';
+ }
+ });
-return {
- View : View
-};
+ return {
+ View : View
+ };
});
\ No newline at end of file
diff --git a/client/galaxy/scripts/mvc/webhooks.js b/client/galaxy/scripts/mvc/webhooks.js
index fe5bdd46b076..de97487a6dad 100644
--- a/client/galaxy/scripts/mvc/webhooks.js
+++ b/client/galaxy/scripts/mvc/webhooks.js
@@ -18,6 +18,11 @@ define([], function() {
initialize: function(options) {
var me = this;
+ var toolId = options.toolId || '';
+ var toolVersion = options.toolVersion || '';
+
+ this.$el.attr('tool_id', toolId);
+ this.$el.attr('tool_version', toolVersion);
this.model = new WebhookModel();
this.model.urlRoot = options.urlRoot;
@@ -34,7 +39,7 @@ define([], function() {
this.$el.html('');
if (webhook.styles) $('', {type: 'text/css'}).text(webhook.styles).appendTo('head');
if (webhook.script) $('', {type: 'text/javascript'}).text(webhook.script).appendTo('head');
-
+
return this;
}
});
@@ -44,7 +49,7 @@ define([], function() {
webhooks.url = Galaxy.root + options.url;
webhooks.fetch({
- async: (typeof options.async != 'undefined') ? options.async : true,
+ async: options.async ? options.async : true,
success: options.callback
});
};
diff --git a/client/galaxy/scripts/onload.js b/client/galaxy/scripts/onload.js
index 1c978684c0a3..695bef35dfb0 100644
--- a/client/galaxy/scripts/onload.js
+++ b/client/galaxy/scripts/onload.js
@@ -183,4 +183,14 @@ $(document).ready( function() {
}
}
}
+
+ // Load all webhooks with the type 'onload'
+ $.getJSON('/api/webhooks/onload/all', function(webhooks) {
+ _.each(webhooks, function(webhook) {
+ if (webhook.activate && webhook.script) {
+ $('', {type: 'text/javascript'}).text(webhook.script).appendTo('head');
+ $('', {type: 'text/css'}).text(webhook.styles).appendTo('head');
+ }
+ });
+ });
});
diff --git a/client/galaxy/style/less/ui.less b/client/galaxy/style/less/ui.less
index 7db625e343a9..26bd93aabd98 100644
--- a/client/galaxy/style/less/ui.less
+++ b/client/galaxy/style/less/ui.less
@@ -746,8 +746,11 @@
width: 100%;
.ui-form-slider-text {
&:extend(.ui-input);
- width: 100px;
+ }
+
+ .ui-form-slider-left {
float: left;
+ width: 100px;
}
.ui-form-slider-element {
diff --git a/client/webpack.config.js b/client/webpack.config.js
index c5fc0c7cf0e6..dafdfa9e8b4d 100644
--- a/client/webpack.config.js
+++ b/client/webpack.config.js
@@ -21,6 +21,7 @@ var webpack = require( 'webpack' ),
'libs/bootstrap',
'libs/bootstrap-tour',
'libs/jquery.complexify',
+ 'libs/jquery/jquery.autocomplete',
// mvc
'libs/underscore',
'libs/backbone',
diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
index da58ad5944ca..9c80d81ddbb8 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -602,11 +602,18 @@
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
-
+
diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample
index 1be56ca42a14..fdcd030b57f2 100644
--- a/config/galaxy.ini.sample
+++ b/config/galaxy.ini.sample
@@ -349,10 +349,10 @@ paste.app_factory = galaxy.web.buildapp:app_factory
# Interactive environment plugins root directory: where to look for interactive
# environment plugins. By default none will be loaded. Set to
-# config/plugins/interactive_environments to load Galaxy's stock plugins
-# (currently just Jupyter). These will require Docker to be configured and
-# have security considerations, so proceed with caution. The path is relative to the
-# Galaxy root dir. To use an absolute path begin the path with '/'. This is a comma
+# config/plugins/interactive_environments to load Galaxy's stock plugins.
+# These will require Docker to be configured and have security considerations,
+# so proceed with caution. The path is relative to the Galaxy root dir. To use
+# an absolute path begin the path with '/'. This is a comma
# separated list.
#interactive_environment_plugins_directory =
diff --git a/config/job_conf.xml.sample_advanced b/config/job_conf.xml.sample_advanced
index 67cc64cc9002..bdb4f8f0bbe7 100644
--- a/config/job_conf.xml.sample_advanced
+++ b/config/job_conf.xml.sample_advanced
@@ -280,8 +280,16 @@
password
+ true
+
-
+
+
+ true
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/config/plugins/webhooks/demo/search/config/searchover.yaml b/config/plugins/webhooks/demo/search/config/searchover.yaml
index a4ba5bb5aa7f..64745187f5b7 100644
--- a/config/plugins/webhooks/demo/search/config/searchover.yaml
+++ b/config/plugins/webhooks/demo/search/config/searchover.yaml
@@ -7,7 +7,7 @@ icon: fa-search
tooltip: Click to activate search and press Ctrl + Alt + q to open the overlay
function: >
- $.getJSON(Galaxy.root + "/api/webhooks", function( data ) {
+ $.getJSON(Galaxy.root + "api/webhooks", function( data ) {
for( var item in data ) {
var webhook = data[item];
if( webhook.name === "searchover" ) {
diff --git a/config/plugins/webhooks/demo/tool_list/config/tool_list.yml b/config/plugins/webhooks/demo/tool_list/config/tool_list.yml
index 180df1a56ba2..cc3577068b44 100644
--- a/config/plugins/webhooks/demo/tool_list/config/tool_list.yml
+++ b/config/plugins/webhooks/demo/tool_list/config/tool_list.yml
@@ -1,5 +1,5 @@
name: tool_list
-type:
+type:
- masthead
activate: true
@@ -13,10 +13,10 @@ function: >
'be patient, this might take a moment.');
}, 1);
- $.getJSON(Galaxy.root + "/api/webhooks/tool_list/get_data", function(data) {
+ $.getJSON(Galaxy.root + "api/webhooks/tool_list/get_data", function(data) {
var popup = window.open('tool_list.html');
- var html = '
' +
- 'Create a Docker flavour of this instance:
' +
+ var html = '
' +
+ 'Create a Docker flavour of this instance:
' +
'
The textarea on ' +
'the right shows the list of installed tools on this Galaxy instance.' +
'You can use it to build a custom Galaxy flavour based on the same ' +
@@ -30,8 +30,8 @@ function: >
'with
\n')
+ for index, fname in enumerate(dir_items):
+ if index % 2 == 0:
+ bgcolor = '#D8D8D8'
+ else:
+ bgcolor = '#FFFFFF'
+ # Can't have an href link here because there is no route
+ # defined for files contained within multiple subdirectory
+ # levels of the primary dataset. Something like this is
+ # close, but not quite correct:
+ # href = url_for(controller='dataset', action='display',
+ # dataset_id=trans.security.encode_id(data.dataset.id),
+ # preview=preview, filename=fname, to_ext=to_ext)
+ tmp_fh.write('
%s
\n' % (bgcolor, fname))
+ tmp_fh.write('
\n')
+ tmp_fh.close()
+ return open(tmp_file_name)
mime = mimetypes.guess_type( file_path )[0]
if not mime:
try:
diff --git a/lib/galaxy/datatypes/plant_tribes.py b/lib/galaxy/datatypes/plant_tribes.py
new file mode 100644
index 000000000000..f1c33411cf84
--- /dev/null
+++ b/lib/galaxy/datatypes/plant_tribes.py
@@ -0,0 +1,213 @@
+import logging
+import os
+import re
+
+from galaxy.datatypes.data import get_file_peek, Text
+from galaxy.datatypes.metadata import MetadataElement, MetadataParameter
+from galaxy.datatypes.text import Html
+from galaxy.util import nice_size
+
+log = logging.getLogger(__name__)
+
+
+class Smat(Text):
+ file_ext = "smat"
+
+ def display_peek(self, dataset):
+ try:
+ return dataset.peek
+ except:
+ return "ESTScan scores matrices (%s)" % (nice_size(dataset.get_size()))
+
+ def set_peek(self, dataset, is_multi_byte=False):
+ if not dataset.dataset.purged:
+ dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
+ dataset.blurb = "ESTScan scores matrices"
+ else:
+ dataset.peek = 'file does not exist'
+ dataset.blurb = 'file purged from disc'
+
+ def sniff(self, filename):
+ """
+ The use of ESTScan implies the creation of scores matrices which
+ reflect the codons preferences in the studied organisms. The
+ ESTScan package includes scripts for generating these files. The
+ output of these scripts consists of the matrices, one for each
+ isochor, and which look like this:
+
+ FORMAT: hse_4is.conf CODING REGION 6 3 1 s C+G: 0 44
+ -1 0 2 -2
+ 2 1 -8 0
+
+ >>> from galaxy.datatypes.sniff import get_test_fname
+ >>> fname = get_test_fname('test_space.txt')
+ >>> Smat().sniff(fname)
+ False
+ >>> fname = get_test_fname('test_tab.bed')
+ >>> Smat().sniff(fname)
+ False
+ >>> fname = get_test_fname('1.smat')
+ >>> Smat().sniff(fname)
+ True
+ """
+ line_no = 0
+ with open(filename, "r") as fh:
+ for line in fh:
+ line_no += 1
+ if line_no > 10000:
+ return True
+ if line_no == 1 and not line.startswith('FORMAT'):
+ # The first line is always the start of a format section.
+ return False
+ if not line.startswith('FORMAT'):
+ if line.find('\t') >= 0:
+ # Smat files are not tabular.
+ return False
+ items = line.split()
+ if len(items) != 4:
+ return False
+ for item in items:
+ # Make sure each item is an integer.
+ if re.match(r"[-+]?\d+$", item) is None:
+ return False
+ return True
+
+
+class PlantTribes(Html):
+ """
+ PlantTribes abstract class.
+ """
+ composite_type = 'basic'
+ MetadataElement(name="num_files", default=0, desc="Number of files in files_path directory", param=MetadataParameter, readonly=True, visible=False, no_value=0)
+
+ def set_meta(self, dataset, overwrite=True, **kwd):
+ try:
+ efp = dataset.extra_files_path
+ if os.path.exists(efp):
+ dataset.metadata.num_files = len(os.listdir(efp))
+ except Exception as e:
+ log.warning("set_meta fname: %s %s" % (dataset.file_name if dataset and dataset.file_name else 'Unkwown', str(e)))
+
+
+class PlantTribesOrtho(PlantTribes):
+ """
+ PlantTribes sequences classified into precomputed, orthologous gene family
+ clusters.
+ """
+ file_ext = "ptortho"
+
+ def set_peek(self, dataset, is_multi_byte=False):
+ super(PlantTribesOrtho, self).set_peek(dataset, is_multi_byte=is_multi_byte)
+ dataset.blurb = "Proteins orthogroup fasta files: %d items" % dataset.metadata.num_files
+
+
+class PlantTribesOrthoCodingSequence(PlantTribes):
+ """
+ PlantTribes sequences classified into precomputed, orthologous gene family
+ clusters and corresponding coding sequences.
+ """
+ file_ext = "ptorthocs"
+
+ def set_peek(self, dataset, is_multi_byte=False):
+ super(PlantTribesOrthoCodingSequence, self).set_peek(dataset, is_multi_byte=is_multi_byte)
+ dataset.blurb = "Protein and coding sequences orthogroup fasta files: %d items" % dataset.metadata.num_files
+
+
+class PlantTribesTargetedGeneFamilies(PlantTribes):
+ """
+ PlantTribes targeted gene families.
+ """
+ file_ext = "pttgf"
+
+ def set_peek(self, dataset, is_multi_byte=False):
+ super(PlantTribesTargetedGeneFamilies, self).set_peek(dataset, is_multi_byte=is_multi_byte)
+ dataset.blurb = "Targeted gene families"
+
+
+class PlantTribesPhylogeneticTree(PlantTribes):
+ """
+ PlantTribes multiple sequence alignments and inferred maximum likelihood
+ phylogenies for orthogroups.
+ """
+ file_ext = "pttree"
+
+ def set_peek(self, dataset, is_multi_byte=False):
+ super(PlantTribesPhylogeneticTree, self).set_peek(dataset, is_multi_byte=is_multi_byte)
+ dataset.blurb = "Phylogenetic trees: %d items" % dataset.metadata.num_files
+
+
+class PlantTribesPhylip(PlantTribes):
+ """
+ PlantTribes orthogroup phylip multiple sequence alignments.
+ """
+ file_ext = "ptphylip"
+
+ def set_peek(self, dataset, is_multi_byte=False):
+ super(PlantTribesPhylip, self).set_peek(dataset, is_multi_byte=is_multi_byte)
+ dataset.blurb = "Orthogroup phylip multiple sequence alignments: %d items" % dataset.metadata.num_files
+
+
+class PlantTribesMultipleSequenceAlignment(PlantTribes):
+ """
+ PlantTribes multiple sequence alignments.
+ """
+ file_ext = "ptalign"
+
+ def set_peek(self, dataset, is_multi_byte=False):
+ super(PlantTribesMultipleSequenceAlignment, self).set_peek(dataset, is_multi_byte=is_multi_byte)
+ dataset.blurb = "Proteins orthogroup alignments: %d items" % dataset.metadata.num_files
+
+
+class PlantTribesMultipleSequenceAlignmentCodonAlignment(PlantTribes):
+ """
+ PlantTribes multiple sequence alignments with codon alignments.
+ """
+ file_ext = "ptalignca"
+
+ def set_peek(self, dataset, is_multi_byte=False):
+ super(PlantTribesMultipleSequenceAlignmentCodonAlignment, self).set_peek(dataset, is_multi_byte=is_multi_byte)
+ dataset.blurb = "Protein and coding sequences orthogroup alignments: %d items" % dataset.metadata.num_files
+
+
+class PlantTribesMultipleSequenceAlignmentTrimmed(PlantTribes):
+ """
+ PlantTribes trimmed multiple sequence alignments.
+ """
+ file_ext = "ptaligntrimmed"
+
+ def set_peek(self, dataset, is_multi_byte=False):
+ super(PlantTribesMultipleSequenceAlignmentTrimmed, self).set_peek(dataset, is_multi_byte=is_multi_byte)
+ dataset.blurb = "Trimmed proteins orthogroup alignments: %d items" % dataset.metadata.num_files
+
+
+class PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment(PlantTribes):
+ """
+ PlantTribes trimmed multiple sequence alignments with codon alignments.
+ """
+ file_ext = "ptaligntrimmedca"
+
+ def set_peek(self, dataset, is_multi_byte=False):
+ super(PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment, self).set_peek(dataset, is_multi_byte=is_multi_byte)
+ dataset.blurb = "Trimmed protein and coding sequences orthogroup alignments: %d items" % dataset.metadata.num_files
+
+
+class PlantTribesMultipleSequenceAlignmentFiltered(PlantTribes):
+ """
+ PlantTribes filtered multiple sequence alignments.
+ """
+ file_ext = "ptalignfiltered"
+
+ def set_peek(self, dataset, is_multi_byte=False):
+ super(PlantTribesMultipleSequenceAlignmentFiltered, self).set_peek(dataset, is_multi_byte=is_multi_byte)
+ dataset.blurb = "Filtered proteins orthogroup alignments: %d items" % dataset.metadata.num_files
+
+
+class PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment(PlantTribes):
+ """
+ PlantTribes filtered multiple sequence alignments with codon alignments.
+ """
+ file_ext = "ptalignfilteredca"
+
+ def set_peek(self, dataset, is_multi_byte=False):
+ super(PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment, self).set_peek(dataset, is_multi_byte=is_multi_byte)
+ dataset.blurb = "Filtered protein and coding sequences orthogroup alignments: %d items" % dataset.metadata.num_files
diff --git a/lib/galaxy/datatypes/text.py b/lib/galaxy/datatypes/text.py
index 351f83f4debb..bffb3ad24bc0 100644
--- a/lib/galaxy/datatypes/text.py
+++ b/lib/galaxy/datatypes/text.py
@@ -69,6 +69,10 @@ def set_peek( self, dataset, is_multi_byte=False ):
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disc'
+ def get_mime(self):
+ """Returns the mime type of the datatype"""
+ return 'application/json'
+
def sniff( self, filename ):
"""
Try to load the string with the json module. If successful it's a json file.
@@ -542,113 +546,3 @@ def set_peek( self, dataset, is_multi_byte=False ):
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disc'
-
-
-class Smat(Text):
- file_ext = "smat"
-
- def display_peek(self, dataset):
- try:
- return dataset.peek
- except:
- return "ESTScan scores matrices (%s)" % (nice_size(dataset.get_size()))
-
- def set_peek(self, dataset, is_multi_byte=False):
- if not dataset.dataset.purged:
- dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
- dataset.blurb = "ESTScan scores matrices"
- else:
- dataset.peek = 'file does not exist'
- dataset.blurb = 'file purged from disc'
-
- def sniff(self, filename):
- """
- The use of ESTScan implies the creation of scores matrices which
- reflect the codons preferences in the studied organisms. The
- ESTScan package includes scripts for generating these files. The
- output of these scripts consists of the matrices, one for each
- isochor, and which look like this:
-
- FORMAT: hse_4is.conf CODING REGION 6 3 1 s C+G: 0 44
- -1 0 2 -2
- 2 1 -8 0
-
- >>> from galaxy.datatypes.sniff import get_test_fname
- >>> fname = get_test_fname('test_space.txt')
- >>> Smat().sniff(fname)
- False
- >>> fname = get_test_fname('test_tab.bed')
- >>> Smat().sniff(fname)
- False
- >>> fname = get_test_fname('1.smat')
- >>> Smat().sniff(fname)
- True
- """
- line_no = 0
- with open(filename, "r") as fh:
- line_no += 1
- if line_no > 10000:
- return True
- line = fh.readline(500)
- if line_no == 1 and not line.startswith('FORMAT'):
- # The first line is always the start of a format section.
- return False
- if not line.startswith('FORMAT'):
- if line.find('\t') >= 0:
- # Smat files are not tabular.
- return False
- items = line.split()
- if len(items) != 4:
- return False
- for item in items:
- # Make sure each item is an integer.
- if re.match(r"[-+]?\d+$", item) is None:
- return False
- return True
-
-
-class PlantTribesOrtho(Html):
- """
- PlantTribes sequences classified into precomputed, orthologous gene family
- clusters.
- """
- file_ext = "ptortho"
-
- def set_peek(self, dataset, is_multi_byte=False):
- super(PlantTribesOrtho, self).set_peek(dataset, is_multi_byte=is_multi_byte)
- dataset.blurb = "PlantTribes gene family clusters: %d files" % dataset.metadata.data_lines
-
-
-class PlantTribesOrthoCodingSequence(Html):
- """
- PlantTribes sequences classified into precomputed, orthologous gene family
- clusters and corresponding coding sequences.
- """
- file_ext = "ptorthocs"
-
- def set_peek(self, dataset, is_multi_byte=False):
- super(PlantTribesOrthoCodingSequence, self).set_peek(dataset, is_multi_byte=is_multi_byte)
- dataset.blurb = "PlantTribes gene family clusters with corresponding coding sequences: %d files" % dataset.metadata.data_lines
-
-
-class PlantTribesPhylogeneticTree(Html):
- """
- PlantTribes multiple sequence alignments and inferred maximum likelihood
- phylogenies for orthogroups.
- """
- file_ext = "pttree"
-
- def set_peek(self, dataset, is_multi_byte=False):
- super(PlantTribesPhylogeneticTree, self).set_peek(dataset, is_multi_byte=is_multi_byte)
- dataset.blurb = "PlantTribes phylogenetic trees: %d files" % dataset.metadata.data_lines
-
-
-class PlantTribesMultipleSequenceAlignment(Html):
- """
- PlantTribes multiple sequence alignments for orthogroups.
- """
- file_ext = "ptalign"
-
- def set_peek(self, dataset, is_multi_byte=False):
- super(PlantTribesMultipleSequenceAlignment, self).set_peek(dataset, is_multi_byte=is_multi_byte)
- dataset.blurb = "PlantTribes multiple sequence alignments: %d files" % dataset.metadata.data_lines
diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 9383418d5d26..6c7747152e51 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -180,6 +180,8 @@ def __parse_job_conf_xml(self, tree):
if plugin.get('type') == 'runner':
workers = plugin.get('workers', plugins.get('workers', JobConfiguration.DEFAULT_NWORKERS))
runner_kwds = self.__get_params(plugin)
+ if not self.__is_enabled(runner_kwds):
+ continue
runner_info = dict(id=plugin.get('id'),
load=plugin.get('load'),
workers=int(workers),
@@ -223,7 +225,11 @@ def __parse_job_conf_xml(self, tree):
if metrics_elements:
job_metrics.set_destination_conf_element( id, metrics_elements[ 0 ] )
job_destination = JobDestination(**dict(destination.items()))
- job_destination['params'] = self.__get_params(destination)
+ params = self.__get_params(destination)
+ if not self.__is_enabled(params):
+ continue
+
+ job_destination['params'] = params
job_destination['env'] = self.__get_envs(destination)
destination_resubmits = self.__get_resubmits(destination)
if destination_resubmits:
@@ -490,6 +496,15 @@ def __get_resubmits(self, parent):
) )
return rval
+ def __is_enabled(self, params):
+ """Check for an enabled parameter - pop it out - and return as boolean."""
+ enabled = True
+ if "enabled" in params:
+ raw_enabled = params.pop("enabled")
+ enabled = util.asbool(raw_enabled)
+
+ return enabled
+
@property
def default_job_tool_configuration(self):
"""
diff --git a/lib/galaxy/jobs/actions/post.py b/lib/galaxy/jobs/actions/post.py
index 73672a1cf09d..380803ccb29b 100644
--- a/lib/galaxy/jobs/actions/post.py
+++ b/lib/galaxy/jobs/actions/post.py
@@ -330,7 +330,7 @@ class TagDatasetAction(DefaultJobAction):
@classmethod
def execute(cls, app, sa_session, action, job, replacement_dict):
if action.action_arguments:
- tags = [t.strip() for t in action.action_arguments.get('tags', '').split(',')]
+ tags = [t.replace('#', 'name:') if t.startswith('#') else t for t in [t.strip() for t in action.action_arguments.get('tags', '').split(',') if t.strip()]]
if tags:
for dataset_assoc in job.output_datasets:
if action.output_name == '' or dataset_assoc.name == action.output_name:
diff --git a/lib/galaxy/jobs/runners/chronos.py b/lib/galaxy/jobs/runners/chronos.py
index 7f41a55517c5..0a04fe89b590 100644
--- a/lib/galaxy/jobs/runners/chronos.py
+++ b/lib/galaxy/jobs/runners/chronos.py
@@ -115,8 +115,12 @@ def __init__(self, app, nworkers, **kwargs):
kwargs[self.RUNNER_PARAM_SPEC_KEY] = {}
kwargs[self.RUNNER_PARAM_SPEC_KEY].update(self.RUNNER_PARAM_SPEC)
super(ChronosJobRunner, self).__init__(app, nworkers, **kwargs)
+ protocol = 'http' if self.runner_params.get('insecure', True) else 'https'
self._chronos_client = chronos.connect(
- self.runner_params['chronos'])
+ self.runner_params['chronos'],
+ username=self.runner_params.get('username'),
+ password=self.runner_params.get('password'),
+ proto=protocol)
self._init_monitor_thread()
self._init_worker_threads()
diff --git a/lib/galaxy/managers/collections_util.py b/lib/galaxy/managers/collections_util.py
index a6a9571cb013..a3e19c160fa5 100644
--- a/lib/galaxy/managers/collections_util.py
+++ b/lib/galaxy/managers/collections_util.py
@@ -65,6 +65,32 @@ def validate_input_element_identifiers( element_identifiers ):
validate_input_element_identifiers( element_identifier[ "element_identifiers" ] )
+def get_hda_and_element_identifiers(dataset_collection_instance):
+ name = dataset_collection_instance.name
+ names = []
+ hdas = []
+ collection = dataset_collection_instance.collection
+ if collection.has_subcollections:
+ for element in collection.elements:
+ subnames, subhdas = get_subcollections(element.child_collection, name="%s/%s" % (name, element.element_identifier))
+ names.extend(subnames)
+ hdas.extend(subhdas)
+ else:
+ for element in collection.elements:
+ names.append("%s/%s" % (name, element.element_identifier))
+ hdas.append(element.dataset_instance)
+ return names, hdas
+
+
+def get_subcollections(collection, name=""):
+ names = []
+ hdas = []
+ for element in collection.elements:
+ names.append("%s/%s" % (name, element.element_identifier))
+ hdas.append(element.dataset_instance)
+ return names, hdas
+
+
def dictify_dataset_collection_instance( dataset_collection_instance, parent, security, view="element" ):
dict_value = dataset_collection_instance.to_dict( view=view )
encoded_id = security.encode_id( dataset_collection_instance.id )
diff --git a/lib/galaxy/tools/toolbox/cache.py b/lib/galaxy/tools/cache.py
similarity index 100%
rename from lib/galaxy/tools/toolbox/cache.py
rename to lib/galaxy/tools/cache.py
diff --git a/lib/galaxy/tools/deps/conda_util.py b/lib/galaxy/tools/deps/conda_util.py
index 00ca742f24e7..00efe51b8ca2 100644
--- a/lib/galaxy/tools/deps/conda_util.py
+++ b/lib/galaxy/tools/deps/conda_util.py
@@ -488,7 +488,7 @@ def cleanup_failed_install(conda_target, conda_context=None):
cleanup_failed_install_of_environment(conda_target.install_environment, conda_context=conda_context)
-def best_search_result(conda_target, conda_context=None, channels_override=None):
+def best_search_result(conda_target, conda_context=None, channels_override=None, offline=False):
"""Find best "conda search" result for specified target.
Return ``None`` if no results match.
@@ -498,6 +498,8 @@ def best_search_result(conda_target, conda_context=None, channels_override=None)
conda_context.ensure_channels_configured()
search_cmd = [conda_context.conda_exec, "search", "--full-name", "--json"]
+ if offline:
+ search_cmd.append("--offline")
if channels_override:
search_cmd.append("--override-channels")
for channel in channels_override:
diff --git a/lib/galaxy/tools/deps/container_resolvers/mulled.py b/lib/galaxy/tools/deps/container_resolvers/mulled.py
index d30355700437..fc551cb883a7 100644
--- a/lib/galaxy/tools/deps/container_resolvers/mulled.py
+++ b/lib/galaxy/tools/deps/container_resolvers/mulled.py
@@ -2,6 +2,7 @@
import collections
import logging
+import os
import six
@@ -18,9 +19,10 @@
)
from ..mulled.mulled_build_tool import requirements_to_mulled_targets
from ..mulled.util import (
- image_name,
mulled_tags_for,
split_tag,
+ v1_image_name,
+ v2_image_name,
)
from ..requirements import ContainerDescription
@@ -28,13 +30,29 @@
CachedMulledImageSingleTarget = collections.namedtuple("CachedMulledImageSingleTarget", ["package_name", "version", "build", "image_identifier"])
-CachedMulledImageMultiTarget = collections.namedtuple("CachedMulledImageMultiTarget", ["hash", "image_identifier"])
+CachedV1MulledImageMultiTarget = collections.namedtuple("CachedV1MulledImageMultiTarget", ["hash", "build", "image_identifier"])
+CachedV2MulledImageMultiTarget = collections.namedtuple("CachedV2MulledImageMultiTarget", ["image_name", "version_hash", "build", "image_identifier"])
CachedMulledImageSingleTarget.multi_target = False
-CachedMulledImageMultiTarget.multi_target = True
+CachedV1MulledImageMultiTarget.multi_target = "v1"
+CachedV2MulledImageMultiTarget.multi_target = "v2"
-def list_cached_mulled_images(namespace=None):
+@property
+def _package_hash(target):
+ # Make this work for Singularity file name or fully qualified Docker repository
+ # image names.
+ image_name = target.image_name
+ if "/" not in image_name:
+ return image_name
+ else:
+ return image_name.rsplit("/")[-1]
+
+
+CachedV2MulledImageMultiTarget.package_hash = _package_hash
+
+
+def list_docker_cached_mulled_images(namespace=None, hash_func="v2"):
command = build_docker_images_command(truncate=True, sudo=False)
command = "%s | tail -n +2 | tr -s ' ' | cut -d' ' -f1,2" % command
images_and_versions = check_output(command)
@@ -43,24 +61,65 @@ def list_cached_mulled_images(namespace=None):
def output_line_to_image(line):
image_name, version = line.split(" ", 1)
identifier = "%s:%s" % (image_name, version)
- url, namespace, package_description = image_name.split("/")
+ image = identifier_to_cached_target(identifier, hash_func, namespace=namespace)
+ return image
- if package_description.startswith("mulled-v1-"):
- hash = package_description
- image = CachedMulledImageMultiTarget(hash, identifier)
- else:
- build = None
- if not version or version == "latest":
- version = None
+ # TODO: Sort on build ...
+ raw_images = [output_line_to_image(_) for _ in filter(name_filter, images_and_versions.splitlines())]
+ return [i for i in raw_images if i is not None]
- if version and "--" in version:
- version, build = split_tag(version)
- image = CachedMulledImageSingleTarget(image_name, version, build, identifier)
+def identifier_to_cached_target(identifier, hash_func, namespace=None):
+ if ":" in identifier:
+ image_name, version = identifier.rsplit(":", 1)
+ else:
+ image_name = identifier
+ version = None
- return image
+ if not version or version == "latest":
+ version = None
+
+ image = None
+ prefix = ""
+ if namespace is not None:
+ prefix = "quay.io/%s/" % namespace
+ if image_name.startswith(prefix + "mulled-v1-"):
+ if hash_func == "v2":
+ return None
- return [output_line_to_image(_) for _ in filter(name_filter, images_and_versions.splitlines())]
+ hash = image_name
+ build = None
+ if version and version.isdigit():
+ build = version
+ image = CachedV1MulledImageMultiTarget(hash, build, identifier)
+ elif image_name.startswith(prefix + "mulled-v2-"):
+ if hash_func == "v1":
+ return None
+
+ version_hash = None
+ build = None
+
+ if version and "-" in version:
+ version_hash, build = version.rsplit("-", 1)
+ elif version.isdigit():
+ version_hash, build = None, version
+ elif version:
+ log.debug("Unparsable mulled image tag encountered [%s]" % version)
+
+ image = CachedV2MulledImageMultiTarget(image_name, version_hash, build, identifier)
+ else:
+ build = None
+ if version and "--" in version:
+ version, build = split_tag(version)
+
+ image = CachedMulledImageSingleTarget(image_name, version, build, identifier)
+ return image
+
+
+def list_cached_mulled_images_from_path(directory, hash_func="v2"):
+ contents = os.listdir(directory)
+ raw_images = map(lambda name: identifier_to_cached_target(name, hash_func), contents)
+ return [i for i in raw_images if i is not None]
def get_filter(namespace):
@@ -68,11 +127,10 @@ def get_filter(namespace):
return lambda name: name.startswith(prefix) and name.count("/") == 2
-def cached_container_description(targets, namespace):
+def find_best_matching_cached_image(targets, cached_images, hash_func):
if len(targets) == 0:
return None
- cached_images = list_cached_mulled_images(namespace)
image = None
if len(targets) == 1:
target = targets[0]
@@ -84,15 +142,46 @@ def cached_container_description(targets, namespace):
if not target.version or target.version == cached_image.version:
image = cached_image
break
- else:
- name = image_name(targets)
+ elif hash_func == "v2":
+ name = v2_image_name(targets)
+ if ":" in name:
+ package_hash, version_hash = name.split(":", 2)
+ else:
+ package_hash, version_hash = name, None
+
for cached_image in cached_images:
- if not cached_image.multi_target:
+ if cached_image.multi_target != "v2":
+ continue
+
+ if version_hash is None:
+ # Just match on package hash...
+ if package_hash == cached_image.package_hash:
+ image = cached_image
+ break
+ else:
+ # Match on package and version hash...
+ if package_hash == cached_image.package_hash and version_hash == cached_image.version_hash:
+ image = cached_image
+ break
+
+ elif hash_func == "v1":
+ name = v1_image_name(targets)
+ for cached_image in cached_images:
+ if cached_image.multi_target != "v1":
continue
if name == cached_image.hash:
image = cached_image
break
+ return image
+
+
+def docker_cached_container_description(targets, namespace, hash_func="v2"):
+ if len(targets) == 0:
+ return None
+
+ cached_images = list_docker_cached_mulled_images(namespace, hash_func=hash_func)
+ image = find_best_matching_cached_image(targets, cached_images, hash_func)
container = None
if image:
@@ -104,35 +193,81 @@ def cached_container_description(targets, namespace):
return container
+def singularity_cached_container_description(targets, cache_directory, hash_func="v2"):
+ if len(targets) == 0:
+ return None
+
+ if not os.path.exists(cache_directory):
+ return None
+
+ cached_images = list_cached_mulled_images_from_path(cache_directory, hash_func=hash_func)
+ image = find_best_matching_cached_image(targets, cached_images, hash_func)
+
+ container = None
+ if image:
+ container = ContainerDescription(
+ os.path.abspath(os.path.join(cache_directory, image.image_identifier)),
+ type="singularity",
+ )
+
+ return container
+
+
@six.python_2_unicode_compatible
-class CachedMulledContainerResolver(ContainerResolver):
+class CachedMulledDockerContainerResolver(ContainerResolver):
resolver_type = "cached_mulled"
+ container_type = "docker"
- def __init__(self, app_info=None, namespace=None):
- super(CachedMulledContainerResolver, self).__init__(app_info)
+ def __init__(self, app_info=None, namespace="biocontainers", hash_func="v2"):
+ super(CachedMulledDockerContainerResolver, self).__init__(app_info)
self.namespace = namespace
+ self.hash_func = hash_func
def resolve(self, enabled_container_types, tool_info):
if tool_info.requires_galaxy_python_environment:
return None
targets = mulled_targets(tool_info)
- return cached_container_description(targets, self.namespace)
+ return docker_cached_container_description(targets, self.namespace, hash_func=self.hash_func)
def __str__(self):
- return "CachedMulledContainerResolver[namespace=%s]" % self.namespace
+ return "CachedMulledDockerContainerResolver[namespace=%s]" % self.namespace
@six.python_2_unicode_compatible
-class MulledContainerResolver(ContainerResolver):
+class CachedMulledSingularityContainerResolver(ContainerResolver):
+
+ resolver_type = "cached_mulled_singularity"
+ container_type = "singularity"
+
+ def __init__(self, app_info=None, hash_func="v2"):
+ super(CachedMulledSingularityContainerResolver, self).__init__(app_info)
+ self.cache_directory = os.path.join(app_info.container_image_cache_path, "singularity", "mulled")
+ self.hash_func = hash_func
+
+ def resolve(self, enabled_container_types, tool_info):
+ if tool_info.requires_galaxy_python_environment:
+ return None
+
+ targets = mulled_targets(tool_info)
+ return singularity_cached_container_description(targets, self.cache_directory, hash_func=self.hash_func)
+
+ def __str__(self):
+ return "CachedMulledSingularityContainerResolver[cache_directory=%s]" % self.cache_directory
+
+
+@six.python_2_unicode_compatible
+class MulledDockerContainerResolver(ContainerResolver):
"""Look for mulled images matching tool dependencies."""
resolver_type = "mulled"
+ container_type = "docker"
- def __init__(self, app_info=None, namespace="biocontainers"):
- super(MulledContainerResolver, self).__init__(app_info)
+ def __init__(self, app_info=None, namespace="biocontainers", hash_func="v2"):
+ super(MulledDockerContainerResolver, self).__init__(app_info)
self.namespace = namespace
+ self.hash_func = hash_func
def resolve(self, enabled_container_types, tool_info):
if tool_info.requires_galaxy_python_environment:
@@ -162,36 +297,109 @@ def resolve(self, enabled_container_types, tool_info):
version, build = split_tag(tags[0])
name = "%s:%s--%s" % (target.package_name, version, build)
else:
- base_image_name = image_name(targets)
- tags = mulled_tags_for(self.namespace, base_image_name)
- if tags:
- name = "%s:%s" % (base_image_name, tags[0])
+ def tags_if_available(image_name):
+ if ":" in image_name:
+ repo_name, tag_prefix = image_name.split(":", 2)
+ else:
+ repo_name = image_name
+ tag_prefix = None
+ tags = mulled_tags_for(self.namespace, repo_name, tag_prefix=tag_prefix)
+ return tags
+
+ if self.hash_func == "v2":
+ base_image_name = v2_image_name(targets)
+ tags = tags_if_available(base_image_name)
+ if tags:
+ if ":" in base_image_name:
+ # base_image_name of form :, expand tag
+ # to include build number in tag.
+ name = "%s:%s" % (base_image_name.split(":")[0], tags[0])
+ else:
+ # base_image_name of form , simply add build number
+ # as tag to fully qualify image.
+ name = "%s:%s" % (base_image_name, tags[0])
+ elif self.hash_func == "v1":
+ base_image_name = v1_image_name(targets)
+ tags = tags_if_available(base_image_name)
+ if tags:
+ name = "%s:%s" % (base_image_name, tags[0])
if name:
return ContainerDescription(
"quay.io/%s/%s" % (self.namespace, name),
- type="docker",
+ type=self.container_type,
)
def __str__(self):
- return "MulledContainerResolver[namespace=%s]" % self.namespace
+ return "MulledDockerContainerResolver[namespace=%s]" % self.namespace
@six.python_2_unicode_compatible
-class BuildMulledContainerResolver(ContainerResolver):
- """Look for mulled images matching tool dependencies."""
+class BuildMulledDockerContainerResolver(ContainerResolver):
+ """Build for Docker mulled images matching tool dependencies."""
resolver_type = "build_mulled"
+ container_type = "docker"
- def __init__(self, app_info=None, namespace="local", **kwds):
- super(BuildMulledContainerResolver, self).__init__(app_info)
+ def __init__(self, app_info=None, namespace="local", hash_func="v2", **kwds):
+ super(BuildMulledDockerContainerResolver, self).__init__(app_info)
self._involucro_context_kwds = {
'involucro_bin': self._get_config_option("involucro_path", None)
}
self.namespace = namespace
+ self.hash_func = hash_func
self._mulled_kwds = {
'namespace': namespace,
'channels': self._get_config_option("channels", DEFAULT_CHANNELS, prefix="mulled"),
+ 'hash_func': self.hash_func,
+ 'command': 'build-and-test',
+ }
+ self.auto_init = self._get_config_option("auto_init", DEFAULT_CHANNELS, prefix="involucro")
+
+ def resolve(self, enabled_container_types, tool_info):
+ if tool_info.requires_galaxy_python_environment:
+ return None
+
+ targets = mulled_targets(tool_info)
+ if len(targets) == 0:
+ return None
+
+ mull_targets(
+ targets,
+ involucro_context=self._get_involucro_context(),
+ **self._mulled_kwds
+ )
+ return docker_cached_container_description(targets, self.namespace, hash_func=self.hash_func)
+
+ def _get_involucro_context(self):
+ involucro_context = InvolucroContext(**self._involucro_context_kwds)
+ self.enabled = ensure_installed(involucro_context, self.auto_init)
+ return involucro_context
+
+ def __str__(self):
+ return "BuildDockerContainerResolver[namespace=%s]" % self.namespace
+
+
+@six.python_2_unicode_compatible
+class BuildMulledSingularityContainerResolver(ContainerResolver):
+ """Build for Singularity mulled images matching tool dependencies."""
+
+ resolver_type = "build_mulled_singularity"
+ container_type = "singularity"
+
+ def __init__(self, app_info=None, hash_func="v2", **kwds):
+ super(BuildMulledSingularityContainerResolver, self).__init__(app_info)
+ self._involucro_context_kwds = {
+ 'involucro_bin': self._get_config_option("involucro_path", None)
+ }
+ self.cache_directory = os.path.join(app_info.container_image_cache_path, "singularity", "mulled")
+ self.hash_func = hash_func
+ self._mulled_kwds = {
+ 'channels': self._get_config_option("channels", DEFAULT_CHANNELS, prefix="mulled"),
+ 'hash_func': self.hash_func,
+ 'command': 'build-and-test',
+ 'singularity': True,
+ 'singularity_image_dir': self.cache_directory,
}
self.auto_init = self._get_config_option("auto_init", DEFAULT_CHANNELS, prefix="involucro")
@@ -208,7 +416,7 @@ def resolve(self, enabled_container_types, tool_info):
involucro_context=self._get_involucro_context(),
**self._mulled_kwds
)
- return cached_container_description(targets, self.namespace)
+ return singularity_cached_container_description(targets, self.cache_directory, hash_func=self.hash_func)
def _get_involucro_context(self):
involucro_context = InvolucroContext(**self._involucro_context_kwds)
@@ -216,7 +424,7 @@ def _get_involucro_context(self):
return involucro_context
def __str__(self):
- return "BuildContainerResolver[namespace=%s]" % self.namespace
+ return "BuildDockerContainerResolver[cache_directory=%s]" % self.cache_directory
def mulled_targets(tool_info):
@@ -224,7 +432,9 @@ def mulled_targets(tool_info):
__all__ = (
- "CachedMulledContainerResolver",
- "MulledContainerResolver",
- "BuildMulledContainerResolver",
+ "CachedMulledDockerContainerResolver",
+ "CachedMulledSingularityContainerResolver",
+ "MulledDockerContainerResolver",
+ "BuildMulledDockerContainerResolver",
+ "BuildMulledSingularityContainerResolver",
)
diff --git a/lib/galaxy/tools/deps/containers.py b/lib/galaxy/tools/deps/containers.py
index 12ff447d515f..ba9647396003 100644
--- a/lib/galaxy/tools/deps/containers.py
+++ b/lib/galaxy/tools/deps/containers.py
@@ -10,23 +10,28 @@
import six
from galaxy.util import asbool
+from galaxy.util import in_directory
from galaxy.util import plugin_config
from .container_resolvers.explicit import ExplicitContainerResolver
from .container_resolvers.mulled import (
- BuildMulledContainerResolver,
- CachedMulledContainerResolver,
- MulledContainerResolver,
+ BuildMulledDockerContainerResolver,
+ BuildMulledSingularityContainerResolver,
+ CachedMulledDockerContainerResolver,
+ CachedMulledSingularityContainerResolver,
+ MulledDockerContainerResolver,
)
from .requirements import ContainerDescription
from .requirements import DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES, DEFAULT_CONTAINER_SHELL
from ..deps import docker_util
+from ..deps import singularity_util
log = logging.getLogger(__name__)
DOCKER_CONTAINER_TYPE = "docker"
+SINGULARITY_CONTAINER_TYPE = "singularity"
DEFAULT_CONTAINER_TYPE = DOCKER_CONTAINER_TYPE
-ALL_CONTAINER_TYPES = [DOCKER_CONTAINER_TYPE]
+ALL_CONTAINER_TYPES = [DOCKER_CONTAINER_TYPE, SINGULARITY_CONTAINER_TYPE]
LOAD_CACHED_IMAGE_COMMAND_TEMPLATE = '''
python << EOF
@@ -216,9 +221,11 @@ def __default_containers_resolvers(self):
]
if self.enable_beta_mulled_containers:
default_resolvers.extend([
- CachedMulledContainerResolver(self.app_info),
- MulledContainerResolver(self.app_info, namespace="biocontainers"),
- BuildMulledContainerResolver(self.app_info),
+ CachedMulledDockerContainerResolver(self.app_info, namespace="biocontainers"),
+ MulledDockerContainerResolver(self.app_info, namespace="biocontainers"),
+ BuildMulledDockerContainerResolver(self.app_info),
+ CachedMulledSingularityContainerResolver(self.app_info),
+ BuildMulledSingularityContainerResolver(self.app_info),
])
return default_resolvers
@@ -229,6 +236,9 @@ def __resolvers_dict( self ):
def find_best_container_description(self, enabled_container_types, tool_info):
"""Yield best container description of supplied types matching tool info."""
for container_resolver in self.container_resolvers:
+ if hasattr(container_resolver, "container_type"):
+ if container_resolver.container_type not in enabled_container_types:
+ continue
container_description = container_resolver.resolve(enabled_container_types, tool_info)
log.info("Checking with container resolver [%s] found description [%s]" % (container_resolver, container_description))
if container_description:
@@ -315,7 +325,105 @@ def containerize_command(self, command):
"""
-class DockerContainer(Container):
+def preprocess_volumes(volumes_raw_str, container_type):
+ """Process Galaxy volume specification string to either Docker or Singularity specification.
+
+ Galaxy allows the mount try "default_ro" which translates to ro for Docker and
+ ro for Singularity iff no subdirectories are rw (Singularity does not allow ro
+ parent directories with rw subdirectories).
+
+ >>> preprocess_volumes("/a/b", DOCKER_CONTAINER_TYPE)
+ '/a/b:rw'
+ >>> preprocess_volumes("/a/b:ro,/a/b/c:rw", DOCKER_CONTAINER_TYPE)
+ '/a/b:ro,/a/b/c:rw'
+ >>> preprocess_volumes("/a/b:default_ro,/a/b/c:rw", DOCKER_CONTAINER_TYPE)
+ '/a/b:ro,/a/b/c:rw'
+ >>> preprocess_volumes("/a/b:default_ro,/a/b/c:rw", SINGULARITY_CONTAINER_TYPE)
+ '/a/b:rw,/a/b/c:rw'
+ """
+
+ volumes_raw_strs = [v.strip() for v in volumes_raw_str.split(",")]
+ volumes = []
+ rw_paths = []
+
+ for volume_raw_str in volumes_raw_strs:
+ volume_parts = volume_raw_str.split(":")
+ if len(volume_parts) > 2:
+ raise Exception("Unparsable volumes string in configuration [%s]" % volumes_raw_str)
+ if len(volume_parts) == 1:
+ volume_parts.append("rw")
+ volumes.append(volume_parts)
+ if volume_parts[1] == "rw":
+ rw_paths.append(volume_parts[0])
+
+ for volume in volumes:
+ path = volume[0]
+ how = volume[1]
+
+ if how == "default_ro":
+ how = "ro"
+ if container_type == SINGULARITY_CONTAINER_TYPE:
+ for rw_path in rw_paths:
+ if in_directory(rw_path, path):
+ how = "rw"
+
+ volume[1] = how
+
+ return ",".join([":".join(v) for v in volumes])
+
+
+class HasDockerLikeVolumes:
+ """Mixin to share functionality related to Docker volume handling.
+
+ Singularity seems to have a fairly compatible syntax for volume handling.
+ """
+
+ def _expand_volume_str(self, value):
+ if not value:
+ return value
+
+ template = string.Template(value)
+ variables = dict()
+
+ def add_var(name, value):
+ if value:
+ variables[name] = os.path.abspath(value)
+
+ add_var("working_directory", self.job_info.working_directory)
+ add_var("job_directory", self.job_info.job_directory)
+ add_var("tool_directory", self.job_info.tool_directory)
+ add_var("galaxy_root", self.app_info.galaxy_root_dir)
+ add_var("default_file_path", self.app_info.default_file_path)
+ add_var("library_import_dir", self.app_info.library_import_dir)
+
+ if self.job_info.job_directory and self.job_info.job_directory_type == "pulsar":
+ # We have a Pulsar job directory, so everything needed (excluding index
+ # files) should be available in job_directory...
+ defaults = "$job_directory:default_ro,$tool_directory:default_ro,$job_directory/outputs:rw,$working_directory:rw"
+ else:
+ defaults = "$galaxy_root:default_ro,$tool_directory:default_ro"
+ if self.job_info.job_directory:
+ defaults += ",$job_directory:default_ro"
+ if self.app_info.outputs_to_working_directory:
+ # Should need default_file_path (which is of course an estimate given
+ # object stores anyway).
+ defaults += ",$working_directory:rw,$default_file_path:default_ro"
+ else:
+ defaults += ",$working_directory:rw,$default_file_path:rw"
+
+ if self.app_info.library_import_dir:
+ defaults += ",$library_import_dir:default_ro"
+
+ # Define $defaults that can easily be extended with external library and
+ # index data without deployer worrying about above details.
+ variables["defaults"] = string.Template(defaults).safe_substitute(variables)
+
+ return template.safe_substitute(variables)
+
+
+class DockerContainer(Container, HasDockerLikeVolumes):
+
+ container_type = DOCKER_CONTAINER_TYPE
def containerize_command(self, command):
def prop(name, default):
@@ -338,9 +446,10 @@ def prop(name, default):
if not working_directory:
raise Exception("Cannot containerize command [%s] without defined working directory." % working_directory)
- volumes_raw = self.__expand_str(self.destination_info.get("docker_volumes", "$defaults"))
+ volumes_raw = self._expand_volume_str(self.destination_info.get("docker_volumes", "$defaults"))
+ preprocessed_volumes_str = preprocess_volumes(volumes_raw, self.container_type)
# TODO: Remove redundant volumes...
- volumes = docker_util.DockerVolume.volumes_from_str(volumes_raw)
+ volumes = docker_util.DockerVolume.volumes_from_str(preprocessed_volumes_str)
volumes_from = self.destination_info.get("docker_volumes_from", docker_util.DEFAULT_VOLUMES_FROM)
docker_host_props = dict(
@@ -394,57 +503,61 @@ def __get_destination_overridable_property(self, name):
else:
return getattr(self.app_info, name)
- def __expand_str(self, value):
- if not value:
- return value
- template = string.Template(value)
- variables = dict()
+def docker_cache_path(cache_directory, container_id):
+ file_container_id = container_id.replace("/", "_slash_")
+ cache_file_name = "docker_%s.tar" % file_container_id
+ return os.path.join(cache_directory, cache_file_name)
- def add_var(name, value):
- if value:
- variables[name] = os.path.abspath(value)
- add_var("working_directory", self.job_info.working_directory)
- add_var("job_directory", self.job_info.job_directory)
- add_var("tool_directory", self.job_info.tool_directory)
- add_var("galaxy_root", self.app_info.galaxy_root_dir)
- add_var("default_file_path", self.app_info.default_file_path)
- add_var("library_import_dir", self.app_info.library_import_dir)
+class SingularityContainer(Container, HasDockerLikeVolumes):
- if self.job_info.job_directory and self.job_info.job_directory_type == "pulsar":
- # We have a Pulsar job directory, so everything needed (excluding index
- # files) should be available in job_directory...
- defaults = "$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw"
- else:
- defaults = "$galaxy_root:ro,$tool_directory:ro"
- if self.job_info.job_directory:
- defaults += ",$job_directory:ro"
- if self.app_info.outputs_to_working_directory:
- # Should need default_file_path (which is a course estimate given
- # object stores anyway).
- defaults += ",$working_directory:rw,$default_file_path:ro"
- else:
- defaults += ",$working_directory:rw,$default_file_path:rw"
+ container_type = SINGULARITY_CONTAINER_TYPE
- if self.app_info.library_import_dir:
- defaults += ",$library_import_dir:ro"
+ def containerize_command(self, command):
+ def prop(name, default):
+ destination_name = "singularity_%s" % name
+ return self.destination_info.get(destination_name, default)
- # Define $defaults that can easily be extended with external library and
- # index data without deployer worrying about above details.
- variables["defaults"] = string.Template(defaults).safe_substitute(variables)
+ env = []
+ for pass_through_var in self.tool_info.env_pass_through:
+ env.append((pass_through_var, "$%s" % pass_through_var))
- return template.safe_substitute(variables)
+ # Allow destinations to explicitly set environment variables just for
+ # docker container. Better approach is to set for destination and then
+ # pass through only what tool needs however. (See todo in ToolInfo.)
+ for key, value in six.iteritems(self.destination_info):
+ if key.startswith("singularity_env_"):
+ real_key = key[len("singularity_env_"):]
+ env.append((real_key, value))
+
+ working_directory = self.job_info.working_directory
+ if not working_directory:
+ raise Exception("Cannot containerize command [%s] without defined working directory." % working_directory)
+ volumes_raw = self._expand_volume_str(self.destination_info.get("singularity_volumes", "$defaults"))
+ volumes = docker_util.DockerVolume.volumes_from_str(volumes_raw)
-def docker_cache_path(cache_directory, container_id):
- file_container_id = container_id.replace("/", "_slash_")
- cache_file_name = "docker_%s.tar" % file_container_id
- return os.path.join(cache_directory, cache_file_name)
+ singularity_target_kwds = dict(
+ singularity_cmd=prop("cmd", singularity_util.DEFAULT_SINGULARITY_COMMAND),
+ sudo=asbool(prop("sudo", singularity_util.DEFAULT_SUDO)),
+ sudo_cmd=prop("sudo_cmd", singularity_util.DEFAULT_SUDO_COMMAND),
+ )
+ run_command = singularity_util.build_singularity_run_command(
+ command,
+ self.container_id,
+ volumes=volumes,
+ env=env,
+ working_directory=working_directory,
+ run_extra_arguments=prop("run_extra_arguments", singularity_util.DEFAULT_RUN_EXTRA_ARGUMENTS),
+ **singularity_target_kwds
+ )
+ return run_command
CONTAINER_CLASSES = dict(
docker=DockerContainer,
+ singularity=SingularityContainer,
)
diff --git a/lib/galaxy/tools/deps/docker_util.py b/lib/galaxy/tools/deps/docker_util.py
index 5d27d2b353ad..629cc59d81d3 100644
--- a/lib/galaxy/tools/deps/docker_util.py
+++ b/lib/galaxy/tools/deps/docker_util.py
@@ -28,7 +28,7 @@ def __init__(self, path, to_path=None, how=DEFAULT_VOLUME_MOUNT_TYPE):
self.from_path = path
self.to_path = to_path or path
if not DockerVolume.__valid_how(how):
- raise ValueError("Invalid way to specify docker volume %s" % how)
+ raise ValueError("Invalid way to specify Docker volume %s" % how)
self.how = how
@staticmethod
@@ -41,7 +41,7 @@ def volumes_from_str(volumes_as_str):
@staticmethod
def volume_from_str(as_str):
if not as_str:
- raise ValueError("Failed to parse docker volume from %s" % as_str)
+ raise ValueError("Failed to parse Docker volume from %s" % as_str)
parts = as_str.split(":", 2)
kwds = dict(path=parts[0])
if len(parts) == 2:
diff --git a/lib/galaxy/tools/deps/mulled/invfile.lua b/lib/galaxy/tools/deps/mulled/invfile.lua
index 693d7ecf6f9c..4370e2cf161a 100644
--- a/lib/galaxy/tools/deps/mulled/invfile.lua
+++ b/lib/galaxy/tools/deps/mulled/invfile.lua
@@ -45,6 +45,19 @@ if conda_image == '' then
conda_image = 'continuumio/miniconda:latest'
end
+
+local singularity_image = VAR.SINGULARITY_IMAGE
+if singularity_image == '' then
+ singularity_image = 'quay.io/biocontainers/singularity:2.3--0'
+end
+
+local singularity_image_dir = VAR.SINGULARITY_IMAGE_DIR
+if singularity_image_dir == '' then
+ singularity_image_dir = 'singularity_import'
+end
+
+
+
local destination_base_image = VAR.DEST_BASE_IMAGE
if destination_base_image == '' then
destination_base_image = 'bgruening/busybox-bash:0.1'
@@ -85,6 +98,24 @@ inv.task('build')
.inImage(destination_base_image)
.as(repo)
+if VAR.SINGULARITY ~= '' then
+ inv.task('singularity')
+ .using(singularity_image)
+ .withHostConfig({binds = {"build:/data",singularity_image_dir .. ":/import"}, privileged = true})
+ .withConfig({entrypoint = {'/bin/sh', '-c'}})
+ -- for small containers (less than 7MB), double the size otherwise, add a little bit more as half the conda size
+ .run("size=$(du -sc /data/dist/ | tail -n 1 | cut -f 1 | awk '{print int($1/1024)}' ) && if [ $size -lt '7' ]; then echo $(($size*2)); else echo $(($size+$size*7/10)); fi")
+ .run("singularity create --size `size=$(du -sc /data/dist/ | tail -n 1 | cut -f 1 | awk '{print int($1/1024)}' ) && if [ $size -lt '7' ]; then echo $(($size*2)); else echo $(($size+$size*7/10)); fi` /import/" .. VAR.SINGULARITY_IMAGE_NAME)
+ .run('mkdir -p /usr/local/var/singularity/mnt/container && singularity bootstrap /import/' .. VAR.SINGULARITY_IMAGE_NAME .. ' /import/Singularity')
+ .run('chown ' .. VAR.USER_ID .. ' /import/' .. VAR.SINGULARITY_IMAGE_NAME)
+end
+
+inv.task('cleanup')
+ .using(conda_image)
+ .withHostConfig({binds = {"build:/data"}})
+ .run('rm', '-rf', '/data/dist')
+
+
if VAR.TEST_BINDS == '' then
inv.task('test')
.using(repo)
@@ -103,9 +134,14 @@ inv.task('push')
inv.task('build-and-test')
.runTask('build')
+ .runTask('singularity')
+ .runTask('cleanup')
.runTask('test')
+
inv.task('all')
.runTask('build')
+ .runTask('singularity')
+ .runTask('cleanup')
.runTask('test')
.runTask('push')
diff --git a/lib/galaxy/tools/deps/mulled/mulled_build.py b/lib/galaxy/tools/deps/mulled/mulled_build.py
index f2cc20f304fb..9fb8724dedac 100644
--- a/lib/galaxy/tools/deps/mulled/mulled_build.py
+++ b/lib/galaxy/tools/deps/mulled/mulled_build.py
@@ -12,6 +12,7 @@
import json
import os
+import shutil
import string
import subprocess
import sys
@@ -24,8 +25,17 @@
from galaxy.tools.deps import commands, installable
+from galaxy.util import safe_makedirs
+
from ._cli import arg_parser
-from .util import build_target, conda_build_target_str, image_name
+from .util import (
+ build_target,
+ conda_build_target_str,
+ create_repository,
+ quay_repository,
+ v1_image_name,
+ v2_image_name,
+)
from ..conda_compat import MetaData
DIRNAME = os.path.dirname(__file__)
@@ -37,6 +47,24 @@
DEFAULT_WORKING_DIR = '/source/'
IS_OS_X = _platform == "darwin"
INVOLUCRO_VERSION = "1.1.2"
+DEST_BASE_IMAGE = os.environ.get('DEST_BASE_IMAGE', None)
+
+SINGULARITY_TEMPLATE = """Bootstrap: docker
+From: bgruening/busybox-bash:0.1
+
+%%setup
+
+ echo "Copying conda environment"
+ mkdir -p /tmp/conda
+ cp -r /data/dist/* /tmp/conda/
+
+%%post
+ mkdir -p /usr/local
+ cp -R /tmp/conda/* /usr/local/
+
+%%test
+ %(container_test)s
+"""
def involucro_link():
@@ -111,23 +139,57 @@ def conda_versions(pkg_name, file_name):
return ret
+class BuildExistsException(Exception):
+ """Exception indicating mull_targets is skipping an existing build.
+
+ If mull_targets is called with rebuild=False and the target built is already published
+ an instance of this exception is thrown.
+ """
+
+
def mull_targets(
targets, involucro_context=None,
- command="build", channels=DEFAULT_CHANNELS, namespace="mulled",
+ command="build", channels=DEFAULT_CHANNELS, namespace="biocontainers",
test='true', test_files=None, image_build=None, name_override=None,
repository_template=DEFAULT_REPOSITORY_TEMPLATE, dry_run=False,
- conda_version=None, verbose=False, binds=DEFAULT_BINDS
+ conda_version=None, verbose=False, binds=DEFAULT_BINDS, rebuild=True,
+ oauth_token=None, hash_func="v2", singularity=False,
+ singularity_image_dir="singularity_import",
):
targets = list(targets)
if involucro_context is None:
involucro_context = InvolucroContext()
+ image_function = v1_image_name if hash_func == "v1" else v2_image_name
+ if len(targets) > 1 and image_build is None:
+ # Force an image build in this case - this seems hacky probably
+ # shouldn't work this way but single case broken else wise.
+ image_build = "0"
+
repo_template_kwds = {
"namespace": namespace,
- "image": image_name(targets, image_build=image_build, name_override=name_override)
+ "image": image_function(targets, image_build=image_build, name_override=name_override)
}
repo = string.Template(repository_template).safe_substitute(repo_template_kwds)
+ if not rebuild or "push" in command:
+ repo_name = repo_template_kwds["image"].split(":", 1)[0]
+ repo_data = quay_repository(repo_template_kwds["namespace"], repo_name)
+ if not rebuild:
+ tags = repo_data.get("tags", [])
+
+ target_tag = None
+ if ":" in repo_template_kwds["image"]:
+ image_name_parts = repo_template_kwds["image"].split(":")
+ assert len(image_name_parts) == 2, ": not allowed in image name [%s]" % repo_template_kwds["image"]
+ target_tag = image_name_parts[1]
+
+ if tags and (target_tag is None or target_tag in tags):
+ raise BuildExistsException()
+ if "push" in command and "error_type" in repo_data and oauth_token:
+ # Explicitly create the repository so it can be built as public.
+ create_repository(repo_template_kwds["namespace"], repo_name, oauth_token)
+
for channel in channels:
if channel.startswith('file://'):
bind_path = channel.lstrip('file://')
@@ -144,8 +206,17 @@ def mull_targets(
'-set', "REPO='%s'" % repo,
'-set', "BINDS='%s'" % bind_str,
]
+
+ if DEST_BASE_IMAGE:
+ involucro_args.extend(["-set", "DEST_BASE_IMAGE='%s'" % DEST_BASE_IMAGE])
if verbose:
involucro_args.extend(["-set", "VERBOSE='1'"])
+ if singularity:
+ singularity_image_name = repo_template_kwds['image']
+ involucro_args.extend(["-set", "SINGULARITY='1'"])
+ involucro_args.extend(["-set", "SINGULARITY_IMAGE_NAME='%s'" % singularity_image_name])
+ involucro_args.extend(["-set", "SINGULARITY_IMAGE_DIR='%s'" % singularity_image_dir])
+ involucro_args.extend(["-set", "USER_ID='%s:%s'" % (os.getuid(), os.getgid() )])
if conda_version is not None:
verbose = "--verbose" if verbose else "--quiet"
involucro_args.extend(["-set", "PREINSTALL='conda install %s --yes conda=%s'" % (verbose, conda_version)])
@@ -165,7 +236,18 @@ def mull_targets(
print(" ".join(involucro_context.build_command(involucro_args)))
if not dry_run:
ensure_installed(involucro_context, True)
- return involucro_context.exec_command(involucro_args)
+ if singularity:
+ if not os.path.exists(singularity_image_dir):
+ safe_makedirs(singularity_image_dir)
+ with open(os.path.join(singularity_image_dir, 'Singularity'), 'w+') as sin_def:
+ fill_template = SINGULARITY_TEMPLATE % {'container_test': test}
+ sin_def.write(fill_template)
+ ret = involucro_context.exec_command(involucro_args)
+ if singularity:
+ # we can not remove this folder as it contains the image wich is owned by root
+ pass
+ # shutil.rmtree('./singularity_import')
+ return ret
return 0
@@ -194,7 +276,14 @@ def build_command(self, involucro_args):
def exec_command(self, involucro_args):
cmd = self.build_command(involucro_args)
- return self.shell_exec(" ".join(cmd))
+ # Create ./build dir manually, otherwise Docker will do it as root
+ os.mkdir('./build')
+ try:
+ res = self.shell_exec(" ".join(cmd))
+ finally:
+ # delete build directory in any case
+ shutil.rmtree('./build')
+ return res
def is_installed(self):
return os.path.exists(self.involucro_bin)
@@ -212,9 +301,10 @@ def ensure_installed(involucro_context, auto_init):
def install_involucro(involucro_context=None, to_path=None):
- to_path = involucro_context.involucro_bin
- download_cmd = " ".join(commands.download_command(involucro_link(), to=to_path, quote_url=True))
- full_cmd = "%s && chmod +x %s" % (download_cmd, to_path)
+ install_path = os.path.abspath(involucro_context.involucro_bin)
+ involucro_context.involucro_bin = install_path
+ download_cmd = " ".join(commands.download_command(involucro_link(), to=install_path, quote_url=True))
+ full_cmd = "%s && chmod +x %s" % (download_cmd, install_path)
return involucro_context.shell_exec(full_cmd)
@@ -222,13 +312,15 @@ def add_build_arguments(parser):
"""Base arguments describing how to 'mull'."""
parser.add_argument('--involucro-path', dest="involucro_path", default=None,
help="Path to involucro (if not set will look in working directory and on PATH).")
- parser.add_argument('--force-rebuild', dest="force_rebuild", action="store_true",
- help="Rebuild package even if already published.")
parser.add_argument('--dry-run', dest='dry_run', action="store_true",
help='Just print commands instead of executing them.')
parser.add_argument('--verbose', dest='verbose', action="store_true",
help='Cause process to be verbose.')
- parser.add_argument('-n', '--namespace', dest='namespace', default="mulled",
+ parser.add_argument('--singularity', action="store_true",
+ help='Additionally build a singularity image.')
+ parser.add_argument('--singularity-image-dir', dest="singularity_image_dir",
+ help="Directory to write singularity images too.")
+ parser.add_argument('-n', '--namespace', dest='namespace', default="biocontainers",
help='quay.io namespace.')
parser.add_argument('-r', '--repository_template', dest='repository_template', default=DEFAULT_REPOSITORY_TEMPLATE,
help='Docker repository target for publication (only quay.io or compat. API is currently supported).')
@@ -238,6 +330,10 @@ def add_build_arguments(parser):
help='Dependent conda channels.')
parser.add_argument('--conda-version', dest="conda_version", default=None,
help="Change to specified version of Conda before installing packages.")
+ parser.add_argument('--oauth-token', dest="oauth_token", default=None,
+ help="If set, use this token when communicating with quay.io API.")
+ parser.add_argument('--check-published', dest="rebuild", action='store_false')
+ parser.add_argument('--hash', dest="hash", choices=["v1", "v2"], default="v2")
def add_single_image_arguments(parser):
@@ -273,6 +369,8 @@ def args_to_mull_targets_kwds(args):
kwds["namespace"] = args.namespace
if hasattr(args, "dry_run"):
kwds["dry_run"] = args.dry_run
+ if hasattr(args, "singularity"):
+ kwds["singularity"] = args.singularity
if hasattr(args, "test"):
kwds["test"] = args.test
if hasattr(args, "test_files"):
@@ -289,6 +387,14 @@ def args_to_mull_targets_kwds(args):
kwds["repository_template"] = args.repository_template
if hasattr(args, "conda_version"):
kwds["conda_version"] = args.conda_version
+ if hasattr(args, "oauth_token"):
+ kwds["oauth_token"] = args.oauth_token
+ if hasattr(args, "rebuild"):
+ kwds["rebuild"] = args.rebuild
+ if hasattr(args, "hash"):
+ kwds["hash_func"] = args.hash
+ if hasattr(args, "singularity_image_dir") and args.singularity_image_dir:
+ kwds["singularity_image_dir"] = args.singularity_image_dir
kwds["involucro_context"] = context_from_args(args)
diff --git a/lib/galaxy/tools/deps/mulled/mulled_build_channel.py b/lib/galaxy/tools/deps/mulled/mulled_build_channel.py
index 6463d3ea58d2..23e3021187bf 100644
--- a/lib/galaxy/tools/deps/mulled/mulled_build_channel.py
+++ b/lib/galaxy/tools/deps/mulled/mulled_build_channel.py
@@ -87,6 +87,8 @@ def add_channel_arguments(parser):
parser.add_argument('--diff-hours', dest='diff_hours', default="25",
help='If finding all recently changed recipes, use this number of hours.')
parser.add_argument('--recipes-dir', dest="recipes_dir", default="./bioconda-recipes")
+ parser.add_argument('--force-rebuild', dest="force_rebuild", action="store_true",
+ help="Rebuild package even if already published.")
def main(argv=None):
diff --git a/lib/galaxy/tools/deps/mulled/mulled_build_files.py b/lib/galaxy/tools/deps/mulled/mulled_build_files.py
index 931da7647c16..3ae94e6bc89a 100644
--- a/lib/galaxy/tools/deps/mulled/mulled_build_files.py
+++ b/lib/galaxy/tools/deps/mulled/mulled_build_files.py
@@ -20,6 +20,7 @@
from .mulled_build import (
add_build_arguments,
args_to_mull_targets_kwds,
+ BuildExistsException,
mull_targets,
target_str_to_targets,
)
@@ -33,8 +34,16 @@ def main(argv=None):
parser.add_argument('files', metavar="FILES", default=".",
help="Path to directory (or single file) of TSV files describing composite recipes.")
args = parser.parse_args()
- for targets in generate_targets(args.files):
- mull_targets(targets, **args_to_mull_targets_kwds(args))
+ for (targets, image_build, name_override) in generate_targets(args.files):
+ try:
+ mull_targets(
+ targets,
+ image_build=image_build,
+ name_override=name_override,
+ **args_to_mull_targets_kwds(args)
+ )
+ except BuildExistsException:
+ continue
def generate_targets(target_source):
@@ -59,14 +68,14 @@ def generate_targets(target_source):
def line_to_targets(line_str):
line = _parse_line(line_str)
- return target_str_to_targets(line)
+ return (target_str_to_targets(line.targets), line.image_build, line.name_override)
_Line = collections.namedtuple("_Line", ["targets", "image_build", "name_override"])
def _parse_line(line_str):
- line_parts = line_str.split(" ")
+ line_parts = line_str.split("\t")
assert len(line_parts) < 3, "Too many fields in line [%s], expect at most 3 - targets, image build number, and name override." % line_str
line_parts += [None] * (3 - len(line_parts))
return _Line(*line_parts)
diff --git a/lib/galaxy/tools/deps/mulled/mulled_build_tool.py b/lib/galaxy/tools/deps/mulled/mulled_build_tool.py
index fbe353d38c75..58de0eba9cd7 100644
--- a/lib/galaxy/tools/deps/mulled/mulled_build_tool.py
+++ b/lib/galaxy/tools/deps/mulled/mulled_build_tool.py
@@ -32,7 +32,8 @@ def main(argv=None):
tool_source = get_tool_source(args.tool)
requirements, _ = tool_source.parse_requirements_and_containers()
targets = requirements_to_mulled_targets(requirements)
- mull_targets(targets, **args_to_mull_targets_kwds(args))
+ kwds = args_to_mull_targets_kwds(args)
+ mull_targets(targets, **kwds)
def requirements_to_mulled_targets(requirements):
diff --git a/lib/galaxy/tools/deps/mulled/mulled_search.py b/lib/galaxy/tools/deps/mulled/mulled_search.py
old mode 100644
new mode 100755
index 724956a13351..4e0662d12b5e
--- a/lib/galaxy/tools/deps/mulled/mulled_search.py
+++ b/lib/galaxy/tools/deps/mulled/mulled_search.py
@@ -112,8 +112,8 @@ def get_additional_repository_information(self, repository_string):
def main(argv=None):
parser = argparse.ArgumentParser(description='Searches in a given quay organization for a repository')
- parser.add_argument('-o', '--organization', dest='organization_string', default="mulled",
- help='Change organization. Default is mulled.')
+ parser.add_argument('-o', '--organization', dest='organization_string', default="biocontainers",
+ help='Change organization. Default is biocontainers.')
parser.add_argument('--non-strict', dest='non_strict', action="store_true",
help='Autocorrection of typos activated. Lists more results but can be confusing.\
For too many queries quay.io blocks the request and the results can be incomplete.')
diff --git a/lib/galaxy/tools/deps/mulled/util.py b/lib/galaxy/tools/deps/mulled/util.py
index 6ea62f241c9e..46ede34a55d7 100644
--- a/lib/galaxy/tools/deps/mulled/util.py
+++ b/lib/galaxy/tools/deps/mulled/util.py
@@ -12,16 +12,22 @@
requests = None
+def create_repository(namespace, repo_name, oauth_token):
+ assert oauth_token
+ headers = {'Authorization': 'Bearer %s' % oauth_token}
+ data = {
+ "repository": repo_name,
+ "namespace": namespace,
+ "description": "",
+ "visibility": "public",
+ }
+ requests.post("https://quay.io/api/v1/repository", json=data, headers=headers)
+
+
def quay_versions(namespace, pkg_name):
"""Get all version tags for a Docker image stored on quay.io for supplied package name."""
- if requests is None:
- raise Exception("requets library is unavailable, functionality not available.")
+ data = quay_repository(namespace, pkg_name)
- assert namespace is not None
- assert pkg_name is not None
- url = 'https://quay.io/api/v1/repository/%s/%s' % (namespace, pkg_name)
- response = requests.get(url, timeout=None)
- data = response.json()
if 'error_type' in data and data['error_type'] == "invalid_token":
return []
@@ -31,12 +37,26 @@ def quay_versions(namespace, pkg_name):
return [tag for tag in data['tags'] if tag != 'latest']
-def mulled_tags_for(namespace, image):
+def quay_repository(namespace, pkg_name):
+ if requests is None:
+ raise Exception("requets library is unavailable, functionality not available.")
+
+ assert namespace is not None
+ assert pkg_name is not None
+ url = 'https://quay.io/api/v1/repository/%s/%s' % (namespace, pkg_name)
+ response = requests.get(url, timeout=None)
+ data = response.json()
+ return data
+
+
+def mulled_tags_for(namespace, image, tag_prefix=None):
"""Fetch remote tags available for supplied image name.
The result will be sorted so newest tags are first.
"""
tags = quay_versions(namespace, image)
+ if tag_prefix is not None:
+ tags = [t for t in tags if t.startswith(tag_prefix)]
tags = version_sorted(tags)
return tags
@@ -77,25 +97,49 @@ def conda_build_target_str(target):
return rval
-def image_name(targets, image_build=None, name_override=None):
+def _simple_image_name(targets, image_build=None):
+ target = targets[0]
+ suffix = ""
+ if target.version is not None:
+ if image_build is not None:
+ print("WARNING: Hard-coding image build instead of using Conda build - this is not recommended.")
+ suffix = image_build
+ else:
+ suffix += ":%s" % target.version
+ build = target.build
+ if build is not None:
+ suffix += "--%s" % build
+ return "%s%s" % (target.package_name, suffix)
+
+
+def v1_image_name(targets, image_build=None, name_override=None):
+ """Generate mulled hash version 1 container identifier for supplied arguments.
+
+ If a single target is specified, simply use the supplied name and version as
+ the repository name and tag respectively. If multiple targets are supplied,
+ hash the package names and versions together as the repository name. For mulled
+ version 1 containers the image build is the repository tag (if supplied).
+
+ >>> single_targets = [build_target("samtools", version="1.3.1")]
+ >>> v1_image_name(single_targets)
+ 'samtools:1.3.1'
+ >>> multi_targets = [build_target("samtools", version="1.3.1"), build_target("bwa", version="0.7.13")]
+ >>> v1_image_name(multi_targets)
+ 'mulled-v1-b06ecbd9141f0dbbc0c287375fc0813adfcbdfbd'
+ >>> multi_targets_on_versionless = [build_target("samtools", version="1.3.1"), build_target("bwa")]
+ >>> v1_image_name(multi_targets_on_versionless)
+ 'mulled-v1-bda945976caa5734347fbf7f35066d9f58519e0c'
+ >>> multi_targets_versionless = [build_target("samtools"), build_target("bwa")]
+ >>> v1_image_name(multi_targets_versionless)
+ 'mulled-v1-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40'
+ """
if name_override is not None:
print("WARNING: Overriding mulled image name, auto-detection of 'mulled' package attributes will fail to detect result.")
return name_override
targets = list(targets)
if len(targets) == 1:
- target = targets[0]
- suffix = ""
- if target.version is not None:
- if image_build is not None:
- print("WARNING: Hard-coding image build instead of using Conda build - this is not recommended.")
- suffix = image_build
- else:
- suffix += ":%s" % target.version
- build = target.build
- if build is not None:
- suffix += "--%s" % build
- return "%s%s" % (target.package_name, suffix)
+ return _simple_image_name(targets, image_build=image_build)
else:
targets_order = sorted(targets, key=lambda t: t.package_name)
requirements_buffer = "\n".join(map(conda_build_target_str, targets_order))
@@ -105,6 +149,66 @@ def image_name(targets, image_build=None, name_override=None):
return "mulled-v1-%s%s" % (m.hexdigest(), suffix)
+def v2_image_name(targets, image_build=None, name_override=None):
+ """Generate mulled hash version 2 container identifier for supplied arguments.
+
+ If a single target is specified, simply use the supplied name and version as
+ the repository name and tag respectively. If multiple targets are supplied,
+ hash the package names as the repository name and hash the package versions (if set)
+ as the tag.
+
+ >>> single_targets = [build_target("samtools", version="1.3.1")]
+ >>> v2_image_name(single_targets)
+ 'samtools:1.3.1'
+ >>> multi_targets = [build_target("samtools", version="1.3.1"), build_target("bwa", version="0.7.13")]
+ >>> v2_image_name(multi_targets)
+ 'mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:4d0535c94ef45be8459f429561f0894c3fe0ebcf'
+ >>> multi_targets_on_versionless = [build_target("samtools", version="1.3.1"), build_target("bwa")]
+ >>> v2_image_name(multi_targets_on_versionless)
+ 'mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:b0c847e4fb89c343b04036e33b2daa19c4152cf5'
+ >>> multi_targets_versionless = [build_target("samtools"), build_target("bwa")]
+ >>> v2_image_name(multi_targets_versionless)
+ 'mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40'
+ """
+ if name_override is not None:
+ print("WARNING: Overriding mulled image name, auto-detection of 'mulled' package attributes will fail to detect result.")
+ return name_override
+
+ targets = list(targets)
+ if len(targets) == 1:
+ return _simple_image_name(targets, image_build=image_build)
+ else:
+ targets_order = sorted(targets, key=lambda t: t.package_name)
+ package_name_buffer = "\n".join(map(lambda t: t.package_name, targets_order))
+ package_hash = hashlib.sha1()
+ package_hash.update(package_name_buffer.encode())
+
+ versions = map(lambda t: t.version, targets_order)
+ if any(versions):
+ # Only hash versions if at least one package has versions...
+ version_name_buffer = "\n".join(map(lambda t: t.version or "null", targets_order))
+ version_hash = hashlib.sha1()
+ version_hash.update(version_name_buffer.encode())
+ version_hash_str = version_hash.hexdigest()
+ else:
+ version_hash_str = ""
+
+ if not image_build:
+ build_suffix = ""
+ elif version_hash_str:
+ # tagged verson is -
+ build_suffix = "-%s" % image_build
+ else:
+ # tagged version is simply the build
+ build_suffix = image_build
+ suffix = ""
+ if version_hash_str or build_suffix:
+ suffix = ":%s%s" % (version_hash_str, build_suffix)
+ return "mulled-v2-%s%s" % (package_hash.hexdigest(), suffix)
+
+
+image_name = v1_image_name # deprecated
+
__all__ = (
"build_target",
"conda_build_target_str",
@@ -113,5 +217,7 @@ def image_name(targets, image_build=None, name_override=None):
"quay_versions",
"split_tag",
"Target",
+ "v1_image_name",
+ "v2_image_name",
"version_sorted",
)
diff --git a/lib/galaxy/tools/deps/singularity_util.py b/lib/galaxy/tools/deps/singularity_util.py
new file mode 100644
index 000000000000..d850c5c7b9c0
--- /dev/null
+++ b/lib/galaxy/tools/deps/singularity_util.py
@@ -0,0 +1,58 @@
+from six.moves import shlex_quote
+
+
+DEFAULT_WORKING_DIRECTORY = None
+DEFAULT_SINGULARITY_COMMAND = "singularity"
+DEFAULT_SUDO = False
+DEFAULT_SUDO_COMMAND = "sudo"
+DEFAULT_RUN_EXTRA_ARGUMENTS = None
+
+
+def build_singularity_run_command(
+ container_command,
+ image,
+ volumes=[],
+ env=[],
+ working_directory=DEFAULT_WORKING_DIRECTORY,
+ singularity_cmd=DEFAULT_SINGULARITY_COMMAND,
+ run_extra_arguments=DEFAULT_RUN_EXTRA_ARGUMENTS,
+ sudo=DEFAULT_SUDO,
+ sudo_cmd=DEFAULT_SUDO_COMMAND,
+):
+ command_parts = []
+ # http://singularity.lbl.gov/docs-environment-metadata
+ for (key, value) in env:
+ command_parts.extend(["SINGULARITYENV_%s=%s" % (key, value)])
+ command_parts += _singularity_prefix(
+ singularity_cmd=singularity_cmd,
+ sudo=sudo,
+ sudo_cmd=sudo_cmd,
+ )
+ command_parts.append("exec")
+ for volume in volumes:
+ command_parts.extend(["-B", shlex_quote(str(volume))])
+ if working_directory:
+ command_parts.extend(["--pwd", shlex_quote(working_directory)])
+ if run_extra_arguments:
+ command_parts.append(run_extra_arguments)
+ full_image = image
+ command_parts.append(shlex_quote(full_image))
+ command_parts.append(container_command)
+ return " ".join(command_parts)
+
+
+def _singularity_prefix(
+ singularity_cmd=DEFAULT_SINGULARITY_COMMAND,
+ sudo=DEFAULT_SUDO,
+ sudo_cmd=DEFAULT_SUDO_COMMAND,
+ **kwds
+):
+ """Prefix to issue a singularity command."""
+ command_parts = []
+ if sudo:
+ command_parts.append(sudo_cmd)
+ command_parts.append(singularity_cmd)
+ return command_parts
+
+
+__all__ = ("build_singularity_run_command",)
diff --git a/lib/galaxy/tools/xsd/galaxy.xsd b/lib/galaxy/tools/xsd/galaxy.xsd
index 3dc11bcf1fb1..3d7bc3ef7a16 100644
--- a/lib/galaxy/tools/xsd/galaxy.xsd
+++ b/lib/galaxy/tools/xsd/galaxy.xsd
@@ -296,7 +296,7 @@ resolver.
- This value describes the type of container that the tool may be executed in and currently must be 'docker'.
+ This value describes the type of container that the tool may be executed in and currently must be ``docker``.
@@ -354,7 +354,7 @@ Read more about configuring Galaxy to run Docker jobs
+
+
+
- This value is the name of the executable code file, and is called in the exec_before_process(), exec_before_job(), exec_after_process() and exec_after_job()( methods.
+ This value is the name of the executable code file, and is called in the ``exec_before_process()``, ``exec_before_job()``, ``exec_after_process()`` and ``exec_after_job()`` methods.
+
+
+
+
+
+ **Deprecated** Map a hook to a function defined in the code file.
+
+
+
+ Function defined in the code file to which the ``exec_after_process`` hook should be mapped
@@ -1169,7 +1182,7 @@ it may be inconvenient to upload the entiry file and this can be used instead.
`__.
+If ``compare`` is set to ``diff``, attempt to decompress both produced output and expected output files if needed before performing the diff. This flag is useful for testing gzipped outputs that are non-deterministic despite having deterministic decompressed contents. This is available in Galaxy 17.05+ and was introduced in [pull request #3550](https://github.com/galaxyproject/galaxy/pull/3550).
]]>
@@ -1956,7 +1969,7 @@ variable:
--color $adv.plot_color
```
-Further examples can be found in the [test case](https://github.com/galaxyproject/galaxy/blob/master/test/functional/tools/section.xml) from [PR #35](https://github.com/galaxyproject/galaxy/pull/35)
+Further examples can be found in the [test case](https://github.com/galaxyproject/galaxy/blob/master/test/functional/tools/section.xml) from [pull request #35](https://github.com/galaxyproject/galaxy/pull/35).
]]>
@@ -2646,7 +2659,7 @@ For newer tools with ``profile>=16.04``, the default behavior is ``exit_code``.
Legacy tools default to ``default`` behavior described above (erroring if the tool
produces any standard error output).
-See [PR 117](https://github.com/galaxyproject/galaxy/pull/117) for more implementation
+See [pull request 117](https://github.com/galaxyproject/galaxy/pull/117) for more implementation
information and discussion on the ``detect_errors`` attribute.
#### ``strict``
@@ -4972,7 +4985,7 @@ the desired input parameter (e.g. ``input="out_format"`` above).
This must be a possible value of the ``input``
parameter (e.g. ``value="interval"`` above), or of the deprecated ``input_dataset``'s
-``attribute.
+attribute.
diff --git a/lib/galaxy/web/framework/helpers/grids.py b/lib/galaxy/web/framework/helpers/grids.py
index ea569363724c..16934753d65f 100644
--- a/lib/galaxy/web/framework/helpers/grids.py
+++ b/lib/galaxy/web/framework/helpers/grids.py
@@ -7,7 +7,7 @@
from sqlalchemy.sql.expression import and_, false, func, null, or_, true
from galaxy.model.item_attrs import RuntimeException, UsesAnnotations, UsesItemRatings
-from galaxy.util import sanitize_text, unicodify
+from galaxy.util import restore_text, sanitize_text, unicodify
from galaxy.util.odict import odict
from galaxy.web.framework import decorators, url_for
from galaxy.web.framework.helpers import iff
@@ -65,6 +65,7 @@ def __call__( self, trans, **kwargs ):
# FIXME: pretty sure this is only here to pass along, can likely be eliminated
status = kwargs.get( 'status', None )
message = kwargs.get( 'message', None )
+ dict_format = kwargs.get( 'dict_format', False )
# Build a base filter and sort key that is the combination of the saved state and defaults.
# Saved state takes preference over defaults.
base_filter = {}
@@ -285,31 +286,147 @@ def url( *args, **kwargs ):
# utf-8 unicode; however, this would require encoding the object as utf-8 before returning the grid
# results via a controller method, which is require substantial changes. Hence, for now, return grid
# as str.
- page = trans.fill_template( iff( async_request, self.async_template, self.template ),
- grid=self,
- query=query,
- cur_page_num=page_num,
- num_pages=num_pages,
- num_page_links=self.num_page_links,
- default_filter_dict=self.default_filter,
- cur_filter_dict=cur_filter_dict,
- sort_key=sort_key,
- current_item=current_item,
- ids=kwargs.get( 'id', [] ),
- url=url,
- status=status,
- message=message,
- info_text=self.info_text,
- use_panels=self.use_panels,
- use_hide_message=self.use_hide_message,
- advanced_search=self.advanced_search,
- show_item_checkboxes=( self.show_item_checkboxes or
- kwargs.get( 'show_item_checkboxes', '' ) in [ 'True', 'true' ] ),
- # Pass back kwargs so that grid template can set and use args without
- # grid explicitly having to pass them.
- kwargs=kwargs )
+ if not dict_format:
+ page = trans.fill_template( iff( async_request, self.async_template, self.template ),
+ grid=self,
+ query=query,
+ cur_page_num=page_num,
+ num_pages=num_pages,
+ num_page_links=self.num_page_links,
+ default_filter_dict=self.default_filter,
+ cur_filter_dict=cur_filter_dict,
+ sort_key=sort_key,
+ current_item=current_item,
+ ids=kwargs.get( 'id', [] ),
+ url=url,
+ status=status,
+ message=message,
+ info_text=self.info_text,
+ use_panels=self.use_panels,
+ use_hide_message=self.use_hide_message,
+ advanced_search=self.advanced_search,
+ show_item_checkboxes=( self.show_item_checkboxes or
+ kwargs.get( 'show_item_checkboxes', '' ) in [ 'True', 'true' ] ),
+ # Pass back kwargs so that grid template can set and use args without
+ # grid explicitly having to pass them.
+ kwargs=kwargs )
+ trans.log_action( trans.get_user(), text_type( "grid.view" ), context, params )
+ return page
+
+ grid_config = {
+ 'title' : self.title,
+ 'url_base' : trans.request.path_url,
+ 'async' : self.use_async,
+ 'async_ops' : [],
+ 'categorical_filters' : {},
+ 'filters' : cur_filter_dict,
+ 'sort_key' : sort_key,
+ 'show_item_checkboxes' : self.show_item_checkboxes or kwargs.get( 'show_item_checkboxes', '' ) in [ 'True', 'true' ],
+ 'cur_page_num' : page_num,
+ 'num_pages' : num_pages,
+ 'num_page_links' : self.num_page_links,
+ 'status' : status,
+ 'message' : restore_text(message),
+ 'global_actions' : [],
+ 'operations' : [],
+ 'items' : [],
+ 'columns' : [],
+ 'model_class' : str( self.model_class ),
+ 'use_paging' : self.use_paging,
+ 'legend' : self.legend,
+ 'current_item_id' : False,
+ 'use_hide_message' : self.use_hide_message,
+ 'default_filter_dict' : self.default_filter,
+ 'advanced_search' : self.advanced_search,
+ 'info_text' : self.info_text,
+ 'url' : url(dict()),
+ 'refresh_frames' : kwargs.get( 'refresh_frames', [] )
+ }
+ if current_item:
+ grid_config['current_item_id'] = current_item.id
+ for column in self.columns:
+ href = None
+ extra = ''
+ if column.sortable:
+ if sort_key.endswith(column.key):
+ if not sort_key.startswith("-"):
+ href = url( sort=( "-" + column.key ) )
+ extra = "↓"
+ else:
+ href = url( sort=( column.key ) )
+ extra = "↑"
+ else:
+ href = url( sort=column.key )
+ grid_config['columns'].append({
+ 'key' : column.key,
+ 'visible' : column.visible,
+ 'nowrap' : column.nowrap,
+ 'attach_popup' : column.attach_popup,
+ 'label_id_prefix' : column.label_id_prefix,
+ 'sortable' : column.sortable,
+ 'label' : column.label,
+ 'filterable' : column.filterable,
+ 'is_text' : isinstance(column, TextColumn),
+ 'href' : href,
+ 'extra' : extra
+ })
+ for operation in self.operations:
+ grid_config['operations'].append({
+ 'allow_multiple' : operation.allow_multiple,
+ 'allow_popup' : operation.allow_popup,
+ 'target' : operation.target,
+ 'label' : operation.label,
+ 'confirm' : operation.confirm,
+ 'global_operation' : False
+ })
+ if operation.allow_multiple:
+ grid_config['show_item_checkboxes'] = True
+ if operation.global_operation:
+ grid_config['global_operation'] = url( ** (operation.global_operation()) )
+ for action in self.global_actions:
+ grid_config['global_actions'].append({
+ 'url_args' : url(**action.url_args),
+ 'label' : action.label,
+ 'target' : action.target
+ })
+ for operation in [op for op in self.operations if op.async_compatible]:
+ grid_config['async_ops'].append(operation.label.lower())
+ for column in self.columns:
+ if column.filterable is not None and not isinstance( column, TextColumn ):
+ grid_config['categorical_filters'][column.key] = dict([ (filter.label, filter.args) for filter in column.get_accepted_filters() ])
+ for i, item in enumerate( query ):
+ item_dict = {
+ 'id' : item.id,
+ 'encode_id' : trans.security.encode_id(item.id),
+ 'link' : [],
+ 'operation_config' : {},
+ 'column_config' : {}
+ }
+ for column in self.columns:
+ if column.visible:
+ link = column.get_link(trans, self, item)
+ if link:
+ link = url(**link)
+ else:
+ link = None
+ target = column.target
+ value = column.get_value( trans, self, item )
+ if isinstance(value, str):
+ value = unicode(value, 'utf-8')
+ value = value.replace('/', '//')
+ item_dict['column_config'][column.label] = {
+ 'link' : link,
+ 'value' : value,
+ 'target' : target
+ }
+ for operation in self.operations:
+ item_dict['operation_config'][operation.label] = {
+ 'allowed' : operation.allowed(item),
+ 'url_args' : url( **operation.get_url_args( item ) )
+ }
+ grid_config['items'].append(item_dict)
trans.log_action( trans.get_user(), text_type( "grid.view" ), context, params )
- return page
+ return grid_config
def get_ids( self, **kwargs ):
id = []
diff --git a/lib/galaxy/webapps/galaxy/api/history_contents.py b/lib/galaxy/webapps/galaxy/api/history_contents.py
index 42c5a3705943..e7bb9489aa62 100644
--- a/lib/galaxy/webapps/galaxy/api/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/history_contents.py
@@ -12,6 +12,7 @@
from galaxy.web import _future_expose_api as expose_api
from galaxy.web import _future_expose_api_raw as expose_api_raw
from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous
+from galaxy.web import _future_expose_api_raw_anonymous as expose_api_raw_anonymous
from galaxy.web.base.controller import BaseAPIController
from galaxy.web.base.controller import UsesLibraryMixin
@@ -23,8 +24,11 @@
from galaxy.managers import hdas
from galaxy.managers import hdcas
from galaxy.managers import folders
-from galaxy.managers.collections_util import api_payload_to_create_params
-from galaxy.managers.collections_util import dictify_dataset_collection_instance
+from galaxy.managers.collections_util import (
+ api_payload_to_create_params,
+ dictify_dataset_collection_instance,
+ get_hda_and_element_identifiers
+)
import logging
log = logging.getLogger( __name__ )
@@ -130,7 +134,7 @@ def show( self, trans, id, history_id, **kwd ):
.. note:: Anonymous users are allowed to get their current history contents
:type id: str
- :param ids: the encoded id of the HDA to return
+ :param id: the encoded id of the HDA to return
:type history_id: str
:param history_id: encoded id string of the HDA's History
@@ -166,6 +170,51 @@ def __show_dataset_collection( self, trans, id, history_id, **kwd ):
trans.response.status = 500
return { 'error': str( e ) }
+ @expose_api_raw_anonymous
+ def download_dataset_collection(self, trans, id, history_id, **kwd):
+ """
+ * GET /api/histories/{history_id}/contents/{id}/download
+
+ Download the content of a HistoryDatasetCollection as a tgz archive
+ while maintaining approximate collection structure.
+
+ :param id: encoded HistoryDatasetCollectionAssociation (HDCA) id
+ :param history_id: encoded id string of the HDCA's History
+ """
+ try:
+ service = trans.app.dataset_collections_service
+ dataset_collection_instance = service.get_dataset_collection_instance(
+ trans=trans,
+ instance_type='history',
+ id=id,
+ )
+ return self.__stream_dataset_collection(trans, dataset_collection_instance)
+
+ except Exception as e:
+ log.exception( "Error in API while creating dataset collection archive" )
+ trans.response.status = 500
+ return { 'error': str( e ) }
+
+ def __stream_dataset_collection(self, trans, dataset_collection_instance):
+ archive_type_string = 'w|gz'
+ archive_ext = 'tgz'
+ if self.app.config.upstream_gzip:
+ archive_type_string = 'w|'
+ archive_ext = 'tar'
+ archive = StreamBall(mode=archive_type_string)
+ names, hdas = get_hda_and_element_identifiers(dataset_collection_instance)
+ for name, hda in zip(names, hdas):
+ if hda.state != hda.states.OK:
+ continue
+ for file_path, relpath in hda.datatype.to_archive(trans=trans, dataset=hda, name=name):
+ archive.add(file=file_path, relpath=relpath)
+ archive_name = "%s: %s.%s" % (dataset_collection_instance.hid, dataset_collection_instance.name, archive_ext)
+ trans.response.set_content_type("application/x-tar")
+ trans.response.headers["Content-Disposition"] = 'attachment; filename="{}"'.format(archive_name)
+ archive.wsgi_status = trans.response.wsgi_status()
+ archive.wsgi_headeritems = trans.response.wsgi_headeritems()
+ return archive.stream
+
@expose_api_anonymous
def create( self, trans, history_id, payload, **kwd ):
"""
diff --git a/lib/galaxy/webapps/galaxy/api/webhooks.py b/lib/galaxy/webapps/galaxy/api/webhooks.py
index ec0bbdaa0e9b..98e3ad1a1d2c 100644
--- a/lib/galaxy/webapps/galaxy/api/webhooks.py
+++ b/lib/galaxy/webapps/galaxy/api/webhooks.py
@@ -57,15 +57,22 @@ def get_all_by_type(self, trans, webhook_type, **kwd):
@expose_api_anonymous_and_sessionless
def get_data(self, trans, webhook_name, **kwd):
"""
- *GET /api/webhooks/{webhook_name}/get_data
+ *GET /api/webhooks/{webhook_name}/get_data/{params}
Returns the result of executing helper function
"""
+ params = {}
+
+ for key, value in kwd.items():
+ params[key] = value
+
webhook = [
webhook
for webhook in self.app.webhooks_registry.webhooks
if webhook.name == webhook_name
]
+
return imp.load_source('helper', webhook[0].helper).main(
trans,
webhook[0],
+ params,
) if webhook and webhook[0].helper != '' else {}
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index 2f7d4457ab79..79b0842a1880 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -108,6 +108,8 @@ def paste_app_factory( global_conf, **kwargs ):
webapp.add_client_route( '/user' )
webapp.add_client_route( '/user/{form_id}' )
webapp.add_client_route( '/workflow' )
+ webapp.add_client_route( '/pages/{action_id}' )
+ webapp.add_client_route( '/datasets/{action_id}' )
webapp.add_client_route( '/workflow/configure_menu' )
webapp.add_client_route( '/custom_builds' )
@@ -344,6 +346,10 @@ def populate_api_routes( webapp, app ):
controller='history_contents', action='archive')
webapp.mapper.connect( '/api/histories/{history_id}/contents/archive/{filename}{.format}',
controller='history_contents', action='archive')
+ webapp.mapper.connect("/api/histories/{history_id}/contents/dataset_collections/{id}/download",
+ controller='history_contents',
+ action='download_dataset_collection',
+ conditions=dict(method=["GET"]))
# ---- visualizations registry ---- generic template renderer
# @deprecated: this route should be considered deprecated
diff --git a/lib/galaxy/webapps/galaxy/controllers/dataset.py b/lib/galaxy/webapps/galaxy/controllers/dataset.py
index 03011ec06d3b..2eff5f295bab 100644
--- a/lib/galaxy/webapps/galaxy/controllers/dataset.py
+++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py
@@ -53,7 +53,6 @@ def get_accepted_filters( self ):
# Grid definition
title = "Saved Datasets"
model_class = model.HistoryDatasetAssociation
- template = '/dataset/grid.mako'
default_sort_key = "-update_time"
columns = [
grids.TextColumn( "Name", key="name",
@@ -463,6 +462,7 @@ def __ok_to_edit_metadata( dataset_id ):
return trans.show_error_message( "You do not have permission to edit this dataset's ( id: %s ) information." % str( dataset_id ) )
@web.expose
+ @web.json
@web.require_login( "see all available datasets" )
def list( self, trans, **kwargs ):
"""List all available datasets"""
@@ -501,9 +501,10 @@ def list( self, trans, **kwargs ):
status, message = trans.webapp.controllers['history']._list_switch( trans, histories )
# Current history changed, refresh history frame; if switching to a dataset, set hda seek.
- trans.template_context['refresh_frames'] = ['history']
+ kwargs['refresh_frames'] = ['history']
if operation == "switch":
hda_ids = [ trans.security.encode_id( hda.id ) for hda in hdas ]
+ # TODO: Highlighting does not work, has to be revisited
trans.template_context[ 'seek_hda_ids' ] = hda_ids
elif operation == "copy to current history":
#
@@ -517,9 +518,10 @@ def list( self, trans, **kwargs ):
status, message = self._copy_datasets( trans, hda_ids, target_histories )
# Current history changed, refresh history frame.
- trans.template_context['refresh_frames'] = ['history']
+ kwargs['refresh_frames'] = ['history']
# Render the list view
+ kwargs[ 'dict_format' ] = True
return self.stored_list_grid( trans, status=status, message=message, **kwargs )
@web.expose
diff --git a/lib/galaxy/webapps/galaxy/controllers/page.py b/lib/galaxy/webapps/galaxy/controllers/page.py
index 9aa9c1999b44..7d9c1b459577 100644
--- a/lib/galaxy/webapps/galaxy/controllers/page.py
+++ b/lib/galaxy/webapps/galaxy/controllers/page.py
@@ -46,13 +46,13 @@ def get_value( self, trans, grid, item ):
key="free-text-search", visible=False, filterable="standard" )
)
global_actions = [
- grids.GridAction( "Add new page", dict( action='create' ) )
+ grids.GridAction( "Add new page", dict( action='create' ), target="inbound" )
]
operations = [
grids.DisplayByUsernameAndSlugGridOperation( "View", allow_multiple=False ),
- grids.GridOperation( "Edit content", allow_multiple=False, url_args=dict( action='edit_content') ),
- grids.GridOperation( "Edit attributes", allow_multiple=False, url_args=dict( action='edit') ),
- grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ),
+ grids.GridOperation( "Edit content", allow_multiple=False, url_args=dict( action='edit_content' ) ),
+ grids.GridOperation( "Edit attributes", allow_multiple=False, url_args=dict( action='edit' ) ),
+ grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), url_args=dict( action='sharing' ) ),
grids.GridOperation( "Delete", confirm="Are you sure you want to delete this page?" ),
]
@@ -308,6 +308,7 @@ def __init__( self, app ):
self.hda_manager = managers.hdas.HDAManager( app )
@web.expose
+ @web.json
@web.require_login()
def list( self, trans, *args, **kwargs ):
""" List user's pages. """
@@ -320,13 +321,10 @@ def list( self, trans, *args, **kwargs ):
item = session.query( model.Page ).get( self.decode_id( id ) )
if operation == "delete":
item.deleted = True
- if operation == "share or publish":
- return self.sharing( trans, **kwargs )
session.flush()
- # HACK: to prevent the insertion of an entire html document inside another
- kwargs[ 'embedded' ] = True
- # Build grid HTML.
+ # Build grid dictionary.
+ kwargs[ 'dict_format' ] = True
grid = self._page_list( trans, *args, **kwargs )
# Build list of pages shared with user.
@@ -339,17 +337,17 @@ def list( self, trans, *args, **kwargs ):
.all()
# Render grid wrapped in panels
- return trans.fill_template( "page/index.mako", embedded_grid=grid, shared_by_others=shared_by_others )
+ grid[ 'shared_by_others' ] = [ {
+ 'username' : p.page.user.username,
+ 'slug' : p.page.slug,
+ 'title' : p.page.title } for p in shared_by_others ]
+ return grid
@web.expose
+ @web.json
def list_published( self, trans, *args, **kwargs ):
- kwargs[ 'embedded' ] = True
- grid = self._all_published_list( trans, *args, **kwargs )
- if 'async' in kwargs:
- return grid
-
- # Render grid wrapped in panels
- return trans.fill_template( "page/list_published.mako", embedded_grid=grid )
+ kwargs[ 'dict_format' ] = True
+ return self._all_published_list( trans, *args, **kwargs )
@web.expose
@web.require_login( "create pages" )
@@ -388,7 +386,7 @@ def create( self, trans, page_title="", page_slug="", page_annotation="" ):
session.flush()
# Display the management page
# trans.set_message( "Page '%s' created" % page.title )
- return trans.response.send_redirect( web.url_for(controller='page', action='list' ) )
+ return trans.response.send_redirect( web.url_for(controller='pages', action='list' ) )
return trans.show_form(
web.FormBuilder( web.url_for(controller='page', action='create'), "Create new page", submit_text="Submit" )
.add_text( "page_title", "Page title", value=page_title, error=page_title_err )
@@ -433,7 +431,7 @@ def edit( self, trans, id, page_title="", page_slug="", page_annotation="" ):
self.add_item_annotation( trans.sa_session, trans.get_user(), page, page_annotation )
session.flush()
# Redirect to page list.
- return trans.response.send_redirect( web.url_for(controller='page', action='list' ) )
+ return trans.response.send_redirect( web.url_for(controller='pages', action='list' ) )
else:
page_title = page.title
page_slug = page.slug
@@ -498,7 +496,7 @@ def sharing( self, trans, id, **kwargs ):
session.flush()
return trans.fill_template( "/sharing_base.mako",
- item=page, use_panels=True )
+ item=page, controller_list='pages', use_panels=True )
@web.expose
@web.require_login( "use Galaxy pages" )
diff --git a/scripts/api/library_upload_dir.py b/scripts/api/library_upload_dir.py
index c4b6ad842342..05a3e0cb56b7 100644
--- a/scripts/api/library_upload_dir.py
+++ b/scripts/api/library_upload_dir.py
@@ -134,7 +134,7 @@ def upload(self):
# So that we can check if it really needs to be uploaded.
already_uploaded = memo_key in self.memo_path.keys()
fid = self.memoized_path(basepath, base_folder=self.folder_id)
- print('[%s/%s] %s/%s uploaded=%' % (idx + 1, len(all_files), fid, fname, already_uploaded))
+ print('[%s/%s] %s/%s uploaded=%s' % (idx + 1, len(all_files), fid, fname, already_uploaded))
if not already_uploaded:
if self.non_local:
diff --git a/static/maps/layout/menu.js.map b/static/maps/layout/menu.js.map
index 0fc28d76be0e..53c702dd2cc9 100644
--- a/static/maps/layout/menu.js.map
+++ b/static/maps/layout/menu.js.map
@@ -1 +1 @@
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diff --git a/static/maps/mvc/collection/collection-view.js.map b/static/maps/mvc/collection/collection-view.js.map
index 49540193d3a3..70767e293b69 100644
--- a/static/maps/mvc/collection/collection-view.js.map
+++ b/static/maps/mvc/collection/collection-view.js.map
@@ -1 +1 @@
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diff --git a/static/maps/mvc/dataset/dataset-li.js.map b/static/maps/mvc/dataset/dataset-li.js.map
index 2f856fdc18e1..0b655fec2820 100644
--- a/static/maps/mvc/dataset/dataset-li.js.map
+++ b/static/maps/mvc/dataset/dataset-li.js.map
@@ -1 +1 @@
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diff --git a/static/maps/mvc/form/form-input.js.map b/static/maps/mvc/form/form-input.js.map
index 0eb52534e88c..f996e2a9eca3 100644
--- a/static/maps/mvc/form/form-input.js.map
+++ b/static/maps/mvc/form/form-input.js.map
@@ -1 +1 @@
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diff --git a/static/maps/mvc/grid/grid-template.js.map b/static/maps/mvc/grid/grid-template.js.map
index 3e46cf610cbc..cb54e841e493 100644
--- a/static/maps/mvc/grid/grid-template.js.map
+++ b/static/maps/mvc/grid/grid-template.js.map
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diff --git a/static/maps/mvc/grid/grid-view.js.map b/static/maps/mvc/grid/grid-view.js.map
index a3cc8abf674c..288d36cc9994 100644
--- a/static/maps/mvc/grid/grid-view.js.map
+++ b/static/maps/mvc/grid/grid-view.js.map
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diff --git a/static/maps/mvc/history/hda-li.js.map b/static/maps/mvc/history/hda-li.js.map
index dcdd3fc759ec..365860dd1fbf 100644
--- a/static/maps/mvc/history/hda-li.js.map
+++ b/static/maps/mvc/history/hda-li.js.map
@@ -1 +1 @@
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diff --git a/static/maps/mvc/history/hdca-li.js.map b/static/maps/mvc/history/hdca-li.js.map
index bc276d1ce638..3a635ac3d29c 100644
--- a/static/maps/mvc/history/hdca-li.js.map
+++ b/static/maps/mvc/history/hdca-li.js.map
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diff --git a/static/maps/mvc/page/page-list.js.map b/static/maps/mvc/page/page-list.js.map
new file mode 100644
index 000000000000..6c2004e9f4c5
--- /dev/null
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diff --git a/static/maps/mvc/tool/tool-form-base.js.map b/static/maps/mvc/tool/tool-form-base.js.map
index 1d48845b1db9..3636f2d60194 100644
--- a/static/maps/mvc/tool/tool-form-base.js.map
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diff --git a/static/maps/mvc/tool/tool-form-composite.js.map b/static/maps/mvc/tool/tool-form-composite.js.map
index 84bff3b56813..c566e6e5f8b8 100644
--- a/static/maps/mvc/tool/tool-form-composite.js.map
+++ b/static/maps/mvc/tool/tool-form-composite.js.map
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\ No newline at end of file
diff --git a/static/maps/mvc/tool/tool-form.js.map b/static/maps/mvc/tool/tool-form.js.map
index 753d6f60f584..76d3535c97a5 100644
--- a/static/maps/mvc/tool/tool-form.js.map
+++ b/static/maps/mvc/tool/tool-form.js.map
@@ -1 +1 @@
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diff --git a/static/maps/mvc/ui/ui-slider.js.map b/static/maps/mvc/ui/ui-slider.js.map
index 2c1fea48a381..f0137b629ad3 100644
--- a/static/maps/mvc/ui/ui-slider.js.map
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diff --git a/static/maps/mvc/webhooks.js.map b/static/maps/mvc/webhooks.js.map
index 9f51bb7ad0b8..7911f11f0a11 100644
--- a/static/maps/mvc/webhooks.js.map
+++ b/static/maps/mvc/webhooks.js.map
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diff --git a/static/maps/onload.js.map b/static/maps/onload.js.map
index 9723faf76e76..4b2c8609f101 100644
--- a/static/maps/onload.js.map
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diff --git a/static/scripts/bundled/admin.bundled.js b/static/scripts/bundled/admin.bundled.js
index c793acffcefc..f437f0f19d8b 100644
--- a/static/scripts/bundled/admin.bundled.js
+++ b/static/scripts/bundled/admin.bundled.js
@@ -1,2 +1,2 @@
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Validation failed."),void(i&&i());if(t.action!==Galaxy.root+"tool_runner/index"){var l=a("").attr({action:t.action,method:t.method,enctype:t.enctype});return r.each(o.inputs,function(e,t){l.append(a("").attr({name:t,value:e}))}),l.hide().appendTo("body").submit().remove(),void(i&&i())}Galaxy.emit.debug("tool-form::submit()","Validation complete.",o),e.request({type:"POST",url:Galaxy.root+"api/tools",data:o,success:function(e){if(i&&i(),n.$el.children().hide(),n.$el.append(n._templateSuccess(e)),e.jobs&&e.jobs.length>0){n.$el.append(a("",{id:"webhook-view"}));new s.WebhookView({urlRoot:Galaxy.root+"api/webhooks/tool"})}parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()},error:function(e){i&&i(),Galaxy.emit.debug("tool-form::submit","Submission failed.",e);var t=!1;if(e&&e.err_data){var s=n.form.data.matchResponse(e.err_data);for(var a in s){n.form.highlight(a,s[a]),t=!0;break}}t||n.modal.show({title:"Job submission failed",body:n._templateError(o,e&&e.err_msg),buttons:{Close:function(){n.modal.hide()}}})}})},validate:function(e){var t=e.inputs,i=-1,n=null;for(var s in t){var o=t[s],a=this.form.data.match(s),r=this.form.field_list[a],l=this.form.input_list[a];if(a&&l&&r){if(!l.optional&&null==o)return this.form.highlight(a),!1;if(o&&o.batch){var c=o.values.length,d=c>0&&o.values[0]&&o.values[0].src;if(d)if(null===n)n=d;else if(n!==d)return this.form.highlight(a,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(i===-1)i=c;else if(i!==c)return this.form.highlight(a,"Please make sure that you select the same number of inputs for all batch mode fields. 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No jobs found.")},_templateError:function(e,t){return a("").addClass("errormessagelarge").append(a("").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. "+(t||""))).append(a("").text(JSON.stringify(e,null,4)))}});return{View:l}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2))},,function(e,t,i){var n,s;(function(o,a){n=[i(4)],s=function(e){var t=o.View.extend({initialize:function(t){this.options=e.merge(t,{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",selectable:!0,cls_tr:""}),this.setElement(this._template()),this.$thead=this.$("thead"),this.$tbody=this.$("tbody"),this.$tmessage=this.$("tmessage"),this.row=this._row(),this.row_count=0},events:{click:"_onclick",dblclick:"_ondblclick"},addHeader:function(e){this.row.append(a("
',"Warning: This is a experimental feature. Most Galaxy tools will not annotate"," citations explicitly at this time. When writing up your analysis, please manually"," review your histories and find all references"," that should be cited in order to completely describe your work. Also, please remember to",' cite Galaxy.',"
"],"element");return o.extend({},t.DatasetListItemView.prototype.templates,{titleBar:e})}();var u=c.extend({className:c.prototype.className+" dataset-collection-element",_swapNewRender:function(e){c.prototype._swapNewRender.call(this,e);var t=this.model.get("state")||"ok";return this.$el.addClass("state-"+t),this.$el},toString:function(){var e=this.model?this.model+"":"(no model)";return"NestedDCDCEListItemView("+e+")"}});return{DCListItemView:c,DCEListItemView:d,DatasetDCEListItemView:h,NestedDCDCEListItemView:u}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1),i(1))},function(e,t,i){var n,s;(function(o,a,r){n=[i(75),i(6),i(5)],s=function(e,t,i){"use strict";var n={defaults:{model_class:"DatasetCollectionElement",element_identifier:null,element_index:null,element_type:null},_mergeObject:function(e){return o.extend(e,e.object,{element_id:e.id}),delete e.object,e},constructor:function(e,t){e=this._mergeObject(e),this.idAttribute="element_id",a.Model.apply(this,arguments)},parse:function(e,t){var i=e;return i=this._mergeObject(i)}},s=a.Model.extend(t.LoggableMixin).extend(n).extend({_logNamespace:"collections"}),l=a.Collection.extend(t.LoggableMixin).extend({_logNamespace:"collections",model:s,toString:function(){return["DatasetCollectionElementCollection(",this.length,")"].join("")}}),c=e.DatasetAssociation.extend(t.mixin(n,{url:function(){return this.has("history_id")?Galaxy.root+"api/histories/"+this.get("history_id")+"/contents/"+this.get("id"):(console.warn("no endpoint for non-hdas within a collection yet"),Galaxy.root+"api/datasets")},defaults:o.extend({},e.DatasetAssociation.prototype.defaults,n.defaults),_downloadQueryParameters:function(){return"?to_ext="+this.get("file_ext")+"&hdca_id="+this.get("parent_hdca_id")+"&element_identifier="+this.get("element_identifier")},constructor:function(e,t){this.debug("\t DatasetDCE.constructor:",e,t),n.constructor.call(this,e,t)},hasDetails:function(){return this.elements&&this.elements.length},toString:function(){var e=this.get("element_identifier");return["DatasetDCE(",e,")"].join("")}})),d=l.extend({model:c,toString:function(){return["DatasetDCECollection(",this.length,")"].join("")}}),h=a.Model.extend(t.LoggableMixin).extend(t.SearchableModelMixin).extend({_logNamespace:"collections",defaults:{collection_type:null,deleted:!1},collectionClass:l,initialize:function(e,t){this.debug(this+"(DatasetCollection).initialize:",e,t,this),this.elements=this._createElementsModel(),this.on("change:elements",function(){this.log("change:elements"),this.elements=this._createElementsModel()})},_createElementsModel:function(){this.debug(this+"._createElementsModel",this.collectionClass,this.get("elements"),this.elements);var e=this.get("elements")||[];this.unset("elements",{silent:!0});var t=this;return o.each(e,function(e,i){o.extend(e,{parent_hdca_id:t.get("id")})}),this.elements=new this.collectionClass(e),this.elements},toJSON:function(){var e=a.Model.prototype.toJSON.call(this);return this.elements&&(e.elements=this.elements.toJSON()),e},inReadyState:function(){var e=this.get("populated");return this.isDeletedOrPurged()||e},hasDetails:function(){return 0!==this.elements.length},getVisibleContents:function(e){return this.elements},parse:function(e,t){var i=a.Model.prototype.parse.call(this,e,t);return i.create_time&&(i.create_time=new Date(i.create_time)),i.update_time&&(i.update_time=new Date(i.update_time)),i},delete:function(e){return this.get("deleted")?r.when():this.save({deleted:!0},e)},undelete:function(e){return!this.get("deleted")||this.get("purged")?r.when():this.save({deleted:!1},e)},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},searchAttributes:["name"],toString:function(){var e=[this.get("id"),this.get("name")||this.get("element_identifier")];return"DatasetCollection("+e.join(",")+")"}}),u=h.extend({collectionClass:d,toString:function(){return"List"+h.prototype.toString.call(this)}}),p=u.extend({toString:function(){return"Pair"+h.prototype.toString.call(this)}}),f=h.extend(t.mixin(n,{constructor:function(e,t){this.debug("\t NestedDCDCE.constructor:",e,t),n.constructor.call(this,e,t)},toString:function(){var e=this.object?""+this.object:this.get("element_identifier");return["NestedDCDCE(",e,")"].join("")}})),g=l.extend({model:f,toString:function(){return["NestedDCDCECollection(",this.length,")"].join("")}}),m=p.extend(t.mixin(n,{constructor:function(e,t){this.debug("\t NestedPairDCDCE.constructor:",e,t),n.constructor.call(this,e,t)},toString:function(){var e=this.object?""+this.object:this.get("element_identifier");return["NestedPairDCDCE(",e,")"].join("")}})),v=g.extend({model:m,toString:function(){return["NestedPairDCDCECollection(",this.length,")"].join("")}}),_=h.extend({collectionClass:v,toString:function(){return["ListPairedDatasetCollection(",this.get("name"),")"].join("")}}),y=u.extend(t.mixin(n,{constructor:function(e,t){this.debug("\t NestedListDCDCE.constructor:",e,t),n.constructor.call(this,e,t)},toString:function(){var e=this.object?""+this.object:this.get("element_identifier");return["NestedListDCDCE(",e,")"].join("")}})),w=g.extend({model:y,toString:function(){return["NestedListDCDCECollection(",this.length,")"].join("")}}),b=h.extend({collectionClass:w,toString:function(){return["ListOfListsDatasetCollection(",this.get("name"),")"].join("")}});return{ListDatasetCollection:u,PairDatasetCollection:p,ListPairedDatasetCollection:_,ListOfListsDatasetCollection:b}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(3),i(1))},function(e,t,i){var n,s;(function(o,a,r,l){n=[i(44),i(11),i(6),i(72),i(8),i(90),i(5),i(87)],s=function(e,t,i,n,s,c,d){"use strict";function h(e,t){var i=e.toJSON(),n=m(i,{defaultHideSourceItems:t,creationFn:function(t,i,n){return t=t.map(function(e){return{id:e.id,name:e.name,src:"dataset"===e.history_content_type?"hda":"hdca"}}),e.createHDCA(t,"list",i,n)}});return n}var u="collections",p=o.View.extend(i.LoggableMixin).extend({_logNamespace:u,tagName:"li",className:"collection-element",initialize:function(e){this.element=e.element||{},this.selected=e.selected||!1},render:function(){return this.$el.attr("data-element-id",this.element.id).attr("draggable",!0).html(this.template({element:this.element})),this.selected&&this.$el.addClass("selected"),this},template:a.template(['',"<%- element.name 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creator")},oncreate:function(){},oncancel:function(){},autoscrollDist:24,highlightClr:"rgba( 64, 255, 255, 1.0 )"},footerSettings:{".hide-originals":"hideOriginals"},initialize:function(e){this.metric("ListCollectionCreator.initialize",e);var t=this;a.each(this.defaultAttributes,function(i,n){i=e[n]||i,t[n]=i}),t.initialElements=e.elements||[],this._setUpCommonSettings(e),this._instanceSetUp(),this._elementsSetUp(),this._setUpBehaviors()},_instanceSetUp:function(){this.selectedIds={},this.$dragging=null,this.blocking=!1},_elementsSetUp:function(){this.invalidElements=[],this.workingElements=[],this.elementViews=[],this.workingElements=this.initialElements.slice(0),this._ensureElementIds(),this._validateElements(),this._mangleDuplicateNames(),this._sortElements()},_ensureElementIds:function(){return this.workingElements.forEach(function(e){e.hasOwnProperty("id")||(e.id=a.uniqueId())}),this.workingElements},_validateElements:function(){var e=this;return e.invalidElements=[],this.workingElements=this.workingElements.filter(function(t){var i=e._isElementInvalid(t);return i&&e.invalidElements.push({element:t,text:i}),!i}),this.workingElements},_isElementInvalid:function(e){if("dataset"!==e.history_content_type)return d("is not a dataset");var i=e.state===t.OK||a.contains(t.NOT_READY_STATES,e.state);return i?e.deleted||e.purged?d("has been deleted or purged"):null:d("has errored, is paused, or is not accessible")},_mangleDuplicateNames:function(){var e=900,t=1,i={};this.workingElements.forEach(function(n){for(var s=n.name;i.hasOwnProperty(s);)if(s=n.name+" ("+t+")",t+=1,t>=e)throw new Error("Safety hit in while loop - thats impressive");n.name=s,i[n.name]=!0})},_sortElements:function(e){},render:function(e,t){return this.workingElements.length .clear-selected").show():this.$(".collection-elements-controls > .clear-selected").hide()},_renderList:function(e,t){var i=this,n=l(""),s=i.$list();a.each(this.elementViews,function(e){e.destroy(),i.removeElementView(e)}),i.workingElements.forEach(function(e){var t=i._createElementView(e);n.append(t.$el)}),i._renderClearSelected(),s.empty().append(n.children()),a.invoke(i.elementViews,"render"),s.height()>s.css("max-height")?s.css("border-width","1px 0px 1px 0px"):s.css("border-width","0px")},_createElementView:function(e){var t=new this.elementViewClass({element:e,selected:a.has(this.selectedIds,e.id)});return this.elementViews.push(t),this._listenToElementView(t),t},_listenToElementView:function(e){var t=this;t.listenTo(e,{select:function(e){var i=e.source.element;e.selected?t.selectedIds[i.id]=!0:delete t.selectedIds[i.id],t.trigger("elements:select",e)},discard:function(e){t.trigger("elements:discard",e)}})},addElementView:function(e){},removeElementView:function(e){delete this.selectedIds[e.element.id],this._renderClearSelected(),this.elementViews=a.without(this.elementViews,e),this.stopListening(e)},_renderNoElementsLeft:function(){this._disableNameAndCreate(!0),this.$(".collection-elements").append(this.templates.noElementsLeft())},_elementToJSON:function(e){return e},createList:function(e){if(!this.workingElements.length){var t=d("No valid elements for final list")+". ";return t+=''+d("Cancel")+" ",t+=d("or"),t+=' '+d("start over")+".",void this._showAlert(t)}var i=this,n=this.workingElements.map(function(e){return i._elementToJSON(e)});return i.blocking=!0,i.creationFn(n,e,i.hideOriginals).always(function(){i.blocking=!1}).fail(function(e,t,n){i.trigger("error",{xhr:e,status:t,message:d("An error occurred while creating this collection")})}).done(function(e,t,n){i.trigger("collection:created",e,t,n),i.metric("collection:created",e),"function"==typeof i.oncreate&&i.oncreate.call(this,e,t,n)})},_setUpBehaviors:function(){return this.on("error",this._errorHandler),this.once("rendered",function(){this.trigger("rendered:initial",this)}),this.on("elements:select",function(e){this._renderClearSelected()}),this.on("elements:discard",function(e){var t=e.source.element;this.removeElementView(e.source),this.workingElements=a.without(this.workingElements,t),this.workingElements.length||this._renderNoElementsLeft()}),this},_errorHandler:function(e){this.error(e);var t=this;if(content=e.message||d("An error occurred"),e.xhr){var i=e.xhr,n=e.message;0===i.readyState&&0===i.status?content+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes."):i.responseJSON?content+=":
",d(["Collections of datasets are permanent, ordered lists of datasets that can be passed to tools and ","workflows in order to have analyses done on each member of the entire group. This interface allows ","you to create a collection and re-order the final collection."].join("")),"
","
","
",d(["Rename elements in the list by clicking on ",'the existing name.'].join("")),"
","
",d(["Discard elements from the final created list by clicking on the ",'"Discard" button.'].join("")),"
","
",d(["Reorder the list by clicking and dragging elements. Select multiple elements by clicking on ",'them and you can then move those selected by dragging the ',"entire group. Deselect them by clicking them again or by clicking the ",'the "Clear selected" link.'].join("")),"
","
",d(['Click the "Start over" link to begin again as if you had just opened ',"the interface."].join("")),"
","
",d(['Click the "Cancel" button to exit the interface.'].join("")),"
","
","
",d(['Once your collection is complete, enter a name and ','click "Create list".'].join("")),"
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','',"<% if( _.size( problems ) ){ %>",d("The following selections could not be included due to problems"),":","
<% _.each( problems, function( problem ){ %>","
<%- problem.element.name %>: <%- problem.text %>
","<% }); %>
","<% } else if( _.size( elements ) < 1 ){ %>",d("No datasets were selected"),".","<% } %>"," ",d("At least one element is needed for the collection"),". ",d("You may need to "),'',d("cancel")," ",d("and reselect new elements"),".","","
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",'"].join(""))}),toString:function(){return"ListCollectionCreator"}}),g=function(e,t,i){var n,o=l.Deferred(),r=Galaxy.modal||new s.View;return t=a.defaults(t||{},{elements:e,oncancel:function(){r.hide(),o.reject("cancelled")},oncreate:function(e,t){r.hide(),o.resolve(t)}}),n=new i(t),r.show({title:t.title||d("Create a collection"),body:n.$el,width:"80%",height:"100%",closing_events:!0}),n.render(),window._collectionCreator=n,o},m=function(e,t){return t=t||{},t.title=d("Create a collection from a list of datasets"),g(e,t,f)};return{DatasetCollectionElementView:p,ListCollectionCreator:f,collectionCreatorModal:g,listCollectionCreatorModal:m,createListCollection:h}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2),i(1),i(1))},function(e,t,i){var n,s;(function(o,a,r,l){n=[i(47),i(11),i(17),i(6),i(5)],s=function(e,t,i,n,s){"use strict";var c="dataset",d=e.ListItemView,h=d.extend({_logNamespace:c,className:d.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log(this+".initialize:",e),d.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank"},_setUpListeners:function(){d.prototype._setUpListeners.call(this);var e=this;return e.listenTo(e.model,{change:function(t){e.model.changedAttributes().state&&e.model.inReadyState()&&e.expanded&&!e.model.hasDetails()?e.model.fetch({silent:!0}).done(function(){e.render()}):o.has(t.changed,"tags")&&1===o.keys(t.changed).length?e.$(".nametags").html(e._renderNametags()):e.render()}})},_fetchModelDetails:function(){var e=this;return e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):a.when()},remove:function(e,t){var i=this;e=e||this.fxSpeed,this.$el.fadeOut(e,function(){r.View.prototype.remove.call(i),t&&t.call(i)})},_swapNewRender:function(e){return d.prototype._swapNewRender.call(this,e),this.model.has("state")&&this.$el.addClass("state-"+this.model.get("state")),
-this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var e=this.model.get("state");if(e===t.NOT_VIEWABLE||e===t.DISCARDED||!this.model.get("accessible"))return null;var n={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged"))n.disabled=!0,n.title=s("Cannot display datasets removed from disk");else if(e===t.UPLOAD)n.disabled=!0,n.title=s("This dataset must finish uploading before it can be viewed");else if(e===t.NEW)n.disabled=!0,n.title=s("This dataset is not yet viewable");else{n.title=s("View data"),n.href=this.model.urls.display;var o=this;n.onclick=function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.addDataset(o.model.get("id")),e.preventDefault())}}return n.faIcon="fa-eye",i(n)},_renderDetails:function(){if(this.model.get("state")===t.NOT_VIEWABLE)return l(this.templates.noAccess(this.model.toJSON(),this));var e=d.prototype._renderDetails.call(this);return e.find(".actions .left").empty().append(this._renderSecondaryActions()),e.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages()),e.find(".display-applications").html(this._renderDisplayApplications()),this._setUpBehaviors(e),e},_renderSummary:function(){var e=this.model.toJSON(),t=this.templates.summaries[e.state];return(t=t||this.templates.summaries.unknown)(e,this)},_renderDetailMessages:function(){var e=this,t=l(''),i=e.model.toJSON();return o.each(e.templates.detailMessages,function(n){t.append(l(n(i,e)))}),t},_renderDisplayApplications:function(){return this.model.isDeletedOrPurged()?"":[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){switch(this.debug("_renderSecondaryActions"),this.model.get("state")){case t.NOT_VIEWABLE:return[];case t.OK:case t.FAILED_METADATA:case t.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return i({title:s("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle",onclick:function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Dataset details",url:this.href}),e.preventDefault(),e.stopPropagation())}})},_renderDownloadButton:function(){return this.model.get("purged")||!this.model.hasData()?null:o.isEmpty(this.model.get("meta_files"))?l(['','',""].join("")):this._renderMetaFileDownloadButton()},_renderMetaFileDownloadButton:function(){var e=this.model.urls;return l(['
"].join(""),{variable:"tool"})});return{ToolParameter:r,IntegerToolParameter:d,SelectToolParameter:u,Tool:p,ToolCollection:f,ToolSearch:v,ToolPanel:_,ToolPanelView:$,ToolFormView:k}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1))},function(e,t,i){var n,s;(function(o,a){n=[i(4)],s=function(e){return o.View.extend({colors:{standard:["c00000","ff0000","ffc000","ffff00","92d050","00b050","00b0f0","0070c0","002060","7030a0"],base:["ffffff","000000","eeece1","1f497d","4f81bd","c0504d","9bbb59","8064a2","4bacc6","f79646"],theme:[["f2f2f2","7f7f7f","ddd9c3","c6d9f0","dbe5f1","f2dcdb","ebf1dd","e5e0ec","dbeef3","fdeada"],["d8d8d8","595959","c4bd97","8db3e2","b8cce4","e5b9b7","d7e3bc","ccc1d9","b7dde8","fbd5b5"],["bfbfbf","3f3f3f","938953","548dd4","95b3d7","d99694","c3d69b","b2a2c7","92cddc","fac08f"],["a5a5a5","262626","494429","17365d","366092","953734","76923c","5f497a","31859b","e36c09"],["7f7f7e","0c0c0c","1d1b10","0f243e","244061","632423","4f6128","3f3151","205867","974806"]]},initialize:function(t){this.options=e.merge(t,{}),this.setElement(this._template()),this.$panel=this.$(".ui-color-picker-panel"),this.$view=this.$(".ui-color-picker-view"),this.$value=this.$(".ui-color-picker-value"),this.$header=this.$(".ui-color-picker-header"),this._build(),this.visible=!1,this.value(this.options.value),this.$boxes=this.$(".ui-color-picker-box");var i=this;this.$boxes.on("click",function(){i.value(a(this).css("background-color")),i.$header.trigger("click")}),this.$header.on("click",function(){i.visible=!i.visible,i.visible?i.$view.fadeIn("fast"):i.$view.fadeOut("fast")})},value:function(e){return void 0!==e&&null!==e&&(this.$value.css("background-color",e),this.$(".ui-color-picker-box").empty(),this.$(this._getValue()).html(this._templateCheck()),this.options.onchange&&this.options.onchange(e)),this._getValue()},_getValue:function(){function e(e){return("0"+parseInt(e).toString(16)).slice(-2)}var t=this.$value.css("background-color");return t=t.match(/^rgb\((\d+),\s*(\d+),\s*(\d+)\)$/),t?"#"+e(t[1])+e(t[2])+e(t[3]):null},_build:function(){this._content({colors:this.colors.base});for(var e in this.colors.theme){var t={};0==e?t.bottom=!0:e!=this.colors.theme.length-1?(t.top=!0,t.bottom=!0):t.top=!0,t.colors=this.colors.theme[e],this._content(t)}this._content({colors:this.colors.standard})},_content:function(e){var t=e.colors,i=a(this._templateContent()),n=i.find(".line");this.$panel.append(i);for(var s in t){var o=a(this._templateBox(t[s]));e.top&&(o.css("border-top","none"),o.css("border-top-left-radius","0px"),o.css("border-top-right-radius","0px")),e.bottom&&(o.css("border-bottom","none"),o.css("border-bottom-left-radius","0px"),o.css("border-bottom-right-radius","0px")),n.append(o)}return i},_templateCheck:function(){return''},_templateContent:function(){return'
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-this.listenTo(this.model,"change:type change:optional change:multiple change:extensions",this._changeType,this),this.render(),this.on("change",function(){e.onchange&&e.onchange(i.value())})},render:function(){this._changeType(),this._changeValue(),this._changeWait()},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},update:function(e){this.model.set("data",e)},value:function(e){void 0!==e&&this.model.set("value",e);var t=this.model.get("current");if(this.config[t]){var i=this.fields[t].value();if(null!==i&&(i=a.isArray(i)?i:[i],i.length>0)){var n=this._batch({values:[]});for(var s in i){var o=this.history[i[s]+"_"+this.config[t].src];if(!o)return Galaxy.emit.debug("ui-select-content::value()","Requested details not found for '"+i[s]+"'."),null;n.values.push(o)}return n.values.sort(function(e,t){return e.hid-t.hid}),n}}else Galaxy.emit.debug("ui-select-content::value()","Invalid value/source '"+e+"'.");return null},_changeCurrent:function(){var e=this;r.each(this.fields,function(t,i){e.model.get("current")==i?(t.$el.show(),r.each(e.$batch,function(t,n){t[e.config[i].batch==n?"show":"hide"]()}),e.button_type.value(i)):t.$el.hide()})},_changeType:function(){var n=this,o=(this.model.get("flavor")?this.model.get("flavor")+"_":"")+String(this.model.get("type"))+(this.model.get("multiple")?"_multiple":"");s[o]?this.config=s[o]:(this.config=s.data,Galaxy.emit.debug("ui-select-content::_changeType()","Invalid configuration/type id '"+o+"'."));var a=n.model.get("data"),l=e.textify(this.model.get("extensions")),c=this.model.get("src_labels");this.fields=[],this.button_data=[],r.each(this.config,function(e,t){n.button_data.push({value:t,icon:e.icon,tooltip:e.tooltip}),n.fields.push(new i.View({optional:n.model.get("optional"),multiple:e.multiple,searchable:!e.multiple||a&&a[e.src]&&a[e.src].length>n.model.get("pagelimit"),selectall:!1,error_text:"No "+(l?l+" ":"")+(c[e.src]||"content")+" available.",onchange:function(){n.trigger("change")}}))}),this.button_type=new t.RadioButton.View({value:this.model.get("current"),data:this.button_data,onchange:function(e){n.model.set("current",e),n.trigger("change")}}),this.$el.empty();var d=0;this.fields.length>1&&(this.$el.append(this.button_type.$el),d=Math.max(0,36*this.fields.length)+"px"),r.each(this.fields,function(e){n.$el.append(e.$el.css({"margin-left":d}))}),r.each(this.$batch,function(e,t){n.$el.append(e.css({"margin-left":d}))}),this.model.set("current",0),this._changeCurrent(),this._changeData()},_changeWait:function(){var e=this;r.each(this.fields,function(t){t[e.model.get("wait")?"wait":"unwait"]()})},_changeData:function(){var e=this.model.get("data"),t=this,i={};r.each(e,function(e,n){i[n]=[],r.each(e,function(e){i[n].push({hid:e.hid,keep:e.keep,label:e.hid+": "+e.name,value:e.id,tags:e.tags}),t.history[e.id+"_"+n]=e})}),r.each(this.config,function(e,n){i[e.src]&&t.fields[n].add(i[e.src],function(e,t){return t.hid-e.hid})})},_changeValue:function(){var e=this.model.get("value");if(e&&e.values&&e.values.length>0){var t=[];r.each(e.values,function(e){t.push(e.id)});for(var i=e.values[0].src,n=e.values.length>1,s=0;s
This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at '+this.options.ftp_upload_site+' using your Galaxy credentials (email address and password).
'}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2))},function(e,t,i){var n,s;(function(o,a,r){n=[i(4)],s=function(e){return o.View.extend({options:{class_check:"fa-check-square-o",class_uncheck:"fa-square-o",parameters:[{id:"space_to_tab",title:"Convert spaces to tabs"},{id:"to_posix_lines",title:"Use POSIX standard"}]},initialize:function(e){this.model=e.model,this.setElement(a("").addClass("upload-settings")),this.$el.append(a("").addClass("upload-settings-cover")),this.$el.append(a("
','<% if( collection.collection_type === "list" ){ %>',s("a list of datasets"),'<% } else if( collection.collection_type === "paired" ){ %>',s("a pair of datasets"),'<% } else if( collection.collection_type === "list:paired" ){ %>',s("a list of paired datasets"),'<% } else if( collection.collection_type === "list:list" ){ %>',s("a list of dataset lists"),"<% } %>","
","
",'',"
"],"collection");return o.extend(o.clone(r.prototype.templates),{controls:e})}();var c=l.extend({DatasetDCEViewClass:i.DatasetDCEListItemView,toString:function(){return"ListCollectionView("+(this.model?this.model.get("name"):"")+")"}}),d=c.extend({toString:function(){return"PairCollectionView("+(this.model?this.model.get("name"):"")+")"}}),h=l.extend({NestedDCDCEViewClass:i.NestedDCDCEListItemView.extend({foldoutPanelClass:d}),toString:function(){return"ListOfPairsCollectionView("+(this.model?this.model.get("name"):"")+")"}}),u=l.extend({NestedDCDCEViewClass:i.NestedDCDCEListItemView.extend({foldoutPanelClass:d}),toString:function(){return"ListOfListsCollectionView("+(this.model?this.model.get("name"):"")+")"}});return{CollectionView:l,ListCollectionView:c,PairCollectionView:d,ListOfPairsCollectionView:h,ListOfListsCollectionView:u}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2))},function(e,t,i){var n,s;(function(o,a){n=[i(11),i(38),i(48),i(70),i(17),i(6),i(5)],s=function(e,t,i,n,s,r,l){"use strict";var c=t.DatasetListItemView,d=c.extend({initialize:function(e){c.prototype.initialize.call(this,e),this.hasUser=e.hasUser,this.purgeAllowed=e.purgeAllowed||!1,this.tagsEditorShown=e.tagsEditorShown||!1,this.annotationEditorShown=e.annotationEditorShown||!1},_renderPrimaryActions:function(){var t=c.prototype._renderPrimaryActions.call(this);return this.model.get("state")===e.NOT_VIEWABLE?t:c.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){if(this.model.get("state")===e.DISCARDED||!this.model.get("accessible"))return null;var t=this.model.get("purged"),i=this.model.get("deleted"),n={title:l("Edit attributes"),href:this.model.urls.edit,target:this.linkTarget,faIcon:"fa-pencil",classes:"edit-btn"};return i||t?(n.disabled=!0,t?n.title=l("Cannot edit attributes of datasets removed from disk"):i&&(n.title=l("Undelete dataset to edit attributes"))):o.contains([e.UPLOAD,e.NEW],this.model.get("state"))&&(n.disabled=!0,n.title=l("This dataset is not yet editable")),s(n)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var e=this,t=this.model.isDeletedOrPurged();return s({title:l(t?"Dataset is already deleted":"Delete"),disabled:t,faIcon:"fa-times",classes:"delete-btn",onclick:function(){e.$el.find(".icon-btn.delete-btn").trigger("mouseout"),e.model.delete()}})},_renderDetails:function(){var t=c.prototype._renderDetails.call(this),i=this.model.get("state");return!this.model.isDeletedOrPurged()&&o.contains([e.OK,e.FAILED_METADATA],i)&&(this._renderTags(t),this._renderAnnotation(t),this._makeDbkeyEditLink(t)),this._setUpBehaviors(t),t},_renderToolHelpButton:function(){var e=this.model.attributes.dataset_id,t=this.model.attributes.creating_job,i=this,n=function(t){var n='
';t.name&&t.help?(n+="Tool help for "+t.name+"",n+=t.help):n+="Tool help is unavailable for this dataset.",n+="
",i.$el.find(".details").append(a.parseHTML(n))},o=function(e){a.ajax({url:Galaxy.root+"api/tools/"+e.tool_id+"/build"}).done(function(e){n(e)}).fail(function(){n({})})};return null===Galaxy.user.id?null:s({title:"Tool Help",classes:"icon-btn",href:"#",faIcon:"fa-question",onclick:function(){i.$el.find(".toolhelp").length>0?i.$el.find(".toolhelp").toggle():a.ajax({url:Galaxy.root+"api/jobs/"+t}).done(function(e){o(e)}).fail(function(){console.log('Failed at recovering job information from the Galaxy API for job id "'+t+'".')})}})},_renderSecondaryActions:function(){var t=c.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case e.UPLOAD:case e.NOT_VIEWABLE:return t;case e.ERROR:return t.unshift(this._renderErrButton()),t.concat([this._renderRerunButton(),this._renderToolHelpButton()]);case e.OK:case e.FAILED_METADATA:return t.concat([this._renderRerunButton(),this._renderVisualizationsButton(),this._renderToolHelpButton()])}return t.concat([this._renderRerunButton(),this._renderToolHelpButton()])},_renderErrButton:function(){return s({title:l("View or report this error"),href:this.model.urls.report_error,classes:"report-error-btn",
-target:this.linkTarget,faIcon:"fa-bug"})},_renderRerunButton:function(){var e=this.model.get("creating_job");if(this.model.get("rerunnable"))return s({title:l("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,faIcon:"fa-refresh",onclick:function(t){t.preventDefault(),Galaxy.router.push("/",{job_id:e})}})},_renderVisualizationsButton:function(){var e=this.model.get("visualizations");if(this.model.isDeletedOrPurged()||!this.hasUser||!this.model.hasData()||o.isEmpty(e))return null;if(!o.isObject(e[0]))return this.warn("Visualizations have been switched off"),null;var t=a(this.templates.visualizations(e,this));return t.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(t.find(".visualization-link").addBack(".visualization-link")),t},_addScratchBookFn:function(e){e.click(function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Visualization",url:a(this).attr("href")}),e.preventDefault(),e.stopPropagation())})},_renderTags:function(e){if(this.hasUser){var t=this;this.tagsEditor=new i.TagsEditor({model:this.model,el:e.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.tagsEditorShown=!0},onhide:function(){t.tagsEditorShown=!1},$activator:s({title:l("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(e){if(this.hasUser){var t=this;this.annotationEditor=new n.AnnotationEditor({model:this.model,el:e.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.annotationEditorShown=!0},onhide:function(){t.annotationEditorShown=!1},$activator:s({title:l("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(e){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var t=a('?').attr("href",this.model.urls.edit).attr("target",this.linkTarget);e.find(".dbkey .value").replaceWith(t)}},events:o.extend(o.clone(c.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(e){this.trigger("edit",this,e)},"click .delete-btn":function(e){this.trigger("delete",this,e)},"click .rerun-btn":function(e){this.trigger("rerun",this,e)},"click .report-err-btn":function(e){this.trigger("report-err",this,e)},"click .visualization-btn":function(e){this.trigger("visualize",this,e)},"click .dbkey a":function(e){this.trigger("edit",this,e)}}),_clickUndeleteLink:function(e){return this.model.undelete(),!1},_clickPurgeLink:function(e){return confirm(l("This will permanently remove the data in your dataset. Are you sure?"))&&this.model.purge(),!1},toString:function(){var e=this.model?this.model+"":"(no model)";return"HDAEditView("+e+")"}});return d.prototype.templates=function(){var e=o.extend({},c.prototype.templates.warnings,{failed_metadata:r.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','
"}}),this.$(".select2-container .select2-search input").off("blur")):(this.$select.find("option").remove(),r.each(this.data,function(t){e.$select.append(o("").attr("value",t.value).html(r.escape(t.label)))})),this.model.set("disabled",0==this.length()),this._changeValue()},_changeDisabled:function(){this.model.get("searchable")?this.$select.select2(this.model.get("disabled")?"disable":"enable"):this.$select.prop("disabled",this.model.get("disabled"))},_changeWait:function(){this.$dropdown.removeClass().addClass("icon-dropdown fa").addClass(this.model.get("wait")?"fa-spinner fa-spin":"fa-caret-down")},_changeVisible:function(){this.$el[this.model.get("visible")?"show":"hide"](),this.$select[this.model.get("visible")?"show":"hide"]()},_changeValue:function(){if(this._setValue(this.model.get("value")),this.model.get("multiple")){if(this.all_button){var e=this._getValue();this.all_button.value(o.isArray(e)?e.length:0,this.length())}}else null!==this._getValue()||this.model.get("optional")||this._setValue(this.first())},value:function(e){return void 0!==e&&this.model.set("value",e),this._getValue()},first:function(){return this.data.length>0?this.data[0].value:null},exists:function(e){return r.findWhere(this.data,{value:e})},text:function(){var e=this._getValue(),t=this.exists(o.isArray(e)?e[0]:e);return t?t.label:""},show:function(){this.model.set("visible",!0)},hide:function(){this.model.set("visible",!1)},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},disabled:function(){return this.model.get("disabled")},enable:function(){this.model.set("disabled",!1)},disable:function(){this.model.set("disabled",!0)},add:function(e,t){r.each(this.model.get("data"),function(t){t.keep&&!r.findWhere(e,{value:t.value})&&e.push(t)}),t&&e&&e.sort(t),this.model.set("data",e)},update:function(e){this.model.set("data",e)},setOnChange:function(e){this.model.set("onchange",e)},length:function(){return o.isArray(this.model.get("data"))?this.model.get("data").length:0},_setValue:function(e){var t=this;if(null!==e&&void 0!==e||(e="__null__"),this.model.get("multiple")?e=o.isArray(e)?e:[e]:o.isArray(e)&&(e=e.length>0?e[0]:"__null__"),this.model.get("searchable")){if(o.isArray(e))val=[],r.each(e,function(e){var i=r.findWhere(t.data2,{id:e});i&&val.push(i)}),e=val;else{var i=r.findWhere(this.data2,{id:e});e=i}this.$select.select2("data",e)}else this.$select.val(e)},_getValue:function(){var t=null;if(this.model.get("searchable")){var i=this.$select.select2("data");i&&(o.isArray(i)?(t=[],i.sort(function(e,t){return e.order-t.order}),r.each(i,function(e){t.push(e.id)})):t=i.id)}else t=this.$select.val();return e.isEmpty(t)?null:t}});return{View:i}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2))},function(e,t,i){var n,s;(function(i){n=[],s=function(){var e=i.Model.extend({defaults:{extension:"auto",genome:"?",url_paste:"",status:"init",info:null,file_name:"",file_mode:"",file_size:0,file_type:null,file_path:"",file_data:null,percentage:0,space_to_tab:!1,to_posix_lines:!0,enabled:!0},reset:function(e){this.clear().set(this.defaults).set(e)}}),t=i.Collection.extend({model:e});return{Model:e,Collection:t}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3))},function(e,t,i){var n,s;(function(a,o,r){n=[i(4),i(7),i(8),i(49),i(28)],s=function(e,t,i,n,s){var l=a.View.extend({initialize:function(s){var a=this;this.modal=parent.Galaxy.modal||new i.View,this.form=new n(e.merge({listen_to_history:!0,always_refresh:!1,customize:function(e){var i=e.model.attributes;i.buttons={execute:execute_btn=new t.Button({icon:"fa-check",tooltip:"Execute: "+i.name+" ("+i.version+")",title:"Execute",cls:"ui-button btn btn-primary",floating:"clear",onclick:function(){execute_btn.wait(),e.portlet.disable(),a.submit(i,function(){execute_btn.unwait(),e.portlet.enable()})}})},i.job_id&&i.job_remap&&i.inputs.push({label:"Resume dependencies from this job",name:"rerun_remap_job_id",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["Yes",i.job_id],["No","__ignore__"]],help:"The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run."})},postchange:function(t,i){var n={tool_id:i.model.get("id"),tool_version:i.model.get("version"),inputs:o.extend(!0,{},i.data.create())};i.wait(!0),Galaxy.emit.debug("tool-form::postchange()","Sending current state.",n),e.request({type:"POST",url:Galaxy.root+"api/tools/"+i.model.get("id")+"/build",data:n,success:function(e){i.update(e),i.wait(!1),Galaxy.emit.debug("tool-form::postchange()","Received new model.",e),t.resolve()},error:function(e){Galaxy.emit.debug("tool-form::postchange()","Refresh request failed.",e),t.reject()}})}},s)),this.deferred=this.form.deferred,this.setElement(""),this.$el.append(this.form.$el)},submit:function(t,i){var n=this,a={tool_id:t.id,tool_version:t.version,inputs:this.form.data.create()};if(this.form.trigger("reset"),!n.validate(a))return Galaxy.emit.debug("tool-form::submit()","Submission canceled. Validation failed."),void(i&&i());if(t.action!==Galaxy.root+"tool_runner/index"){var l=o("").attr({action:t.action,method:t.method,enctype:t.enctype});return r.each(a.inputs,function(e,t){l.append(o("").attr({name:t,value:e}))}),l.hide().appendTo("body").submit().remove(),void(i&&i())}Galaxy.emit.debug("tool-form::submit()","Validation complete.",a),e.request({type:"POST",url:Galaxy.root+"api/tools",data:a,success:function(e){if(i&&i(),n.$el.children().hide(),n.$el.append(n._templateSuccess(e)),e.jobs&&e.jobs.length>0){n.$el.append(o("",{id:"webhook-view"}));new s.WebhookView({urlRoot:Galaxy.root+"api/webhooks/tool",toolId:a.tool_id})}parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()},error:function(e){i&&i(),Galaxy.emit.debug("tool-form::submit","Submission failed.",e);var t=!1;if(e&&e.err_data){var s=n.form.data.matchResponse(e.err_data);for(var o in s){n.form.highlight(o,s[o]),t=!0;break}}t||n.modal.show({title:"Job submission failed",body:n._templateError(a,e&&e.err_msg),buttons:{Close:function(){n.modal.hide()}}})}})},validate:function(e){var t=e.inputs,i=-1,n=null;for(var s in t){var a=t[s],o=this.form.data.match(s),r=this.form.field_list[o],l=this.form.input_list[o];if(o&&l&&r){if(!l.optional&&null==a)return this.form.highlight(o),!1;if(a&&a.batch){var c=a.values.length,d=c>0&&a.values[0]&&a.values[0].src;if(d)if(null===n)n=d;else if(n!==d)return this.form.highlight(o,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(i===-1)i=c;else if(i!==c)return this.form.highlight(o,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains "+c+" selection(s) while a previous field contains "+i+"."),!1}}else Galaxy.emit.debug("tool-form::validate()","Retrieving input objects failed.")}return!0},_templateSuccess:function(e){if(e.jobs&&e.jobs.length>0){var t=e.jobs.length,i=1==t?"1 job has":t+" jobs have",n=o("").addClass("donemessagelarge").append(o("").text(i+" been successfully added to the queue - resulting in the following datasets:"));return r.each(e.outputs,function(e){n.append(o("").addClass("messagerow").append(o("").text(e.hid+": "+e.name)))}),n.append(o("").append("").text("You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.")),n}return this._templateError(e,"Invalid success response. No jobs found.")},_templateError:function(e,t){return o("").addClass("errormessagelarge").append(o("").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. "+(t||""))).append(o("").text(JSON.stringify(e,null,4)))}});return{View:l}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2))},,function(e,t,i){var n,s;(function(a,o){n=[i(4)],s=function(e){var t=a.View.extend({initialize:function(t){this.options=e.merge(t,{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",selectable:!0,cls_tr:""}),this.setElement(this._template()),this.$thead=this.$("thead"),this.$tbody=this.$("tbody"),this.$tmessage=this.$("tmessage"),this.row=this._row(),this.row_count=0},events:{click:"_onclick",dblclick:"_ondblclick"},addHeader:function(e){this.row.append(o("
',"Warning: This is a experimental feature. Most Galaxy tools will not annotate"," citations explicitly at this time. When writing up your analysis, please manually"," review your histories and find all references"," that should be cited in order to completely describe your work. Also, please remember to",' cite Galaxy.',"
"],"element");return a.extend({},t.DatasetListItemView.prototype.templates,{titleBar:e})}();var u=c.extend({className:c.prototype.className+" dataset-collection-element",_swapNewRender:function(e){c.prototype._swapNewRender.call(this,e);var t=this.model.get("state")||"ok";return this.$el.addClass("state-"+t),this.$el},toString:function(){var e=this.model?this.model+"":"(no model)";return"NestedDCDCEListItemView("+e+")"}});return{DCListItemView:c,DCEListItemView:d,DatasetDCEListItemView:h,NestedDCDCEListItemView:u}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1),i(1))},function(e,t,i){var n,s;(function(a,o,r){n=[i(76),i(6),i(5)],s=function(e,t,i){"use strict";var n={defaults:{model_class:"DatasetCollectionElement",element_identifier:null,element_index:null,element_type:null},_mergeObject:function(e){return a.extend(e,e.object,{element_id:e.id}),delete e.object,e},constructor:function(e,t){e=this._mergeObject(e),this.idAttribute="element_id",o.Model.apply(this,arguments)},parse:function(e,t){var i=e;return i=this._mergeObject(i)}},s=o.Model.extend(t.LoggableMixin).extend(n).extend({_logNamespace:"collections"}),l=o.Collection.extend(t.LoggableMixin).extend({_logNamespace:"collections",model:s,toString:function(){return["DatasetCollectionElementCollection(",this.length,")"].join("")}}),c=e.DatasetAssociation.extend(t.mixin(n,{url:function(){return this.has("history_id")?Galaxy.root+"api/histories/"+this.get("history_id")+"/contents/"+this.get("id"):(console.warn("no endpoint for non-hdas within a collection yet"),Galaxy.root+"api/datasets")},defaults:a.extend({},e.DatasetAssociation.prototype.defaults,n.defaults),_downloadQueryParameters:function(){return"?to_ext="+this.get("file_ext")+"&hdca_id="+this.get("parent_hdca_id")+"&element_identifier="+this.get("element_identifier")},constructor:function(e,t){this.debug("\t DatasetDCE.constructor:",e,t),n.constructor.call(this,e,t)},hasDetails:function(){return this.elements&&this.elements.length},toString:function(){var e=this.get("element_identifier");return["DatasetDCE(",e,")"].join("")}})),d=l.extend({model:c,toString:function(){return["DatasetDCECollection(",this.length,")"].join("")}}),h=o.Model.extend(t.LoggableMixin).extend(t.SearchableModelMixin).extend({_logNamespace:"collections",defaults:{collection_type:null,deleted:!1},collectionClass:l,initialize:function(e,t){this.debug(this+"(DatasetCollection).initialize:",e,t,this),this.elements=this._createElementsModel(),this.on("change:elements",function(){this.log("change:elements"),this.elements=this._createElementsModel()})},_createElementsModel:function(){this.debug(this+"._createElementsModel",this.collectionClass,this.get("elements"),this.elements);var e=this.get("elements")||[];this.unset("elements",{silent:!0});var t=this;return a.each(e,function(e,i){a.extend(e,{parent_hdca_id:t.get("id")})}),this.elements=new this.collectionClass(e),this.elements},toJSON:function(){var e=o.Model.prototype.toJSON.call(this);return this.elements&&(e.elements=this.elements.toJSON()),e},inReadyState:function(){var e=this.get("populated");return this.isDeletedOrPurged()||e},hasDetails:function(){return 0!==this.elements.length},getVisibleContents:function(e){return this.elements},parse:function(e,t){var i=o.Model.prototype.parse.call(this,e,t);return i.create_time&&(i.create_time=new Date(i.create_time)),i.update_time&&(i.update_time=new Date(i.update_time)),i},delete:function(e){return this.get("deleted")?r.when():this.save({deleted:!0},e)},undelete:function(e){return!this.get("deleted")||this.get("purged")?r.when():this.save({deleted:!1},e)},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},searchAttributes:["name"],toString:function(){var e=[this.get("id"),this.get("name")||this.get("element_identifier")];return"DatasetCollection("+e.join(",")+")"}}),u=h.extend({collectionClass:d,toString:function(){return"List"+h.prototype.toString.call(this)}}),p=u.extend({toString:function(){return"Pair"+h.prototype.toString.call(this)}}),f=h.extend(t.mixin(n,{constructor:function(e,t){this.debug("\t NestedDCDCE.constructor:",e,t),n.constructor.call(this,e,t)},toString:function(){var e=this.object?""+this.object:this.get("element_identifier");return["NestedDCDCE(",e,")"].join("")}})),g=l.extend({model:f,toString:function(){return["NestedDCDCECollection(",this.length,")"].join("")}}),m=p.extend(t.mixin(n,{constructor:function(e,t){this.debug("\t NestedPairDCDCE.constructor:",e,t),n.constructor.call(this,e,t)},toString:function(){var e=this.object?""+this.object:this.get("element_identifier");return["NestedPairDCDCE(",e,")"].join("")}})),v=g.extend({model:m,toString:function(){return["NestedPairDCDCECollection(",this.length,")"].join("")}}),_=h.extend({collectionClass:v,toString:function(){return["ListPairedDatasetCollection(",this.get("name"),")"].join("")}}),y=u.extend(t.mixin(n,{constructor:function(e,t){this.debug("\t NestedListDCDCE.constructor:",e,t),n.constructor.call(this,e,t)},toString:function(){var e=this.object?""+this.object:this.get("element_identifier");return["NestedListDCDCE(",e,")"].join("")}})),b=g.extend({model:y,toString:function(){return["NestedListDCDCECollection(",this.length,")"].join("")}}),w=h.extend({collectionClass:b,toString:function(){return["ListOfListsDatasetCollection(",this.get("name"),")"].join("")}});return{ListDatasetCollection:u,PairDatasetCollection:p,ListPairedDatasetCollection:_,ListOfListsDatasetCollection:w}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(3),i(1))},function(e,t,i){var n,s;(function(a,o,r,l){n=[i(44),i(11),i(6),i(73),i(8),i(91),i(5),i(88)],s=function(e,t,i,n,s,c,d){"use strict";function h(e,t){var i=e.toJSON(),n=m(i,{defaultHideSourceItems:t,creationFn:function(t,i,n){return t=t.map(function(e){return{id:e.id,name:e.name,src:"dataset"===e.history_content_type?"hda":"hdca"}}),e.createHDCA(t,"list",i,n)}});return n}var u="collections",p=a.View.extend(i.LoggableMixin).extend({_logNamespace:u,tagName:"li",className:"collection-element",initialize:function(e){this.element=e.element||{},this.selected=e.selected||!1},render:function(){return this.$el.attr("data-element-id",this.element.id).attr("draggable",!0).html(this.template({element:this.element})),this.selected&&this.$el.addClass("selected"),this},template:o.template(['',"<%- element.name %>","",'"].join("")),select:function(e){this.$el.toggleClass("selected",e),this.trigger("select",{source:this,selected:this.$el.hasClass("selected")})},discard:function(){var e=this,t=this.$el.parent().width();this.$el.animate({"margin-right":t},"fast",function(){e.trigger("discard",{source:e}),e.destroy()})},destroy:function(){this.off(),this.$el.remove()},events:{click:"_click","click .name":"_clickName","click .discard":"_clickDiscard",dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_click:function(e){e.stopPropagation(),this.select(e)},_clickName:function(e){e.stopPropagation(),e.preventDefault();var t=([d("Enter a new name for the element"),":\n(",d("Note that changing the name here will not rename the dataset"),")"].join(""),prompt(d("Enter a new name for the element")+":",this.element.name));t&&(this.element.name=t,this.render())},_clickDiscard:function(e){e.stopPropagation(),this.discard()},_dragstart:function(e){e.originalEvent&&(e=e.originalEvent),e.dataTransfer.effectAllowed="move",e.dataTransfer.setData("text/plain",JSON.stringify(this.element)),this.$el.addClass("dragging"),this.$el.parent().trigger("collection-element.dragstart",[this])},_dragend:function(e){this.$el.removeClass("dragging"),this.$el.parent().trigger("collection-element.dragend",[this])},_sendToParent:function(e){this.$el.parent().trigger(e)},toString:function(){return"DatasetCollectionElementView()"}}),f=a.View.extend(i.LoggableMixin).extend(n.CollectionCreatorMixin).extend({_logNamespace:u,elementViewClass:p,collectionClass:e.HistoryListDatasetCollection,className:"list-collection-creator collection-creator flex-row-container",minElements:1,defaultAttributes:{creationFn:function(){throw new TypeError("no creation fn for creator")},oncreate:function(){},oncancel:function(){},autoscrollDist:24,highlightClr:"rgba( 64, 255, 255, 1.0 )"},footerSettings:{".hide-originals":"hideOriginals"},initialize:function(e){this.metric("ListCollectionCreator.initialize",e);var t=this;o.each(this.defaultAttributes,function(i,n){i=e[n]||i,t[n]=i}),t.initialElements=e.elements||[],this._setUpCommonSettings(e),this._instanceSetUp(),this._elementsSetUp(),this._setUpBehaviors()},_instanceSetUp:function(){this.selectedIds={},this.$dragging=null,this.blocking=!1},_elementsSetUp:function(){this.invalidElements=[],this.workingElements=[],this.elementViews=[],this.workingElements=this.initialElements.slice(0),this._ensureElementIds(),this._validateElements(),this._mangleDuplicateNames(),this._sortElements()},_ensureElementIds:function(){return this.workingElements.forEach(function(e){e.hasOwnProperty("id")||(e.id=o.uniqueId())}),this.workingElements},_validateElements:function(){var e=this;return e.invalidElements=[],this.workingElements=this.workingElements.filter(function(t){var i=e._isElementInvalid(t);return i&&e.invalidElements.push({element:t,text:i}),!i}),this.workingElements},_isElementInvalid:function(e){if("dataset"!==e.history_content_type)return d("is not a dataset");var i=e.state===t.OK||o.contains(t.NOT_READY_STATES,e.state);return i?e.deleted||e.purged?d("has been deleted or purged"):null:d("has errored, is paused, or is not accessible")},_mangleDuplicateNames:function(){var e=900,t=1,i={};this.workingElements.forEach(function(n){for(var s=n.name;i.hasOwnProperty(s);)if(s=n.name+" ("+t+")",t+=1,t>=e)throw new Error("Safety hit in while loop - thats impressive");n.name=s,i[n.name]=!0})},_sortElements:function(e){},render:function(e,t){return this.workingElements.length .clear-selected").show():this.$(".collection-elements-controls > .clear-selected").hide()},_renderList:function(e,t){var i=this,n=l(""),s=i.$list();o.each(this.elementViews,function(e){e.destroy(),i.removeElementView(e)}),i.workingElements.forEach(function(e){var t=i._createElementView(e);n.append(t.$el)}),i._renderClearSelected(),s.empty().append(n.children()),o.invoke(i.elementViews,"render"),s.height()>s.css("max-height")?s.css("border-width","1px 0px 1px 0px"):s.css("border-width","0px")},_createElementView:function(e){var t=new this.elementViewClass({element:e,selected:o.has(this.selectedIds,e.id)});return this.elementViews.push(t),this._listenToElementView(t),t},_listenToElementView:function(e){var t=this;t.listenTo(e,{select:function(e){var i=e.source.element;e.selected?t.selectedIds[i.id]=!0:delete t.selectedIds[i.id],t.trigger("elements:select",e)},discard:function(e){t.trigger("elements:discard",e)}})},addElementView:function(e){},removeElementView:function(e){delete this.selectedIds[e.element.id],this._renderClearSelected(),this.elementViews=o.without(this.elementViews,e),this.stopListening(e)},_renderNoElementsLeft:function(){this._disableNameAndCreate(!0),this.$(".collection-elements").append(this.templates.noElementsLeft())},_elementToJSON:function(e){return e},createList:function(e){if(!this.workingElements.length){var t=d("No valid elements for final list")+". ";return t+=''+d("Cancel")+" ",t+=d("or"),t+=' '+d("start over")+".",void this._showAlert(t)}var i=this,n=this.workingElements.map(function(e){return i._elementToJSON(e)});return i.blocking=!0,i.creationFn(n,e,i.hideOriginals).always(function(){i.blocking=!1}).fail(function(e,t,n){i.trigger("error",{xhr:e,status:t,message:d("An error occurred while creating this collection")})}).done(function(e,t,n){i.trigger("collection:created",e,t,n),i.metric("collection:created",e),"function"==typeof i.oncreate&&i.oncreate.call(this,e,t,n)})},_setUpBehaviors:function(){return this.on("error",this._errorHandler),this.once("rendered",function(){this.trigger("rendered:initial",this)}),this.on("elements:select",function(e){this._renderClearSelected()}),this.on("elements:discard",function(e){var t=e.source.element;this.removeElementView(e.source),this.workingElements=o.without(this.workingElements,t),this.workingElements.length||this._renderNoElementsLeft()}),this},_errorHandler:function(e){this.error(e);var t=this;if(content=e.message||d("An error occurred"),e.xhr){var i=e.xhr,n=e.message;0===i.readyState&&0===i.status?content+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes."):i.responseJSON?content+=":
",d(["Collections of datasets are permanent, ordered lists of datasets that can be passed to tools and ","workflows in order to have analyses done on each member of the entire group. This interface allows ","you to create a collection and re-order the final collection."].join("")),"
","
","
",d(["Rename elements in the list by clicking on ",'the existing name.'].join("")),"
","
",d(["Discard elements from the final created list by clicking on the ",'"Discard" button.'].join("")),"
","
",d(["Reorder the list by clicking and dragging elements. Select multiple elements by clicking on ",'them and you can then move those selected by dragging the ',"entire group. Deselect them by clicking them again or by clicking the ",'the "Clear selected" link.'].join("")),"
","
",d(['Click the "Start over" link to begin again as if you had just opened ',"the interface."].join("")),"
","
",d(['Click the "Cancel" button to exit the interface.'].join("")),"
","
","
",d(['Once your collection is complete, enter a name and ','click "Create list".'].join("")),"
"].join("")),invalidElements:o.template([d("The following selections could not be included due to problems:"),"
','',"<% if( _.size( problems ) ){ %>",d("The following selections could not be included due to problems"),":","
<% _.each( problems, function( problem ){ %>","
<%- problem.element.name %>: <%- problem.text %>
","<% }); %>
","<% } else if( _.size( elements ) < 1 ){ %>",d("No datasets were selected"),".","<% } %>"," ",d("At least one element is needed for the collection"),". ",d("You may need to "),'',d("cancel")," ",d("and reselect new elements"),".","","
","
",'"].join(""))}),toString:function(){return"ListCollectionCreator"}}),g=function(e,t,i){var n,a=l.Deferred(),r=Galaxy.modal||new s.View;return t=o.defaults(t||{},{elements:e,oncancel:function(){r.hide(),a.reject("cancelled")},oncreate:function(e,t){r.hide(),a.resolve(t)}}),n=new i(t),r.show({title:t.title||d("Create a collection"),body:n.$el,width:"80%",height:"100%",closing_events:!0}),n.render(),window._collectionCreator=n,a},m=function(e,t){return t=t||{},t.title=d("Create a collection from a list of datasets"),g(e,t,f)};return{DatasetCollectionElementView:p,ListCollectionCreator:f,collectionCreatorModal:g,listCollectionCreatorModal:m,createListCollection:h}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2),i(1),i(1))},function(e,t,i){var n,s;(function(a,o,r,l){n=[i(47),i(11),i(17),i(6),i(5)],s=function(e,t,i,n,s){"use strict";var c="dataset",d=e.ListItemView,h=d.extend({_logNamespace:c,className:d.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log(this+".initialize:",e),d.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank"},_setUpListeners:function(){d.prototype._setUpListeners.call(this);var e=this;return e.listenTo(e.model,{change:function(t){e.model.changedAttributes().state&&e.model.inReadyState()&&e.expanded&&!e.model.hasDetails()?e.model.fetch({silent:!0}).done(function(){e.render()}):a.has(t.changed,"tags")&&1===a.keys(t.changed).length?e.$(".nametags").html(e._renderNametags()):e.render()}})},_fetchModelDetails:function(){var e=this;return e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):o.when()},remove:function(e,t){var i=this;e=e||this.fxSpeed,this.$el.fadeOut(e,function(){r.View.prototype.remove.call(i),t&&t.call(i)})},_swapNewRender:function(e){return d.prototype._swapNewRender.call(this,e),this.model.has("state")&&this.$el.addClass("state-"+this.model.get("state")),
+this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var e=this.model.get("state");if(e===t.NOT_VIEWABLE||e===t.DISCARDED||!this.model.get("accessible"))return null;var n={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged"))n.disabled=!0,n.title=s("Cannot display datasets removed from disk");else if(e===t.UPLOAD)n.disabled=!0,n.title=s("This dataset must finish uploading before it can be viewed");else if(e===t.NEW)n.disabled=!0,n.title=s("This dataset is not yet viewable");else{n.title=s("View data"),n.href=this.model.urls.display;var a=this;n.onclick=function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.addDataset(a.model.get("id")),e.preventDefault())}}return n.faIcon="fa-eye",i(n)},_renderDetails:function(){if(this.model.get("state")===t.NOT_VIEWABLE)return l(this.templates.noAccess(this.model.toJSON(),this));var e=d.prototype._renderDetails.call(this);return e.find(".actions .left").empty().append(this._renderSecondaryActions()),e.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages()),e.find(".display-applications").html(this._renderDisplayApplications()),this._setUpBehaviors(e),e},_renderSummary:function(){var e=this.model.toJSON(),t=this.templates.summaries[e.state];return(t=t||this.templates.summaries.unknown)(e,this)},_renderDetailMessages:function(){var e=this,t=l(''),i=e.model.toJSON();return a.each(e.templates.detailMessages,function(n){t.append(l(n(i,e)))}),t},_renderDisplayApplications:function(){return this.model.isDeletedOrPurged()?"":[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){switch(this.debug("_renderSecondaryActions"),this.model.get("state")){case t.NOT_VIEWABLE:return[];case t.OK:case t.FAILED_METADATA:case t.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return i({title:s("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle",onclick:function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Dataset details",url:this.href}),e.preventDefault(),e.stopPropagation())}})},_renderDownloadButton:function(){return this.model.get("purged")||!this.model.hasData()?null:a.isEmpty(this.model.get("meta_files"))?l(['','',""].join("")):this._renderMetaFileDownloadButton()},_renderMetaFileDownloadButton:function(){var e=this.model.urls;return l(['
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+i.removeClass("fa-minus-square").addClass("fa-plus-square"))},_templateOptions:function(){function t(e,t){var i=e.find(".button-"+t);i.on("click",function(){s._setState(t,!i.data("is_expanded"))})}function n(a,r,l){l=l||[];for(i in r){var c=r[i],d=c.options&&c.options.length>0,h=l.slice(0);s.header_index[c.value]=h.slice(0);var u=o("");if(d){var p=e.uid(),f=o("").addClass("button-"+p).addClass("ui-drilldown-button fa fa-plus-square"),g=o("").addClass("subgroup-"+p).addClass("ui-drilldown-subgroup");u.append(o("").append(f).append(s._templateOption({label:c.name,value:c.value}))),h.push(p),n(g,c.options,h),u.append(g),t(u,p)}else u.append(s._templateOption({label:c.name,value:c.value}));a.append(u)}}var s=this;this.header_index={};var a=o("");return n(a,this.model.get("data")),a},_template:function(){return o("").addClass("ui-options-list drilldown-container").attr("id",this.model.id)}});return{View:n}}.apply(t,s),!(void 0!==a&&(e.exports=a))}).call(t,n(1),n(2))},function(e,t,i){var n,s;(function(a,o,r){n=[i(4),i(7),i(23)],s=function(e,t,i){var n={DISABLED:"disabled",ENABLED:"enabled",LINKED:"linked"},s={data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:n.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:n.LINKED},{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:n.LINKED}],data_multiple:[{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:n.DISABLED},{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collections",multiple:!0,batch:n.DISABLED}],data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:n.DISABLED}],workflow_data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:n.DISABLED}],workflow_data_multiple:[{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:n.DISABLED}],workflow_data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:n.DISABLED}],module_data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:n.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:n.ENABLED}],module_data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:n.DISABLED},{src:"hdca",icon:"fa-folder",tooltip:"Multiple collections",multiple:!0,batch:n.ENABLED}]},l=a.View.extend({initialize:function(e){var i=this;this.model=e&&e.model||new a.Model({src_labels:{hda:"dataset",hdca:"dataset collection"},pagelimit:100,statustimer:1e3}).set(e),this.setElement(o("").addClass("ui-select-content")),this.button_product=new t.RadioButton.View({value:"false",data:[{icon:"fa fa-chain",value:"false",tooltip:"Linked inputs will be run in matched order with other datasets e.g. use this for matching forward and reverse reads."},{icon:"fa fa-chain-broken",value:"true",tooltip:"Unlinked dataset inputs will be run against *all* other inputs."}]});var n=o("").addClass("ui-form-info").append(o("").addClass("fa fa-sitemap")).append(o("").html("This is a batch mode input field. Separate jobs will be triggered for each dataset selection."));this.$batch={linked:n.clone(),enabled:n.clone().append(o("").append(o("").addClass("ui-form-title").html("Batch options:")).append(this.button_product.$el)).append(o("").css("clear","both"))},this.$el.on("dragenter",function(e){this.lastenter=e.target,i.$el.addClass("ui-dragover")}).on("dragover",function(e){e.preventDefault()}).on("dragleave",function(e){this.lastenter===e.target&&i.$el.removeClass("ui-dragover")}).on("drop",function(e){i._handleDrop(e)}),this.history={},this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:current",this._changeCurrent,this),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:type change:optional change:multiple change:extensions",this._changeType,this),this.render(),this.on("change",function(){e.onchange&&e.onchange(i.value())})},render:function(){this._changeType(),this._changeValue(),this._changeWait()},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},update:function(e){this.model.set("data",e)},value:function(e){void 0!==e&&this.model.set("value",e);var t=this.model.get("current");if(this.config[t]){var i=this.fields[t].value();if(null!==i&&(i=o.isArray(i)?i:[i],i.length>0)){var n=this._batch({values:[]});for(var s in i){var a=this.history[i[s]+"_"+this.config[t].src];if(!a)return Galaxy.emit.debug("ui-select-content::value()","Requested details not found for '"+i[s]+"'."),null;n.values.push(a)}return n.values.sort(function(e,t){return e.hid-t.hid}),n}}else Galaxy.emit.debug("ui-select-content::value()","Invalid value/source '"+e+"'.");return null},_changeCurrent:function(){var e=this;r.each(this.fields,function(t,i){e.model.get("current")==i?(t.$el.show(),r.each(e.$batch,function(t,n){t[e.config[i].batch==n?"show":"hide"]()}),e.button_type.value(i)):t.$el.hide()})},_changeType:function(){var n=this,a=(this.model.get("flavor")?this.model.get("flavor")+"_":"")+String(this.model.get("type"))+(this.model.get("multiple")?"_multiple":"");s[a]?this.config=s[a]:(this.config=s.data,Galaxy.emit.debug("ui-select-content::_changeType()","Invalid configuration/type id '"+a+"'."));var o=n.model.get("data"),l=e.textify(this.model.get("extensions")),c=this.model.get("src_labels");this.fields=[],this.button_data=[],r.each(this.config,function(e,t){n.button_data.push({value:t,icon:e.icon,tooltip:e.tooltip}),n.fields.push(new i.View({optional:n.model.get("optional"),multiple:e.multiple,searchable:!e.multiple||o&&o[e.src]&&o[e.src].length>n.model.get("pagelimit"),selectall:!1,error_text:"No "+(l?l+" ":"")+(c[e.src]||"content")+" available.",onchange:function(){n.trigger("change")}}))}),this.button_type=new t.RadioButton.View({value:this.model.get("current"),data:this.button_data,onchange:function(e){n.model.set("current",e),n.trigger("change")}}),this.$el.empty();var d=0;this.fields.length>1&&(this.$el.append(this.button_type.$el),d=Math.max(0,36*this.fields.length)+"px"),r.each(this.fields,function(e){n.$el.append(e.$el.css({"margin-left":d}))}),r.each(this.$batch,function(e,t){n.$el.append(e.css({"margin-left":d}))}),this.model.set("current",0),this._changeCurrent(),this._changeData()},_changeWait:function(){var e=this;r.each(this.fields,function(t){t[e.model.get("wait")?"wait":"unwait"]()})},_changeData:function(){var e=this.model.get("data"),t=this,i={};r.each(e,function(e,n){i[n]=[],r.each(e,function(e){i[n].push({hid:e.hid,keep:e.keep,label:e.hid+": "+e.name,value:e.id,tags:e.tags}),t.history[e.id+"_"+n]=e})}),r.each(this.config,function(e,n){i[e.src]&&t.fields[n].add(i[e.src],function(e,t){return t.hid-e.hid})})},_changeValue:function(){var e=this.model.get("value");if(e&&e.values&&e.values.length>0){var t=[];r.each(e.values,function(e){t.push(e.id)});for(var i=e.values[0].src,n=e.values.length>1,s=0;s
This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at '+this.options.ftp_upload_site+' using your Galaxy credentials (email address and password).
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"],"collection");
+return a.extend(a.clone(r.prototype.templates),{controls:e})}();var c=l.extend({DatasetDCEViewClass:i.DatasetDCEListItemView,toString:function(){return"ListCollectionView("+(this.model?this.model.get("name"):"")+")"}}),d=c.extend({toString:function(){return"PairCollectionView("+(this.model?this.model.get("name"):"")+")"}}),h=l.extend({NestedDCDCEViewClass:i.NestedDCDCEListItemView.extend({foldoutPanelClass:d}),toString:function(){return"ListOfPairsCollectionView("+(this.model?this.model.get("name"):"")+")"}}),u=l.extend({NestedDCDCEViewClass:i.NestedDCDCEListItemView.extend({foldoutPanelClass:d}),toString:function(){return"ListOfListsCollectionView("+(this.model?this.model.get("name"):"")+")"}});return{CollectionView:l,ListCollectionView:c,PairCollectionView:d,ListOfPairsCollectionView:h,ListOfListsCollectionView:u}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2))},function(e,t,i){var n,s;(function(a,o){n=[i(11),i(38),i(48),i(71),i(17),i(6),i(5)],s=function(e,t,i,n,s,r,l){"use strict";var c=t.DatasetListItemView,d=c.extend({initialize:function(e){c.prototype.initialize.call(this,e),this.hasUser=e.hasUser,this.purgeAllowed=e.purgeAllowed||!1,this.tagsEditorShown=e.tagsEditorShown||!1,this.annotationEditorShown=e.annotationEditorShown||!1},_renderPrimaryActions:function(){var t=c.prototype._renderPrimaryActions.call(this);return this.model.get("state")===e.NOT_VIEWABLE?t:c.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){if(this.model.get("state")===e.DISCARDED||!this.model.get("accessible"))return null;var t=this.model.get("purged"),i=this.model.get("deleted"),n={title:l("Edit attributes"),href:this.model.urls.edit,target:this.linkTarget,faIcon:"fa-pencil",classes:"edit-btn"};return i||t?(n.disabled=!0,t?n.title=l("Cannot edit attributes of datasets removed from disk"):i&&(n.title=l("Undelete dataset to edit attributes"))):a.contains([e.UPLOAD,e.NEW],this.model.get("state"))&&(n.disabled=!0,n.title=l("This dataset is not yet editable")),s(n)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var e=this,t=this.model.isDeletedOrPurged();return s({title:l(t?"Dataset is already deleted":"Delete"),disabled:t,faIcon:"fa-times",classes:"delete-btn",onclick:function(){e.$el.find(".icon-btn.delete-btn").trigger("mouseout"),e.model.delete()}})},_renderDetails:function(){var t=c.prototype._renderDetails.call(this),i=this.model.get("state");return!this.model.isDeletedOrPurged()&&a.contains([e.OK,e.FAILED_METADATA],i)&&(this._renderTags(t),this._renderAnnotation(t),this._makeDbkeyEditLink(t)),this._setUpBehaviors(t),t},_renderToolHelpButton:function(){var e=this.model.attributes.dataset_id,t=this.model.attributes.creating_job,i=this,n=function(t){var n='
';t.name&&t.help?(n+="Tool help for "+t.name+"",n+=t.help):n+="Tool help is unavailable for this dataset.",n+="
",i.$el.find(".details").append(o.parseHTML(n))},a=function(e){o.ajax({url:Galaxy.root+"api/tools/"+e.tool_id+"/build"}).done(function(e){n(e)}).fail(function(){n({})})};return null===Galaxy.user.id?null:s({title:"Tool Help",classes:"icon-btn",href:"#",faIcon:"fa-question",onclick:function(){i.$el.find(".toolhelp").length>0?i.$el.find(".toolhelp").toggle():o.ajax({url:Galaxy.root+"api/jobs/"+t}).done(function(e){a(e)}).fail(function(){console.log('Failed at recovering job information from the Galaxy API for job id "'+t+'".')})}})},_renderSecondaryActions:function(){var t=c.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case e.UPLOAD:case e.NOT_VIEWABLE:return t;case e.ERROR:return t.unshift(this._renderErrButton()),t.concat([this._renderRerunButton(),this._renderToolHelpButton()]);case e.OK:case e.FAILED_METADATA:return t.concat([this._renderRerunButton(),this._renderVisualizationsButton(),this._renderToolHelpButton()])}return t.concat([this._renderRerunButton(),this._renderToolHelpButton()])},_renderErrButton:function(){return s({title:l("View or report this error"),href:this.model.urls.report_error,classes:"report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_renderRerunButton:function(){var e=this.model.get("creating_job");if(this.model.get("rerunnable"))return s({title:l("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,faIcon:"fa-refresh",onclick:function(t){t.preventDefault(),Galaxy.router.push("/",{job_id:e})}})},_renderVisualizationsButton:function(){var e=this.model.get("visualizations");if(this.model.isDeletedOrPurged()||!this.hasUser||!this.model.hasData()||a.isEmpty(e))return null;if(!a.isObject(e[0]))return this.warn("Visualizations have been switched off"),null;var t=o(this.templates.visualizations(e,this));return t.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(t.find(".visualization-link").addBack(".visualization-link")),t},_addScratchBookFn:function(e){e.click(function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Visualization",url:o(this).attr("href")}),e.preventDefault(),e.stopPropagation())})},_renderTags:function(e){if(this.hasUser){var t=this;this.tagsEditor=new i.TagsEditor({model:this.model,el:e.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.tagsEditorShown=!0},onhide:function(){t.tagsEditorShown=!1},$activator:s({title:l("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(e){if(this.hasUser){var t=this;this.annotationEditor=new n.AnnotationEditor({model:this.model,el:e.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.annotationEditorShown=!0},onhide:function(){t.annotationEditorShown=!1},$activator:s({title:l("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(e){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var t=o('?').attr("href",this.model.urls.edit).attr("target",this.linkTarget);e.find(".dbkey .value").replaceWith(t)}},events:a.extend(a.clone(c.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(e){this.trigger("edit",this,e)},"click .delete-btn":function(e){this.trigger("delete",this,e)},"click .rerun-btn":function(e){this.trigger("rerun",this,e)},"click .report-err-btn":function(e){this.trigger("report-err",this,e)},"click .visualization-btn":function(e){this.trigger("visualize",this,e)},"click .dbkey a":function(e){this.trigger("edit",this,e)}}),_clickUndeleteLink:function(e){return this.model.undelete(),!1},_clickPurgeLink:function(e){return confirm(l("This will permanently remove the data in your dataset. Are you sure?"))&&this.model.purge(),!1},toString:function(){var e=this.model?this.model+"":"(no model)";return"HDAEditView("+e+")"}});return d.prototype.templates=function(){var e=a.extend({},c.prototype.templates.warnings,{failed_metadata:r.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','
"]);return a.extend(a.clone(l.prototype.templates),{controls:e})}(),{ListPanel:l,ModelListPanel:c}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2),i(1))},,function(e,t,i){var n,s;(function(o,a){n=[i(5)],s=function(e){"use strict";function t(t,i,n){return Galaxy.modal.show({title:i,body:t,closing_events:!0,buttons:{Ok:function(){Galaxy.modal.hide()}}}),Galaxy.modal.$el.addClass("error-modal"),n&&(Galaxy.modal.$(".error-details").add(Galaxy.modal.$('button:contains("Details")')).remove(),o("").addClass("error-details").hide().appendTo(Galaxy.modal.$(".modal-content")).append([o("").text(h),o("").text(JSON.stringify(n,null," "))]),o('").appendTo(Galaxy.modal.$(".buttons")).click(function(){Galaxy.modal.$(".error-details").toggle()})),Galaxy.modal}function i(i,n,s){if(i){if(i=e(i),n=e(n)||e("Error:"),window.Galaxy&&Galaxy.modal)return t(i,n,s);alert(n+"\n\n"+i),console.log("error details:",JSON.stringify(s))}}function n(){return i(e("You appear to be offline. Please check your connection and try again."),e("Offline?"))}function s(){return i(e("Galaxy is currently unreachable. Please try again in a few minutes.")+" "+c,e("Cannot connect to Galaxy"))}function r(t,n,s,o,a){o=o||d,o+=" "+c,a=a||e("An error occurred");var r=l(t,n,s);return i(o,a,r)}function l(e,t,i){return{raven:a.result(window.Raven,"lastEventId"),userAgent:navigator.userAgent,onLine:navigator.onLine,version:a.result(Galaxy.config,"version_major"),xhr:a.omit(t,a.functions(t)),options:a.omit(i,"xhr"),url:a.result(Galaxy.lastAjax,"url"),data:a.result(Galaxy.lastAjax,"data"),model:a.result(e,"toJSON",e+""),user:a.omit(a.result(Galaxy.user,"toJSON"),"email")}}var c=e("Please contact a Galaxy administrator if the problem persists."),d=e("An error occurred while updating information with the server."),h=e("The following information can assist the developers in finding the source of the error:");return{errorModal:i,offlineErrorModal:n,badGatewayErrorModal:s,ajaxErrorModal:r}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(1),i(2))},function(e,t,i){var n,s;(function(i,o,a,r){n=[],s=function(){var e=i.View.extend({initialize:function(e,t){this.$button=e,this.$button.length||(this.$button=o("")),this.options=t||[],this.$button.data("popupmenu",this);var i=this;this.$button.click(function(e){return o(".popmenu-wrapper").remove(),i._renderAndShow(e),!1})},_renderAndShow:function(e){this.render(),this.$el.appendTo("body").css(this._getShownPosition(e)).show(),this._setUpCloseBehavior()},render:function(){if(this.$el.addClass("popmenu-wrapper").hide().css({position:"absolute"}).html(this.template(this.$button.attr("id"),this.options)),this.options.length){var e=this;this.$el.find("li").each(function(t,i){var n=e.options[t];n.func&&o(this).children("a.popupmenu-option").click(function(t){n.func.call(e,t,n),t.preventDefault()})})}return this},template:function(e,t){return['
",s(["Collections of paired datasets are ordered lists of dataset pairs (often forward and reverse reads). ","These collections can be passed to tools and workflows in order to have analyses done on each member of ","the entire group. This interface allows you to create a collection, choose which datasets are paired, ","and re-order the final collection."].join("")),"
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",s(['Unpaired datasets are shown in the unpaired section ',"(hover over the underlined words to highlight below). ",'Paired datasets are shown in the paired section.',"
To pair datasets, you can:","
Click a dataset in the ",'forward column ',"to select it then click a dataset in the ",'reverse column.',"
",'
Click one of the "Pair these datasets" buttons in the ','middle column ',"to pair the datasets in a particular row.","
",'
Click "Auto-pair" ',"to have your datasets automatically paired based on name.","
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",s(["
You can filter what is shown in the unpaired sections by:","
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","
Choosing from a list of preset filters by clicking the ",'"Choose filters" link.',"
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",s(['You can include or remove the file extensions (e.g. ".fastq") from your pair names by toggling the ','"Remove file extensions from pair names?" control.'].join("")),"
","
",s(['Once your collection is complete, enter a name and ','click "Create list". ',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"
"].join(""))})}),f=function(e,t){var i,n=r.Deferred();if(t=a.defaults(t||{},{datasets:e,oncancel:function(){Galaxy.modal.hide(),n.reject("cancelled")},oncreate:function(e,t){Galaxy.modal.hide(),n.resolve(t)}}),!window.Galaxy||!Galaxy.modal)throw new Error("Galaxy or Galaxy.modal not found");return i=new p(t),Galaxy.modal.show({title:"Create a collection of paired datasets",body:i.$el,width:"80%",height:"800px",closing_events:!0}),i.render(),window.creator=i,n};return{PairedCollectionCreator:p,pairedCollectionCreatorModal:f,createListOfPairsCollection:d}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2),i(1),i(1))},function(e,t,i){var n,s;(function(o,a,r){n=[i(37),i(44),i(6),i(5)],s=function(e,t,i,n){"use strict";function s(e,t){var i=e.toJSON(),n=u(i,{defaultHideSourceItems:t,creationFn:function(t,i,n){return t=[{name:"forward",src:"hda",id:t[0].id},{name:"reverse",src:"hda",id:t[1].id}],e.createHDCA(t,"paired",i,n)}});return n}var l="collections",c=o.View.extend(i.LoggableMixin).extend({_logNamespace:l,tagName:"li",className:"collection-element",initialize:function(e){this.element=e.element||{},this.identifier=e.identifier},render:function(){return this.$el.attr("data-element-id",this.element.id).html(this.template({identifier:this.identifier,element:this.element})),this},template:a.template(['<%- identifier %>','<%- element.name %>'].join("")),destroy:function(){this.off(),this.$el.remove()},toString:function(){return"DatasetCollectionElementView()"}}),d=e.ListCollectionCreator,h=d.extend({elementViewClass:c,collectionClass:t.HistoryPairDatasetCollection,className:"pair-collection-creator collection-creator flex-row-container",_mangleDuplicateNames:function(){},render:function(e,t){return 2===this.workingElements.length?d.prototype.render.call(this,e,t):this._renderInvalid(e,t)},_renderList:function(e,t){var i=this,n=r(""),s=i.$list();a.each(this.elementViews,function(e){e.destroy(),i.removeElementView(e)}),n.append(i._createForwardElementView().$el),n.append(i._createReverseElementView().$el),s.empty().append(n.children()),a.invoke(i.elementViews,"render")},_createForwardElementView:function(){return this._createElementView(this.workingElements[0],{identifier:"forward"})},_createReverseElementView:function(){return this._createElementView(this.workingElements[1],{identifier:"reverse"})},_createElementView:function(e,t){var i=new this.elementViewClass(a.extend(t,{element:e}));return this.elementViews.push(i),i},swap:function(){this.workingElements=[this.workingElements[1],this.workingElements[0]],this._renderList()},events:a.extend(a.clone(d.prototype.events),{"click .swap":"swap"}),templates:a.extend(a.clone(d.prototype.templates),{middle:a.template(['
",n(["Pair collections are permanent collections containing two datasets: one forward and one reverse. ","Often these are forward and reverse reads. The pair collections can be passed to tools and ","workflows in order to have analyses done on both datasets. This interface allows ","you to create a pair, name it, and swap which is forward and which reverse."].join("")),"
","
","
",n(['Click the "Swap" link to make your forward dataset the reverse ',"and the reverse dataset forward."].join("")),"
","
",n(['Click the "Cancel" button to exit the interface.'].join("")),"
","
","
",n(['Once your collection is complete, enter a name and ','click "Create list".'].join("")),"
"].join("")),invalidInitial:a.template(['
','
','',"<% if( _.size( problems ) ){ %>",n("The following selections could not be included due to problems"),"
<% _.each( problems, function( problem ){ %>","
<%- problem.element.name %>: <%- problem.text %>
","<% }); %>
","<% } else if( _.size( elements ) === 0 ){ %>",n("No datasets were selected"),".","<% } else if( _.size( elements ) === 1 ){ %>",n("Only one dataset was selected"),": <%- elements[0].name %>","<% } else if( _.size( elements ) > 2 ){ %>",n("Too many datasets were selected"),': <%- _.pluck( elements, "name" ).join( ", ") %>',"<% } %>"," ",n("Two (and only two) elements are needed for the pair"),". ",n("You may need to "),'',n("cancel")," ",n("and reselect new elements"),".","","
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",'"].join(""))}),toString:function(){return"PairCollectionCreator"}}),u=function(t,i){return i=i||{},i.title=n("Create a collection from a pair of datasets"),e.collectionCreatorModal(t,i,h)};return{PairCollectionCreator:h,pairCollectionCreatorModal:u,createPairCollection:s}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2),i(1))},function(e,t,i){var n,s;(function(o,a,r){n=[i(8),i(83),i(5)],s=function(e,t,i){"use strict";var n={defaultName:o.template("Copy of '<%- name %>'"),title:o.template(i("Copying history")+' "<%- name %>"'),submitLabel:i("Copy"),errorMessage:i("History could not be copied."),progressive:i("Copying history"),activeLabel:i("Copy only the active, non-deleted datasets"),allLabel:i("Copy all datasets including deleted ones"),anonWarning:i("As an anonymous user, unless you login or register, you will lose your current history ")+i("after copying this history. "),_template:o.template(["<% if( isAnon ){ %>",'
";this.modal.$(".modal-body").empty().append(e).css({"margin-top":"8px"})},dialog:function(e,n,s){function l(){var i=e.$("#copy-modal-title").val();if(!i)return void e.$(".invalid-title").show();var s="copy-all"===e.$('input[name="copy-what"]:checked').val();e.$("button").prop("disabled",!0),c._showAjaxIndicator(),n.copy(!0,i,s).done(function(e){d.resolve(e)}).fail(function(e,o,a){var r={name:i,copyAllDatasets:s};t.ajaxErrorModal(n,e,r,c.errorMessage),d.rejectWith(d,arguments)}).done(function(){g&&e.hide()})}s=s||{};var c=this,d=a.Deferred(),h=s.nameFn||this.defaultName,u=h({name:n.get("name")}),p=s.allDatasets?"copy-all":"copy-non-deleted",f=!!o.isUndefined(s.allowAll)||s.allowAll,g=!!o.isUndefined(s.autoClose)||s.autoClose;this.modal=e;var m=s.closing_callback;return e.show(o.extend(s,{title:this.title({name:n.get("name")}),body:r(c._template({name:u,isAnon:Galaxy.user.isAnonymous(),allowAll:f,copyWhat:p,activeLabel:this.activeLabel,allLabel:this.allLabel,anonWarning:this.anonWarning})),buttons:o.object([[i("Cancel"),function(){e.hide()}],[this.submitLabel,l]]),height:"auto",closing_events:!0,closing_callback:function(e){e&&d.reject({cancelled:!0}),m&&m(e)}})),e.$("#copy-modal-title").focus().select(),e.$("#copy-modal-title").on("keydown",function(e){13===e.keyCode&&(e.preventDefault(),l())}),d}},s=o.extend({},n,{defaultName:o.template("imported: <%- name %>"),title:o.template(i("Importing history")+' "<%- name %>"'),submitLabel:i("Import"),errorMessage:i("History could not be imported."),progressive:i("Importing history"),activeLabel:i("Import only the active, non-deleted datasets"),allLabel:i("Import all datasets including deleted ones"),anonWarning:i("As an anonymous user, unless you login or register, you will lose your current history ")+i("after importing this history. ")}),l=function(t,i){i=i||{};var o=window.parent.Galaxy.modal||new e.View({});return i.useImport?s.dialog(o,t,i):n.dialog(o,t,i)};return l}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1),i(1))},function(e,t,i){var n,s;(function(o,a){n=[i(74),i(76),i(6),i(5)],s=function(e,t,i,n){"use strict";var s=e.DatasetListItemEdit,r=s.extend({className:s.prototype.className+" history-content",_fetchModelDetails:function(){var e=this;return e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):e.model.has("rerunnable")?o.when():e.model.fetch({silent:!0,data:{keys:["rerunnable","creating_job"].join(",")}})},events:a.extend(a.clone(s.prototype.events),{"click .unhide-link":function(e){return this.model.unhide(),!1}}),toString:function(){var e=this.model?this.model+"":"(no model)";return"HDAListItemEdit("+e+")"}});return r.prototype.templates=function(){var e=a.extend({},s.prototype.templates.warnings,{hidden:i.wrapTemplate(["<% if( !dataset.visible ){ %>",'
"],"history"),i=h.wrapTemplate(['','",''],"pages");return o.extend(o.clone(p.prototype.templates),{el:e,controls:t,pagination:i})}(),{HistoryView:f}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1))},function(e,t,i){var n,s;(function(o,a){n=[i(84),i(114),i(6),i(5),i(28)],s=function(e,t,i,n,s){"use strict";function r(e,t,i){return a.clone(l).filter(function(n){return!(e&&!n.anon)&&(!(!t&&n.purge)&&(n.href&&(n.href=i+n.href,n.target="galaxy_main"),n.confirm&&(n.func=function(){confirm(n.confirm)&&(galaxy_main.location=n.href)}),!0))})}var l=[{html:n("History Lists"),header:!0},{html:n("Saved Histories"),href:"history/list"},{html:n("Histories Shared with Me"),href:"history/list_shared"},{html:n("Current History"),header:!0,anon:!0},{html:n("Create New"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.createNewHistory()}},{html:n("Copy History"),func:function(){t(Galaxy.currHistoryPanel.model).done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:n("Share or Publish"),href:"history/sharing"},{html:n("Show Structure"),href:"history/display_structured",anon:!0},{html:n("Extract Workflow"),href:"workflow/build_from_current_history"},{html:n("Delete"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(n("Really delete the current history?"))&&(galaxy_main.window.location.href="history/delete?id="+Galaxy.currHistoryPanel.model.id)}},{html:n("Delete Permanently"),purge:!0,anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(n("Really delete the current history permanently? This cannot be undone."))&&(galaxy_main.window.location.href="history/delete?purge=True&id="+Galaxy.currHistoryPanel.model.id)}},{html:n("Dataset Actions"),header:!0,anon:!0},{html:n("Copy Datasets"),href:"dataset/copy_datasets"},{html:n("Dataset Security"),href:"root/history_set_default_permissions"},{html:n("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:!0},{html:n("Collapse Expanded Datasets"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.collapseAll()}},{html:n("Unhide Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(n("Really unhide all hidden datasets?"))&&o.post(Galaxy.root+"history/adjust_hidden",{user_action:"unhide"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:n("Delete Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(n("Really delete all hidden datasets?"))&&o.post(Galaxy.root+"history/adjust_hidden",{user_action:"delete"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:n("Purge Deleted Datasets"),confirm:n("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:!0,anon:!0},{html:n("Downloads"),header:!0},{html:n("Export Tool Citations"),href:"history/citations",anon:!0},{html:n("Export History to File"),href:"history/export_archive?preview=True",anon:!0},{html:n("Other Actions"),header:!0},{html:n("Import from File"),href:"history/import_archive"}];s.add({url:"api/webhooks/history-menu/all",async:!1,callback:function(e){var t=[];o.each(e.models,function(e,i){var s=i.toJSON();s.activate&&t.push({html:n(s.config.title),anon:!0})}),t.length>0&&(t.unshift({html:n("Webhooks"),header:!0}),o.merge(l,t))}});var c=function(t,i){i=i||{};var n=void 0===i.anonymous||i.anonymous,s=i.purgeAllowed||!1,o=r(n,s,Galaxy.root);return new e(t,o)};return c}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(1),i(2))},function(e,t,i){var n,s;(function(o,a){n=[i(4)],s=function(e){var t=o.View.extend({initialize:function(e){this.collection=new o.Collection,this.model=e&&e.model||new o.Model({onchange:null,visible:!0}).set(e),this.setElement(a(this._template())),this.$nav=this.$(".tab-navigation"),this.$content=this.$(".tab-content"),this.$el.on("click",function(){a(".tooltip").hide()}),this.render(),this.listenTo(this.model,"change",this.render,this),this.listenTo(this.collection,"add",this._add,this),this.listenTo(this.collection,"remove",this._remove,this),this.listenTo(this.collection,"change",this._change,this),this.listenTo(this.collection,"reset",this._reset,this),this.listenTo(this.collection,"add remove reset",this.render,this)},render:function(){var e=this.model.get("current");e=this.$("#"+e).length>0?e:this.first(),e&&(this.$nav.children().removeClass("active"),this.$content.children().removeClass("active"),this.$("#tab-"+e).addClass("active"),this.$("#"+e).addClass("active")),this.$el[this.model.get("visible")?"fadeIn":"fadeOut"]("fast"),this.$nav[this.size()>1?"show":"hide"]()},current:function(){return this.model.get("current")},show:function(e){e&&(this.model.set({current:e,visible:!0}),this.model.get("onchange")&&this.model.get("onchange")(e))},hide:function(){this.model.set("visible",!1)},first:function(){var e=this.collection.first();return e&&e.id},size:function(){return this.collection.length},add:function(e){this.collection.add(e)},del:function(e){this.collection.remove(e)},delAll:function(){this.collection.reset()},showTab:function(e){this.collection.get(e).set("hidden",!1)},hideTab:function(e){this.collection.get(e).set("hidden",!0)},_add:function(e){var t=this,i=e.attributes;this.$content.append(a("").attr("id",i.id).addClass("tab-pane").append(i.$el)),this.$nav.append(a(this._template_tab(i)).show().tooltip({title:i.tooltip,placement:"bottom",container:t.$el}).on("click",function(e){e.preventDefault(),t.show(i.id)})),1==this.size()&&this.show(i.id)},_remove:function(e){this.$("#tab-"+e.id).remove(),this.$("#"+e.id).remove()},_reset:function(){this.$nav.empty(),this.$content.empty()},_change:function(e){this.$("#tab-"+e.id)[e.get("hidden")?"hide":"show"]()},_template:function(){return a("").addClass("ui-tabs tabbable tabs-left").append(a("
").addClass("tab-navigation nav nav-tabs")).append(a("").addClass("tab-content"))},_template_tab:function(e){var t=a("").addClass("tab-element").attr("id","tab-"+e.id).append(a("").attr("id","tab-title-link-"+e.id)),i=t.find("a");return e.icon&&i.append(a("").addClass("tab-icon fa").addClass(e.icon)),i.append(a("").attr("id","tab-title-text-"+e.id).addClass("tab-title-text").append(e.title)),t}});return{View:t}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1))},function(e,t,i){var n,s;(function(o,a,r){n=[i(4),i(24),i(58),i(14),i(15)],s=function(e,t,i,n,s){return o.View.extend({status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},initialize:function(e,t){var i=this;this.app=e,this.model=t.model,this.setElement(this._template(t.model)),this.$mode=this.$(".upload-mode"),this.$title=this.$(".upload-title-extended"),this.$text=this.$(".upload-text"),this.$size=this.$(".upload-size"),this.$info_text=this.$(".upload-info-text"),this.$info_progress=this.$(".upload-info-progress"),this.$text_content=this.$(".upload-text-content"),this.$symbol=this.$(".upload-symbol"),this.$progress_bar=this.$(".upload-progress-bar"),this.$percentage=this.$(".upload-percentage"),this.settings=new n.View({title:"Upload configuration",container:this.$(".upload-settings"),placement:"bottom"});this.app.select_genome.value(),this.app.select_extension.value();this.$symbol.on("click",function(){i._removeRow()}),this.$text_content.on("change input",function(e){i.model.set({url_paste:a(e.target).val(),file_size:a(e.target).val().length})}),this.listenTo(this.model,"change:percentage",function(){i._refreshPercentage()}),this.listenTo(this.model,"change:status",function(){i._refreshStatus()}),this.listenTo(this.model,"change:info",function(){i._refreshInfo()}),this.listenTo(this.model,"change:file_size",function(){i._refreshFileSize()}),this.listenTo(this.model,"remove",function(){i.remove()}),this.app.collection.on("reset",function(){i.remove()})},render:function(){var t=this.model.attributes;this.$title.html(r.escape(t.file_name)),this.$size.html(e.bytesToString(t.file_size)),this.$mode.removeClass().addClass("upload-mode").addClass("text-primary"),"new"==t.file_mode?(this.$text.css({width:this.$el.width()-16+"px",top:this.$el.height()-8+"px"}).show(),this.$el.height(this.$el.height()-8+this.$text.height()+16),this.$mode.addClass("fa fa-edit")):"local"==t.file_mode?this.$mode.addClass("fa fa-laptop"):"ftp"==t.file_mode&&this.$mode.addClass("fa fa-folder-open-o")},_refreshInfo:function(){var e=this.model.get("info");e?this.$info_text.html("Failed: "+e).show():this.$info_text.hide()},_refreshPercentage:function(){var e=parseInt(this.model.get("percentage"));this.$progress_bar.css({width:e+"%"}),this.$percentage.html(100!=e?e+"%":"Adding to history...")},_refreshStatus:function(){var e=this.model.get("status");this.$symbol.removeClass().addClass("upload-symbol").addClass(this.status_classes[e]),this.model.set("enabled","init"==e);var t=this.model.get("enabled");this.$text_content.attr("disabled",!t),"success"==e&&(this.$el.addClass("success"),this.$percentage.html("100%")),"error"==e&&(this.$el.addClass("danger"),this.$info_progress.hide())},_refreshFileSize:function(){this.$size.html(e.bytesToString(this.model.get("file_size")))},_removeRow:function(){["init","success","error"].indexOf(this.model.get("status"))!==-1&&this.app.collection.remove(this.model)},_showSettings:function(){this.settings.visible?this.settings.hide():(this.settings.empty(),this.settings.append(new i(this).$el),this.settings.show())},_template:function(e){return'
You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.
0%
'}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2))},function(e,t,i){var n,s;(function(o,a,r){n=[i(4),i(24),i(122),i(57),i(14),i(15),i(7),i(37),i(62)],s=function(e,t,i,n,s,l,c,d){return o.View.extend({upload_size:0,collection:new t.Collection,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(e){var t=this;this.app=e,this.options=e.options,this.list_extensions=e.list_extensions,this.list_genomes=e.list_genomes,this.ui_button=e.ui_button,this.ftp_upload_site=e.currentFtp(),this.setElement(this._template()),this.btnLocal=new c.Button({id:"btn-local",title:"Choose local files",onclick:function(){t.uploadbox.select()},icon:"fa fa-laptop"}),this.btnFtp=new c.Button({id:"btn-ftp",title:"Choose FTP files",onclick:function(){t._eventFtp()},icon:"fa fa-folder-open-o"}),this.btnCreate=new c.Button({id:"btn-new",title:"Paste/Fetch data",onclick:function(){t._eventCreate()},icon:"fa fa-edit"}),this.btnStart=new c.Button({id:"btn-start",title:"Start",onclick:function(){t._eventStart()}}),this.btnBuild=new c.Button({id:"btn-build",title:"Build",onclick:function(){t._eventBuild()}}),this.btnStop=new c.Button({id:"btn-stop",title:"Pause",onclick:function(){t._eventStop()}}),this.btnReset=new c.Button({id:"btn-reset",title:"Reset",onclick:function(){t._eventReset()}}),this.btnClose=new c.Button({id:"btn-close",title:"Close",onclick:function(){t.app.modal.hide()}}),a.each([this.btnLocal,this.btnFtp,this.btnCreate,this.btnStop,this.btnReset,this.btnStart,this.btnBuild,this.btnClose],function(e){t.$(".upload-buttons").prepend(e.$el)}),this.uploadbox=this.$(".upload-box").uploadbox({url:this.app.options.nginx_upload_path,announce:function(e,i){t._eventAnnounce(e,i)},initialize:function(e){return t.app.toData([t.collection.get(e)],t.history_id)},progress:function(e,i){t._eventProgress(e,i)},success:function(e,i){t._eventSuccess(e,i)},error:function(e,i){t._eventError(e,i)},complete:function(){t._eventComplete()},ondragover:function(){t.$(".upload-box").addClass("highlight")},ondragleave:function(){t.$(".upload-box").removeClass("highlight")}}),console.log(this.list_extensions),this.ftp=new s.View({title:"FTP files",container:this.btnFtp.$el}),this.select_extension=new l.View({css:"upload-footer-selection-compressed",container:this.$(".upload-footer-extension"),data:a.filter(this.list_extensions,function(e){return!e.composite_files}),value:this.options.default_extension,onchange:function(e){t.updateExtension(e)}}),this.collectionType="list",this.select_collection=new l.View({css:"upload-footer-selection-compressed",container:this.$(".upload-footer-collection-type"),data:[{id:"list",text:"List"},{id:"paired",text:"Paired"},{id:"list:paired",text:"List of Pairs"}],value:"list",onchange:function(e){t.updateCollectionType(e)}}),this.$(".upload-footer-extension-info").on("click",function(e){t.showExtensionInfo({$el:r(e.target),title:t.select_extension.text(),extension:t.select_extension.value(),placement:"top"})}).on("mousedown",function(e){e.preventDefault()}),this.select_genome=new l.View({css:"upload-footer-selection",container:this.$(".upload-footer-genome"),data:this.list_genomes,value:this.options.default_genome,onchange:function(e){t.updateGenome(e)}}),this.collection.on("remove",function(e){t._eventRemove(e)}),this._updateScreen()},_eventAnnounce:function(e,n){this.counter.announce++;var s=new t.Model({id:e,file_name:n.name,file_size:n.size,file_mode:n.mode||"local",file_path:n.path,file_data:n,extension:this.select_extension.value(),genome:this.select_genome.value()});this.collection.add(s);var o=new i(this,{model:s});this.$(".upload-table > tbody:first").append(o.$el),this._updateScreen(),o.render()},_eventProgress:function(e,t){var i=this.collection.get(e);i.set("percentage",t),this.ui_button.model.set("percentage",this._uploadPercentage(t,i.get("file_size")))},_eventSuccess:function(e,t){var i=a.pluck(t.outputs,"hid"),n=this.collection.get(e);n.set({percentage:100,status:"success",hids:i}),this.ui_button.model.set("percentage",this._uploadPercentage(100,n.get("file_size"))),this.upload_completed+=100*n.get("file_size"),this.counter.announce--,this.counter.success++,this._updateScreen(),Galaxy.currHistoryPanel.refreshContents()},_eventError:function(e,t){var i=this.collection.get(e);i.set({percentage:100,status:"error",info:t}),this.ui_button.model.set({percentage:this._uploadPercentage(100,i.get("file_size")),status:"danger"}),this.upload_completed+=100*i.get("file_size"),this.counter.announce--,this.counter.error++,this._updateScreen()},_eventComplete:function(){this.collection.each(function(e){
-"queued"==e.get("status")&&e.set("status","init")}),this.counter.running=0,this._updateScreen()},_eventBuild:function(){var e=[];a.forEach(this.collection.models,function(t){e.push.apply(e,t.get("hids"))});var t=a.map(e,function(e){return Galaxy.currHistoryPanel.collection.getByHid(e)}),i=new Galaxy.currHistoryPanel.collection.constructor(t);i.historyId=Galaxy.currHistoryPanel.collection.historyId,Galaxy.currHistoryPanel.buildCollection(this.collectionType,i,!0),this.counter.running=0,this._updateScreen(),this._eventReset(),this.app.modal.hide()},_eventRemove:function(e){var t=e.get("status");"success"==t?this.counter.success--:"error"==t?this.counter.error--:this.counter.announce--,this.uploadbox.remove(e.id),this._updateScreen()},showExtensionInfo:function(e){var t=this,i=e.$el,n=e.extension,o=e.title,r=a.findWhere(t.list_extensions,{id:n});this.extension_popup&&this.extension_popup.remove(),this.extension_popup=new s.View({placement:e.placement||"bottom",container:i}),this.extension_popup.title(o),this.extension_popup.empty(),this.extension_popup.append(this._templateDescription(r)),this.extension_popup.show()},_eventFtp:function(){if(this.ftp.visible)this.ftp.hide();else{this.ftp.empty();var e=this;this.ftp.append(new n({collection:this.collection,ftp_upload_site:this.ftp_upload_site,onadd:function(t){e.uploadbox.add([{mode:"ftp",name:t.path,size:t.size,path:t.path}])},onremove:function(t){e.collection.remove(t)}}).$el),this.ftp.show()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(!(0==this.counter.announce||this.counter.running>0)){var e=this;this.upload_size=0,this.upload_completed=0,this.collection.each(function(t){"init"==t.get("status")&&(t.set("status","queued"),e.upload_size+=t.get("file_size"))}),this.ui_button.model.set({percentage:0,status:"success"}),this.counter.running=this.counter.announce,this.history_id=this.app.currentHistory(),this.uploadbox.start(),this._updateScreen()}},_eventStop:function(){this.counter.running>0&&(this.ui_button.model.set("status","info"),r(".upload-top-info").html("Queue will pause after completing the current file..."),this.uploadbox.stop())},_eventReset:function(){0==this.counter.running&&(this.collection.reset(),this.counter.reset(),this.uploadbox.reset(),this.select_extension.value(this.options.default_extension),this.select_genome.value(this.options.default_genome),this.ui_button.model.set("percentage",0),this._updateScreen())},updateExtension:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("extension")!=i.options.default_extension&&t||n.set("extension",e)})},updateCollectionType:function(e){this.collectionType=e},updateGenome:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("genome")!=i.options.default_genome&&t||n.set("genome",e)})},_updateScreen:function(){var e="";e=0==this.counter.announce?this.uploadbox.compatible()?" ":"Browser does not support Drag & Drop. Try Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+.":0==this.counter.running?"You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed.":"Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining.",this.$(".upload-top-info").html(e);var t=0==this.counter.running&&this.counter.announce+this.counter.success+this.counter.error>0,i=0==this.counter.running&&this.counter.announce>0,n=0==this.counter.running&&0==this.counter.announce&&this.counter.success>0&&0==this.counter.error,s=0==this.counter.running,o=this.counter.announce+this.counter.success+this.counter.error>0;this.btnReset[t?"enable":"disable"](),this.btnStart[i?"enable":"disable"](),this.btnStart.$el[i?"addClass":"removeClass"]("btn-primary"),this.btnBuild[n?"enable":"disable"](),this.btnBuild.$el[n?"addClass":"removeClass"]("btn-primary"),this.btnStop[this.counter.running>0?"enable":"disable"](),this.btnLocal[s?"enable":"disable"](),this.btnFtp[s?"enable":"disable"](),this.btnCreate[s?"enable":"disable"](),this.btnFtp.$el[this.ftp_upload_site?"show":"hide"](),this.$(".upload-table")[o?"show":"hide"](),this.$(".upload-helper")[o?"hide":"show"]()},_uploadPercentage:function(e,t){return(this.upload_completed+e*t)/this.upload_size},_templateDescription:function(e){if(e.description){var t=e.description;return e.description_url&&(t+=' (read more)'),t}return"There is no description available for this file extension."},_template:function(){return'
Drop files here
Name
Size
Status
'}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2),i(1))},function(e,t,i){var n,s;(function(o,a,r){n=[i(4),i(58),i(57),i(14),i(7),i(15),i(62)],s=function(e,t,i,n,s,l){return o.View.extend({status_classes:{init:"upload-mode fa fa-exclamation text-primary",ready:"upload-mode fa fa-check text-success",running:"upload-mode fa fa-spinner fa-spin",success:"upload-mode fa fa-check",error:"upload-mode fa fa-exclamation-triangle"},initialize:function(e,t){var i=this;this.app=e,this.model=t.model,this.setElement(this._template()),this.$source=this.$(".upload-source"),this.$settings=this.$(".upload-settings"),this.$status=this.$(".upload-status"),this.$text=this.$(".upload-text"),this.$text_content=this.$(".upload-text-content"),this.$info_text=this.$(".upload-info-text"),this.$info_progress=this.$(".upload-info-progress"),this.$file_name=this.$(".upload-file-name"),this.$file_desc=this.$(".upload-file-desc"),this.$file_size=this.$(".upload-file-size"),this.$progress_bar=this.$(".upload-progress-bar"),this.$percentage=this.$(".upload-percentage"),this.uploadinput=this.$el.uploadinput({ondragover:function(){i.model.get("enabled")&&i.$el.addClass("warning")},ondragleave:function(){i.$el.removeClass("warning")},onchange:function(e){"running"!=i.model.get("status")&&e&&e.length>0&&(i.model.reset({file_data:e[0],file_name:e[0].name,file_size:e[0].size,file_mode:e[0].mode||"local"}),i._refreshReady())}}),this.button_menu=new s.ButtonMenu({icon:"fa-caret-down",title:"Select",pull:"left"}),this.$source.append(this.button_menu.$el),this.button_menu.addMenu({icon:"fa-laptop",title:"Choose local file",onclick:function(){i.uploadinput.dialog()}}),this.app.ftp_upload_site&&this.button_menu.addMenu({icon:"fa-folder-open-o",title:"Choose FTP file",onclick:function(){i._showFtp()}}),this.button_menu.addMenu({icon:"fa-edit",title:"Paste/Fetch data",onclick:function(){i.model.reset({file_mode:"new",file_name:"New File"})}}),this.ftp=new n.View({title:"Choose FTP file:",container:this.$source.find(".ui-button-menu"),placement:"right"}),this.settings=new n.View({title:"Upload configuration",container:this.$settings,placement:"bottom"}),this.$text_content.on("change input",function(e){i.model.set({url_paste:a(e.target).val(),file_size:a(e.target).val().length}),i._refreshReady()}),this.$settings.on("click",function(e){i._showSettings()}).on("mousedown",function(e){e.preventDefault()}),this.listenTo(this.model,"change:percentage",function(){i._refreshPercentage()}),this.listenTo(this.model,"change:status",function(){i._refreshStatus()}),this.listenTo(this.model,"change:info",function(){i._refreshInfo()}),this.listenTo(this.model,"change:file_name",function(){i._refreshFileName()}),this.listenTo(this.model,"change:file_mode",function(){i._refreshMode()}),this.listenTo(this.model,"change:file_size",function(){i._refreshFileSize()}),this.listenTo(this.model,"remove",function(){i.remove()}),this.app.collection.on("reset",function(){i.remove()})},render:function(){this.$el.attr("id","upload-row-"+this.model.id),this.$file_name.html(r.escape(this.model.get("file_name")||"-")),this.$file_desc.html(this.model.get("file_desc")||"Unavailable"),this.$file_size.html(e.bytesToString(this.model.get("file_size"))),this.$status.removeClass().addClass(this.status_classes.init)},remove:function(){o.View.prototype.remove.apply(this)},_refreshReady:function(){this.app.collection.each(function(e){e.set("status",e.get("file_size")>0&&"ready"||"init")})},_refreshMode:function(){var e=this.model.get("file_mode");"new"==e?(this.height=this.$el.height(),this.$text.css({width:this.$el.width()-16+"px",top:this.$el.height()-8+"px"}).show(),this.$el.height(this.$el.height()-8+this.$text.height()+16),this.$text_content.val("").trigger("keyup")):(this.$el.height(this.height),this.$text.hide())},_refreshInfo:function(){var e=this.model.get("info");e?this.$info_text.html("Failed: "+e).show():this.$info_text.hide()},_refreshPercentage:function(){var e=parseInt(this.model.get("percentage"));0!=e?this.$progress_bar.css({width:e+"%"}):(this.$progress_bar.addClass("no-transition"),this.$progress_bar.css({width:"0%"}),this.$progress_bar[0].offsetHeight,this.$progress_bar.removeClass("no-transition")),this.$percentage.html(100!=e?e+"%":"Adding to history...")},_refreshStatus:function(){var e=this.model.get("status");this.$status.removeClass().addClass(this.status_classes[e]),this.model.set("enabled","running"!=e),this.$text_content.attr("disabled",!this.model.get("enabled")),this.$el.removeClass("success danger warning"),"running"!=e&&"ready"!=e||this.model.set("percentage",0),this.$source.find(".button")["running"==e?"addClass":"removeClass"]("disabled"),"success"==e&&(this.$el.addClass("success"),this.model.set("percentage",100),this.$percentage.html("100%")),"error"==e?(this.$el.addClass("danger"),this.model.set("percentage",0),this.$info_progress.hide(),this.$info_text.show()):(this.$info_progress.show(),this.$info_text.hide())},_refreshFileName:function(){this.$file_name.html(this.model.get("file_name")||"-")},_refreshFileSize:function(){this.$file_size.html(e.bytesToString(this.model.get("file_size")))},_showFtp:function(){if(this.ftp.visible)this.ftp.hide();else{var e=this;this.ftp.empty(),this.ftp.append(new i({ftp_upload_site:this.app.ftp_upload_site,onchange:function(t){e.ftp.hide(),"running"!=e.model.get("status")&&t&&(e.model.reset({file_mode:"ftp",file_name:t.path,file_size:t.size,file_path:t.path}),e._refreshReady())}}).$el),this.ftp.show()}},_showSettings:function(){this.settings.visible?this.settings.hide():(this.settings.empty(),this.settings.append(new t(this).$el),this.settings.show())},_template:function(){return'
You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.
0%
'}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2))},function(e,t,i){var n,s;(function(o,a,r){n=[i(4),i(24),i(124),i(14),i(15),i(7)],s=function(e,t,i,n,s,l){return o.View.extend({collection:new t.Collection,initialize:function(e){var t=this;this.app=e,this.options=e.options,this.list_extensions=e.list_extensions,this.list_genomes=e.list_genomes,this.ftp_upload_site=e.currentFtp(),this.setElement(this._template()),this.btnStart=new l.Button({title:"Start",onclick:function(){t._eventStart()}}),this.btnClose=new l.Button({title:"Close",onclick:function(){t.app.modal.hide()}}),a.each([this.btnStart,this.btnClose],function(e){t.$(".upload-buttons").prepend(e.$el)}),this.select_extension=new s.View({css:"upload-footer-selection",container:this.$(".upload-footer-extension"),data:a.filter(this.list_extensions,function(e){return e.composite_files}),onchange:function(e){t.collection.reset();var i=a.findWhere(t.list_extensions,{id:e});i&&i.composite_files&&a.each(i.composite_files,function(e){t.collection.add({id:t.collection.size(),file_desc:e.description||e.name})})}}),this.$(".upload-footer-extension-info").on("click",function(e){t._showExtensionInfo({$el:r(e.target),title:t.select_extension.text(),extension:t.select_extension.value(),placement:"top"})}).on("mousedown",function(e){e.preventDefault()}),this.select_genome=new s.View({css:"upload-footer-selection",container:this.$(".upload-footer-genome"),data:this.list_genomes,value:this.options.default_genome}),this.listenTo(this.collection,"add",function(e){t._eventAnnounce(e)}),this.listenTo(this.collection,"change add",function(){t.render()}),this.select_extension.options.onchange(this.select_extension.value()),this.render()},render:function(){var e=this.collection.first();e&&"running"==e.get("status")?(this.select_genome.disable(),this.select_extension.disable()):(this.select_genome.enable(),this.select_extension.enable()),this.collection.where({status:"ready"}).length==this.collection.length&&this.collection.length>0?(this.btnStart.enable(),this.btnStart.$el.addClass("btn-primary")):(this.btnStart.disable(),this.btnStart.$el.removeClass("btn-primary")),this.$(".upload-table")[this.collection.length>0?"show":"hide"]()},_eventAnnounce:function(e){var t=new i(this,{model:e});this.$(".upload-table > tbody:first").append(t.$el),this.$(".upload-table")[this.collection.length>0?"show":"hide"](),t.render()},_eventStart:function(){var e=this;this.collection.each(function(t){t.set({genome:e.select_genome.value(),extension:e.select_extension.value()})}),r.uploadpost({url:this.app.options.nginx_upload_path,data:this.app.toData(this.collection.filter()),success:function(t){e._eventSuccess(t)},error:function(t){e._eventError(t)},progress:function(t){e._eventProgress(t)}})},_eventProgress:function(e){this.collection.each(function(t){t.set("percentage",e)})},_eventSuccess:function(e){this.collection.each(function(e){e.set("status","success")}),Galaxy.currHistoryPanel.refreshContents()},_eventError:function(e){this.collection.each(function(t){t.set({status:"error",info:e})})},_showExtensionInfo:function(e){var t=e.$el,i=e.extension,s=e.title,o=a.findWhere(this.list_extensions,{id:i});this.extension_popup&&this.extension_popup.remove(),this.extension_popup=new n.View({placement:e.placement||"bottom",container:t,destroy:!0}),this.extension_popup.title(s),this.extension_popup.empty(),this.extension_popup.append(this._templateDescription(o)),this.extension_popup.show()},_templateDescription:function(e){if(e.description){var t=e.description;return e.description_url&&(t+=' (read more)'),t}return"There is no description available for this file extension."},_template:function(){return'
Description
Name
Size
Settings
Status
'}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2),i(1))},function(e,t,i){var n,s;(function(o,a,r){n=[i(4),i(24),i(58),i(14),i(15)],s=function(e,t,i,n,s){return o.View.extend({status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},initialize:function(e,t){var i=this;this.app=e,this.model=t.model,this.setElement(this._template(t.model)),this.$mode=this.$(".upload-mode"),this.$title=this.$(".upload-title"),this.$text=this.$(".upload-text"),this.$size=this.$(".upload-size"),this.$info_text=this.$(".upload-info-text"),this.$info_progress=this.$(".upload-info-progress"),this.$text_content=this.$(".upload-text-content"),this.$settings=this.$(".upload-settings"),this.$symbol=this.$(".upload-symbol"),this.$progress_bar=this.$(".upload-progress-bar"),this.$percentage=this.$(".upload-percentage"),this.settings=new n.View({title:"Upload configuration",container:this.$(".upload-settings"),placement:"bottom"});var o=this.app.select_genome.value(),r=this.app.select_extension.value();this.select_genome=new s.View({css:"upload-genome",data:i.app.list_genomes,container:this.$(".upload-genome"),value:o,onchange:function(e){i.model.set("genome",e)}}),this.select_extension=new s.View({css:"upload-extension",data:i.app.list_extensions,container:this.$(".upload-extension"),value:r,onchange:function(e){i.model.set("extension",e)}}),this.model.set({genome:o,extension:r}),this.$symbol.on("click",function(){i._removeRow()}),this.$(".upload-extension-info").on("click",function(e){i.app.showExtensionInfo({$el:a(e.target),title:i.select_extension.text(),extension:i.select_extension.value()})}).on("mousedown",function(e){e.preventDefault()}),this.$settings.on("click",function(e){i._showSettings()}).on("mousedown",function(e){e.preventDefault()}),this.$text_content.on("change input",function(e){i.model.set({url_paste:a(e.target).val(),file_size:a(e.target).val().length})}),this.listenTo(this.model,"change:percentage",function(){i._refreshPercentage()}),this.listenTo(this.model,"change:status",function(){i._refreshStatus()}),this.listenTo(this.model,"change:info",function(){i._refreshInfo()}),this.listenTo(this.model,"change:genome",function(){i._refreshGenome()}),this.listenTo(this.model,"change:extension",function(){i._refreshExtension()}),this.listenTo(this.model,"change:file_size",function(){i._refreshFileSize()}),this.listenTo(this.model,"remove",function(){i.remove()}),this.app.collection.on("reset",function(){i.remove()})},render:function(){var t=this.model.attributes;this.$title.html(r.escape(t.file_name)),this.$size.html(e.bytesToString(t.file_size)),this.$mode.removeClass().addClass("upload-mode").addClass("text-primary"),"new"==t.file_mode?(this.$text.css({width:this.$el.width()-16+"px",top:this.$el.height()-8+"px"}).show(),this.$el.height(this.$el.height()-8+this.$text.height()+16),this.$mode.addClass("fa fa-edit")):"local"==t.file_mode?this.$mode.addClass("fa fa-laptop"):"ftp"==t.file_mode&&this.$mode.addClass("fa fa-folder-open-o")},remove:function(){this.select_genome.remove(),this.select_extension.remove(),o.View.prototype.remove.apply(this)},_refreshExtension:function(){this.select_extension.value(this.model.get("extension"))},_refreshGenome:function(){this.select_genome.value(this.model.get("genome"))},_refreshInfo:function(){var e=this.model.get("info");e?this.$info_text.html("Failed: "+e).show():this.$info_text.hide()},_refreshPercentage:function(){var e=parseInt(this.model.get("percentage"));this.$progress_bar.css({width:e+"%"}),this.$percentage.html(100!=e?e+"%":"Adding to history...")},_refreshStatus:function(){var e=this.model.get("status");this.$symbol.removeClass().addClass("upload-symbol").addClass(this.status_classes[e]),this.model.set("enabled","init"==e);var t=this.model.get("enabled");this.$text_content.attr("disabled",!t),t?(this.select_genome.enable(),this.select_extension.enable()):(this.select_genome.disable(),this.select_extension.disable()),"success"==e&&(this.$el.addClass("success"),this.$percentage.html("100%")),"error"==e&&(this.$el.addClass("danger"),this.$info_progress.hide())},_refreshFileSize:function(){this.$size.html(e.bytesToString(this.model.get("file_size")))},_removeRow:function(){["init","success","error"].indexOf(this.model.get("status"))!==-1&&this.app.collection.remove(this.model)},_showSettings:function(){this.settings.visible?this.settings.hide():(this.settings.empty(),this.settings.append(new i(this).$el),this.settings.show())},_template:function(e){return'
You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.
0%
'}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2))},function(e,t,i){var n,s;(function(o,a,r){n=[i(4),i(24),i(126),i(57),i(14),i(15),i(7),i(62)],s=function(e,t,i,n,s,l,c){return o.View.extend({upload_size:0,collection:new t.Collection,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(e){var t=this;this.app=e,this.options=e.options,this.list_extensions=e.list_extensions,this.list_genomes=e.list_genomes,this.ui_button=e.ui_button,this.ftp_upload_site=e.currentFtp(),this.setElement(this._template()),this.btnLocal=new c.Button({id:"btn-local",title:"Choose local file",onclick:function(){t.uploadbox.select()},icon:"fa fa-laptop"}),this.btnFtp=new c.Button({id:"btn-ftp",title:"Choose FTP file",onclick:function(){t._eventFtp()},icon:"fa fa-folder-open-o"}),this.btnCreate=new c.Button({id:"btn-new",title:"Paste/Fetch data",onclick:function(){t._eventCreate()},icon:"fa fa-edit"}),this.btnStart=new c.Button({id:"btn-start",title:"Start",onclick:function(){t._eventStart()}}),this.btnStop=new c.Button({id:"btn-stop",title:"Pause",onclick:function(){t._eventStop()}}),this.btnReset=new c.Button({id:"btn-reset",title:"Reset",onclick:function(){t._eventReset()}}),this.btnClose=new c.Button({id:"btn-close",title:"Close",onclick:function(){t.app.modal.hide()}}),a.each([this.btnLocal,this.btnFtp,this.btnCreate,this.btnStop,this.btnReset,this.btnStart,this.btnClose],function(e){t.$(".upload-buttons").prepend(e.$el)}),this.uploadbox=this.$(".upload-box").uploadbox({url:this.app.options.nginx_upload_path,announce:function(e,i){t._eventAnnounce(e,i)},initialize:function(e){return t.app.toData([t.collection.get(e)],t.history_id)},progress:function(e,i){t._eventProgress(e,i)},success:function(e,i){t._eventSuccess(e,i)},error:function(e,i){t._eventError(e,i)},complete:function(){t._eventComplete()},ondragover:function(){t.$(".upload-box").addClass("highlight")},ondragleave:function(){t.$(".upload-box").removeClass("highlight")}}),this.ftp=new s.View({title:"FTP files",container:this.btnFtp.$el}),this.select_extension=new l.View({css:"upload-footer-selection",container:this.$(".upload-footer-extension"),data:a.filter(this.list_extensions,function(e){return!e.composite_files}),value:this.options.default_extension,onchange:function(e){t.updateExtension(e)}}),this.$(".upload-footer-extension-info").on("click",function(e){t.showExtensionInfo({$el:r(e.target),title:t.select_extension.text(),extension:t.select_extension.value(),placement:"top"})}).on("mousedown",function(e){e.preventDefault()}),this.select_genome=new l.View({css:"upload-footer-selection",container:this.$(".upload-footer-genome"),data:this.list_genomes,value:this.options.default_genome,onchange:function(e){t.updateGenome(e)}}),this.collection.on("remove",function(e){t._eventRemove(e)}),this._updateScreen()},_eventAnnounce:function(e,n){this.counter.announce++;var s=new t.Model({id:e,file_name:n.name,file_size:n.size,file_mode:n.mode||"local",file_path:n.path,file_data:n});this.collection.add(s);var o=new i(this,{model:s});this.$(".upload-table > tbody:first").append(o.$el),this._updateScreen(),o.render()},_eventProgress:function(e,t){var i=this.collection.get(e);i.set("percentage",t),this.ui_button.model.set("percentage",this._uploadPercentage(t,i.get("file_size")))},_eventSuccess:function(e,t){var i=this.collection.get(e);i.set({percentage:100,status:"success"}),this.ui_button.model.set("percentage",this._uploadPercentage(100,i.get("file_size"))),this.upload_completed+=100*i.get("file_size"),this.counter.announce--,this.counter.success++,this._updateScreen(),Galaxy.currHistoryPanel.refreshContents()},_eventError:function(e,t){var i=this.collection.get(e);i.set({percentage:100,status:"error",info:t}),this.ui_button.model.set({percentage:this._uploadPercentage(100,i.get("file_size")),status:"danger"}),this.upload_completed+=100*i.get("file_size"),this.counter.announce--,this.counter.error++,this._updateScreen()},_eventComplete:function(){this.collection.each(function(e){"queued"==e.get("status")&&e.set("status","init")}),this.counter.running=0,this._updateScreen()},_eventRemove:function(e){var t=e.get("status");"success"==t?this.counter.success--:"error"==t?this.counter.error--:this.counter.announce--,this.uploadbox.remove(e.id),this._updateScreen()},showExtensionInfo:function(e){var t=this,i=e.$el,n=e.extension,o=e.title,r=a.findWhere(t.list_extensions,{id:n});this.extension_popup&&this.extension_popup.remove(),this.extension_popup=new s.View({placement:e.placement||"bottom",container:i}),this.extension_popup.title(o),this.extension_popup.empty(),this.extension_popup.append(this._templateDescription(r)),this.extension_popup.show()},_eventFtp:function(){if(this.ftp.visible)this.ftp.hide();else{this.ftp.empty();var e=this;this.ftp.append(new n({collection:this.collection,ftp_upload_site:this.ftp_upload_site,onadd:function(t){e.uploadbox.add([{mode:"ftp",name:t.path,size:t.size,path:t.path}])},onremove:function(t){e.collection.remove(t)}}).$el),this.ftp.show()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(!(0==this.counter.announce||this.counter.running>0)){var e=this;this.upload_size=0,this.upload_completed=0,this.collection.each(function(t){"init"==t.get("status")&&(t.set("status","queued"),e.upload_size+=t.get("file_size"))}),this.ui_button.model.set({percentage:0,status:"success"}),this.counter.running=this.counter.announce,this.history_id=this.app.currentHistory(),this.uploadbox.start(),this._updateScreen()}},_eventStop:function(){this.counter.running>0&&(this.ui_button.model.set("status","info"),r(".upload-top-info").html("Queue will pause after completing the current file..."),this.uploadbox.stop())},_eventReset:function(){0==this.counter.running&&(this.collection.reset(),this.counter.reset(),this.uploadbox.reset(),this.select_extension.value(this.options.default_extension),this.select_genome.value(this.options.default_genome),this.ui_button.model.set("percentage",0),this._updateScreen())},updateExtension:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("extension")!=i.options.default_extension&&t||n.set("extension",e)})},updateGenome:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("genome")!=i.options.default_genome&&t||n.set("genome",e)})},_updateScreen:function(){var e="";e=0==this.counter.announce?this.uploadbox.compatible()?" ":"Browser does not support Drag & Drop. Try Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+.":0==this.counter.running?"You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed.":"Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining.",this.$(".upload-top-info").html(e);var t=0==this.counter.running&&this.counter.announce+this.counter.success+this.counter.error>0,i=0==this.counter.running&&this.counter.announce>0,n=0==this.counter.running,s=this.counter.announce+this.counter.success+this.counter.error>0;this.btnReset[t?"enable":"disable"](),this.btnStart[i?"enable":"disable"](),this.btnStart.$el[i?"addClass":"removeClass"]("btn-primary"),this.btnStop[this.counter.running>0?"enable":"disable"](),this.btnLocal[n?"enable":"disable"](),this.btnFtp[n?"enable":"disable"](),this.btnCreate[n?"enable":"disable"](),this.btnFtp.$el[this.ftp_upload_site?"show":"hide"](),this.$(".upload-table")[s?"show":"hide"](),this.$(".upload-helper")[s?"hide":"show"]()},_uploadPercentage:function(e,t){return(this.upload_completed+e*t)/this.upload_size},_templateDescription:function(e){if(e.description){var t=e.description;return e.description_url&&(t+=' (read more)'),t}return"There is no description available for this file extension."},_template:function(){return'
Drop files here
Name
Size
Type
Genome
Settings
Status
'}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2),i(1))},function(e,t,i){var n,s;(function(i,o){n=[],s=function(){var e=i.View.extend({initialize:function(e){var t=this;this.model=e&&e.model||new i.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",percentage:0,status:"",onunload:function(){},onclick:function(){}}).set(e),this.setElement(this._template()),this.$progress=this.$(".progress-bar"),this.listenTo(this.model,"change",this.render,this),this.render(),o(window).on("beforeunload",function(){return t.model.get("onunload")()})},render:function(){var e=this.model.attributes;this.$el.off("click").on("click",function(t){e.onclick(t)}).tooltip({title:this.model.get("tooltip"),placement:"bottom"}),this.$progress.removeClass().addClass("progress-bar").addClass("progress-bar-notransition").addClass(""!=e.status&&"progress-bar-"+e.status).css({width:e.percentage+"%"})},_template:function(){return'
'}});return{View:e}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1))},function(e,t,i){var n,s;(function(o){n=[i(4),i(8),i(121),i(128),i(127),i(125),i(123)],s=function(e,t,i,n,s,a,r){return o.View.extend({options:{
-nginx_upload_path:"",ftp_upload_site:"n/a",default_genome:"?",default_extension:"auto",height:500,width:900,auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. 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";this.modal.$(".modal-body").empty().append(e).css({"margin-top":"8px"})},dialog:function(e,n,s){function l(){var i=e.$("#copy-modal-title").val();if(!i)return void e.$(".invalid-title").show();var s="copy-all"===e.$('input[name="copy-what"]:checked').val();e.$("button").prop("disabled",!0),c._showAjaxIndicator(),n.copy(!0,i,s).done(function(e){d.resolve(e)}).fail(function(e,a,o){var r={name:i,copyAllDatasets:s};t.ajaxErrorModal(n,e,r,c.errorMessage),d.rejectWith(d,arguments)}).done(function(){g&&e.hide()})}s=s||{};var c=this,d=o.Deferred(),h=s.nameFn||this.defaultName,u=h({name:n.get("name")
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"],"history"),i=h.wrapTemplate(['','",''],"pages");return a.extend(a.clone(p.prototype.templates),{el:e,controls:t,pagination:i})}(),{HistoryView:f}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1))},function(e,t,i){var n,s;(function(a,o){n=[i(51),i(118),i(6),i(5),i(28)],s=function(e,t,i,n,s){"use strict";function r(e,t,i){return o.clone(l).filter(function(n){return!(e&&!n.anon)&&(!(!t&&n.purge)&&(n.href&&(n.href=i+n.href,n.target="galaxy_main"),n.confirm&&(n.func=function(){confirm(n.confirm)&&(galaxy_main.location=n.href)}),!0))})}var l=[{html:n("History Lists"),header:!0},{html:n("Saved Histories"),href:"history/list"},{html:n("Histories Shared with Me"),href:"history/list_shared"},{html:n("Current History"),header:!0,anon:!0},{html:n("Create New"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.createNewHistory()}},{html:n("Copy History"),func:function(){t(Galaxy.currHistoryPanel.model).done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:n("Share or Publish"),href:"history/sharing"},{html:n("Show Structure"),href:"history/display_structured",
+anon:!0},{html:n("Extract Workflow"),href:"workflow/build_from_current_history"},{html:n("Delete"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(n("Really delete the current history?"))&&(galaxy_main.window.location.href="history/delete?id="+Galaxy.currHistoryPanel.model.id)}},{html:n("Delete Permanently"),purge:!0,anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(n("Really delete the current history permanently? This cannot be undone."))&&(galaxy_main.window.location.href="history/delete?purge=True&id="+Galaxy.currHistoryPanel.model.id)}},{html:n("Dataset Actions"),header:!0,anon:!0},{html:n("Copy Datasets"),href:"dataset/copy_datasets"},{html:n("Dataset Security"),href:"root/history_set_default_permissions"},{html:n("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:!0},{html:n("Collapse Expanded Datasets"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.collapseAll()}},{html:n("Unhide Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(n("Really unhide all hidden datasets?"))&&a.post(Galaxy.root+"history/adjust_hidden",{user_action:"unhide"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:n("Delete Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(n("Really delete all hidden datasets?"))&&a.post(Galaxy.root+"history/adjust_hidden",{user_action:"delete"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:n("Purge Deleted Datasets"),confirm:n("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:!0,anon:!0},{html:n("Downloads"),header:!0},{html:n("Export Tool Citations"),href:"history/citations",anon:!0},{html:n("Export History to File"),href:"history/export_archive?preview=True",anon:!0},{html:n("Other Actions"),header:!0},{html:n("Import from File"),href:"history/import_archive"}];s.add({url:"api/webhooks/history-menu/all",async:!1,callback:function(e){var t=[];a.each(e.models,function(e,i){var s=i.toJSON();s.activate&&t.push({html:n(s.config.title),anon:!0})}),t.length>0&&(t.unshift({html:n("Webhooks"),header:!0}),a.merge(l,t))}});var c=function(t,i){i=i||{};var n=void 0===i.anonymous||i.anonymous,s=i.purgeAllowed||!1,a=r(n,s,Galaxy.root);return new e(t,a)};return c}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(1),i(2))},function(e,t,i){var n,s;(function(a,o,r){n=[i(4),i(77)],s=function(e,t){var i=a.View.extend({initialize:function(t){var i=this;this.setElement(o("")),this.model=new a.Model,e.get({url:Galaxy.root+"page/list",success:function(e){e.dict_format=!0,i.model.set(e),i.render()}})},render:function(){var e=new t(this.model.attributes);this.$el.empty().append(e.$el),this.$el.append(this._templateShared())},_templateShared:function(){var e=o("
")}),e.append(i)}else e.append("No pages have been shared with you.");return e}});return{View:i}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2))},function(e,t,i){var n,s;(function(a,o){n=[i(4)],s=function(e){var t=a.View.extend({initialize:function(e){this.collection=new a.Collection,this.model=e&&e.model||new a.Model({onchange:null,visible:!0}).set(e),this.setElement(o(this._template())),this.$nav=this.$(".tab-navigation"),this.$content=this.$(".tab-content"),this.$el.on("click",function(){o(".tooltip").hide()}),this.render(),this.listenTo(this.model,"change",this.render,this),this.listenTo(this.collection,"add",this._add,this),this.listenTo(this.collection,"remove",this._remove,this),this.listenTo(this.collection,"change",this._change,this),this.listenTo(this.collection,"reset",this._reset,this),this.listenTo(this.collection,"add remove reset",this.render,this)},render:function(){var e=this.model.get("current");e=this.$("#"+e).length>0?e:this.first(),e&&(this.$nav.children().removeClass("active"),this.$content.children().removeClass("active"),this.$("#tab-"+e).addClass("active"),this.$("#"+e).addClass("active")),this.$el[this.model.get("visible")?"fadeIn":"fadeOut"]("fast"),this.$nav[this.size()>1?"show":"hide"]()},current:function(){return this.model.get("current")},show:function(e){e&&(this.model.set({current:e,visible:!0}),this.model.get("onchange")&&this.model.get("onchange")(e))},hide:function(){this.model.set("visible",!1)},first:function(){var e=this.collection.first();return e&&e.id},size:function(){return this.collection.length},add:function(e){this.collection.add(e)},del:function(e){this.collection.remove(e)},delAll:function(){this.collection.reset()},showTab:function(e){this.collection.get(e).set("hidden",!1)},hideTab:function(e){this.collection.get(e).set("hidden",!0)},_add:function(e){var t=this,i=e.attributes;this.$content.append(o("").attr("id",i.id).addClass("tab-pane").append(i.$el)),this.$nav.append(o(this._template_tab(i)).show().tooltip({title:i.tooltip,placement:"bottom",container:t.$el}).on("click",function(e){e.preventDefault(),t.show(i.id)})),1==this.size()&&this.show(i.id)},_remove:function(e){this.$("#tab-"+e.id).remove(),this.$("#"+e.id).remove()},_reset:function(){this.$nav.empty(),this.$content.empty()},_change:function(e){this.$("#tab-"+e.id)[e.get("hidden")?"hide":"show"]()},_template:function(){return o("").addClass("ui-tabs tabbable tabs-left").append(o("
").addClass("tab-navigation nav nav-tabs")).append(o("").addClass("tab-content"))},_template_tab:function(e){var t=o("").addClass("tab-element").attr("id","tab-"+e.id).append(o("").attr("id","tab-title-link-"+e.id)),i=t.find("a");return e.icon&&i.append(o("").addClass("tab-icon fa").addClass(e.icon)),i.append(o("").attr("id","tab-title-text-"+e.id).addClass("tab-title-text").append(e.title)),t}});return{View:t}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1))},function(e,t,i){var n,s;(function(a,o,r){n=[i(4),i(24),i(59),i(14),i(15)],s=function(e,t,i,n,s){return a.View.extend({status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},initialize:function(e,t){var i=this;this.app=e,this.model=t.model,this.setElement(this._template(t.model)),this.$mode=this.$(".upload-mode"),this.$title=this.$(".upload-title-extended"),this.$text=this.$(".upload-text"),this.$size=this.$(".upload-size"),this.$info_text=this.$(".upload-info-text"),this.$info_progress=this.$(".upload-info-progress"),this.$text_content=this.$(".upload-text-content"),this.$symbol=this.$(".upload-symbol"),this.$progress_bar=this.$(".upload-progress-bar"),this.$percentage=this.$(".upload-percentage"),this.settings=new n.View({title:"Upload configuration",container:this.$(".upload-settings"),placement:"bottom"});this.app.select_genome.value(),this.app.select_extension.value();this.$symbol.on("click",function(){i._removeRow()}),this.$text_content.on("change input",function(e){i.model.set({url_paste:o(e.target).val(),file_size:o(e.target).val().length})}),this.listenTo(this.model,"change:percentage",function(){i._refreshPercentage()}),this.listenTo(this.model,"change:status",function(){i._refreshStatus()}),this.listenTo(this.model,"change:info",function(){i._refreshInfo()}),this.listenTo(this.model,"change:file_size",function(){i._refreshFileSize()}),this.listenTo(this.model,"remove",function(){i.remove()}),this.app.collection.on("reset",function(){i.remove()})},render:function(){var t=this.model.attributes;this.$title.html(r.escape(t.file_name)),this.$size.html(e.bytesToString(t.file_size)),this.$mode.removeClass().addClass("upload-mode").addClass("text-primary"),"new"==t.file_mode?(this.$text.css({width:this.$el.width()-16+"px",top:this.$el.height()-8+"px"}).show(),this.$el.height(this.$el.height()-8+this.$text.height()+16),this.$mode.addClass("fa fa-edit")):"local"==t.file_mode?this.$mode.addClass("fa fa-laptop"):"ftp"==t.file_mode&&this.$mode.addClass("fa fa-folder-open-o")},_refreshInfo:function(){var e=this.model.get("info");e?this.$info_text.html("Failed: "+e).show():this.$info_text.hide()},_refreshPercentage:function(){var e=parseInt(this.model.get("percentage"));this.$progress_bar.css({width:e+"%"}),this.$percentage.html(100!=e?e+"%":"Adding to history...")},_refreshStatus:function(){var e=this.model.get("status");this.$symbol.removeClass().addClass("upload-symbol").addClass(this.status_classes[e]),this.model.set("enabled","init"==e);var t=this.model.get("enabled");this.$text_content.attr("disabled",!t),"success"==e&&(this.$el.addClass("success"),this.$percentage.html("100%")),"error"==e&&(this.$el.addClass("danger"),this.$info_progress.hide())},_refreshFileSize:function(){this.$size.html(e.bytesToString(this.model.get("file_size")))},_removeRow:function(){["init","success","error"].indexOf(this.model.get("status"))!==-1&&this.app.collection.remove(this.model)},_showSettings:function(){this.settings.visible?this.settings.hide():(this.settings.empty(),this.settings.append(new i(this).$el),this.settings.show())},_template:function(e){return'
You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.
0%
'}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2))},function(e,t,i){var n,s;(function(a,o,r){n=[i(4),i(24),i(127),i(58),i(14),i(15),i(7),i(37),i(63)],s=function(e,t,i,n,s,l,c,d){return a.View.extend({upload_size:0,collection:new t.Collection,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(e){var t=this;this.app=e,this.options=e.options,this.list_extensions=e.list_extensions,this.list_genomes=e.list_genomes,this.ui_button=e.ui_button,this.ftp_upload_site=e.currentFtp(),this.setElement(this._template()),this.btnLocal=new c.Button({id:"btn-local",title:"Choose local files",onclick:function(){t.uploadbox.select()},icon:"fa fa-laptop"}),this.btnFtp=new c.Button({id:"btn-ftp",title:"Choose FTP files",onclick:function(){t._eventFtp()},icon:"fa fa-folder-open-o"}),this.btnCreate=new c.Button({id:"btn-new",title:"Paste/Fetch data",onclick:function(){t._eventCreate()},icon:"fa fa-edit"}),this.btnStart=new c.Button({id:"btn-start",title:"Start",onclick:function(){t._eventStart()}}),this.btnBuild=new c.Button({id:"btn-build",title:"Build",onclick:function(){t._eventBuild()}}),this.btnStop=new c.Button({id:"btn-stop",title:"Pause",onclick:function(){t._eventStop()}}),this.btnReset=new c.Button({id:"btn-reset",title:"Reset",onclick:function(){t._eventReset()}}),this.btnClose=new c.Button({id:"btn-close",title:"Close",onclick:function(){t.app.modal.hide()}}),o.each([this.btnLocal,this.btnFtp,this.btnCreate,this.btnStop,this.btnReset,this.btnStart,this.btnBuild,this.btnClose],function(e){t.$(".upload-buttons").prepend(e.$el)}),this.uploadbox=this.$(".upload-box").uploadbox({url:this.app.options.nginx_upload_path,announce:function(e,i){t._eventAnnounce(e,i)},initialize:function(e){return t.app.toData([t.collection.get(e)],t.history_id)},progress:function(e,i){t._eventProgress(e,i)},success:function(e,i){t._eventSuccess(e,i)},error:function(e,i){t._eventError(e,i)},complete:function(){t._eventComplete()},ondragover:function(){t.$(".upload-box").addClass("highlight")},ondragleave:function(){t.$(".upload-box").removeClass("highlight")}}),console.log(this.list_extensions),this.ftp=new s.View({title:"FTP files",container:this.btnFtp.$el}),this.select_extension=new l.View({css:"upload-footer-selection-compressed",container:this.$(".upload-footer-extension"),data:o.filter(this.list_extensions,function(e){return!e.composite_files}),value:this.options.default_extension,onchange:function(e){t.updateExtension(e)}}),this.collectionType="list",this.select_collection=new l.View({css:"upload-footer-selection-compressed",container:this.$(".upload-footer-collection-type"),data:[{id:"list",text:"List"},{id:"paired",text:"Paired"},{id:"list:paired",text:"List of Pairs"}],value:"list",onchange:function(e){t.updateCollectionType(e)}}),this.$(".upload-footer-extension-info").on("click",function(e){t.showExtensionInfo({$el:r(e.target),title:t.select_extension.text(),extension:t.select_extension.value(),placement:"top"})}).on("mousedown",function(e){e.preventDefault()}),this.select_genome=new l.View({css:"upload-footer-selection",container:this.$(".upload-footer-genome"),data:this.list_genomes,value:this.options.default_genome,onchange:function(e){t.updateGenome(e)}}),this.collection.on("remove",function(e){t._eventRemove(e)}),this._updateScreen()},_eventAnnounce:function(e,n){this.counter.announce++;var s=new t.Model({id:e,file_name:n.name,file_size:n.size,file_mode:n.mode||"local",file_path:n.path,file_data:n,extension:this.select_extension.value(),genome:this.select_genome.value()});this.collection.add(s);var a=new i(this,{model:s});this.$(".upload-table > tbody:first").append(a.$el),this._updateScreen(),a.render()},_eventProgress:function(e,t){var i=this.collection.get(e);i.set("percentage",t),this.ui_button.model.set("percentage",this._uploadPercentage(t,i.get("file_size")))},_eventSuccess:function(e,t){var i=o.pluck(t.outputs,"hid"),n=this.collection.get(e);n.set({percentage:100,status:"success",hids:i}),this.ui_button.model.set("percentage",this._uploadPercentage(100,n.get("file_size"))),this.upload_completed+=100*n.get("file_size"),this.counter.announce--,this.counter.success++,this._updateScreen(),Galaxy.currHistoryPanel.refreshContents()},_eventError:function(e,t){var i=this.collection.get(e);i.set({percentage:100,status:"error",info:t}),this.ui_button.model.set({percentage:this._uploadPercentage(100,i.get("file_size")),status:"danger"}),this.upload_completed+=100*i.get("file_size"),this.counter.announce--,this.counter.error++,this._updateScreen()},_eventComplete:function(){this.collection.each(function(e){"queued"==e.get("status")&&e.set("status","init")}),this.counter.running=0,this._updateScreen()},_eventBuild:function(){var e=[];o.forEach(this.collection.models,function(t){e.push.apply(e,t.get("hids"))});var t=o.map(e,function(e){return Galaxy.currHistoryPanel.collection.getByHid(e)}),i=new Galaxy.currHistoryPanel.collection.constructor(t);i.historyId=Galaxy.currHistoryPanel.collection.historyId,Galaxy.currHistoryPanel.buildCollection(this.collectionType,i,!0),this.counter.running=0,this._updateScreen(),this._eventReset(),this.app.modal.hide()},_eventRemove:function(e){var t=e.get("status");"success"==t?this.counter.success--:"error"==t?this.counter.error--:this.counter.announce--,this.uploadbox.remove(e.id),this._updateScreen()},showExtensionInfo:function(e){var t=this,i=e.$el,n=e.extension,a=e.title,r=o.findWhere(t.list_extensions,{id:n});this.extension_popup&&this.extension_popup.remove(),this.extension_popup=new s.View({placement:e.placement||"bottom",container:i}),this.extension_popup.title(a),this.extension_popup.empty(),this.extension_popup.append(this._templateDescription(r)),this.extension_popup.show()},_eventFtp:function(){if(this.ftp.visible)this.ftp.hide();else{this.ftp.empty();var e=this;this.ftp.append(new n({collection:this.collection,ftp_upload_site:this.ftp_upload_site,onadd:function(t){e.uploadbox.add([{mode:"ftp",name:t.path,size:t.size,path:t.path}])},onremove:function(t){e.collection.remove(t)}}).$el),this.ftp.show()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(!(0==this.counter.announce||this.counter.running>0)){var e=this;this.upload_size=0,this.upload_completed=0,this.collection.each(function(t){"init"==t.get("status")&&(t.set("status","queued"),e.upload_size+=t.get("file_size"))}),this.ui_button.model.set({percentage:0,status:"success"}),this.counter.running=this.counter.announce,this.history_id=this.app.currentHistory(),this.uploadbox.start(),this._updateScreen()}},_eventStop:function(){this.counter.running>0&&(this.ui_button.model.set("status","info"),r(".upload-top-info").html("Queue will pause after completing the current file..."),this.uploadbox.stop())},_eventReset:function(){0==this.counter.running&&(this.collection.reset(),this.counter.reset(),this.uploadbox.reset(),this.select_extension.value(this.options.default_extension),this.select_genome.value(this.options.default_genome),this.ui_button.model.set("percentage",0),this._updateScreen())},updateExtension:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("extension")!=i.options.default_extension&&t||n.set("extension",e)})},updateCollectionType:function(e){this.collectionType=e},updateGenome:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("genome")!=i.options.default_genome&&t||n.set("genome",e)})},_updateScreen:function(){var e="";e=0==this.counter.announce?this.uploadbox.compatible()?" ":"Browser does not support Drag & Drop. Try Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+.":0==this.counter.running?"You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed.":"Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining.",this.$(".upload-top-info").html(e);var t=0==this.counter.running&&this.counter.announce+this.counter.success+this.counter.error>0,i=0==this.counter.running&&this.counter.announce>0,n=0==this.counter.running&&0==this.counter.announce&&this.counter.success>0&&0==this.counter.error,s=0==this.counter.running,a=this.counter.announce+this.counter.success+this.counter.error>0;this.btnReset[t?"enable":"disable"](),this.btnStart[i?"enable":"disable"](),this.btnStart.$el[i?"addClass":"removeClass"]("btn-primary"),this.btnBuild[n?"enable":"disable"](),this.btnBuild.$el[n?"addClass":"removeClass"]("btn-primary"),this.btnStop[this.counter.running>0?"enable":"disable"](),this.btnLocal[s?"enable":"disable"](),this.btnFtp[s?"enable":"disable"](),this.btnCreate[s?"enable":"disable"](),this.btnFtp.$el[this.ftp_upload_site?"show":"hide"](),this.$(".upload-table")[a?"show":"hide"](),this.$(".upload-helper")[a?"hide":"show"]()},_uploadPercentage:function(e,t){return(this.upload_completed+e*t)/this.upload_size},_templateDescription:function(e){if(e.description){var t=e.description;return e.description_url&&(t+=' (read more)'),t}return"There is no description available for this file extension."},_template:function(){return'
Drop files here
Name
Size
Status
'}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2),i(1))},function(e,t,i){var n,s;(function(a,o,r){n=[i(4),i(59),i(58),i(14),i(7),i(15),i(63)],s=function(e,t,i,n,s,l){return a.View.extend({status_classes:{init:"upload-mode fa fa-exclamation text-primary",ready:"upload-mode fa fa-check text-success",running:"upload-mode fa fa-spinner fa-spin",success:"upload-mode fa fa-check",error:"upload-mode fa fa-exclamation-triangle"},initialize:function(e,t){var i=this;this.app=e,this.model=t.model,this.setElement(this._template()),this.$source=this.$(".upload-source"),this.$settings=this.$(".upload-settings"),this.$status=this.$(".upload-status"),this.$text=this.$(".upload-text"),this.$text_content=this.$(".upload-text-content"),this.$info_text=this.$(".upload-info-text"),this.$info_progress=this.$(".upload-info-progress"),this.$file_name=this.$(".upload-file-name"),this.$file_desc=this.$(".upload-file-desc"),this.$file_size=this.$(".upload-file-size"),this.$progress_bar=this.$(".upload-progress-bar"),this.$percentage=this.$(".upload-percentage"),this.uploadinput=this.$el.uploadinput({ondragover:function(){i.model.get("enabled")&&i.$el.addClass("warning")},ondragleave:function(){i.$el.removeClass("warning")},onchange:function(e){"running"!=i.model.get("status")&&e&&e.length>0&&(i.model.reset({file_data:e[0],file_name:e[0].name,file_size:e[0].size,file_mode:e[0].mode||"local"}),i._refreshReady())}}),this.button_menu=new s.ButtonMenu({icon:"fa-caret-down",title:"Select",pull:"left"}),this.$source.append(this.button_menu.$el),this.button_menu.addMenu({icon:"fa-laptop",title:"Choose local file",onclick:function(){i.uploadinput.dialog()}}),this.app.ftp_upload_site&&this.button_menu.addMenu({icon:"fa-folder-open-o",title:"Choose FTP file",onclick:function(){i._showFtp()}}),this.button_menu.addMenu({icon:"fa-edit",title:"Paste/Fetch data",onclick:function(){i.model.reset({file_mode:"new",file_name:"New File"})}}),this.ftp=new n.View({title:"Choose FTP file:",container:this.$source.find(".ui-button-menu"),placement:"right"}),this.settings=new n.View({title:"Upload configuration",container:this.$settings,placement:"bottom"}),this.$text_content.on("change input",function(e){i.model.set({url_paste:o(e.target).val(),file_size:o(e.target).val().length}),i._refreshReady()}),this.$settings.on("click",function(e){i._showSettings()}).on("mousedown",function(e){e.preventDefault()}),this.listenTo(this.model,"change:percentage",function(){i._refreshPercentage()}),this.listenTo(this.model,"change:status",function(){i._refreshStatus()}),this.listenTo(this.model,"change:info",function(){i._refreshInfo()}),this.listenTo(this.model,"change:file_name",function(){i._refreshFileName()}),this.listenTo(this.model,"change:file_mode",function(){i._refreshMode()}),this.listenTo(this.model,"change:file_size",function(){i._refreshFileSize()}),this.listenTo(this.model,"remove",function(){i.remove()}),this.app.collection.on("reset",function(){i.remove()})},render:function(){this.$el.attr("id","upload-row-"+this.model.id),this.$file_name.html(r.escape(this.model.get("file_name")||"-")),this.$file_desc.html(this.model.get("file_desc")||"Unavailable"),this.$file_size.html(e.bytesToString(this.model.get("file_size"))),this.$status.removeClass().addClass(this.status_classes.init)},remove:function(){a.View.prototype.remove.apply(this)},_refreshReady:function(){this.app.collection.each(function(e){e.set("status",e.get("file_size")>0&&"ready"||"init")})},_refreshMode:function(){var e=this.model.get("file_mode");"new"==e?(this.height=this.$el.height(),this.$text.css({width:this.$el.width()-16+"px",top:this.$el.height()-8+"px"}).show(),this.$el.height(this.$el.height()-8+this.$text.height()+16),this.$text_content.val("").trigger("keyup")):(this.$el.height(this.height),this.$text.hide())},_refreshInfo:function(){var e=this.model.get("info");e?this.$info_text.html("Failed: "+e).show():this.$info_text.hide()},_refreshPercentage:function(){var e=parseInt(this.model.get("percentage"));0!=e?this.$progress_bar.css({width:e+"%"}):(this.$progress_bar.addClass("no-transition"),this.$progress_bar.css({width:"0%"}),this.$progress_bar[0].offsetHeight,this.$progress_bar.removeClass("no-transition")),this.$percentage.html(100!=e?e+"%":"Adding to history...")},_refreshStatus:function(){var e=this.model.get("status");this.$status.removeClass().addClass(this.status_classes[e]),this.model.set("enabled","running"!=e),this.$text_content.attr("disabled",!this.model.get("enabled")),this.$el.removeClass("success danger warning"),"running"!=e&&"ready"!=e||this.model.set("percentage",0),this.$source.find(".button")["running"==e?"addClass":"removeClass"]("disabled"),"success"==e&&(this.$el.addClass("success"),this.model.set("percentage",100),this.$percentage.html("100%")),"error"==e?(this.$el.addClass("danger"),this.model.set("percentage",0),this.$info_progress.hide(),this.$info_text.show()):(this.$info_progress.show(),this.$info_text.hide())},_refreshFileName:function(){this.$file_name.html(this.model.get("file_name")||"-")},_refreshFileSize:function(){this.$file_size.html(e.bytesToString(this.model.get("file_size")))},_showFtp:function(){if(this.ftp.visible)this.ftp.hide();else{var e=this;this.ftp.empty(),this.ftp.append(new i({ftp_upload_site:this.app.ftp_upload_site,onchange:function(t){e.ftp.hide(),"running"!=e.model.get("status")&&t&&(e.model.reset({file_mode:"ftp",file_name:t.path,file_size:t.size,file_path:t.path}),e._refreshReady())}}).$el),this.ftp.show()}},_showSettings:function(){this.settings.visible?this.settings.hide():(this.settings.empty(),this.settings.append(new t(this).$el),this.settings.show())},_template:function(){return'
You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.
0%
'}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2))},function(e,t,i){var n,s;(function(a,o,r){n=[i(4),i(24),i(129),i(14),i(15),i(7)],s=function(e,t,i,n,s,l){return a.View.extend({collection:new t.Collection,initialize:function(e){var t=this;this.app=e,this.options=e.options,this.list_extensions=e.list_extensions,this.list_genomes=e.list_genomes,this.ftp_upload_site=e.currentFtp(),this.setElement(this._template()),this.btnStart=new l.Button({title:"Start",onclick:function(){t._eventStart()}}),this.btnClose=new l.Button({title:"Close",onclick:function(){t.app.modal.hide()}}),o.each([this.btnStart,this.btnClose],function(e){t.$(".upload-buttons").prepend(e.$el)}),this.select_extension=new s.View({css:"upload-footer-selection",container:this.$(".upload-footer-extension"),data:o.filter(this.list_extensions,function(e){return e.composite_files}),onchange:function(e){t.collection.reset();var i=o.findWhere(t.list_extensions,{id:e});i&&i.composite_files&&o.each(i.composite_files,function(e){t.collection.add({id:t.collection.size(),file_desc:e.description||e.name})})}}),this.$(".upload-footer-extension-info").on("click",function(e){t._showExtensionInfo({$el:r(e.target),title:t.select_extension.text(),extension:t.select_extension.value(),placement:"top"})}).on("mousedown",function(e){e.preventDefault()}),this.select_genome=new s.View({css:"upload-footer-selection",container:this.$(".upload-footer-genome"),data:this.list_genomes,value:this.options.default_genome}),this.listenTo(this.collection,"add",function(e){t._eventAnnounce(e)}),this.listenTo(this.collection,"change add",function(){t.render()}),this.select_extension.options.onchange(this.select_extension.value()),this.render()},render:function(){var e=this.collection.first();e&&"running"==e.get("status")?(this.select_genome.disable(),this.select_extension.disable()):(this.select_genome.enable(),this.select_extension.enable()),this.collection.where({status:"ready"}).length==this.collection.length&&this.collection.length>0?(this.btnStart.enable(),this.btnStart.$el.addClass("btn-primary")):(this.btnStart.disable(),this.btnStart.$el.removeClass("btn-primary")),this.$(".upload-table")[this.collection.length>0?"show":"hide"]()},_eventAnnounce:function(e){var t=new i(this,{model:e});this.$(".upload-table > tbody:first").append(t.$el),this.$(".upload-table")[this.collection.length>0?"show":"hide"](),t.render()},_eventStart:function(){var e=this;this.collection.each(function(t){t.set({genome:e.select_genome.value(),extension:e.select_extension.value()})}),r.uploadpost({url:this.app.options.nginx_upload_path,data:this.app.toData(this.collection.filter()),success:function(t){e._eventSuccess(t)},error:function(t){e._eventError(t)},progress:function(t){e._eventProgress(t)}})},_eventProgress:function(e){this.collection.each(function(t){t.set("percentage",e)})},_eventSuccess:function(e){this.collection.each(function(e){e.set("status","success")}),Galaxy.currHistoryPanel.refreshContents()},_eventError:function(e){this.collection.each(function(t){t.set({status:"error",info:e})})},_showExtensionInfo:function(e){var t=e.$el,i=e.extension,s=e.title,a=o.findWhere(this.list_extensions,{id:i});this.extension_popup&&this.extension_popup.remove(),this.extension_popup=new n.View({placement:e.placement||"bottom",container:t,destroy:!0}),this.extension_popup.title(s),this.extension_popup.empty(),this.extension_popup.append(this._templateDescription(a)),this.extension_popup.show()},_templateDescription:function(e){if(e.description){var t=e.description;return e.description_url&&(t+=' (read more)'),t}return"There is no description available for this file extension."},_template:function(){return'
Description
Name
Size
Settings
Status
'}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2),i(1))},function(e,t,i){var n,s;(function(a,o,r){n=[i(4),i(24),i(59),i(14),i(15)],s=function(e,t,i,n,s){return a.View.extend({status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},initialize:function(e,t){var i=this;this.app=e,this.model=t.model,this.setElement(this._template(t.model)),this.$mode=this.$(".upload-mode"),this.$title=this.$(".upload-title"),this.$text=this.$(".upload-text"),this.$size=this.$(".upload-size"),
+this.$info_text=this.$(".upload-info-text"),this.$info_progress=this.$(".upload-info-progress"),this.$text_content=this.$(".upload-text-content"),this.$settings=this.$(".upload-settings"),this.$symbol=this.$(".upload-symbol"),this.$progress_bar=this.$(".upload-progress-bar"),this.$percentage=this.$(".upload-percentage"),this.settings=new n.View({title:"Upload configuration",container:this.$(".upload-settings"),placement:"bottom"});var a=this.app.select_genome.value(),r=this.app.select_extension.value();this.select_genome=new s.View({css:"upload-genome",data:i.app.list_genomes,container:this.$(".upload-genome"),value:a,onchange:function(e){i.model.set("genome",e)}}),this.select_extension=new s.View({css:"upload-extension",data:i.app.list_extensions,container:this.$(".upload-extension"),value:r,onchange:function(e){i.model.set("extension",e)}}),this.model.set({genome:a,extension:r}),this.$symbol.on("click",function(){i._removeRow()}),this.$(".upload-extension-info").on("click",function(e){i.app.showExtensionInfo({$el:o(e.target),title:i.select_extension.text(),extension:i.select_extension.value()})}).on("mousedown",function(e){e.preventDefault()}),this.$settings.on("click",function(e){i._showSettings()}).on("mousedown",function(e){e.preventDefault()}),this.$text_content.on("change input",function(e){i.model.set({url_paste:o(e.target).val(),file_size:o(e.target).val().length})}),this.listenTo(this.model,"change:percentage",function(){i._refreshPercentage()}),this.listenTo(this.model,"change:status",function(){i._refreshStatus()}),this.listenTo(this.model,"change:info",function(){i._refreshInfo()}),this.listenTo(this.model,"change:genome",function(){i._refreshGenome()}),this.listenTo(this.model,"change:extension",function(){i._refreshExtension()}),this.listenTo(this.model,"change:file_size",function(){i._refreshFileSize()}),this.listenTo(this.model,"remove",function(){i.remove()}),this.app.collection.on("reset",function(){i.remove()})},render:function(){var t=this.model.attributes;this.$title.html(r.escape(t.file_name)),this.$size.html(e.bytesToString(t.file_size)),this.$mode.removeClass().addClass("upload-mode").addClass("text-primary"),"new"==t.file_mode?(this.$text.css({width:this.$el.width()-16+"px",top:this.$el.height()-8+"px"}).show(),this.$el.height(this.$el.height()-8+this.$text.height()+16),this.$mode.addClass("fa fa-edit")):"local"==t.file_mode?this.$mode.addClass("fa fa-laptop"):"ftp"==t.file_mode&&this.$mode.addClass("fa fa-folder-open-o")},remove:function(){this.select_genome.remove(),this.select_extension.remove(),a.View.prototype.remove.apply(this)},_refreshExtension:function(){this.select_extension.value(this.model.get("extension"))},_refreshGenome:function(){this.select_genome.value(this.model.get("genome"))},_refreshInfo:function(){var e=this.model.get("info");e?this.$info_text.html("Failed: "+e).show():this.$info_text.hide()},_refreshPercentage:function(){var e=parseInt(this.model.get("percentage"));this.$progress_bar.css({width:e+"%"}),this.$percentage.html(100!=e?e+"%":"Adding to history...")},_refreshStatus:function(){var e=this.model.get("status");this.$symbol.removeClass().addClass("upload-symbol").addClass(this.status_classes[e]),this.model.set("enabled","init"==e);var t=this.model.get("enabled");this.$text_content.attr("disabled",!t),t?(this.select_genome.enable(),this.select_extension.enable()):(this.select_genome.disable(),this.select_extension.disable()),"success"==e&&(this.$el.addClass("success"),this.$percentage.html("100%")),"error"==e&&(this.$el.addClass("danger"),this.$info_progress.hide())},_refreshFileSize:function(){this.$size.html(e.bytesToString(this.model.get("file_size")))},_removeRow:function(){["init","success","error"].indexOf(this.model.get("status"))!==-1&&this.app.collection.remove(this.model)},_showSettings:function(){this.settings.visible?this.settings.hide():(this.settings.empty(),this.settings.append(new i(this).$el),this.settings.show())},_template:function(e){return'
You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.
0%
'}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2))},function(e,t,i){var n,s;(function(a,o,r){n=[i(4),i(24),i(131),i(58),i(14),i(15),i(7),i(63)],s=function(e,t,i,n,s,l,c){return a.View.extend({upload_size:0,collection:new t.Collection,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(e){var t=this;this.app=e,this.options=e.options,this.list_extensions=e.list_extensions,this.list_genomes=e.list_genomes,this.ui_button=e.ui_button,this.ftp_upload_site=e.currentFtp(),this.setElement(this._template()),this.btnLocal=new c.Button({id:"btn-local",title:"Choose local file",onclick:function(){t.uploadbox.select()},icon:"fa fa-laptop"}),this.btnFtp=new c.Button({id:"btn-ftp",title:"Choose FTP file",onclick:function(){t._eventFtp()},icon:"fa fa-folder-open-o"}),this.btnCreate=new c.Button({id:"btn-new",title:"Paste/Fetch data",onclick:function(){t._eventCreate()},icon:"fa fa-edit"}),this.btnStart=new c.Button({id:"btn-start",title:"Start",onclick:function(){t._eventStart()}}),this.btnStop=new c.Button({id:"btn-stop",title:"Pause",onclick:function(){t._eventStop()}}),this.btnReset=new c.Button({id:"btn-reset",title:"Reset",onclick:function(){t._eventReset()}}),this.btnClose=new c.Button({id:"btn-close",title:"Close",onclick:function(){t.app.modal.hide()}}),o.each([this.btnLocal,this.btnFtp,this.btnCreate,this.btnStop,this.btnReset,this.btnStart,this.btnClose],function(e){t.$(".upload-buttons").prepend(e.$el)}),this.uploadbox=this.$(".upload-box").uploadbox({url:this.app.options.nginx_upload_path,announce:function(e,i){t._eventAnnounce(e,i)},initialize:function(e){return t.app.toData([t.collection.get(e)],t.history_id)},progress:function(e,i){t._eventProgress(e,i)},success:function(e,i){t._eventSuccess(e,i)},error:function(e,i){t._eventError(e,i)},complete:function(){t._eventComplete()},ondragover:function(){t.$(".upload-box").addClass("highlight")},ondragleave:function(){t.$(".upload-box").removeClass("highlight")}}),this.ftp=new s.View({title:"FTP files",container:this.btnFtp.$el}),this.select_extension=new l.View({css:"upload-footer-selection",container:this.$(".upload-footer-extension"),data:o.filter(this.list_extensions,function(e){return!e.composite_files}),value:this.options.default_extension,onchange:function(e){t.updateExtension(e)}}),this.$(".upload-footer-extension-info").on("click",function(e){t.showExtensionInfo({$el:r(e.target),title:t.select_extension.text(),extension:t.select_extension.value(),placement:"top"})}).on("mousedown",function(e){e.preventDefault()}),this.select_genome=new l.View({css:"upload-footer-selection",container:this.$(".upload-footer-genome"),data:this.list_genomes,value:this.options.default_genome,onchange:function(e){t.updateGenome(e)}}),this.collection.on("remove",function(e){t._eventRemove(e)}),this._updateScreen()},_eventAnnounce:function(e,n){this.counter.announce++;var s=new t.Model({id:e,file_name:n.name,file_size:n.size,file_mode:n.mode||"local",file_path:n.path,file_data:n});this.collection.add(s);var a=new i(this,{model:s});this.$(".upload-table > tbody:first").append(a.$el),this._updateScreen(),a.render()},_eventProgress:function(e,t){var i=this.collection.get(e);i.set("percentage",t),this.ui_button.model.set("percentage",this._uploadPercentage(t,i.get("file_size")))},_eventSuccess:function(e,t){var i=this.collection.get(e);i.set({percentage:100,status:"success"}),this.ui_button.model.set("percentage",this._uploadPercentage(100,i.get("file_size"))),this.upload_completed+=100*i.get("file_size"),this.counter.announce--,this.counter.success++,this._updateScreen(),Galaxy.currHistoryPanel.refreshContents()},_eventError:function(e,t){var i=this.collection.get(e);i.set({percentage:100,status:"error",info:t}),this.ui_button.model.set({percentage:this._uploadPercentage(100,i.get("file_size")),status:"danger"}),this.upload_completed+=100*i.get("file_size"),this.counter.announce--,this.counter.error++,this._updateScreen()},_eventComplete:function(){this.collection.each(function(e){"queued"==e.get("status")&&e.set("status","init")}),this.counter.running=0,this._updateScreen()},_eventRemove:function(e){var t=e.get("status");"success"==t?this.counter.success--:"error"==t?this.counter.error--:this.counter.announce--,this.uploadbox.remove(e.id),this._updateScreen()},showExtensionInfo:function(e){var t=this,i=e.$el,n=e.extension,a=e.title,r=o.findWhere(t.list_extensions,{id:n});this.extension_popup&&this.extension_popup.remove(),this.extension_popup=new s.View({placement:e.placement||"bottom",container:i}),this.extension_popup.title(a),this.extension_popup.empty(),this.extension_popup.append(this._templateDescription(r)),this.extension_popup.show()},_eventFtp:function(){if(this.ftp.visible)this.ftp.hide();else{this.ftp.empty();var e=this;this.ftp.append(new n({collection:this.collection,ftp_upload_site:this.ftp_upload_site,onadd:function(t){e.uploadbox.add([{mode:"ftp",name:t.path,size:t.size,path:t.path}])},onremove:function(t){e.collection.remove(t)}}).$el),this.ftp.show()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(!(0==this.counter.announce||this.counter.running>0)){var e=this;this.upload_size=0,this.upload_completed=0,this.collection.each(function(t){"init"==t.get("status")&&(t.set("status","queued"),e.upload_size+=t.get("file_size"))}),this.ui_button.model.set({percentage:0,status:"success"}),this.counter.running=this.counter.announce,this.history_id=this.app.currentHistory(),this.uploadbox.start(),this._updateScreen()}},_eventStop:function(){this.counter.running>0&&(this.ui_button.model.set("status","info"),r(".upload-top-info").html("Queue will pause after completing the current file..."),this.uploadbox.stop())},_eventReset:function(){0==this.counter.running&&(this.collection.reset(),this.counter.reset(),this.uploadbox.reset(),this.select_extension.value(this.options.default_extension),this.select_genome.value(this.options.default_genome),this.ui_button.model.set("percentage",0),this._updateScreen())},updateExtension:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("extension")!=i.options.default_extension&&t||n.set("extension",e)})},updateGenome:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("genome")!=i.options.default_genome&&t||n.set("genome",e)})},_updateScreen:function(){var e="";e=0==this.counter.announce?this.uploadbox.compatible()?" ":"Browser does not support Drag & Drop. Try Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+.":0==this.counter.running?"You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed.":"Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining.",this.$(".upload-top-info").html(e);var t=0==this.counter.running&&this.counter.announce+this.counter.success+this.counter.error>0,i=0==this.counter.running&&this.counter.announce>0,n=0==this.counter.running,s=this.counter.announce+this.counter.success+this.counter.error>0;this.btnReset[t?"enable":"disable"](),this.btnStart[i?"enable":"disable"](),this.btnStart.$el[i?"addClass":"removeClass"]("btn-primary"),this.btnStop[this.counter.running>0?"enable":"disable"](),this.btnLocal[n?"enable":"disable"](),this.btnFtp[n?"enable":"disable"](),this.btnCreate[n?"enable":"disable"](),this.btnFtp.$el[this.ftp_upload_site?"show":"hide"](),this.$(".upload-table")[s?"show":"hide"](),this.$(".upload-helper")[s?"hide":"show"]()},_uploadPercentage:function(e,t){return(this.upload_completed+e*t)/this.upload_size},_templateDescription:function(e){if(e.description){var t=e.description;return e.description_url&&(t+=' (read more)'),t}return"There is no description available for this file extension."},_template:function(){return'
Drop files here
Name
Size
Type
Genome
Settings
Status
'}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2),i(1))},function(e,t,i){var n,s;(function(i,a){n=[],s=function(){var e=i.View.extend({initialize:function(e){var t=this;this.model=e&&e.model||new i.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",percentage:0,status:"",onunload:function(){},onclick:function(){}}).set(e),this.setElement(this._template()),this.$progress=this.$(".progress-bar"),this.listenTo(this.model,"change",this.render,this),this.render(),a(window).on("beforeunload",function(){return t.model.get("onunload")()})},render:function(){var e=this.model.attributes;this.$el.off("click").on("click",function(t){e.onclick(t)}).tooltip({title:this.model.get("tooltip"),placement:"bottom"}),this.$progress.removeClass().addClass("progress-bar").addClass("progress-bar-notransition").addClass(""!=e.status&&"progress-bar-"+e.status).css({width:e.percentage+"%"})},_template:function(){return'
'}});return{View:e}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1))},function(e,t,i){var n,s;(function(a){n=[i(4),i(8),i(126),i(133),i(132),i(130),i(128)],s=function(e,t,i,n,s,o,r){return a.View.extend({options:{nginx_upload_path:"",ftp_upload_site:"n/a",default_genome:"?",default_extension:"auto",height:500,width:900,auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."}},list_extensions:[],list_genomes:[],initialize:function(t){var i=this;this.options=e.merge(t,this.options),this.ui_button=new n.View({onclick:function(e){e.preventDefault(),i.show()},onunload:function(){var e=i.ui_button.model.get("percentage",0);if(e>0&&e<100)return"Several uploads are queued."}}),this.setElement(this.ui_button.$el);var i=this;e.get({url:Galaxy.root+"api/datatypes?extension_only=False",success:function(e){for(key in e)i.list_extensions.push({id:e[key].extension,text:e[key].extension,description:e[key].description,description_url:e[key].description_url,composite_files:e[key].composite_files});i.list_extensions.sort(function(e,t){var i=e.text&&e.text.toLowerCase(),n=t.text&&t.text.toLowerCase();return i>n?1:it.text?1:e.text0){var n={};n.dbkey=e[0].get("genome",null),n.file_type=e[0].get("extension",null);for(var s in e){var a=e[s];if(a.set("status","running"),!(a.get("file_size")>0)){i.error_message="Upload content incomplete.",a.set("status","error"),a.set("info",i.error_message);break}var o="files_"+s+"|";switch(n[o+"type"]="upload_dataset",n[o+"space_to_tab"]=a.get("space_to_tab")&&"Yes"||null,n[o+"to_posix_lines"]=a.get("to_posix_lines")&&"Yes"||null,a.get("file_mode")){case"new":n[o+"url_paste"]=a.get("url_paste");break;case"ftp":n[o+"ftp_files"]=a.get("file_path");break;case"local":i.files.push({name:o+"file_data",file:a.get("file_data")})}}i.payload.inputs=JSON.stringify(n)}return i}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3))},function(e,t,i){var n,s;(function(a,o){n=[i(4),i(7),i(20),i(27)],s=function(e,t,i,n){var s=a.Collection.extend({comparator:function(e,t){return e=e.get("name"),t=t.get("name"),e>t?1:e").append(o("").text("Current Custom Builds")).append(this.table.$el).append(this.$installed=o("").append(o("").text("System Installed Builds").addClass("ui-margin-top")).append(this.installed_builds.$el)).append(o("").text("Add a Custom Build").addClass("ui-margin-top")).append(o("").addClass("ui-column").append(o("").addClass("ui-column-left").append(this.message.$el).append(this.$form=o("").addClass("ui-margin-top"))).append(this.$help=o("").addClass("ui-column-right")))),this.listenTo(this.collection,"add remove reset",function(){i._renderTable()}),this.listenTo(this.model,"change",function(){i._renderForm()}),this.collection.fetch(),this.model.fetch()},render:function(){this._renderTable(),this._renderForm()},_renderTable:function(){var e=this;this.table.delAll(),this.collection.sort(),this.collection.each(function(i){e.table.add(i.id),e.table.add(i.get("name")),e.table.add(void 0!==i.get("count")?i.get("count"):"Processing..."),e.table.add(new t.ButtonIcon({icon:"fa-trash-o",cls:"ui-button-icon-plain",tooltip:"Delete custom build.",onclick:function(){i.destroy()}}).$el),e.table.append(i.id)})},_renderForm:function(){var e=this,n="fasta",s=new i({inputs:[{type:"text",name:"name",label:"Name",help:"Specify a build name e.g. Hamster."},{type:"text",name:"id",label:"Key",help:"Specify a build key e.g. hamster_v1."},{name:"len",type:"conditional",test_param:{name:"type",label:"Definition",help:"Provide the data source.",type:"select",value:n,data:[{value:"fasta",label:"FASTA-file from history"},{value:"file",label:"Len-file from disk"},{value:"text",label:"Len-file by copy/paste"}]},cases:[{value:"fasta",inputs:[{type:"select",name:"value",label:"FASTA-file",data:this.model.get("fasta_hdas")}]},{value:"file",inputs:[{type:"upload",name:"value",label:"Len-file",data:this.model.get("len_hdas")}]},{value:"text",inputs:[{type:"text",area:!0,name:"value",label:"Edit/Paste"}]}]}],buttons:{save:new t.Button({icon:"fa-save",tooltip:"Create new Build",title:"Save",cls:"ui-button btn btn-primary",floating:"clear",onclick:function(){var t=s.data.create();t.id&&t.name?e.collection.create(t,{wait:!0,success:function(t){t.get("message")?e.message.update({message:t.get("message"),status:"warning"}):e.message.update({message:"Successfully added a new custom build.",status:"success"})},error:function(t,i){var n=i&&i.responseJSON&&i.responseJSON.err_msg;e.message.update({message:n||"Failed to create custom build.",status:"danger"})}}):e.message.update({message:"All inputs are required.",status:"danger"})}})},onchange:function(){var t=s.data.match("len|type");if(t){var i=s.field_list[t];e._renderHelp(i.value())}}});this.$form.empty().append(s.$el);var a=this.model.get("installed_builds");a&&a.length?(this.$installed.show(),this.installed_builds.update(this.model.get("installed_builds"))):this.$installed.hide(),this._renderHelp(n)},_renderHelp:function(e){this.$help.empty().addClass("alert alert-info").html("fasta"==e?this._templateFasta():this._templateLen())},_templateLen:function(){return"
Length Format
The length format is two-column, separated by whitespace, of the form:
chrom/contig length of chrom/contig
For example, the first few entries of mm9.len are as follows:
Trackster uses this information to populate the select box for chrom/contig, andto set the maximum basepair of the track browser. You may either upload a .len fileof this format (Len File option), or directly enter the information into the box (Len Entry option).
"},_templateFasta:function(){return"
FASTA format
This is a multi-fasta file from your current history that provides the genomesequences for each chromosome/contig in your build.
Here is a snippet from an example multi-fasta file:
"}});return{View:r}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1))},function(e,t,i){var n,s;(function(a,o,r){n=[i(20),i(7)],s=function(e,t){var i=a.Model.extend({initialize:function(e){e=e||{},e.user_id=e.user_id||Galaxy.user.id,this.set({user_id:e.user_id,information:{title:"Manage information",description:"Edit your email, addresses and custom parameters or change your username.",url:"api/users/"+e.user_id+"/information/inputs",icon:"fa-user"},password:{title:"Change password",description:"Allows you to change your login credentials.",icon:"fa-unlock-alt",url:"api/users/"+e.user_id+"/password/inputs",submit_title:"Save password"},communication:{title:"Change communication settings",description:"Enable or disable the communication feature to chat with other users.",url:"api/users/"+e.user_id+"/communication/inputs",icon:"fa-comments-o"},permissions:{title:"Set dataset permissions for new histories",description:"Grant others default access to newly created histories. Changes made here will only affect histories created after these settings have been stored.",url:"api/users/"+e.user_id+"/permissions/inputs",icon:"fa-users",submit_title:"Save permissions"},api_key:{title:"Manage API key",description:"Access your current API key or create a new one.",url:"api/users/"+e.user_id+"/api_key/inputs",icon:"fa-key",submit_title:"Create a new key",submit_icon:"fa-check"},toolbox_filters:{title:"Manage Toolbox filters",description:"Customize your Toolbox by displaying or omitting sets of Tools.",url:"api/users/"+e.user_id+"/toolbox_filters/inputs",icon:"fa-filter",submit_title:"Save filters"},openids:{title:"Manage OpenIDs",description:"Associate OpenIDs with your account.",icon:"fa-openid",onclick:function(){window.location.href=Galaxy.root+"user/openid_manage?cntrller=user&use_panels=True"}},custom_builds:{title:"Manage custom builds",description:"Add or remove custom builds using history datasets.",icon:"fa-cubes",onclick:function(){window.location.href=Galaxy.root+"custom_builds"}},logout:{title:"Sign out",description:"Click here to sign out of all sessions.",icon:"fa-sign-out",onclick:function(){Galaxy.modal.show({title:"Sign out",body:"Do you want to continue and sign out of all active sessions?",buttons:{Cancel:function(){Galaxy.modal.hide()},"Sign out":function(){window.location.href=Galaxy.root+"user/logout"}}})}}})}}),n=a.View.extend({initialize:function(){this.model=new i,this.message=new t.Message,this.setElement(""),this.render()},render:function(){var e=this,t=Galaxy.config;o.getJSON(Galaxy.root+"api/users/"+Galaxy.user.id,function(i){e.$preferences=o("").addClass("ui-panel").append(e.message.$el).append(o("").append("User preferences")).append(o("").append("You are logged in as "+r.escape(i.email)+".")).append(e.$table=o("
You are using '+e.nice_total_disk_usage+" of disk space in this Galaxy instance. "+(Galaxy.config.enable_quotas?"Your disk quota is: "+e.quota+". ":"")+'Is your usage more than expected? See the documentation for tips on how to find all of the data in your account.
")):t.html("")},confirm_delete:function(e,t){var i=e.$el.find(".link-confirm-"+t.id),n=e.$el.find(".link-confirm-shared-"+t.id);i.click(function(){return confirm("Are you sure you want to delete workflow '"+t.name+"'?")}),n.click(function(){return confirm("Are you sure you want to remove the shared workflow '"+t.name+"'?")})},search_workflow:function(e,t,i,n){t.on("keyup",function(){var e=a(this).val();if(e.length>=n){var t=new RegExp(e,"i");i.hide(),i.filter(function(){return t.test(a(this).text())}).show()}else i.show()})},get_querystring:function(e){return decodeURIComponent(window.location.search.replace(new RegExp("^(?:.*[&\\?]"+encodeURIComponent(e).replace(/[\.\+\*]/g,"\\$&")+"(?:\\=([^&]*))?)?.*$","i"),"$1"))},adjust_actiondropdown:function(e){e.on("show.bs.dropdown",function(){e.css("overflow","inherit")}),e.on("hide.bs.dropdown",function(){e.css("overflow","auto")})},_templateNoWorkflow:function(){return'
');\n\t }\n\t }\n\t\n\t // Render first chunk.\n\t var self = this,\n\t first_chunk = this.model.get('first_data_chunk');\n\t if (first_chunk) {\n\t // First chunk is bootstrapped, so render now.\n\t this._renderChunk(first_chunk);\n\t } else {\n\t // No bootstrapping, so get first chunk and then render.\n\t $.when(self.model.get_next_chunk()).then(function (result) {\n\t self._renderChunk(result);\n\t });\n\t }\n\t\n\t // -- Show new chunks during scrolling. --\n\t\n\t // Set up chunk loading when scrolling using the scrolling element.\n\t this.scroll_elt.scroll(function () {\n\t self.attempt_to_fetch();\n\t });\n\t },\n\t\n\t /**\n\t * Returns true if user has scrolled to the bottom of the view.\n\t */\n\t scrolled_to_bottom: function () {\n\t return false;\n\t },\n\t\n\t // -- Helper functions. --\n\t\n\t _renderCell: function (cell_contents, index, colspan) {\n\t var $cell = $('
').text(cell_contents);\n\t var column_types = this.model.get_metadata('column_types');\n\t if (colspan !== undefined) {\n\t $cell.attr('colspan', colspan).addClass('stringalign');\n\t } else if (column_types) {\n\t if (index < column_types.length) {\n\t if (column_types[index] === 'str' || column_types[index] === 'list') {\n\t /* Left align all str columns, right align the rest */\n\t $cell.addClass('stringalign');\n\t }\n\t }\n\t }\n\t return $cell;\n\t },\n\t\n\t _renderRow: function (line) {\n\t // Check length of cells to ensure this is a complete row.\n\t var cells = line.split('\\t'),\n\t row = $('
'),\n\t num_columns = this.model.get_metadata('columns');\n\t\n\t if (this.row_count % 2 !== 0) {\n\t row.addClass('dark_row');\n\t }\n\t\n\t if (cells.length === num_columns) {\n\t _.each(cells, function (cell_contents, index) {\n\t row.append(this._renderCell(cell_contents, index));\n\t }, this);\n\t } else if (cells.length > num_columns) {\n\t // SAM file or like format with optional metadata included.\n\t _.each(cells.slice(0, num_columns - 1), function (cell_contents, index) {\n\t row.append(this._renderCell(cell_contents, index));\n\t }, this);\n\t row.append(this._renderCell(cells.slice(num_columns - 1).join('\\t'), num_columns - 1));\n\t } else if (cells.length === 1) {\n\t // Comment line, just return the one cell.\n\t row.append(this._renderCell(line, 0, num_columns));\n\t } else {\n\t // cells.length is greater than one, but less than num_columns. Render cells and pad tds.\n\t // Possibly a SAM file or like format with optional metadata missing.\n\t // Could also be a tabular file with a line with missing columns.\n\t _.each(cells, function (cell_contents, index) {\n\t row.append(this._renderCell(cell_contents, index));\n\t }, this);\n\t _.each(_.range(num_columns - cells.length), function () {\n\t row.append($('
'));\n\t });\n\t }\n\t\n\t this.row_count++;\n\t return row;\n\t },\n\t\n\t _renderChunk: function (chunk) {\n\t var data_table = this.$el.find('table');\n\t _.each(chunk.ck_data.split('\\n'), function (line, index) {\n\t if (line !== '') {\n\t data_table.append(this._renderRow(line));\n\t }\n\t }, this);\n\t }\n\t });\n\t\n\t /**\n\t * Tabular view that is placed at the top level of page. Scrolling occurs\n\t * view top-level elements outside of view.\n\t */\n\t var TopLevelTabularDatasetChunkedView = TabularDatasetChunkedView.extend({\n\t\n\t initialize: function (options) {\n\t TabularDatasetChunkedView.prototype.initialize.call(this, options);\n\t\n\t // Scrolling happens in top-level elements.\n\t scroll_elt = _.find(this.$el.parents(), function (p) {\n\t return $(p).css('overflow') === 'auto';\n\t });\n\t\n\t // If no scrolling element found, use window.\n\t if (!scroll_elt) {\n\t scroll_elt = window;\n\t }\n\t\n\t // Wrap scrolling element for easy access.\n\t this.scroll_elt = $(scroll_elt);\n\t },\n\t\n\t /**\n\t * Returns true if user has scrolled to the bottom of the view.\n\t */\n\t scrolled_to_bottom: function () {\n\t return this.$el.height() - this.scroll_elt.scrollTop() - this.scroll_elt.height() <= 0;\n\t }\n\t\n\t });\n\t\n\t /**\n\t * Tabular view tnat is embedded in a page. Scrolling occurs in view's el.\n\t */\n\t var EmbeddedTabularDatasetChunkedView = TabularDatasetChunkedView.extend({\n\t\n\t initialize: function (options) {\n\t TabularDatasetChunkedView.prototype.initialize.call(this, options);\n\t\n\t // Because view is embedded, set up div to do scrolling.\n\t this.scroll_elt = this.$el.css({\n\t position: 'relative',\n\t overflow: 'scroll',\n\t height: options.height || '500px'\n\t });\n\t },\n\t\n\t /**\n\t * Returns true if user has scrolled to the bottom of the view.\n\t */\n\t scrolled_to_bottom: function () {\n\t return this.$el.scrollTop() + this.$el.innerHeight() >= this.el.scrollHeight;\n\t }\n\t\n\t });\n\t\n\t // button for trackster visualization\n\t var TabularButtonTracksterView = Backbone.View.extend({\n\t\n\t // gene region columns\n\t col: {\n\t chrom: null,\n\t start: null,\n\t end: null\n\t },\n\t\n\t // url for trackster\n\t url_viz: null,\n\t\n\t // dataset id\n\t dataset_id: null,\n\t\n\t // database key\n\t genome_build: null,\n\t\n\t // data type\n\t file_ext: null,\n\t\n\t // backbone initialize\n\t initialize: function (options) {\n\t // check if environment is available\n\t var Galaxy = parent.Galaxy;\n\t\n\t // link galaxy modal or create one\n\t if (Galaxy && Galaxy.modal) {\n\t this.modal = Galaxy.modal;\n\t }\n\t\n\t // link galaxy frames\n\t if (Galaxy && Galaxy.frame) {\n\t this.frame = Galaxy.frame;\n\t }\n\t\n\t // check\n\t if (!this.modal || !this.frame) {\n\t return;\n\t }\n\t\n\t // model/metadata\n\t var model = options.model;\n\t var metadata = model.get('metadata');\n\t\n\t // check for datatype\n\t if (!model.get('file_ext')) {\n\t return;\n\t }\n\t\n\t // get data type\n\t this.file_ext = model.get('file_ext');\n\t\n\t // check for bed-file format\n\t if (this.file_ext == 'bed') {\n\t // verify that metadata exists\n\t if (metadata.get('chromCol') && metadata.get('startCol') && metadata.get('endCol')) {\n\t // read in columns\n\t this.col.chrom = metadata.get('chromCol') - 1;\n\t this.col.start = metadata.get('startCol') - 1;\n\t this.col.end = metadata.get('endCol') - 1;\n\t } else {\n\t console.log('TabularButtonTrackster : Bed-file metadata incomplete.');\n\t return;\n\t }\n\t }\n\t\n\t // check for vcf-file format\n\t if (this.file_ext == 'vcf') {\n\t // search array\n\t function search(str, array) {\n\t for (var j = 0; j < array.length; j++) if (array[j].match(str)) return j;\n\t return -1;\n\t };\n\t\n\t // load\n\t this.col.chrom = search('Chrom', metadata.get('column_names'));\n\t this.col.start = search('Pos', metadata.get('column_names'));\n\t this.col.end = null;\n\t\n\t // verify that metadata exists\n\t if (this.col.chrom == -1 || this.col.start == -1) {\n\t console.log('TabularButtonTrackster : VCF-file metadata incomplete.');\n\t return;\n\t }\n\t }\n\t\n\t // check\n\t if (this.col.chrom === undefined) {\n\t return;\n\t }\n\t\n\t // get dataset id\n\t if (model.id) {\n\t this.dataset_id = model.id;\n\t } else {\n\t console.log('TabularButtonTrackster : Dataset identification is missing.');\n\t return;\n\t }\n\t\n\t // get url\n\t if (model.get('url_viz')) {\n\t this.url_viz = model.get('url_viz');\n\t } else {\n\t console.log('TabularButtonTrackster : Url for visualization controller is missing.');\n\t return;\n\t }\n\t\n\t // get genome_build / database key\n\t if (model.get('genome_build')) {\n\t this.genome_build = model.get('genome_build');\n\t }\n\t\n\t // create the icon\n\t var btn_viz = new mod_icon_btn.IconButtonView({\n\t model: new mod_icon_btn.IconButton({\n\t title: 'Visualize',\n\t icon_class: 'chart_curve',\n\t id: 'btn_viz'\n\t })\n\t });\n\t\n\t // set element\n\t this.setElement(options.$el);\n\t\n\t // add to element\n\t this.$el.append(btn_viz.render().$el);\n\t\n\t // hide the button\n\t this.hide();\n\t },\n\t\n\t // backbone events\n\t events: {\n\t 'mouseover tr': 'show',\n\t 'mouseleave': 'hide'\n\t },\n\t\n\t // show button\n\t show: function (e) {\n\t // is numeric\n\t function is_numeric(n) {\n\t return !isNaN(parseFloat(n)) && isFinite(n);\n\t };\n\t\n\t // check\n\t if (this.col.chrom === null) return;\n\t\n\t // get selected data line\n\t var row = $(e.target).parent();\n\t\n\t // verify that location has been found\n\t var chrom = row.children().eq(this.col.chrom).html();\n\t var start = row.children().eq(this.col.start).html();\n\t\n\t // end is optional\n\t var end = this.col.end ? row.children().eq(this.col.end).html() : start;\n\t\n\t // double check location\n\t if (!chrom.match(\"^#\") && chrom !== \"\" && is_numeric(start)) {\n\t\n\t // get target gene region\n\t var btn_viz_pars = {\n\t dataset_id: this.dataset_id,\n\t gene_region: chrom + \":\" + start + \"-\" + end\n\t };\n\t\n\t // get button position\n\t var offset = row.offset();\n\t var left = offset.left - 10;\n\t var top = offset.top - $(window).scrollTop() + 3;\n\t\n\t // update css\n\t $('#btn_viz').css({ 'position': 'fixed', 'top': top + 'px', 'left': left + 'px' });\n\t $('#btn_viz').off('click');\n\t $('#btn_viz').click(this.create_trackster_action(this.url_viz, btn_viz_pars, this.genome_build));\n\t\n\t // show the button\n\t $('#btn_viz').show();\n\t } else {\n\t // hide the button\n\t $('#btn_viz').hide();\n\t }\n\t },\n\t\n\t // hide button\n\t hide: function () {\n\t this.$el.find('#btn_viz').hide();\n\t },\n\t\n\t // create action\n\t create_trackster_action: function (vis_url, dataset_params, dbkey) {\n\t // link this\n\t var self = this;\n\t\n\t // create function\n\t return function () {\n\t var listTracksParams = {};\n\t if (dbkey) {\n\t listTracksParams['f-dbkey'] = dbkey;\n\t }\n\t $.ajax({\n\t url: vis_url + '/list_tracks?' + $.param(listTracksParams),\n\t dataType: 'html',\n\t error: function () {\n\t // show error message\n\t self.modal.show({\n\t title: 'Something went wrong!',\n\t body: 'Unfortunately we could not add this dataset to the track browser. Please try again or contact us.',\n\t buttons: {\n\t 'Cancel': function () {\n\t self.modal.hide();\n\t }\n\t }\n\t });\n\t },\n\t success: function (table_html) {\n\t self.modal.show({\n\t title: 'View Data in a New or Saved Visualization',\n\t buttons: {\n\t 'Cancel': function () {\n\t self.modal.hide();\n\t },\n\t 'View in saved visualization': function () {\n\t // show modal with saved visualizations\n\t self.modal.show({\n\t title: 'Add Data to Saved Visualization',\n\t body: table_html,\n\t buttons: {\n\t 'Cancel': function () {\n\t self.modal.hide();\n\t },\n\t 'Add to visualization': function () {\n\t // hide\n\t self.modal.hide();\n\t\n\t // search selected fields\n\t self.modal.$el.find('input[name=id]:checked').each(function () {\n\t // get visualization id\n\t var vis_id = $(this).val();\n\t dataset_params.id = vis_id;\n\t\n\t // add widget\n\t self.frame.add({\n\t title: 'Trackster',\n\t type: 'url',\n\t content: vis_url + '/trackster?' + $.param(dataset_params)\n\t });\n\t });\n\t }\n\t }\n\t });\n\t },\n\t 'View in new visualization': function () {\n\t // hide\n\t self.modal.hide();\n\t\n\t // add widget\n\t self.frame.add({\n\t title: 'Trackster',\n\t type: 'url',\n\t content: vis_url + '/trackster?' + $.param(dataset_params)\n\t });\n\t }\n\t }\n\t });\n\t }\n\t });\n\t return false;\n\t };\n\t }\n\t });\n\t\n\t // -- Utility functions. --\n\t\n\t /**\n\t * Create a model, attach it to a view, render view, and attach it to a parent element.\n\t */\n\t var createModelAndView = function (model, view, model_config, parent_elt) {\n\t // Create model, view.\n\t var a_view = new view({\n\t model: new model(model_config)\n\t });\n\t\n\t // Render view and add to parent element.\n\t a_view.render();\n\t if (parent_elt) {\n\t parent_elt.append(a_view.$el);\n\t }\n\t\n\t return a_view;\n\t };\n\t\n\t /**\n\t * Create a tabular dataset chunked view (and requisite tabular dataset model)\n\t * and appends to parent_elt.\n\t */\n\t var createTabularDatasetChunkedView = function (options) {\n\t // If no model, create and set model from dataset config.\n\t if (!options.model) {\n\t options.model = new TabularDataset(options.dataset_config);\n\t }\n\t\n\t var parent_elt = options.parent_elt;\n\t var embedded = options.embedded;\n\t\n\t // Clean up options so that only needed options are passed to view.\n\t delete options.embedded;\n\t delete options.parent_elt;\n\t delete options.dataset_config;\n\t\n\t // Create and set up view.\n\t var view = embedded ? new EmbeddedTabularDatasetChunkedView(options) : new TopLevelTabularDatasetChunkedView(options);\n\t view.render();\n\t\n\t if (parent_elt) {\n\t parent_elt.append(view.$el);\n\t // If we're sticking this in another element, once it's appended check\n\t // to make sure we've filled enough space.\n\t // Without this, the scroll elements don't work.\n\t view.expand_to_container();\n\t }\n\t\n\t return view;\n\t };\n\t\n\t return {\n\t Dataset: Dataset,\n\t TabularDataset: TabularDataset,\n\t DatasetCollection: DatasetCollection,\n\t TabularDatasetChunkedView: TabularDatasetChunkedView,\n\t createTabularDatasetChunkedView: createTabularDatasetChunkedView\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ }),\n/* 11 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;!(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t\n\t 'use strict';\n\t //==============================================================================\n\t /** Map of possible HDA/collection/job states to their string equivalents.\n\t * A port of galaxy.model.Dataset.states.\n\t */\n\t\n\t var STATES = {\n\t // NOT ready states\n\t /** is uploading and not ready */\n\t UPLOAD: 'upload',\n\t /** the job that will produce the dataset queued in the runner */\n\t QUEUED: 'queued',\n\t /** the job that will produce the dataset is running */\n\t RUNNING: 'running',\n\t /** metadata for the dataset is being discovered/set */\n\t SETTING_METADATA: 'setting_metadata',\n\t\n\t // ready states\n\t /** was created without a tool */\n\t NEW: 'new',\n\t /** has no data */\n\t EMPTY: 'empty',\n\t /** has successfully completed running */\n\t OK: 'ok',\n\t\n\t /** the job that will produce the dataset paused */\n\t PAUSED: 'paused',\n\t /** metadata discovery/setting failed or errored (but otherwise ok) */\n\t FAILED_METADATA: 'failed_metadata',\n\t //TODO: not in trans.app.model.Dataset.states - is in database\n\t /** not accessible to the current user (i.e. due to permissions) */\n\t NOT_VIEWABLE: 'noPermission',\n\t /** deleted while uploading */\n\t DISCARDED: 'discarded',\n\t /** the tool producing this dataset failed */\n\t ERROR: 'error'\n\t };\n\t\n\t STATES.READY_STATES = [STATES.OK, STATES.EMPTY, STATES.PAUSED, STATES.FAILED_METADATA, STATES.NOT_VIEWABLE, STATES.DISCARDED, STATES.ERROR];\n\t\n\t STATES.NOT_READY_STATES = [STATES.UPLOAD, STATES.QUEUED, STATES.RUNNING, STATES.SETTING_METADATA, STATES.NEW];\n\t\n\t //==============================================================================\n\t return STATES;\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\n/***/ }),\n/* 12 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {/** This module contains all button views. */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t /** This renders the default button which is used e.g. at the bottom of the upload modal. */\n\t var ButtonDefault = Backbone.View.extend({\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model({\n\t id: Utils.uid(),\n\t title: '',\n\t floating: 'right',\n\t icon: '',\n\t cls: 'btn btn-default',\n\t wait: false,\n\t wait_text: 'Sending...',\n\t wait_cls: 'btn btn-info',\n\t disabled: false,\n\t percentage: -1\n\t }).set(options);\n\t this.setElement($('').attr('type', 'button').append(this.$icon = $('')).append(this.$title = $('')).append(this.$progress = $('').append(this.$progress_bar = $(''))));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var self = this;\n\t var options = this.model.attributes;\n\t this.$el.removeClass().addClass('ui-button-default').addClass(options.disabled && 'disabled').attr('id', options.id).attr('disabled', options.disabled).css('float', options.floating).off('click').on('click', function () {\n\t $('.tooltip').hide();\n\t options.onclick && !self.disabled && options.onclick();\n\t }).tooltip({ title: options.tooltip, placement: 'bottom' });\n\t this.$progress.addClass('progress').css('display', options.percentage !== -1 ? 'block' : 'none');\n\t this.$progress_bar.addClass('progress-bar').css({ width: options.percentage + '%' });\n\t this.$icon.removeClass().addClass('icon fa');\n\t this.$title.removeClass().addClass('title');\n\t if (options.wait) {\n\t this.$el.addClass(options.wait_cls).prop('disabled', true);\n\t this.$icon.addClass('fa-spinner fa-spin ui-margin-right');\n\t this.$title.html(options.wait_text);\n\t } else {\n\t this.$el.addClass(options.cls);\n\t this.$icon.addClass(options.icon);\n\t this.$title.html(options.title);\n\t options.icon && options.title && this.$icon.addClass('ui-margin-right');\n\t }\n\t },\n\t\n\t /** Show button */\n\t show: function () {\n\t this.$el.show();\n\t },\n\t\n\t /** Hide button */\n\t hide: function () {\n\t this.$el.hide();\n\t },\n\t\n\t /** Disable button */\n\t disable: function () {\n\t this.model.set('disabled', true);\n\t },\n\t\n\t /** Enable button */\n\t enable: function () {\n\t this.model.set('disabled', false);\n\t },\n\t\n\t /** Show spinner to indicate that the button is not ready to be clicked */\n\t wait: function () {\n\t this.model.set('wait', true);\n\t },\n\t\n\t /** Hide spinner to indicate that the button is ready to be clicked */\n\t unwait: function () {\n\t this.model.set('wait', false);\n\t },\n\t\n\t /** Change icon */\n\t setIcon: function (icon) {\n\t this.model.set('icon', icon);\n\t }\n\t });\n\t\n\t /** This button allows the right-click/open-in-new-tab feature, its used e.g. for panel buttons. */\n\t var ButtonLink = ButtonDefault.extend({\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model({\n\t id: Utils.uid(),\n\t title: '',\n\t icon: '',\n\t cls: ''\n\t }).set(options);\n\t this.setElement($('').append(this.$icon = $('')));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var options = this.model.attributes;\n\t this.$el.removeClass().addClass(options.cls).attr({ id: options.id,\n\t href: options.href || 'javascript:void(0)',\n\t title: options.title,\n\t target: options.target || '_top',\n\t disabled: options.disabled }).tooltip({ placement: 'bottom' }).off('click').on('click', function () {\n\t options.onclick && !options.disabled && options.onclick();\n\t });\n\t this.$icon.removeClass().addClass(options.icon);\n\t }\n\t });\n\t\n\t /** The check button is used in the tool form and allows to distinguish between multiple states e.g. all, partially and nothing selected. */\n\t var ButtonCheck = Backbone.View.extend({\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model({\n\t id: Utils.uid(),\n\t title: 'Select/Unselect all',\n\t icons: ['fa-square-o', 'fa-minus-square-o', 'fa-check-square-o'],\n\t value: 0,\n\t onchange: function () {}\n\t }).set(options);\n\t this.setElement($('').append(this.$icon = $('')).append(this.$title = $('')));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t\n\t render: function (options) {\n\t var self = this;\n\t var options = this.model.attributes;\n\t this.$el.addClass('ui-button-check').off('click').on('click', function () {\n\t self.model.set('value', self.model.get('value') === 0 && 2 || 0);\n\t options.onclick && options.onclick();\n\t });\n\t this.$title.html(options.title);\n\t this.$icon.removeClass().addClass('icon fa ui-margin-right').addClass(options.icons[options.value]);\n\t },\n\t\n\t /* Sets a new value and/or returns the value.\n\t * @param{Integer} new_val - Set a new value 0=unchecked, 1=partial and 2=checked.\n\t * OR:\n\t * @param{Integer} new_val - Number of selected options.\n\t * @param{Integer} total - Total number of available options.\n\t */\n\t value: function (new_val, total) {\n\t if (new_val !== undefined) {\n\t if (total && new_val !== 0) {\n\t new_val = new_val !== total && 1 || 2;\n\t }\n\t this.model.set('value', new_val);\n\t this.model.get('onchange')(this.model.get('value'));\n\t }\n\t return this.model.get('value');\n\t }\n\t });\n\t\n\t /** This renders a differently styled, more compact button version. */\n\t var ButtonIcon = ButtonDefault.extend({\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model({\n\t id: Utils.uid(),\n\t title: '',\n\t floating: 'right',\n\t icon: '',\n\t cls: 'ui-button-icon',\n\t disabled: false\n\t }).set(options);\n\t this.setElement($('').append(this.$button = $('').append(this.$icon = $('')).append(this.$title = $(''))));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t\n\t render: function (options) {\n\t var self = this;\n\t var options = this.model.attributes;\n\t this.$el.removeClass().addClass(options.cls).addClass(options.disabled && 'disabled').attr('disabled', options.disabled).attr('id', options.id).css('float', options.floating).off('click').on('click', function () {\n\t $('.tooltip').hide();\n\t !options.disabled && options.onclick && options.onclick();\n\t });\n\t this.$button.addClass('button').tooltip({ title: options.tooltip, placement: 'bottom' });\n\t this.$icon.removeClass().addClass('icon fa').addClass(options.icon);\n\t this.$title.addClass('title').html(options.title);\n\t options.icon && options.title && this.$icon.addClass('ui-margin-right');\n\t }\n\t });\n\t\n\t /** This class creates a button with dropdown menu. */\n\t var ButtonMenu = ButtonDefault.extend({\n\t $menu: null,\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model({\n\t id: '',\n\t title: '',\n\t floating: 'right',\n\t pull: 'right',\n\t icon: null,\n\t onclick: null,\n\t cls: 'ui-button-icon ui-button-menu',\n\t tooltip: '',\n\t target: '',\n\t href: '',\n\t onunload: null,\n\t visible: true,\n\t tag: ''\n\t }).set(options);\n\t this.collection = new Backbone.Collection();\n\t this.setElement($('').append(this.$root = $('').append(this.$icon = $('')).append(this.$title = $(''))));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.listenTo(this.collection, 'change add remove reset', this.render, this);\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var self = this;\n\t var options = this.model.attributes;\n\t this.$el.removeClass().addClass('dropdown').addClass(options.cls).attr('id', options.id).css({ float: options.floating,\n\t display: options.visible && this.collection.where({ visible: true }).length > 0 ? 'block' : 'none' });\n\t this.$root.addClass('root button dropdown-toggle').attr('data-toggle', 'dropdown').tooltip({ title: options.tooltip, placement: 'bottom' }).off('click').on('click', function (e) {\n\t $('.tooltip').hide();\n\t e.preventDefault();\n\t options.onclick && options.onclick();\n\t });\n\t this.$icon.removeClass().addClass('icon fa').addClass(options.icon);\n\t this.$title.removeClass().addClass('title').html(options.title);\n\t options.icon && options.title && this.$icon.addClass('ui-margin-right');\n\t this.$menu && this.$menu.remove();\n\t if (this.collection.length > 0) {\n\t this.$menu = $('
').addClass('menu dropdown-menu').addClass('pull-' + self.model.get('pull')).attr('role', 'menu');\n\t this.$el.append(this.$menu);\n\t }\n\t this.collection.each(function (submodel) {\n\t var suboptions = submodel.attributes;\n\t if (suboptions.visible) {\n\t var $link = $('').addClass('dropdown-item').attr({ href: suboptions.href, target: suboptions.target }).append($('').addClass('fa').addClass(suboptions.icon).css('display', suboptions.icon ? 'inline-block' : 'none')).append(suboptions.title).on('click', function (e) {\n\t if (suboptions.onclick) {\n\t e.preventDefault();\n\t suboptions.onclick();\n\t }\n\t });\n\t self.$menu.append($('').append($link));\n\t suboptions.divider && self.$menu.append($('').addClass('divider'));\n\t }\n\t });\n\t },\n\t\n\t /** Add a new menu item */\n\t addMenu: function (options) {\n\t this.collection.add(Utils.merge(options, {\n\t title: '',\n\t target: '',\n\t href: '',\n\t onclick: null,\n\t divider: false,\n\t visible: true,\n\t icon: null,\n\t cls: 'button-menu btn-group'\n\t }));\n\t }\n\t });\n\t\n\t return {\n\t ButtonDefault: ButtonDefault,\n\t ButtonLink: ButtonLink,\n\t ButtonIcon: ButtonIcon,\n\t ButtonCheck: ButtonCheck,\n\t ButtonMenu: ButtonMenu\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1)))\n\n/***/ }),\n/* 13 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, $) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [\n\t //jquery\n\t //backbone\n\t], __WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t //=============================================================================\n\t /**\n\t * backbone model for icon buttons\n\t */\n\t var IconButton = Backbone.Model.extend({\n\t defaults: {\n\t title: \"\",\n\t icon_class: \"\",\n\t on_click: null,\n\t menu_options: null,\n\t is_menu_button: true,\n\t id: null,\n\t href: null,\n\t target: null,\n\t enabled: true,\n\t visible: true,\n\t tooltip_config: {}\n\t }\n\t });\n\t\n\t /**\n\t * backbone view for icon buttons\n\t */\n\t var IconButtonView = Backbone.View.extend({\n\t\n\t initialize: function () {\n\t // better rendering this way\n\t this.model.attributes.tooltip_config = { placement: 'bottom' };\n\t this.model.bind('change', this.render, this);\n\t },\n\t\n\t render: function () {\n\t // hide tooltip\n\t this.$el.tooltip('hide');\n\t\n\t var new_elem = this.template(this.model.toJSON());\n\t // configure tooltip\n\t new_elem.tooltip(this.model.get('tooltip_config'));\n\t this.$el.replaceWith(new_elem);\n\t this.setElement(new_elem);\n\t return this;\n\t },\n\t\n\t events: {\n\t 'click': 'click'\n\t },\n\t\n\t click: function (event) {\n\t // if on_click pass to that function\n\t if (_.isFunction(this.model.get('on_click'))) {\n\t this.model.get('on_click')(event);\n\t return false;\n\t }\n\t // otherwise, bubble up ( to href or whatever )\n\t return true;\n\t },\n\t\n\t // generate html element\n\t template: function (options) {\n\t var buffer = 'title=\"' + options.title + '\" class=\"icon-button';\n\t\n\t if (options.is_menu_button) {\n\t buffer += ' menu-button';\n\t }\n\t\n\t buffer += ' ' + options.icon_class;\n\t\n\t if (!options.enabled) {\n\t buffer += '_disabled';\n\t }\n\t\n\t // close class tag\n\t buffer += '\"';\n\t\n\t if (options.id) {\n\t buffer += ' id=\"' + options.id + '\"';\n\t }\n\t\n\t buffer += ' href=\"' + options.href + '\"';\n\t // add target for href\n\t if (options.target) {\n\t buffer += ' target=\"' + options.target + '\"';\n\t }\n\t // set visibility\n\t if (!options.visible) {\n\t buffer += ' style=\"display: none;\"';\n\t }\n\t\n\t // enabled/disabled\n\t if (options.enabled) {\n\t buffer = '';\n\t } else {\n\t buffer = '';\n\t }\n\t\n\t // return element\n\t return $(buffer);\n\t }\n\t });\n\t\n\t // define collection\n\t var IconButtonCollection = Backbone.Collection.extend({\n\t model: IconButton\n\t });\n\t\n\t /**\n\t * menu with multiple icon buttons\n\t * views are not needed nor used for individual buttons\n\t */\n\t var IconButtonMenuView = Backbone.View.extend({\n\t\n\t tagName: 'div',\n\t\n\t initialize: function () {\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t // initialize icon buttons\n\t var self = this;\n\t this.collection.each(function (button) {\n\t // create and add icon button to menu\n\t var elt = $('').attr('href', 'javascript:void(0)').attr('title', button.attributes.title).addClass('icon-button menu-button').addClass(button.attributes.icon_class).appendTo(self.$el).click(button.attributes.on_click);\n\t\n\t // configure tooltip\n\t if (button.attributes.tooltip_config) {\n\t elt.tooltip(button.attributes.tooltip_config);\n\t }\n\t\n\t // add popup menu to icon\n\t var menu_options = button.get('options');\n\t if (menu_options) {\n\t make_popupmenu(elt, menu_options);\n\t }\n\t });\n\t\n\t // return\n\t return this;\n\t }\n\t });\n\t\n\t /**\n\t * Returns an IconButtonMenuView for the provided configuration.\n\t * Configuration is a list of dictionaries where each dictionary\n\t * defines an icon button. Each dictionary must have the following\n\t * elements: icon_class, title, and on_click.\n\t */\n\t var create_icon_buttons_menu = function (config, global_config) {\n\t // initialize global configuration\n\t if (!global_config) global_config = {};\n\t\n\t // create and initialize menu\n\t var buttons = new IconButtonCollection(_.map(config, function (button_config) {\n\t return new IconButton(_.extend(button_config, global_config));\n\t }));\n\t\n\t // return menu\n\t return new IconButtonMenuView({ collection: buttons });\n\t };\n\t\n\t //=============================================================================\n\t return {\n\t IconButton: IconButton,\n\t IconButtonView: IconButtonView,\n\t IconButtonCollection: IconButtonCollection,\n\t IconButtonMenuView: IconButtonMenuView,\n\t create_icon_buttons_menu: create_icon_buttons_menu\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ }),\n/* 14 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, $) {/**\n\t * Popover wrapper\n\t*/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t var View = Backbone.View.extend({\n\t optionsDefault: {\n\t with_close: true,\n\t title: null,\n\t placement: 'top',\n\t container: 'body',\n\t body: null\n\t },\n\t\n\t initialize: function (options) {\n\t this.setElement(this._template());\n\t this.uid = Utils.uid();\n\t this.options = _.defaults(options || {}, this.optionsDefault);\n\t this.options.container.parent().append(this.el);\n\t this.$title = this.$('.popover-title-label');\n\t this.$close = this.$('.popover-close');\n\t this.$body = this.$('.popover-content');\n\t\n\t // add initial content\n\t this.options.body && this.append(this.options.body);\n\t\n\t // add event to hide if click is outside of popup and not on container\n\t var self = this;\n\t $('body').on('mousedown.' + this.uid, function (e) {\n\t // the 'is' for buttons that trigger popups\n\t // the 'has' for icons within a button that triggers a popup\n\t self.visible && !$(self.options.container).is(e.target) && !$(self.el).is(e.target) && $(self.el).has(e.target).length === 0 && self.hide();\n\t });\n\t },\n\t\n\t /**\n\t * Render popover\n\t */\n\t render: function () {\n\t this.$title.html(this.options.title);\n\t this.$el.removeClass().addClass('ui-popover popover fade in').addClass(this.options.placement);\n\t this.$el.css(this._get_placement(this.options.placement));\n\t\n\t // configure close option\n\t var self = this;\n\t if (this.options.with_close) {\n\t this.$close.on('click', function () {\n\t self.hide();\n\t }).show();\n\t } else {\n\t this.$close.off().hide();\n\t }\n\t },\n\t\n\t /**\n\t * Set the popover title\n\t * @params{ String } newTitle - New popover title\n\t */\n\t title: function (newTitle) {\n\t if (newTitle !== undefined) {\n\t this.options.title = newTitle;\n\t this.$title.html(newTitle);\n\t }\n\t },\n\t\n\t /**\n\t * Show popover\n\t */\n\t show: function () {\n\t this.render();\n\t this.$el.show();\n\t this.visible = true;\n\t },\n\t\n\t /**\n\t * Hide popover\n\t */\n\t hide: function () {\n\t this.$el.hide();\n\t this.visible = false;\n\t },\n\t\n\t /**\n\t * Append new content to the popover\n\t * @params{ Object } $el - Dom element\n\t */\n\t append: function ($el) {\n\t this.$body.append($el);\n\t },\n\t\n\t /**\n\t * Remove all content\n\t */\n\t empty: function () {\n\t this.$body.empty();\n\t },\n\t\n\t /**\n\t * Remove popover\n\t */\n\t remove: function () {\n\t $('body').off('mousedown.' + this.uid);\n\t this.$el.remove();\n\t },\n\t\n\t /**\n\t * Improve popover location/placement\n\t */\n\t _get_placement: function (placement) {\n\t // get popover dimensions\n\t var width = this._get_width(this.$el);\n\t var height = this.$el.height();\n\t\n\t // get container details\n\t var $container = this.options.container;\n\t var container_width = this._get_width($container);\n\t var container_height = this._get_height($container);\n\t var container_position = $container.position();\n\t\n\t // get position\n\t var top = left = 0;\n\t if (['top', 'bottom'].indexOf(placement) != -1) {\n\t left = container_position.left - width + (container_width + width) / 2;\n\t switch (placement) {\n\t case 'top':\n\t top = container_position.top - height - 5;\n\t break;\n\t case 'bottom':\n\t top = container_position.top + container_height + 5;\n\t break;\n\t }\n\t } else {\n\t top = container_position.top - height + (container_height + height) / 2;\n\t switch (placement) {\n\t case 'right':\n\t left = container_position.left + container_width;\n\t break;\n\t }\n\t }\n\t return { top: top, left: left };\n\t },\n\t\n\t /**\n\t * Returns padding/margin corrected width\n\t */\n\t _get_width: function ($el) {\n\t return $el.width() + parseInt($el.css('padding-left')) + parseInt($el.css('margin-left')) + parseInt($el.css('padding-right')) + parseInt($el.css('margin-right'));\n\t },\n\t\n\t /**\n\t * Returns padding corrected height\n\t */\n\t _get_height: function ($el) {\n\t return $el.height() + parseInt($el.css('padding-top')) + parseInt($el.css('padding-bottom'));\n\t },\n\t\n\t /**\n\t * Return the popover template\n\t */\n\t _template: function (options) {\n\t return '
' + '
' + '
' + '
' + '' + '
' + '
' + '
';\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ }),\n/* 15 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _) {// dependencies\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t\n\t /**\n\t * A plugin for initializing select2 input items.\n\t * Make sure the select2 library itself is loaded beforehand.\n\t * Also the element to which select2 will be appended has to \n\t * be created before select2 initialization (and passed as option).\n\t */\n\t var View = Backbone.View.extend({\n\t // options\n\t optionsDefault: {\n\t css: '',\n\t placeholder: 'No data available',\n\t data: [],\n\t value: null,\n\t multiple: false,\n\t minimumInputLength: 0,\n\t // example format of initial data: \"id:name,55:anotherrole@role.com,27:role@role.com\"\n\t initialData: ''\n\t },\n\t\n\t // initialize\n\t initialize: function (options) {\n\t // configure options\n\t this.options = Utils.merge(options, this.optionsDefault);\n\t\n\t // create new element\n\t this.setElement(this._template(this.options));\n\t\n\t // check if container exists\n\t if (!this.options.container) {\n\t console.log('ui-select::initialize() : container not specified.');\n\t return;\n\t }\n\t\n\t // add to dom\n\t this.options.container.append(this.$el);\n\t\n\t // link selection dictionary\n\t this.select_data = this.options.data;\n\t\n\t // refresh\n\t this._refresh();\n\t\n\t if (!this.options.multiple) {\n\t // initial value\n\t if (this.options.value) {\n\t this._setValue(this.options.value);\n\t }\n\t\n\t // add change event\n\t var self = this;\n\t if (this.options.onchange) {\n\t this.$el.on('change', function () {\n\t self.options.onchange(self.value());\n\t });\n\t }\n\t }\n\t },\n\t\n\t // value\n\t value: function (new_value) {\n\t // get current id/value\n\t var before = this._getValue();\n\t\n\t // check if new_value is defined\n\t if (new_value !== undefined) {\n\t this._setValue(new_value);\n\t }\n\t\n\t // get current id/value\n\t var after = this._getValue();\n\t\n\t // fire onchange\n\t if (after != before && this.options.onchange) {\n\t this.options.onchange(after);\n\t }\n\t\n\t // return current value\n\t return after;\n\t },\n\t\n\t // label\n\t text: function () {\n\t return this.$el.select2('data').text;\n\t },\n\t\n\t // disabled\n\t disabled: function () {\n\t return !this.$el.select2('enable');\n\t },\n\t\n\t // enable\n\t enable: function () {\n\t this.$el.select2('enable', true);\n\t },\n\t\n\t // disable\n\t disable: function () {\n\t this.$el.select2('enable', false);\n\t },\n\t\n\t // add\n\t add: function (options) {\n\t // add options\n\t this.select_data.push({\n\t id: options.id,\n\t text: options.text\n\t });\n\t\n\t // refresh\n\t this._refresh();\n\t },\n\t\n\t // remove\n\t del: function (id) {\n\t // search option\n\t var index = this._getIndex(id);\n\t\n\t // check if found\n\t if (index != -1) {\n\t // remove options\n\t this.select_data.splice(index, 1);\n\t\n\t // refresh\n\t this._refresh();\n\t }\n\t },\n\t\n\t // remove\n\t remove: function () {\n\t this.$el.select2('destroy');\n\t },\n\t\n\t // update\n\t update: function (options) {\n\t // copy options\n\t this.select_data = [];\n\t for (var key in options.data) {\n\t this.select_data.push(options.data[key]);\n\t }\n\t\n\t // refresh\n\t this._refresh();\n\t },\n\t\n\t // refresh\n\t _refresh: function () {\n\t // add select2 data based on type of input\n\t if (!this.options.multiple) {\n\t var selected = this._getValue();\n\t var select_opt = {\n\t data: this.select_data,\n\t containerCssClass: this.options.css,\n\t placeholder: this.options.placeholder,\n\t dropdownAutoWidth: true\n\t };\n\t this.$el.select2(select_opt);\n\t // select previous value (if exists)\n\t this._setValue(selected);\n\t } else {\n\t var select_opt = {\n\t multiple: this.options.multiple,\n\t containerCssClass: this.options.css,\n\t placeholder: this.options.placeholder,\n\t minimumInputLength: this.options.minimumInputLength,\n\t ajax: this.options.ajax,\n\t dropdownCssClass: this.options.dropdownCssClass,\n\t escapeMarkup: this.options.escapeMarkup,\n\t formatResult: this.options.formatResult,\n\t formatSelection: this.options.formatSelection,\n\t initSelection: this.options.initSelection,\n\t initialData: this.options.initialData\n\t };\n\t this.$el.select2(select_opt);\n\t }\n\t },\n\t\n\t // get index\n\t _getIndex: function (value) {\n\t // returns the index of the searched value\n\t _.findIndex(this.select_data, { id: value });\n\t },\n\t\n\t // get value\n\t _getValue: function () {\n\t return this.$el.select2('val');\n\t },\n\t\n\t // set value\n\t _setValue: function (new_value) {\n\t var index = this._getIndex(new_value);\n\t if (index == -1) {\n\t if (this.select_data.length > 0) {\n\t new_value = this.select_data[0].id;\n\t }\n\t }\n\t this.$el.select2('val', new_value);\n\t },\n\t\n\t // element\n\t _template: function (options) {\n\t return '';\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2)))\n\n/***/ }),\n/* 16 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_FACTORY__, __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;// from: https://raw.githubusercontent.com/umdjs/umd/master/jqueryPlugin.js\n\t// Uses AMD or browser globals to create a jQuery plugin.\n\t(function (factory) {\n\t if (true) {\n\t //TODO: So...this turns out to be an all or nothing thing. If I load jQuery in the define below, it will\n\t // (of course) wipe the old jquery *and all the plugins loaded into it*. So the define below *is still\n\t // relying on jquery being loaded globally* in order to preserve plugins.\n\t !(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(1)], __WEBPACK_AMD_DEFINE_FACTORY__ = (factory), __WEBPACK_AMD_DEFINE_RESULT__ = (typeof __WEBPACK_AMD_DEFINE_FACTORY__ === 'function' ? (__WEBPACK_AMD_DEFINE_FACTORY__.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__)) : __WEBPACK_AMD_DEFINE_FACTORY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t } else {\n\t // Browser globals\n\t factory(jQuery);\n\t }\n\t})(function (jQuery) {\n\t 'use_strict';\n\t\n\t var $ = jQuery;\n\t\n\t // ============================================================================\n\t /**\n\t * Make an element with text editable: (a) when user clicks on text, a textbox/area\n\t * is provided for editing; (b) when enter key pressed, element's text is set and on_finish\n\t * is called.\n\t */\n\t $.fn.make_text_editable = function (config_dict) {\n\t // Get config options.\n\t var num_cols = \"num_cols\" in config_dict ? config_dict.num_cols : 30,\n\t num_rows = \"num_rows\" in config_dict ? config_dict.num_rows : 4,\n\t use_textarea = \"use_textarea\" in config_dict ? config_dict.use_textarea : false,\n\t on_finish = \"on_finish\" in config_dict ? config_dict.on_finish : null,\n\t help_text = \"help_text\" in config_dict ? config_dict.help_text : null;\n\t\n\t // Add element behavior.\n\t var container = $(this);\n\t container.addClass(\"editable-text\").click(function (e) {\n\t // If there's already an input element, editing is active, so do nothing.\n\t if ($(this).children(\":input\").length > 0) {\n\t return;\n\t }\n\t\n\t container.removeClass(\"editable-text\");\n\t\n\t // Handler for setting element text.\n\t var set_text = function (new_text) {\n\t container.find(\":input\").remove();\n\t\n\t if (new_text !== \"\") {\n\t container.text(new_text);\n\t } else {\n\t // No text; need a line so that there is a click target.\n\t container.html(\" \");\n\t }\n\t container.addClass(\"editable-text\");\n\t\n\t if (on_finish) {\n\t on_finish(new_text);\n\t }\n\t };\n\t\n\t // Create input element(s) for editing.\n\t var cur_text = \"cur_text\" in config_dict ? config_dict.cur_text : container.text(),\n\t input_elt,\n\t button_elt;\n\t\n\t if (use_textarea) {\n\t input_elt = $(\"\").attr({ rows: num_rows, cols: num_cols }).text($.trim(cur_text)).keyup(function (e) {\n\t if (e.keyCode === 27) {\n\t // Escape key.\n\t set_text(cur_text);\n\t }\n\t });\n\t button_elt = $(\"\").text(\"Done\").click(function () {\n\t set_text(input_elt.val());\n\t // Return false so that click does not propogate to container.\n\t return false;\n\t });\n\t } else {\n\t input_elt = $(\"\").attr({ value: $.trim(cur_text), size: num_cols }).blur(function () {\n\t set_text(cur_text);\n\t }).keyup(function (e) {\n\t if (e.keyCode === 27) {\n\t // Escape key.\n\t $(this).trigger(\"blur\");\n\t } else if (e.keyCode === 13) {\n\t // Enter key.\n\t set_text($(this).val());\n\t }\n\t\n\t // Do not propogate event to avoid unwanted side effects.\n\t e.stopPropagation();\n\t });\n\t }\n\t\n\t // Replace text with input object(s) and focus & select.\n\t container.text(\"\");\n\t container.append(input_elt);\n\t if (button_elt) {\n\t container.append(button_elt);\n\t }\n\t input_elt.focus();\n\t input_elt.select();\n\t\n\t // Do not propogate to elements below b/c that blurs input and prevents it from being used.\n\t e.stopPropagation();\n\t });\n\t\n\t // Add help text if there some.\n\t if (help_text) {\n\t container.attr(\"title\", help_text).tooltip();\n\t }\n\t\n\t return container;\n\t };\n\t\n\t // ============================================================================\n\t});\n\n/***/ }),\n/* 17 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_FACTORY__, __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function($, _) {(function (root, factory) {\n\t if (true) {\n\t !(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_FACTORY__ = (factory), __WEBPACK_AMD_DEFINE_RESULT__ = (typeof __WEBPACK_AMD_DEFINE_FACTORY__ === 'function' ? (__WEBPACK_AMD_DEFINE_FACTORY__.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__)) : __WEBPACK_AMD_DEFINE_FACTORY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t } else {\n\t root.faIconButton = factory();\n\t }\n\t})(this, function () {\n\t //============================================================================\n\t /** Returns a jQuery object containing a clickable font-awesome button.\n\t * options:\n\t * tooltipConfig : option map for bootstrap tool tip\n\t * classes : array of class names (will always be classed as icon-btn)\n\t * disabled : T/F - add the 'disabled' class?\n\t * title : tooltip/title string\n\t * target : optional href target\n\t * href : optional href\n\t * faIcon : which font awesome icon to use\n\t * onclick : function to call when the button is clicked\n\t */\n\t var faIconButton = function (options) {\n\t options = options || {};\n\t options.tooltipConfig = options.tooltipConfig || { placement: 'bottom' };\n\t\n\t options.classes = ['icon-btn'].concat(options.classes || []);\n\t if (options.disabled) {\n\t options.classes.push('disabled');\n\t }\n\t\n\t var html = ['',\n\t // could go with something less specific here - like 'html'\n\t '', ''].join('');\n\t var $button = $(html).tooltip(options.tooltipConfig);\n\t if (_.isFunction(options.onclick)) {\n\t $button.click(options.onclick);\n\t }\n\t return $button;\n\t };\n\t\n\t //============================================================================\n\t return faIconButton;\n\t});\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1), __webpack_require__(2)))\n\n/***/ }),\n/* 18 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {!(__WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t\n\t /**\n\t * Stringifies a number adding commas for digit grouping as per North America.\n\t */\n\t function commatize(number) {\n\t number += ''; // Convert to string\n\t var rgx = /(\\d+)(\\d{3})/;\n\t while (rgx.test(number)) {\n\t number = number.replace(rgx, '$1' + ',' + '$2');\n\t }\n\t return number;\n\t }\n\t\n\t /**\n\t * Helper to determine if object is jQuery deferred.\n\t */\n\t var is_deferred = function (d) {\n\t return 'promise' in d;\n\t };\n\t\n\t /**\n\t * Implementation of a server-state based deferred. Server is repeatedly polled, and when\n\t * condition is met, deferred is resolved.\n\t */\n\t var ServerStateDeferred = Backbone.Model.extend({\n\t defaults: {\n\t ajax_settings: {},\n\t interval: 1000,\n\t success_fn: function (result) {\n\t return true;\n\t }\n\t },\n\t\n\t /**\n\t * Returns a deferred that resolves when success function returns true.\n\t */\n\t go: function () {\n\t var deferred = $.Deferred(),\n\t self = this,\n\t ajax_settings = self.get('ajax_settings'),\n\t success_fn = self.get('success_fn'),\n\t interval = self.get('interval'),\n\t _go = function () {\n\t $.ajax(ajax_settings).success(function (result) {\n\t if (success_fn(result)) {\n\t // Result is good, so resolve.\n\t deferred.resolve(result);\n\t } else {\n\t // Result not good, try again.\n\t setTimeout(_go, interval);\n\t }\n\t });\n\t };\n\t _go();\n\t return deferred;\n\t }\n\t });\n\t\n\t /**\n\t * Returns a random color in hexadecimal format that is sufficiently different from a single color\n\t * or set of colors.\n\t * @param colors a color or list of colors in the format '#RRGGBB'\n\t */\n\t var get_random_color = function (colors) {\n\t // Default for colors is white.\n\t if (!colors) {\n\t colors = \"#ffffff\";\n\t }\n\t\n\t // If needed, create list of colors.\n\t if (typeof colors === \"string\") {\n\t colors = [colors];\n\t }\n\t\n\t // Convert colors to numbers.\n\t for (var i = 0; i < colors.length; i++) {\n\t colors[i] = parseInt(colors[i].slice(1), 16);\n\t }\n\t\n\t // -- Perceived brightness and difference formulas are from\n\t // -- http://www.w3.org/WAI/ER/WD-AERT/#color-contrast\n\t\n\t // Compute perceived color brightness (based on RGB-YIQ transformation):\n\t var brightness = function (r, g, b) {\n\t return (r * 299 + g * 587 + b * 114) / 1000;\n\t };\n\t\n\t // Compute color difference:\n\t var difference = function (r1, g1, b1, r2, g2, b2) {\n\t return Math.max(r1, r2) - Math.min(r1, r2) + (Math.max(g1, g2) - Math.min(g1, g2)) + (Math.max(b1, b2) - Math.min(b1, b2));\n\t };\n\t\n\t // Create new random color.\n\t var new_color,\n\t nr,\n\t ng,\n\t nb,\n\t other_color,\n\t or,\n\t og,\n\t ob,\n\t n_brightness,\n\t o_brightness,\n\t diff,\n\t ok = false,\n\t num_tries = 0;\n\t do {\n\t // New color is never white b/c random in [0,1)\n\t new_color = Math.round(Math.random() * 0xffffff);\n\t nr = (new_color & 0xff0000) >> 16;\n\t ng = (new_color & 0x00ff00) >> 8;\n\t nb = new_color & 0x0000ff;\n\t n_brightness = brightness(nr, ng, nb);\n\t ok = true;\n\t for (i = 0; i < colors.length; i++) {\n\t other_color = colors[i];\n\t or = (other_color & 0xff0000) >> 16;\n\t og = (other_color & 0x00ff00) >> 8;\n\t ob = other_color & 0x0000ff;\n\t o_brightness = brightness(or, og, ob);\n\t diff = difference(nr, ng, nb, or, og, ob);\n\t // These thresholds may need to be adjusted. Brightness difference range is 125;\n\t // color difference range is 500.\n\t if (Math.abs(n_brightness - o_brightness) < 40 || diff < 200) {\n\t ok = false;\n\t break;\n\t }\n\t }\n\t\n\t num_tries++;\n\t } while (!ok && num_tries <= 10);\n\t\n\t // Add 0x1000000 to left pad number with 0s.\n\t return '#' + (0x1000000 + new_color).toString(16).substr(1, 6);\n\t };\n\t\n\t return {\n\t commatize: commatize,\n\t is_deferred: is_deferred,\n\t ServerStateDeferred: ServerStateDeferred,\n\t get_random_color: get_random_color\n\t };\n\t}.call(exports, __webpack_require__, exports, module), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1)))\n\n/***/ }),\n/* 19 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(33), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (parseBibtex, baseMVC, _l) {\n\t /* global Backbone */\n\t // we use amd here to require, but bibtex uses a global or commonjs pattern.\n\t // webpack will load via commonjs and plain requirejs will load as global. Check both\n\t parseBibtex = parseBibtex || window.BibtexParser;\n\t\n\t var logNamespace = 'citation';\n\t //==============================================================================\n\t /** @class model for tool citations.\n\t * @name Citation\n\t * @augments Backbone.Model\n\t */\n\t var Citation = Backbone.Model.extend(baseMVC.LoggableMixin).extend({\n\t _logNamespace: logNamespace,\n\t\n\t defaults: {\n\t content: ''\n\t },\n\t\n\t initialize: function () {\n\t var parsed;\n\t try {\n\t // TODO: to model.parse/.validate\n\t parsed = parseBibtex(this.attributes.content);\n\t } catch (err) {\n\t return;\n\t }\n\t // bibtex returns successfully parsed in .entries and any parsing errors in .errors\n\t if (parsed.errors.length) {\n\t // the gen. form of these errors seems to be [ line, col, char, error message ]\n\t var errors = parsed.errors.reduce(function (all, current) {\n\t return all + '; ' + current;\n\t });\n\t // throw new Error( 'Error parsing bibtex: ' + errors );\n\t this.log('Error parsing bibtex: ' + errors);\n\t }\n\t\n\t this._fields = {};\n\t this.entry = _.first(parsed.entries);\n\t if (this.entry) {\n\t var rawFields = this.entry.Fields;\n\t for (var key in rawFields) {\n\t var value = rawFields[key];\n\t var lowerKey = key.toLowerCase();\n\t this._fields[lowerKey] = value;\n\t }\n\t }\n\t },\n\t entryType: function () {\n\t return this.entry ? this.entry.EntryType : undefined;\n\t },\n\t fields: function () {\n\t return this._fields;\n\t }\n\t });\n\t\n\t //==============================================================================\n\t /** @class Backbone collection of citations.\n\t */\n\t var BaseCitationCollection = Backbone.Collection.extend(baseMVC.LoggableMixin).extend({\n\t _logNamespace: logNamespace,\n\t\n\t /** root api url */\n\t urlRoot: Galaxy.root + 'api',\n\t partial: true, // Assume some tools in history/workflow may not be properly annotated yet.\n\t model: Citation\n\t });\n\t\n\t var HistoryCitationCollection = BaseCitationCollection.extend({\n\t /** complete api url */\n\t url: function () {\n\t return this.urlRoot + '/histories/' + this.history_id + '/citations';\n\t }\n\t });\n\t\n\t var ToolCitationCollection = BaseCitationCollection.extend({\n\t /** complete api url */\n\t url: function () {\n\t return this.urlRoot + '/tools/' + this.tool_id + '/citations';\n\t },\n\t partial: false });\n\t\n\t //==============================================================================\n\t\n\t return {\n\t Citation: Citation,\n\t HistoryCitationCollection: HistoryCitationCollection,\n\t ToolCitationCollection: ToolCitationCollection\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2)))\n\n/***/ }),\n/* 20 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, $) {/**\n\t This is the main class of the form plugin. It is referenced as 'app' in lower level modules.\n\t*/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(9), __webpack_require__(7), __webpack_require__(43), __webpack_require__(39)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Portlet, Ui, FormSection, FormData) {\n\t return Backbone.View.extend({\n\t initialize: function (options) {\n\t this.model = new Backbone.Model({\n\t initial_errors: false,\n\t cls: 'ui-portlet-limited',\n\t icon: null,\n\t always_refresh: true,\n\t message_status: 'warning'\n\t }).set(options);\n\t this.setElement('');\n\t this.render();\n\t },\n\t\n\t /** Update available options */\n\t update: function (new_model) {\n\t var self = this;\n\t this.data.matchModel(new_model, function (node, input_id) {\n\t var input = self.input_list[input_id];\n\t if (input && input.options) {\n\t if (!_.isEqual(input.options, node.options)) {\n\t input.options = node.options;\n\t var field = self.field_list[input_id];\n\t if (field.update) {\n\t var new_options = [];\n\t if (['data', 'data_collection', 'drill_down'].indexOf(input.type) != -1) {\n\t new_options = input.options;\n\t } else {\n\t for (var i in node.options) {\n\t var opt = node.options[i];\n\t if (opt.length > 2) {\n\t new_options.push({ label: opt[0], value: opt[1] });\n\t }\n\t }\n\t }\n\t field.update(new_options);\n\t field.trigger('change');\n\t Galaxy.emit.debug('form-view::update()', 'Updating options for ' + input_id);\n\t }\n\t }\n\t }\n\t });\n\t },\n\t\n\t /** Set form into wait mode */\n\t wait: function (active) {\n\t for (var i in this.input_list) {\n\t var field = this.field_list[i];\n\t var input = this.input_list[i];\n\t if (input.is_dynamic && field.wait && field.unwait) {\n\t field[active ? 'wait' : 'unwait']();\n\t }\n\t }\n\t },\n\t\n\t /** Highlight and scroll to input element (currently only used for error notifications) */\n\t highlight: function (input_id, message, silent) {\n\t var input_element = this.element_list[input_id];\n\t if (input_element) {\n\t input_element.error(message || 'Please verify this parameter.');\n\t this.portlet.expand();\n\t this.trigger('expand', input_id);\n\t if (!silent) {\n\t var $panel = this.$el.parents().filter(function () {\n\t return ['auto', 'scroll'].indexOf($(this).css('overflow')) != -1;\n\t }).first();\n\t $panel.animate({ scrollTop: $panel.scrollTop() + input_element.$el.offset().top - 120 }, 500);\n\t }\n\t }\n\t },\n\t\n\t /** Highlights errors */\n\t errors: function (options) {\n\t this.trigger('reset');\n\t if (options && options.errors) {\n\t var error_messages = this.data.matchResponse(options.errors);\n\t for (var input_id in this.element_list) {\n\t var input = this.element_list[input_id];\n\t if (error_messages[input_id]) {\n\t this.highlight(input_id, error_messages[input_id], true);\n\t }\n\t }\n\t }\n\t },\n\t\n\t /** Render tool form */\n\t render: function () {\n\t var self = this;\n\t this.off('change');\n\t this.off('reset');\n\t // contains the dom field elements as created by the parameter factory i.e. form-parameters\n\t this.field_list = {};\n\t // contains input definitions/dictionaries as provided by the parameters to_dict() function through the api\n\t this.input_list = {};\n\t // contains the dom elements of each input element i.e. form-input which wraps the actual input field\n\t this.element_list = {};\n\t // converts the form into a json data structure\n\t this.data = new FormData.Manager(this);\n\t this._renderForm();\n\t this.data.create();\n\t this.model.get('initial_errors') && this.errors(this.model.attributes);\n\t // add listener which triggers on checksum change, and reset the form input wrappers\n\t var current_check = this.data.checksum();\n\t this.on('change', function (input_id) {\n\t var input = self.input_list[input_id];\n\t if (!input || input.refresh_on_change || self.model.get('always_refresh')) {\n\t var new_check = self.data.checksum();\n\t if (new_check != current_check) {\n\t current_check = new_check;\n\t self.model.get('onchange') && self.model.get('onchange')();\n\t }\n\t }\n\t });\n\t this.on('reset', function () {\n\t _.each(self.element_list, function (input_element) {\n\t input_element.reset();\n\t });\n\t });\n\t return this;\n\t },\n\t\n\t /** Renders/appends dom elements of the form */\n\t _renderForm: function () {\n\t $('.tooltip').remove();\n\t var options = this.model.attributes;\n\t this.message = new Ui.UnescapedMessage();\n\t this.section = new FormSection.View(this, { inputs: options.inputs });\n\t this.portlet = new Portlet.View({\n\t icon: options.icon,\n\t title: options.title,\n\t cls: options.cls,\n\t operations: options.operations,\n\t buttons: options.buttons,\n\t collapsible: options.collapsible,\n\t collapsed: options.collapsed,\n\t onchange_title: options.onchange_title\n\t });\n\t this.portlet.append(this.message.$el);\n\t this.portlet.append(this.section.$el);\n\t this.$el.empty();\n\t options.inputs && this.$el.append(this.portlet.$el);\n\t options.message && this.message.update({ persistent: true, status: options.message_status, message: options.message });\n\t Galaxy.emit.debug('form-view::initialize()', 'Completed');\n\t }\n\t });\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ }),\n/* 21 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {// dependencies\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(9), __webpack_require__(7)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Portlet, Ui) {\n\t\n\t // ui list element\n\t var View = Backbone.View.extend({\n\t // create portlet to keep track of selected list elements\n\t initialize: function (options) {\n\t // link this\n\t var self = this;\n\t\n\t // initialize options\n\t this.options = options;\n\t this.name = options.name || 'element';\n\t this.multiple = options.multiple || false;\n\t\n\t // create message handler\n\t this.message = new Ui.Message();\n\t\n\t // create portlet\n\t this.portlet = new Portlet.View({ cls: 'ui-portlet-section' });\n\t\n\t // create select field containing the options which can be inserted into the list\n\t this.select = new Ui.Select.View({ optional: options.optional });\n\t\n\t // create insert new list element button\n\t this.button = new Ui.ButtonIcon({\n\t icon: 'fa fa-sign-in',\n\t floating: 'left',\n\t tooltip: 'Insert new ' + this.name,\n\t onclick: function () {\n\t self.add({\n\t id: self.select.value(),\n\t name: self.select.text()\n\t });\n\t }\n\t });\n\t\n\t // build main element\n\t this.setElement(this._template(options));\n\t this.$('.ui-list-message').append(this.message.$el);\n\t this.$('.ui-list-portlet').append(this.portlet.$el);\n\t this.$('.ui-list-button').append(this.button.$el);\n\t this.$('.ui-list-select').append(this.select.$el);\n\t },\n\t\n\t /** Return/Set currently selected list elements */\n\t value: function (val) {\n\t // set new value\n\t if (val !== undefined) {\n\t this.portlet.empty();\n\t if ($.isArray(val)) {\n\t for (var i in val) {\n\t var v = val[i];\n\t var v_id = null;\n\t var v_name = null;\n\t if ($.type(v) != 'string') {\n\t v_id = v.id;\n\t v_name = v.name;\n\t } else {\n\t v_id = v_name = v;\n\t }\n\t if (v_id != null) {\n\t this.add({\n\t id: v_id,\n\t name: v_name\n\t });\n\t }\n\t }\n\t }\n\t this._refresh();\n\t }\n\t // get current value\n\t var lst = [];\n\t this.$('.ui-list-id').each(function () {\n\t lst.push({\n\t id: $(this).prop('id'),\n\t name: $(this).find('.ui-list-name').html()\n\t });\n\t });\n\t if (lst.length == 0) {\n\t return null;\n\t }\n\t return lst;\n\t },\n\t\n\t /** Add row */\n\t add: function (options) {\n\t var self = this;\n\t if (this.$('[id=\"' + options.id + '\"]').length === 0) {\n\t if (!Utils.isEmpty(options.id)) {\n\t var $el = $(this._templateRow({\n\t id: options.id,\n\t name: options.name\n\t }));\n\t $el.on('click', function () {\n\t $el.remove();\n\t self._refresh();\n\t });\n\t $el.on('mouseover', function () {\n\t $el.addClass('portlet-highlight');\n\t });\n\t $el.on('mouseout', function () {\n\t $el.removeClass('portlet-highlight');\n\t });\n\t this.portlet.append($el);\n\t this._refresh();\n\t } else {\n\t this.message.update({ message: 'Please select a valid ' + this.name + '.', status: 'danger' });\n\t }\n\t } else {\n\t this.message.update({ message: 'This ' + this.name + ' is already in the list.' });\n\t }\n\t },\n\t\n\t /** Update available options */\n\t update: function (options) {\n\t this.select.update(options);\n\t },\n\t\n\t /** Refresh view */\n\t _refresh: function () {\n\t if (this.$('.ui-list-id').length > 0) {\n\t !this.multiple && this.button.disable();\n\t this.$('.ui-list-portlet').show();\n\t } else {\n\t this.button.enable();\n\t this.$('.ui-list-portlet').hide();\n\t }\n\t this.options.onchange && this.options.onchange();\n\t },\n\t\n\t /** Main Template */\n\t _template: function (options) {\n\t return '
\");\n\t return this;\n\t },\n\t formattedReference: function () {\n\t var model = this.model;\n\t var entryType = model.entryType();\n\t var fields = model.fields();\n\t\n\t var ref = \"\";\n\t // Code inspired by...\n\t // https://github.com/vkaravir/bib-publication-list/blob/master/src/bib-publication-list.js\n\t var authorsAndYear = this._asSentence((fields.author ? fields.author : \"\") + (fields.year ? \" (\" + fields.year + \")\" : \"\")) + \" \";\n\t var title = fields.title || \"\";\n\t var pages = fields.pages ? \"pp. \" + fields.pages : \"\";\n\t var address = fields.address;\n\t if (entryType == \"article\") {\n\t var volume = (fields.volume ? fields.volume : \"\") + (fields.number ? \" (\" + fields.number + \")\" : \"\") + (pages ? \", \" + pages : \"\");\n\t ref = authorsAndYear + this._asSentence(title) + (fields.journal ? \"In \" + fields.journal + \", \" : \"\") + this._asSentence(volume) + this._asSentence(fields.address) + \"<\\/em>\";\n\t } else if (entryType == \"inproceedings\" || entryType == \"proceedings\") {\n\t ref = authorsAndYear + this._asSentence(title) + (fields.booktitle ? \"In \" + fields.booktitle + \", \" : \"\") + (pages ? pages : \"\") + (address ? \", \" + address : \"\") + \".<\\/em>\";\n\t } else if (entryType == \"mastersthesis\" || entryType == \"phdthesis\") {\n\t ref = authorsAndYear + this._asSentence(title) + (fields.howpublished ? fields.howpublished + \". \" : \"\") + (fields.note ? fields.note + \".\" : \"\");\n\t } else if (entryType == \"techreport\") {\n\t ref = authorsAndYear + this._asSentence(title) + this._asSentence(fields.institution) + this._asSentence(fields.number) + this._asSentence(fields.type);\n\t } else if (entryType == \"book\" || entryType == \"inbook\" || entryType == \"incollection\") {\n\t ref = authorsAndYear + \" \" + this._formatBookInfo(fields);\n\t } else {\n\t ref = authorsAndYear + \" \" + this._asSentence(title) + this._asSentence(fields.howpublished) + this._asSentence(fields.note);\n\t }\n\t var doiUrl = \"\";\n\t if (fields.doi) {\n\t doiUrl = 'http://dx.doi.org/' + fields.doi;\n\t ref += '[doi:' + fields.doi + \"]\";\n\t }\n\t var url = fields.url || doiUrl;\n\t if (url) {\n\t ref += '[Link]';\n\t }\n\t return ref;\n\t },\n\t _formatBookInfo: function (fields) {\n\t var info = \"\";\n\t if (fields.chapter) {\n\t info += fields.chapter + \" in \";\n\t }\n\t if (fields.title) {\n\t info += \"\" + fields.title + \"<\\/em>\";\n\t }\n\t if (fields.editor) {\n\t info += \", Edited by \" + fields.editor + \", \";\n\t }\n\t if (fields.publisher) {\n\t info += \", \" + fields.publisher;\n\t }\n\t if (fields.pages) {\n\t info += \", pp. \" + fields.pages + \"\";\n\t }\n\t if (fields.series) {\n\t info += \", \" + fields.series + \"<\\/em>\";\n\t }\n\t if (fields.volume) {\n\t info += \", Vol.\" + fields.volume;\n\t }\n\t if (fields.issn) {\n\t info += \", ISBN: \" + fields.issn;\n\t }\n\t return info + \".\";\n\t },\n\t _asSentence: function (str) {\n\t return str && str.trim() ? str + \". \" : \"\";\n\t }\n\t });\n\t\n\t var CitationListView = Backbone.View.extend({\n\t el: '#citations',\n\t /**\n\t * Set up view.\n\t */\n\t initialize: function () {\n\t this.listenTo(this.collection, 'add', this.renderCitation);\n\t },\n\t\n\t events: {\n\t 'click .citations-to-bibtex': 'showBibtex',\n\t 'click .citations-to-formatted': 'showFormatted'\n\t },\n\t\n\t renderCitation: function (citation) {\n\t var citationView = new CitationView({ model: citation });\n\t this.$(\".citations-formatted\").append(citationView.render().el);\n\t var rawTextarea = this.$(\".citations-bibtex-text\");\n\t rawTextarea.val(rawTextarea.val() + \"\\n\\r\" + citation.attributes.content);\n\t },\n\t\n\t render: function () {\n\t this.$el.html(this.citationsElement());\n\t this.collection.each(function (item) {\n\t this.renderCitation(item);\n\t }, this);\n\t this.showFormatted();\n\t },\n\t\n\t showBibtex: function () {\n\t this.$(\".citations-to-formatted\").show();\n\t this.$(\".citations-to-bibtex\").hide();\n\t this.$(\".citations-bibtex\").show();\n\t this.$(\".citations-formatted\").hide();\n\t this.$(\".citations-bibtex-text\").select();\n\t },\n\t\n\t showFormatted: function () {\n\t this.$(\".citations-to-formatted\").hide();\n\t this.$(\".citations-to-bibtex\").show();\n\t this.$(\".citations-bibtex\").hide();\n\t this.$(\".citations-formatted\").show();\n\t },\n\t\n\t partialWarningElement: function () {\n\t if (this.collection.partial) {\n\t return ['
', 'Warning: This is a experimental feature. Most Galaxy tools will not annotate', ' citations explicitly at this time. When writing up your analysis, please manually', ' review your histories and find all references', ' that should be cited in order to completely describe your work. Also, please remember to', ' cite Galaxy.', '
'], 'collection');\n\t\n\t // use element identifier\n\t var subtitleTemplate = BASE_MVC.wrapTemplate(['
', '<% var countText = collection.element_count? ( collection.element_count + \" \" ) : \"\"; %>', '<% if( collection.collection_type === \"list\" ){ %>', _l('a list of <%- countText %>datasets'), '<% } else if( collection.collection_type === \"paired\" ){ %>', _l('a pair of datasets'), '<% } else if( collection.collection_type === \"list:paired\" ){ %>', _l('a list of <%- countText %>dataset pairs'), '<% } else if( collection.collection_type === \"list:list\" ){ %>', _l('a list of <%- countText %>dataset lists'), '<% } %>', '
'], 'collection');\n\t\n\t return _.extend({}, FoldoutListItemView.prototype.templates, {\n\t warnings: warnings,\n\t titleBar: titleBarTemplate,\n\t subtitle: subtitleTemplate\n\t });\n\t }();\n\t\n\t //==============================================================================\n\t /** @class Read only view for DatasetCollectionElement.\n\t */\n\t var DCEListItemView = ListItemView.extend(\n\t /** @lends DCEListItemView.prototype */{\n\t\n\t /** add the DCE class to the list item */\n\t className: ListItemView.prototype.className + \" dataset-collection-element\",\n\t\n\t /** set up */\n\t initialize: function (attributes) {\n\t if (attributes.logger) {\n\t this.logger = this.model.logger = attributes.logger;\n\t }\n\t this.log('DCEListItemView.initialize:', attributes);\n\t ListItemView.prototype.initialize.call(this, attributes);\n\t },\n\t\n\t // ......................................................................... misc\n\t /** String representation */\n\t toString: function () {\n\t var modelString = this.model ? this.model + '' : '(no model)';\n\t return 'DCEListItemView(' + modelString + ')';\n\t }\n\t });\n\t\n\t // ............................................................................ TEMPLATES\n\t /** underscore templates */\n\t DCEListItemView.prototype.templates = function () {\n\t\n\t // use the element identifier here - since that will persist and the user will need it\n\t var titleBarTemplate = BASE_MVC.wrapTemplate(['
', '
', '<%- element.element_identifier %>', '
', '', '
'], 'element');\n\t\n\t return _.extend({}, ListItemView.prototype.templates, {\n\t titleBar: titleBarTemplate\n\t });\n\t }();\n\t\n\t //==============================================================================\n\t /** @class Read only view for a DatasetCollectionElement that is also an DatasetAssociation\n\t * (a dataset contained in a dataset collection).\n\t */\n\t var DatasetDCEListItemView = DATASET_LI.DatasetListItemView.extend(\n\t /** @lends DatasetDCEListItemView.prototype */{\n\t\n\t className: DATASET_LI.DatasetListItemView.prototype.className + \" dataset-collection-element\",\n\t\n\t /** set up */\n\t initialize: function (attributes) {\n\t if (attributes.logger) {\n\t this.logger = this.model.logger = attributes.logger;\n\t }\n\t this.log('DatasetDCEListItemView.initialize:', attributes);\n\t DATASET_LI.DatasetListItemView.prototype.initialize.call(this, attributes);\n\t },\n\t\n\t /** In this override, only get details if in the ready state.\n\t * Note: fetch with no 'change' event triggering to prevent automatic rendering.\n\t */\n\t _fetchModelDetails: function () {\n\t var view = this;\n\t if (view.model.inReadyState() && !view.model.hasDetails()) {\n\t return view.model.fetch({ silent: true });\n\t }\n\t return jQuery.when();\n\t },\n\t\n\t // ......................................................................... misc\n\t /** String representation */\n\t toString: function () {\n\t var modelString = this.model ? this.model + '' : '(no model)';\n\t return 'DatasetDCEListItemView(' + modelString + ')';\n\t }\n\t });\n\t\n\t // ............................................................................ TEMPLATES\n\t /** underscore templates */\n\t DatasetDCEListItemView.prototype.templates = function () {\n\t\n\t // use the element identifier here and not the dataset name\n\t //TODO:?? can we steal the DCE titlebar?\n\t var titleBarTemplate = BASE_MVC.wrapTemplate(['
', '', '
', '<%- element.element_identifier %>', '
', '
'], 'element');\n\t\n\t return _.extend({}, DATASET_LI.DatasetListItemView.prototype.templates, {\n\t titleBar: titleBarTemplate\n\t });\n\t }();\n\t\n\t //==============================================================================\n\t /** @class Read only view for a DatasetCollectionElement that is also a DatasetCollection\n\t * (a nested DC).\n\t */\n\t var NestedDCDCEListItemView = DCListItemView.extend(\n\t /** @lends NestedDCDCEListItemView.prototype */{\n\t\n\t className: DCListItemView.prototype.className + \" dataset-collection-element\",\n\t\n\t /** In this override, add the state as a class for use with state-based CSS */\n\t _swapNewRender: function ($newRender) {\n\t DCListItemView.prototype._swapNewRender.call(this, $newRender);\n\t var state = this.model.get('state') || 'ok';\n\t this.$el.addClass('state-' + state);\n\t return this.$el;\n\t },\n\t\n\t // ......................................................................... misc\n\t /** String representation */\n\t toString: function () {\n\t var modelString = this.model ? this.model + '' : '(no model)';\n\t return 'NestedDCDCEListItemView(' + modelString + ')';\n\t }\n\t });\n\t\n\t //==============================================================================\n\t return {\n\t DCListItemView: DCListItemView,\n\t DCEListItemView: DCEListItemView,\n\t DatasetDCEListItemView: DatasetDCEListItemView,\n\t NestedDCDCEListItemView: NestedDCDCEListItemView\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(1)))\n\n/***/ }),\n/* 36 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_, Backbone, jQuery) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(75), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (DATASET_MODEL, BASE_MVC, _l) {\n\t 'use strict';\n\t\n\t //==============================================================================\n\t /*\n\t Notes:\n\t \n\t Terminology:\n\t DatasetCollection/DC : a container of datasets or nested DatasetCollections\n\t Element/DatasetCollectionElement/DCE : an item contained in a DatasetCollection\n\t HistoryDatasetCollectionAssociation/HDCA: a DatasetCollection contained in a history\n\t \n\t \n\t This all seems too complex unfortunately:\n\t \n\t - Terminology collision between DatasetCollections (DCs) and Backbone Collections.\n\t - In the DatasetCollections API JSON, DC Elements use a 'Has A' stucture to *contain*\n\t either a dataset or a nested DC. This would make the hierarchy much taller. I've\n\t decided to merge the contained JSON with the DC element json - making the 'has a'\n\t relation into an 'is a' relation. This seems simpler to me and allowed a lot of\n\t DRY in both models and views, but may make tracking or tracing within these models\n\t more difficult (since DatasetCollectionElements are now *also* DatasetAssociations\n\t or DatasetCollections (nested)). This also violates the rule of thumb about\n\t favoring aggregation over inheritance.\n\t - Currently, there are three DatasetCollection subclasses: List, Pair, and ListPaired.\n\t These each should a) be usable on their own, b) be usable in the context of\n\t nesting within a collection model (at least in the case of ListPaired), and\n\t c) be usable within the context of other container models (like History or\n\t LibraryFolder, etc.). I've tried to separate/extract classes in order to\n\t handle those three situations, but it's proven difficult to do in a simple,\n\t readable manner.\n\t - Ideally, histories and libraries would inherit from the same server models as\n\t dataset collections do since they are (in essence) dataset collections themselves -\n\t making the whole nested structure simpler. This would be a large, error-prone\n\t refactoring and migration.\n\t \n\t Many of the classes and heirarchy are meant as extension points so, while the\n\t relations and flow may be difficult to understand initially, they'll allow us to\n\t handle the growth or flux dataset collection in the future (w/o actually implementing\n\t any YAGNI).\n\t \n\t */\n\t //_________________________________________________________________________________________________ ELEMENTS\n\t /** @class mixin for Dataset collection elements.\n\t * When collection elements are passed from the API, the underlying element is\n\t * in a sub-object 'object' (IOW, a DCE representing an HDA will have HDA json in element.object).\n\t * This mixin uses the constructor and parse methods to merge that JSON with the DCE attribtues\n\t * effectively changing a DCE from a container to a subclass (has a --> is a).\n\t */\n\t\n\t var DatasetCollectionElementMixin = {\n\t\n\t /** default attributes used by elements in a dataset collection */\n\t defaults: {\n\t model_class: 'DatasetCollectionElement',\n\t element_identifier: null,\n\t element_index: null,\n\t element_type: null\n\t },\n\t\n\t /** merge the attributes of the sub-object 'object' into this model */\n\t _mergeObject: function (attributes) {\n\t // if we don't preserve and correct ids here, the element id becomes the object id\n\t // and collision in backbone's _byId will occur and only\n\t _.extend(attributes, attributes.object, { element_id: attributes.id });\n\t delete attributes.object;\n\t return attributes;\n\t },\n\t\n\t /** override to merge this.object into this */\n\t constructor: function (attributes, options) {\n\t // console.debug( '\\t DatasetCollectionElement.constructor:', attributes, options );\n\t attributes = this._mergeObject(attributes);\n\t this.idAttribute = 'element_id';\n\t Backbone.Model.apply(this, arguments);\n\t },\n\t\n\t /** when the model is fetched, merge this.object into this */\n\t parse: function (response, options) {\n\t var attributes = response;\n\t attributes = this._mergeObject(attributes);\n\t return attributes;\n\t }\n\t };\n\t\n\t /** @class Concrete class of Generic DatasetCollectionElement */\n\t var DatasetCollectionElement = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(DatasetCollectionElementMixin).extend({ _logNamespace: 'collections' });\n\t\n\t //==============================================================================\n\t /** @class Base/Abstract Backbone collection for Generic DCEs. */\n\t var DCECollection = Backbone.Collection.extend(BASE_MVC.LoggableMixin).extend(\n\t /** @lends DCECollection.prototype */{\n\t _logNamespace: 'collections',\n\t\n\t model: DatasetCollectionElement,\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return ['DatasetCollectionElementCollection(', this.length, ')'].join('');\n\t }\n\t });\n\t\n\t //==============================================================================\n\t /** @class Backbone model for a dataset collection element that is a dataset (HDA).\n\t */\n\t var DatasetDCE = DATASET_MODEL.DatasetAssociation.extend(BASE_MVC.mixin(DatasetCollectionElementMixin,\n\t /** @lends DatasetDCE.prototype */{\n\t\n\t /** url fn */\n\t url: function () {\n\t // won't always be an hda\n\t if (!this.has('history_id')) {\n\t console.warn('no endpoint for non-hdas within a collection yet');\n\t // (a little silly since this api endpoint *also* points at hdas)\n\t return Galaxy.root + 'api/datasets';\n\t }\n\t return Galaxy.root + 'api/histories/' + this.get('history_id') + '/contents/' + this.get('id');\n\t },\n\t\n\t defaults: _.extend({}, DATASET_MODEL.DatasetAssociation.prototype.defaults, DatasetCollectionElementMixin.defaults),\n\t\n\t _downloadQueryParameters: function () {\n\t return '?to_ext=' + this.get('file_ext') + '&hdca_id=' + this.get('parent_hdca_id') + '&element_identifier=' + this.get('element_identifier');\n\t },\n\t\n\t // because all objects have constructors (as this hashmap would even if this next line wasn't present)\n\t // the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model\n\t // - re-apply manually for now\n\t /** call the mixin constructor */\n\t constructor: function (attributes, options) {\n\t this.debug('\\t DatasetDCE.constructor:', attributes, options);\n\t //DATASET_MODEL.DatasetAssociation.prototype.constructor.call( this, attributes, options );\n\t DatasetCollectionElementMixin.constructor.call(this, attributes, options);\n\t },\n\t\n\t /** Does this model already contain detailed data (as opposed to just summary level data)? */\n\t hasDetails: function () {\n\t return this.elements && this.elements.length;\n\t },\n\t\n\t /** String representation. */\n\t toString: function () {\n\t var objStr = this.get('element_identifier');\n\t return ['DatasetDCE(', objStr, ')'].join('');\n\t }\n\t }));\n\t\n\t //==============================================================================\n\t /** @class DCECollection of DatasetDCE's (a list of datasets, a pair of datasets).\n\t */\n\t var DatasetDCECollection = DCECollection.extend(\n\t /** @lends DatasetDCECollection.prototype */{\n\t model: DatasetDCE,\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return ['DatasetDCECollection(', this.length, ')'].join('');\n\t }\n\t });\n\t\n\t //_________________________________________________________________________________________________ COLLECTIONS\n\t /** @class Backbone model for Dataset Collections.\n\t * The DC API returns an array of JSON objects under the attribute elements.\n\t * This model:\n\t * - removes that array/attribute ('elements') from the model,\n\t * - creates a bbone collection (of the class defined in the 'collectionClass' attribute),\n\t * - passes that json onto the bbone collection\n\t * - caches the bbone collection in this.elements\n\t */\n\t var DatasetCollection = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(BASE_MVC.SearchableModelMixin).extend( /** @lends DatasetCollection.prototype */{\n\t _logNamespace: 'collections',\n\t\n\t /** default attributes for a model */\n\t defaults: {\n\t /* 'list', 'paired', or 'list:paired' */\n\t collection_type: null,\n\t //??\n\t deleted: false\n\t },\n\t\n\t /** Which class to use for elements */\n\t collectionClass: DCECollection,\n\t\n\t /** set up: create elements instance var and (on changes to elements) update them */\n\t initialize: function (model, options) {\n\t this.debug(this + '(DatasetCollection).initialize:', model, options, this);\n\t this.elements = this._createElementsModel();\n\t this.on('change:elements', function () {\n\t this.log('change:elements');\n\t //TODO: prob. better to update the collection instead of re-creating it\n\t this.elements = this._createElementsModel();\n\t });\n\t },\n\t\n\t /** move elements model attribute to full collection */\n\t _createElementsModel: function () {\n\t this.debug(this + '._createElementsModel', this.collectionClass, this.get('elements'), this.elements);\n\t //TODO: same patterns as DatasetCollectionElement _createObjectModel - refactor to BASE_MVC.hasSubModel?\n\t var elements = this.get('elements') || [];\n\t this.unset('elements', { silent: true });\n\t var self = this;\n\t _.each(elements, function (element, index) {\n\t _.extend(element, { \"parent_hdca_id\": self.get(\"id\") });\n\t });\n\t this.elements = new this.collectionClass(elements);\n\t //this.debug( 'collectionClass:', this.collectionClass + '', this.elements );\n\t return this.elements;\n\t },\n\t\n\t // ........................................................................ common queries\n\t /** pass the elements back within the model json when this is serialized */\n\t toJSON: function () {\n\t var json = Backbone.Model.prototype.toJSON.call(this);\n\t if (this.elements) {\n\t json.elements = this.elements.toJSON();\n\t }\n\t return json;\n\t },\n\t\n\t /** Is this collection in a 'ready' state no processing (for the collection) is left\n\t * to do on the server.\n\t */\n\t inReadyState: function () {\n\t var populated = this.get('populated');\n\t return this.isDeletedOrPurged() || populated;\n\t },\n\t\n\t //TODO:?? the following are the same interface as DatasetAssociation - can we combine?\n\t /** Does the DC contain any elements yet? Is a fetch() required? */\n\t hasDetails: function () {\n\t return this.elements.length !== 0;\n\t },\n\t\n\t /** Given the filters, what models in this.elements would be returned? */\n\t getVisibleContents: function (filters) {\n\t // filters unused for now\n\t return this.elements;\n\t },\n\t\n\t // ........................................................................ ajax\n\t /** override to use actual Dates objects for create/update times */\n\t parse: function (response, options) {\n\t var parsed = Backbone.Model.prototype.parse.call(this, response, options);\n\t if (parsed.create_time) {\n\t parsed.create_time = new Date(parsed.create_time);\n\t }\n\t if (parsed.update_time) {\n\t parsed.update_time = new Date(parsed.update_time);\n\t }\n\t return parsed;\n\t },\n\t\n\t /** save this dataset, _Mark_ing it as deleted (just a flag) */\n\t 'delete': function (options) {\n\t if (this.get('deleted')) {\n\t return jQuery.when();\n\t }\n\t return this.save({ deleted: true }, options);\n\t },\n\t /** save this dataset, _Mark_ing it as undeleted */\n\t undelete: function (options) {\n\t if (!this.get('deleted') || this.get('purged')) {\n\t return jQuery.when();\n\t }\n\t return this.save({ deleted: false }, options);\n\t },\n\t\n\t /** Is this collection deleted or purged? */\n\t isDeletedOrPurged: function () {\n\t return this.get('deleted') || this.get('purged');\n\t },\n\t\n\t // ........................................................................ searchable\n\t /** searchable attributes for collections */\n\t searchAttributes: ['name'],\n\t\n\t // ........................................................................ misc\n\t /** String representation */\n\t toString: function () {\n\t var idAndName = [this.get('id'), this.get('name') || this.get('element_identifier')];\n\t return 'DatasetCollection(' + idAndName.join(',') + ')';\n\t }\n\t });\n\t\n\t //==============================================================================\n\t /** Model for a DatasetCollection containing datasets (non-nested).\n\t */\n\t var ListDatasetCollection = DatasetCollection.extend(\n\t /** @lends ListDatasetCollection.prototype */{\n\t\n\t /** override since we know the collection will only contain datasets */\n\t collectionClass: DatasetDCECollection,\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return 'List' + DatasetCollection.prototype.toString.call(this);\n\t }\n\t });\n\t\n\t //==============================================================================\n\t /** Model for a DatasetCollection containing fwd/rev datasets (a list of 2).\n\t */\n\t var PairDatasetCollection = ListDatasetCollection.extend(\n\t /** @lends PairDatasetCollection.prototype */{\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return 'Pair' + DatasetCollection.prototype.toString.call(this);\n\t }\n\t });\n\t\n\t //_________________________________________________________________________________________________ NESTED COLLECTIONS\n\t // this is where things get weird, man. Weird.\n\t //TODO: it might be possible to compact all the following...I think.\n\t //==============================================================================\n\t /** @class Backbone model for a Generic DatasetCollectionElement that is also a DatasetCollection\n\t * (a nested collection). Currently only list:paired.\n\t */\n\t var NestedDCDCE = DatasetCollection.extend(BASE_MVC.mixin(DatasetCollectionElementMixin,\n\t /** @lends NestedDCDCE.prototype */{\n\t\n\t // because all objects have constructors (as this hashmap would even if this next line wasn't present)\n\t // the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model\n\t // - re-apply manually it now\n\t /** call the mixin constructor */\n\t constructor: function (attributes, options) {\n\t this.debug('\\t NestedDCDCE.constructor:', attributes, options);\n\t DatasetCollectionElementMixin.constructor.call(this, attributes, options);\n\t },\n\t\n\t /** String representation. */\n\t toString: function () {\n\t var objStr = this.object ? '' + this.object : this.get('element_identifier');\n\t return ['NestedDCDCE(', objStr, ')'].join('');\n\t }\n\t }));\n\t\n\t //==============================================================================\n\t /** @class Backbone collection containing Generic NestedDCDCE's (nested dataset collections).\n\t */\n\t var NestedDCDCECollection = DCECollection.extend(\n\t /** @lends NestedDCDCECollection.prototype */{\n\t\n\t /** This is a collection of nested collections */\n\t model: NestedDCDCE,\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return ['NestedDCDCECollection(', this.length, ')'].join('');\n\t }\n\t });\n\t\n\t //==============================================================================\n\t /** @class Backbone model for a paired dataset collection within a list:paired dataset collection.\n\t */\n\t var NestedPairDCDCE = PairDatasetCollection.extend(BASE_MVC.mixin(DatasetCollectionElementMixin,\n\t /** @lends NestedPairDCDCE.prototype */{\n\t //TODO:?? possibly rename to NestedDatasetCollection?\n\t\n\t // because all objects have constructors (as this hashmap would even if this next line wasn't present)\n\t // the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model\n\t // - re-apply manually it now\n\t /** This is both a collection and a collection element - call the constructor */\n\t constructor: function (attributes, options) {\n\t this.debug('\\t NestedPairDCDCE.constructor:', attributes, options);\n\t //DatasetCollection.constructor.call( this, attributes, options );\n\t DatasetCollectionElementMixin.constructor.call(this, attributes, options);\n\t },\n\t\n\t /** String representation. */\n\t toString: function () {\n\t var objStr = this.object ? '' + this.object : this.get('element_identifier');\n\t return ['NestedPairDCDCE(', objStr, ')'].join('');\n\t }\n\t }));\n\t\n\t //==============================================================================\n\t /** @class Backbone collection for a backbone collection containing paired dataset collections.\n\t */\n\t var NestedPairDCDCECollection = NestedDCDCECollection.extend(\n\t /** @lends PairDCDCECollection.prototype */{\n\t\n\t /** We know this collection is composed of only nested pair collections */\n\t model: NestedPairDCDCE,\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return ['NestedPairDCDCECollection(', this.length, ')'].join('');\n\t }\n\t });\n\t\n\t //==============================================================================\n\t /** @class Backbone Model for a DatasetCollection (list) that contains DatasetCollections (pairs).\n\t */\n\t var ListPairedDatasetCollection = DatasetCollection.extend(\n\t /** @lends ListPairedDatasetCollection.prototype */{\n\t\n\t /** list:paired is the only collection that itself contains collections */\n\t collectionClass: NestedPairDCDCECollection,\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return ['ListPairedDatasetCollection(', this.get('name'), ')'].join('');\n\t }\n\t });\n\t\n\t //==============================================================================\n\t /** @class Backbone model for a list dataset collection within a list:list dataset collection. */\n\t var NestedListDCDCE = ListDatasetCollection.extend(BASE_MVC.mixin(DatasetCollectionElementMixin,\n\t /** @lends NestedListDCDCE.prototype */{\n\t\n\t /** This is both a collection and a collection element - call the constructor */\n\t constructor: function (attributes, options) {\n\t this.debug('\\t NestedListDCDCE.constructor:', attributes, options);\n\t DatasetCollectionElementMixin.constructor.call(this, attributes, options);\n\t },\n\t\n\t /** String representation. */\n\t toString: function () {\n\t var objStr = this.object ? '' + this.object : this.get('element_identifier');\n\t return ['NestedListDCDCE(', objStr, ')'].join('');\n\t }\n\t }));\n\t\n\t //==============================================================================\n\t /** @class Backbone collection containing list dataset collections. */\n\t var NestedListDCDCECollection = NestedDCDCECollection.extend({\n\t\n\t /** We know this collection is composed of only nested pair collections */\n\t model: NestedListDCDCE,\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return ['NestedListDCDCECollection(', this.length, ')'].join('');\n\t }\n\t });\n\t\n\t //==============================================================================\n\t /** @class Backbone Model for a DatasetCollection (list) that contains other lists. */\n\t var ListOfListsDatasetCollection = DatasetCollection.extend({\n\t\n\t /** list:paired is the only collection that itself contains collections */\n\t collectionClass: NestedListDCDCECollection,\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return ['ListOfListsDatasetCollection(', this.get('name'), ')'].join('');\n\t }\n\t });\n\t\n\t //==============================================================================\n\t return {\n\t ListDatasetCollection: ListDatasetCollection,\n\t PairDatasetCollection: PairDatasetCollection,\n\t ListPairedDatasetCollection: ListPairedDatasetCollection,\n\t ListOfListsDatasetCollection: ListOfListsDatasetCollection\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(3), __webpack_require__(1)))\n\n/***/ }),\n/* 37 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, $, jQuery) {\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(44), __webpack_require__(11), __webpack_require__(6), __webpack_require__(72), __webpack_require__(8), __webpack_require__(90), __webpack_require__(5), __webpack_require__(87)], __WEBPACK_AMD_DEFINE_RESULT__ = function (HDCA, STATES, BASE_MVC, baseCreator, UI_MODAL, naturalSort, _l) {\n\t\n\t 'use strict';\n\t\n\t var logNamespace = 'collections';\n\t\n\t /*==============================================================================\n\t TODO:\n\t use proper Element model and not just json\n\t straighten out createFn, collection.createHDCA\n\t possibly stop using modals for this\n\t It would be neat to do a drag and drop\n\t \n\t ==============================================================================*/\n\t /** A view for both DatasetDCEs and NestedDCDCEs\n\t * (things that implement collection-model:DatasetCollectionElementMixin)\n\t */\n\t var DatasetCollectionElementView = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({\n\t _logNamespace: logNamespace,\n\t\n\t //TODO: use proper class (DatasetDCE or NestedDCDCE (or the union of both))\n\t tagName: 'li',\n\t className: 'collection-element',\n\t\n\t initialize: function (attributes) {\n\t this.element = attributes.element || {};\n\t this.selected = attributes.selected || false;\n\t },\n\t\n\t render: function () {\n\t this.$el.attr('data-element-id', this.element.id).attr('draggable', true).html(this.template({ element: this.element }));\n\t if (this.selected) {\n\t this.$el.addClass('selected');\n\t }\n\t return this;\n\t },\n\t\n\t //TODO: lots of unused space in the element - possibly load details and display them horiz.\n\t template: _.template(['', '<%- element.name %>', '', ''].join('')),\n\t\n\t /** select this element and pub */\n\t select: function (toggle) {\n\t this.$el.toggleClass('selected', toggle);\n\t this.trigger('select', {\n\t source: this,\n\t selected: this.$el.hasClass('selected')\n\t });\n\t },\n\t\n\t /** animate the removal of this element and pub */\n\t discard: function () {\n\t var view = this,\n\t parentWidth = this.$el.parent().width();\n\t this.$el.animate({ 'margin-right': parentWidth }, 'fast', function () {\n\t view.trigger('discard', {\n\t source: view\n\t });\n\t view.destroy();\n\t });\n\t },\n\t\n\t /** remove the DOM and any listeners */\n\t destroy: function () {\n\t this.off();\n\t this.$el.remove();\n\t },\n\t\n\t events: {\n\t 'click': '_click',\n\t 'click .name': '_clickName',\n\t 'click .discard': '_clickDiscard',\n\t\n\t 'dragstart': '_dragstart',\n\t 'dragend': '_dragend',\n\t 'dragover': '_sendToParent',\n\t 'drop': '_sendToParent'\n\t },\n\t\n\t /** select when the li is clicked */\n\t _click: function (ev) {\n\t ev.stopPropagation();\n\t this.select(ev);\n\t },\n\t\n\t /** rename a pair when the name is clicked */\n\t _clickName: function (ev) {\n\t ev.stopPropagation();\n\t ev.preventDefault();\n\t var promptString = [_l('Enter a new name for the element'), ':\\n(', _l('Note that changing the name here will not rename the dataset'), ')'].join(''),\n\t response = prompt(_l('Enter a new name for the element') + ':', this.element.name);\n\t if (response) {\n\t this.element.name = response;\n\t this.render();\n\t }\n\t //TODO: cancelling with ESC leads to closure of the creator...\n\t },\n\t\n\t /** discard when the discard button is clicked */\n\t _clickDiscard: function (ev) {\n\t ev.stopPropagation();\n\t this.discard();\n\t },\n\t\n\t /** dragging pairs for re-ordering */\n\t _dragstart: function (ev) {\n\t if (ev.originalEvent) {\n\t ev = ev.originalEvent;\n\t }\n\t ev.dataTransfer.effectAllowed = 'move';\n\t ev.dataTransfer.setData('text/plain', JSON.stringify(this.element));\n\t\n\t this.$el.addClass('dragging');\n\t this.$el.parent().trigger('collection-element.dragstart', [this]);\n\t },\n\t\n\t /** dragging for re-ordering */\n\t _dragend: function (ev) {\n\t this.$el.removeClass('dragging');\n\t this.$el.parent().trigger('collection-element.dragend', [this]);\n\t },\n\t\n\t /** manually bubble up an event to the parent/container */\n\t _sendToParent: function (ev) {\n\t this.$el.parent().trigger(ev);\n\t },\n\t\n\t /** string rep */\n\t toString: function () {\n\t return 'DatasetCollectionElementView()';\n\t }\n\t });\n\t\n\t // ============================================================================\n\t /** An interface for building collections.\n\t */\n\t var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(baseCreator.CollectionCreatorMixin).extend({\n\t _logNamespace: logNamespace,\n\t\n\t /** the class used to display individual elements */\n\t elementViewClass: DatasetCollectionElementView,\n\t /** the class this creator will create and save */\n\t collectionClass: HDCA.HistoryListDatasetCollection,\n\t className: 'list-collection-creator collection-creator flex-row-container',\n\t\n\t /** minimum number of valid elements to start with in order to build a collection of this type */\n\t minElements: 1,\n\t\n\t defaultAttributes: {\n\t //TODO: remove - use new collectionClass().save()\n\t /** takes elements and creates the proper collection - returns a promise */\n\t creationFn: function () {\n\t throw new TypeError('no creation fn for creator');\n\t },\n\t /** fn to call when the collection is created (scoped to this) */\n\t oncreate: function () {},\n\t /** fn to call when the cancel button is clicked (scoped to this) - if falsy, no btn is displayed */\n\t oncancel: function () {},\n\t /** distance from list edge to begin autoscrolling list */\n\t autoscrollDist: 24,\n\t /** Color passed to hoverhighlight */\n\t highlightClr: 'rgba( 64, 255, 255, 1.0 )'\n\t },\n\t\n\t footerSettings: {\n\t '.hide-originals': 'hideOriginals'\n\t },\n\t\n\t /** set up initial options, instance vars, behaviors */\n\t initialize: function (attributes) {\n\t this.metric('ListCollectionCreator.initialize', attributes);\n\t var creator = this;\n\t _.each(this.defaultAttributes, function (value, key) {\n\t value = attributes[key] || value;\n\t creator[key] = value;\n\t });\n\t\n\t /** unordered, original list - cache to allow reversal */\n\t creator.initialElements = attributes.elements || [];\n\t\n\t this._setUpCommonSettings(attributes);\n\t this._instanceSetUp();\n\t this._elementsSetUp();\n\t this._setUpBehaviors();\n\t },\n\t\n\t /** set up instance vars */\n\t _instanceSetUp: function () {\n\t /** Ids of elements that have been selected by the user - to preserve over renders */\n\t this.selectedIds = {};\n\t /** DOM elements currently being dragged */\n\t this.$dragging = null;\n\t /** Used for blocking UI events during ajax/operations (don't post twice) */\n\t this.blocking = false;\n\t },\n\t\n\t // ------------------------------------------------------------------------ process raw list\n\t /** set up main data */\n\t _elementsSetUp: function () {\n\t //this.debug( '-- _dataSetUp' );\n\t /** a list of invalid elements and the reasons they aren't valid */\n\t this.invalidElements = [];\n\t //TODO: handle fundamental problem of syncing DOM, views, and list here\n\t /** data for list in progress */\n\t this.workingElements = [];\n\t /** views for workingElements */\n\t this.elementViews = [];\n\t\n\t // copy initial list, sort, add ids if needed\n\t this.workingElements = this.initialElements.slice(0);\n\t this._ensureElementIds();\n\t this._validateElements();\n\t this._mangleDuplicateNames();\n\t this._sortElements();\n\t },\n\t\n\t /** add ids to dataset objs in initial list if none */\n\t _ensureElementIds: function () {\n\t this.workingElements.forEach(function (element) {\n\t if (!element.hasOwnProperty('id')) {\n\t element.id = _.uniqueId();\n\t }\n\t });\n\t return this.workingElements;\n\t },\n\t\n\t /** separate working list into valid and invalid elements for this collection */\n\t _validateElements: function () {\n\t var creator = this,\n\t existingNames = {};\n\t creator.invalidElements = [];\n\t\n\t this.workingElements = this.workingElements.filter(function (element) {\n\t var problem = creator._isElementInvalid(element);\n\t if (problem) {\n\t creator.invalidElements.push({\n\t element: element,\n\t text: problem\n\t });\n\t }\n\t return !problem;\n\t });\n\t return this.workingElements;\n\t },\n\t\n\t /** describe what is wrong with a particular element if anything */\n\t _isElementInvalid: function (element) {\n\t if (element.history_content_type !== 'dataset') {\n\t return _l(\"is not a dataset\");\n\t }\n\t var validState = element.state === STATES.OK || _.contains(STATES.NOT_READY_STATES, element.state);\n\t if (!validState) {\n\t return _l(\"has errored, is paused, or is not accessible\");\n\t }\n\t if (element.deleted || element.purged) {\n\t return _l(\"has been deleted or purged\");\n\t }\n\t return null;\n\t },\n\t\n\t /** mangle duplicate names using a mac-like '(counter)' addition to any duplicates */\n\t _mangleDuplicateNames: function () {\n\t var SAFETY = 900,\n\t counter = 1,\n\t existingNames = {};\n\t this.workingElements.forEach(function (element) {\n\t var currName = element.name;\n\t while (existingNames.hasOwnProperty(currName)) {\n\t currName = element.name + ' (' + counter + ')';\n\t counter += 1;\n\t if (counter >= SAFETY) {\n\t throw new Error('Safety hit in while loop - thats impressive');\n\t }\n\t }\n\t element.name = currName;\n\t existingNames[element.name] = true;\n\t });\n\t },\n\t\n\t /** sort a list of elements */\n\t _sortElements: function (list) {\n\t // // currently only natural sort by name\n\t // this.workingElements.sort( function( a, b ){ return naturalSort( a.name, b.name ); });\n\t // return this.workingElements;\n\t },\n\t\n\t // ------------------------------------------------------------------------ rendering\n\t // templates : ListCollectionCreator.templates,\n\t /** render the entire interface */\n\t render: function (speed, callback) {\n\t //this.debug( '-- _render' );\n\t if (this.workingElements.length < this.minElements) {\n\t return this._renderInvalid(speed, callback);\n\t }\n\t\n\t this.$el.empty().html(this.templates.main());\n\t this._renderHeader(speed);\n\t this._renderMiddle(speed);\n\t this._renderFooter(speed);\n\t this._addPluginComponents();\n\t this.$('.collection-name').focus();\n\t this.trigger('rendered', this);\n\t return this;\n\t },\n\t\n\t /** render a simplified interface aimed at telling the user why they can't move forward */\n\t _renderInvalid: function (speed, callback) {\n\t //this.debug( '-- _render' );\n\t this.$el.empty().html(this.templates.invalidInitial({\n\t problems: this.invalidElements,\n\t elements: this.workingElements\n\t }));\n\t if (typeof this.oncancel === 'function') {\n\t this.$('.cancel-create.btn').show();\n\t }\n\t this.trigger('rendered', this);\n\t return this;\n\t },\n\t\n\t /** render the header section */\n\t _renderHeader: function (speed, callback) {\n\t var $header = this.$('.header').empty().html(this.templates.header()).find('.help-content').prepend($(this.templates.helpContent()));\n\t //TODO: should only show once despite calling _renderHeader again\n\t if (this.invalidElements.length) {\n\t this._invalidElementsAlert();\n\t }\n\t return $header;\n\t },\n\t\n\t /** render the middle including the elements */\n\t _renderMiddle: function (speed, callback) {\n\t var $middle = this.$('.middle').empty().html(this.templates.middle());\n\t this._renderList(speed);\n\t return $middle;\n\t },\n\t\n\t /** add any jQuery/bootstrap/custom plugins to elements rendered */\n\t _addPluginComponents: function () {\n\t this.$('.help-content i').hoverhighlight('.collection-creator', this.highlightClr);\n\t },\n\t\n\t /** build and show an alert describing any elements that could not be included due to problems */\n\t _invalidElementsAlert: function () {\n\t this._showAlert(this.templates.invalidElements({ problems: this.invalidElements }), 'alert-warning');\n\t },\n\t\n\t _disableNameAndCreate: function (disable) {\n\t disable = !_.isUndefined(disable) ? disable : true;\n\t if (disable) {\n\t this.$('.collection-name').prop('disabled', true);\n\t this.$('.create-collection').toggleClass('disabled', true);\n\t // } else {\n\t // this.$( '.collection-name' ).prop( 'disabled', false );\n\t // this.$( '.create-collection' ).removeClass( 'disable' );\n\t }\n\t },\n\t\n\t // ------------------------------------------------------------------------ rendering elements\n\t /** conv. to the main list display DOM */\n\t $list: function () {\n\t return this.$('.collection-elements');\n\t },\n\t\n\t /** show or hide the clear selected control based on the num of selected elements */\n\t _renderClearSelected: function () {\n\t if (_.size(this.selectedIds)) {\n\t this.$('.collection-elements-controls > .clear-selected').show();\n\t } else {\n\t this.$('.collection-elements-controls > .clear-selected').hide();\n\t }\n\t },\n\t\n\t /** render the elements in order (or a warning if no elements found) */\n\t _renderList: function (speed, callback) {\n\t //this.debug( '-- _renderList' );\n\t var creator = this,\n\t $tmp = jQuery(''),\n\t $list = creator.$list();\n\t\n\t _.each(this.elementViews, function (view) {\n\t view.destroy();\n\t creator.removeElementView(view);\n\t });\n\t\n\t // if( !this.workingElements.length ){\n\t // this._renderNoValidElements();\n\t // return;\n\t // }\n\t\n\t creator.workingElements.forEach(function (element) {\n\t var elementView = creator._createElementView(element);\n\t $tmp.append(elementView.$el);\n\t });\n\t\n\t creator._renderClearSelected();\n\t $list.empty().append($tmp.children());\n\t _.invoke(creator.elementViews, 'render');\n\t\n\t if ($list.height() > $list.css('max-height')) {\n\t $list.css('border-width', '1px 0px 1px 0px');\n\t } else {\n\t $list.css('border-width', '0px');\n\t }\n\t },\n\t\n\t /** create an element view, cache in elementViews, set up listeners, and return */\n\t _createElementView: function (element) {\n\t var elementView = new this.elementViewClass({\n\t //TODO: use non-generic class or not all\n\t // model : COLLECTION.DatasetDCE( element )\n\t element: element,\n\t selected: _.has(this.selectedIds, element.id)\n\t });\n\t this.elementViews.push(elementView);\n\t this._listenToElementView(elementView);\n\t return elementView;\n\t },\n\t\n\t /** listen to any element events */\n\t _listenToElementView: function (view) {\n\t var creator = this;\n\t creator.listenTo(view, {\n\t select: function (data) {\n\t var element = data.source.element;\n\t if (data.selected) {\n\t creator.selectedIds[element.id] = true;\n\t } else {\n\t delete creator.selectedIds[element.id];\n\t }\n\t creator.trigger('elements:select', data);\n\t },\n\t discard: function (data) {\n\t creator.trigger('elements:discard', data);\n\t }\n\t });\n\t },\n\t\n\t /** add a new element view based on the json in element */\n\t addElementView: function (element) {\n\t //TODO: workingElements is sorted, add element in appropo index\n\t // add element, sort elements, find element index\n\t // var view = this._createElementView( element );\n\t // return view;\n\t },\n\t\n\t /** stop listening to view and remove from caches */\n\t removeElementView: function (view) {\n\t delete this.selectedIds[view.element.id];\n\t this._renderClearSelected();\n\t\n\t this.elementViews = _.without(this.elementViews, view);\n\t this.stopListening(view);\n\t },\n\t\n\t /** render a message in the list that no elements remain to create a collection */\n\t _renderNoElementsLeft: function () {\n\t this._disableNameAndCreate(true);\n\t this.$('.collection-elements').append(this.templates.noElementsLeft());\n\t },\n\t\n\t // /** render a message in the list that no valid elements were found to create a collection */\n\t // _renderNoValidElements : function(){\n\t // this._disableNameAndCreate( true );\n\t // this.$( '.collection-elements' ).append( this.templates.noValidElements() );\n\t // },\n\t\n\t // ------------------------------------------------------------------------ API\n\t /** convert element into JSON compatible with the collections API */\n\t _elementToJSON: function (element) {\n\t // return element.toJSON();\n\t return element;\n\t },\n\t\n\t /** create the collection via the API\n\t * @returns {jQuery.xhr Object} the jquery ajax request\n\t */\n\t createList: function (name) {\n\t if (!this.workingElements.length) {\n\t var message = _l('No valid elements for final list') + '. ';\n\t message += '' + _l('Cancel') + ' ';\n\t message += _l('or');\n\t message += ' ' + _l('start over') + '.';\n\t this._showAlert(message);\n\t return;\n\t }\n\t\n\t var creator = this,\n\t elements = this.workingElements.map(function (element) {\n\t return creator._elementToJSON(element);\n\t });\n\t\n\t creator.blocking = true;\n\t return creator.creationFn(elements, name, creator.hideOriginals).always(function () {\n\t creator.blocking = false;\n\t }).fail(function (xhr, status, message) {\n\t creator.trigger('error', {\n\t xhr: xhr,\n\t status: status,\n\t message: _l('An error occurred while creating this collection')\n\t });\n\t }).done(function (response, message, xhr) {\n\t creator.trigger('collection:created', response, message, xhr);\n\t creator.metric('collection:created', response);\n\t if (typeof creator.oncreate === 'function') {\n\t creator.oncreate.call(this, response, message, xhr);\n\t }\n\t });\n\t },\n\t\n\t // ------------------------------------------------------------------------ events\n\t /** set up event handlers on self */\n\t _setUpBehaviors: function () {\n\t this.on('error', this._errorHandler);\n\t\n\t this.once('rendered', function () {\n\t this.trigger('rendered:initial', this);\n\t });\n\t\n\t this.on('elements:select', function (data) {\n\t this._renderClearSelected();\n\t });\n\t\n\t this.on('elements:discard', function (data) {\n\t var element = data.source.element;\n\t this.removeElementView(data.source);\n\t\n\t this.workingElements = _.without(this.workingElements, element);\n\t if (!this.workingElements.length) {\n\t this._renderNoElementsLeft();\n\t }\n\t });\n\t\n\t //this.on( 'all', function(){\n\t // this.info( arguments );\n\t //});\n\t return this;\n\t },\n\t\n\t /** handle errors with feedback and details to the user (if available) */\n\t _errorHandler: function (data) {\n\t this.error(data);\n\t\n\t var creator = this;\n\t content = data.message || _l('An error occurred');\n\t if (data.xhr) {\n\t var xhr = data.xhr,\n\t message = data.message;\n\t if (xhr.readyState === 0 && xhr.status === 0) {\n\t content += ': ' + _l('Galaxy could not be reached and may be updating.') + _l(' Try again in a few minutes.');\n\t } else if (xhr.responseJSON) {\n\t content += ':
' + JSON.stringify(xhr.responseJSON) + '
';\n\t } else {\n\t content += ': ' + message;\n\t }\n\t }\n\t creator._showAlert(content, 'alert-danger');\n\t },\n\t\n\t events: {\n\t // header\n\t 'click .more-help': '_clickMoreHelp',\n\t 'click .less-help': '_clickLessHelp',\n\t 'click .main-help': '_toggleHelp',\n\t 'click .header .alert button': '_hideAlert',\n\t\n\t 'click .reset': 'reset',\n\t 'click .clear-selected': 'clearSelectedElements',\n\t\n\t // elements - selection\n\t 'click .collection-elements': 'clearSelectedElements',\n\t\n\t // elements - drop target\n\t // 'dragenter .collection-elements': '_dragenterElements',\n\t // 'dragleave .collection-elements': '_dragleaveElements',\n\t 'dragover .collection-elements': '_dragoverElements',\n\t 'drop .collection-elements': '_dropElements',\n\t\n\t // these bubble up from the elements as custom events\n\t 'collection-element.dragstart .collection-elements': '_elementDragstart',\n\t 'collection-element.dragend .collection-elements': '_elementDragend',\n\t\n\t // footer\n\t 'change .collection-name': '_changeName',\n\t 'keydown .collection-name': '_nameCheckForEnter',\n\t 'change .hide-originals': '_changeHideOriginals',\n\t 'click .cancel-create': '_cancelCreate',\n\t 'click .create-collection': '_clickCreate' //,\n\t },\n\t\n\t // ........................................................................ elements\n\t /** reset all data to the initial state */\n\t reset: function () {\n\t this._instanceSetUp();\n\t this._elementsSetUp();\n\t this.render();\n\t },\n\t\n\t /** deselect all elements */\n\t clearSelectedElements: function (ev) {\n\t this.$('.collection-elements .collection-element').removeClass('selected');\n\t this.$('.collection-elements-controls > .clear-selected').hide();\n\t },\n\t\n\t //_dragenterElements : function( ev ){\n\t // //this.debug( '_dragenterElements:', ev );\n\t //},\n\t //TODO: if selected are dragged out of the list area - remove the placeholder - cuz it won't work anyway\n\t // _dragleaveElements : function( ev ){\n\t // //this.debug( '_dragleaveElements:', ev );\n\t // },\n\t\n\t /** track the mouse drag over the list adding a placeholder to show where the drop would occur */\n\t _dragoverElements: function (ev) {\n\t //this.debug( '_dragoverElements:', ev );\n\t ev.preventDefault();\n\t\n\t var $list = this.$list();\n\t this._checkForAutoscroll($list, ev.originalEvent.clientY);\n\t var $nearest = this._getNearestElement(ev.originalEvent.clientY);\n\t\n\t //TODO: no need to re-create - move instead\n\t this.$('.element-drop-placeholder').remove();\n\t var $placeholder = $('');\n\t if (!$nearest.length) {\n\t $list.append($placeholder);\n\t } else {\n\t $nearest.before($placeholder);\n\t }\n\t },\n\t\n\t /** If the mouse is near enough to the list's top or bottom, scroll the list */\n\t _checkForAutoscroll: function ($element, y) {\n\t var AUTOSCROLL_SPEED = 2,\n\t offset = $element.offset(),\n\t scrollTop = $element.scrollTop(),\n\t upperDist = y - offset.top,\n\t lowerDist = offset.top + $element.outerHeight() - y;\n\t if (upperDist >= 0 && upperDist < this.autoscrollDist) {\n\t $element.scrollTop(scrollTop - AUTOSCROLL_SPEED);\n\t } else if (lowerDist >= 0 && lowerDist < this.autoscrollDist) {\n\t $element.scrollTop(scrollTop + AUTOSCROLL_SPEED);\n\t }\n\t },\n\t\n\t /** get the nearest element based on the mouse's Y coordinate.\n\t * If the y is at the end of the list, return an empty jQuery object.\n\t */\n\t _getNearestElement: function (y) {\n\t var WIGGLE = 4,\n\t lis = this.$('.collection-elements li.collection-element').toArray();\n\t for (var i = 0; i < lis.length; i++) {\n\t var $li = $(lis[i]),\n\t top = $li.offset().top,\n\t halfHeight = Math.floor($li.outerHeight() / 2) + WIGGLE;\n\t if (top + halfHeight > y && top - halfHeight < y) {\n\t return $li;\n\t }\n\t }\n\t return $();\n\t },\n\t\n\t /** drop (dragged/selected elements) onto the list, re-ordering the internal list */\n\t _dropElements: function (ev) {\n\t if (ev.originalEvent) {\n\t ev = ev.originalEvent;\n\t }\n\t // both required for firefox\n\t ev.preventDefault();\n\t ev.dataTransfer.dropEffect = 'move';\n\t\n\t // insert before the nearest element or after the last.\n\t var $nearest = this._getNearestElement(ev.clientY);\n\t if ($nearest.length) {\n\t this.$dragging.insertBefore($nearest);\n\t } else {\n\t // no nearest before - insert after last element\n\t this.$dragging.insertAfter(this.$('.collection-elements .collection-element').last());\n\t }\n\t // resync the creator's list based on the new DOM order\n\t this._syncOrderToDom();\n\t return false;\n\t },\n\t\n\t /** resync the creator's list of elements based on the DOM order */\n\t _syncOrderToDom: function () {\n\t var creator = this,\n\t newElements = [];\n\t //TODO: doesn't seem wise to use the dom to store these - can't we sync another way?\n\t this.$('.collection-elements .collection-element').each(function () {\n\t var id = $(this).attr('data-element-id'),\n\t element = _.findWhere(creator.workingElements, { id: id });\n\t if (element) {\n\t newElements.push(element);\n\t } else {\n\t console.error('missing element: ', id);\n\t }\n\t });\n\t this.workingElements = newElements;\n\t this._renderList();\n\t },\n\t\n\t /** drag communication with element sub-views: dragstart */\n\t _elementDragstart: function (ev, element) {\n\t // auto select the element causing the event and move all selected\n\t element.select(true);\n\t this.$dragging = this.$('.collection-elements .collection-element.selected');\n\t },\n\t\n\t /** drag communication with element sub-views: dragend - remove the placeholder */\n\t _elementDragend: function (ev, element) {\n\t $('.element-drop-placeholder').remove();\n\t this.$dragging = null;\n\t },\n\t\n\t // ------------------------------------------------------------------------ templates\n\t //TODO: move to require text plugin and load these as text\n\t //TODO: underscore currently unnecc. bc no vars are used\n\t //TODO: better way of localizing text-nodes in long strings\n\t /** underscore template fns attached to class */\n\t templates: _.extend({}, baseCreator.CollectionCreatorMixin._creatorTemplates, {\n\t\n\t /** the header (not including help text) */\n\t header: _.template(['
'].join('')),\n\t\n\t /** help content */\n\t helpContent: _.template(['
', _l(['Collections of datasets are permanent, ordered lists of datasets that can be passed to tools and ', 'workflows in order to have analyses done on each member of the entire group. This interface allows ', 'you to create a collection and re-order the final collection.'].join('')), '
', '
', '
', _l(['Rename elements in the list by clicking on ', 'the existing name.'].join('')), '
', '
', _l(['Discard elements from the final created list by clicking on the ', '\"Discard\" button.'].join('')), '
', '
', _l(['Reorder the list by clicking and dragging elements. Select multiple elements by clicking on ', 'them and you can then move those selected by dragging the ', 'entire group. Deselect them by clicking them again or by clicking the ', 'the \"Clear selected\" link.'].join('')), '
', '
', _l(['Click the \"Start over\" link to begin again as if you had just opened ', 'the interface.'].join('')), '
', '
', _l(['Click the \"Cancel\" button to exit the interface.'].join('')), '
', '
', '
', _l(['Once your collection is complete, enter a name and ', 'click \"Create list\".'].join('')), '
'].join('')),\n\t\n\t /** shown in list when all elements are discarded */\n\t invalidElements: _.template([_l('The following selections could not be included due to problems:'), '
<% _.each( problems, function( problem ){ %>', '
<%- problem.element.name %>: <%- problem.text %>
', '<% }); %>
'].join('')),\n\t\n\t /** shown in list when all elements are discarded */\n\t noElementsLeft: _.template(['
'].join('')),\n\t\n\t /** a simplified page communicating what went wrong and why the user needs to reselect something else */\n\t invalidInitial: _.template(['
', '
', '', '<% if( _.size( problems ) ){ %>', _l('The following selections could not be included due to problems'), ':', '
<% _.each( problems, function( problem ){ %>', '
<%- problem.element.name %>: <%- problem.text %>
', '<% }); %>
', '<% } else if( _.size( elements ) < 1 ){ %>', _l('No datasets were selected'), '.', '<% } %>', ' ', _l('At least one element is needed for the collection'), '. ', _l('You may need to '), '', _l('cancel'), ' ', _l('and reselect new elements'), '.', '', '
', '
', ''].join(''))\n\t }),\n\t\n\t // ------------------------------------------------------------------------ misc\n\t /** string rep */\n\t toString: function () {\n\t return 'ListCollectionCreator';\n\t }\n\t });\n\t\n\t //=============================================================================\n\t /** Create a modal and load its body with the given CreatorClass creator type\n\t * @returns {Deferred} resolved when creator has built a collection.\n\t */\n\t var collectionCreatorModal = function _collectionCreatorModal(elements, options, CreatorClass) {\n\t\n\t var deferred = jQuery.Deferred(),\n\t modal = Galaxy.modal || new UI_MODAL.View(),\n\t creator;\n\t\n\t options = _.defaults(options || {}, {\n\t elements: elements,\n\t oncancel: function () {\n\t modal.hide();\n\t deferred.reject('cancelled');\n\t },\n\t oncreate: function (creator, response) {\n\t modal.hide();\n\t deferred.resolve(response);\n\t }\n\t });\n\t\n\t creator = new CreatorClass(options);\n\t modal.show({\n\t title: options.title || _l('Create a collection'),\n\t body: creator.$el,\n\t width: '80%',\n\t height: '100%',\n\t closing_events: true\n\t });\n\t creator.render();\n\t window._collectionCreator = creator;\n\t\n\t //TODO: remove modal header\n\t return deferred;\n\t };\n\t\n\t /** List collection flavor of collectionCreatorModal. */\n\t var listCollectionCreatorModal = function _listCollectionCreatorModal(elements, options) {\n\t options = options || {};\n\t options.title = _l('Create a collection from a list of datasets');\n\t return collectionCreatorModal(elements, options, ListCollectionCreator);\n\t };\n\t\n\t //==============================================================================\n\t /** Use a modal to create a list collection, then add it to the given history contents.\n\t * @returns {Deferred} resolved when the collection is added to the history.\n\t */\n\t function createListCollection(contents, defaultHideSourceItems) {\n\t var elements = contents.toJSON(),\n\t promise = listCollectionCreatorModal(elements, {\n\t defaultHideSourceItems: defaultHideSourceItems,\n\t creationFn: function (elements, name, hideSourceItems) {\n\t elements = elements.map(function (element) {\n\t return {\n\t id: element.id,\n\t name: element.name,\n\t //TODO: this allows for list:list even if the filter above does not - reconcile\n\t src: element.history_content_type === 'dataset' ? 'hda' : 'hdca'\n\t };\n\t });\n\t return contents.createHDCA(elements, 'list', name, hideSourceItems);\n\t }\n\t });\n\t return promise;\n\t }\n\t\n\t //==============================================================================\n\t return {\n\t DatasetCollectionElementView: DatasetCollectionElementView,\n\t ListCollectionCreator: ListCollectionCreator,\n\t\n\t collectionCreatorModal: collectionCreatorModal,\n\t listCollectionCreatorModal: listCollectionCreatorModal,\n\t createListCollection: createListCollection\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2), __webpack_require__(1), __webpack_require__(1)))\n\n/***/ }),\n/* 38 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_, jQuery, Backbone, $) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(47), __webpack_require__(11), __webpack_require__(17), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (LIST_ITEM, STATES, faIconButton, BASE_MVC, _l) {\n\t 'use strict';\n\t\n\t var logNamespace = 'dataset';\n\t /*==============================================================================\n\t TODO:\n\t straighten out state rendering and templates used\n\t inaccessible/STATES.NOT_VIEWABLE is a special case\n\t simplify button rendering\n\t \n\t ==============================================================================*/\n\t var _super = LIST_ITEM.ListItemView;\n\t /** @class Read only list view for either LDDAs, HDAs, or HDADCEs.\n\t * Roughly, any DatasetInstance (and not a raw Dataset).\n\t */\n\t var DatasetListItemView = _super.extend(\n\t /** @lends DatasetListItemView.prototype */{\n\t _logNamespace: logNamespace,\n\t\n\t className: _super.prototype.className + \" dataset\",\n\t //TODO:?? doesn't exactly match an hda's type_id\n\t id: function () {\n\t return ['dataset', this.model.get('id')].join('-');\n\t },\n\t\n\t /** Set up: instance vars, options, and event handlers */\n\t initialize: function (attributes) {\n\t if (attributes.logger) {\n\t this.logger = this.model.logger = attributes.logger;\n\t }\n\t this.log(this + '.initialize:', attributes);\n\t _super.prototype.initialize.call(this, attributes);\n\t\n\t /** where should pages from links be displayed? (default to new tab/window) */\n\t this.linkTarget = attributes.linkTarget || '_blank';\n\t },\n\t\n\t /** event listeners */\n\t _setUpListeners: function () {\n\t _super.prototype._setUpListeners.call(this);\n\t var self = this;\n\t\n\t // re-rendering on any model changes\n\t return self.listenTo(self.model, {\n\t 'change': function (model) {\n\t // if the model moved into the ready state and is expanded without details, fetch those details now\n\t if (self.model.changedAttributes().state && self.model.inReadyState() && self.expanded && !self.model.hasDetails()) {\n\t // normally, will render automatically (due to fetch -> change),\n\t // but! setting_metadata sometimes doesn't cause any other changes besides state\n\t // so, not rendering causes it to seem frozen in setting_metadata state\n\t self.model.fetch({ silent: true }).done(function () {\n\t self.render();\n\t });\n\t } else {\n\t if (_.has(model.changed, 'tags') && _.keys(model.changed).length === 1) {\n\t // If only the tags have changed, rerender specifically\n\t // the titlebar region. Otherwise default to the full\n\t // render.\n\t self.$('.nametags').html(self._renderNametags());\n\t } else {\n\t self.render();\n\t }\n\t }\n\t }\n\t });\n\t },\n\t\n\t // ......................................................................... expandable\n\t /** In this override, only get details if in the ready state, get rerunnable if in other states.\n\t * Note: fetch with no 'change' event triggering to prevent automatic rendering.\n\t */\n\t _fetchModelDetails: function () {\n\t var view = this;\n\t if (view.model.inReadyState() && !view.model.hasDetails()) {\n\t return view.model.fetch({ silent: true });\n\t }\n\t return jQuery.when();\n\t },\n\t\n\t // ......................................................................... removal\n\t /** Remove this view's html from the DOM and remove all event listeners.\n\t * @param {Number or String} speed jq effect speed\n\t * @param {Function} callback an optional function called when removal is done (scoped to this view)\n\t */\n\t remove: function (speed, callback) {\n\t var view = this;\n\t speed = speed || this.fxSpeed;\n\t this.$el.fadeOut(speed, function () {\n\t Backbone.View.prototype.remove.call(view);\n\t if (callback) {\n\t callback.call(view);\n\t }\n\t });\n\t },\n\t\n\t // ......................................................................... rendering\n\t /* TODO:\n\t dataset states are the issue primarily making dataset rendering complex\n\t each state should have it's own way of displaying/set of details\n\t often with different actions that can be applied\n\t throw in deleted/purged/visible and things get complicated easily\n\t I've considered (a couple of times) - creating a view for each state\n\t - but recreating the view during an update...seems wrong\n\t */\n\t /** In this override, add the dataset state as a class for use with state-based CSS */\n\t _swapNewRender: function ($newRender) {\n\t _super.prototype._swapNewRender.call(this, $newRender);\n\t if (this.model.has('state')) {\n\t this.$el.addClass('state-' + this.model.get('state'));\n\t }\n\t return this.$el;\n\t },\n\t\n\t // ................................................................................ titlebar\n\t /** In this override, add the dataset display button. */\n\t _renderPrimaryActions: function () {\n\t // render just the display for read-only\n\t return [this._renderDisplayButton()];\n\t },\n\t\n\t /** Render icon-button to display dataset data */\n\t _renderDisplayButton: function () {\n\t // don't show display if not viewable or not accessible\n\t var state = this.model.get('state');\n\t if (state === STATES.NOT_VIEWABLE || state === STATES.DISCARDED || !this.model.get('accessible')) {\n\t return null;\n\t }\n\t\n\t var displayBtnData = {\n\t target: this.linkTarget,\n\t classes: 'display-btn'\n\t };\n\t\n\t // show a disabled display if the data's been purged\n\t if (this.model.get('purged')) {\n\t displayBtnData.disabled = true;\n\t displayBtnData.title = _l('Cannot display datasets removed from disk');\n\t\n\t // disable if still uploading\n\t } else if (state === STATES.UPLOAD) {\n\t displayBtnData.disabled = true;\n\t displayBtnData.title = _l('This dataset must finish uploading before it can be viewed');\n\t\n\t // disable if still new\n\t } else if (state === STATES.NEW) {\n\t displayBtnData.disabled = true;\n\t displayBtnData.title = _l('This dataset is not yet viewable');\n\t } else {\n\t displayBtnData.title = _l('View data');\n\t\n\t // default link for dataset\n\t displayBtnData.href = this.model.urls.display;\n\t\n\t // add frame manager option onclick event\n\t var self = this;\n\t displayBtnData.onclick = function (ev) {\n\t if (Galaxy.frame && Galaxy.frame.active) {\n\t // Add dataset to frames.\n\t Galaxy.frame.addDataset(self.model.get('id'));\n\t ev.preventDefault();\n\t }\n\t };\n\t }\n\t displayBtnData.faIcon = 'fa-eye';\n\t return faIconButton(displayBtnData);\n\t },\n\t\n\t // ......................................................................... rendering details\n\t /** Render the enclosing div of the hda body and, if expanded, the html in the body\n\t * @returns {jQuery} rendered DOM\n\t */\n\t _renderDetails: function () {\n\t //TODO: generalize to be allow different details for each state\n\t\n\t // no access - render nothing but a message\n\t if (this.model.get('state') === STATES.NOT_VIEWABLE) {\n\t return $(this.templates.noAccess(this.model.toJSON(), this));\n\t }\n\t\n\t var $details = _super.prototype._renderDetails.call(this);\n\t $details.find('.actions .left').empty().append(this._renderSecondaryActions());\n\t $details.find('.summary').html(this._renderSummary()).prepend(this._renderDetailMessages());\n\t $details.find('.display-applications').html(this._renderDisplayApplications());\n\t\n\t this._setUpBehaviors($details);\n\t return $details;\n\t },\n\t\n\t /** Defer to the appropo summary rendering fn based on state */\n\t _renderSummary: function () {\n\t var json = this.model.toJSON(),\n\t summaryRenderFn = this.templates.summaries[json.state];\n\t summaryRenderFn = summaryRenderFn || this.templates.summaries.unknown;\n\t return summaryRenderFn(json, this);\n\t },\n\t\n\t /** Render messages to be displayed only when the details are shown */\n\t _renderDetailMessages: function () {\n\t var view = this,\n\t $warnings = $(''),\n\t json = view.model.toJSON();\n\t //TODO:! unordered (map)\n\t _.each(view.templates.detailMessages, function (templateFn) {\n\t $warnings.append($(templateFn(json, view)));\n\t });\n\t return $warnings;\n\t },\n\t\n\t /** Render the external display application links */\n\t _renderDisplayApplications: function () {\n\t if (this.model.isDeletedOrPurged()) {\n\t return '';\n\t }\n\t // render both old and new display apps using the same template\n\t return [this.templates.displayApplications(this.model.get('display_apps'), this), this.templates.displayApplications(this.model.get('display_types'), this)].join('');\n\t },\n\t\n\t // ......................................................................... secondary/details actions\n\t /** A series of links/buttons for less commonly used actions: re-run, info, etc. */\n\t _renderSecondaryActions: function () {\n\t this.debug('_renderSecondaryActions');\n\t switch (this.model.get('state')) {\n\t case STATES.NOT_VIEWABLE:\n\t return [];\n\t case STATES.OK:\n\t case STATES.FAILED_METADATA:\n\t case STATES.ERROR:\n\t return [this._renderDownloadButton(), this._renderShowParamsButton()];\n\t }\n\t return [this._renderShowParamsButton()];\n\t },\n\t\n\t /** Render icon-button to show the input and output (stdout/err) for the job that created this.\n\t * @returns {jQuery} rendered DOM\n\t */\n\t _renderShowParamsButton: function () {\n\t // gen. safe to show in all cases\n\t return faIconButton({\n\t title: _l('View details'),\n\t classes: 'params-btn',\n\t href: this.model.urls.show_params,\n\t target: this.linkTarget,\n\t faIcon: 'fa-info-circle',\n\t onclick: function (ev) {\n\t if (Galaxy.frame && Galaxy.frame.active) {\n\t Galaxy.frame.add({ title: 'Dataset details', url: this.href });\n\t ev.preventDefault();\n\t ev.stopPropagation();\n\t }\n\t }\n\t });\n\t },\n\t\n\t /** Render icon-button/popupmenu to download the data (and/or the associated meta files (bai, etc.)) for this.\n\t * @returns {jQuery} rendered DOM\n\t */\n\t _renderDownloadButton: function () {\n\t // don't show anything if the data's been purged\n\t if (this.model.get('purged') || !this.model.hasData()) {\n\t return null;\n\t }\n\t\n\t // return either: a popupmenu with links to download assoc. meta files (if there are meta files)\n\t // or a single download icon-button (if there are no meta files)\n\t if (!_.isEmpty(this.model.get('meta_files'))) {\n\t return this._renderMetaFileDownloadButton();\n\t }\n\t\n\t return $(['', '', ''].join(''));\n\t },\n\t\n\t /** Render the download button which opens a dropdown with links to download assoc. meta files (indeces, etc.) */\n\t _renderMetaFileDownloadButton: function () {\n\t var urls = this.model.urls;\n\t return $(['
'], 'dataset');\n\t\n\t // messages to be displayed only within the details section ('below the fold')\n\t var detailMessageTemplates = {\n\t resubmitted: BASE_MVC.wrapTemplate([\n\t // deleted not purged\n\t '<% if( model.resubmitted ){ %>', '
', _l('The job creating this dataset has been resubmitted'), '
', '<% } %>'])\n\t };\n\t\n\t // this is applied to both old and new style display apps\n\t var displayApplicationsTemplate = BASE_MVC.wrapTemplate(['<% _.each( apps, function( app ){ %>', '
', '<% }); %>'], 'apps');\n\t\n\t return _.extend({}, _super.prototype.templates, {\n\t warnings: warnings,\n\t details: detailsTemplate,\n\t noAccess: noAccessTemplate,\n\t summaries: summaryTemplates,\n\t detailMessages: detailMessageTemplates,\n\t displayApplications: displayApplicationsTemplate\n\t });\n\t }();\n\t\n\t // ============================================================================\n\t return {\n\t DatasetListItemView: DatasetListItemView\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3), __webpack_require__(1)))\n\n/***/ }),\n/* 39 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/* This class maps the form dom to an api compatible javascript dictionary. */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t var Manager = Backbone.Model.extend({\n\t initialize: function (app) {\n\t this.app = app;\n\t },\n\t\n\t /** Creates a checksum. */\n\t checksum: function () {\n\t var sum = '';\n\t var self = this;\n\t this.app.section.$el.find('.section-row').each(function () {\n\t var id = $(this).attr('id');\n\t var field = self.app.field_list[id];\n\t if (field) {\n\t sum += id + ':' + JSON.stringify(field.value && field.value()) + ':' + field.collapsed + ';';\n\t }\n\t });\n\t return sum;\n\t },\n\t\n\t /** Convert dom into a dictionary of flat id/value pairs used e.g. on job submission. */\n\t create: function () {\n\t var self = this;\n\t\n\t // get raw dictionary from dom\n\t var dict = {};\n\t this._iterate(this.app.section.$el, dict);\n\t\n\t // add to result dictionary, label elements\n\t var result_dict = {};\n\t this.flat_dict = {};\n\t function add(flat_id, input_id, input_value) {\n\t self.flat_dict[flat_id] = input_id;\n\t result_dict[flat_id] = input_value;\n\t self.app.element_list[input_id] && self.app.element_list[input_id].$el.attr('tour_id', flat_id);\n\t }\n\t // converter between raw dictionary and job dictionary\n\t function convert(identifier, head) {\n\t for (var index in head) {\n\t var node = head[index];\n\t if (node.input) {\n\t var input = node.input;\n\t var flat_id = identifier;\n\t if (identifier != '') {\n\t flat_id += '|';\n\t }\n\t flat_id += input.name;\n\t switch (input.type) {\n\t case 'repeat':\n\t var section_label = 'section-';\n\t var block_indices = [];\n\t var block_prefix = null;\n\t for (var block_label in node) {\n\t var pos = block_label.indexOf(section_label);\n\t if (pos != -1) {\n\t pos += section_label.length;\n\t block_indices.push(parseInt(block_label.substr(pos)));\n\t if (!block_prefix) {\n\t block_prefix = block_label.substr(0, pos);\n\t }\n\t }\n\t }\n\t block_indices.sort(function (a, b) {\n\t return a - b;\n\t });\n\t var index = 0;\n\t for (var i in block_indices) {\n\t convert(flat_id + '_' + index++, node[block_prefix + block_indices[i]]);\n\t }\n\t break;\n\t case 'conditional':\n\t var value = self.app.field_list[input.id].value();\n\t add(flat_id + '|' + input.test_param.name, input.id, value);\n\t var selectedCase = matchCase(input, value);\n\t if (selectedCase != -1) {\n\t convert(flat_id, head[input.id + '-section-' + selectedCase]);\n\t }\n\t break;\n\t case 'section':\n\t convert(!input.flat && flat_id || '', node);\n\t break;\n\t default:\n\t var field = self.app.field_list[input.id];\n\t if (field && field.value) {\n\t var value = field.value();\n\t if (input.ignore === undefined || input.ignore != value) {\n\t if (field.collapsed && input.collapsible_value) {\n\t value = input.collapsible_value;\n\t }\n\t add(flat_id, input.id, value);\n\t if (input.payload) {\n\t for (var p_id in input.payload) {\n\t add(p_id, input.id, input.payload[p_id]);\n\t }\n\t }\n\t }\n\t }\n\t }\n\t }\n\t }\n\t }\n\t convert('', dict);\n\t return result_dict;\n\t },\n\t\n\t /** Matches flat ids to corresponding input element\n\t * @param{string} flat_id - Flat input id to be looked up.\n\t */\n\t match: function (flat_id) {\n\t return this.flat_dict && this.flat_dict[flat_id];\n\t },\n\t\n\t /** Match conditional values to selected cases\n\t */\n\t matchCase: function (input, value) {\n\t return matchCase(input, value);\n\t },\n\t\n\t /** Matches a new tool model to the current input elements e.g. used to update dynamic options\n\t */\n\t matchModel: function (model, callback) {\n\t var self = this;\n\t visitInputs(model.inputs, function (input, name) {\n\t self.flat_dict[name] && callback(input, self.flat_dict[name]);\n\t });\n\t },\n\t\n\t /** Matches identifier from api response to input elements e.g. used to display validation errors\n\t */\n\t matchResponse: function (response) {\n\t var result = {};\n\t var self = this;\n\t function search(id, head) {\n\t if (typeof head === 'string') {\n\t var input_id = self.flat_dict[id];\n\t input_id && (result[input_id] = head);\n\t } else {\n\t for (var i in head) {\n\t var new_id = i;\n\t if (id !== '') {\n\t var separator = '|';\n\t if (head instanceof Array) {\n\t separator = '_';\n\t }\n\t new_id = id + separator + new_id;\n\t }\n\t search(new_id, head[i]);\n\t }\n\t }\n\t }\n\t search('', response);\n\t return result;\n\t },\n\t\n\t /** Map dom tree to dictionary tree with input elements.\n\t */\n\t _iterate: function (parent, dict) {\n\t var self = this;\n\t var children = $(parent).children();\n\t children.each(function () {\n\t var child = this;\n\t var id = $(child).attr('id');\n\t if ($(child).hasClass('section-row')) {\n\t var input = self.app.input_list[id];\n\t dict[id] = input && { input: input } || {};\n\t self._iterate(child, dict[id]);\n\t } else {\n\t self._iterate(child, dict);\n\t }\n\t });\n\t }\n\t });\n\t\n\t /** Match conditional values to selected cases\n\t * @param{dict} input - Definition of conditional input parameter\n\t * @param{dict} value - Current value\n\t */\n\t var matchCase = function (input, value) {\n\t if (input.test_param.type == 'boolean') {\n\t if (value == 'true') {\n\t value = input.test_param.truevalue || 'true';\n\t } else {\n\t value = input.test_param.falsevalue || 'false';\n\t }\n\t }\n\t for (var i in input.cases) {\n\t if (input.cases[i].value == value) {\n\t return i;\n\t }\n\t }\n\t return -1;\n\t };\n\t\n\t /** Visits tool inputs\n\t * @param{dict} inputs - Nested dictionary of input elements\n\t * @param{dict} callback - Called with the mapped dictionary object and corresponding model node\n\t */\n\t var visitInputs = function (inputs, callback, prefix, context) {\n\t context = $.extend(true, {}, context);\n\t _.each(inputs, function (input) {\n\t if (input && input.type && input.name) {\n\t context[input.name] = input;\n\t }\n\t });\n\t for (var key in inputs) {\n\t var node = inputs[key];\n\t node.name = node.name || key;\n\t var name = prefix ? prefix + '|' + node.name : node.name;\n\t switch (node.type) {\n\t case 'repeat':\n\t _.each(node.cache, function (cache, j) {\n\t visitInputs(cache, callback, name + '_' + j, context);\n\t });\n\t break;\n\t case 'conditional':\n\t if (node.test_param) {\n\t callback(node.test_param, name + '|' + node.test_param.name, context);\n\t var selectedCase = matchCase(node, node.test_param.value);\n\t if (selectedCase != -1) {\n\t visitInputs(node.cases[selectedCase].inputs, callback, name, context);\n\t } else {\n\t Galaxy.emit.debug('form-data::visitInputs() - Invalid case for ' + name + '.');\n\t }\n\t } else {\n\t Galaxy.emit.debug('form-data::visitInputs() - Conditional test parameter missing for ' + name + '.');\n\t }\n\t break;\n\t case 'section':\n\t visitInputs(node.inputs, callback, name, context);\n\t break;\n\t default:\n\t callback(node, name, context);\n\t }\n\t }\n\t };\n\t\n\t return {\n\t Manager: Manager,\n\t visitInputs: visitInputs\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1), __webpack_require__(2)))\n\n/***/ }),\n/* 40 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/**\n\t This class creates a form input element wrapper\n\t*/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t return Backbone.View.extend({\n\t initialize: function (app, options) {\n\t this.app = app;\n\t this.app_options = app.model ? app.model.attributes : {};\n\t this.field = options && options.field || new Backbone.View();\n\t this.model = options && options.model || new Backbone.Model({\n\t text_enable: this.app_options.text_enable || 'Enable',\n\t text_disable: this.app_options.text_disable || 'Disable',\n\t cls_enable: this.app_options.cls_enable || 'fa fa-caret-square-o-down',\n\t cls_disable: this.app_options.cls_disable || 'fa fa-caret-square-o-up'\n\t }).set(options);\n\t\n\t // set element and link components\n\t this.setElement(this._template());\n\t this.$field = this.$('.ui-form-field');\n\t this.$info = this.$('.ui-form-info');\n\t this.$preview = this.$('.ui-form-preview');\n\t this.$collapsible = this.$('.ui-form-collapsible');\n\t this.$collapsible_text = this.$('.ui-form-collapsible-text');\n\t this.$collapsible_icon = this.$('.ui-form-collapsible-icon');\n\t this.$title = this.$('.ui-form-title');\n\t this.$title_text = this.$('.ui-form-title-text');\n\t this.$error_text = this.$('.ui-form-error-text');\n\t this.$error = this.$('.ui-form-error');\n\t this.$backdrop = this.$('.ui-form-backdrop');\n\t\n\t // add field element\n\t this.$field.prepend(this.field.$el);\n\t\n\t // decide wether to expand or collapse fields\n\t var collapsible_value = this.model.get('collapsible_value');\n\t this.field.collapsed = collapsible_value !== undefined && JSON.stringify(this.model.get('value')) == JSON.stringify(collapsible_value);\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t\n\t // add click handler\n\t var self = this;\n\t this.$collapsible.on('click', function () {\n\t self.field.collapsed = !self.field.collapsed;\n\t app.trigger && app.trigger('change');\n\t self.render();\n\t });\n\t },\n\t\n\t /** Set backdrop for input element */\n\t backdrop: function () {\n\t this.model.set('backdrop', true);\n\t },\n\t\n\t /** Set error text */\n\t error: function (text) {\n\t this.model.set('error_text', text);\n\t },\n\t\n\t /** Reset this view */\n\t reset: function () {\n\t !this.model.get('fixed') && this.model.set('error_text', null);\n\t },\n\t\n\t render: function () {\n\t // render help\n\t $('.tooltip').hide();\n\t var help_text = this.model.get('help', '');\n\t var help_argument = this.model.get('argument');\n\t if (help_argument && help_text.indexOf('(' + help_argument + ')') == -1) {\n\t help_text += ' (' + help_argument + ')';\n\t }\n\t this.$info.html(help_text);\n\t // render visibility\n\t this.$el[this.model.get('hidden') ? 'hide' : 'show']();\n\t // render preview view for collapsed fields\n\t this.$preview[this.field.collapsed && this.model.get('collapsible_preview') || this.model.get('disabled') ? 'show' : 'hide']().html(_.escape(this.model.get('text_value')));\n\t // render error messages\n\t var error_text = this.model.get('error_text');\n\t this.$error[error_text ? 'show' : 'hide']();\n\t this.$el[error_text ? 'addClass' : 'removeClass']('ui-error');\n\t this.$error_text.html(error_text);\n\t // render backdrop\n\t this.$backdrop[this.model.get('backdrop') ? 'show' : 'hide']();\n\t // render input field\n\t this.field.collapsed || this.model.get('disabled') ? this.$field.hide() : this.$field.show();\n\t // render input field color and style\n\t this.field.model && this.field.model.set({ 'color': this.model.get('color'), 'style': this.model.get('style') });\n\t // render collapsible options\n\t if (!this.model.get('disabled') && this.model.get('collapsible_value') !== undefined) {\n\t var collapsible_state = this.field.collapsed ? 'enable' : 'disable';\n\t this.$title_text.hide();\n\t this.$collapsible.show();\n\t this.$collapsible_text.text(this.model.get('label'));\n\t this.$collapsible_icon.removeClass().addClass('icon').addClass(this.model.get('cls_' + collapsible_state)).attr('data-original-title', this.model.get('text_' + collapsible_state)).tooltip({ placement: 'bottom' });\n\t } else {\n\t this.$title_text.show().text(this.model.get('label'));\n\t this.$collapsible.hide();\n\t }\n\t },\n\t\n\t _template: function () {\n\t return $('').addClass('ui-form-element').append($('').addClass('ui-form-error ui-error').append($('').addClass('fa fa-arrow-down')).append($('').addClass('ui-form-error-text'))).append($('').addClass('ui-form-title').append($('').addClass('ui-form-collapsible').append($('').addClass('ui-form-collapsible-icon')).append($('').addClass('ui-form-collapsible-text'))).append($('').addClass('ui-form-title-text'))).append($('').addClass('ui-form-field').append($('').addClass('ui-form-info')).append($('').addClass('ui-form-backdrop'))).append($('').addClass('ui-form-preview'));\n\t }\n\t });\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1), __webpack_require__(2)))\n\n/***/ }),\n/* 41 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, $) {/**\n\t This class creates input elements. New input parameter types should be added to the types dictionary.\n\t*/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(7), __webpack_require__(53), __webpack_require__(55), __webpack_require__(54), __webpack_require__(51)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Ui, SelectContent, SelectLibrary, SelectFtp, ColorPicker) {\n\t\n\t // create form view\n\t return Backbone.Model.extend({\n\t /** Available parameter types */\n\t types: {\n\t 'text': '_fieldText',\n\t 'password': '_fieldText',\n\t 'select': '_fieldSelect',\n\t 'data_column': '_fieldSelect',\n\t 'genomebuild': '_fieldSelect',\n\t 'data': '_fieldData',\n\t 'data_collection': '_fieldData',\n\t 'integer': '_fieldSlider',\n\t 'float': '_fieldSlider',\n\t 'boolean': '_fieldBoolean',\n\t 'drill_down': '_fieldDrilldown',\n\t 'color': '_fieldColor',\n\t 'hidden': '_fieldHidden',\n\t 'hidden_data': '_fieldHidden',\n\t 'baseurl': '_fieldHidden',\n\t 'library_data': '_fieldLibrary',\n\t 'ftpfile': '_fieldFtp',\n\t 'upload': '_fieldUpload'\n\t },\n\t\n\t /** Returns an input field for a given field type */\n\t create: function (input_def) {\n\t var fieldClass = this.types[input_def.type];\n\t var field = typeof this[fieldClass] === 'function' ? this[fieldClass].call(this, input_def) : null;\n\t if (!field) {\n\t field = input_def.options ? this._fieldSelect(input_def) : this._fieldText(input_def);\n\t Galaxy.emit.debug('form-parameters::_addRow()', 'Auto matched field type (' + input_def.type + ').');\n\t }\n\t input_def.value === undefined && (input_def.value = null);\n\t field.value(input_def.value);\n\t return field;\n\t },\n\t\n\t /** Data input field */\n\t _fieldData: function (input_def) {\n\t return new SelectContent.View({\n\t id: 'field-' + input_def.id,\n\t extensions: input_def.extensions,\n\t optional: input_def.optional,\n\t multiple: input_def.multiple,\n\t type: input_def.type,\n\t flavor: input_def.flavor,\n\t data: input_def.options,\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** Select/Checkbox/Radio options field */\n\t _fieldSelect: function (input_def) {\n\t // show text field e.g. in workflow editor\n\t if (input_def.is_workflow) {\n\t return this._fieldText(input_def);\n\t }\n\t\n\t // customize properties\n\t if (input_def.type == 'data_column') {\n\t input_def.error_text = 'Missing columns in referenced dataset.';\n\t }\n\t\n\t // identify available options\n\t var data = input_def.data;\n\t if (!data) {\n\t data = [];\n\t _.each(input_def.options, function (option) {\n\t data.push({ label: option[0], value: option[1] });\n\t });\n\t }\n\t\n\t // identify display type\n\t var SelectClass = Ui.Select;\n\t switch (input_def.display) {\n\t case 'checkboxes':\n\t SelectClass = Ui.Checkbox;\n\t break;\n\t case 'radio':\n\t SelectClass = Ui.Radio;\n\t break;\n\t case 'radiobutton':\n\t SelectClass = Ui.RadioButton;\n\t break;\n\t }\n\t\n\t // create select field\n\t return new SelectClass.View({\n\t id: 'field-' + input_def.id,\n\t data: data,\n\t error_text: input_def.error_text || 'No options available',\n\t multiple: input_def.multiple,\n\t optional: input_def.optional,\n\t onchange: input_def.onchange,\n\t searchable: input_def.flavor !== 'workflow'\n\t });\n\t },\n\t\n\t /** Drill down options field */\n\t _fieldDrilldown: function (input_def) {\n\t // show text field e.g. in workflow editor\n\t if (input_def.is_workflow) {\n\t return this._fieldText(input_def);\n\t }\n\t\n\t // create drill down field\n\t return new Ui.Drilldown.View({\n\t id: 'field-' + input_def.id,\n\t data: input_def.options,\n\t display: input_def.display,\n\t optional: input_def.optional,\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** Text input field */\n\t _fieldText: function (input_def) {\n\t // field replaces e.g. a select field\n\t if (input_def.options && input_def.data) {\n\t input_def.area = input_def.multiple;\n\t if (Utils.isEmpty(input_def.value)) {\n\t input_def.value = null;\n\t } else {\n\t if ($.isArray(input_def.value)) {\n\t var str_value = '';\n\t for (var i in input_def.value) {\n\t str_value += String(input_def.value[i]);\n\t if (!input_def.multiple) {\n\t break;\n\t }\n\t str_value += '\\n';\n\t }\n\t input_def.value = str_value;\n\t }\n\t }\n\t }\n\t // create input element\n\t return new Ui.Input({\n\t id: 'field-' + input_def.id,\n\t type: input_def.type,\n\t area: input_def.area,\n\t readonly: input_def.readonly,\n\t placeholder: input_def.placeholder,\n\t datalist: input_def.datalist,\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** Slider field */\n\t _fieldSlider: function (input_def) {\n\t return new Ui.Slider.View({\n\t id: 'field-' + input_def.id,\n\t precise: input_def.type == 'float',\n\t is_workflow: input_def.is_workflow,\n\t min: input_def.min,\n\t max: input_def.max,\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** Hidden field */\n\t _fieldHidden: function (input_def) {\n\t return new Ui.Hidden({\n\t id: 'field-' + input_def.id,\n\t info: input_def.info\n\t });\n\t },\n\t\n\t /** Boolean field */\n\t _fieldBoolean: function (input_def) {\n\t return new Ui.RadioButton.View({\n\t id: 'field-' + input_def.id,\n\t data: [{ label: 'Yes', value: 'true' }, { label: 'No', value: 'false' }],\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** Color picker field */\n\t _fieldColor: function (input_def) {\n\t return new ColorPicker({\n\t id: 'field-' + input_def.id,\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** Library dataset field */\n\t _fieldLibrary: function (input_def) {\n\t return new SelectLibrary.View({\n\t id: 'field-' + input_def.id,\n\t optional: input_def.optional,\n\t multiple: input_def.multiple,\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** FTP file field */\n\t _fieldFtp: function (input_def) {\n\t return new SelectFtp.View({\n\t id: 'field-' + input_def.id,\n\t optional: input_def.optional,\n\t multiple: input_def.multiple,\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** Upload file field */\n\t _fieldUpload: function (input_def) {\n\t return new Ui.Upload({\n\t id: 'field-' + input_def.id,\n\t onchange: input_def.onchange\n\t });\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ }),\n/* 42 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/** This class creates a ui component which enables the dynamic creation of portlets */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(9), __webpack_require__(7)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Portlet, Ui) {\n\t var View = Backbone.View.extend({\n\t initialize: function (options) {\n\t this.list = {};\n\t this.options = Utils.merge(options, {\n\t title: 'Repeat',\n\t empty_text: 'Not available.',\n\t max: null,\n\t min: null\n\t });\n\t this.button_new = new Ui.ButtonIcon({\n\t icon: 'fa-plus',\n\t title: 'Insert ' + this.options.title,\n\t tooltip: 'Add new ' + this.options.title + ' block',\n\t floating: 'clear',\n\t cls: 'ui-button-icon form-repeat-add',\n\t onclick: function () {\n\t options.onnew && options.onnew();\n\t }\n\t });\n\t this.setElement($('').append(this.$list = $('')).append($('').append(this.button_new.$el)));\n\t },\n\t\n\t /** Number of repeat blocks */\n\t size: function () {\n\t return _.size(this.list);\n\t },\n\t\n\t /** Add new repeat block */\n\t add: function (options) {\n\t if (!options.id || this.list[options.id]) {\n\t Galaxy.emit.debug('form-repeat::add()', 'Duplicate or invalid repeat block id.');\n\t return;\n\t }\n\t var button_delete = new Ui.ButtonIcon({\n\t icon: 'fa-trash-o',\n\t tooltip: 'Delete this repeat block',\n\t cls: 'ui-button-icon-plain form-repeat-delete',\n\t onclick: function () {\n\t options.ondel && options.ondel();\n\t }\n\t });\n\t var portlet = new Portlet.View({\n\t id: options.id,\n\t title: 'placeholder',\n\t cls: options.cls || 'ui-portlet-repeat',\n\t operations: { button_delete: button_delete }\n\t });\n\t portlet.append(options.$el);\n\t portlet.$el.addClass('section-row').hide();\n\t this.list[options.id] = portlet;\n\t this.$list.append(portlet.$el.fadeIn('fast'));\n\t this.options.max > 0 && this.size() >= this.options.max && this.button_new.disable();\n\t this._refresh();\n\t },\n\t\n\t /** Delete repeat block */\n\t del: function (id) {\n\t if (!this.list[id]) {\n\t Galaxy.emit.debug('form-repeat::del()', 'Invalid repeat block id.');\n\t return;\n\t }\n\t this.$list.find('#' + id).remove();\n\t delete this.list[id];\n\t this.button_new.enable();\n\t this._refresh();\n\t },\n\t\n\t /** Remove all */\n\t delAll: function () {\n\t for (var id in this.list) {\n\t this.del(id);\n\t }\n\t },\n\t\n\t /** Hides add/del options */\n\t hideOptions: function () {\n\t this.button_new.$el.hide();\n\t _.each(this.list, function (portlet) {\n\t portlet.hideOperation('button_delete');\n\t });\n\t _.isEmpty(this.list) && this.$el.append($('').addClass('ui-form-info').html(this.options.empty_text));\n\t },\n\t\n\t /** Refresh view */\n\t _refresh: function () {\n\t var index = 0;\n\t for (var id in this.list) {\n\t var portlet = this.list[id];\n\t portlet.title(++index + ': ' + this.options.title);\n\t portlet[this.size() > this.options.min ? 'showOperation' : 'hideOperation']('button_delete');\n\t }\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1), __webpack_require__(2)))\n\n/***/ }),\n/* 43 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _, jQuery) {/**\n\t This class creates a form section and populates it with input elements. It also handles repeat blocks and conditionals by recursively creating new sub sections.\n\t*/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(7), __webpack_require__(9), __webpack_require__(42), __webpack_require__(40), __webpack_require__(41)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Ui, Portlet, Repeat, InputElement, Parameters) {\n\t var View = Backbone.View.extend({\n\t initialize: function (app, options) {\n\t this.app = app;\n\t this.inputs = options.inputs;\n\t this.parameters = new Parameters();\n\t this.setElement($(''));\n\t this.render();\n\t },\n\t\n\t /** Render section view */\n\t render: function () {\n\t var self = this;\n\t this.$el.empty();\n\t _.each(this.inputs, function (input) {\n\t self.add(input);\n\t });\n\t },\n\t\n\t /** Add a new input element */\n\t add: function (input) {\n\t var input_def = jQuery.extend(true, {}, input);\n\t input_def.id = input.id = Utils.uid();\n\t this.app.input_list[input_def.id] = input_def;\n\t switch (input_def.type) {\n\t case 'conditional':\n\t this._addConditional(input_def);\n\t break;\n\t case 'repeat':\n\t this._addRepeat(input_def);\n\t break;\n\t case 'section':\n\t this._addSection(input_def);\n\t break;\n\t default:\n\t this._addRow(input_def);\n\t }\n\t },\n\t\n\t /** Add a conditional block */\n\t _addConditional: function (input_def) {\n\t var self = this;\n\t input_def.test_param.id = input_def.id;\n\t this.app.model.get('sustain_conditionals') && (input_def.test_param.disabled = true);\n\t var field = this._addRow(input_def.test_param);\n\t\n\t // set onchange event for test parameter\n\t field.model && field.model.set('onchange', function (value) {\n\t var selectedCase = self.app.data.matchCase(input_def, value);\n\t for (var i in input_def.cases) {\n\t var case_def = input_def.cases[i];\n\t var section_row = self.$('#' + input_def.id + '-section-' + i);\n\t var nonhidden = false;\n\t for (var j in case_def.inputs) {\n\t if (!case_def.inputs[j].hidden) {\n\t nonhidden = true;\n\t break;\n\t }\n\t }\n\t if (i == selectedCase && nonhidden) {\n\t section_row.fadeIn('fast');\n\t } else {\n\t section_row.hide();\n\t }\n\t }\n\t self.app.trigger('change');\n\t });\n\t\n\t // add conditional sub sections\n\t for (var i in input_def.cases) {\n\t var sub_section = new View(this.app, { inputs: input_def.cases[i].inputs });\n\t this._append(sub_section.$el.addClass('ui-form-section'), input_def.id + '-section-' + i);\n\t }\n\t\n\t // trigger refresh on conditional input field after all input elements have been created\n\t field.trigger('change');\n\t },\n\t\n\t /** Add a repeat block */\n\t _addRepeat: function (input_def) {\n\t var self = this;\n\t var block_index = 0;\n\t\n\t // create repeat block element\n\t var repeat = new Repeat.View({\n\t title: input_def.title || 'Repeat',\n\t min: input_def.min,\n\t max: input_def.max,\n\t onnew: function () {\n\t create(input_def.inputs);self.app.trigger('change');\n\t }\n\t });\n\t\n\t // helper function to create new repeat blocks\n\t function create(inputs) {\n\t var sub_section_id = input_def.id + '-section-' + block_index++;\n\t var sub_section = new View(self.app, { inputs: inputs });\n\t repeat.add({ id: sub_section_id,\n\t $el: sub_section.$el,\n\t ondel: function () {\n\t repeat.del(sub_section_id);self.app.trigger('change');\n\t } });\n\t }\n\t\n\t //\n\t // add parsed/minimum number of repeat blocks\n\t //\n\t var n_cache = _.size(input_def.cache);\n\t for (var i = 0; i < Math.max(Math.max(n_cache, input_def.min || 0), input_def.default || 0); i++) {\n\t create(i < n_cache ? input_def.cache[i] : input_def.inputs);\n\t }\n\t\n\t // hide options\n\t this.app.model.get('sustain_repeats') && repeat.hideOptions();\n\t\n\t // create input field wrapper\n\t var input_element = new InputElement(this.app, {\n\t label: input_def.title || input_def.name,\n\t help: input_def.help,\n\t field: repeat\n\t });\n\t this._append(input_element.$el, input_def.id);\n\t },\n\t\n\t /** Add a customized section */\n\t _addSection: function (input_def) {\n\t var portlet = new Portlet.View({\n\t title: input_def.title || input_def.name,\n\t cls: 'ui-portlet-section',\n\t collapsible: true,\n\t collapsible_button: true,\n\t collapsed: !input_def.expanded\n\t });\n\t portlet.append(new View(this.app, { inputs: input_def.inputs }).$el);\n\t portlet.append($('').addClass('ui-form-info').html(input_def.help));\n\t this.app.on('expand', function (input_id) {\n\t portlet.$('#' + input_id).length > 0 && portlet.expand();\n\t });\n\t this._append(portlet.$el, input_def.id);\n\t },\n\t\n\t /** Add a single input field element */\n\t _addRow: function (input_def) {\n\t var self = this;\n\t var id = input_def.id;\n\t input_def.onchange = input_def.onchange || function () {\n\t self.app.trigger('change', id);\n\t };\n\t var field = this.parameters.create(input_def);\n\t this.app.field_list[id] = field;\n\t var input_element = new InputElement(this.app, {\n\t name: input_def.name,\n\t label: input_def.hide_label ? '' : input_def.label || input_def.name,\n\t value: input_def.value,\n\t text_value: input_def.text_value,\n\t collapsible_value: input_def.collapsible_value,\n\t collapsible_preview: input_def.collapsible_preview,\n\t help: input_def.help,\n\t argument: input_def.argument,\n\t disabled: input_def.disabled,\n\t color: input_def.color,\n\t style: input_def.style,\n\t backdrop: input_def.backdrop,\n\t hidden: input_def.hidden,\n\t fixed: input_def.fixed,\n\t field: field\n\t });\n\t this.app.element_list[id] = input_element;\n\t this._append(input_element.$el, input_def.id);\n\t return field;\n\t },\n\t\n\t /** Append a new element to the form i.e. input element, repeat block, conditionals etc. */\n\t _append: function ($el, id) {\n\t this.$el.append($el.addClass('section-row').attr('id', id));\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ }),\n/* 44 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(36), __webpack_require__(79), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (DC_MODEL, HISTORY_CONTENT, _l) {\n\t\n\t 'use strict';\n\t\n\t /*==============================================================================\n\t \n\t Models for DatasetCollections contained within a history.\n\t \n\t TODO:\n\t these might be compactable to one class if some duplication with\n\t collection-model is used.\n\t \n\t ==============================================================================*/\n\t\n\t var hcontentMixin = HISTORY_CONTENT.HistoryContentMixin,\n\t ListDC = DC_MODEL.ListDatasetCollection,\n\t PairDC = DC_MODEL.PairDatasetCollection,\n\t ListPairedDC = DC_MODEL.ListPairedDatasetCollection,\n\t ListOfListsDC = DC_MODEL.ListOfListsDatasetCollection;\n\t\n\t //==============================================================================\n\t /** Override to post to contents route w/o id. */\n\t function buildHDCASave(_super) {\n\t return function _save(attributes, options) {\n\t if (this.isNew()) {\n\t options = options || {};\n\t options.url = this.urlRoot + this.get('history_id') + '/contents';\n\t attributes = attributes || {};\n\t attributes.type = 'dataset_collection';\n\t }\n\t return _super.call(this, attributes, options);\n\t };\n\t }\n\t\n\t //==============================================================================\n\t /** @class Backbone model for List Dataset Collection within a History.\n\t */\n\t var HistoryListDatasetCollection = ListDC.extend(hcontentMixin).extend(\n\t /** @lends HistoryListDatasetCollection.prototype */{\n\t\n\t defaults: _.extend(_.clone(ListDC.prototype.defaults), {\n\t history_content_type: 'dataset_collection',\n\t collection_type: 'list',\n\t model_class: 'HistoryDatasetCollectionAssociation'\n\t }),\n\t\n\t /** Override to post to contents route w/o id. */\n\t save: buildHDCASave(ListDC.prototype.save),\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return 'History' + ListDC.prototype.toString.call(this);\n\t }\n\t });\n\t\n\t //==============================================================================\n\t /** @class Backbone model for Pair Dataset Collection within a History.\n\t * @constructs\n\t */\n\t var HistoryPairDatasetCollection = PairDC.extend(hcontentMixin).extend(\n\t /** @lends HistoryPairDatasetCollection.prototype */{\n\t\n\t defaults: _.extend(_.clone(PairDC.prototype.defaults), {\n\t history_content_type: 'dataset_collection',\n\t collection_type: 'paired',\n\t model_class: 'HistoryDatasetCollectionAssociation'\n\t }),\n\t\n\t /** Override to post to contents route w/o id. */\n\t save: buildHDCASave(PairDC.prototype.save),\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return 'History' + PairDC.prototype.toString.call(this);\n\t }\n\t });\n\t\n\t //==============================================================================\n\t /** @class Backbone model for List of Pairs Dataset Collection within a History. */\n\t var HistoryListPairedDatasetCollection = ListPairedDC.extend(hcontentMixin).extend({\n\t\n\t defaults: _.extend(_.clone(ListPairedDC.prototype.defaults), {\n\t history_content_type: 'dataset_collection',\n\t collection_type: 'list:paired',\n\t model_class: 'HistoryDatasetCollectionAssociation'\n\t }),\n\t\n\t /** Override to post to contents route w/o id. */\n\t save: buildHDCASave(ListPairedDC.prototype.save),\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return 'History' + ListPairedDC.prototype.toString.call(this);\n\t }\n\t });\n\t\n\t //==============================================================================\n\t /** @class Backbone model for List of Lists Dataset Collection within a History. */\n\t var HistoryListOfListsDatasetCollection = ListOfListsDC.extend(hcontentMixin).extend({\n\t\n\t defaults: _.extend(_.clone(ListOfListsDC.prototype.defaults), {\n\t history_content_type: 'dataset_collection',\n\t collection_type: 'list:list',\n\t model_class: 'HistoryDatasetCollectionAssociation'\n\t }),\n\t\n\t /** Override to post to contents route w/o id. */\n\t save: buildHDCASave(ListOfListsDC.prototype.save),\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return ['HistoryListOfListsDatasetCollection(', this.get('name'), ')'].join('');\n\t }\n\t });\n\t\n\t //==============================================================================\n\t return {\n\t HistoryListDatasetCollection: HistoryListDatasetCollection,\n\t HistoryPairDatasetCollection: HistoryPairDatasetCollection,\n\t HistoryListPairedDatasetCollection: HistoryListPairedDatasetCollection,\n\t HistoryListOfListsDatasetCollection: HistoryListOfListsDatasetCollection\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2)))\n\n/***/ }),\n/* 45 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_, jQuery, Backbone) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(71), __webpack_require__(77), __webpack_require__(44), __webpack_require__(46), __webpack_require__(6), __webpack_require__(139)], __WEBPACK_AMD_DEFINE_RESULT__ = function (CONTROLLED_FETCH_COLLECTION, HDA_MODEL, HDCA_MODEL, HISTORY_PREFS, BASE_MVC, AJAX_QUEUE) {\n\t 'use strict';\n\t\n\t //==============================================================================\n\t\n\t var _super = CONTROLLED_FETCH_COLLECTION.PaginatedCollection;\n\t /** @class Backbone collection for history content.\n\t * NOTE: history content seems like a dataset collection, but differs in that it is mixed:\n\t * each element can be either an HDA (dataset) or a DatasetCollection and co-exist on\n\t * the same level.\n\t * Dataset collections on the other hand are not mixed and (so far) can only contain either\n\t * HDAs or child dataset collections on one level.\n\t * This is why this does not inherit from any of the DatasetCollections (currently).\n\t */\n\t var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({\n\t _logNamespace: 'history',\n\t\n\t // ........................................................................ composite collection\n\t /** since history content is a mix, override model fn into a factory, creating based on history_content_type */\n\t model: function (attrs, options) {\n\t if (attrs.history_content_type === \"dataset\") {\n\t return new HDA_MODEL.HistoryDatasetAssociation(attrs, options);\n\t } else if (attrs.history_content_type === \"dataset_collection\") {\n\t switch (attrs.collection_type) {\n\t case 'list':\n\t return new HDCA_MODEL.HistoryListDatasetCollection(attrs, options);\n\t case 'paired':\n\t return new HDCA_MODEL.HistoryPairDatasetCollection(attrs, options);\n\t case 'list:paired':\n\t return new HDCA_MODEL.HistoryListPairedDatasetCollection(attrs, options);\n\t case 'list:list':\n\t return new HDCA_MODEL.HistoryListOfListsDatasetCollection(attrs, options);\n\t }\n\t // This is a hack inside a hack:\n\t // Raise a plain object with validationError to fake a model.validationError\n\t // (since we don't have a model to use validate with)\n\t // (the outer hack being the mixed content/model function in this collection)\n\t var msg = 'Unknown collection_type: ' + attrs.collection_type;\n\t console.warn(msg, attrs);\n\t return { validationError: msg };\n\t }\n\t return { validationError: 'Unknown history_content_type: ' + attrs.history_content_type };\n\t },\n\t\n\t // ........................................................................ set up\n\t limitPerPage: 500,\n\t\n\t /** @type {Integer} how many contents per call to fetch when using progressivelyFetchDetails */\n\t limitPerProgressiveFetch: 500,\n\t\n\t /** @type {String} order used here and when fetching from server */\n\t order: 'hid',\n\t\n\t /** root api url */\n\t urlRoot: Galaxy.root + 'api/histories',\n\t\n\t /** complete api url */\n\t url: function () {\n\t return this.urlRoot + '/' + this.historyId + '/contents';\n\t },\n\t\n\t /** Set up */\n\t initialize: function (models, options) {\n\t options = options || {};\n\t _super.prototype.initialize.call(this, models, options);\n\t\n\t this.history = options.history || null;\n\t this.setHistoryId(options.historyId || null);\n\t /** @type {Boolean} does this collection contain and fetch deleted elements */\n\t this.includeDeleted = options.includeDeleted || this.includeDeleted;\n\t /** @type {Boolean} does this collection contain and fetch non-visible elements */\n\t this.includeHidden = options.includeHidden || this.includeHidden;\n\t\n\t // backbonejs uses collection.model.prototype.idAttribute to determine if a model is *already* in a collection\n\t // and either merged or replaced. In this case, our 'model' is a function so we need to add idAttribute\n\t // manually here - if we don't, contents will not merge but be replaced/swapped.\n\t this.model.prototype.idAttribute = 'type_id';\n\t },\n\t\n\t setHistoryId: function (newId) {\n\t this.historyId = newId;\n\t this._setUpWebStorage();\n\t },\n\t\n\t /** Set up client side storage. Currently PersistanStorage keyed under 'history:' */\n\t _setUpWebStorage: function (initialSettings) {\n\t // TODO: use initialSettings\n\t if (!this.historyId) {\n\t return;\n\t }\n\t this.storage = new HISTORY_PREFS.HistoryPrefs({\n\t id: HISTORY_PREFS.HistoryPrefs.historyStorageKey(this.historyId)\n\t });\n\t this.trigger('new-storage', this.storage, this);\n\t\n\t this.on({\n\t 'include-deleted': function (newVal) {\n\t this.storage.includeDeleted(newVal);\n\t },\n\t 'include-hidden': function (newVal) {\n\t this.storage.includeHidden(newVal);\n\t }\n\t });\n\t\n\t this.includeDeleted = this.storage.includeDeleted() || false;\n\t this.includeHidden = this.storage.includeHidden() || false;\n\t return this;\n\t },\n\t\n\t // ........................................................................ common queries\n\t /** @type {Object} map of collection available sorting orders containing comparator fns */\n\t comparators: _.extend(_.clone(_super.prototype.comparators), {\n\t 'name': BASE_MVC.buildComparator('name', { ascending: true }),\n\t 'name-dsc': BASE_MVC.buildComparator('name', { ascending: false }),\n\t 'hid': BASE_MVC.buildComparator('hid', { ascending: false }),\n\t 'hid-asc': BASE_MVC.buildComparator('hid', { ascending: true })\n\t }),\n\t\n\t /** Get every model in this collection not in a 'ready' state (running). */\n\t running: function () {\n\t return this.filter(function (c) {\n\t return !c.inReadyState();\n\t });\n\t },\n\t\n\t /** return contents that are not ready and not deleted/hidden */\n\t runningAndActive: function () {\n\t return this.filter(function (c) {\n\t return !c.inReadyState() && c.get('visible')\n\t // TODO: deletedOrPurged?\n\t && !c.get('deleted');\n\t });\n\t },\n\t\n\t /** Get the model with the given hid\n\t * @param {Int} hid the hid to search for\n\t * @returns {HistoryDatasetAssociation} the model with the given hid or undefined if not found\n\t */\n\t getByHid: function (hid) {\n\t // note: there *can* be more than one content with a given hid, this finds the first based on order\n\t return this.findWhere({ hid: hid });\n\t },\n\t\n\t /** return true if all contents have details */\n\t haveDetails: function () {\n\t return this.all(function (c) {\n\t return c.hasDetails();\n\t });\n\t },\n\t\n\t // ........................................................................ hidden / deleted\n\t /** return a new contents collection of only hidden items */\n\t hidden: function () {\n\t return this.filter(function (c) {\n\t return c.hidden();\n\t });\n\t },\n\t\n\t /** return a new contents collection of only hidden items */\n\t deleted: function () {\n\t return this.filter(function (c) {\n\t return c.get('deleted');\n\t });\n\t },\n\t\n\t /** return a new contents collection of only hidden items */\n\t visibleAndUndeleted: function () {\n\t return this.filter(function (c) {\n\t return c.get('visible') &&\n\t // TODO: deletedOrPurged?\n\t !c.get('deleted');\n\t });\n\t },\n\t\n\t /** create a setter in order to publish the change */\n\t setIncludeDeleted: function (setting, options) {\n\t if (_.isBoolean(setting) && setting !== this.includeDeleted) {\n\t this.includeDeleted = setting;\n\t if (_.result(options, 'silent')) {\n\t return;\n\t }\n\t this.trigger('include-deleted', setting, this);\n\t }\n\t },\n\t\n\t /** create a setter in order to publish the change */\n\t setIncludeHidden: function (setting, options) {\n\t if (_.isBoolean(setting) && setting !== this.includeHidden) {\n\t this.includeHidden = setting;\n\t options = options || {};\n\t if (_.result(options, 'silent')) {\n\t return;\n\t }\n\t this.trigger('include-hidden', setting, this);\n\t }\n\t },\n\t\n\t // ........................................................................ ajax\n\t // ............ controlled fetch collection\n\t /** override to get expanded ids from sessionStorage and pass to API as details */\n\t fetch: function (options) {\n\t options = options || {};\n\t if (this.historyId && !options.details) {\n\t var prefs = HISTORY_PREFS.HistoryPrefs.get(this.historyId).toJSON();\n\t if (!_.isEmpty(prefs.expandedIds)) {\n\t options.details = _.values(prefs.expandedIds).join(',');\n\t }\n\t }\n\t return _super.prototype.fetch.call(this, options);\n\t },\n\t\n\t // ............. ControlledFetch stuff\n\t /** override to include the API versioning flag */\n\t _buildFetchData: function (options) {\n\t return _.extend(_super.prototype._buildFetchData.call(this, options), {\n\t v: 'dev'\n\t });\n\t },\n\t\n\t /** Extend to include details and version */\n\t _fetchParams: _super.prototype._fetchParams.concat([\n\t // TODO: remove (the need for) both\n\t /** version */\n\t 'v',\n\t /** dataset ids to get full details of */\n\t 'details']),\n\t\n\t /** override to add deleted/hidden filters */\n\t _buildFetchFilters: function (options) {\n\t var superFilters = _super.prototype._buildFetchFilters.call(this, options) || {};\n\t var filters = {};\n\t if (!this.includeDeleted) {\n\t filters.deleted = false;\n\t filters.purged = false;\n\t }\n\t if (!this.includeHidden) {\n\t filters.visible = true;\n\t }\n\t return _.defaults(superFilters, filters);\n\t },\n\t\n\t // ............ paginated collection\n\t getTotalItemCount: function () {\n\t return this.history.contentsShown();\n\t },\n\t\n\t // ............ history contents specific ajax\n\t /** override to filter requested contents to those updated after the Date 'since' */\n\t fetchUpdated: function (since, options) {\n\t if (since) {\n\t options = options || { filters: {} };\n\t options.remove = false;\n\t options.filters = {\n\t 'update_time-ge': since.toISOString(),\n\t // workflows will produce hidden datasets (non-output datasets) that still\n\t // need to be updated in the collection or they'll update forever\n\t // we can remove the default visible filter by using an 'empty' value\n\t visible: ''\n\t };\n\t }\n\t return this.fetch(options);\n\t },\n\t\n\t /** fetch all the deleted==true contents of this collection */\n\t fetchDeleted: function (options) {\n\t options = options || {};\n\t var self = this;\n\t options.filters = _.extend(options.filters, {\n\t // all deleted, purged or not\n\t deleted: true,\n\t purged: undefined\n\t });\n\t options.remove = false;\n\t\n\t self.trigger('fetching-deleted', self);\n\t return self.fetch(options).always(function () {\n\t self.trigger('fetching-deleted-done', self);\n\t });\n\t },\n\t\n\t /** fetch all the visible==false contents of this collection */\n\t fetchHidden: function (options) {\n\t options = options || {};\n\t var self = this;\n\t options.filters = _.extend(options.filters, {\n\t visible: false\n\t });\n\t options.remove = false;\n\t\n\t self.trigger('fetching-hidden', self);\n\t return self.fetch(options).always(function () {\n\t self.trigger('fetching-hidden-done', self);\n\t });\n\t },\n\t\n\t /** fetch detailed model data for all contents in this collection */\n\t fetchAllDetails: function (options) {\n\t options = options || {};\n\t var detailsFlag = { details: 'all' };\n\t options.data = _.extend(options.data || {}, detailsFlag);\n\t return this.fetch(options);\n\t },\n\t\n\t /** specialty fetch method for retrieving the element_counts of all hdcas in the history */\n\t fetchCollectionCounts: function (options) {\n\t options = options || {};\n\t options.keys = ['type_id', 'element_count'].join(',');\n\t options.filters = _.extend(options.filters || {}, {\n\t history_content_type: 'dataset_collection'\n\t });\n\t options.remove = false;\n\t return this.fetch(options);\n\t },\n\t\n\t // ............. quasi-batch ops\n\t // TODO: to batch\n\t /** helper that fetches using filterParams then calls save on each fetched using updateWhat as the save params */\n\t _filterAndUpdate: function (filterParams, updateWhat) {\n\t var self = this;\n\t var idAttribute = self.model.prototype.idAttribute;\n\t var updateArgs = [updateWhat];\n\t\n\t return self.fetch({ filters: filterParams, remove: false }).then(function (fetched) {\n\t // convert filtered json array to model array\n\t fetched = fetched.reduce(function (modelArray, currJson, i) {\n\t var model = self.get(currJson[idAttribute]);\n\t return model ? modelArray.concat(model) : modelArray;\n\t }, []);\n\t return self.ajaxQueue('save', updateArgs, fetched);\n\t });\n\t },\n\t\n\t /** using a queue, perform ajaxFn on each of the models in this collection */\n\t ajaxQueue: function (ajaxFn, args, collection) {\n\t collection = collection || this.models;\n\t return new AJAX_QUEUE.AjaxQueue(collection.slice().reverse().map(function (content, i) {\n\t var fn = _.isString(ajaxFn) ? content[ajaxFn] : ajaxFn;\n\t return function () {\n\t return fn.apply(content, args);\n\t };\n\t })).deferred;\n\t },\n\t\n\t /** fetch contents' details in batches of limitPerCall - note: only get searchable details here */\n\t progressivelyFetchDetails: function (options) {\n\t options = options || {};\n\t var deferred = jQuery.Deferred();\n\t var self = this;\n\t var limit = options.limitPerCall || self.limitPerProgressiveFetch;\n\t // TODO: only fetch tags and annotations if specifically requested\n\t var searchAttributes = HDA_MODEL.HistoryDatasetAssociation.prototype.searchAttributes;\n\t var detailKeys = searchAttributes.join(',');\n\t\n\t function _recursivelyFetch(offset) {\n\t offset = offset || 0;\n\t var _options = _.extend(_.clone(options), {\n\t view: 'summary',\n\t keys: detailKeys,\n\t limit: limit,\n\t offset: offset,\n\t reset: offset === 0,\n\t remove: false\n\t });\n\t\n\t _.defer(function () {\n\t self.fetch.call(self, _options).fail(deferred.reject).done(function (response) {\n\t deferred.notify(response, limit, offset);\n\t if (response.length !== limit) {\n\t self.allFetched = true;\n\t deferred.resolve(response, limit, offset);\n\t } else {\n\t _recursivelyFetch(offset + limit);\n\t }\n\t });\n\t });\n\t }\n\t _recursivelyFetch();\n\t return deferred;\n\t },\n\t\n\t /** does some bit of JSON represent something that can be copied into this contents collection */\n\t isCopyable: function (contentsJSON) {\n\t var copyableModelClasses = ['HistoryDatasetAssociation', 'HistoryDatasetCollectionAssociation'];\n\t return _.isObject(contentsJSON) && contentsJSON.id && _.contains(copyableModelClasses, contentsJSON.model_class);\n\t },\n\t\n\t /** copy an existing, accessible hda into this collection */\n\t copy: function (json) {\n\t // TODO: somehow showhorn all this into 'save'\n\t var id, type, contentType;\n\t if (_.isString(json)) {\n\t id = json;\n\t contentType = 'hda';\n\t type = 'dataset';\n\t } else {\n\t id = json.id;\n\t contentType = {\n\t 'HistoryDatasetAssociation': 'hda',\n\t 'LibraryDatasetDatasetAssociation': 'ldda',\n\t 'HistoryDatasetCollectionAssociation': 'hdca'\n\t }[json.model_class] || 'hda';\n\t type = contentType === 'hdca' ? 'dataset_collection' : 'dataset';\n\t }\n\t var collection = this,\n\t xhr = jQuery.ajax(this.url(), {\n\t method: 'POST',\n\t contentType: 'application/json',\n\t data: JSON.stringify({\n\t content: id,\n\t source: contentType,\n\t type: type\n\t })\n\t }).done(function (response) {\n\t collection.add([response], { parse: true });\n\t }).fail(function (error, status, message) {\n\t collection.trigger('error', collection, xhr, {}, 'Error copying contents', { type: type, id: id, source: contentType });\n\t });\n\t return xhr;\n\t },\n\t\n\t /** create a new HDCA in this collection */\n\t createHDCA: function (elementIdentifiers, collectionType, name, hideSourceItems, options) {\n\t // normally collection.create returns the new model, but we need the promise from the ajax, so we fake create\n\t //precondition: elementIdentifiers is an array of plain js objects\n\t // in the proper form to create the collectionType\n\t var hdca = this.model({\n\t history_content_type: 'dataset_collection',\n\t collection_type: collectionType,\n\t history_id: this.historyId,\n\t name: name,\n\t hide_source_items: hideSourceItems || false,\n\t // should probably be able to just send in a bunch of json here and restruct per class\n\t // note: element_identifiers is now (incorrectly) an attribute\n\t element_identifiers: elementIdentifiers\n\t // do not create the model on the client until the ajax returns\n\t });\n\t return hdca.save(options);\n\t },\n\t\n\t // ........................................................................ searching\n\t /** return true if all contents have the searchable attributes */\n\t haveSearchDetails: function () {\n\t return this.allFetched && this.all(function (content) {\n\t // null (which is a valid returned annotation value)\n\t // will return false when using content.has( 'annotation' )\n\t //TODO: a bit hacky - formalize\n\t return _.has(content.attributes, 'annotation');\n\t });\n\t },\n\t\n\t /** return a new collection of contents whose attributes contain the substring matchesWhat */\n\t matches: function (matchesWhat) {\n\t return this.filter(function (content) {\n\t return content.matches(matchesWhat);\n\t });\n\t },\n\t\n\t // ........................................................................ misc\n\t /** In this override, copy the historyId to the clone */\n\t clone: function () {\n\t var clone = Backbone.Collection.prototype.clone.call(this);\n\t clone.historyId = this.historyId;\n\t return clone;\n\t },\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return ['HistoryContents(', [this.historyId, this.length].join(), ')'].join('');\n\t }\n\t });\n\t\n\t //==============================================================================\n\t return {\n\t HistoryContents: HistoryContents\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3)))\n\n/***/ }),\n/* 46 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(6)], __WEBPACK_AMD_DEFINE_RESULT__ = function (BASE_MVC) {\n\t\n\t 'use strict';\n\t\n\t var logNamespace = 'history';\n\t\n\t // ============================================================================\n\t /** session storage for individual history preferences */\n\t var HistoryPrefs = BASE_MVC.SessionStorageModel.extend(\n\t /** @lends HistoryPrefs.prototype */{\n\t //TODO:?? move to user prefs?\n\t defaults: {\n\t //TODO:?? expandedIds to array?\n\t expandedIds: {},\n\t show_deleted: false,\n\t show_hidden: false\n\t },\n\t\n\t /** add an hda id to the hash of expanded hdas */\n\t addExpanded: function (model) {\n\t //TODO: use type_id and not model\n\t var current = this.get('expandedIds');\n\t current[model.id] = model.get('id');\n\t this.save('expandedIds', current);\n\t },\n\t\n\t /** remove an hda id from the hash of expanded hdas */\n\t removeExpanded: function (model) {\n\t var current = this.get('expandedIds');\n\t delete current[model.id];\n\t this.save('expandedIds', current);\n\t },\n\t\n\t isExpanded: function (contentId) {\n\t return _.result(this.get('expandedIds'), contentId, false);\n\t },\n\t\n\t allExpanded: function () {\n\t return _.values(this.get('expandedIds'));\n\t },\n\t\n\t clearExpanded: function () {\n\t this.set('expandedIds', {});\n\t },\n\t\n\t includeDeleted: function (val) {\n\t // moving the invocation here so other components don't need to know the key\n\t // TODO: change this key later\n\t if (!_.isUndefined(val)) {\n\t this.set('show_deleted', val);\n\t }\n\t return this.get('show_deleted');\n\t },\n\t\n\t includeHidden: function (val) {\n\t // TODO: change this key later\n\t if (!_.isUndefined(val)) {\n\t this.set('show_hidden', val);\n\t }\n\t return this.get('show_hidden');\n\t },\n\t\n\t toString: function () {\n\t return 'HistoryPrefs(' + this.id + ')';\n\t }\n\t\n\t }, {\n\t // ........................................................................ class vars\n\t // class lvl for access w/o instantiation\n\t storageKeyPrefix: 'history:',\n\t\n\t /** key string to store each histories settings under */\n\t historyStorageKey: function historyStorageKey(historyId) {\n\t if (!historyId) {\n\t throw new Error('HistoryPrefs.historyStorageKey needs valid id: ' + historyId);\n\t }\n\t // single point of change\n\t return HistoryPrefs.storageKeyPrefix + historyId;\n\t },\n\t\n\t /** return the existing storage for the history with the given id (or create one if it doesn't exist) */\n\t get: function get(historyId) {\n\t return new HistoryPrefs({ id: HistoryPrefs.historyStorageKey(historyId) });\n\t },\n\t\n\t /** clear all history related items in sessionStorage */\n\t clearAll: function clearAll(historyId) {\n\t for (var key in sessionStorage) {\n\t if (key.indexOf(HistoryPrefs.storageKeyPrefix) === 0) {\n\t sessionStorage.removeItem(key);\n\t }\n\t }\n\t }\n\t });\n\t\n\t //==============================================================================\n\t return {\n\t HistoryPrefs: HistoryPrefs\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2)))\n\n/***/ }),\n/* 47 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _, jQuery) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (BASE_MVC, _l) {\n\t\n\t 'use strict';\n\t\n\t var logNamespace = 'list';\n\t //==============================================================================\n\t /** A view which, when first rendered, shows only summary data/attributes, but\n\t * can be expanded to show further details (and optionally fetch those\n\t * details from the server).\n\t */\n\t var ExpandableView = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({\n\t _logNamespace: logNamespace,\n\t\n\t //TODO: Although the reasoning behind them is different, this shares a lot with HiddenUntilActivated above: combine them\n\t //PRECONDITION: model must have method hasDetails\n\t //PRECONDITION: subclasses must have templates.el and templates.details\n\t\n\t initialize: function (attributes) {\n\t /** are the details of this view expanded/shown or not? */\n\t this.expanded = attributes.expanded || false;\n\t this.log('\\t expanded:', this.expanded);\n\t this.fxSpeed = attributes.fxSpeed !== undefined ? attributes.fxSpeed : this.fxSpeed;\n\t },\n\t\n\t // ........................................................................ render main\n\t /** jq fx speed */\n\t fxSpeed: 'fast',\n\t\n\t /** Render this content, set up ui.\n\t * @param {Number or String} speed the speed of the render\n\t */\n\t render: function (speed) {\n\t var $newRender = this._buildNewRender();\n\t this._setUpBehaviors($newRender);\n\t this._queueNewRender($newRender, speed);\n\t return this;\n\t },\n\t\n\t /** Build a temp div containing the new children for the view's $el.\n\t * If the view is already expanded, build the details as well.\n\t */\n\t _buildNewRender: function () {\n\t // create a new render using a skeleton template, render title buttons, render body, and set up events, etc.\n\t var $newRender = $(this.templates.el(this.model.toJSON(), this));\n\t if (this.expanded) {\n\t this.$details($newRender).replaceWith(this._renderDetails().show());\n\t }\n\t return $newRender;\n\t },\n\t\n\t /** Fade out the old el, swap in the new contents, then fade in.\n\t * @param {Number or String} speed jq speed to use for rendering effects\n\t * @fires rendered when rendered\n\t */\n\t _queueNewRender: function ($newRender, speed) {\n\t speed = speed === undefined ? this.fxSpeed : speed;\n\t var view = this;\n\t\n\t if (speed === 0) {\n\t view._swapNewRender($newRender);\n\t view.trigger('rendered', view);\n\t } else {\n\t $(view).queue('fx', [function (next) {\n\t view.$el.fadeOut(speed, next);\n\t }, function (next) {\n\t view._swapNewRender($newRender);\n\t next();\n\t }, function (next) {\n\t view.$el.fadeIn(speed, next);\n\t }, function (next) {\n\t view.trigger('rendered', view);\n\t next();\n\t }]);\n\t }\n\t },\n\t\n\t /** empty out the current el, move the $newRender's children in */\n\t _swapNewRender: function ($newRender) {\n\t return this.$el.empty().attr('class', _.isFunction(this.className) ? this.className() : this.className).append($newRender.children());\n\t },\n\t\n\t /** set up js behaviors, event handlers for elements within the given container\n\t * @param {jQuery} $container jq object that contains the elements to process (defaults to this.$el)\n\t */\n\t _setUpBehaviors: function ($where) {\n\t $where = $where || this.$el;\n\t // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.)\n\t //make_popup_menus( $where );\n\t $where.find('[title]').tooltip({ placement: 'bottom' });\n\t },\n\t\n\t // ......................................................................... details\n\t /** shortcut to details DOM (as jQ) */\n\t $details: function ($where) {\n\t $where = $where || this.$el;\n\t return $where.find('> .details');\n\t },\n\t\n\t /** build the DOM for the details and set up behaviors on it */\n\t _renderDetails: function () {\n\t var $newDetails = $(this.templates.details(this.model.toJSON(), this));\n\t this._setUpBehaviors($newDetails);\n\t return $newDetails;\n\t },\n\t\n\t // ......................................................................... expansion/details\n\t /** Show or hide the details\n\t * @param {Boolean} expand if true, expand; if false, collapse\n\t */\n\t toggleExpanded: function (expand) {\n\t expand = expand === undefined ? !this.expanded : expand;\n\t if (expand) {\n\t this.expand();\n\t } else {\n\t this.collapse();\n\t }\n\t return this;\n\t },\n\t\n\t /** Render and show the full, detailed body of this view including extra data and controls.\n\t * note: if the model does not have detailed data, fetch that data before showing the body\n\t * @fires expanded when a body has been expanded\n\t */\n\t expand: function () {\n\t var view = this;\n\t return view._fetchModelDetails().always(function () {\n\t view._expand();\n\t });\n\t },\n\t\n\t /** Check for model details and, if none, fetch them.\n\t * @returns {jQuery.promise} the model.fetch.xhr if details are being fetched, an empty promise if not\n\t */\n\t _fetchModelDetails: function () {\n\t if (!this.model.hasDetails()) {\n\t return this.model.fetch();\n\t }\n\t return jQuery.when();\n\t },\n\t\n\t /** Inner fn called when expand (public) has fetched the details */\n\t _expand: function () {\n\t var view = this,\n\t $newDetails = view._renderDetails();\n\t view.$details().replaceWith($newDetails);\n\t // needs to be set after the above or the slide will not show\n\t view.expanded = true;\n\t view.$details().slideDown(view.fxSpeed, function () {\n\t view.trigger('expanded', view);\n\t });\n\t },\n\t\n\t /** Hide the body/details of an HDA.\n\t * @fires collapsed when a body has been collapsed\n\t */\n\t collapse: function () {\n\t this.debug(this + '(ExpandableView).collapse');\n\t var view = this;\n\t view.expanded = false;\n\t this.$details().slideUp(view.fxSpeed, function () {\n\t view.trigger('collapsed', view);\n\t });\n\t }\n\t\n\t });\n\t\n\t //==============================================================================\n\t /** A view that is displayed in some larger list/grid/collection.\n\t * Inherits from Expandable, Selectable, Draggable.\n\t * The DOM contains warnings, a title bar, and a series of primary action controls.\n\t * Primary actions are meant to be easily accessible item functions (such as delete)\n\t * that are rendered in the title bar.\n\t *\n\t * Details are rendered when the user clicks the title bar or presses enter/space when\n\t * the title bar is in focus.\n\t *\n\t * Designed as a base class for history panel contents - but usable elsewhere (I hope).\n\t */\n\t var ListItemView = ExpandableView.extend(BASE_MVC.mixin(BASE_MVC.SelectableViewMixin, BASE_MVC.DraggableViewMixin, {\n\t\n\t tagName: 'div',\n\t className: 'list-item',\n\t\n\t /** Set up the base class and all mixins */\n\t initialize: function (attributes) {\n\t ExpandableView.prototype.initialize.call(this, attributes);\n\t BASE_MVC.SelectableViewMixin.initialize.call(this, attributes);\n\t BASE_MVC.DraggableViewMixin.initialize.call(this, attributes);\n\t this._setUpListeners();\n\t },\n\t\n\t /** event listeners */\n\t _setUpListeners: function () {\n\t // hide the primary actions in the title bar when selectable and narrow\n\t this.on('selectable', function (isSelectable) {\n\t if (isSelectable) {\n\t this.$('.primary-actions').hide();\n\t } else {\n\t this.$('.primary-actions').show();\n\t }\n\t }, this);\n\t return this;\n\t },\n\t\n\t // ........................................................................ rendering\n\t /** In this override, call methods to build warnings, titlebar and primary actions */\n\t _buildNewRender: function () {\n\t var $newRender = ExpandableView.prototype._buildNewRender.call(this);\n\t $newRender.children('.warnings').replaceWith(this._renderWarnings());\n\t $newRender.children('.title-bar').replaceWith(this._renderTitleBar());\n\t $newRender.children('.primary-actions').append(this._renderPrimaryActions());\n\t $newRender.find('> .title-bar .subtitle').replaceWith(this._renderSubtitle());\n\t return $newRender;\n\t },\n\t\n\t /** In this override, render the selector controls and set up dragging before the swap */\n\t _swapNewRender: function ($newRender) {\n\t ExpandableView.prototype._swapNewRender.call(this, $newRender);\n\t if (this.selectable) {\n\t this.showSelector(0);\n\t }\n\t if (this.draggable) {\n\t this.draggableOn();\n\t }\n\t return this.$el;\n\t },\n\t\n\t /** Render any warnings the item may need to show (e.g. \"I'm deleted\") */\n\t _renderWarnings: function () {\n\t var view = this,\n\t $warnings = $(''),\n\t json = view.model.toJSON();\n\t //TODO:! unordered (map)\n\t _.each(view.templates.warnings, function (templateFn) {\n\t $warnings.append($(templateFn(json, view)));\n\t });\n\t return $warnings;\n\t },\n\t\n\t /** Render the title bar (the main/exposed SUMMARY dom element) */\n\t _renderTitleBar: function () {\n\t return $(this.templates.titleBar(this.model.toJSON(), this));\n\t },\n\t\n\t /** Return an array of jQ objects containing common/easily-accessible item controls */\n\t _renderPrimaryActions: function () {\n\t // override this\n\t return [];\n\t },\n\t\n\t /** Render the title bar (the main/exposed SUMMARY dom element) */\n\t _renderSubtitle: function () {\n\t return $(this.templates.subtitle(this.model.toJSON(), this));\n\t },\n\t\n\t // ......................................................................... events\n\t /** event map */\n\t events: {\n\t // expand the body when the title is clicked or when in focus and space or enter is pressed\n\t 'click .title-bar': '_clickTitleBar',\n\t 'keydown .title-bar': '_keyDownTitleBar',\n\t 'click .selector': 'toggleSelect'\n\t },\n\t\n\t /** expand when the title bar is clicked */\n\t _clickTitleBar: function (event) {\n\t event.stopPropagation();\n\t if (event.altKey) {\n\t this.toggleSelect(event);\n\t if (!this.selectable) {\n\t this.showSelector();\n\t }\n\t } else {\n\t this.toggleExpanded();\n\t }\n\t },\n\t\n\t /** expand when the title bar is in focus and enter or space is pressed */\n\t _keyDownTitleBar: function (event) {\n\t // bail (with propagation) if keydown and not space or enter\n\t var KEYCODE_SPACE = 32,\n\t KEYCODE_RETURN = 13;\n\t if (event && event.type === 'keydown' && (event.keyCode === KEYCODE_SPACE || event.keyCode === KEYCODE_RETURN)) {\n\t this.toggleExpanded();\n\t event.stopPropagation();\n\t return false;\n\t }\n\t return true;\n\t },\n\t\n\t // ......................................................................... misc\n\t /** String representation */\n\t toString: function () {\n\t var modelString = this.model ? this.model + '' : '(no model)';\n\t return 'ListItemView(' + modelString + ')';\n\t }\n\t }));\n\t\n\t // ............................................................................ TEMPLATES\n\t /** underscore templates */\n\t ListItemView.prototype.templates = function () {\n\t\n\t var elTemplato = BASE_MVC.wrapTemplate(['
',\n\t // space for title bar buttons - gen. floated to the right\n\t '', '',\n\t\n\t // expandable area for more details\n\t '', '
']);\n\t\n\t var warnings = {};\n\t\n\t var titleBarTemplate = BASE_MVC.wrapTemplate([\n\t // adding a tabindex here allows focusing the title bar and the use of keydown to expand the dataset display\n\t '
',\n\t //TODO: prob. belongs in dataset-list-item\n\t '', '
', '<%- element.name %>', '
', '', '
'], 'element');\n\t\n\t var subtitleTemplate = BASE_MVC.wrapTemplate([\n\t // override this\n\t '']);\n\t\n\t var detailsTemplate = BASE_MVC.wrapTemplate([\n\t // override this\n\t '']);\n\t\n\t return {\n\t el: elTemplato,\n\t warnings: warnings,\n\t titleBar: titleBarTemplate,\n\t subtitle: subtitleTemplate,\n\t details: detailsTemplate\n\t };\n\t }();\n\t\n\t //==============================================================================\n\t /** A view that is displayed in some larger list/grid/collection.\n\t * *AND* can display some sub-list of it's own when expanded (e.g. dataset collections).\n\t * This list will 'foldout' when the item is expanded depending on this.foldoutStyle:\n\t * If 'foldout': will expand vertically to show the nested list\n\t * If 'drilldown': will overlay the parent list\n\t *\n\t * Inherits from ListItemView.\n\t *\n\t * _renderDetails does the work of creating this.details: a sub-view that shows the nested list\n\t */\n\t var FoldoutListItemView = ListItemView.extend({\n\t\n\t /** If 'foldout': show the sub-panel inside the expanded item\n\t * If 'drilldown': only fire events and handle by pub-sub\n\t * (allow the panel containing this item to attach it, hide itself, etc.)\n\t */\n\t foldoutStyle: 'foldout',\n\t /** Panel view class to instantiate for the sub-panel */\n\t foldoutPanelClass: null,\n\t\n\t /** override to:\n\t * add attributes foldoutStyle and foldoutPanelClass for config poly\n\t * disrespect attributes.expanded if drilldown\n\t */\n\t initialize: function (attributes) {\n\t if (this.foldoutStyle === 'drilldown') {\n\t this.expanded = false;\n\t }\n\t this.foldoutStyle = attributes.foldoutStyle || this.foldoutStyle;\n\t this.foldoutPanelClass = attributes.foldoutPanelClass || this.foldoutPanelClass;\n\t\n\t ListItemView.prototype.initialize.call(this, attributes);\n\t this.foldout = this._createFoldoutPanel();\n\t },\n\t\n\t /** in this override, attach the foldout panel when rendering details */\n\t _renderDetails: function () {\n\t if (this.foldoutStyle === 'drilldown') {\n\t return $();\n\t }\n\t var $newDetails = ListItemView.prototype._renderDetails.call(this);\n\t return this._attachFoldout(this.foldout, $newDetails);\n\t },\n\t\n\t /** In this override, handle collection expansion. */\n\t _createFoldoutPanel: function () {\n\t var model = this.model;\n\t var FoldoutClass = this._getFoldoutPanelClass(model),\n\t options = this._getFoldoutPanelOptions(model),\n\t foldout = new FoldoutClass(_.extend(options, {\n\t model: model\n\t }));\n\t return foldout;\n\t },\n\t\n\t /** Stub to return proper foldout panel class */\n\t _getFoldoutPanelClass: function () {\n\t // override\n\t return this.foldoutPanelClass;\n\t },\n\t\n\t /** Stub to return proper foldout panel options */\n\t _getFoldoutPanelOptions: function () {\n\t return {\n\t // propagate foldout style down\n\t foldoutStyle: this.foldoutStyle,\n\t fxSpeed: this.fxSpeed\n\t };\n\t },\n\t\n\t /** Render the foldout panel inside the view, hiding controls */\n\t _attachFoldout: function (foldout, $whereTo) {\n\t $whereTo = $whereTo || this.$('> .details');\n\t this.foldout = foldout.render(0);\n\t foldout.$('> .controls').hide();\n\t return $whereTo.append(foldout.$el);\n\t },\n\t\n\t /** In this override, branch on foldoutStyle to show expanded */\n\t expand: function () {\n\t var view = this;\n\t return view._fetchModelDetails().always(function () {\n\t if (view.foldoutStyle === 'foldout') {\n\t view._expand();\n\t } else if (view.foldoutStyle === 'drilldown') {\n\t view._expandByDrilldown();\n\t }\n\t });\n\t },\n\t\n\t /** For drilldown, set up close handler and fire expanded:drilldown\n\t * containing views can listen to this and handle other things\n\t * (like hiding themselves) by listening for expanded/collapsed:drilldown\n\t */\n\t _expandByDrilldown: function () {\n\t var view = this;\n\t // attachment and rendering done by listener\n\t view.listenTo(view.foldout, 'close', function () {\n\t view.trigger('collapsed:drilldown', view, view.foldout);\n\t });\n\t view.trigger('expanded:drilldown', view, view.foldout);\n\t }\n\t\n\t });\n\t\n\t // ............................................................................ TEMPLATES\n\t /** underscore templates */\n\t FoldoutListItemView.prototype.templates = function () {\n\t\n\t var detailsTemplate = BASE_MVC.wrapTemplate(['
',\n\t // override with more info (that goes above the panel)\n\t '
'], 'collection');\n\t\n\t return _.extend({}, ListItemView.prototype.templates, {\n\t details: detailsTemplate\n\t });\n\t }();\n\t\n\t //==============================================================================\n\t return {\n\t ExpandableView: ExpandableView,\n\t ListItemView: ListItemView,\n\t FoldoutListItemView: FoldoutListItemView\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ }),\n/* 48 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (baseMVC, _l) {\n\t // =============================================================================\n\t /** A view on any model that has a 'tags' attribute (a list of tag strings)\n\t * Incorporates the select2 jQuery plugin for tags display/editing:\n\t * http://ivaynberg.github.io/select2/\n\t */\n\t var TagsEditor = Backbone.View.extend(baseMVC.LoggableMixin).extend(baseMVC.HiddenUntilActivatedViewMixin).extend({\n\t\n\t tagName: 'div',\n\t className: 'tags-display',\n\t\n\t /** Set up listeners, parse options */\n\t initialize: function (options) {\n\t //console.debug( this, options );\n\t // only listen to the model only for changes to tags - re-render\n\t if (options.usePrompt === false) {\n\t this.label = '';\n\t } else {\n\t this.label = '';\n\t }\n\t this.hiddenUntilActivated(options.$activator, options);\n\t },\n\t\n\t /** Build the DOM elements, call select to on the created input, and set up behaviors */\n\t render: function () {\n\t var self = this;\n\t this.$el.html(this._template());\n\t\n\t this.$input().select2({\n\t placeholder: 'Add tags',\n\t width: '100%',\n\t tags: function () {\n\t // initialize possible tags in the dropdown based on all the tags the user has used so far\n\t return self._getTagsUsed();\n\t }\n\t });\n\t\n\t this._setUpBehaviors();\n\t return this;\n\t },\n\t\n\t _hashToName: function (tag) {\n\t if (tag.startsWith('#')) {\n\t return 'name:' + tag.slice(1);\n\t }\n\t return tag;\n\t },\n\t\n\t _nameToHash: function (tag) {\n\t if (tag.startsWith('name:')) {\n\t tag = '#' + tag.slice(5);\n\t }\n\t return tag;\n\t },\n\t\n\t /** @returns {String} the html text used to build the view's DOM */\n\t _template: function () {\n\t return [this.label,\n\t // set up initial tags by adding as CSV to input vals (necc. to init select2)\n\t ''].join('');\n\t },\n\t\n\t /** @returns {String} the sorted, comma-separated tags from the model */\n\t tagsToCSV: function () {\n\t var self = this;\n\t var tagsArray = this.model.get('tags');\n\t if (!_.isArray(tagsArray) || _.isEmpty(tagsArray)) {\n\t return '';\n\t }\n\t return tagsArray.map(function (tag) {\n\t return _.escape(self._nameToHash(tag));\n\t }).sort().join(',');\n\t },\n\t\n\t /** @returns {jQuery} the input for this view */\n\t $input: function () {\n\t return this.$el.find('input.tags-input');\n\t },\n\t\n\t /** @returns {String[]} all tags used by the current user */\n\t _getTagsUsed: function () {\n\t //TODO: global\n\t var self = this;\n\t return _.map(Galaxy.user.get('tags_used'), self._nameToHash);\n\t },\n\t\n\t /** set up any event listeners on the view's DOM (mostly handled by select2) */\n\t _setUpBehaviors: function () {\n\t var self = this;\n\t this.$input().on('change', function (event) {\n\t // Modify any 'hashtag' 'nametags'\n\t event.val = _.map(event.val, self._hashToName);\n\t // save the model's tags in either remove or added event\n\t self.model.save({ tags: event.val });\n\t // if it's new, add the tag to the users tags\n\t if (event.added) {\n\t //??: solve weird behavior in FF on test.galaxyproject.org where\n\t // event.added.text is string object: 'String{ 0=\"o\", 1=\"n\", 2=\"e\" }'\n\t self._addNewTagToTagsUsed(event.added.text + '');\n\t }\n\t });\n\t },\n\t\n\t /** add a new tag (if not already there) to the list of all tags used by the user\n\t * @param {String} newTag the tag to add to the list of used\n\t */\n\t _addNewTagToTagsUsed: function (newTag) {\n\t //TODO: global\n\t var tagsUsed = Galaxy.user.get('tags_used');\n\t if (!_.contains(tagsUsed, newTag)) {\n\t tagsUsed.push(newTag);\n\t tagsUsed.sort();\n\t Galaxy.user.set('tags_used', tagsUsed);\n\t }\n\t },\n\t\n\t /** shut down event listeners and remove this view's DOM */\n\t remove: function () {\n\t this.$input.off();\n\t this.stopListening(this.model);\n\t Backbone.View.prototype.remove.call(this);\n\t },\n\t\n\t /** string rep */\n\t toString: function () {\n\t return ['TagsEditor(', this.model + '', ')'].join('');\n\t }\n\t });\n\t\n\t // =============================================================================\n\t return {\n\t TagsEditor: TagsEditor\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2)))\n\n/***/ }),\n/* 49 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function($, _) {/**\n\t This is the base class of the tool form plugin. This class is e.g. inherited by the regular and the workflow tool form.\n\t*/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(60), __webpack_require__(7), __webpack_require__(20), __webpack_require__(19), __webpack_require__(34)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Deferred, Ui, FormBase, CitationModel, CitationView) {\n\t return FormBase.extend({\n\t initialize: function (options) {\n\t var self = this;\n\t this.deferred = new Deferred();\n\t FormBase.prototype.initialize.call(this, options);\n\t if (this.model.get('inputs')) {\n\t this._buildForm(this.model.attributes);\n\t } else {\n\t this.deferred.execute(function (process) {\n\t self._buildModel(process, self.model.attributes, true);\n\t });\n\t }\n\t // listen to history panel\n\t if (this.model.get('listen_to_history') && parent.Galaxy && parent.Galaxy.currHistoryPanel) {\n\t this.listenTo(parent.Galaxy.currHistoryPanel.collection, 'change', function () {\n\t self.model.get('onchange')();\n\t });\n\t }\n\t // destroy dom elements\n\t this.$el.on('remove', function () {\n\t self.remove();\n\t });\n\t },\n\t\n\t /** Wait for deferred build processes before removal */\n\t remove: function () {\n\t var self = this;\n\t this.$el.hide();\n\t this.deferred.execute(function () {\n\t FormBase.prototype.remove.call(self);\n\t Galaxy.emit.debug('tool-form-base::remove()', 'Destroy view.');\n\t });\n\t },\n\t\n\t /** Build form */\n\t _buildForm: function (options) {\n\t var self = this;\n\t this.model.set(options);\n\t this.model.set({\n\t title: options.title || '' + options.name + ' ' + options.description + ' (Galaxy Version ' + options.version + ')',\n\t operations: !this.model.get('hide_operations') && this._operations(),\n\t onchange: function () {\n\t self.deferred.reset();\n\t self.deferred.execute(function (process) {\n\t self.model.get('postchange')(process, self);\n\t });\n\t }\n\t });\n\t this.model.get('customize') && this.model.get('customize')(this);\n\t this.render();\n\t if (!this.model.get('collapsible')) {\n\t this.$el.append($('').addClass('ui-margin-top-large').append(this._footer()));\n\t }\n\t },\n\t\n\t /** Builds a new model through api call and recreates the entire form */\n\t _buildModel: function (process, new_options, hide_message) {\n\t var self = this;\n\t var options = this.model.attributes;\n\t options.version = new_options.version;\n\t options.id = new_options.id;\n\t\n\t // build request url\n\t var build_url = '';\n\t var build_data = {};\n\t if (options.job_id) {\n\t build_url = Galaxy.root + 'api/jobs/' + options.job_id + '/build_for_rerun';\n\t } else {\n\t build_url = Galaxy.root + 'api/tools/' + options.id + '/build';\n\t if (Galaxy.params && Galaxy.params.tool_id == options.id) {\n\t build_data = $.extend({}, Galaxy.params);\n\t options.version && (build_data['tool_version'] = options.version);\n\t }\n\t }\n\t\n\t // get initial model\n\t Utils.get({\n\t url: build_url,\n\t data: build_data,\n\t success: function (data) {\n\t if (!data.display) {\n\t window.location = Galaxy.root;\n\t return;\n\t }\n\t self._buildForm(data);\n\t !hide_message && self.message.update({\n\t status: 'success',\n\t message: 'Now you are using \\'' + options.name + '\\' version ' + options.version + ', id \\'' + options.id + '\\'.',\n\t persistent: false\n\t });\n\t Galaxy.emit.debug('tool-form-base::_buildModel()', 'Initial tool model ready.', data);\n\t process.resolve();\n\t },\n\t error: function (response, status) {\n\t var error_message = response && response.err_msg || 'Uncaught error.';\n\t if (status == 401) {\n\t window.location = Galaxy.root + 'user/login?' + $.param({ redirect: Galaxy.root + '?tool_id=' + options.id });\n\t } else if (self.$el.is(':empty')) {\n\t self.$el.prepend(new Ui.Message({\n\t message: error_message,\n\t status: 'danger',\n\t persistent: true,\n\t large: true\n\t }).$el);\n\t } else {\n\t Galaxy.modal && Galaxy.modal.show({\n\t title: 'Tool request failed',\n\t body: error_message,\n\t buttons: {\n\t 'Close': function () {\n\t Galaxy.modal.hide();\n\t }\n\t }\n\t });\n\t }\n\t Galaxy.emit.debug('tool-form-base::_buildModel()', 'Initial tool model request failed.', response);\n\t process.reject();\n\t }\n\t });\n\t },\n\t\n\t /** Create tool operation menu */\n\t _operations: function () {\n\t var self = this;\n\t var options = this.model.attributes;\n\t\n\t // button for version selection\n\t var versions_button = new Ui.ButtonMenu({\n\t icon: 'fa-cubes',\n\t title: !options.narrow && 'Versions' || null,\n\t tooltip: 'Select another tool version'\n\t });\n\t if (!options.sustain_version && options.versions && options.versions.length > 1) {\n\t for (var i in options.versions) {\n\t var version = options.versions[i];\n\t if (version != options.version) {\n\t versions_button.addMenu({\n\t title: 'Switch to ' + version,\n\t version: version,\n\t icon: 'fa-cube',\n\t onclick: function () {\n\t // here we update the tool version (some tools encode the version also in the id)\n\t var id = options.id.replace(options.version, this.version);\n\t var version = this.version;\n\t // queue model request\n\t self.deferred.reset();\n\t self.deferred.execute(function (process) {\n\t self._buildModel(process, { id: id, version: version });\n\t });\n\t }\n\t });\n\t }\n\t }\n\t } else {\n\t versions_button.$el.hide();\n\t }\n\t\n\t // button for options e.g. search, help\n\t var menu_button = new Ui.ButtonMenu({\n\t icon: 'fa-caret-down',\n\t title: !options.narrow && 'Options' || null,\n\t tooltip: 'View available options'\n\t });\n\t if (options.biostar_url) {\n\t menu_button.addMenu({\n\t icon: 'fa-question-circle',\n\t title: 'Question?',\n\t onclick: function () {\n\t window.open(options.biostar_url + '/p/new/post/');\n\t }\n\t });\n\t menu_button.addMenu({\n\t icon: 'fa-search',\n\t title: 'Search',\n\t onclick: function () {\n\t window.open(options.biostar_url + '/local/search/page/?q=' + options.name);\n\t }\n\t });\n\t };\n\t menu_button.addMenu({\n\t icon: 'fa-share',\n\t title: 'Share',\n\t onclick: function () {\n\t prompt('Copy to clipboard: Ctrl+C, Enter', window.location.origin + Galaxy.root + 'root?tool_id=' + options.id);\n\t }\n\t });\n\t\n\t // add admin operations\n\t if (Galaxy.user && Galaxy.user.get('is_admin')) {\n\t menu_button.addMenu({\n\t icon: 'fa-download',\n\t title: 'Download',\n\t onclick: function () {\n\t window.location.href = Galaxy.root + 'api/tools/' + options.id + '/download';\n\t }\n\t });\n\t menu_button.addMenu({\n\t icon: 'fa-refresh',\n\t title: 'Reload XML',\n\t onclick: function () {\n\t Utils.get({\n\t url: Galaxy.root + 'api/tools/' + options.id + '/reload',\n\t success: function (response) {\n\t self.message.update({ persistent: false, message: 'Tool XML has been reloaded.', status: 'success' });\n\t },\n\t error: function (response) {\n\t self.message.update({ persistent: false, message: response.err_msg, status: 'danger' });\n\t }\n\t });\n\t }\n\t });\n\t }\n\t\n\t // button for version selection\n\t if (options.requirements && options.requirements.length > 0) {\n\t menu_button.addMenu({\n\t icon: 'fa-info-circle',\n\t title: 'Requirements',\n\t onclick: function () {\n\t if (!this.requirements_visible || self.portlet.collapsed) {\n\t this.requirements_visible = true;\n\t self.portlet.expand();\n\t self.message.update({ persistent: true, message: self._templateRequirements(options), status: 'info' });\n\t } else {\n\t this.requirements_visible = false;\n\t self.message.update({ message: '' });\n\t }\n\t }\n\t });\n\t }\n\t\n\t // add toolshed url\n\t if (options.sharable_url) {\n\t menu_button.addMenu({\n\t icon: 'fa-external-link',\n\t title: 'See in Tool Shed',\n\t onclick: function () {\n\t window.open(options.sharable_url);\n\t }\n\t });\n\t }\n\t\n\t return {\n\t menu: menu_button,\n\t versions: versions_button\n\t };\n\t },\n\t\n\t /** Create footer */\n\t _footer: function () {\n\t var options = this.model.attributes;\n\t var $el = $('').append(this._templateHelp(options));\n\t if (options.citations) {\n\t var $citations = $('');\n\t var citations = new CitationModel.ToolCitationCollection();\n\t citations.tool_id = options.id;\n\t var citation_list_view = new CitationView.CitationListView({ el: $citations, collection: citations });\n\t citation_list_view.render();\n\t citations.fetch();\n\t $el.append($citations);\n\t }\n\t return $el;\n\t },\n\t\n\t /** Templates */\n\t _templateHelp: function (options) {\n\t var $tmpl = $('').addClass('ui-form-help').append(options.help);\n\t $tmpl.find('a').attr('target', '_blank');\n\t return $tmpl;\n\t },\n\t\n\t _templateRequirements: function (options) {\n\t var nreq = options.requirements.length;\n\t if (nreq > 0) {\n\t var requirements_message = 'This tool requires ';\n\t _.each(options.requirements, function (req, i) {\n\t requirements_message += req.name + (req.version ? ' (Version ' + req.version + ')' : '') + (i < nreq - 2 ? ', ' : i == nreq - 2 ? ' and ' : '');\n\t });\n\t var requirements_link = $('').attr('target', '_blank').attr('href', 'https://galaxyproject.org/tools/requirements/').text('here');\n\t return $('').append(requirements_message + '. Click ').append(requirements_link).append(' for more information.');\n\t }\n\t return 'No requirements found.';\n\t }\n\t });\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1), __webpack_require__(2)))\n\n/***/ }),\n/* 50 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {/**\n\t * Model, view, and controller objects for Galaxy tools and tool panel.\n\t */\n\t\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(2), __webpack_require__(18), __webpack_require__(10), __webpack_require__(25)], __WEBPACK_AMD_DEFINE_RESULT__ = function (_, util, data, ToolForm) {\n\t 'use strict';\n\t\n\t /**\n\t * Mixin for tracking model visibility.\n\t */\n\t\n\t var VisibilityMixin = {\n\t hidden: false,\n\t\n\t show: function () {\n\t this.set(\"hidden\", false);\n\t },\n\t\n\t hide: function () {\n\t this.set(\"hidden\", true);\n\t },\n\t\n\t toggle: function () {\n\t this.set(\"hidden\", !this.get(\"hidden\"));\n\t },\n\t\n\t is_visible: function () {\n\t return !this.attributes.hidden;\n\t }\n\t\n\t };\n\t\n\t /**\n\t * A tool parameter.\n\t */\n\t var ToolParameter = Backbone.Model.extend({\n\t defaults: {\n\t name: null,\n\t label: null,\n\t type: null,\n\t value: null,\n\t html: null,\n\t num_samples: 5\n\t },\n\t\n\t initialize: function (options) {\n\t this.attributes.html = unescape(this.attributes.html);\n\t },\n\t\n\t copy: function () {\n\t return new ToolParameter(this.toJSON());\n\t },\n\t\n\t set_value: function (value) {\n\t this.set('value', value || '');\n\t }\n\t });\n\t\n\t var ToolParameterCollection = Backbone.Collection.extend({\n\t model: ToolParameter\n\t });\n\t\n\t /**\n\t * A data tool parameter.\n\t */\n\t var DataToolParameter = ToolParameter.extend({});\n\t\n\t /**\n\t * An integer tool parameter.\n\t */\n\t var IntegerToolParameter = ToolParameter.extend({\n\t set_value: function (value) {\n\t this.set('value', parseInt(value, 10));\n\t },\n\t\n\t /**\n\t * Returns samples from a tool input.\n\t */\n\t get_samples: function () {\n\t return d3.scale.linear().domain([this.get('min'), this.get('max')]).ticks(this.get('num_samples'));\n\t }\n\t });\n\t\n\t var FloatToolParameter = IntegerToolParameter.extend({\n\t set_value: function (value) {\n\t this.set('value', parseFloat(value));\n\t }\n\t });\n\t\n\t /**\n\t * A select tool parameter.\n\t */\n\t var SelectToolParameter = ToolParameter.extend({\n\t /**\n\t * Returns tool options.\n\t */\n\t get_samples: function () {\n\t return _.map(this.get('options'), function (option) {\n\t return option[0];\n\t });\n\t }\n\t });\n\t\n\t // Set up dictionary of parameter types.\n\t ToolParameter.subModelTypes = {\n\t 'integer': IntegerToolParameter,\n\t 'float': FloatToolParameter,\n\t 'data': DataToolParameter,\n\t 'select': SelectToolParameter\n\t };\n\t\n\t /**\n\t * A Galaxy tool.\n\t */\n\t var Tool = Backbone.Model.extend({\n\t // Default attributes.\n\t defaults: {\n\t id: null,\n\t name: null,\n\t description: null,\n\t target: null,\n\t inputs: [],\n\t outputs: []\n\t },\n\t\n\t urlRoot: Galaxy.root + 'api/tools',\n\t\n\t initialize: function (options) {\n\t\n\t // Set parameters.\n\t this.set('inputs', new ToolParameterCollection(_.map(options.inputs, function (p) {\n\t var p_class = ToolParameter.subModelTypes[p.type] || ToolParameter;\n\t return new p_class(p);\n\t })));\n\t },\n\t\n\t /**\n\t *\n\t */\n\t toJSON: function () {\n\t var rval = Backbone.Model.prototype.toJSON.call(this);\n\t\n\t // Convert inputs to JSON manually.\n\t rval.inputs = this.get('inputs').map(function (i) {\n\t return i.toJSON();\n\t });\n\t return rval;\n\t },\n\t\n\t /**\n\t * Removes inputs of a particular type; this is useful because not all inputs can be handled by\n\t * client and server yet.\n\t */\n\t remove_inputs: function (types) {\n\t var tool = this,\n\t incompatible_inputs = tool.get('inputs').filter(function (input) {\n\t return types.indexOf(input.get('type')) !== -1;\n\t });\n\t tool.get('inputs').remove(incompatible_inputs);\n\t },\n\t\n\t /**\n\t * Returns object copy, optionally including only inputs that can be sampled.\n\t */\n\t copy: function (only_samplable_inputs) {\n\t var copy = new Tool(this.toJSON());\n\t\n\t // Return only samplable inputs if flag is set.\n\t if (only_samplable_inputs) {\n\t var valid_inputs = new Backbone.Collection();\n\t copy.get('inputs').each(function (input) {\n\t if (input.get_samples()) {\n\t valid_inputs.push(input);\n\t }\n\t });\n\t copy.set('inputs', valid_inputs);\n\t }\n\t\n\t return copy;\n\t },\n\t\n\t apply_search_results: function (results) {\n\t _.indexOf(results, this.attributes.id) !== -1 ? this.show() : this.hide();\n\t return this.is_visible();\n\t },\n\t\n\t /**\n\t * Set a tool input's value.\n\t */\n\t set_input_value: function (name, value) {\n\t this.get('inputs').find(function (input) {\n\t return input.get('name') === name;\n\t }).set('value', value);\n\t },\n\t\n\t /**\n\t * Set many input values at once.\n\t */\n\t set_input_values: function (inputs_dict) {\n\t var self = this;\n\t _.each(_.keys(inputs_dict), function (input_name) {\n\t self.set_input_value(input_name, inputs_dict[input_name]);\n\t });\n\t },\n\t\n\t /**\n\t * Run tool; returns a Deferred that resolves to the tool's output(s).\n\t */\n\t run: function () {\n\t return this._run();\n\t },\n\t\n\t /**\n\t * Rerun tool using regions and a target dataset.\n\t */\n\t rerun: function (target_dataset, regions) {\n\t return this._run({\n\t action: 'rerun',\n\t target_dataset_id: target_dataset.id,\n\t regions: regions\n\t });\n\t },\n\t\n\t /**\n\t * Returns input dict for tool's inputs.\n\t */\n\t get_inputs_dict: function () {\n\t var input_dict = {};\n\t this.get('inputs').each(function (input) {\n\t input_dict[input.get('name')] = input.get('value');\n\t });\n\t return input_dict;\n\t },\n\t\n\t /**\n\t * Run tool; returns a Deferred that resolves to the tool's output(s).\n\t * NOTE: this method is a helper method and should not be called directly.\n\t */\n\t _run: function (additional_params) {\n\t // Create payload.\n\t var payload = _.extend({\n\t tool_id: this.id,\n\t inputs: this.get_inputs_dict()\n\t }, additional_params);\n\t\n\t // Because job may require indexing datasets, use server-side\n\t // deferred to ensure that job is run. Also use deferred that\n\t // resolves to outputs from tool.\n\t var run_deferred = $.Deferred(),\n\t ss_deferred = new util.ServerStateDeferred({\n\t ajax_settings: {\n\t url: this.urlRoot,\n\t data: JSON.stringify(payload),\n\t dataType: \"json\",\n\t contentType: 'application/json',\n\t type: \"POST\"\n\t },\n\t interval: 2000,\n\t success_fn: function (response) {\n\t return response !== \"pending\";\n\t }\n\t });\n\t\n\t // Run job and resolve run_deferred to tool outputs.\n\t $.when(ss_deferred.go()).then(function (result) {\n\t run_deferred.resolve(new data.DatasetCollection(result));\n\t });\n\t return run_deferred;\n\t }\n\t });\n\t _.extend(Tool.prototype, VisibilityMixin);\n\t\n\t /**\n\t * Tool view.\n\t */\n\t var ToolView = Backbone.View.extend({});\n\t\n\t /**\n\t * Wrap collection of tools for fast access/manipulation.\n\t */\n\t var ToolCollection = Backbone.Collection.extend({\n\t model: Tool\n\t });\n\t\n\t /**\n\t * Label or section header in tool panel.\n\t */\n\t var ToolSectionLabel = Backbone.Model.extend(VisibilityMixin);\n\t\n\t /**\n\t * Section of tool panel with elements (labels and tools).\n\t */\n\t var ToolSection = Backbone.Model.extend({\n\t defaults: {\n\t elems: [],\n\t open: false\n\t },\n\t\n\t clear_search_results: function () {\n\t _.each(this.attributes.elems, function (elt) {\n\t elt.show();\n\t });\n\t\n\t this.show();\n\t this.set(\"open\", false);\n\t },\n\t\n\t apply_search_results: function (results) {\n\t var all_hidden = true,\n\t cur_label;\n\t _.each(this.attributes.elems, function (elt) {\n\t if (elt instanceof ToolSectionLabel) {\n\t cur_label = elt;\n\t cur_label.hide();\n\t } else if (elt instanceof Tool) {\n\t if (elt.apply_search_results(results)) {\n\t all_hidden = false;\n\t if (cur_label) {\n\t cur_label.show();\n\t }\n\t }\n\t }\n\t });\n\t\n\t if (all_hidden) {\n\t this.hide();\n\t } else {\n\t this.show();\n\t this.set(\"open\", true);\n\t }\n\t }\n\t });\n\t _.extend(ToolSection.prototype, VisibilityMixin);\n\t\n\t /**\n\t * Tool search that updates results when query is changed. Result value of null\n\t * indicates that query was not run; if not null, results are from search using\n\t * query.\n\t */\n\t var ToolSearch = Backbone.Model.extend({\n\t defaults: {\n\t search_hint_string: \"search tools\",\n\t min_chars_for_search: 3,\n\t clear_btn_url: \"\",\n\t visible: true,\n\t query: \"\",\n\t results: null,\n\t // ESC (27) will clear the input field and tool search filters\n\t clear_key: 27\n\t },\n\t\n\t urlRoot: Galaxy.root + 'api/tools',\n\t\n\t initialize: function () {\n\t this.on(\"change:query\", this.do_search);\n\t },\n\t\n\t /**\n\t * Do the search and update the results.\n\t */\n\t do_search: function () {\n\t var query = this.attributes.query;\n\t\n\t // If query is too short, do not search.\n\t if (query.length < this.attributes.min_chars_for_search) {\n\t this.set(\"results\", null);\n\t return;\n\t }\n\t\n\t // Do search via AJAX.\n\t var q = query;\n\t // Stop previous ajax-request\n\t if (this.timer) {\n\t clearTimeout(this.timer);\n\t }\n\t // Start a new ajax-request in X ms\n\t $(\"#search-clear-btn\").hide();\n\t $(\"#search-spinner\").show();\n\t var self = this;\n\t this.timer = setTimeout(function () {\n\t // log the search to analytics if present\n\t if (typeof ga !== 'undefined') {\n\t ga('send', 'pageview', Galaxy.root + '?q=' + q);\n\t }\n\t $.get(self.urlRoot, { q: q }, function (data) {\n\t self.set(\"results\", data);\n\t $(\"#search-spinner\").hide();\n\t $(\"#search-clear-btn\").show();\n\t }, \"json\");\n\t }, 400);\n\t },\n\t\n\t clear_search: function () {\n\t this.set(\"query\", \"\");\n\t this.set(\"results\", null);\n\t }\n\t\n\t });\n\t _.extend(ToolSearch.prototype, VisibilityMixin);\n\t\n\t /**\n\t * Tool Panel.\n\t */\n\t var ToolPanel = Backbone.Model.extend({\n\t\n\t initialize: function (options) {\n\t this.attributes.tool_search = options.tool_search;\n\t this.attributes.tool_search.on(\"change:results\", this.apply_search_results, this);\n\t this.attributes.tools = options.tools;\n\t this.attributes.layout = new Backbone.Collection(this.parse(options.layout));\n\t },\n\t\n\t /**\n\t * Parse tool panel dictionary and return collection of tool panel elements.\n\t */\n\t parse: function (response) {\n\t // Recursive function to parse tool panel elements.\n\t var self = this,\n\t\n\t // Helper to recursively parse tool panel.\n\t parse_elt = function (elt_dict) {\n\t var type = elt_dict.model_class;\n\t // There are many types of tools; for now, anything that ends in 'Tool'\n\t // is treated as a generic tool.\n\t if (type.indexOf('Tool') === type.length - 4) {\n\t return self.attributes.tools.get(elt_dict.id);\n\t } else if (type === 'ToolSection') {\n\t // Parse elements.\n\t var elems = _.map(elt_dict.elems, parse_elt);\n\t elt_dict.elems = elems;\n\t return new ToolSection(elt_dict);\n\t } else if (type === 'ToolSectionLabel') {\n\t return new ToolSectionLabel(elt_dict);\n\t }\n\t };\n\t\n\t return _.map(response, parse_elt);\n\t },\n\t\n\t clear_search_results: function () {\n\t this.get('layout').each(function (panel_elt) {\n\t if (panel_elt instanceof ToolSection) {\n\t panel_elt.clear_search_results();\n\t } else {\n\t // Label or tool, so just show.\n\t panel_elt.show();\n\t }\n\t });\n\t },\n\t\n\t apply_search_results: function () {\n\t var results = this.get('tool_search').get('results');\n\t if (results === null) {\n\t this.clear_search_results();\n\t return;\n\t }\n\t\n\t var cur_label = null;\n\t this.get('layout').each(function (panel_elt) {\n\t if (panel_elt instanceof ToolSectionLabel) {\n\t cur_label = panel_elt;\n\t cur_label.hide();\n\t } else if (panel_elt instanceof Tool) {\n\t if (panel_elt.apply_search_results(results)) {\n\t if (cur_label) {\n\t cur_label.show();\n\t }\n\t }\n\t } else {\n\t // Starting new section, so clear current label.\n\t cur_label = null;\n\t panel_elt.apply_search_results(results);\n\t }\n\t });\n\t }\n\t });\n\t\n\t /**\n\t * View classes for Galaxy tools and tool panel.\n\t *\n\t * Views use the templates defined below for rendering. Views update as needed\n\t * based on (a) model/collection events and (b) user interactions; in this sense,\n\t * they are controllers are well and the HTML is the real view in the MVC architecture.\n\t */\n\t\n\t /**\n\t * Base view that handles visibility based on model's hidden attribute.\n\t */\n\t var BaseView = Backbone.View.extend({\n\t initialize: function () {\n\t this.model.on(\"change:hidden\", this.update_visible, this);\n\t this.update_visible();\n\t },\n\t update_visible: function () {\n\t this.model.attributes.hidden ? this.$el.hide() : this.$el.show();\n\t }\n\t });\n\t\n\t /**\n\t * Link to a tool.\n\t */\n\t var ToolLinkView = BaseView.extend({\n\t tagName: 'div',\n\t\n\t render: function () {\n\t // create element\n\t var $link = $('');\n\t $link.append(templates.tool_link(this.model.toJSON()));\n\t\n\t var formStyle = this.model.get('form_style', null);\n\t // open upload dialog for upload tool\n\t if (this.model.id === 'upload1') {\n\t $link.find('a').on('click', function (e) {\n\t e.preventDefault();\n\t Galaxy.upload.show();\n\t });\n\t } else if (formStyle === 'regular') {\n\t // regular tools\n\t var self = this;\n\t $link.find('a').on('click', function (e) {\n\t e.preventDefault();\n\t Galaxy.router.push('/', { tool_id: self.model.id, version: self.model.get('version') });\n\t });\n\t }\n\t\n\t // add element\n\t this.$el.append($link);\n\t return this;\n\t }\n\t });\n\t\n\t /**\n\t * Panel label/section header.\n\t */\n\t var ToolSectionLabelView = BaseView.extend({\n\t tagName: 'div',\n\t className: 'toolPanelLabel',\n\t\n\t render: function () {\n\t this.$el.append($(\"\").text(this.model.attributes.text));\n\t return this;\n\t }\n\t });\n\t\n\t /**\n\t * Panel section.\n\t */\n\t var ToolSectionView = BaseView.extend({\n\t tagName: 'div',\n\t className: 'toolSectionWrapper',\n\t\n\t initialize: function () {\n\t BaseView.prototype.initialize.call(this);\n\t this.model.on(\"change:open\", this.update_open, this);\n\t },\n\t\n\t render: function () {\n\t // Build using template.\n\t this.$el.append(templates.panel_section(this.model.toJSON()));\n\t\n\t // Add tools to section.\n\t var section_body = this.$el.find(\".toolSectionBody\");\n\t _.each(this.model.attributes.elems, function (elt) {\n\t if (elt instanceof Tool) {\n\t var tool_view = new ToolLinkView({ model: elt, className: \"toolTitle\" });\n\t tool_view.render();\n\t section_body.append(tool_view.$el);\n\t } else if (elt instanceof ToolSectionLabel) {\n\t var label_view = new ToolSectionLabelView({ model: elt });\n\t label_view.render();\n\t section_body.append(label_view.$el);\n\t } else {\n\t // TODO: handle nested section bodies?\n\t }\n\t });\n\t return this;\n\t },\n\t\n\t events: {\n\t 'click .toolSectionTitle > a': 'toggle'\n\t },\n\t\n\t /**\n\t * Toggle visibility of tool section.\n\t */\n\t toggle: function () {\n\t this.model.set(\"open\", !this.model.attributes.open);\n\t },\n\t\n\t /**\n\t * Update whether section is open or close.\n\t */\n\t update_open: function () {\n\t this.model.attributes.open ? this.$el.children(\".toolSectionBody\").slideDown(\"fast\") : this.$el.children(\".toolSectionBody\").slideUp(\"fast\");\n\t }\n\t });\n\t\n\t var ToolSearchView = Backbone.View.extend({\n\t tagName: 'div',\n\t id: 'tool-search',\n\t className: 'bar',\n\t\n\t events: {\n\t 'click': 'focus_and_select',\n\t 'keyup :input': 'query_changed',\n\t 'change :input': 'query_changed',\n\t 'click #search-clear-btn': 'clear'\n\t },\n\t\n\t render: function () {\n\t this.$el.append(templates.tool_search(this.model.toJSON()));\n\t if (!this.model.is_visible()) {\n\t this.$el.hide();\n\t }\n\t\n\t // Adjust top for issue 2907 depending on whether the messagebox is visible.\n\t if ($(\"#messagebox\").is(\":visible\")) {\n\t this.$el.css(\"top\", \"95px\");\n\t }\n\t\n\t this.$el.find('[title]').tooltip();\n\t return this;\n\t },\n\t\n\t focus_and_select: function () {\n\t this.$el.find(\":input\").focus().select();\n\t },\n\t\n\t clear: function () {\n\t this.model.clear_search();\n\t this.$el.find(\":input\").val('');\n\t this.focus_and_select();\n\t return false;\n\t },\n\t\n\t query_changed: function (evData) {\n\t // check for the 'clear key' (ESC) first\n\t if (this.model.attributes.clear_key && this.model.attributes.clear_key === evData.which) {\n\t this.clear();\n\t return false;\n\t }\n\t this.model.set(\"query\", this.$el.find(\":input\").val());\n\t }\n\t });\n\t\n\t /**\n\t * Tool panel view. Events triggered include:\n\t * tool_link_click(click event, tool_model)\n\t */\n\t var ToolPanelView = Backbone.View.extend({\n\t tagName: 'div',\n\t className: 'toolMenu',\n\t\n\t /**\n\t * Set up view.\n\t */\n\t initialize: function () {\n\t this.model.get('tool_search').on(\"change:results\", this.handle_search_results, this);\n\t },\n\t\n\t render: function () {\n\t var self = this;\n\t\n\t // Render search.\n\t var search_view = new ToolSearchView({ model: this.model.get('tool_search') });\n\t search_view.render();\n\t self.$el.append(search_view.$el);\n\t\n\t // Render panel.\n\t this.model.get('layout').each(function (panel_elt) {\n\t if (panel_elt instanceof ToolSection) {\n\t var section_title_view = new ToolSectionView({ model: panel_elt });\n\t section_title_view.render();\n\t self.$el.append(section_title_view.$el);\n\t } else if (panel_elt instanceof Tool) {\n\t var tool_view = new ToolLinkView({ model: panel_elt, className: \"toolTitleNoSection\" });\n\t tool_view.render();\n\t self.$el.append(tool_view.$el);\n\t } else if (panel_elt instanceof ToolSectionLabel) {\n\t var label_view = new ToolSectionLabelView({ model: panel_elt });\n\t label_view.render();\n\t self.$el.append(label_view.$el);\n\t }\n\t });\n\t\n\t // Setup tool link click eventing.\n\t self.$el.find(\"a.tool-link\").click(function (e) {\n\t // Tool id is always the first class.\n\t var tool_id = $(this).attr('class').split(/\\s+/)[0],\n\t tool = self.model.get('tools').get(tool_id);\n\t\n\t self.trigger(\"tool_link_click\", e, tool);\n\t });\n\t\n\t return this;\n\t },\n\t\n\t handle_search_results: function () {\n\t var results = this.model.get('tool_search').get('results');\n\t if (results && results.length === 0) {\n\t $(\"#search-no-results\").show();\n\t } else {\n\t $(\"#search-no-results\").hide();\n\t }\n\t }\n\t });\n\t\n\t /**\n\t * View for working with a tool: setting parameters and inputs and executing the tool.\n\t */\n\t var ToolFormView = Backbone.View.extend({\n\t className: 'toolForm',\n\t\n\t render: function () {\n\t this.$el.children().remove();\n\t this.$el.append(templates.tool_form(this.model.toJSON()));\n\t }\n\t });\n\t\n\t /**\n\t * Integrated tool menu + tool execution.\n\t */\n\t var IntegratedToolMenuAndView = Backbone.View.extend({\n\t className: 'toolMenuAndView',\n\t\n\t initialize: function () {\n\t this.tool_panel_view = new ToolPanelView({ collection: this.collection });\n\t this.tool_form_view = new ToolFormView();\n\t },\n\t\n\t render: function () {\n\t // Render and append tool panel.\n\t this.tool_panel_view.render();\n\t this.tool_panel_view.$el.css(\"float\", \"left\");\n\t this.$el.append(this.tool_panel_view.$el);\n\t\n\t // Append tool form view.\n\t this.tool_form_view.$el.hide();\n\t this.$el.append(this.tool_form_view.$el);\n\t\n\t // On tool link click, show tool.\n\t var self = this;\n\t this.tool_panel_view.on(\"tool_link_click\", function (e, tool) {\n\t // Prevents click from activating link:\n\t e.preventDefault();\n\t // Show tool that was clicked on:\n\t self.show_tool(tool);\n\t });\n\t },\n\t\n\t /**\n\t * Fetch and display tool.\n\t */\n\t show_tool: function (tool) {\n\t var self = this;\n\t tool.fetch().done(function () {\n\t self.tool_form_view.model = tool;\n\t self.tool_form_view.render();\n\t self.tool_form_view.$el.show();\n\t $('#left').width(\"650px\");\n\t });\n\t }\n\t });\n\t\n\t // TODO: move into relevant views\n\t var templates = {\n\t // the search bar at the top of the tool panel\n\t tool_search: _.template(['\" autocomplete=\"off\" type=\"text\" />', '',\n\t //TODO: replace with icon\n\t ''].join('')),\n\t\n\t // the category level container in the tool panel (e.g. 'Get Data', 'Text Manipulation')\n\t panel_section: _.template(['
'].join('')),\n\t\n\t // a single tool's link in the tool panel; will load the tool form in the center panel\n\t tool_link: _.template(['', '<% _.each( labels, function( label ){ %>', '\">', '<%- label %>', '', '<% }); %>', '', ' tool-link\" href=\"<%= link %>\" target=\"<%- target %>\" minsizehint=\"<%- min_width %>\">', '<%- name %>', '', ' <%- description %>'].join('')),\n\t\n\t // the tool form for entering tool parameters, viewing help and executing the tool\n\t // loaded when a tool link is clicked in the tool panel\n\t tool_form: _.template(['
';\n\t },\n\t\n\t /** Template of info message */\n\t _templateInfo: function () {\n\t return '
' + 'Your FTP directory does not contain any files.' + '
';\n\t },\n\t\n\t /** Template of main view */\n\t _template: function () {\n\t return '
' + '' + '
This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at ' + this.options.ftp_upload_site + ' using your Galaxy credentials (email address and password).
' + '
' + '
';\n\t }\n\t });\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1), __webpack_require__(2)))\n\n/***/ }),\n/* 58 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/** This renders the content of the settings popup, allowing users to specify flags i.e. for space-to-tab conversion **/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t return Backbone.View.extend({\n\t options: {\n\t class_check: 'fa-check-square-o',\n\t class_uncheck: 'fa-square-o',\n\t parameters: [{\n\t id: 'space_to_tab',\n\t title: 'Convert spaces to tabs'\n\t }, {\n\t id: 'to_posix_lines',\n\t title: 'Use POSIX standard'\n\t }]\n\t },\n\t\n\t initialize: function (options) {\n\t var self = this;\n\t this.model = options.model;\n\t this.setElement($('').addClass('upload-settings'));\n\t this.$el.append($('').addClass('upload-settings-cover'));\n\t this.$el.append($('
').append(parameter.title)));\n\t });\n\t this.$cover[this.model.get('enabled') && 'hide' || 'show']();\n\t }\n\t });\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1), __webpack_require__(2)))\n\n/***/ }),\n/* 59 */,\n/* 60 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {/**\n\t * This class defines a queue to ensure that multiple deferred callbacks are executed sequentially.\n\t */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t return Backbone.Model.extend({\n\t initialize: function () {\n\t this.active = {};\n\t this.last = null;\n\t },\n\t\n\t /** Adds a callback to the queue. Upon execution a deferred object is parsed to the callback i.e. callback( deferred ).\n\t * If the callback does not take any arguments, the deferred is resolved instantly.\n\t */\n\t execute: function (callback) {\n\t var self = this;\n\t var id = Utils.uid();\n\t var has_deferred = callback.length > 0;\n\t\n\t // register process\n\t this.active[id] = true;\n\t\n\t // deferred process\n\t var process = $.Deferred();\n\t process.promise().always(function () {\n\t delete self.active[id];\n\t has_deferred && Galaxy.emit.debug('deferred::execute()', this.state().charAt(0).toUpperCase() + this.state().slice(1) + ' ' + id);\n\t });\n\t\n\t // deferred queue\n\t $.when(this.last).always(function () {\n\t if (self.active[id]) {\n\t has_deferred && Galaxy.emit.debug('deferred::execute()', 'Running ' + id);\n\t callback(process);\n\t !has_deferred && process.resolve();\n\t } else {\n\t process.reject();\n\t }\n\t });\n\t this.last = process.promise();\n\t },\n\t\n\t /** Resets the promise queue. All currently queued but unexecuted callbacks/promises will be rejected.\n\t */\n\t reset: function () {\n\t Galaxy.emit.debug('deferred::execute()', 'Reset');\n\t for (var i in this.active) {\n\t this.active[i] = false;\n\t }\n\t },\n\t\n\t /** Returns true if all processes are done.\n\t */\n\t ready: function () {\n\t return $.isEmptyObject(this.active);\n\t }\n\t });\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1)))\n\n/***/ }),\n/* 61 */,\n/* 62 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\t/* WEBPACK VAR INJECTION */(function(jQuery, _) {/*\n\t galaxy upload plugins - requires FormData and XMLHttpRequest\n\t*/\n\t;(function ($) {\n\t // add event properties\n\t jQuery.event.props.push(\"dataTransfer\");\n\t\n\t /**\n\t Posts file data to the API\n\t */\n\t $.uploadpost = function (config) {\n\t // parse options\n\t var cnf = $.extend({}, {\n\t data: {},\n\t success: function () {},\n\t error: function () {},\n\t progress: function () {},\n\t url: null,\n\t maxfilesize: 2048,\n\t error_filesize: 'File exceeds 2GB. Please use a FTP client.',\n\t error_default: 'Please make sure the file is available.',\n\t error_server: 'Upload request failed.',\n\t error_login: 'Uploads require you to log in.'\n\t }, config);\n\t\n\t // link data\n\t var data = cnf.data;\n\t\n\t // check errors\n\t if (data.error_message) {\n\t cnf.error(data.error_message);\n\t return;\n\t }\n\t\n\t // construct form data\n\t var form = new FormData();\n\t for (var key in data.payload) {\n\t form.append(key, data.payload[key]);\n\t }\n\t\n\t // add files to submission\n\t var sizes = 0;\n\t for (var key in data.files) {\n\t var d = data.files[key];\n\t form.append(d.name, d.file, d.file.name);\n\t sizes += d.file.size;\n\t }\n\t\n\t // check file size, unless it's an ftp file\n\t if (sizes > 1048576 * cnf.maxfilesize) {\n\t cnf.error(cnf.error_filesize);\n\t return;\n\t }\n\t\n\t // prepare request\n\t xhr = new XMLHttpRequest();\n\t xhr.open('POST', cnf.url, true);\n\t xhr.setRequestHeader('Accept', 'application/json');\n\t xhr.setRequestHeader('Cache-Control', 'no-cache');\n\t xhr.setRequestHeader('X-Requested-With', 'XMLHttpRequest');\n\t\n\t // captures state changes\n\t xhr.onreadystatechange = function () {\n\t // check for request completed, server connection closed\n\t if (xhr.readyState == xhr.DONE) {\n\t // parse response\n\t var response = null;\n\t if (xhr.responseText) {\n\t try {\n\t response = jQuery.parseJSON(xhr.responseText);\n\t } catch (e) {\n\t response = xhr.responseText;\n\t }\n\t }\n\t // pass any error to the error option\n\t if (xhr.status < 200 || xhr.status > 299) {\n\t var text = xhr.statusText;\n\t if (xhr.status == 403) {\n\t text = cnf.error_login;\n\t } else if (xhr.status == 0) {\n\t text = cnf.error_server;\n\t } else if (!text) {\n\t text = cnf.error_default;\n\t }\n\t cnf.error(text + ' (' + xhr.status + ')');\n\t } else {\n\t cnf.success(response);\n\t }\n\t }\n\t };\n\t\n\t // prepare upload progress\n\t xhr.upload.addEventListener('progress', function (e) {\n\t if (e.lengthComputable) {\n\t cnf.progress(Math.round(e.loaded * 100 / e.total));\n\t }\n\t }, false);\n\t\n\t // send request\n\t Galaxy.emit.debug('uploadbox::uploadpost()', 'Posting following data.', cnf);\n\t xhr.send(form);\n\t };\n\t\n\t /**\n\t Handles the upload events drag/drop etc.\n\t */\n\t $.fn.uploadinput = function (options) {\n\t // initialize\n\t var el = this;\n\t var opts = $.extend({}, {\n\t ondragover: function () {},\n\t ondragleave: function () {},\n\t onchange: function () {},\n\t multiple: false\n\t }, options);\n\t\n\t // append hidden upload field\n\t var $input = $('');\n\t el.append($input.change(function (e) {\n\t opts.onchange(e.target.files);\n\t $(this).val('');\n\t }));\n\t\n\t // drag/drop events\n\t el.on('drop', function (e) {\n\t opts.ondragleave(e);\n\t if (e.dataTransfer) {\n\t opts.onchange(e.dataTransfer.files);\n\t e.preventDefault();\n\t }\n\t });\n\t el.on('dragover', function (e) {\n\t e.preventDefault();\n\t opts.ondragover(e);\n\t });\n\t el.on('dragleave', function (e) {\n\t e.stopPropagation();\n\t opts.ondragleave(e);\n\t });\n\t\n\t // exports\n\t return {\n\t dialog: function () {\n\t $input.trigger('click');\n\t }\n\t };\n\t };\n\t\n\t /**\n\t Handles the upload queue and events such as drag/drop etc.\n\t */\n\t $.fn.uploadbox = function (options) {\n\t // parse options\n\t var opts = $.extend({}, {\n\t dragover: function () {},\n\t dragleave: function () {},\n\t announce: function (d) {},\n\t initialize: function (d) {},\n\t progress: function (d, m) {},\n\t success: function (d, m) {},\n\t error: function (d, m) {\n\t alert(m);\n\t },\n\t complete: function () {}\n\t }, options);\n\t\n\t // file queue\n\t var queue = {};\n\t\n\t // queue index/length counter\n\t var queue_index = 0;\n\t var queue_length = 0;\n\t\n\t // indicates if queue is currently running\n\t var queue_running = false;\n\t var queue_stop = false;\n\t\n\t // element\n\t var uploadinput = $(this).uploadinput({\n\t multiple: true,\n\t onchange: function (files) {\n\t add(files);\n\t },\n\t ondragover: options.ondragover,\n\t ondragleave: options.ondragleave\n\t });\n\t\n\t // add new files to upload queue\n\t function add(files) {\n\t if (files && files.length && !queue_running) {\n\t var current_index = queue_index;\n\t _.each(files, function (file, key) {\n\t if (file.mode !== 'new' && _.filter(queue, function (f) {\n\t return f.name === file.name && f.size === file.size;\n\t }).length) {\n\t file.duplicate = true;\n\t }\n\t });\n\t _.each(files, function (file) {\n\t if (!file.duplicate) {\n\t var index = String(queue_index++);\n\t queue[index] = file;\n\t opts.announce(index, queue[index]);\n\t queue_length++;\n\t }\n\t });\n\t return current_index;\n\t }\n\t }\n\t\n\t // remove file from queue\n\t function remove(index) {\n\t if (queue[index]) {\n\t delete queue[index];\n\t queue_length--;\n\t }\n\t }\n\t\n\t // process an upload, recursive\n\t function process() {\n\t // validate\n\t if (queue_length == 0 || queue_stop) {\n\t queue_stop = false;\n\t queue_running = false;\n\t opts.complete();\n\t return;\n\t } else {\n\t queue_running = true;\n\t }\n\t\n\t // get an identifier from the queue\n\t var index = -1;\n\t for (var key in queue) {\n\t index = key;\n\t break;\n\t }\n\t\n\t // get current file from queue\n\t var file = queue[index];\n\t\n\t // remove from queue\n\t remove(index);\n\t\n\t // create and submit data\n\t $.uploadpost({\n\t url: opts.url,\n\t data: opts.initialize(index),\n\t success: function (message) {\n\t opts.success(index, message);process();\n\t },\n\t error: function (message) {\n\t opts.error(index, message);process();\n\t },\n\t progress: function (percentage) {\n\t opts.progress(index, percentage);\n\t }\n\t });\n\t }\n\t\n\t /*\n\t public interface\n\t */\n\t\n\t // open file browser for selection\n\t function select() {\n\t uploadinput.dialog();\n\t }\n\t\n\t // remove all entries from queue\n\t function reset(index) {\n\t for (index in queue) {\n\t remove(index);\n\t }\n\t }\n\t\n\t // initiate upload process\n\t function start() {\n\t if (!queue_running) {\n\t queue_running = true;\n\t process();\n\t }\n\t }\n\t\n\t // stop upload process\n\t function stop() {\n\t queue_stop = true;\n\t }\n\t\n\t // set options\n\t function configure(options) {\n\t opts = $.extend({}, opts, options);\n\t return opts;\n\t }\n\t\n\t // verify browser compatibility\n\t function compatible() {\n\t return window.File && window.FormData && window.XMLHttpRequest && window.FileList;\n\t }\n\t\n\t // export functions\n\t return {\n\t 'select': select,\n\t 'add': add,\n\t 'remove': remove,\n\t 'start': start,\n\t 'stop': stop,\n\t 'reset': reset,\n\t 'configure': configure,\n\t 'compatible': compatible\n\t };\n\t };\n\t})(jQuery);\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1), __webpack_require__(2)))\n\n/***/ }),\n/* 63 */,\n/* 64 */,\n/* 65 */,\n/* 66 */,\n/* 67 */,\n/* 68 */,\n/* 69 */,\n/* 70 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(6), __webpack_require__(5), __webpack_require__(16)], __WEBPACK_AMD_DEFINE_RESULT__ = function (baseMVC, _l) {\n\t // =============================================================================\n\t /** A view on any model that has a 'annotation' attribute\n\t */\n\t var AnnotationEditor = Backbone.View.extend(baseMVC.LoggableMixin).extend(baseMVC.HiddenUntilActivatedViewMixin).extend({\n\t\n\t tagName: 'div',\n\t className: 'annotation-display',\n\t\n\t /** Set up listeners, parse options */\n\t initialize: function (options) {\n\t options = options || {};\n\t this.tooltipConfig = options.tooltipConfig || { placement: 'bottom' };\n\t //console.debug( this, options );\n\t // only listen to the model only for changes to annotations\n\t this.listenTo(this.model, 'change:annotation', function () {\n\t this.render();\n\t });\n\t this.hiddenUntilActivated(options.$activator, options);\n\t },\n\t\n\t /** Build the DOM elements, call select to on the created input, and set up behaviors */\n\t render: function () {\n\t var view = this;\n\t this.$el.html(this._template());\n\t\n\t //TODO: handle empties better\n\t this.$annotation().make_text_editable({\n\t use_textarea: true,\n\t on_finish: function (newAnnotation) {\n\t view.$annotation().text(newAnnotation);\n\t view.model.save({ annotation: newAnnotation }, { silent: true }).fail(function () {\n\t view.$annotation().text(view.model.previous('annotation'));\n\t });\n\t }\n\t });\n\t return this;\n\t },\n\t\n\t /** @returns {String} the html text used to build the view's DOM */\n\t _template: function () {\n\t var annotation = this.model.get('annotation');\n\t return [\n\t //TODO: make prompt optional\n\t '',\n\t // set up initial tags by adding as CSV to input vals (necc. to init select2)\n\t '
', _.escape(annotation), '
'].join('');\n\t },\n\t\n\t /** @returns {jQuery} the main element for this view */\n\t $annotation: function () {\n\t return this.$el.find('.annotation');\n\t },\n\t\n\t /** shut down event listeners and remove this view's DOM */\n\t remove: function () {\n\t this.$annotation.off();\n\t this.stopListening(this.model);\n\t Backbone.View.prototype.remove.call(this);\n\t },\n\t\n\t /** string rep */\n\t toString: function () {\n\t return ['AnnotationEditor(', this.model + '', ')'].join('');\n\t }\n\t });\n\t // =============================================================================\n\t return {\n\t AnnotationEditor: AnnotationEditor\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2)))\n\n/***/ }),\n/* 71 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(jQuery) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(2), __webpack_require__(3), __webpack_require__(6)], __WEBPACK_AMD_DEFINE_RESULT__ = function (_, Backbone, BASE_MVC) {\n\t 'use strict';\n\t\n\t //=============================================================================\n\t /**\n\t * A Collection that can be limited/offset/re-ordered/filtered.\n\t * @type {Backbone.Collection}\n\t */\n\t\n\t var ControlledFetchCollection = Backbone.Collection.extend({\n\t\n\t /** call setOrder on initialization to build the comparator based on options */\n\t initialize: function (models, options) {\n\t Backbone.Collection.prototype.initialize.call(this, models, options);\n\t this.setOrder(options.order || this.order, { silent: true });\n\t },\n\t\n\t /** set up to track order changes and re-sort when changed */\n\t _setUpListeners: function () {\n\t return this.on({\n\t 'changed-order': this.sort\n\t });\n\t },\n\t\n\t /** override to provide order and offsets based on instance vars, set limit if passed,\n\t * and set allFetched/fire 'all-fetched' when xhr returns\n\t */\n\t fetch: function (options) {\n\t options = this._buildFetchOptions(options);\n\t // console.log( 'fetch options:', options );\n\t return Backbone.Collection.prototype.fetch.call(this, options);\n\t },\n\t\n\t /** build ajax data/parameters from options */\n\t _buildFetchOptions: function (options) {\n\t // note: we normally want options passed in to override the defaults built here\n\t // so most of these fns will generate defaults\n\t options = _.clone(options) || {};\n\t var self = this;\n\t\n\t // jquery ajax option; allows multiple q/qv for filters (instead of 'q[]')\n\t options.traditional = true;\n\t\n\t // options.data\n\t // we keep limit, offset, etc. in options *as well as move it into data* because:\n\t // - it makes fetch calling convenient to add it to a single options map (instead of as mult. args)\n\t // - it allows the std. event handlers (for fetch, etc.) to have access\n\t // to the pagination options too\n\t // (i.e. this.on( 'sync', function( options ){ if( options.limit ){ ... } }))\n\t // however, when we send to xhr/jquery we copy them to data also so that they become API query params\n\t options.data = options.data || self._buildFetchData(options);\n\t // console.log( 'data:', options.data );\n\t\n\t // options.data.filters --> options.data.q, options.data.qv\n\t var filters = this._buildFetchFilters(options);\n\t // console.log( 'filters:', filters );\n\t if (!_.isEmpty(filters)) {\n\t _.extend(options.data, this._fetchFiltersToAjaxData(filters));\n\t }\n\t // console.log( 'data:', options.data );\n\t return options;\n\t },\n\t\n\t /** Build the dictionary to send to fetch's XHR as data */\n\t _buildFetchData: function (options) {\n\t var defaults = {};\n\t if (this.order) {\n\t defaults.order = this.order;\n\t }\n\t return _.defaults(_.pick(options, this._fetchParams), defaults);\n\t },\n\t\n\t /** These attribute keys are valid params to fetch/API-index */\n\t _fetchParams: [\n\t /** model dependent string to control the order of models returned */\n\t 'order',\n\t /** limit the number of models returned from a fetch */\n\t 'limit',\n\t /** skip this number of models when fetching */\n\t 'offset',\n\t /** what series of attributes to return (model dependent) */\n\t 'view',\n\t /** individual keys to return for the models (see api/histories.index) */\n\t 'keys'],\n\t\n\t /** add any needed filters here based on collection state */\n\t _buildFetchFilters: function (options) {\n\t // override\n\t return _.clone(options.filters || {});\n\t },\n\t\n\t /** Convert dictionary filters to qqv style arrays */\n\t _fetchFiltersToAjaxData: function (filters) {\n\t // return as a map so ajax.data can extend from it\n\t var filterMap = {\n\t q: [],\n\t qv: []\n\t };\n\t _.each(filters, function (v, k) {\n\t // don't send if filter value is empty\n\t if (v === undefined || v === '') {\n\t return;\n\t }\n\t // json to python\n\t if (v === true) {\n\t v = 'True';\n\t }\n\t if (v === false) {\n\t v = 'False';\n\t }\n\t if (v === null) {\n\t v = 'None';\n\t }\n\t // map to k/v arrays (q/qv)\n\t filterMap.q.push(k);\n\t filterMap.qv.push(v);\n\t });\n\t return filterMap;\n\t },\n\t\n\t /** override to reset allFetched flag to false */\n\t reset: function (models, options) {\n\t this.allFetched = false;\n\t return Backbone.Collection.prototype.reset.call(this, models, options);\n\t },\n\t\n\t // ........................................................................ order\n\t order: null,\n\t\n\t /** @type {Object} map of collection available sorting orders containing comparator fns */\n\t comparators: {\n\t 'update_time': BASE_MVC.buildComparator('update_time', { ascending: false }),\n\t 'update_time-asc': BASE_MVC.buildComparator('update_time', { ascending: true }),\n\t 'create_time': BASE_MVC.buildComparator('create_time', { ascending: false }),\n\t 'create_time-asc': BASE_MVC.buildComparator('create_time', { ascending: true })\n\t },\n\t\n\t /** set the order and comparator for this collection then sort with the new order\n\t * @event 'changed-order' passed the new order and the collection\n\t */\n\t setOrder: function (order, options) {\n\t options = options || {};\n\t var collection = this;\n\t var comparator = collection.comparators[order];\n\t if (_.isUndefined(comparator)) {\n\t throw new Error('unknown order: ' + order);\n\t }\n\t // if( _.isUndefined( comparator ) ){ return; }\n\t if (comparator === collection.comparator) {\n\t return;\n\t }\n\t\n\t var oldOrder = collection.order;\n\t collection.order = order;\n\t collection.comparator = comparator;\n\t\n\t if (!options.silent) {\n\t collection.trigger('changed-order', options);\n\t }\n\t return collection;\n\t }\n\t\n\t });\n\t\n\t //=============================================================================\n\t /**\n\t *\n\t */\n\t var PaginatedCollection = ControlledFetchCollection.extend({\n\t\n\t /** @type {Number} limit used for each page's fetch */\n\t limitPerPage: 500,\n\t\n\t initialize: function (models, options) {\n\t ControlledFetchCollection.prototype.initialize.call(this, models, options);\n\t this.currentPage = options.currentPage || 0;\n\t },\n\t\n\t getTotalItemCount: function () {\n\t return this.length;\n\t },\n\t\n\t shouldPaginate: function () {\n\t return this.getTotalItemCount() >= this.limitPerPage;\n\t },\n\t\n\t getLastPage: function () {\n\t return Math.floor(this.getTotalItemCount() / this.limitPerPage);\n\t },\n\t\n\t getPageCount: function () {\n\t return this.getLastPage() + 1;\n\t },\n\t\n\t getPageLimitOffset: function (pageNum) {\n\t pageNum = this.constrainPageNum(pageNum);\n\t return {\n\t limit: this.limitPerPage,\n\t offset: pageNum * this.limitPerPage\n\t };\n\t },\n\t\n\t constrainPageNum: function (pageNum) {\n\t return Math.max(0, Math.min(pageNum, this.getLastPage()));\n\t },\n\t\n\t /** fetch the next page of data */\n\t fetchPage: function (pageNum, options) {\n\t var self = this;\n\t pageNum = self.constrainPageNum(pageNum);\n\t self.currentPage = pageNum;\n\t options = _.defaults(options || {}, self.getPageLimitOffset(pageNum));\n\t\n\t self.trigger('fetching-more');\n\t return self.fetch(options).always(function () {\n\t self.trigger('fetching-more-done');\n\t });\n\t },\n\t\n\t fetchCurrentPage: function (options) {\n\t return this.fetchPage(this.currentPage, options);\n\t },\n\t\n\t fetchPrevPage: function (options) {\n\t return this.fetchPage(this.currentPage - 1, options);\n\t },\n\t\n\t fetchNextPage: function (options) {\n\t return this.fetchPage(this.currentPage + 1, options);\n\t }\n\t });\n\t\n\t //=============================================================================\n\t /**\n\t * A Collection that will load more elements without reseting.\n\t */\n\t var InfinitelyScrollingCollection = ControlledFetchCollection.extend({\n\t\n\t /** @type {Number} limit used for the first fetch (or a reset) */\n\t limitOnFirstFetch: null,\n\t /** @type {Number} limit used for each subsequent fetch */\n\t limitPerFetch: 100,\n\t\n\t initialize: function (models, options) {\n\t ControlledFetchCollection.prototype.initialize.call(this, models, options);\n\t /** @type {Integer} number of contents to return from the first fetch */\n\t this.limitOnFirstFetch = options.limitOnFirstFetch || this.limitOnFirstFetch;\n\t /** @type {Integer} limit for every fetch after the first */\n\t this.limitPerFetch = options.limitPerFetch || this.limitPerFetch;\n\t /** @type {Boolean} are all contents fetched? */\n\t this.allFetched = false;\n\t /** @type {Integer} what was the offset of the last content returned */\n\t this.lastFetched = options.lastFetched || 0;\n\t },\n\t\n\t /** build ajax data/parameters from options */\n\t _buildFetchOptions: function (options) {\n\t // options (options for backbone.fetch and jquery.ajax generally)\n\t // backbone option; false here to make fetching an addititive process\n\t options.remove = options.remove || false;\n\t return ControlledFetchCollection.prototype._buildFetchOptions.call(this, options);\n\t },\n\t\n\t /** fetch the first 'page' of data */\n\t fetchFirst: function (options) {\n\t // console.log( 'ControlledFetchCollection.fetchFirst:', options );\n\t options = options ? _.clone(options) : {};\n\t this.allFetched = false;\n\t this.lastFetched = 0;\n\t return this.fetchMore(_.defaults(options, {\n\t reset: true,\n\t limit: this.limitOnFirstFetch\n\t }));\n\t },\n\t\n\t /** fetch the next page of data */\n\t fetchMore: function (options) {\n\t // console.log( 'ControlledFetchCollection.fetchMore:', options );\n\t options = _.clone(options || {});\n\t var collection = this;\n\t\n\t // console.log( 'fetchMore, options.reset:', options.reset );\n\t if (!options.reset && collection.allFetched) {\n\t return jQuery.when();\n\t }\n\t\n\t // TODO: this fails in the edge case where\n\t // the first fetch offset === limit (limit 4, offset 4, collection.length 4)\n\t options.offset = options.reset ? 0 : options.offset || collection.lastFetched;\n\t var limit = options.limit = options.limit || collection.limitPerFetch || null;\n\t // console.log( 'fetchMore, limit:', limit, 'offset:', options.offset );\n\t\n\t collection.trigger('fetching-more');\n\t return collection.fetch(options).always(function () {\n\t collection.trigger('fetching-more-done');\n\t })\n\t // maintain allFetched flag and trigger if all were fetched this time\n\t .done(function _postFetchMore(fetchedData) {\n\t var numFetched = _.isArray(fetchedData) ? fetchedData.length : 0;\n\t collection.lastFetched += numFetched;\n\t // console.log( 'fetchMore, lastFetched:', collection.lastFetched );\n\t // anything less than a full page means we got all there is to get\n\t if (!limit || numFetched < limit) {\n\t collection.allFetched = true;\n\t collection.trigger('all-fetched', this);\n\t }\n\t });\n\t },\n\t\n\t /** fetch all the collection */\n\t fetchAll: function (options) {\n\t // whitelist options to prevent allowing limit/offset/filters\n\t // (use vanilla fetch instead)\n\t options = options || {};\n\t var self = this;\n\t options = _.pick(options, 'silent');\n\t options.filters = {};\n\t return self.fetch(options).done(function (fetchData) {\n\t self.allFetched = true;\n\t self.trigger('all-fetched', self);\n\t });\n\t }\n\t });\n\t\n\t //==============================================================================\n\t return {\n\t ControlledFetchCollection: ControlledFetchCollection,\n\t PaginatedCollection: PaginatedCollection,\n\t InfinitelyScrollingCollection: InfinitelyScrollingCollection\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1)))\n\n/***/ }),\n/* 72 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t\n\t /* For presentation-related functionality shared across collection creators.\n\t Particularily overlapping functionality related to name processing and help.\n\t */\n\t var CollectionCreatorMixin = {\n\t\n\t /** add (or clear if clear is truthy) a validation warning to the DOM element described in what */\n\t _validationWarning: function (what, clear) {\n\t var VALIDATION_CLASS = 'validation-warning';\n\t if (what === 'name') {\n\t what = this.$('.collection-name').add(this.$('.collection-name-prompt'));\n\t this.$('.collection-name').focus().select();\n\t }\n\t if (clear) {\n\t what = what || this.$('.' + VALIDATION_CLASS);\n\t what.removeClass(VALIDATION_CLASS);\n\t } else {\n\t what.addClass(VALIDATION_CLASS);\n\t }\n\t },\n\t\n\t _changeHideOriginals: function (ev) {\n\t this.hideOriginals = this.$('.hide-originals').prop(\"checked\");\n\t },\n\t\n\t // ........................................................................ footer\n\t /** handle a collection name change */\n\t _changeName: function (ev) {\n\t this._validationWarning('name', !!this._getName());\n\t },\n\t\n\t /** check for enter key press when in the collection name and submit */\n\t _nameCheckForEnter: function (ev) {\n\t if (ev.keyCode === 13 && !this.blocking) {\n\t this._clickCreate();\n\t }\n\t },\n\t\n\t /** get the current collection name */\n\t _getName: function () {\n\t return _.escape(this.$('.collection-name').val());\n\t },\n\t\n\t // ........................................................................ header\n\t /** expand help */\n\t _clickMoreHelp: function (ev) {\n\t ev.stopPropagation();\n\t this.$('.main-help').addClass('expanded');\n\t this.$('.more-help').hide();\n\t },\n\t /** collapse help */\n\t _clickLessHelp: function (ev) {\n\t ev.stopPropagation();\n\t this.$('.main-help').removeClass('expanded');\n\t this.$('.more-help').show();\n\t },\n\t /** toggle help */\n\t _toggleHelp: function (ev) {\n\t ev.stopPropagation();\n\t this.$('.main-help').toggleClass('expanded');\n\t this.$('.more-help').toggle();\n\t },\n\t\n\t /** show an alert on the top of the interface containing message (alertClass is bootstrap's alert-*) */\n\t _showAlert: function (message, alertClass) {\n\t alertClass = alertClass || 'alert-danger';\n\t this.$('.main-help').hide();\n\t this.$('.header .alert').attr('class', 'alert alert-dismissable').addClass(alertClass).show().find('.alert-message').html(message);\n\t },\n\t /** hide the alerts at the top */\n\t _hideAlert: function (message) {\n\t this.$('.main-help').show();\n\t this.$('.header .alert').hide();\n\t },\n\t\n\t _cancelCreate: function (ev) {\n\t if (typeof this.oncancel === 'function') {\n\t this.oncancel.call(this);\n\t }\n\t },\n\t\n\t /** attempt to create the current collection */\n\t _clickCreate: function (ev) {\n\t var name = this._getName();\n\t if (!name) {\n\t this._validationWarning('name');\n\t } else if (!this.blocking) {\n\t this.createList(name);\n\t }\n\t },\n\t\n\t _setUpCommonSettings: function (attributes) {\n\t this.hideOriginals = attributes.defaultHideSourceItems || false;\n\t },\n\t\n\t /** render the footer, completion controls, and cancel controls */\n\t _renderFooter: function (speed, callback) {\n\t var instance = this;\n\t var $footer = this.$('.footer').empty().html(this.templates.footer());\n\t _.each(this.footerSettings, function (property, selector) {\n\t this.$(selector).prop('checked', instance[property]);\n\t });\n\t if (typeof this.oncancel === 'function') {\n\t this.$('.cancel-create.btn').show();\n\t }\n\t return $footer;\n\t },\n\t\n\t _creatorTemplates: {\n\t main: _.template(['', '', ''].join(''))\n\t }\n\t\n\t };\n\t\n\t //==============================================================================\n\t return {\n\t CollectionCreatorMixin: CollectionCreatorMixin\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2)))\n\n/***/ }),\n/* 73 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(81), __webpack_require__(36), __webpack_require__(35), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (LIST_VIEW, DC_MODEL, DC_LI, BASE_MVC, _l) {\n\t\n\t 'use strict';\n\t\n\t var logNamespace = 'collections';\n\t /* =============================================================================\n\t TODO:\n\t \n\t ============================================================================= */\n\t /** @class non-editable, read-only View/Controller for a dataset collection.\n\t */\n\t var _super = LIST_VIEW.ModelListPanel;\n\t var CollectionView = _super.extend(\n\t /** @lends CollectionView.prototype */{\n\t //MODEL is either a DatasetCollection (or subclass) or a DatasetCollectionElement (list of pairs)\n\t _logNamespace: logNamespace,\n\t\n\t className: _super.prototype.className + ' dataset-collection-panel',\n\t\n\t /** sub view class used for datasets */\n\t DatasetDCEViewClass: DC_LI.DatasetDCEListItemView,\n\t /** sub view class used for nested collections */\n\t NestedDCDCEViewClass: DC_LI.NestedDCDCEListItemView,\n\t /** key of attribute in model to assign to this.collection */\n\t modelCollectionKey: 'elements',\n\t\n\t // ......................................................................... SET UP\n\t /** Set up the view, set up storage, bind listeners to HistoryContents events\n\t * @param {Object} attributes optional settings for the panel\n\t */\n\t initialize: function (attributes) {\n\t _super.prototype.initialize.call(this, attributes);\n\t this.linkTarget = attributes.linkTarget || '_blank';\n\t\n\t this.hasUser = attributes.hasUser;\n\t /** A stack of panels that currently cover or hide this panel */\n\t this.panelStack = [];\n\t /** The text of the link to go back to the panel containing this one */\n\t this.parentName = attributes.parentName;\n\t /** foldout or drilldown */\n\t this.foldoutStyle = attributes.foldoutStyle || 'foldout';\n\t },\n\t\n\t _queueNewRender: function ($newRender, speed) {\n\t speed = speed === undefined ? this.fxSpeed : speed;\n\t var panel = this;\n\t panel.log('_queueNewRender:', $newRender, speed);\n\t\n\t // TODO: jquery@1.12 doesn't change display when the elem has display: flex\n\t // this causes display: block for those elems after the use of show/hide animations\n\t // animations are removed from this view for now until fixed\n\t panel._swapNewRender($newRender);\n\t panel.trigger('rendered', panel);\n\t },\n\t\n\t // ------------------------------------------------------------------------ sub-views\n\t /** In this override, use model.getVisibleContents */\n\t _filterCollection: function () {\n\t //TODO: should *not* be model.getVisibleContents - visibility is not model related\n\t return this.model.getVisibleContents();\n\t },\n\t\n\t /** override to return proper view class based on element_type */\n\t _getItemViewClass: function (model) {\n\t //this.debug( this + '._getItemViewClass:', model );\n\t //TODO: subclasses use DCEViewClass - but are currently unused - decide\n\t switch (model.get('element_type')) {\n\t case 'hda':\n\t return this.DatasetDCEViewClass;\n\t case 'dataset_collection':\n\t return this.NestedDCDCEViewClass;\n\t }\n\t throw new TypeError('Unknown element type:', model.get('element_type'));\n\t },\n\t\n\t /** override to add link target and anon */\n\t _getItemViewOptions: function (model) {\n\t var options = _super.prototype._getItemViewOptions.call(this, model);\n\t return _.extend(options, {\n\t linkTarget: this.linkTarget,\n\t hasUser: this.hasUser,\n\t //TODO: could move to only nested: list:paired\n\t foldoutStyle: this.foldoutStyle\n\t });\n\t },\n\t\n\t // ------------------------------------------------------------------------ collection sub-views\n\t /** In this override, add/remove expanded/collapsed model ids to/from web storage */\n\t _setUpItemViewListeners: function (view) {\n\t var panel = this;\n\t _super.prototype._setUpItemViewListeners.call(panel, view);\n\t\n\t // use pub-sub to: handle drilldown expansion and collapse\n\t panel.listenTo(view, {\n\t 'expanded:drilldown': function (v, drilldown) {\n\t this._expandDrilldownPanel(drilldown);\n\t },\n\t 'collapsed:drilldown': function (v, drilldown) {\n\t this._collapseDrilldownPanel(drilldown);\n\t }\n\t });\n\t return this;\n\t },\n\t\n\t /** Handle drill down by hiding this panels list and controls and showing the sub-panel */\n\t _expandDrilldownPanel: function (drilldown) {\n\t this.panelStack.push(drilldown);\n\t // hide this panel's controls and list, set the name for back navigation, and attach to the $el\n\t this.$('> .controls').add(this.$list()).hide();\n\t drilldown.parentName = this.model.get('name');\n\t this.$el.append(drilldown.render().$el);\n\t },\n\t\n\t /** Handle drilldown close by freeing the panel and re-rendering this panel */\n\t _collapseDrilldownPanel: function (drilldown) {\n\t this.panelStack.pop();\n\t this.render();\n\t },\n\t\n\t // ------------------------------------------------------------------------ panel events\n\t /** event map */\n\t events: {\n\t 'click .navigation .back': 'close'\n\t },\n\t\n\t /** close/remove this collection panel */\n\t close: function (event) {\n\t this.remove();\n\t this.trigger('close');\n\t },\n\t\n\t // ........................................................................ misc\n\t /** string rep */\n\t toString: function () {\n\t return 'CollectionView(' + (this.model ? this.model.get('name') : '') + ')';\n\t }\n\t });\n\t\n\t //------------------------------------------------------------------------------ TEMPLATES\n\t CollectionView.prototype.templates = function () {\n\t\n\t var controlsTemplate = BASE_MVC.wrapTemplate(['
', '<% if( collection.collection_type === \"list\" ){ %>', _l('a list of datasets'), '<% } else if( collection.collection_type === \"paired\" ){ %>', _l('a pair of datasets'), '<% } else if( collection.collection_type === \"list:paired\" ){ %>', _l('a list of paired datasets'), '<% } else if( collection.collection_type === \"list:list\" ){ %>', _l('a list of dataset lists'), '<% } %>', '
', '
', '', '
'], 'collection');\n\t\n\t return _.extend(_.clone(_super.prototype.templates), {\n\t controls: controlsTemplate\n\t });\n\t }();\n\t\n\t // =============================================================================\n\t /** @class non-editable, read-only View/Controller for a dataset collection. */\n\t var ListCollectionView = CollectionView.extend(\n\t /** @lends ListCollectionView.prototype */{\n\t\n\t //TODO: not strictly needed - due to switch in CollectionView._getContentClass\n\t /** sub view class used for datasets */\n\t DatasetDCEViewClass: DC_LI.DatasetDCEListItemView,\n\t\n\t // ........................................................................ misc\n\t /** string rep */\n\t toString: function () {\n\t return 'ListCollectionView(' + (this.model ? this.model.get('name') : '') + ')';\n\t }\n\t });\n\t\n\t // =============================================================================\n\t /** @class non-editable, read-only View/Controller for a dataset collection. */\n\t var PairCollectionView = ListCollectionView.extend(\n\t /** @lends PairCollectionView.prototype */{\n\t\n\t // ........................................................................ misc\n\t /** string rep */\n\t toString: function () {\n\t return 'PairCollectionView(' + (this.model ? this.model.get('name') : '') + ')';\n\t }\n\t });\n\t\n\t // =============================================================================\n\t /** @class non-editable, read-only View/Controller for a dataset collection. */\n\t var ListOfPairsCollectionView = CollectionView.extend(\n\t /** @lends ListOfPairsCollectionView.prototype */{\n\t\n\t //TODO: not strictly needed - due to switch in CollectionView._getContentClass\n\t /** sub view class used for nested collections */\n\t NestedDCDCEViewClass: DC_LI.NestedDCDCEListItemView.extend({\n\t foldoutPanelClass: PairCollectionView\n\t }),\n\t\n\t // ........................................................................ misc\n\t /** string rep */\n\t toString: function () {\n\t return 'ListOfPairsCollectionView(' + (this.model ? this.model.get('name') : '') + ')';\n\t }\n\t });\n\t\n\t // =============================================================================\n\t /** @class non-editable, read-only View/Controller for a list of lists dataset collection. */\n\t var ListOfListsCollectionView = CollectionView.extend({\n\t\n\t /** sub view class used for nested collections */\n\t NestedDCDCEViewClass: DC_LI.NestedDCDCEListItemView.extend({\n\t foldoutPanelClass: PairCollectionView\n\t }),\n\t\n\t /** string rep */\n\t toString: function () {\n\t return 'ListOfListsCollectionView(' + (this.model ? this.model.get('name') : '') + ')';\n\t }\n\t });\n\t\n\t //==============================================================================\n\t return {\n\t CollectionView: CollectionView,\n\t ListCollectionView: ListCollectionView,\n\t PairCollectionView: PairCollectionView,\n\t ListOfPairsCollectionView: ListOfPairsCollectionView,\n\t ListOfListsCollectionView: ListOfListsCollectionView\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2)))\n\n/***/ }),\n/* 74 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_, $) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(11), __webpack_require__(38), __webpack_require__(48), __webpack_require__(70), __webpack_require__(17), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (STATES, DATASET_LI, TAGS, ANNOTATIONS, faIconButton, BASE_MVC, _l) {\n\t\n\t 'use strict';\n\t //==============================================================================\n\t\n\t var _super = DATASET_LI.DatasetListItemView;\n\t /** @class Editing view for DatasetAssociation.\n\t */\n\t var DatasetListItemEdit = _super.extend(\n\t /** @lends DatasetListItemEdit.prototype */{\n\t\n\t /** set up: options */\n\t initialize: function (attributes) {\n\t _super.prototype.initialize.call(this, attributes);\n\t this.hasUser = attributes.hasUser;\n\t\n\t /** allow user purge of dataset files? */\n\t this.purgeAllowed = attributes.purgeAllowed || false;\n\t\n\t //TODO: move to HiddenUntilActivatedViewMixin\n\t /** should the tags editor be shown or hidden initially? */\n\t this.tagsEditorShown = attributes.tagsEditorShown || false;\n\t /** should the tags editor be shown or hidden initially? */\n\t this.annotationEditorShown = attributes.annotationEditorShown || false;\n\t },\n\t\n\t // ......................................................................... titlebar actions\n\t /** In this override, add the other two primary actions: edit and delete */\n\t _renderPrimaryActions: function () {\n\t var actions = _super.prototype._renderPrimaryActions.call(this);\n\t if (this.model.get('state') === STATES.NOT_VIEWABLE) {\n\t return actions;\n\t }\n\t // render the display, edit attr and delete icon-buttons\n\t return _super.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(), this._renderDeleteButton()]);\n\t },\n\t\n\t //TODO: move titleButtons into state renderers, remove state checks in the buttons\n\t\n\t /** Render icon-button to edit the attributes (format, permissions, etc.) this dataset. */\n\t _renderEditButton: function () {\n\t // don't show edit while uploading, in-accessible\n\t // DO show if in error (ala previous history panel)\n\t if (this.model.get('state') === STATES.DISCARDED || !this.model.get('accessible')) {\n\t return null;\n\t }\n\t\n\t var purged = this.model.get('purged'),\n\t deleted = this.model.get('deleted'),\n\t editBtnData = {\n\t title: _l('Edit attributes'),\n\t href: this.model.urls.edit,\n\t target: this.linkTarget,\n\t faIcon: 'fa-pencil',\n\t classes: 'edit-btn'\n\t };\n\t\n\t // disable if purged or deleted and explain why in the tooltip\n\t if (deleted || purged) {\n\t editBtnData.disabled = true;\n\t if (purged) {\n\t editBtnData.title = _l('Cannot edit attributes of datasets removed from disk');\n\t } else if (deleted) {\n\t editBtnData.title = _l('Undelete dataset to edit attributes');\n\t }\n\t\n\t // disable if still uploading or new\n\t } else if (_.contains([STATES.UPLOAD, STATES.NEW], this.model.get('state'))) {\n\t editBtnData.disabled = true;\n\t editBtnData.title = _l('This dataset is not yet editable');\n\t }\n\t return faIconButton(editBtnData);\n\t },\n\t\n\t /** Render icon-button to delete this hda. */\n\t _renderDeleteButton: function () {\n\t // don't show delete if...\n\t if (!this.model.get('accessible')) {\n\t return null;\n\t }\n\t\n\t var self = this,\n\t deletedAlready = this.model.isDeletedOrPurged();\n\t return faIconButton({\n\t title: !deletedAlready ? _l('Delete') : _l('Dataset is already deleted'),\n\t disabled: deletedAlready,\n\t faIcon: 'fa-times',\n\t classes: 'delete-btn',\n\t onclick: function () {\n\t // ...bler... tooltips being left behind in DOM (hover out never called on deletion)\n\t self.$el.find('.icon-btn.delete-btn').trigger('mouseout');\n\t self.model['delete']();\n\t }\n\t });\n\t },\n\t\n\t // ......................................................................... details\n\t /** In this override, add tags and annotations controls, make the ? dbkey a link to editing page */\n\t _renderDetails: function () {\n\t //TODO: generalize to be allow different details for each state\n\t var $details = _super.prototype._renderDetails.call(this),\n\t state = this.model.get('state');\n\t\n\t if (!this.model.isDeletedOrPurged() && _.contains([STATES.OK, STATES.FAILED_METADATA], state)) {\n\t this._renderTags($details);\n\t this._renderAnnotation($details);\n\t this._makeDbkeyEditLink($details);\n\t }\n\t\n\t this._setUpBehaviors($details);\n\t return $details;\n\t },\n\t\n\t /**************************************************************************\n\t * Render help button to show tool help text without rerunning the tool.\n\t * Issue #2100\n\t */\n\t _renderToolHelpButton: function () {\n\t var datasetID = this.model.attributes.dataset_id;\n\t var jobID = this.model.attributes.creating_job;\n\t var self = this;\n\t\n\t var parseToolBuild = function (data) {\n\t var helpString = '
';\n\t if (data.name && data.help) {\n\t helpString += 'Tool help for ' + data.name + '';\n\t helpString += data.help;\n\t } else {\n\t helpString += 'Tool help is unavailable for this dataset.';\n\t }\n\t helpString += '
';\n\t self.$el.find('.details').append($.parseHTML(helpString));\n\t };\n\t var parseToolID = function (data) {\n\t $.ajax({\n\t url: Galaxy.root + 'api/tools/' + data.tool_id + '/build'\n\t }).done(function (data) {\n\t parseToolBuild(data);\n\t }).fail(function () {\n\t parseToolBuild({});\n\t });\n\t };\n\t if (Galaxy.user.id === null) {\n\t return null;\n\t }\n\t return faIconButton({\n\t title: 'Tool Help',\n\t classes: 'icon-btn',\n\t href: '#',\n\t faIcon: 'fa-question',\n\t onclick: function () {\n\t var divString = 'thdiv-' + datasetID;\n\t if (self.$el.find(\".toolhelp\").length > 0) {\n\t self.$el.find(\".toolhelp\").toggle();\n\t } else {\n\t $.ajax({\n\t url: Galaxy.root + 'api/jobs/' + jobID\n\t }).done(function (data) {\n\t parseToolID(data);\n\t }).fail(function () {\n\t console.log('Failed at recovering job information from the Galaxy API for job id \"' + jobID + '\".');\n\t });\n\t }\n\t }\n\t });\n\t },\n\t //*************************************************************************\n\t\n\t /** Add less commonly used actions in the details section based on state */\n\t _renderSecondaryActions: function () {\n\t var actions = _super.prototype._renderSecondaryActions.call(this);\n\t switch (this.model.get('state')) {\n\t case STATES.UPLOAD:\n\t case STATES.NOT_VIEWABLE:\n\t return actions;\n\t case STATES.ERROR:\n\t // error button comes first\n\t actions.unshift(this._renderErrButton());\n\t return actions.concat([this._renderRerunButton(), this._renderToolHelpButton()]);\n\t case STATES.OK:\n\t case STATES.FAILED_METADATA:\n\t return actions.concat([this._renderRerunButton(), this._renderVisualizationsButton(), this._renderToolHelpButton()]);\n\t }\n\t return actions.concat([this._renderRerunButton(), this._renderToolHelpButton()]);\n\t },\n\t\n\t /** Render icon-button to report an error on this dataset to the galaxy admin. */\n\t _renderErrButton: function () {\n\t return faIconButton({\n\t title: _l('View or report this error'),\n\t href: this.model.urls.report_error,\n\t classes: 'report-error-btn',\n\t target: this.linkTarget,\n\t faIcon: 'fa-bug'\n\t });\n\t },\n\t\n\t /** Render icon-button to re-run the job that created this dataset. */\n\t _renderRerunButton: function () {\n\t var creating_job = this.model.get('creating_job');\n\t if (this.model.get('rerunnable')) {\n\t return faIconButton({\n\t title: _l('Run this job again'),\n\t href: this.model.urls.rerun,\n\t classes: 'rerun-btn',\n\t target: this.linkTarget,\n\t faIcon: 'fa-refresh',\n\t onclick: function (ev) {\n\t ev.preventDefault();\n\t Galaxy.router.push('/', { job_id: creating_job });\n\t }\n\t });\n\t }\n\t },\n\t\n\t /** Render an icon-button or popupmenu of links based on the applicable visualizations */\n\t _renderVisualizationsButton: function () {\n\t //TODO: someday - lazyload visualizations\n\t var visualizations = this.model.get('visualizations');\n\t if (this.model.isDeletedOrPurged() || !this.hasUser || !this.model.hasData() || _.isEmpty(visualizations)) {\n\t return null;\n\t }\n\t if (!_.isObject(visualizations[0])) {\n\t this.warn('Visualizations have been switched off');\n\t return null;\n\t }\n\t\n\t var $visualizations = $(this.templates.visualizations(visualizations, this));\n\t //HACK: need to re-write those directed at galaxy_main with linkTarget\n\t $visualizations.find('[target=\"galaxy_main\"]').attr('target', this.linkTarget);\n\t // use addBack here to include the root $visualizations elem (for the case of 1 visualization)\n\t this._addScratchBookFn($visualizations.find('.visualization-link').addBack('.visualization-link'));\n\t return $visualizations;\n\t },\n\t\n\t /** add scratchbook functionality to visualization links */\n\t _addScratchBookFn: function ($links) {\n\t var li = this;\n\t $links.click(function (ev) {\n\t if (Galaxy.frame && Galaxy.frame.active) {\n\t Galaxy.frame.add({\n\t title: 'Visualization',\n\t url: $(this).attr('href')\n\t });\n\t ev.preventDefault();\n\t ev.stopPropagation();\n\t }\n\t });\n\t },\n\t\n\t //TODO: if possible move these to readonly view - but display the owner's tags/annotation (no edit)\n\t /** Render the tags list/control */\n\t _renderTags: function ($where) {\n\t if (!this.hasUser) {\n\t return;\n\t }\n\t var view = this;\n\t this.tagsEditor = new TAGS.TagsEditor({\n\t model: this.model,\n\t el: $where.find('.tags-display'),\n\t onshowFirstTime: function () {\n\t this.render();\n\t },\n\t // persist state on the hda view (and not the editor) since these are currently re-created each time\n\t onshow: function () {\n\t view.tagsEditorShown = true;\n\t },\n\t onhide: function () {\n\t view.tagsEditorShown = false;\n\t },\n\t $activator: faIconButton({\n\t title: _l('Edit dataset tags'),\n\t classes: 'tag-btn',\n\t faIcon: 'fa-tags'\n\t }).appendTo($where.find('.actions .right'))\n\t });\n\t if (this.tagsEditorShown) {\n\t this.tagsEditor.toggle(true);\n\t }\n\t },\n\t\n\t /** Render the annotation display/control */\n\t _renderAnnotation: function ($where) {\n\t if (!this.hasUser) {\n\t return;\n\t }\n\t var view = this;\n\t this.annotationEditor = new ANNOTATIONS.AnnotationEditor({\n\t model: this.model,\n\t el: $where.find('.annotation-display'),\n\t onshowFirstTime: function () {\n\t this.render();\n\t },\n\t // persist state on the hda view (and not the editor) since these are currently re-created each time\n\t onshow: function () {\n\t view.annotationEditorShown = true;\n\t },\n\t onhide: function () {\n\t view.annotationEditorShown = false;\n\t },\n\t $activator: faIconButton({\n\t title: _l('Edit dataset annotation'),\n\t classes: 'annotate-btn',\n\t faIcon: 'fa-comment'\n\t }).appendTo($where.find('.actions .right'))\n\t });\n\t if (this.annotationEditorShown) {\n\t this.annotationEditor.toggle(true);\n\t }\n\t },\n\t\n\t /** If the format/dbkey/genome_build isn't set, make the display a link to the edit page */\n\t _makeDbkeyEditLink: function ($details) {\n\t // make the dbkey a link to editing\n\t if (this.model.get('metadata_dbkey') === '?' && !this.model.isDeletedOrPurged()) {\n\t var editableDbkey = $('?').attr('href', this.model.urls.edit).attr('target', this.linkTarget);\n\t $details.find('.dbkey .value').replaceWith(editableDbkey);\n\t }\n\t },\n\t\n\t // ......................................................................... events\n\t /** event map */\n\t events: _.extend(_.clone(_super.prototype.events), {\n\t 'click .undelete-link': '_clickUndeleteLink',\n\t 'click .purge-link': '_clickPurgeLink',\n\t\n\t 'click .edit-btn': function (ev) {\n\t this.trigger('edit', this, ev);\n\t },\n\t 'click .delete-btn': function (ev) {\n\t this.trigger('delete', this, ev);\n\t },\n\t 'click .rerun-btn': function (ev) {\n\t this.trigger('rerun', this, ev);\n\t },\n\t 'click .report-err-btn': function (ev) {\n\t this.trigger('report-err', this, ev);\n\t },\n\t 'click .visualization-btn': function (ev) {\n\t this.trigger('visualize', this, ev);\n\t },\n\t 'click .dbkey a': function (ev) {\n\t this.trigger('edit', this, ev);\n\t }\n\t }),\n\t\n\t /** listener for item undelete (in the messages section) */\n\t _clickUndeleteLink: function (ev) {\n\t this.model.undelete();\n\t return false;\n\t },\n\t\n\t /** listener for item purge (in the messages section) */\n\t _clickPurgeLink: function (ev) {\n\t if (confirm(_l('This will permanently remove the data in your dataset. Are you sure?'))) {\n\t this.model.purge();\n\t }\n\t return false;\n\t },\n\t\n\t // ......................................................................... misc\n\t /** string rep */\n\t toString: function () {\n\t var modelString = this.model ? this.model + '' : '(no model)';\n\t return 'HDAEditView(' + modelString + ')';\n\t }\n\t });\n\t\n\t // ............................................................................ TEMPLATES\n\t /** underscore templates */\n\t DatasetListItemEdit.prototype.templates = function () {\n\t\n\t var warnings = _.extend({}, _super.prototype.templates.warnings, {\n\t failed_metadata: BASE_MVC.wrapTemplate([\n\t // in this override, provide a link to the edit page\n\t '<% if( dataset.state === \"failed_metadata\" ){ %>', '
', '<% } %>'], 'dataset'),\n\t\n\t deleted: BASE_MVC.wrapTemplate([\n\t // in this override, provide links to undelete or purge the dataset\n\t '<% if( dataset.deleted && !dataset.purged ){ %>',\n\t // deleted not purged\n\t '
', '<% } %>'], 'visualizations');\n\t\n\t return _.extend({}, _super.prototype.templates, {\n\t warnings: warnings,\n\t visualizations: visualizationsTemplate\n\t });\n\t }();\n\t\n\t //==============================================================================\n\t return {\n\t DatasetListItemEdit: DatasetListItemEdit\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1)))\n\n/***/ }),\n/* 75 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, jQuery) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(11), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (STATES, BASE_MVC, _l) {\n\t 'use strict';\n\t\n\t var logNamespace = 'dataset';\n\t //==============================================================================\n\t var searchableMixin = BASE_MVC.SearchableModelMixin;\n\t /** @class base model for any DatasetAssociation (HDAs, LDDAs, DatasetCollectionDAs).\n\t * No knowledge of what type (HDA/LDDA/DCDA) should be needed here.\n\t * The DA's are made searchable (by attribute) by mixing in SearchableModelMixin.\n\t */\n\t var DatasetAssociation = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(BASE_MVC.mixin(searchableMixin, /** @lends DatasetAssociation.prototype */{\n\t _logNamespace: logNamespace,\n\t\n\t /** default attributes for a model */\n\t defaults: {\n\t state: STATES.NEW,\n\t deleted: false,\n\t purged: false,\n\t name: '(unnamed dataset)',\n\t accessible: true,\n\t // sniffed datatype (sam, tabular, bed, etc.)\n\t data_type: '',\n\t file_ext: '',\n\t file_size: 0,\n\t\n\t // array of associated file types (eg. [ 'bam_index', ... ])\n\t meta_files: [],\n\t\n\t misc_blurb: '',\n\t misc_info: '',\n\t\n\t tags: []\n\t // do NOT default on annotation, as this default is valid and will be passed on 'save'\n\t // which is incorrect behavior when the model is only partially fetched (annos are not passed in summary data)\n\t //annotation : ''\n\t },\n\t\n\t /** instance vars and listeners */\n\t initialize: function (attributes, options) {\n\t this.debug(this + '(Dataset).initialize', attributes, options);\n\t\n\t //!! this state is not in trans.app.model.Dataset.states - set it here -\n\t if (!this.get('accessible')) {\n\t this.set('state', STATES.NOT_VIEWABLE);\n\t }\n\t\n\t /** Datasets rely/use some web controllers - have the model generate those URLs on startup */\n\t this.urls = this._generateUrls();\n\t\n\t this._setUpListeners();\n\t },\n\t\n\t /** returns misc. web urls for rendering things like re-run, display, etc. */\n\t _generateUrls: function () {\n\t var id = this.get('id');\n\t if (!id) {\n\t return {};\n\t }\n\t var urls = {\n\t 'purge': 'datasets/' + id + '/purge_async',\n\t 'display': 'datasets/' + id + '/display/?preview=True',\n\t 'edit': 'datasets/' + id + '/edit',\n\t 'download': 'datasets/' + id + '/display' + this._downloadQueryParameters(),\n\t 'report_error': 'dataset/errors?id=' + id,\n\t 'rerun': 'tool_runner/rerun?id=' + id,\n\t 'show_params': 'datasets/' + id + '/show_params',\n\t 'visualization': 'visualization',\n\t 'meta_download': 'dataset/get_metadata_file?hda_id=' + id + '&metadata_name='\n\t };\n\t _.each(urls, function (value, key) {\n\t urls[key] = Galaxy.root + value;\n\t });\n\t this.urls = urls;\n\t return urls;\n\t },\n\t\n\t _downloadQueryParameters: function () {\n\t return '?to_ext=' + this.get('file_ext');\n\t },\n\t\n\t /** set up any event listeners\n\t * event: state:ready fired when this DA moves into/is already in a ready state\n\t */\n\t _setUpListeners: function () {\n\t // if the state has changed and the new state is a ready state, fire an event\n\t this.on('change:state', function (currModel, newState) {\n\t this.log(this + ' has changed state:', currModel, newState);\n\t if (this.inReadyState()) {\n\t this.trigger('state:ready', currModel, newState, this.previous('state'));\n\t }\n\t });\n\t // the download url (currently) relies on having a correct file extension\n\t this.on('change:id change:file_ext', function (currModel) {\n\t this._generateUrls();\n\t });\n\t },\n\t\n\t // ........................................................................ common queries\n\t /** override to add urls */\n\t toJSON: function () {\n\t var json = Backbone.Model.prototype.toJSON.call(this);\n\t //console.warn( 'returning json?' );\n\t //return json;\n\t return _.extend(json, {\n\t urls: this.urls\n\t });\n\t },\n\t\n\t /** Is this dataset deleted or purged? */\n\t isDeletedOrPurged: function () {\n\t return this.get('deleted') || this.get('purged');\n\t },\n\t\n\t /** Is this dataset in a 'ready' state; where 'Ready' states are states where no\n\t * processing (for the ds) is left to do on the server.\n\t */\n\t inReadyState: function () {\n\t var ready = _.contains(STATES.READY_STATES, this.get('state'));\n\t return this.isDeletedOrPurged() || ready;\n\t },\n\t\n\t /** Does this model already contain detailed data (as opposed to just summary level data)? */\n\t hasDetails: function () {\n\t // if it's inaccessible assume it has everything it needs\n\t if (!this.get('accessible')) {\n\t return true;\n\t }\n\t return this.has('annotation');\n\t },\n\t\n\t /** Convenience function to match dataset.has_data. */\n\t hasData: function () {\n\t return this.get('file_size') > 0;\n\t },\n\t\n\t // ........................................................................ ajax\n\t fetch: function (options) {\n\t var dataset = this;\n\t return Backbone.Model.prototype.fetch.call(this, options).always(function () {\n\t dataset._generateUrls();\n\t });\n\t },\n\t\n\t /** override to use actual Dates objects for create/update times */\n\t parse: function (response, options) {\n\t var parsed = Backbone.Model.prototype.parse.call(this, response, options);\n\t if (parsed.create_time) {\n\t parsed.create_time = new Date(parsed.create_time);\n\t }\n\t if (parsed.update_time) {\n\t parsed.update_time = new Date(parsed.update_time);\n\t }\n\t return parsed;\n\t },\n\t\n\t /** override to wait by default */\n\t save: function (attrs, options) {\n\t options = options || {};\n\t options.wait = _.isUndefined(options.wait) ? true : options.wait;\n\t return Backbone.Model.prototype.save.call(this, attrs, options);\n\t },\n\t\n\t //NOTE: subclasses of DA's will need to implement url and urlRoot in order to have these work properly\n\t /** save this dataset, _Mark_ing it as deleted (just a flag) */\n\t 'delete': function (options) {\n\t if (this.get('deleted')) {\n\t return jQuery.when();\n\t }\n\t return this.save({ deleted: true }, options);\n\t },\n\t /** save this dataset, _Mark_ing it as undeleted */\n\t undelete: function (options) {\n\t if (!this.get('deleted') || this.get('purged')) {\n\t return jQuery.when();\n\t }\n\t return this.save({ deleted: false }, options);\n\t },\n\t\n\t /** remove the file behind this dataset from the filesystem (if permitted) */\n\t purge: function _purge(options) {\n\t //TODO: use, override model.destroy, HDA.delete({ purge: true })\n\t if (this.get('purged')) {\n\t return jQuery.when();\n\t }\n\t options = options || {};\n\t options.url = this.urls.purge;\n\t\n\t //TODO: ideally this would be a DELETE call to the api\n\t // using purge async for now\n\t var hda = this,\n\t xhr = jQuery.ajax(options);\n\t xhr.done(function (message, status, responseObj) {\n\t hda.set({ deleted: true, purged: true });\n\t });\n\t xhr.fail(function (xhr, status, message) {\n\t // Exception messages are hidden within error page including: '...not allowed in this Galaxy instance.'\n\t // unbury and re-add to xhr\n\t var error = _l(\"Unable to purge dataset\");\n\t var messageBuriedInUnfortunatelyFormattedError = 'Removal of datasets by users ' + 'is not allowed in this Galaxy instance';\n\t if (xhr.responseJSON && xhr.responseJSON.error) {\n\t error = xhr.responseJSON.error;\n\t } else if (xhr.responseText.indexOf(messageBuriedInUnfortunatelyFormattedError) !== -1) {\n\t error = messageBuriedInUnfortunatelyFormattedError;\n\t }\n\t xhr.responseText = error;\n\t hda.trigger('error', hda, xhr, options, _l(error), { error: error });\n\t });\n\t return xhr;\n\t },\n\t\n\t // ........................................................................ searching\n\t /** what attributes of an HDA will be used in a text search */\n\t searchAttributes: ['name', 'file_ext', 'genome_build', 'misc_blurb', 'misc_info', 'annotation', 'tags'],\n\t\n\t /** our attr keys don't often match the labels we display to the user - so, when using\n\t * attribute specifiers ('name=\"bler\"') in a term, allow passing in aliases for the\n\t * following attr keys.\n\t */\n\t searchAliases: {\n\t title: 'name',\n\t format: 'file_ext',\n\t database: 'genome_build',\n\t blurb: 'misc_blurb',\n\t description: 'misc_blurb',\n\t info: 'misc_info',\n\t tag: 'tags'\n\t },\n\t\n\t // ........................................................................ misc\n\t /** String representation */\n\t toString: function () {\n\t var nameAndId = this.get('id') || '';\n\t if (this.get('name')) {\n\t nameAndId = '\"' + this.get('name') + '\",' + nameAndId;\n\t }\n\t return 'Dataset(' + nameAndId + ')';\n\t }\n\t }));\n\t\n\t //==============================================================================\n\t /** @class Backbone collection for dataset associations.\n\t */\n\t var DatasetAssociationCollection = Backbone.Collection.extend(BASE_MVC.LoggableMixin).extend(\n\t /** @lends HistoryContents.prototype */{\n\t _logNamespace: logNamespace,\n\t\n\t model: DatasetAssociation,\n\t\n\t /** root api url */\n\t urlRoot: Galaxy.root + 'api/datasets',\n\t\n\t /** url fn */\n\t url: function () {\n\t return this.urlRoot;\n\t },\n\t\n\t // ........................................................................ common queries\n\t /** Get the ids of every item in this collection\n\t * @returns array of encoded ids\n\t */\n\t ids: function () {\n\t return this.map(function (item) {\n\t return item.get('id');\n\t });\n\t },\n\t\n\t /** Get contents that are not ready\n\t * @returns array of content models\n\t */\n\t notReady: function () {\n\t return this.filter(function (content) {\n\t return !content.inReadyState();\n\t });\n\t },\n\t\n\t /** return true if any datasets don't have details */\n\t haveDetails: function () {\n\t return this.all(function (dataset) {\n\t return dataset.hasDetails();\n\t });\n\t },\n\t\n\t // ........................................................................ ajax\n\t /** using a queue, perform ajaxFn on each of the models in this collection */\n\t ajaxQueue: function (ajaxFn, options) {\n\t var deferred = jQuery.Deferred(),\n\t startingLength = this.length,\n\t responses = [];\n\t\n\t if (!startingLength) {\n\t deferred.resolve([]);\n\t return deferred;\n\t }\n\t\n\t // use reverse order (stylistic choice)\n\t var ajaxFns = this.chain().reverse().map(function (dataset, i) {\n\t return function () {\n\t var xhr = ajaxFn.call(dataset, options);\n\t // if successful, notify using the deferred to allow tracking progress\n\t xhr.done(function (response) {\n\t deferred.notify({ curr: i, total: startingLength, response: response, model: dataset });\n\t });\n\t // (regardless of previous error or success) if not last ajax call, shift and call the next\n\t // if last fn, resolve deferred\n\t xhr.always(function (response) {\n\t responses.push(response);\n\t if (ajaxFns.length) {\n\t ajaxFns.shift()();\n\t } else {\n\t deferred.resolve(responses);\n\t }\n\t });\n\t };\n\t }).value();\n\t // start the queue\n\t ajaxFns.shift()();\n\t\n\t return deferred;\n\t },\n\t\n\t // ........................................................................ sorting/filtering\n\t /** return a new collection of datasets whose attributes contain the substring matchesWhat */\n\t matches: function (matchesWhat) {\n\t return this.filter(function (dataset) {\n\t return dataset.matches(matchesWhat);\n\t });\n\t },\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return ['DatasetAssociationCollection(', this.length, ')'].join('');\n\t }\n\t });\n\t\n\t //==============================================================================\n\t return {\n\t DatasetAssociation: DatasetAssociation,\n\t DatasetAssociationCollection: DatasetAssociationCollection\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ }),\n/* 76 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(38), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (DATASET_LI, BASE_MVC, _l) {\n\t\n\t 'use strict';\n\t\n\t //==============================================================================\n\t\n\t var _super = DATASET_LI.DatasetListItemView;\n\t /** @class Read only view for HistoryDatasetAssociation.\n\t * Since there are no controls on the HDAView to hide the dataset,\n\t * the primary thing this class does (currently) is override templates\n\t * to render the HID.\n\t */\n\t var HDAListItemView = _super.extend(\n\t /** @lends HDAListItemView.prototype */{\n\t\n\t className: _super.prototype.className + \" history-content\",\n\t\n\t initialize: function (attributes, options) {\n\t _super.prototype.initialize.call(this, attributes, options);\n\t },\n\t\n\t // ......................................................................... misc\n\t /** String representation */\n\t toString: function () {\n\t var modelString = this.model ? this.model + '' : '(no model)';\n\t return 'HDAListItemView(' + modelString + ')';\n\t }\n\t });\n\t\n\t // ............................................................................ TEMPLATES\n\t /** underscore templates */\n\t HDAListItemView.prototype.templates = function () {\n\t\n\t var titleBarTemplate = BASE_MVC.wrapTemplate([\n\t // adding the hid display to the title\n\t '
', '', '
',\n\t //TODO: remove whitespace and use margin-right\n\t '<%- dataset.hid %> ', '<%- dataset.name %>', '
'], 'dataset');\n\t\n\t var warnings = _.extend({}, _super.prototype.templates.warnings, {\n\t hidden: BASE_MVC.wrapTemplate([\n\t // add a warning when hidden\n\t '<% if( !dataset.visible ){ %>', '
', _l('This dataset has been hidden'), '
', '<% } %>'], 'dataset')\n\t });\n\t\n\t return _.extend({}, _super.prototype.templates, {\n\t titleBar: titleBarTemplate,\n\t warnings: warnings\n\t });\n\t }();\n\t\n\t //==============================================================================\n\t return {\n\t HDAListItemView: HDAListItemView\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2)))\n\n/***/ }),\n/* 77 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(75), __webpack_require__(79), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (DATASET, HISTORY_CONTENT, BASE_MVC, _l) {\n\t 'use strict';\n\t\n\t //==============================================================================\n\t\n\t var _super = DATASET.DatasetAssociation,\n\t hcontentMixin = HISTORY_CONTENT.HistoryContentMixin;\n\t /** @class (HDA) model for a Galaxy dataset contained in and related to a history.\n\t */\n\t var HistoryDatasetAssociation = _super.extend(BASE_MVC.mixin(hcontentMixin,\n\t /** @lends HistoryDatasetAssociation.prototype */{\n\t\n\t /** default attributes for a model */\n\t defaults: _.extend({}, _super.prototype.defaults, hcontentMixin.defaults, {\n\t history_content_type: 'dataset',\n\t model_class: 'HistoryDatasetAssociation'\n\t })\n\t }));\n\t\n\t //==============================================================================\n\t return {\n\t HistoryDatasetAssociation: HistoryDatasetAssociation\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2)))\n\n/***/ }),\n/* 78 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(11), __webpack_require__(35), __webpack_require__(73), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (STATES, DC_LI, DC_VIEW, BASE_MVC, _l) {\n\t\n\t 'use strict';\n\t\n\t //==============================================================================\n\t\n\t var _super = DC_LI.DCListItemView;\n\t /** @class Read only view for HistoryDatasetCollectionAssociation (a dataset collection inside a history).\n\t */\n\t var HDCAListItemView = _super.extend(\n\t /** @lends HDCAListItemView.prototype */{\n\t\n\t className: _super.prototype.className + \" history-content\",\n\t\n\t /** event listeners */\n\t _setUpListeners: function () {\n\t _super.prototype._setUpListeners.call(this);\n\t this.listenTo(this.model, {\n\t 'change:tags change:populated change:visible': function (model, options) {\n\t this.render();\n\t }\n\t });\n\t },\n\t\n\t /** Override to provide the proper collections panels as the foldout */\n\t _getFoldoutPanelClass: function () {\n\t switch (this.model.get('collection_type')) {\n\t case 'list':\n\t return DC_VIEW.ListCollectionView;\n\t case 'paired':\n\t return DC_VIEW.PairCollectionView;\n\t case 'list:paired':\n\t return DC_VIEW.ListOfPairsCollectionView;\n\t case 'list:list':\n\t return DC_VIEW.ListOfListsCollectionView;\n\t }\n\t throw new TypeError('Uknown collection_type: ' + this.model.get('collection_type'));\n\t },\n\t\n\t /** In this override, add the state as a class for use with state-based CSS */\n\t _swapNewRender: function ($newRender) {\n\t _super.prototype._swapNewRender.call(this, $newRender);\n\t //TODO: model currently has no state\n\t var state = !this.model.get('populated') ? STATES.RUNNING : STATES.OK;\n\t //if( this.model.has( 'state' ) ){\n\t this.$el.addClass('state-' + state);\n\t //}\n\t return this.$el;\n\t },\n\t\n\t // ......................................................................... misc\n\t /** String representation */\n\t toString: function () {\n\t var modelString = this.model ? this.model + '' : '(no model)';\n\t return 'HDCAListItemView(' + modelString + ')';\n\t }\n\t });\n\t\n\t /** underscore templates */\n\t HDCAListItemView.prototype.templates = function () {\n\t\n\t var warnings = _.extend({}, _super.prototype.templates.warnings, {\n\t hidden: BASE_MVC.wrapTemplate([\n\t // add a warning when hidden\n\t '<% if( !collection.visible ){ %>', '
', _l('This collection has been hidden'), '
', '<% } %>'], 'collection')\n\t });\n\t\n\t // could steal this from hda-base (or use mixed content)\n\t var titleBarTemplate = BASE_MVC.wrapTemplate([\n\t // adding the hid display to the title\n\t '
', '', '
',\n\t //TODO: remove whitespace and use margin-right\n\t '<%- collection.hid %> ', '<%- collection.name %>', '
'], 'collection');\n\t\n\t return _.extend({}, _super.prototype.templates, {\n\t warnings: warnings,\n\t titleBar: titleBarTemplate\n\t });\n\t }();\n\t\n\t //==============================================================================\n\t return {\n\t HDCAListItemView: HDCAListItemView\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2)))\n\n/***/ }),\n/* 79 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(jQuery) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(11), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (STATES, BASE_MVC, _l) {\n\t 'use strict';\n\t\n\t //==============================================================================\n\t /** @class Mixin for HistoryContents content (HDAs, HDCAs).\n\t */\n\t\n\t var HistoryContentMixin = {\n\t\n\t /** default attributes for a model */\n\t defaults: {\n\t /** parent (containing) history */\n\t history_id: null,\n\t /** some content_type (HistoryContents can contain mixed model classes) */\n\t history_content_type: null,\n\t /** indicating when/what order the content was generated in the context of the history */\n\t hid: null,\n\t /** whether the user wants the content shown (visible) */\n\t visible: true\n\t },\n\t\n\t // ........................................................................ mixed content element\n\t // In order to be part of a MIXED bbone collection, we can't rely on the id\n\t // (which may collide btwn models of different classes)\n\t // Instead, use type_id which prefixes the history_content_type so the bbone collection can differentiate\n\t idAttribute: 'type_id',\n\t\n\t // ........................................................................ common queries\n\t /** the more common alias of visible */\n\t hidden: function () {\n\t return !this.get('visible');\n\t },\n\t\n\t //TODO: remove\n\t /** based on includeDeleted, includeHidden (gen. from the container control),\n\t * would this ds show in the list of ds's?\n\t * @param {Boolean} includeDeleted are we showing deleted hdas?\n\t * @param {Boolean} includeHidden are we showing hidden hdas?\n\t */\n\t isVisible: function (includeDeleted, includeHidden) {\n\t var isVisible = true;\n\t if (!includeDeleted && (this.get('deleted') || this.get('purged'))) {\n\t isVisible = false;\n\t }\n\t if (!includeHidden && !this.get('visible')) {\n\t isVisible = false;\n\t }\n\t return isVisible;\n\t },\n\t\n\t // ........................................................................ ajax\n\t //TODO?: these are probably better done on the leaf classes\n\t /** history content goes through the 'api/histories' API */\n\t urlRoot: Galaxy.root + 'api/histories/',\n\t\n\t /** full url spec. for this content */\n\t url: function () {\n\t var url = this.urlRoot + this.get('history_id') + '/contents/' + this.get('history_content_type') + 's/' + this.get('id');\n\t return url;\n\t },\n\t\n\t /** save this content as not visible */\n\t hide: function (options) {\n\t if (!this.get('visible')) {\n\t return jQuery.when();\n\t }\n\t return this.save({ visible: false }, options);\n\t },\n\t /** save this content as visible */\n\t unhide: function (options) {\n\t if (this.get('visible')) {\n\t return jQuery.when();\n\t }\n\t return this.save({ visible: true }, options);\n\t },\n\t\n\t // ........................................................................ misc\n\t toString: function () {\n\t return [this.get('type_id'), this.get('hid'), this.get('name')].join(':');\n\t }\n\t };\n\t\n\t //==============================================================================\n\t return {\n\t HistoryContentMixin: HistoryContentMixin\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1)))\n\n/***/ }),\n/* 80 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, jQuery, _, $) {\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(45), __webpack_require__(46), __webpack_require__(71), __webpack_require__(4), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (HISTORY_CONTENTS, HISTORY_PREFS, CONTROLLED_FETCH_COLLECTION, UTILS, BASE_MVC, _l) {\n\t 'use strict';\n\t\n\t //==============================================================================\n\t /** @class Model for a Galaxy history resource - both a record of user\n\t * tool use and a collection of the datasets those tools produced.\n\t * @name History\n\t * @augments Backbone.Model\n\t */\n\t\n\t var History = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(BASE_MVC.mixin(BASE_MVC.SearchableModelMixin, /** @lends History.prototype */{\n\t _logNamespace: 'history',\n\t\n\t /** ms between fetches when checking running jobs/datasets for updates */\n\t UPDATE_DELAY: 4000,\n\t\n\t // values from api (may need more)\n\t defaults: {\n\t model_class: 'History',\n\t id: null,\n\t name: 'Unnamed History',\n\t state: 'new',\n\t\n\t deleted: false,\n\t contents_active: {},\n\t contents_states: {}\n\t },\n\t\n\t urlRoot: Galaxy.root + 'api/histories',\n\t\n\t contentsClass: HISTORY_CONTENTS.HistoryContents,\n\t\n\t /** What model fields to search with */\n\t searchAttributes: ['name', 'annotation', 'tags'],\n\t\n\t /** Adding title and singular tag */\n\t searchAliases: {\n\t title: 'name',\n\t tag: 'tags'\n\t },\n\t\n\t // ........................................................................ set up/tear down\n\t /** Set up the model\n\t * @param {Object} historyJSON model data for this History\n\t * @param {Object} options any extra settings including logger\n\t */\n\t initialize: function (historyJSON, options) {\n\t options = options || {};\n\t this.logger = options.logger || null;\n\t this.log(this + \".initialize:\", historyJSON, options);\n\t\n\t /** HistoryContents collection of the HDAs contained in this history. */\n\t this.contents = new this.contentsClass([], {\n\t history: this,\n\t historyId: this.get('id'),\n\t order: options.order\n\t });\n\t\n\t this._setUpListeners();\n\t this._setUpCollectionListeners();\n\t\n\t /** cached timeout id for the dataset updater */\n\t this.updateTimeoutId = null;\n\t },\n\t\n\t /** set up any event listeners for this history including those to the contained HDAs\n\t * events: error:contents if an error occurred with the contents collection\n\t */\n\t _setUpListeners: function () {\n\t // if the model's id changes ('current' or null -> an actual id), update the contents history_id\n\t return this.on({\n\t 'error': function (model, xhr, options, msg, details) {\n\t this.clearUpdateTimeout();\n\t },\n\t 'change:id': function (model, newId) {\n\t if (this.contents) {\n\t this.contents.historyId = newId;\n\t }\n\t }\n\t });\n\t },\n\t\n\t /** event handlers for the contents submodels */\n\t _setUpCollectionListeners: function () {\n\t if (!this.contents) {\n\t return this;\n\t }\n\t // bubble up errors\n\t return this.listenTo(this.contents, {\n\t 'error': function () {\n\t this.trigger.apply(this, jQuery.makeArray(arguments));\n\t }\n\t });\n\t },\n\t\n\t // ........................................................................ derived attributes\n\t /** */\n\t contentsShown: function () {\n\t var contentsActive = this.get('contents_active');\n\t var shown = contentsActive.active || 0;\n\t shown += this.contents.includeDeleted ? contentsActive.deleted : 0;\n\t shown += this.contents.includeHidden ? contentsActive.hidden : 0;\n\t return shown;\n\t },\n\t\n\t /** convert size in bytes to a more human readable version */\n\t nice_size: function () {\n\t var size = this.get('size');\n\t return size ? UTILS.bytesToString(size, true, 2) : _l('(empty)');\n\t },\n\t\n\t /** override to add nice_size */\n\t toJSON: function () {\n\t return _.extend(Backbone.Model.prototype.toJSON.call(this), {\n\t nice_size: this.nice_size()\n\t });\n\t },\n\t\n\t /** override to allow getting nice_size */\n\t get: function (key) {\n\t if (key === 'nice_size') {\n\t return this.nice_size();\n\t }\n\t return Backbone.Model.prototype.get.apply(this, arguments);\n\t },\n\t\n\t // ........................................................................ common queries\n\t /** T/F is this history owned by the current user (Galaxy.user)\n\t * Note: that this will return false for an anon user even if the history is theirs.\n\t */\n\t ownedByCurrUser: function () {\n\t // no currUser\n\t if (!Galaxy || !Galaxy.user) {\n\t return false;\n\t }\n\t // user is anon or history isn't owned\n\t if (Galaxy.user.isAnonymous() || Galaxy.user.id !== this.get('user_id')) {\n\t return false;\n\t }\n\t return true;\n\t },\n\t\n\t /** Return the number of running jobs assoc with this history (note: unknown === 0) */\n\t numOfUnfinishedJobs: function () {\n\t var unfinishedJobIds = this.get('non_ready_jobs');\n\t return unfinishedJobIds ? unfinishedJobIds.length : 0;\n\t },\n\t\n\t /** Return the number of running hda/hdcas in this history (note: unknown === 0) */\n\t numOfUnfinishedShownContents: function () {\n\t return this.contents.runningAndActive().length || 0;\n\t },\n\t\n\t // ........................................................................ updates\n\t _fetchContentRelatedAttributes: function () {\n\t var contentRelatedAttrs = ['size', 'non_ready_jobs', 'contents_active', 'hid_counter'];\n\t return this.fetch({ data: $.param({ keys: contentRelatedAttrs.join(',') }) });\n\t },\n\t\n\t /** check for any changes since the last time we updated (or fetch all if ) */\n\t refresh: function (options) {\n\t // console.log( this + '.refresh' );\n\t options = options || {};\n\t var self = this;\n\t\n\t // note if there was no previous update time, all summary contents will be fetched\n\t var lastUpdateTime = self.lastUpdateTime;\n\t // if we don't flip this, then a fully-fetched list will not be re-checked via fetch\n\t this.contents.allFetched = false;\n\t var fetchFn = self.contents.currentPage !== 0 ? function () {\n\t return self.contents.fetchPage(self.contents.currentPage);\n\t } : function () {\n\t return self.contents.fetchUpdated(lastUpdateTime);\n\t };\n\t // note: if there was no previous update time, all summary contents will be fetched\n\t return fetchFn().done(function (response, status, xhr) {\n\t var serverResponseDatetime;\n\t try {\n\t serverResponseDatetime = new Date(xhr.getResponseHeader('Date'));\n\t } catch (err) {}\n\t self.lastUpdateTime = serverResponseDatetime || new Date();\n\t self.checkForUpdates(options);\n\t });\n\t },\n\t\n\t /** continuously fetch updated contents every UPDATE_DELAY ms if this history's datasets or jobs are unfinished */\n\t checkForUpdates: function (options) {\n\t // console.log( this + '.checkForUpdates' );\n\t options = options || {};\n\t var delay = this.UPDATE_DELAY;\n\t var self = this;\n\t if (!self.id) {\n\t return;\n\t }\n\t\n\t function _delayThenUpdate() {\n\t // prevent buildup of updater timeouts by clearing previous if any, then set new and cache id\n\t self.clearUpdateTimeout();\n\t self.updateTimeoutId = setTimeout(function () {\n\t self.refresh(options);\n\t }, delay);\n\t }\n\t\n\t // if there are still datasets in the non-ready state, recurse into this function with the new time\n\t var nonReadyContentCount = this.numOfUnfinishedShownContents();\n\t // console.log( 'nonReadyContentCount:', nonReadyContentCount );\n\t if (nonReadyContentCount > 0) {\n\t _delayThenUpdate();\n\t } else {\n\t // no datasets are running, but currently runnning jobs may still produce new datasets\n\t // see if the history has any running jobs and continue to update if so\n\t // (also update the size for the user in either case)\n\t self._fetchContentRelatedAttributes().done(function (historyData) {\n\t // console.log( 'non_ready_jobs:', historyData.non_ready_jobs );\n\t if (self.numOfUnfinishedJobs() > 0) {\n\t _delayThenUpdate();\n\t } else {\n\t // otherwise, let listeners know that all updates have stopped\n\t self.trigger('ready');\n\t }\n\t });\n\t }\n\t },\n\t\n\t /** clear the timeout and the cached timeout id */\n\t clearUpdateTimeout: function () {\n\t if (this.updateTimeoutId) {\n\t clearTimeout(this.updateTimeoutId);\n\t this.updateTimeoutId = null;\n\t }\n\t },\n\t\n\t // ........................................................................ ajax\n\t /** override to use actual Dates objects for create/update times */\n\t parse: function (response, options) {\n\t var parsed = Backbone.Model.prototype.parse.call(this, response, options);\n\t if (parsed.create_time) {\n\t parsed.create_time = new Date(parsed.create_time);\n\t }\n\t if (parsed.update_time) {\n\t parsed.update_time = new Date(parsed.update_time);\n\t }\n\t return parsed;\n\t },\n\t\n\t /** fetch this histories data (using options) then it's contents (using contentsOptions) */\n\t fetchWithContents: function (options, contentsOptions) {\n\t options = options || {};\n\t var self = this;\n\t\n\t // console.log( this + '.fetchWithContents' );\n\t // TODO: push down to a base class\n\t options.view = 'dev-detailed';\n\t\n\t // fetch history then use history data to fetch (paginated) contents\n\t return this.fetch(options).then(function getContents(history) {\n\t self.contents.history = self;\n\t self.contents.setHistoryId(history.id);\n\t return self.fetchContents(contentsOptions);\n\t });\n\t },\n\t\n\t /** fetch this histories contents, adjusting options based on the stored history preferences */\n\t fetchContents: function (options) {\n\t options = options || {};\n\t var self = this;\n\t\n\t // we're updating, reset the update time\n\t self.lastUpdateTime = new Date();\n\t return self.contents.fetchCurrentPage(options);\n\t },\n\t\n\t /** save this history, _Mark_ing it as deleted (just a flag) */\n\t _delete: function (options) {\n\t if (this.get('deleted')) {\n\t return jQuery.when();\n\t }\n\t return this.save({ deleted: true }, options);\n\t },\n\t /** purge this history, _Mark_ing it as purged and removing all dataset data from the server */\n\t purge: function (options) {\n\t if (this.get('purged')) {\n\t return jQuery.when();\n\t }\n\t return this.save({ deleted: true, purged: true }, options);\n\t },\n\t /** save this history, _Mark_ing it as undeleted */\n\t undelete: function (options) {\n\t if (!this.get('deleted')) {\n\t return jQuery.when();\n\t }\n\t return this.save({ deleted: false }, options);\n\t },\n\t\n\t /** Make a copy of this history on the server\n\t * @param {Boolean} current if true, set the copy as the new current history (default: true)\n\t * @param {String} name name of new history (default: none - server sets to: Copy of )\n\t * @fires copied passed this history and the response JSON from the copy\n\t * @returns {xhr}\n\t */\n\t copy: function (current, name, allDatasets) {\n\t current = current !== undefined ? current : true;\n\t if (!this.id) {\n\t throw new Error('You must set the history ID before copying it.');\n\t }\n\t\n\t var postData = { history_id: this.id };\n\t if (current) {\n\t postData.current = true;\n\t }\n\t if (name) {\n\t postData.name = name;\n\t }\n\t if (!allDatasets) {\n\t postData.all_datasets = false;\n\t }\n\t postData.view = 'dev-detailed';\n\t\n\t var history = this;\n\t var copy = jQuery.post(this.urlRoot, postData);\n\t // if current - queue to setAsCurrent before firing 'copied'\n\t if (current) {\n\t return copy.then(function (response) {\n\t var newHistory = new History(response);\n\t return newHistory.setAsCurrent().done(function () {\n\t history.trigger('copied', history, response);\n\t });\n\t });\n\t }\n\t return copy.done(function (response) {\n\t history.trigger('copied', history, response);\n\t });\n\t },\n\t\n\t setAsCurrent: function () {\n\t var history = this,\n\t xhr = jQuery.getJSON(Galaxy.root + 'history/set_as_current?id=' + this.id);\n\t\n\t xhr.done(function () {\n\t history.trigger('set-as-current', history);\n\t });\n\t return xhr;\n\t },\n\t\n\t // ........................................................................ misc\n\t toString: function () {\n\t return 'History(' + this.get('id') + ',' + this.get('name') + ')';\n\t }\n\t }));\n\t\n\t //==============================================================================\n\t var _collectionSuper = CONTROLLED_FETCH_COLLECTION.InfinitelyScrollingCollection;\n\t /** @class A collection of histories (per user)\n\t * that maintains the current history as the first in the collection.\n\t * New or copied histories become the current history.\n\t */\n\t var HistoryCollection = _collectionSuper.extend(BASE_MVC.LoggableMixin).extend({\n\t _logNamespace: 'history',\n\t\n\t model: History,\n\t /** @type {String} initial order used by collection */\n\t order: 'update_time',\n\t /** @type {Number} limit used for the first fetch (or a reset) */\n\t limitOnFirstFetch: 10,\n\t /** @type {Number} limit used for each subsequent fetch */\n\t limitPerFetch: 10,\n\t\n\t initialize: function (models, options) {\n\t options = options || {};\n\t this.log('HistoryCollection.initialize', models, options);\n\t _collectionSuper.prototype.initialize.call(this, models, options);\n\t\n\t /** @type {boolean} should deleted histories be included */\n\t this.includeDeleted = options.includeDeleted || false;\n\t\n\t /** @type {String} encoded id of the history that's current */\n\t this.currentHistoryId = options.currentHistoryId;\n\t\n\t this.setUpListeners();\n\t // note: models are sent to reset *after* this fn ends; up to this point\n\t // the collection *is empty*\n\t },\n\t\n\t urlRoot: Galaxy.root + 'api/histories',\n\t url: function () {\n\t return this.urlRoot;\n\t },\n\t\n\t /** set up reflexive event handlers */\n\t setUpListeners: function setUpListeners() {\n\t return this.on({\n\t // when a history is deleted, remove it from the collection (if optionally set to do so)\n\t 'change:deleted': function (history) {\n\t // TODO: this becomes complicated when more filters are used\n\t this.debug('change:deleted', this.includeDeleted, history.get('deleted'));\n\t if (!this.includeDeleted && history.get('deleted')) {\n\t this.remove(history);\n\t }\n\t },\n\t // listen for a history copy, setting it to current\n\t 'copied': function (original, newData) {\n\t this.setCurrent(new History(newData, []));\n\t },\n\t // when a history is made current, track the id in the collection\n\t 'set-as-current': function (history) {\n\t var oldCurrentId = this.currentHistoryId;\n\t this.trigger('no-longer-current', oldCurrentId);\n\t this.currentHistoryId = history.id;\n\t }\n\t });\n\t },\n\t\n\t /** override to change view */\n\t _buildFetchData: function (options) {\n\t return _.extend(_collectionSuper.prototype._buildFetchData.call(this, options), {\n\t view: 'dev-detailed'\n\t });\n\t },\n\t\n\t /** override to filter out deleted and purged */\n\t _buildFetchFilters: function (options) {\n\t var superFilters = _collectionSuper.prototype._buildFetchFilters.call(this, options) || {};\n\t var filters = {};\n\t if (!this.includeDeleted) {\n\t filters.deleted = false;\n\t filters.purged = false;\n\t } else {\n\t // force API to return both deleted and non\n\t //TODO: when the API is updated, remove this\n\t filters.deleted = null;\n\t }\n\t return _.defaults(superFilters, filters);\n\t },\n\t\n\t /** override to fetch current as well (as it may be outside the first 10, etc.) */\n\t fetchFirst: function (options) {\n\t var self = this;\n\t // TODO: batch?\n\t var xhr = $.when();\n\t if (this.currentHistoryId) {\n\t xhr = _collectionSuper.prototype.fetchFirst.call(self, {\n\t silent: true,\n\t limit: 1,\n\t filters: {\n\t // without these a deleted current history will return [] here and block the other xhr\n\t 'purged': '',\n\t 'deleted': '',\n\t 'encoded_id-in': this.currentHistoryId\n\t }\n\t });\n\t }\n\t return xhr.then(function () {\n\t options = options || {};\n\t options.offset = 0;\n\t return self.fetchMore(options);\n\t });\n\t },\n\t\n\t /** @type {Object} map of collection available sorting orders containing comparator fns */\n\t comparators: _.extend(_.clone(_collectionSuper.prototype.comparators), {\n\t 'name': BASE_MVC.buildComparator('name', { ascending: true }),\n\t 'name-dsc': BASE_MVC.buildComparator('name', { ascending: false }),\n\t 'size': BASE_MVC.buildComparator('size', { ascending: false }),\n\t 'size-asc': BASE_MVC.buildComparator('size', { ascending: true })\n\t }),\n\t\n\t /** override to always have the current history first */\n\t sort: function (options) {\n\t options = options || {};\n\t var silent = options.silent;\n\t var currentHistory = this.remove(this.get(this.currentHistoryId));\n\t _collectionSuper.prototype.sort.call(this, _.defaults({ silent: true }, options));\n\t this.unshift(currentHistory, { silent: true });\n\t if (!silent) {\n\t this.trigger('sort', this, options);\n\t }\n\t return this;\n\t },\n\t\n\t /** create a new history and by default set it to be the current history */\n\t create: function create(data, hdas, historyOptions, xhrOptions) {\n\t //TODO: .create is actually a collection function that's overridden here\n\t var collection = this,\n\t xhr = jQuery.getJSON(Galaxy.root + 'history/create_new_current');\n\t return xhr.done(function (newData) {\n\t collection.setCurrent(new History(newData, [], historyOptions || {}));\n\t });\n\t },\n\t\n\t /** set the current history to the given history, placing it first in the collection.\n\t * Pass standard bbone options for use in unshift.\n\t * @triggers new-current passed history and this collection\n\t */\n\t setCurrent: function (history, options) {\n\t options = options || {};\n\t // new histories go in the front\n\t this.unshift(history, options);\n\t this.currentHistoryId = history.get('id');\n\t if (!options.silent) {\n\t this.trigger('new-current', history, this);\n\t }\n\t return this;\n\t },\n\t\n\t toString: function toString() {\n\t return 'HistoryCollection(' + this.length + ',current:' + this.currentHistoryId + ')';\n\t }\n\t });\n\t\n\t //==============================================================================\n\t return {\n\t History: History,\n\t HistoryCollection: HistoryCollection\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ }),\n/* 81 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, $) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(47), __webpack_require__(137), __webpack_require__(6), __webpack_require__(5), __webpack_require__(88)], __WEBPACK_AMD_DEFINE_RESULT__ = function (LIST_ITEM, LoadingIndicator, BASE_MVC, _l) {\n\t\n\t 'use strict';\n\t\n\t var logNamespace = 'list';\n\t /* ============================================================================\n\t TODO:\n\t \n\t ============================================================================ */\n\t /** @class View for a list/collection of models and the sub-views of those models.\n\t * Sub-views must (at least have the interface if not) inherit from ListItemView.\n\t * (For a list panel that also includes some 'container' model (History->HistoryContents)\n\t * use ModelWithListPanel)\n\t *\n\t * Allows for:\n\t * searching collection/sub-views\n\t * selecting/multi-selecting sub-views\n\t *\n\t * Currently used:\n\t * for dataset/dataset-choice\n\t * as superclass of ModelListPanel\n\t */\n\t var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend( /** @lends ListPanel.prototype */{\n\t _logNamespace: logNamespace,\n\t\n\t /** class to use for constructing the sub-views */\n\t viewClass: LIST_ITEM.ListItemView,\n\t /** class to used for constructing collection of sub-view models */\n\t collectionClass: Backbone.Collection,\n\t\n\t tagName: 'div',\n\t className: 'list-panel',\n\t\n\t /** (in ms) that jquery effects will use */\n\t fxSpeed: 'fast',\n\t\n\t /** string to display when the collection has no contents */\n\t emptyMsg: _l('This list is empty'),\n\t /** displayed when no items match the search terms */\n\t noneFoundMsg: _l('No matching items found'),\n\t /** string used for search placeholder */\n\t searchPlaceholder: _l('search'),\n\t\n\t // ......................................................................... SET UP\n\t /** Set up the view, set up storage, bind listeners to HistoryContents events\n\t * @param {Object} attributes optional settings for the list\n\t */\n\t initialize: function (attributes, options) {\n\t attributes = attributes || {};\n\t // set the logger if requested\n\t if (attributes.logger) {\n\t this.logger = attributes.logger;\n\t }\n\t this.log(this + '.initialize:', attributes);\n\t\n\t // ---- instance vars\n\t /** how quickly should jquery fx run? */\n\t this.fxSpeed = _.has(attributes, 'fxSpeed') ? attributes.fxSpeed : this.fxSpeed;\n\t\n\t /** filters for displaying subviews */\n\t this.filters = [];\n\t /** current search terms */\n\t this.searchFor = attributes.searchFor || '';\n\t\n\t /** loading indicator */\n\t // this.indicator = new LoadingIndicator( this.$el );\n\t\n\t /** currently showing selectors on items? */\n\t this.selecting = attributes.selecting !== undefined ? attributes.selecting : true;\n\t //this.selecting = false;\n\t\n\t /** cached selected item.model.ids to persist btwn renders */\n\t this.selected = attributes.selected || [];\n\t /** the last selected item.model.id */\n\t this.lastSelected = null;\n\t\n\t /** are sub-views draggable */\n\t this.dragItems = attributes.dragItems || false;\n\t\n\t /** list item view class (when passed models) */\n\t this.viewClass = attributes.viewClass || this.viewClass;\n\t\n\t /** list item views */\n\t this.views = [];\n\t /** list item models */\n\t this.collection = attributes.collection || this._createDefaultCollection();\n\t\n\t /** filter fns run over collection items to see if they should show in the list */\n\t this.filters = attributes.filters || [];\n\t\n\t /** override $scrollContainer fn via attributes - fn should return jq for elem to call scrollTo on */\n\t this.$scrollContainer = attributes.$scrollContainer || this.$scrollContainer;\n\t\n\t /** @type {String} generic title */\n\t this.title = attributes.title || '';\n\t /** @type {String} generic subtitle */\n\t this.subtitle = attributes.subtitle || '';\n\t\n\t this._setUpListeners();\n\t },\n\t\n\t // ------------------------------------------------------------------------ listeners\n\t /** create any event listeners for the list */\n\t _setUpListeners: function () {\n\t this.off();\n\t\n\t //TODO: move errorHandler down into list-view from history-view or\n\t // pass to global error handler (Galaxy)\n\t this.on({\n\t error: function (model, xhr, options, msg, details) {\n\t //this.errorHandler( model, xhr, options, msg, details );\n\t console.error(model, xhr, options, msg, details);\n\t },\n\t // show hide the loading indicator\n\t loading: function () {\n\t this._showLoadingIndicator('loading...', 40);\n\t },\n\t 'loading-done': function () {\n\t this._hideLoadingIndicator(40);\n\t }\n\t });\n\t\n\t // throw the first render up as a diff namespace using once (for outside consumption)\n\t this.once('rendered', function () {\n\t this.trigger('rendered:initial', this);\n\t });\n\t\n\t this._setUpCollectionListeners();\n\t this._setUpViewListeners();\n\t return this;\n\t },\n\t\n\t /** create and return a collection for when none is initially passed */\n\t _createDefaultCollection: function () {\n\t // override\n\t return new this.collectionClass([]);\n\t },\n\t\n\t /** listening for collection events */\n\t _setUpCollectionListeners: function () {\n\t this.log(this + '._setUpCollectionListeners', this.collection);\n\t this.stopListening(this.collection);\n\t\n\t // bubble up error events\n\t this.listenTo(this.collection, {\n\t error: function (model, xhr, options, msg, details) {\n\t this.trigger('error', model, xhr, options, msg, details);\n\t },\n\t update: function (collection, options) {\n\t var changes = options.changes;\n\t // console.info( collection + ', update:', changes, '\\noptions:', options );\n\t // more than one: render everything\n\t if (options.renderAll || changes.added.length + changes.removed.length > 1) {\n\t return this.renderItems();\n\t }\n\t // otherwise, let the single add/remove handlers do it\n\t if (changes.added.length === 1) {\n\t return this.addItemView(_.first(changes.added), collection, options);\n\t }\n\t if (changes.removed.length === 1) {\n\t return this.removeItemView(_.first(changes.removed), collection, options);\n\t }\n\t }\n\t });\n\t return this;\n\t },\n\t\n\t /** listening for sub-view events that bubble up with the 'view:' prefix */\n\t _setUpViewListeners: function () {\n\t this.log(this + '._setUpViewListeners');\n\t\n\t // shift to select a range\n\t this.on({\n\t 'view:selected': function (view, ev) {\n\t if (ev && ev.shiftKey && this.lastSelected) {\n\t var lastSelectedView = this.viewFromModelId(this.lastSelected);\n\t if (lastSelectedView) {\n\t this.selectRange(view, lastSelectedView);\n\t }\n\t } else if (ev && ev.altKey && !this.selecting) {\n\t this.showSelectors();\n\t }\n\t this.selected.push(view.model.id);\n\t this.lastSelected = view.model.id;\n\t },\n\t\n\t 'view:de-selected': function (view, ev) {\n\t this.selected = _.without(this.selected, view.model.id);\n\t }\n\t });\n\t },\n\t\n\t // ------------------------------------------------------------------------ rendering\n\t /** Render this content, set up ui.\n\t * @param {Number or String} speed the speed of the render\n\t */\n\t render: function (speed) {\n\t this.log(this + '.render', speed);\n\t var $newRender = this._buildNewRender();\n\t this._setUpBehaviors($newRender);\n\t this._queueNewRender($newRender, speed);\n\t return this;\n\t },\n\t\n\t /** Build a temp div containing the new children for the view's $el. */\n\t _buildNewRender: function () {\n\t this.debug(this + '(ListPanel)._buildNewRender');\n\t var $newRender = $(this.templates.el({}, this));\n\t this._renderControls($newRender);\n\t this._renderTitle($newRender);\n\t this._renderSubtitle($newRender);\n\t this._renderSearch($newRender);\n\t this.renderItems($newRender);\n\t return $newRender;\n\t },\n\t\n\t /** Build a temp div containing the new children for the view's $el. */\n\t _renderControls: function ($newRender) {\n\t this.debug(this + '(ListPanel)._renderControls');\n\t var $controls = $(this.templates.controls({}, this));\n\t $newRender.find('.controls').replaceWith($controls);\n\t return $controls;\n\t },\n\t\n\t /** return a jQuery object containing the title DOM */\n\t _renderTitle: function ($where) {\n\t //$where = $where || this.$el;\n\t //$where.find( '.title' ).replaceWith( ... )\n\t },\n\t\n\t /** return a jQuery object containing the subtitle DOM (if any) */\n\t _renderSubtitle: function ($where) {\n\t //$where = $where || this.$el;\n\t //$where.find( '.title' ).replaceWith( ... )\n\t },\n\t\n\t /** Fade out the old el, swap in the new contents, then fade in.\n\t * @param {Number or String} speed jq speed to use for rendering effects\n\t * @fires rendered when rendered\n\t */\n\t _queueNewRender: function ($newRender, speed) {\n\t speed = speed === undefined ? this.fxSpeed : speed;\n\t var panel = this;\n\t panel.log('_queueNewRender:', $newRender, speed);\n\t\n\t $(panel).queue('fx', [function (next) {\n\t panel.$el.fadeOut(speed, next);\n\t }, function (next) {\n\t panel._swapNewRender($newRender);\n\t next();\n\t }, function (next) {\n\t panel.$el.fadeIn(speed, next);\n\t }, function (next) {\n\t panel.trigger('rendered', panel);\n\t next();\n\t }]);\n\t },\n\t\n\t /** empty out the current el, move the $newRender's children in */\n\t _swapNewRender: function ($newRender) {\n\t this.$el.empty().attr('class', this.className).append($newRender.children());\n\t if (this.selecting) {\n\t this.showSelectors(0);\n\t }\n\t return this;\n\t },\n\t\n\t /** Set up any behaviors, handlers (ep. plugins) that need to be called when the entire view has been built but\n\t * not attached to the page yet.\n\t */\n\t _setUpBehaviors: function ($where) {\n\t $where = $where || this.$el;\n\t this.$controls($where).find('[title]').tooltip();\n\t // set up the pupup for actions available when multi selecting\n\t this._renderMultiselectActionMenu($where);\n\t return this;\n\t },\n\t\n\t /** render a menu containing the actions available to sets of selected items */\n\t _renderMultiselectActionMenu: function ($where) {\n\t $where = $where || this.$el;\n\t var $menu = $where.find('.list-action-menu'),\n\t actions = this.multiselectActions();\n\t if (!actions.length) {\n\t return $menu.empty();\n\t }\n\t\n\t var $newMenu = $(['
', '', '
', '
', '
'].join(''));\n\t var $actions = actions.map(function (action) {\n\t var html = ['
'].join('');\n\t return $(html).click(function (ev) {\n\t ev.preventDefault();\n\t return action.func(ev);\n\t });\n\t });\n\t $newMenu.find('ul').append($actions);\n\t $menu.replaceWith($newMenu);\n\t return $newMenu;\n\t },\n\t\n\t /** return a list of plain objects used to render multiselect actions menu. Each object should have:\n\t * html: an html string used as the anchor contents\n\t * func: a function called when the anchor is clicked (passed the click event)\n\t */\n\t multiselectActions: function () {\n\t return [];\n\t },\n\t\n\t // ------------------------------------------------------------------------ sub-$element shortcuts\n\t /** the scroll container for this panel - can be $el, $el.parent(), or grandparent depending on context */\n\t $scrollContainer: function ($where) {\n\t // override or set via attributes.$scrollContainer\n\t return ($where || this.$el).parent().parent();\n\t },\n\t /** convenience selector for the section that displays the list controls */\n\t $controls: function ($where) {\n\t return ($where || this.$el).find('> .controls');\n\t },\n\t /** list-items: where the subviews are contained in the view's dom */\n\t $list: function ($where) {\n\t return ($where || this.$el).find('> .list-items');\n\t },\n\t /** container where list messages are attached */\n\t $messages: function ($where) {\n\t //TODO: controls isn't really correct here (only for ModelListPanel)\n\t return ($where || this.$el).find('> .controls .messages');\n\t },\n\t /** the message displayed when no views can be shown (no views, none matching search) */\n\t $emptyMessage: function ($where) {\n\t return ($where || this.$el).find('> .empty-message');\n\t },\n\t\n\t // ------------------------------------------------------------------------ hda sub-views\n\t /** render the subviews for the list's collection */\n\t renderItems: function ($whereTo) {\n\t $whereTo = $whereTo || this.$el;\n\t var panel = this;\n\t panel.log(this + '.renderItems', $whereTo);\n\t\n\t var $list = panel.$list($whereTo);\n\t panel.freeViews();\n\t // console.log( 'views freed' );\n\t //TODO:? cache and re-use views?\n\t var shownModels = panel._filterCollection();\n\t // console.log( 'models filtered:', shownModels );\n\t\n\t panel.views = shownModels.map(function (itemModel) {\n\t var view = panel._createItemView(itemModel);\n\t return view;\n\t });\n\t\n\t $list.empty();\n\t // console.log( 'list emptied' );\n\t if (panel.views.length) {\n\t panel._attachItems($whereTo);\n\t // console.log( 'items attached' );\n\t }\n\t panel._renderEmptyMessage($whereTo).toggle(!panel.views.length);\n\t panel.trigger('views:ready', panel.views);\n\t\n\t // console.log( '------------------------------------------- rendering items' );\n\t return panel.views;\n\t },\n\t\n\t /** Filter the collection to only those models that should be currently viewed */\n\t _filterCollection: function () {\n\t // override this\n\t var panel = this;\n\t return panel.collection.filter(_.bind(panel._filterItem, panel));\n\t },\n\t\n\t /** Should the model be viewable in the current state?\n\t * Checks against this.filters and this.searchFor\n\t */\n\t _filterItem: function (model) {\n\t // override this\n\t var panel = this;\n\t return _.every(panel.filters.map(function (fn) {\n\t return fn.call(model);\n\t })) && (!panel.searchFor || model.matchesAll(panel.searchFor));\n\t },\n\t\n\t /** Create a view for a model and set up it's listeners */\n\t _createItemView: function (model) {\n\t var ViewClass = this._getItemViewClass(model);\n\t var options = _.extend(this._getItemViewOptions(model), {\n\t model: model\n\t });\n\t var view = new ViewClass(options);\n\t this._setUpItemViewListeners(view);\n\t return view;\n\t },\n\t\n\t /** Free a view for a model. Note: does not remove it from the DOM */\n\t _destroyItemView: function (view) {\n\t this.stopListening(view);\n\t this.views = _.without(this.views, view);\n\t },\n\t\n\t _destroyItemViews: function (view) {\n\t var self = this;\n\t self.views.forEach(function (v) {\n\t self.stopListening(v);\n\t });\n\t self.views = [];\n\t return self;\n\t },\n\t\n\t /** free any sub-views the list has */\n\t freeViews: function () {\n\t return this._destroyItemViews();\n\t },\n\t\n\t /** Get the bbone view class based on the model */\n\t _getItemViewClass: function (model) {\n\t // override this\n\t return this.viewClass;\n\t },\n\t\n\t /** Get the options passed to the new view based on the model */\n\t _getItemViewOptions: function (model) {\n\t // override this\n\t return {\n\t //logger : this.logger,\n\t fxSpeed: this.fxSpeed,\n\t expanded: false,\n\t selectable: this.selecting,\n\t selected: _.contains(this.selected, model.id),\n\t draggable: this.dragItems\n\t };\n\t },\n\t\n\t /** Set up listeners for new models */\n\t _setUpItemViewListeners: function (view) {\n\t var panel = this;\n\t // send all events to the panel, re-namspaceing them with the view prefix\n\t this.listenTo(view, 'all', function () {\n\t var args = Array.prototype.slice.call(arguments, 0);\n\t args[0] = 'view:' + args[0];\n\t panel.trigger.apply(panel, args);\n\t });\n\t\n\t // drag multiple - hijack ev.setData to add all selected items\n\t this.listenTo(view, 'draggable:dragstart', function (ev, v) {\n\t //TODO: set multiple drag data here\n\t var json = {},\n\t selected = this.getSelectedModels();\n\t if (selected.length) {\n\t json = selected.toJSON();\n\t } else {\n\t json = [v.model.toJSON()];\n\t }\n\t ev.dataTransfer.setData('text', JSON.stringify(json));\n\t //ev.dataTransfer.setDragImage( v.el, 60, 60 );\n\t }, this);\n\t\n\t return panel;\n\t },\n\t\n\t /** Attach views in this.views to the model based on $whereTo */\n\t _attachItems: function ($whereTo) {\n\t var self = this;\n\t // console.log( '_attachItems:', $whereTo, this.$list( $whereTo ) );\n\t //ASSUMES: $list has been emptied\n\t this.$list($whereTo).append(this.views.map(function (view) {\n\t return self._renderItemView$el(view);\n\t }));\n\t return this;\n\t },\n\t\n\t /** get a given subview's $el (or whatever may wrap it) and return it */\n\t _renderItemView$el: function (view) {\n\t // useful to wrap and override\n\t return view.render(0).$el;\n\t },\n\t\n\t /** render the empty/none-found message */\n\t _renderEmptyMessage: function ($whereTo) {\n\t this.debug('_renderEmptyMessage', $whereTo, this.searchFor);\n\t var text = this.searchFor ? this.noneFoundMsg : this.emptyMsg;\n\t return this.$emptyMessage($whereTo).text(text);\n\t },\n\t\n\t /** expand all item views */\n\t expandAll: function () {\n\t _.each(this.views, function (view) {\n\t view.expand();\n\t });\n\t },\n\t\n\t /** collapse all item views */\n\t collapseAll: function () {\n\t _.each(this.views, function (view) {\n\t view.collapse();\n\t });\n\t },\n\t\n\t // ------------------------------------------------------------------------ collection/views syncing\n\t /** Add a view (if the model should be viewable) to the panel */\n\t addItemView: function (model, collection, options) {\n\t // console.log( this + '.addItemView:', model );\n\t var panel = this;\n\t // get the index of the model in the list of filtered models shown by this list\n\t // in order to insert the view in the proper place\n\t //TODO:? potentially expensive\n\t var modelIndex = panel._filterCollection().indexOf(model);\n\t if (modelIndex === -1) {\n\t return undefined;\n\t }\n\t var view = panel._createItemView(model);\n\t // console.log( 'adding and rendering:', modelIndex, view.toString() );\n\t\n\t $(view).queue('fx', [function (next) {\n\t // hide the empty message first if only view\n\t if (panel.$emptyMessage().is(':visible')) {\n\t panel.$emptyMessage().fadeOut(panel.fxSpeed, next);\n\t } else {\n\t next();\n\t }\n\t }, function (next) {\n\t panel._attachView(view, modelIndex);\n\t next();\n\t }]);\n\t return view;\n\t },\n\t\n\t /** internal fn to add view (to both panel.views and panel.$list) */\n\t _attachView: function (view, modelIndex, useFx) {\n\t // console.log( this + '._attachView:', view, modelIndex, useFx );\n\t useFx = _.isUndefined(useFx) ? true : useFx;\n\t modelIndex = modelIndex || 0;\n\t var panel = this;\n\t\n\t // use the modelIndex to splice into views and insert at the proper index in the DOM\n\t panel.views.splice(modelIndex, 0, view);\n\t panel._insertIntoListAt(modelIndex, panel._renderItemView$el(view).hide());\n\t\n\t panel.trigger('view:attached', view);\n\t if (useFx) {\n\t view.$el.slideDown(panel.fxSpeed, function () {\n\t panel.trigger('view:attached:rendered');\n\t });\n\t } else {\n\t view.$el.show();\n\t panel.trigger('view:attached:rendered');\n\t }\n\t return view;\n\t },\n\t\n\t /** insert a jq object as a child of list-items at the specified *DOM index* */\n\t _insertIntoListAt: function (index, $what) {\n\t // console.log( this + '._insertIntoListAt:', index, $what );\n\t var $list = this.$list();\n\t if (index === 0) {\n\t $list.prepend($what);\n\t } else {\n\t $list.children().eq(index - 1).after($what);\n\t }\n\t return $what;\n\t },\n\t\n\t /** Remove a view from the panel (if found) */\n\t removeItemView: function (model, collection, options) {\n\t var panel = this;\n\t var view = _.find(panel.views, function (v) {\n\t return v.model === model;\n\t });\n\t if (!view) {\n\t return undefined;\n\t }\n\t panel.views = _.without(panel.views, view);\n\t panel.trigger('view:removed', view);\n\t\n\t // potentially show the empty message if no views left\n\t // use anonymous queue here - since remove can happen multiple times\n\t $({}).queue('fx', [function (next) {\n\t view.$el.fadeOut(panel.fxSpeed, next);\n\t }, function (next) {\n\t view.remove();\n\t panel.trigger('view:removed:rendered');\n\t if (!panel.views.length) {\n\t panel._renderEmptyMessage().fadeIn(panel.fxSpeed, next);\n\t } else {\n\t next();\n\t }\n\t }]);\n\t return view;\n\t },\n\t\n\t /** get views based on model.id */\n\t viewFromModelId: function (id) {\n\t return _.find(this.views, function (v) {\n\t return v.model.id === id;\n\t });\n\t },\n\t\n\t /** get views based on model */\n\t viewFromModel: function (model) {\n\t return model ? this.viewFromModelId(model.id) : undefined;\n\t },\n\t\n\t /** get views based on model properties */\n\t viewsWhereModel: function (properties) {\n\t return this.views.filter(function (view) {\n\t return _.isMatch(view.model.attributes, properties);\n\t });\n\t },\n\t\n\t /** A range of views between (and including) viewA and viewB */\n\t viewRange: function (viewA, viewB) {\n\t if (viewA === viewB) {\n\t return viewA ? [viewA] : [];\n\t }\n\t\n\t var indexA = this.views.indexOf(viewA),\n\t indexB = this.views.indexOf(viewB);\n\t\n\t // handle not found\n\t if (indexA === -1 || indexB === -1) {\n\t if (indexA === indexB) {\n\t return [];\n\t }\n\t return indexA === -1 ? [viewB] : [viewA];\n\t }\n\t // reverse if indeces are\n\t //note: end inclusive\n\t return indexA < indexB ? this.views.slice(indexA, indexB + 1) : this.views.slice(indexB, indexA + 1);\n\t },\n\t\n\t // ------------------------------------------------------------------------ searching\n\t /** render a search input for filtering datasets shown\n\t * (see SearchableMixin in base-mvc for implementation of the actual searching)\n\t * return will start the search\n\t * esc will clear the search\n\t * clicking the clear button will clear the search\n\t * uses searchInput in ui.js\n\t */\n\t _renderSearch: function ($where) {\n\t $where.find('.controls .search-input').searchInput({\n\t placeholder: this.searchPlaceholder,\n\t initialVal: this.searchFor,\n\t onfirstsearch: _.bind(this._firstSearch, this),\n\t onsearch: _.bind(this.searchItems, this),\n\t onclear: _.bind(this.clearSearch, this)\n\t });\n\t return $where;\n\t },\n\t\n\t /** What to do on the first search entered */\n\t _firstSearch: function (searchFor) {\n\t // override to load model details if necc.\n\t this.log('onFirstSearch', searchFor);\n\t return this.searchItems(searchFor);\n\t },\n\t\n\t /** filter view list to those that contain the searchFor terms */\n\t searchItems: function (searchFor, force) {\n\t this.log('searchItems', searchFor, this.searchFor, force);\n\t if (!force && this.searchFor === searchFor) {\n\t return this;\n\t }\n\t this.searchFor = searchFor;\n\t this.renderItems();\n\t this.trigger('search:searching', searchFor, this);\n\t var $search = this.$('> .controls .search-query');\n\t if ($search.val() !== searchFor) {\n\t $search.val(searchFor);\n\t }\n\t return this;\n\t },\n\t\n\t /** clear the search filters and show all views that are normally shown */\n\t clearSearch: function (searchFor) {\n\t //this.log( 'onSearchClear', this );\n\t this.searchFor = '';\n\t this.trigger('search:clear', this);\n\t this.$('> .controls .search-query').val('');\n\t this.renderItems();\n\t return this;\n\t },\n\t\n\t // ------------------------------------------------------------------------ selection\n\t /** @type Integer when the number of list item views is >= to this, don't animate selectors */\n\t THROTTLE_SELECTOR_FX_AT: 20,\n\t\n\t /** show selectors on all visible itemViews and associated controls */\n\t showSelectors: function (speed) {\n\t speed = speed !== undefined ? speed : this.fxSpeed;\n\t this.selecting = true;\n\t this.$('.list-actions').slideDown(speed);\n\t speed = this.views.length >= this.THROTTLE_SELECTOR_FX_AT ? 0 : speed;\n\t _.each(this.views, function (view) {\n\t view.showSelector(speed);\n\t });\n\t //this.selected = [];\n\t //this.lastSelected = null;\n\t },\n\t\n\t /** hide selectors on all visible itemViews and associated controls */\n\t hideSelectors: function (speed) {\n\t speed = speed !== undefined ? speed : this.fxSpeed;\n\t this.selecting = false;\n\t this.$('.list-actions').slideUp(speed);\n\t speed = this.views.length >= this.THROTTLE_SELECTOR_FX_AT ? 0 : speed;\n\t _.each(this.views, function (view) {\n\t view.hideSelector(speed);\n\t });\n\t this.selected = [];\n\t this.lastSelected = null;\n\t },\n\t\n\t /** show or hide selectors on all visible itemViews and associated controls */\n\t toggleSelectors: function () {\n\t if (!this.selecting) {\n\t this.showSelectors();\n\t } else {\n\t this.hideSelectors();\n\t }\n\t },\n\t\n\t /** select all visible items */\n\t selectAll: function (event) {\n\t _.each(this.views, function (view) {\n\t view.select(event);\n\t });\n\t },\n\t\n\t /** deselect all visible items */\n\t deselectAll: function (event) {\n\t this.lastSelected = null;\n\t _.each(this.views, function (view) {\n\t view.deselect(event);\n\t });\n\t },\n\t\n\t /** select a range of datasets between A and B */\n\t selectRange: function (viewA, viewB) {\n\t var range = this.viewRange(viewA, viewB);\n\t _.each(range, function (view) {\n\t view.select();\n\t });\n\t return range;\n\t },\n\t\n\t /** return an array of all currently selected itemViews */\n\t getSelectedViews: function () {\n\t return _.filter(this.views, function (v) {\n\t return v.selected;\n\t });\n\t },\n\t\n\t /** return a collection of the models of all currenly selected items */\n\t getSelectedModels: function () {\n\t // console.log( '(getSelectedModels)' );\n\t return new this.collection.constructor(_.map(this.getSelectedViews(), function (view) {\n\t return view.model;\n\t }));\n\t },\n\t\n\t // ------------------------------------------------------------------------ loading indicator\n\t /** hide the $el and display a loading indicator (in the $el's parent) when loading new data */\n\t _showLoadingIndicator: function (msg, speed, callback) {\n\t this.debug('_showLoadingIndicator', this.indicator, msg, speed, callback);\n\t speed = speed !== undefined ? speed : this.fxSpeed;\n\t if (!this.indicator) {\n\t this.indicator = new LoadingIndicator(this.$el);\n\t this.debug('\\t created', this.indicator);\n\t }\n\t if (!this.$el.is(':visible')) {\n\t this.indicator.show(0, callback);\n\t } else {\n\t this.$el.fadeOut(speed);\n\t this.indicator.show(msg, speed, callback);\n\t }\n\t },\n\t\n\t /** hide the loading indicator */\n\t _hideLoadingIndicator: function (speed, callback) {\n\t this.debug('_hideLoadingIndicator', this.indicator, speed, callback);\n\t speed = speed !== undefined ? speed : this.fxSpeed;\n\t if (this.indicator) {\n\t this.indicator.hide(speed, callback);\n\t }\n\t },\n\t\n\t // ------------------------------------------------------------------------ scrolling\n\t /** get the current scroll position of the panel in its parent */\n\t scrollPosition: function () {\n\t return this.$scrollContainer().scrollTop();\n\t },\n\t\n\t /** set the current scroll position of the panel in its parent */\n\t scrollTo: function (pos, speed) {\n\t speed = speed || 0;\n\t this.$scrollContainer().animate({ scrollTop: pos }, speed);\n\t return this;\n\t },\n\t\n\t /** Scrolls the panel to the top. */\n\t scrollToTop: function (speed) {\n\t return this.scrollTo(0, speed);\n\t },\n\t\n\t /** scroll to the given view in list-items */\n\t scrollToItem: function (view, speed) {\n\t if (!view) {\n\t return this;\n\t }\n\t return this;\n\t },\n\t\n\t /** Scrolls the panel to show the content with the given id. */\n\t scrollToId: function (id, speed) {\n\t return this.scrollToItem(this.viewFromModelId(id), speed);\n\t },\n\t\n\t // ------------------------------------------------------------------------ panel events\n\t /** event map */\n\t events: {\n\t 'click .select-all': 'selectAll',\n\t 'click .deselect-all': 'deselectAll'\n\t },\n\t\n\t // ------------------------------------------------------------------------ misc\n\t /** Return a string rep of the panel */\n\t toString: function () {\n\t return 'ListPanel(' + this.collection + ')';\n\t }\n\t });\n\t\n\t // ............................................................................ TEMPLATES\n\t /** underscore templates */\n\t ListPanel.prototype.templates = function () {\n\t\n\t var elTemplate = BASE_MVC.wrapTemplate([\n\t // temp container\n\t '
', '', '', '', '
']);\n\t\n\t var controlsTemplate = BASE_MVC.wrapTemplate(['
']);\n\t\n\t return {\n\t el: elTemplate,\n\t controls: controlsTemplate\n\t };\n\t }();\n\t\n\t //=============================================================================\n\t /** View for a model that has a sub-collection (e.g. History, DatasetCollection)\n\t * Allows:\n\t * the model to be reset\n\t * auto assign panel.collection to panel.model[ panel.modelCollectionKey ]\n\t *\n\t */\n\t var ModelListPanel = ListPanel.extend({\n\t\n\t /** key of attribute in model to assign to this.collection */\n\t modelCollectionKey: 'contents',\n\t\n\t initialize: function (attributes) {\n\t ListPanel.prototype.initialize.call(this, attributes);\n\t this.selecting = attributes.selecting !== undefined ? attributes.selecting : false;\n\t\n\t this.setModel(this.model, attributes);\n\t },\n\t\n\t /** release/free/shutdown old models and set up panel for new models\n\t * @fires new-model with the panel as parameter\n\t */\n\t setModel: function (model, attributes) {\n\t attributes = attributes || {};\n\t this.debug(this + '.setModel:', model, attributes);\n\t\n\t this.freeModel();\n\t this.freeViews();\n\t\n\t if (model) {\n\t var oldModelId = this.model ? this.model.get('id') : null;\n\t\n\t // set up the new model with user, logger, storage, events\n\t this.model = model;\n\t if (this.logger) {\n\t this.model.logger = this.logger;\n\t }\n\t this._setUpModelListeners();\n\t\n\t //TODO: relation btwn model, collection becoming tangled here\n\t // free the collection, and assign the new collection to either\n\t // the model[ modelCollectionKey ], attributes.collection, or an empty vanilla collection\n\t this.stopListening(this.collection);\n\t this.collection = this.model[this.modelCollectionKey] || attributes.collection || this._createDefaultCollection();\n\t this._setUpCollectionListeners();\n\t\n\t if (oldModelId && model.get('id') !== oldModelId) {\n\t this.trigger('new-model', this);\n\t }\n\t }\n\t return this;\n\t },\n\t\n\t /** free the current model and all listeners for it, free any views for the model */\n\t freeModel: function () {\n\t // stop/release the previous model, and clear cache to sub-views\n\t if (this.model) {\n\t this.stopListening(this.model);\n\t //TODO: see base-mvc\n\t //this.model.free();\n\t //this.model = null;\n\t }\n\t return this;\n\t },\n\t\n\t // ------------------------------------------------------------------------ listening\n\t /** listening for model events */\n\t _setUpModelListeners: function () {\n\t // override\n\t this.log(this + '._setUpModelListeners', this.model);\n\t // bounce model errors up to the panel\n\t this.listenTo(this.model, 'error', function () {\n\t var args = Array.prototype.slice.call(arguments, 0);\n\t //args.unshift( 'model:error' );\n\t args.unshift('error');\n\t this.trigger.apply(this, args);\n\t }, this);\n\t\n\t // debugging\n\t if (this.logger) {\n\t this.listenTo(this.model, 'all', function (event) {\n\t this.info(this + '(model)', event, arguments);\n\t });\n\t }\n\t return this;\n\t },\n\t\n\t /** Build a temp div containing the new children for the view's $el.\n\t */\n\t _renderControls: function ($newRender) {\n\t this.debug(this + '(ModelListPanel)._renderControls');\n\t var json = this.model ? this.model.toJSON() : {},\n\t $controls = $(this.templates.controls(json, this));\n\t $newRender.find('.controls').replaceWith($controls);\n\t return $controls;\n\t },\n\t\n\t // ------------------------------------------------------------------------ misc\n\t /** Return a string rep of the panel */\n\t toString: function () {\n\t return 'ModelListPanel(' + this.model + ')';\n\t }\n\t });\n\t\n\t // ............................................................................ TEMPLATES\n\t /** underscore templates */\n\t ModelListPanel.prototype.templates = function () {\n\t\n\t var controlsTemplate = BASE_MVC.wrapTemplate(['
', '
',\n\t //TODO: this is really the only difference - consider factoring titlebar out\n\t '
<%- model.name %>
', '
', '
<%- view.subtitle %>
', '', '', '
', '', '
', '
', '
', '', '', '
', '
', '
', '
', '
']);\n\t\n\t return _.extend(_.clone(ListPanel.prototype.templates), {\n\t controls: controlsTemplate\n\t });\n\t }();\n\t\n\t //=============================================================================\n\t return {\n\t ListPanel: ListPanel,\n\t ModelListPanel: ModelListPanel\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ }),\n/* 82 */,\n/* 83 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function($, _) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (_l) {\n\t 'use strict';\n\t\n\t //TODO: toastr is another possibility - I didn't see where I might add details, tho\n\t\n\t /* ============================================================================\n\t Error modals meant to replace the o-so-easy alerts.\n\t \n\t These are currently styled as errormessages but use the Galaxy.modal\n\t infrastructure to be shown/closed. They're capable of showing details in a\n\t togglable dropdown and the details are formatted in a pre.\n\t \n\t Example:\n\t errorModal( 'Heres a message', 'A Title', { some_details: 'here' });\n\t errorModal( 'Heres a message' ); // no details, title is 'Error'\n\t \n\t There are three specialized forms:\n\t offlineErrorModal a canned response for when there's no connection\n\t badGatewayErrorModal canned response for when Galaxy is restarting\n\t ajaxErrorModal plugable into any Backbone class as an\n\t error event handler by accepting the error args: model, xhr, options\n\t \n\t Examples:\n\t if( navigator.offLine ){ offlineErrorModal(); }\n\t if( xhr.status === 502 ){ badGatewayErrorModal(); }\n\t this.listenTo( this.model, 'error', ajaxErrorModal );\n\t \n\t ============================================================================ */\n\t\n\t var CONTACT_MSG = _l('Please contact a Galaxy administrator if the problem persists.');\n\t var DEFAULT_AJAX_ERR_MSG = _l('An error occurred while updating information with the server.');\n\t var DETAILS_MSG = _l('The following information can assist the developers in finding the source of the error:');\n\t\n\t /** private helper that builds the modal and handles adding details */\n\t function _errorModal(message, title, details) {\n\t // create and return the modal, adding details button only if needed\n\t Galaxy.modal.show({\n\t title: title,\n\t body: message,\n\t closing_events: true,\n\t buttons: { Ok: function () {\n\t Galaxy.modal.hide();\n\t } }\n\t });\n\t Galaxy.modal.$el.addClass('error-modal');\n\t\n\t if (details) {\n\t Galaxy.modal.$('.error-details').add(Galaxy.modal.$('button:contains(\"Details\")')).remove();\n\t $('').addClass('error-details').hide().appendTo(Galaxy.modal.$('.modal-content')).append([$('').text(DETAILS_MSG), $('').text(JSON.stringify(details, null, ' '))]);\n\t\n\t $('').appendTo(Galaxy.modal.$('.buttons')).click(function () {\n\t Galaxy.modal.$('.error-details').toggle();\n\t });\n\t }\n\t return Galaxy.modal;\n\t }\n\t\n\t /** Display a modal showing an error message but fallback to alert if there's no modal */\n\t function errorModal(message, title, details) {\n\t if (!message) {\n\t return;\n\t }\n\t\n\t message = _l(message);\n\t title = _l(title) || _l('Error:');\n\t if (window.Galaxy && Galaxy.modal) {\n\t return _errorModal(message, title, details);\n\t }\n\t\n\t alert(title + '\\n\\n' + message);\n\t console.log('error details:', JSON.stringify(details));\n\t }\n\t\n\t // ----------------------------------------------------------------------------\n\t /** display a modal when the user may be offline */\n\t function offlineErrorModal() {\n\t return errorModal(_l('You appear to be offline. Please check your connection and try again.'), _l('Offline?'));\n\t }\n\t\n\t // ----------------------------------------------------------------------------\n\t /** 502 messages that should be displayed when galaxy is restarting */\n\t function badGatewayErrorModal() {\n\t return errorModal(_l('Galaxy is currently unreachable. Please try again in a few minutes.') + ' ' + CONTACT_MSG, _l('Cannot connect to Galaxy'));\n\t }\n\t\n\t // ----------------------------------------------------------------------------\n\t /** display a modal (with details) about a failed Backbone ajax operation */\n\t function ajaxErrorModal(model, xhr, options, message, title) {\n\t message = message || DEFAULT_AJAX_ERR_MSG;\n\t message += ' ' + CONTACT_MSG;\n\t title = title || _l('An error occurred');\n\t var details = _ajaxDetails(model, xhr, options);\n\t return errorModal(message, title, details);\n\t }\n\t\n\t /** build details which may help debugging the ajax call */\n\t function _ajaxDetails(model, xhr, options) {\n\t return {\n\t //TODO: still can't manage Raven id\n\t raven: _.result(window.Raven, 'lastEventId'),\n\t userAgent: navigator.userAgent,\n\t onLine: navigator.onLine,\n\t version: _.result(Galaxy.config, 'version_major'),\n\t xhr: _.omit(xhr, _.functions(xhr)),\n\t options: _.omit(options, 'xhr'),\n\t // add ajax data from Galaxy object cache\n\t url: _.result(Galaxy.lastAjax, 'url'),\n\t data: _.result(Galaxy.lastAjax, 'data'),\n\t // backbone stuff (auto-redacting email for user)\n\t model: _.result(model, 'toJSON', model + ''),\n\t user: _.omit(_.result(Galaxy.user, 'toJSON'), 'email')\n\t };\n\t }\n\t\n\t //=============================================================================\n\t return {\n\t errorModal: errorModal,\n\t offlineErrorModal: offlineErrorModal,\n\t badGatewayErrorModal: badGatewayErrorModal,\n\t ajaxErrorModal: ajaxErrorModal\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1), __webpack_require__(2)))\n\n/***/ }),\n/* 84 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _, jQuery) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [\n\t //jquery\n\t //backbone\n\t], __WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t // =============================================================================\n\t /**\n\t * view for a popup menu\n\t */\n\t var PopupMenu = Backbone.View.extend({\n\t //TODO: maybe better as singleton off the Galaxy obj\n\t /** Cache the desired button element and options, set up the button click handler\n\t * NOTE: attaches this view as HTML/jQ data on the button for later use.\n\t */\n\t initialize: function ($button, options) {\n\t // default settings\n\t this.$button = $button;\n\t if (!this.$button.length) {\n\t this.$button = $('');\n\t }\n\t this.options = options || [];\n\t this.$button.data('popupmenu', this);\n\t\n\t // set up button click -> open menu behavior\n\t var menu = this;\n\t this.$button.click(function (event) {\n\t // if there's already a menu open, remove it\n\t $('.popmenu-wrapper').remove();\n\t menu._renderAndShow(event);\n\t return false;\n\t });\n\t },\n\t\n\t // render the menu, append to the page body at the click position, and set up the 'click-away' handlers, show\n\t _renderAndShow: function (clickEvent) {\n\t this.render();\n\t this.$el.appendTo('body').css(this._getShownPosition(clickEvent)).show();\n\t this._setUpCloseBehavior();\n\t },\n\t\n\t // render the menu\n\t // this menu doesn't attach itself to the DOM ( see _renderAndShow )\n\t render: function () {\n\t // render the menu body absolute and hidden, fill with template\n\t this.$el.addClass('popmenu-wrapper').hide().css({ position: 'absolute' }).html(this.template(this.$button.attr('id'), this.options));\n\t\n\t // set up behavior on each link/anchor elem\n\t if (this.options.length) {\n\t var menu = this;\n\t //precondition: there should be one option per li\n\t this.$el.find('li').each(function (i, li) {\n\t var option = menu.options[i];\n\t\n\t // if the option has 'func', call that function when the anchor is clicked\n\t if (option.func) {\n\t $(this).children('a.popupmenu-option').click(function (event) {\n\t option.func.call(menu, event, option);\n\t // We must preventDefault otherwise clicking \"cancel\"\n\t // on a purge or something still navigates and causes\n\t // the action.\n\t event.preventDefault();\n\t // bubble up so that an option click will call the close behavior\n\t });\n\t }\n\t });\n\t }\n\t return this;\n\t },\n\t\n\t template: function (id, options) {\n\t return ['
', this._templateOptions(options), '
'].join('');\n\t },\n\t\n\t _templateOptions: function (options) {\n\t if (!options.length) {\n\t return '
(no options)
';\n\t }\n\t return _.map(options, function (option) {\n\t if (option.divider) {\n\t return '';\n\t } else if (option.header) {\n\t return ['
'].join('');\n\t }).join('');\n\t },\n\t\n\t // get the absolute position/offset for the menu\n\t _getShownPosition: function (clickEvent) {\n\t\n\t // display menu horiz. centered on click...\n\t var menuWidth = this.$el.width();\n\t var x = clickEvent.pageX - menuWidth / 2;\n\t\n\t // adjust to handle horiz. scroll and window dimensions ( draw entirely on visible screen area )\n\t x = Math.min(x, $(document).scrollLeft() + $(window).width() - menuWidth - 5);\n\t x = Math.max(x, $(document).scrollLeft() + 5);\n\t return {\n\t top: clickEvent.pageY,\n\t left: x\n\t };\n\t },\n\t\n\t // bind an event handler to all available frames so that when anything is clicked\n\t // the menu is removed from the DOM and the event handler unbinds itself\n\t _setUpCloseBehavior: function () {\n\t var menu = this;\n\t //TODO: alternately: focus hack, blocking overlay, jquery.blockui\n\t\n\t // function to close popup and unbind itself\n\t function closePopup(event) {\n\t $(document).off('click.close_popup');\n\t if (window && window.parent !== window) {\n\t try {\n\t $(window.parent.document).off(\"click.close_popup\");\n\t } catch (err) {}\n\t } else {\n\t try {\n\t $('iframe#galaxy_main').contents().off(\"click.close_popup\");\n\t } catch (err) {}\n\t }\n\t menu.remove();\n\t }\n\t\n\t $('html').one(\"click.close_popup\", closePopup);\n\t if (window && window.parent !== window) {\n\t try {\n\t $(window.parent.document).find('html').one(\"click.close_popup\", closePopup);\n\t } catch (err) {}\n\t } else {\n\t try {\n\t $('iframe#galaxy_main').contents().one(\"click.close_popup\", closePopup);\n\t } catch (err) {}\n\t }\n\t },\n\t\n\t // add a menu option/item at the given index\n\t addItem: function (item, index) {\n\t // append to end if no index\n\t index = index >= 0 ? index : this.options.length;\n\t this.options.splice(index, 0, item);\n\t return this;\n\t },\n\t\n\t // remove a menu option/item at the given index\n\t removeItem: function (index) {\n\t if (index >= 0) {\n\t this.options.splice(index, 1);\n\t }\n\t return this;\n\t },\n\t\n\t // search for a menu option by its html\n\t findIndexByHtml: function (html) {\n\t for (var i = 0; i < this.options.length; i++) {\n\t if (_.has(this.options[i], 'html') && this.options[i].html === html) {\n\t return i;\n\t }\n\t }\n\t return null;\n\t },\n\t\n\t // search for a menu option by its html\n\t findItemByHtml: function (html) {\n\t return this.options[this.findIndexByHtml(html)];\n\t },\n\t\n\t // string representation\n\t toString: function () {\n\t return 'PopupMenu';\n\t }\n\t });\n\t /** shortcut to new for when you don't need to preserve the ref */\n\t PopupMenu.create = function _create($button, options) {\n\t return new PopupMenu($button, options);\n\t };\n\t\n\t // -----------------------------------------------------------------------------\n\t // the following class functions are bridges from the original make_popupmenu and make_popup_menus\n\t // to the newer backbone.js PopupMenu\n\t\n\t /** Create a PopupMenu from simple map initial_options activated by clicking button_element.\n\t * Converts initial_options to object array used by PopupMenu.\n\t * @param {jQuery|DOMElement} button_element element which, when clicked, activates menu\n\t * @param {Object} initial_options map of key -> values, where\n\t * key is option text, value is fn to call when option is clicked\n\t * @returns {PopupMenu} the PopupMenu created\n\t */\n\t PopupMenu.make_popupmenu = function (button_element, initial_options) {\n\t var convertedOptions = [];\n\t _.each(initial_options, function (optionVal, optionKey) {\n\t var newOption = { html: optionKey };\n\t\n\t // keys with null values indicate: header\n\t if (optionVal === null) {\n\t // !optionVal? (null only?)\n\t newOption.header = true;\n\t\n\t // keys with function values indicate: a menu option\n\t } else if (jQuery.type(optionVal) === 'function') {\n\t newOption.func = optionVal;\n\t }\n\t //TODO:?? any other special optionVals?\n\t // there was no divider option originally\n\t convertedOptions.push(newOption);\n\t });\n\t return new PopupMenu($(button_element), convertedOptions);\n\t };\n\t\n\t /** Find all anchors in $parent (using selector) and covert anchors into a PopupMenu options map.\n\t * @param {jQuery} $parent the element that contains the links to convert to options\n\t * @param {String} selector jq selector string to find links\n\t * @returns {Object[]} the options array to initialize a PopupMenu\n\t */\n\t //TODO: lose parent and selector, pass in array of links, use map to return options\n\t PopupMenu.convertLinksToOptions = function ($parent, selector) {\n\t $parent = $($parent);\n\t selector = selector || 'a';\n\t var options = [];\n\t $parent.find(selector).each(function (elem, i) {\n\t var option = {},\n\t $link = $(elem);\n\t\n\t // convert link text to the option text (html) and the href into the option func\n\t option.html = $link.text();\n\t if ($link.attr('href')) {\n\t var linkHref = $link.attr('href'),\n\t linkTarget = $link.attr('target'),\n\t confirmText = $link.attr('confirm');\n\t\n\t option.func = function () {\n\t // if there's a \"confirm\" attribute, throw up a confirmation dialog, and\n\t // if the user cancels - do nothing\n\t if (confirmText && !confirm(confirmText)) {\n\t return;\n\t }\n\t\n\t // if there's no confirm attribute, or the user accepted the confirm dialog:\n\t switch (linkTarget) {\n\t // relocate the center panel\n\t case '_parent':\n\t window.parent.location = linkHref;\n\t break;\n\t\n\t // relocate the entire window\n\t case '_top':\n\t window.top.location = linkHref;\n\t break;\n\t\n\t // relocate this panel\n\t default:\n\t window.location = linkHref;\n\t }\n\t };\n\t }\n\t options.push(option);\n\t });\n\t return options;\n\t };\n\t\n\t /** Create a single popupmenu from existing DOM button and anchor elements\n\t * @param {jQuery} $buttonElement the element that when clicked will open the menu\n\t * @param {jQuery} $menuElement the element that contains the anchors to convert into a menu\n\t * @param {String} menuElementLinkSelector jq selector string used to find anchors to be made into menu options\n\t * @returns {PopupMenu} the PopupMenu (Backbone View) that can render, control the menu\n\t */\n\t PopupMenu.fromExistingDom = function ($buttonElement, $menuElement, menuElementLinkSelector) {\n\t $buttonElement = $($buttonElement);\n\t $menuElement = $($menuElement);\n\t var options = PopupMenu.convertLinksToOptions($menuElement, menuElementLinkSelector);\n\t // we're done with the menu (having converted it to an options map)\n\t $menuElement.remove();\n\t return new PopupMenu($buttonElement, options);\n\t };\n\t\n\t /** Create all popupmenus within a document or a more specific element\n\t * @param {DOMElement} parent the DOM element in which to search for popupmenus to build (defaults to document)\n\t * @param {String} menuSelector jq selector string to find popupmenu menu elements (defaults to \"div[popupmenu]\")\n\t * @param {Function} buttonSelectorBuildFn the function to build the jq button selector.\n\t * Will be passed $menuElement, parent.\n\t * (Defaults to return '#' + $menuElement.attr( 'popupmenu' ); )\n\t * @returns {PopupMenu[]} array of popupmenus created\n\t */\n\t PopupMenu.make_popup_menus = function (parent, menuSelector, buttonSelectorBuildFn) {\n\t parent = parent || document;\n\t // orig. Glx popupmenu menus have a (non-std) attribute 'popupmenu'\n\t // which contains the id of the button that activates the menu\n\t menuSelector = menuSelector || 'div[popupmenu]';\n\t // default to (orig. Glx) matching button to menu by using the popupmenu attr of the menu as the id of the button\n\t buttonSelectorBuildFn = buttonSelectorBuildFn || function ($menuElement, parent) {\n\t return '#' + $menuElement.attr('popupmenu');\n\t };\n\t\n\t // aggregate and return all PopupMenus\n\t var popupMenusCreated = [];\n\t $(parent).find(menuSelector).each(function () {\n\t var $menuElement = $(this),\n\t $buttonElement = $(parent).find(buttonSelectorBuildFn($menuElement, parent));\n\t popupMenusCreated.push(PopupMenu.fromDom($buttonElement, $menuElement));\n\t $buttonElement.addClass('popup');\n\t });\n\t return popupMenusCreated;\n\t };\n\t\n\t // =============================================================================\n\t return PopupMenu;\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ }),\n/* 85 */,\n/* 86 */,\n/* 87 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_FACTORY__, __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(jQuery, $) {(function (factory) {\n\t if (true) {\n\t !(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_FACTORY__ = (factory), __WEBPACK_AMD_DEFINE_RESULT__ = (typeof __WEBPACK_AMD_DEFINE_FACTORY__ === 'function' ? (__WEBPACK_AMD_DEFINE_FACTORY__.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__)) : __WEBPACK_AMD_DEFINE_FACTORY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t } else {\n\t // Browser globals\n\t factory(jQuery);\n\t }\n\t})(function () {\n\t //=============================================================================\n\t\n\t jQuery.fn.extend({\n\t hoverhighlight: function $hoverhighlight(scope, color) {\n\t scope = scope || 'body';\n\t if (!this.length) {\n\t return this;\n\t }\n\t\n\t $(this).each(function () {\n\t var $this = $(this),\n\t targetSelector = $this.data('target');\n\t\n\t if (targetSelector) {\n\t $this.mouseover(function (ev) {\n\t $(targetSelector, scope).css({\n\t background: color\n\t });\n\t }).mouseout(function (ev) {\n\t $(targetSelector).css({\n\t background: ''\n\t });\n\t });\n\t }\n\t });\n\t return this;\n\t }\n\t });\n\t});\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1), __webpack_require__(1)))\n\n/***/ }),\n/* 88 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_FACTORY__, __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function($, jQuery) {// from: https://raw.githubusercontent.com/umdjs/umd/master/jqueryPlugin.js\n\t// Uses AMD or browser globals to create a jQuery plugin.\n\t(function (factory) {\n\t if (true) {\n\t //TODO: So...this turns out to be an all or nothing thing. If I load jQuery in the define below, it will\n\t // (of course) wipe the old jquery *and all the plugins loaded into it*. So the define below *is still\n\t // relying on jquery being loaded globally* in order to preserve plugins.\n\t !(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_FACTORY__ = (factory), __WEBPACK_AMD_DEFINE_RESULT__ = (typeof __WEBPACK_AMD_DEFINE_FACTORY__ === 'function' ? (__WEBPACK_AMD_DEFINE_FACTORY__.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__)) : __WEBPACK_AMD_DEFINE_FACTORY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t } else {\n\t // Browser globals\n\t factory(jQuery);\n\t }\n\t})(function () {\n\t var _l = window._l || function (s) {\n\t return s;\n\t };\n\t\n\t //TODO: consolidate with tool menu functionality, use there\n\t\n\t /** searchInput: (jQuery plugin)\n\t * Creates a search input, a clear button, and loading indicator\n\t * within the selected node.\n\t *\n\t * When the user either presses return or enters some minimal number\n\t * of characters, a callback is called. Pressing ESC when the input\n\t * is focused will clear the input and call a separate callback.\n\t */\n\t function searchInput(parentNode, options) {\n\t var KEYCODE_ESC = 27,\n\t KEYCODE_RETURN = 13,\n\t $parentNode = $(parentNode),\n\t firstSearch = true,\n\t defaults = {\n\t initialVal: '',\n\t name: 'search',\n\t placeholder: 'search',\n\t classes: '',\n\t onclear: function () {},\n\t onfirstsearch: null,\n\t onsearch: function (inputVal) {},\n\t minSearchLen: 0,\n\t escWillClear: true,\n\t oninit: function () {}\n\t };\n\t\n\t // .................................................................... input rendering and events\n\t // visually clear the search, trigger an event, and call the callback\n\t function clearSearchInput(event) {\n\t var $input = $(this).parent().children('input');\n\t $input.val('').trigger('searchInput.clear').blur();\n\t options.onclear();\n\t }\n\t\n\t // search for searchTerms, trigger an event, call the appropo callback (based on whether this is the first)\n\t function search(event, searchTerms) {\n\t if (!searchTerms) {\n\t return clearSearchInput();\n\t }\n\t $(this).trigger('search.search', searchTerms);\n\t if (typeof options.onfirstsearch === 'function' && firstSearch) {\n\t firstSearch = false;\n\t options.onfirstsearch(searchTerms);\n\t } else {\n\t options.onsearch(searchTerms);\n\t }\n\t }\n\t\n\t // .................................................................... input rendering and events\n\t function inputTemplate() {\n\t // class search-query is bootstrap 2.3 style that now lives in base.less\n\t return [''].join('');\n\t }\n\t\n\t // the search input that responds to keyboard events and displays the search value\n\t function $input() {\n\t return $(inputTemplate())\n\t // select all text on a focus\n\t .focus(function (event) {\n\t $(this).select();\n\t })\n\t // attach behaviors to esc, return if desired, search on some min len string\n\t .keyup(function (event) {\n\t event.preventDefault();\n\t event.stopPropagation();\n\t\n\t // esc key will clear if desired\n\t if (event.which === KEYCODE_ESC && options.escWillClear) {\n\t clearSearchInput.call(this, event);\n\t } else {\n\t var searchTerms = $(this).val();\n\t // return key or the search string len > minSearchLen (if not 0) triggers search\n\t if (event.which === KEYCODE_RETURN || options.minSearchLen && searchTerms.length >= options.minSearchLen) {\n\t search.call(this, event, searchTerms);\n\t }\n\t }\n\t }).val(options.initialVal);\n\t }\n\t\n\t // .................................................................... clear button rendering and events\n\t // a button for clearing the search bar, placed on the right hand side\n\t function $clearBtn() {\n\t return $([''].join('')).tooltip({ placement: 'bottom' }).click(function (event) {\n\t clearSearchInput.call(this, event);\n\t });\n\t }\n\t\n\t // .................................................................... loadingIndicator rendering\n\t // a button for clearing the search bar, placed on the right hand side\n\t function $loadingIndicator() {\n\t return $([''].join('')).hide().tooltip({ placement: 'bottom' });\n\t }\n\t\n\t // .................................................................... commands\n\t // visually swap the load, clear buttons\n\t function toggleLoadingIndicator() {\n\t $parentNode.find('.search-loading').toggle();\n\t $parentNode.find('.search-clear').toggle();\n\t }\n\t\n\t // .................................................................... init\n\t // string command (not constructor)\n\t if (jQuery.type(options) === 'string') {\n\t if (options === 'toggle-loading') {\n\t toggleLoadingIndicator();\n\t }\n\t return $parentNode;\n\t }\n\t\n\t // initial render\n\t if (jQuery.type(options) === 'object') {\n\t options = jQuery.extend(true, {}, defaults, options);\n\t }\n\t //NOTE: prepended\n\t return $parentNode.addClass('search-input').prepend([$input(), $clearBtn(), $loadingIndicator()]);\n\t }\n\t\n\t // as jq plugin\n\t jQuery.fn.extend({\n\t searchInput: function $searchInput(options) {\n\t return this.each(function () {\n\t return searchInput(this, options);\n\t });\n\t }\n\t });\n\t});\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1), __webpack_require__(1)))\n\n/***/ }),\n/* 89 */,\n/* 90 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;!(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t // Alphanumeric/natural sort fn\n\t function naturalSort(a, b) {\n\t // setup temp-scope variables for comparison evauluation\n\t var re = /(-?[0-9\\.]+)/g,\n\t x = a.toString().toLowerCase() || '',\n\t y = b.toString().toLowerCase() || '',\n\t nC = String.fromCharCode(0),\n\t xN = x.replace(re, nC + '$1' + nC).split(nC),\n\t yN = y.replace(re, nC + '$1' + nC).split(nC),\n\t xD = new Date(x).getTime(),\n\t yD = xD ? new Date(y).getTime() : null;\n\t // natural sorting of dates\n\t if (yD) {\n\t if (xD < yD) {\n\t return -1;\n\t } else if (xD > yD) {\n\t return 1;\n\t }\n\t }\n\t // natural sorting through split numeric strings and default strings\n\t var oFxNcL, oFyNcL;\n\t for (var cLoc = 0, numS = Math.max(xN.length, yN.length); cLoc < numS; cLoc++) {\n\t oFxNcL = parseFloat(xN[cLoc]) || xN[cLoc];\n\t oFyNcL = parseFloat(yN[cLoc]) || yN[cLoc];\n\t if (oFxNcL < oFyNcL) {\n\t return -1;\n\t } else if (oFxNcL > oFyNcL) {\n\t return 1;\n\t }\n\t }\n\t return 0;\n\t }\n\t\n\t return naturalSort;\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\n/***/ }),\n/* 91 */,\n/* 92 */,\n/* 93 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\t/* WEBPACK VAR INJECTION */(function(Backbone) {var Ui = __webpack_require__(7),\n\t historyOptionsMenu = __webpack_require__(120);\n\tCurrentHistoryView = __webpack_require__(117).CurrentHistoryView, _l = __webpack_require__(5);\n\t\n\t/** the right hand panel in the analysis page that shows the current history */\n\tvar HistoryPanel = Backbone.View.extend({\n\t\n\t initialize: function (page, options) {\n\t var self = this;\n\t this.userIsAnonymous = Galaxy.user.isAnonymous();\n\t this.allow_user_dataset_purge = options.config.allow_user_dataset_purge;\n\t this.root = options.root;\n\t\n\t // view of the current history\n\t this.historyView = new CurrentHistoryView({\n\t className: CurrentHistoryView.prototype.className + ' middle',\n\t purgeAllowed: this.allow_user_dataset_purge,\n\t linkTarget: 'galaxy_main'\n\t });\n\t\n\t // add history panel to Galaxy object\n\t Galaxy.currHistoryPanel = this.historyView;\n\t Galaxy.currHistoryPanel.listenToGalaxy(Galaxy);\n\t\n\t // build buttons\n\t this.buttonRefresh = new Ui.ButtonLink({\n\t id: 'history-refresh-button',\n\t title: 'Refresh history',\n\t cls: 'panel-header-button',\n\t icon: 'fa fa-refresh',\n\t onclick: function () {\n\t self.historyView.loadCurrentHistory();\n\t }\n\t });\n\t this.buttonOptions = new Ui.ButtonLink({\n\t id: 'history-options-button',\n\t title: 'History options',\n\t cls: 'panel-header-button',\n\t target: 'galaxy_main',\n\t icon: 'fa fa-cog',\n\t href: this.root + 'root/history_options'\n\t });\n\t this.buttonViewMulti = new Ui.ButtonLink({\n\t id: 'history-view-multi-button',\n\t title: 'View all histories',\n\t cls: 'panel-header-button',\n\t icon: 'fa fa-columns',\n\t href: this.root + 'history/view_multiple'\n\t });\n\t\n\t // define components\n\t this.model = new Backbone.Model({\n\t cls: 'history-right-panel',\n\t title: _l('History'),\n\t buttons: [this.buttonRefresh, this.buttonOptions, this.buttonViewMulti]\n\t });\n\t\n\t // build body template and connect history view\n\t this.setElement(this._template());\n\t this.historyView.setElement(this.$el);\n\t this.historyView.connectToQuotaMeter(Galaxy.quotaMeter);\n\t this.historyView.loadCurrentHistory();\n\t\n\t // fetch to update the quota meter adding 'current' for any anon-user's id\n\t Galaxy.listenTo(this.historyView, 'history-size-change', function () {\n\t Galaxy.user.fetch({ url: Galaxy.user.urlRoot() + '/' + (Galaxy.user.id || 'current') });\n\t });\n\t },\n\t\n\t render: function () {\n\t this.optionsMenu = historyOptionsMenu(this.buttonOptions.$el, {\n\t anonymous: this.userIsAnonymous,\n\t purgeAllowed: this.allow_user_dataset_purge,\n\t root: this.root\n\t });\n\t this.buttonViewMulti.$el[!this.userIsAnonymous ? 'show' : 'hide']();\n\t },\n\t\n\t /** add history view div */\n\t _template: function (data) {\n\t return [''].join('');\n\t },\n\t\n\t toString: function () {\n\t return 'historyPanel';\n\t }\n\t});\n\t\n\tmodule.exports = HistoryPanel;\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3)))\n\n/***/ }),\n/* 94 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\t/* WEBPACK VAR INJECTION */(function(Backbone, _) {var Tools = __webpack_require__(50),\n\t Upload = __webpack_require__(129),\n\t _l = __webpack_require__(5);\n\t\n\tvar ToolPanel = Backbone.View.extend({\n\t initialize: function (page, options) {\n\t // access configuration options\n\t var config = options.config;\n\t this.root = options.root;\n\t\n\t /** @type {Object[]} descriptions of user's workflows to be shown in the tool menu */\n\t this.stored_workflow_menu_entries = config.stored_workflow_menu_entries || [];\n\t\n\t // create tool search, tool panel, and tool panel view.\n\t var tool_search = new Tools.ToolSearch({\n\t hidden: false\n\t });\n\t var tools = new Tools.ToolCollection(config.toolbox);\n\t this.tool_panel = new Tools.ToolPanel({\n\t tool_search: tool_search,\n\t tools: tools,\n\t layout: config.toolbox_in_panel\n\t });\n\t this.tool_panel_view = new Tools.ToolPanelView({ model: this.tool_panel });\n\t\n\t // add upload modal\n\t this.upload_button = new Upload({\n\t nginx_upload_path: config.nginx_upload_path,\n\t ftp_upload_site: config.ftp_upload_site,\n\t default_genome: config.default_genome,\n\t default_extension: config.default_extension\n\t });\n\t\n\t // add uploader button to Galaxy object\n\t Galaxy.upload = this.upload_button;\n\t\n\t // components for panel definition\n\t this.model = new Backbone.Model({\n\t title: _l('Tools'),\n\t buttons: [this.upload_button]\n\t });\n\t\n\t // build body template\n\t this.setElement(this._template());\n\t },\n\t\n\t render: function () {\n\t // if there are tools, render panel and display everything\n\t var self = this;\n\t if (this.tool_panel.get('layout').size() > 0) {\n\t this.$el.prepend(this.tool_panel_view.$el);\n\t this.tool_panel_view.render();\n\t }\n\t // build the dom for the workflow portion of the tool menu\n\t // add internal workflow list\n\t self.$('#internal-workflows').append(self._templateAllWorkflow({\n\t title: _l('All workflows'),\n\t href: 'workflow'\n\t }));\n\t _.each(this.stored_workflow_menu_entries, function (menu_entry) {\n\t self.$('#internal-workflows').append(self._templateTool({\n\t title: menu_entry.stored_workflow.name,\n\t href: 'workflow/run?id=' + menu_entry.encoded_stored_workflow_id\n\t }));\n\t });\n\t },\n\t\n\t /** build a link to one tool */\n\t _templateTool: function (tool) {\n\t return ['
'].join('');\n\t },\n\t\n\t /** override to include inital menu dom and workflow section */\n\t _template: function () {\n\t return ['
', '
', '
', '', _l('Search did not match any tools.'), '', '
', '
', '
', '
', '
', '', _l('Workflows'), '', '
', '
', '
', '
', '
'].join('');\n\t },\n\t\n\t toString: function () {\n\t return 'toolPanel';\n\t }\n\t});\n\t\n\tmodule.exports = ToolPanel;\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2)))\n\n/***/ }),\n/* 95 */,\n/* 96 */,\n/* 97 */,\n/* 98 */,\n/* 99 */,\n/* 100 */,\n/* 101 */,\n/* 102 */,\n/* 103 */,\n/* 104 */,\n/* 105 */,\n/* 106 */,\n/* 107 */,\n/* 108 */,\n/* 109 */,\n/* 110 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(jQuery, _) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(35), __webpack_require__(74), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (DC_LI, DATASET_LI_EDIT, BASE_MVC, _l) {\n\t\n\t 'use strict';\n\t //==============================================================================\n\t\n\t var DCListItemView = DC_LI.DCListItemView;\n\t /** @class Edit view for DatasetCollection.\n\t */\n\t var DCListItemEdit = DCListItemView.extend(\n\t /** @lends DCListItemEdit.prototype */{\n\t\n\t /** override to add linkTarget */\n\t initialize: function (attributes) {\n\t DCListItemView.prototype.initialize.call(this, attributes);\n\t },\n\t\n\t // ......................................................................... misc\n\t /** String representation */\n\t toString: function () {\n\t var modelString = this.model ? this.model + '' : '(no model)';\n\t return 'DCListItemEdit(' + modelString + ')';\n\t }\n\t });\n\t\n\t //==============================================================================\n\t var DCEListItemView = DC_LI.DCEListItemView;\n\t /** @class Read only view for DatasetCollectionElement.\n\t */\n\t var DCEListItemEdit = DCEListItemView.extend(\n\t /** @lends DCEListItemEdit.prototype */{\n\t //TODO: this might be expendable - compacted with HDAListItemView\n\t\n\t /** set up */\n\t initialize: function (attributes) {\n\t DCEListItemView.prototype.initialize.call(this, attributes);\n\t },\n\t\n\t // ......................................................................... misc\n\t /** String representation */\n\t toString: function () {\n\t var modelString = this.model ? this.model + '' : '(no model)';\n\t return 'DCEListItemEdit(' + modelString + ')';\n\t }\n\t });\n\t\n\t //==============================================================================\n\t // NOTE: this does not inherit from DatasetDCEListItemView as you would expect\n\t //TODO: but should - if we can find something simpler than using diamond\n\t /** @class Editable view for a DatasetCollectionElement that is also an DatasetAssociation\n\t * (a dataset contained in a dataset collection).\n\t */\n\t var DatasetDCEListItemEdit = DATASET_LI_EDIT.DatasetListItemEdit.extend(\n\t /** @lends DatasetDCEListItemEdit.prototype */{\n\t\n\t /** set up */\n\t initialize: function (attributes) {\n\t DATASET_LI_EDIT.DatasetListItemEdit.prototype.initialize.call(this, attributes);\n\t },\n\t\n\t // NOTE: this does not inherit from DatasetDCEListItemView - so we duplicate this here\n\t //TODO: fix\n\t /** In this override, only get details if in the ready state.\n\t * Note: fetch with no 'change' event triggering to prevent automatic rendering.\n\t */\n\t _fetchModelDetails: function () {\n\t var view = this;\n\t if (view.model.inReadyState() && !view.model.hasDetails()) {\n\t return view.model.fetch({ silent: true });\n\t }\n\t return jQuery.when();\n\t },\n\t\n\t /** Override to remove delete button */\n\t _renderDeleteButton: function () {\n\t return null;\n\t },\n\t\n\t // ......................................................................... misc\n\t /** String representation */\n\t toString: function () {\n\t var modelString = this.model ? this.model + '' : '(no model)';\n\t return 'DatasetDCEListItemEdit(' + modelString + ')';\n\t }\n\t });\n\t\n\t // ............................................................................ TEMPLATES\n\t /** underscore templates */\n\t DatasetDCEListItemEdit.prototype.templates = function () {\n\t\n\t return _.extend({}, DATASET_LI_EDIT.DatasetListItemEdit.prototype.templates, {\n\t titleBar: DC_LI.DatasetDCEListItemView.prototype.templates.titleBar\n\t });\n\t }();\n\t\n\t //==============================================================================\n\t /** @class Read only view for a DatasetCollectionElement that is also a DatasetCollection\n\t * (a nested DC).\n\t */\n\t var NestedDCDCEListItemEdit = DC_LI.NestedDCDCEListItemView.extend(\n\t /** @lends NestedDCDCEListItemEdit.prototype */{\n\t\n\t /** String representation */\n\t toString: function () {\n\t var modelString = this.model ? this.model + '' : '(no model)';\n\t return 'NestedDCDCEListItemEdit(' + modelString + ')';\n\t }\n\t });\n\t\n\t //==============================================================================\n\t return {\n\t DCListItemEdit: DCListItemEdit,\n\t DCEListItemEdit: DCEListItemEdit,\n\t DatasetDCEListItemEdit: DatasetDCEListItemEdit,\n\t NestedDCDCEListItemEdit: NestedDCDCEListItemEdit\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1), __webpack_require__(2)))\n\n/***/ }),\n/* 111 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(73), __webpack_require__(36), __webpack_require__(110), __webpack_require__(6), __webpack_require__(48), __webpack_require__(17), __webpack_require__(5), __webpack_require__(16)], __WEBPACK_AMD_DEFINE_RESULT__ = function (DC_VIEW, DC_MODEL, DC_EDIT, BASE_MVC, TAGS, faIconButton, _l) {\n\t\n\t 'use strict';\n\t /* =============================================================================\n\t TODO:\n\t \n\t ============================================================================= */\n\t /** @class editable View/Controller for a dataset collection.\n\t */\n\t\n\t var _super = DC_VIEW.CollectionView;\n\t var CollectionViewEdit = _super.extend(\n\t /** @lends CollectionView.prototype */{\n\t //MODEL is either a DatasetCollection (or subclass) or a DatasetCollectionElement (list of pairs)\n\t\n\t /** logger used to record this.log messages, commonly set to console */\n\t //logger : console,\n\t\n\t /** sub view class used for datasets */\n\t DatasetDCEViewClass: DC_EDIT.DatasetDCEListItemEdit,\n\t /** sub view class used for nested collections */\n\t NestedDCDCEViewClass: DC_EDIT.NestedDCDCEListItemEdit,\n\t\n\t // ......................................................................... SET UP\n\t /** Set up the view, set up storage, bind listeners to HistoryContents events\n\t * @param {Object} attributes optional settings for the panel\n\t */\n\t initialize: function (attributes) {\n\t _super.prototype.initialize.call(this, attributes);\n\t },\n\t\n\t /** In this override, make the collection name editable\n\t */\n\t _setUpBehaviors: function ($where) {\n\t $where = $where || this.$el;\n\t _super.prototype._setUpBehaviors.call(this, $where);\n\t if (!this.model) {\n\t return;\n\t }\n\t\n\t // anon users shouldn't have access to any of the following\n\t if (!Galaxy.user || Galaxy.user.isAnonymous()) {\n\t return;\n\t }\n\t\n\t this.tagsEditorShown = true;\n\t\n\t //TODO: extract\n\t var panel = this,\n\t nameSelector = '> .controls .name';\n\t $where.find(nameSelector).attr('title', _l('Click to rename collection')).tooltip({ placement: 'bottom' }).make_text_editable({\n\t on_finish: function (newName) {\n\t var previousName = panel.model.get('name');\n\t if (newName && newName !== previousName) {\n\t panel.$el.find(nameSelector).text(newName);\n\t panel.model.save({ name: newName }).fail(function () {\n\t panel.$el.find(nameSelector).text(panel.model.previous('name'));\n\t });\n\t } else {\n\t panel.$el.find(nameSelector).text(previousName);\n\t }\n\t }\n\t });\n\t this.tagsEditor = new TAGS.TagsEditor({\n\t model: this.model,\n\t el: $where.find('.tags-display'),\n\t onshowFirstTime: function () {\n\t this.render();\n\t },\n\t usePrompt: false\n\t });\n\t this.tagsEditor.toggle(true);\n\t },\n\t\n\t // ........................................................................ misc\n\t /** string rep */\n\t toString: function () {\n\t return 'CollectionViewEdit(' + (this.model ? this.model.get('name') : '') + ')';\n\t }\n\t });\n\t\n\t // =============================================================================\n\t /** @class non-editable, read-only View/Controller for a dataset collection. */\n\t var ListCollectionViewEdit = CollectionViewEdit.extend(\n\t /** @lends ListCollectionView.prototype */{\n\t\n\t //TODO: not strictly needed - due to switch in CollectionView._getContentClass\n\t /** sub view class used for datasets */\n\t DatasetDCEViewClass: DC_EDIT.DatasetDCEListItemEdit,\n\t\n\t // ........................................................................ misc\n\t /** string rep */\n\t toString: function () {\n\t return 'ListCollectionViewEdit(' + (this.model ? this.model.get('name') : '') + ')';\n\t }\n\t });\n\t\n\t // =============================================================================\n\t /** @class Editable, read-only View/Controller for a dataset collection. */\n\t var PairCollectionViewEdit = ListCollectionViewEdit.extend(\n\t /** @lends PairCollectionViewEdit.prototype */{\n\t\n\t // ........................................................................ misc\n\t /** string rep */\n\t toString: function () {\n\t return 'PairCollectionViewEdit(' + (this.model ? this.model.get('name') : '') + ')';\n\t }\n\t });\n\t\n\t // =============================================================================\n\t /** @class Editable (roughly since these collections are immutable),\n\t * View/Controller for a dataset collection.\n\t */\n\t var NestedPairCollectionViewEdit = PairCollectionViewEdit.extend(\n\t /** @lends NestedPairCollectionViewEdit.prototype */{\n\t\n\t /** Override to remove the editable text from the name/identifier - these collections are considered immutable */\n\t _setUpBehaviors: function ($where) {\n\t _super.prototype._setUpBehaviors.call(this, $where);\n\t },\n\t\n\t // ........................................................................ misc\n\t /** string rep */\n\t toString: function () {\n\t return 'NestedPairCollectionViewEdit(' + (this.model ? this.model.get('name') : '') + ')';\n\t }\n\t });\n\t\n\t // =============================================================================\n\t /** @class editable, View/Controller for a list of pairs dataset collection. */\n\t var ListOfPairsCollectionViewEdit = CollectionViewEdit.extend(\n\t /** @lends ListOfPairsCollectionView.prototype */{\n\t\n\t //TODO: not strictly needed - due to switch in CollectionView._getContentClass\n\t /** sub view class used for nested collections */\n\t NestedDCDCEViewClass: DC_EDIT.NestedDCDCEListItemEdit.extend({\n\t foldoutPanelClass: NestedPairCollectionViewEdit\n\t }),\n\t\n\t // ........................................................................ misc\n\t /** string rep */\n\t toString: function () {\n\t return 'ListOfPairsCollectionViewEdit(' + (this.model ? this.model.get('name') : '') + ')';\n\t }\n\t });\n\t\n\t // =============================================================================\n\t /** @class View/Controller for a list of lists dataset collection. */\n\t var ListOfListsCollectionViewEdit = CollectionViewEdit.extend(\n\t /** @lends ListOfListsCollectionView.prototype */{\n\t\n\t //TODO: not strictly needed - due to switch in CollectionView._getContentClass\n\t /** sub view class used for nested collections */\n\t NestedDCDCEViewClass: DC_EDIT.NestedDCDCEListItemEdit.extend({\n\t foldoutPanelClass: NestedPairCollectionViewEdit\n\t }),\n\t\n\t // ........................................................................ misc\n\t /** string rep */\n\t toString: function () {\n\t return 'ListOfListsCollectionViewEdit(' + (this.model ? this.model.get('name') : '') + ')';\n\t }\n\t });\n\t\n\t //==============================================================================\n\t return {\n\t CollectionViewEdit: CollectionViewEdit,\n\t ListCollectionViewEdit: ListCollectionViewEdit,\n\t PairCollectionViewEdit: PairCollectionViewEdit,\n\t ListOfPairsCollectionViewEdit: ListOfPairsCollectionViewEdit,\n\t ListOfListsCollectionViewEdit: ListOfListsCollectionViewEdit\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\n/***/ }),\n/* 112 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, jQuery, $) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(141), __webpack_require__(90), __webpack_require__(72), __webpack_require__(6), __webpack_require__(5), __webpack_require__(87)], __WEBPACK_AMD_DEFINE_RESULT__ = function (levenshteinDistance, naturalSort, baseCreator, baseMVC, _l) {\n\t\n\t 'use strict';\n\t\n\t var logNamespace = 'collections';\n\t /* ============================================================================\n\t TODO:\n\t \n\t \n\t PROGRAMMATICALLY:\n\t currPanel.once( 'rendered', function(){\n\t currPanel.showSelectors();\n\t currPanel.selectAll();\n\t _.last( currPanel.actionsPopup.options ).func();\n\t });\n\t \n\t ============================================================================ */\n\t /** A view for paired datasets in the collections creator.\n\t */\n\t var PairView = Backbone.View.extend(baseMVC.LoggableMixin).extend({\n\t _logNamespace: logNamespace,\n\t\n\t tagName: 'li',\n\t className: 'dataset paired',\n\t\n\t initialize: function (attributes) {\n\t this.pair = attributes.pair || {};\n\t },\n\t\n\t template: _.template(['<%- pair.forward.name %>', '', '<%- pair.name %>', '', '<%- pair.reverse.name %>'].join('')),\n\t\n\t render: function () {\n\t this.$el.attr('draggable', true).data('pair', this.pair).html(this.template({ pair: this.pair })).addClass('flex-column-container');\n\t return this;\n\t },\n\t\n\t events: {\n\t 'dragstart': '_dragstart',\n\t 'dragend': '_dragend',\n\t 'dragover': '_sendToParent',\n\t 'drop': '_sendToParent'\n\t },\n\t\n\t /** dragging pairs for re-ordering */\n\t _dragstart: function (ev) {\n\t ev.currentTarget.style.opacity = '0.4';\n\t if (ev.originalEvent) {\n\t ev = ev.originalEvent;\n\t }\n\t\n\t ev.dataTransfer.effectAllowed = 'move';\n\t ev.dataTransfer.setData('text/plain', JSON.stringify(this.pair));\n\t\n\t this.$el.parent().trigger('pair.dragstart', [this]);\n\t },\n\t\n\t /** dragging pairs for re-ordering */\n\t _dragend: function (ev) {\n\t ev.currentTarget.style.opacity = '1.0';\n\t this.$el.parent().trigger('pair.dragend', [this]);\n\t },\n\t\n\t /** manually bubble up an event to the parent/container */\n\t _sendToParent: function (ev) {\n\t this.$el.parent().trigger(ev);\n\t },\n\t\n\t /** string rep */\n\t toString: function () {\n\t return 'PairView(' + this.pair.name + ')';\n\t }\n\t });\n\t\n\t // ============================================================================\n\t /** returns an autopair function that uses the provided options.match function */\n\t function autoPairFnBuilder(options) {\n\t options = options || {};\n\t options.createPair = options.createPair || function _defaultCreatePair(params) {\n\t params = params || {};\n\t var a = params.listA.splice(params.indexA, 1)[0],\n\t b = params.listB.splice(params.indexB, 1)[0],\n\t aInBIndex = params.listB.indexOf(a),\n\t bInAIndex = params.listA.indexOf(b);\n\t if (aInBIndex !== -1) {\n\t params.listB.splice(aInBIndex, 1);\n\t }\n\t if (bInAIndex !== -1) {\n\t params.listA.splice(bInAIndex, 1);\n\t }\n\t return this._pair(a, b, { silent: true });\n\t };\n\t // compile these here outside of the loop\n\t var _regexps = [];\n\t function getRegExps() {\n\t if (!_regexps.length) {\n\t _regexps = [new RegExp(this.filters[0]), new RegExp(this.filters[1])];\n\t }\n\t return _regexps;\n\t }\n\t // mangle params as needed\n\t options.preprocessMatch = options.preprocessMatch || function _defaultPreprocessMatch(params) {\n\t var regexps = getRegExps.call(this);\n\t return _.extend(params, {\n\t matchTo: params.matchTo.name.replace(regexps[0], ''),\n\t possible: params.possible.name.replace(regexps[1], '')\n\t });\n\t };\n\t\n\t return function _strategy(params) {\n\t this.debug('autopair _strategy ---------------------------');\n\t params = params || {};\n\t var listA = params.listA,\n\t listB = params.listB,\n\t indexA = 0,\n\t indexB,\n\t bestMatch = {\n\t score: 0.0,\n\t index: null\n\t },\n\t paired = [];\n\t //console.debug( 'params:', JSON.stringify( params, null, ' ' ) );\n\t this.debug('starting list lens:', listA.length, listB.length);\n\t this.debug('bestMatch (starting):', JSON.stringify(bestMatch, null, ' '));\n\t\n\t while (indexA < listA.length) {\n\t var matchTo = listA[indexA];\n\t bestMatch.score = 0.0;\n\t\n\t for (indexB = 0; indexB < listB.length; indexB++) {\n\t var possible = listB[indexB];\n\t this.debug(indexA + ':' + matchTo.name);\n\t this.debug(indexB + ':' + possible.name);\n\t\n\t // no matching with self\n\t if (listA[indexA] !== listB[indexB]) {\n\t bestMatch = options.match.call(this, options.preprocessMatch.call(this, {\n\t matchTo: matchTo,\n\t possible: possible,\n\t index: indexB,\n\t bestMatch: bestMatch\n\t }));\n\t this.debug('bestMatch:', JSON.stringify(bestMatch, null, ' '));\n\t if (bestMatch.score === 1.0) {\n\t this.debug('breaking early due to perfect match');\n\t break;\n\t }\n\t }\n\t }\n\t var scoreThreshold = options.scoreThreshold.call(this);\n\t this.debug('scoreThreshold:', scoreThreshold);\n\t this.debug('bestMatch.score:', bestMatch.score);\n\t\n\t if (bestMatch.score >= scoreThreshold) {\n\t //console.debug( 'autoPairFnBuilder.strategy', listA[ indexA ].name, listB[ bestMatch.index ].name );\n\t paired.push(options.createPair.call(this, {\n\t listA: listA,\n\t indexA: indexA,\n\t listB: listB,\n\t indexB: bestMatch.index\n\t }));\n\t //console.debug( 'list lens now:', listA.length, listB.length );\n\t } else {\n\t indexA += 1;\n\t }\n\t if (!listA.length || !listB.length) {\n\t return paired;\n\t }\n\t }\n\t this.debug('paired:', JSON.stringify(paired, null, ' '));\n\t this.debug('autopair _strategy ---------------------------');\n\t return paired;\n\t };\n\t }\n\t\n\t // ============================================================================\n\t /** An interface for building collections of paired datasets.\n\t */\n\t var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin).extend(baseCreator.CollectionCreatorMixin).extend({\n\t _logNamespace: logNamespace,\n\t\n\t className: 'list-of-pairs-collection-creator collection-creator flex-row-container',\n\t\n\t /** set up initial options, instance vars, behaviors, and autopair (if set to do so) */\n\t initialize: function (attributes) {\n\t this.metric('PairedCollectionCreator.initialize', attributes);\n\t //this.debug( '-- PairedCollectionCreator:', attributes );\n\t\n\t attributes = _.defaults(attributes, {\n\t datasets: [],\n\t filters: this.DEFAULT_FILTERS,\n\t automaticallyPair: true,\n\t strategy: 'lcs',\n\t matchPercentage: 0.9,\n\t twoPassAutopairing: true\n\t });\n\t\n\t /** unordered, original list */\n\t this.initialList = attributes.datasets;\n\t\n\t /** is this from a history? if so, what's its id? */\n\t this.historyId = attributes.historyId;\n\t\n\t /** which filters should be used initially? (String[2] or name in commonFilters) */\n\t this.filters = this.commonFilters[attributes.filters] || this.commonFilters[this.DEFAULT_FILTERS];\n\t if (_.isArray(attributes.filters)) {\n\t this.filters = attributes.filters;\n\t }\n\t\n\t /** try to auto pair the unpaired datasets on load? */\n\t this.automaticallyPair = attributes.automaticallyPair;\n\t\n\t /** what method to use for auto pairing (will be passed aggression level) */\n\t this.strategy = this.strategies[attributes.strategy] || this.strategies[this.DEFAULT_STRATEGY];\n\t if (_.isFunction(attributes.strategy)) {\n\t this.strategy = attributes.strategy;\n\t }\n\t\n\t /** distance/mismatch level allowed for autopairing */\n\t this.matchPercentage = attributes.matchPercentage;\n\t\n\t /** try to autopair using simple first, then this.strategy on the remainder */\n\t this.twoPassAutopairing = attributes.twoPassAutopairing;\n\t\n\t /** remove file extensions (\\.*) from created pair names? */\n\t this.removeExtensions = true;\n\t //this.removeExtensions = false;\n\t\n\t /** fn to call when the cancel button is clicked (scoped to this) - if falsy, no btn is displayed */\n\t this.oncancel = attributes.oncancel;\n\t /** fn to call when the collection is created (scoped to this) */\n\t this.oncreate = attributes.oncreate;\n\t\n\t /** fn to call when the cancel button is clicked (scoped to this) - if falsy, no btn is displayed */\n\t this.autoscrollDist = attributes.autoscrollDist || 24;\n\t\n\t /** is the unpaired panel shown? */\n\t this.unpairedPanelHidden = false;\n\t /** is the paired panel shown? */\n\t this.pairedPanelHidden = false;\n\t\n\t /** DOM elements currently being dragged */\n\t this.$dragging = null;\n\t\n\t /** Used for blocking UI events during ajax/operations (don't post twice) */\n\t this.blocking = false;\n\t\n\t this._setUpCommonSettings(attributes);\n\t this._setUpBehaviors();\n\t this._dataSetUp();\n\t },\n\t\n\t /** map of common filter pairs by name */\n\t commonFilters: {\n\t illumina: ['_1', '_2'],\n\t Rs: ['_R1', '_R2']\n\t },\n\t /** which commonFilter to use by default */\n\t DEFAULT_FILTERS: 'illumina',\n\t\n\t /** map of name->fn for autopairing */\n\t strategies: {\n\t 'simple': 'autopairSimple',\n\t 'lcs': 'autopairLCS',\n\t 'levenshtein': 'autopairLevenshtein'\n\t },\n\t /** default autopair strategy name */\n\t DEFAULT_STRATEGY: 'lcs',\n\t\n\t // ------------------------------------------------------------------------ process raw list\n\t /** set up main data: cache initialList, sort, and autopair */\n\t _dataSetUp: function () {\n\t //this.debug( '-- _dataSetUp' );\n\t\n\t this.paired = [];\n\t this.unpaired = [];\n\t\n\t this.selectedIds = [];\n\t\n\t // sort initial list, add ids if needed, and save new working copy to unpaired\n\t this._sortInitialList();\n\t this._ensureIds();\n\t this.unpaired = this.initialList.slice(0);\n\t\n\t if (this.automaticallyPair) {\n\t this.autoPair();\n\t this.once('rendered:initial', function () {\n\t this.trigger('autopair');\n\t });\n\t }\n\t },\n\t\n\t /** sort initial list */\n\t _sortInitialList: function () {\n\t //this.debug( '-- _sortInitialList' );\n\t this._sortDatasetList(this.initialList);\n\t },\n\t\n\t /** sort a list of datasets */\n\t _sortDatasetList: function (list) {\n\t // currently only natural sort by name\n\t list.sort(function (a, b) {\n\t return naturalSort(a.name, b.name);\n\t });\n\t return list;\n\t },\n\t\n\t /** add ids to dataset objs in initial list if none */\n\t _ensureIds: function () {\n\t this.initialList.forEach(function (dataset) {\n\t if (!dataset.hasOwnProperty('id')) {\n\t dataset.id = _.uniqueId();\n\t }\n\t });\n\t return this.initialList;\n\t },\n\t\n\t /** split initial list into two lists, those that pass forward filters & those passing reverse */\n\t _splitByFilters: function () {\n\t var regexFilters = this.filters.map(function (stringFilter) {\n\t return new RegExp(stringFilter);\n\t }),\n\t split = [[], []];\n\t\n\t function _filter(unpaired, filter) {\n\t return filter.test(unpaired.name);\n\t //return dataset.name.indexOf( filter ) >= 0;\n\t }\n\t this.unpaired.forEach(function _filterEach(unpaired) {\n\t // 90% of the time this seems to work, but:\n\t //TODO: this treats *all* strings as regex which may confuse people - possibly check for // surrounding?\n\t // would need explanation in help as well\n\t regexFilters.forEach(function (filter, i) {\n\t if (_filter(unpaired, filter)) {\n\t split[i].push(unpaired);\n\t }\n\t });\n\t });\n\t return split;\n\t },\n\t\n\t /** add a dataset to the unpaired list in it's proper order */\n\t _addToUnpaired: function (dataset) {\n\t // currently, unpaired is natural sorted by name, use binary search to find insertion point\n\t var binSearchSortedIndex = function (low, hi) {\n\t if (low === hi) {\n\t return low;\n\t }\n\t\n\t var mid = Math.floor((hi - low) / 2) + low,\n\t compared = naturalSort(dataset.name, this.unpaired[mid].name);\n\t\n\t if (compared < 0) {\n\t return binSearchSortedIndex(low, mid);\n\t } else if (compared > 0) {\n\t return binSearchSortedIndex(mid + 1, hi);\n\t }\n\t // walk the equal to find the last\n\t while (this.unpaired[mid] && this.unpaired[mid].name === dataset.name) {\n\t mid++;\n\t }\n\t return mid;\n\t }.bind(this);\n\t\n\t this.unpaired.splice(binSearchSortedIndex(0, this.unpaired.length), 0, dataset);\n\t },\n\t\n\t // ------------------------------------------------------------------------ auto pairing\n\t /** two passes to automatically create pairs:\n\t * use both simpleAutoPair, then the fn mentioned in strategy\n\t */\n\t autoPair: function (strategy) {\n\t // split first using exact matching\n\t var split = this._splitByFilters(),\n\t paired = [];\n\t if (this.twoPassAutopairing) {\n\t paired = this.autopairSimple({\n\t listA: split[0],\n\t listB: split[1]\n\t });\n\t split = this._splitByFilters();\n\t }\n\t\n\t // uncomment to see printlns while running tests\n\t //this.debug = function(){ console.log.apply( console, arguments ); };\n\t\n\t // then try the remainder with something less strict\n\t strategy = strategy || this.strategy;\n\t split = this._splitByFilters();\n\t paired = paired.concat(this[strategy].call(this, {\n\t listA: split[0],\n\t listB: split[1]\n\t }));\n\t return paired;\n\t },\n\t\n\t /** autopair by exact match */\n\t autopairSimple: autoPairFnBuilder({\n\t scoreThreshold: function () {\n\t return 1.0;\n\t },\n\t match: function _match(params) {\n\t params = params || {};\n\t if (params.matchTo === params.possible) {\n\t return {\n\t index: params.index,\n\t score: 1.0\n\t };\n\t }\n\t return params.bestMatch;\n\t }\n\t }),\n\t\n\t /** autopair by levenshtein edit distance scoring */\n\t autopairLevenshtein: autoPairFnBuilder({\n\t scoreThreshold: function () {\n\t return this.matchPercentage;\n\t },\n\t match: function _matches(params) {\n\t params = params || {};\n\t var distance = levenshteinDistance(params.matchTo, params.possible),\n\t score = 1.0 - distance / Math.max(params.matchTo.length, params.possible.length);\n\t if (score > params.bestMatch.score) {\n\t return {\n\t index: params.index,\n\t score: score\n\t };\n\t }\n\t return params.bestMatch;\n\t }\n\t }),\n\t\n\t /** autopair by longest common substrings scoring */\n\t autopairLCS: autoPairFnBuilder({\n\t scoreThreshold: function () {\n\t return this.matchPercentage;\n\t },\n\t match: function _matches(params) {\n\t params = params || {};\n\t var match = this._naiveStartingAndEndingLCS(params.matchTo, params.possible).length,\n\t score = match / Math.max(params.matchTo.length, params.possible.length);\n\t if (score > params.bestMatch.score) {\n\t return {\n\t index: params.index,\n\t score: score\n\t };\n\t }\n\t return params.bestMatch;\n\t }\n\t }),\n\t\n\t /** return the concat'd longest common prefix and suffix from two strings */\n\t _naiveStartingAndEndingLCS: function (s1, s2) {\n\t var fwdLCS = '',\n\t revLCS = '',\n\t i = 0,\n\t j = 0;\n\t while (i < s1.length && i < s2.length) {\n\t if (s1[i] !== s2[i]) {\n\t break;\n\t }\n\t fwdLCS += s1[i];\n\t i += 1;\n\t }\n\t if (i === s1.length) {\n\t return s1;\n\t }\n\t if (i === s2.length) {\n\t return s2;\n\t }\n\t\n\t i = s1.length - 1;\n\t j = s2.length - 1;\n\t while (i >= 0 && j >= 0) {\n\t if (s1[i] !== s2[j]) {\n\t break;\n\t }\n\t revLCS = [s1[i], revLCS].join('');\n\t i -= 1;\n\t j -= 1;\n\t }\n\t return fwdLCS + revLCS;\n\t },\n\t\n\t // ------------------------------------------------------------------------ pairing / unpairing\n\t /** create a pair from fwd and rev, removing them from unpaired, and placing the new pair in paired */\n\t _pair: function (fwd, rev, options) {\n\t options = options || {};\n\t this.debug('_pair:', fwd, rev);\n\t var pair = this._createPair(fwd, rev, options.name);\n\t this.paired.push(pair);\n\t this.unpaired = _.without(this.unpaired, fwd, rev);\n\t if (!options.silent) {\n\t this.trigger('pair:new', pair);\n\t }\n\t return pair;\n\t },\n\t\n\t /** create a pair Object from fwd and rev, adding the name attribute (will guess if not given) */\n\t _createPair: function (fwd, rev, name) {\n\t // ensure existance and don't pair something with itself\n\t if (!(fwd && rev) || fwd === rev) {\n\t throw new Error('Bad pairing: ' + [JSON.stringify(fwd), JSON.stringify(rev)]);\n\t }\n\t name = name || this._guessNameForPair(fwd, rev);\n\t return { forward: fwd, name: name, reverse: rev };\n\t },\n\t\n\t /** try to find a good pair name for the given fwd and rev datasets */\n\t _guessNameForPair: function (fwd, rev, removeExtensions) {\n\t removeExtensions = removeExtensions !== undefined ? removeExtensions : this.removeExtensions;\n\t var fwdName = fwd.name,\n\t revName = rev.name,\n\t lcs = this._naiveStartingAndEndingLCS(fwdName.replace(new RegExp(this.filters[0]), ''), revName.replace(new RegExp(this.filters[1]), ''));\n\t if (removeExtensions) {\n\t var lastDotIndex = lcs.lastIndexOf('.');\n\t if (lastDotIndex > 0) {\n\t var extension = lcs.slice(lastDotIndex, lcs.length);\n\t lcs = lcs.replace(extension, '');\n\t fwdName = fwdName.replace(extension, '');\n\t revName = revName.replace(extension, '');\n\t }\n\t }\n\t return lcs || fwdName + ' & ' + revName;\n\t },\n\t\n\t /** unpair a pair, removing it from paired, and adding the fwd,rev datasets back into unpaired */\n\t _unpair: function (pair, options) {\n\t options = options || {};\n\t if (!pair) {\n\t throw new Error('Bad pair: ' + JSON.stringify(pair));\n\t }\n\t this.paired = _.without(this.paired, pair);\n\t this._addToUnpaired(pair.forward);\n\t this._addToUnpaired(pair.reverse);\n\t\n\t if (!options.silent) {\n\t this.trigger('pair:unpair', [pair]);\n\t }\n\t return pair;\n\t },\n\t\n\t /** unpair all paired datasets */\n\t unpairAll: function () {\n\t var pairs = [];\n\t while (this.paired.length) {\n\t pairs.push(this._unpair(this.paired[0], { silent: true }));\n\t }\n\t this.trigger('pair:unpair', pairs);\n\t },\n\t\n\t // ------------------------------------------------------------------------ API\n\t /** convert a pair into JSON compatible with the collections API */\n\t _pairToJSON: function (pair, src) {\n\t src = src || 'hda';\n\t //TODO: consider making this the pair structure when created instead\n\t return {\n\t collection_type: 'paired',\n\t src: 'new_collection',\n\t name: pair.name,\n\t element_identifiers: [{\n\t name: 'forward',\n\t id: pair.forward.id,\n\t src: src\n\t }, {\n\t name: 'reverse',\n\t id: pair.reverse.id,\n\t src: src\n\t }]\n\t };\n\t },\n\t\n\t /** create the collection via the API\n\t * @returns {jQuery.xhr Object} the jquery ajax request\n\t */\n\t createList: function (name) {\n\t var creator = this,\n\t url = Galaxy.root + 'api/histories/' + this.historyId + '/contents/dataset_collections';\n\t\n\t //TODO: use ListPairedCollection.create()\n\t var ajaxData = {\n\t type: 'dataset_collection',\n\t collection_type: 'list:paired',\n\t hide_source_items: creator.hideOriginals || false,\n\t name: _.escape(name || creator.$('.collection-name').val()),\n\t element_identifiers: creator.paired.map(function (pair) {\n\t return creator._pairToJSON(pair);\n\t })\n\t\n\t };\n\t //this.debug( JSON.stringify( ajaxData ) );\n\t creator.blocking = true;\n\t return jQuery.ajax(url, {\n\t type: 'POST',\n\t contentType: 'application/json',\n\t dataType: 'json',\n\t data: JSON.stringify(ajaxData)\n\t }).always(function () {\n\t creator.blocking = false;\n\t }).fail(function (xhr, status, message) {\n\t creator._ajaxErrHandler(xhr, status, message);\n\t }).done(function (response, message, xhr) {\n\t //this.info( 'ok', response, message, xhr );\n\t creator.trigger('collection:created', response, message, xhr);\n\t creator.metric('collection:created', response);\n\t if (typeof creator.oncreate === 'function') {\n\t creator.oncreate.call(this, response, message, xhr);\n\t }\n\t });\n\t },\n\t\n\t /** handle ajax errors with feedback and details to the user (if available) */\n\t _ajaxErrHandler: function (xhr, status, message) {\n\t this.error(xhr, status, message);\n\t var content = _l('An error occurred while creating this collection');\n\t if (xhr) {\n\t if (xhr.readyState === 0 && xhr.status === 0) {\n\t content += ': ' + _l('Galaxy could not be reached and may be updating.') + _l(' Try again in a few minutes.');\n\t } else if (xhr.responseJSON) {\n\t content += '
' + JSON.stringify(xhr.responseJSON) + '
';\n\t } else {\n\t content += ': ' + message;\n\t }\n\t }\n\t creator._showAlert(content, 'alert-danger');\n\t },\n\t\n\t // ------------------------------------------------------------------------ rendering\n\t /** render the entire interface */\n\t render: function (speed, callback) {\n\t //this.debug( '-- _render' );\n\t //this.$el.empty().html( this.templates.main() );\n\t this.$el.empty().html(this.templates.main());\n\t this._renderHeader(speed);\n\t this._renderMiddle(speed);\n\t this._renderFooter(speed);\n\t this._addPluginComponents();\n\t this.trigger('rendered', this);\n\t return this;\n\t },\n\t\n\t /** render the header section */\n\t _renderHeader: function (speed, callback) {\n\t //this.debug( '-- _renderHeader' );\n\t var $header = this.$('.header').empty().html(this.templates.header()).find('.help-content').prepend($(this.templates.helpContent()));\n\t\n\t this._renderFilters();\n\t return $header;\n\t },\n\t /** fill the filter inputs with the filter values */\n\t _renderFilters: function () {\n\t return this.$('.forward-column .column-header input').val(this.filters[0]).add(this.$('.reverse-column .column-header input').val(this.filters[1]));\n\t },\n\t\n\t /** render the middle including unpaired and paired sections (which may be hidden) */\n\t _renderMiddle: function (speed, callback) {\n\t var $middle = this.$('.middle').empty().html(this.templates.middle());\n\t\n\t // (re-) hide the un/paired panels based on instance vars\n\t if (this.unpairedPanelHidden) {\n\t this.$('.unpaired-columns').hide();\n\t } else if (this.pairedPanelHidden) {\n\t this.$('.paired-columns').hide();\n\t }\n\t\n\t this._renderUnpaired();\n\t this._renderPaired();\n\t return $middle;\n\t },\n\t /** render the unpaired section, showing datasets accrd. to filters, update the unpaired counts */\n\t _renderUnpaired: function (speed, callback) {\n\t //this.debug( '-- _renderUnpaired' );\n\t var creator = this,\n\t $fwd,\n\t $rev,\n\t $prd = [],\n\t split = this._splitByFilters();\n\t // update unpaired counts\n\t this.$('.forward-column .title').text([split[0].length, _l('unpaired forward')].join(' '));\n\t this.$('.forward-column .unpaired-info').text(this._renderUnpairedDisplayStr(this.unpaired.length - split[0].length));\n\t this.$('.reverse-column .title').text([split[1].length, _l('unpaired reverse')].join(' '));\n\t this.$('.reverse-column .unpaired-info').text(this._renderUnpairedDisplayStr(this.unpaired.length - split[1].length));\n\t\n\t this.$('.unpaired-columns .column-datasets').empty();\n\t\n\t // show/hide the auto pair button if any unpaired are left\n\t this.$('.autopair-link').toggle(this.unpaired.length !== 0);\n\t if (this.unpaired.length === 0) {\n\t this._renderUnpairedEmpty();\n\t return;\n\t }\n\t\n\t // create the dataset dom arrays\n\t $rev = split[1].map(function (dataset, i) {\n\t // if there'll be a fwd dataset across the way, add a button to pair the row\n\t if (split[0][i] !== undefined && split[0][i] !== dataset) {\n\t $prd.push(creator._renderPairButton());\n\t }\n\t return creator._renderUnpairedDataset(dataset);\n\t });\n\t $fwd = split[0].map(function (dataset) {\n\t return creator._renderUnpairedDataset(dataset);\n\t });\n\t\n\t if (!$fwd.length && !$rev.length) {\n\t this._renderUnpairedNotShown();\n\t return;\n\t }\n\t // add to appropo cols\n\t //TODO: not the best way to render - consider rendering the entire unpaired-columns section in a fragment\n\t // and swapping out that\n\t this.$('.unpaired-columns .forward-column .column-datasets').append($fwd).add(this.$('.unpaired-columns .paired-column .column-datasets').append($prd)).add(this.$('.unpaired-columns .reverse-column .column-datasets').append($rev));\n\t this._adjUnpairedOnScrollbar();\n\t },\n\t /** return a string to display the count of filtered out datasets */\n\t _renderUnpairedDisplayStr: function (numFiltered) {\n\t return ['(', numFiltered, ' ', _l('filtered out'), ')'].join('');\n\t },\n\t /** return an unattached jQuery DOM element to represent an unpaired dataset */\n\t _renderUnpairedDataset: function (dataset) {\n\t //TODO: to underscore template\n\t return $('').attr('id', 'dataset-' + dataset.id).addClass('dataset unpaired').attr('draggable', true).addClass(dataset.selected ? 'selected' : '').append($('').addClass('dataset-name').text(dataset.name))\n\t //??\n\t .data('dataset', dataset);\n\t },\n\t /** render the button that may go between unpaired datasets, allowing the user to pair a row */\n\t _renderPairButton: function () {\n\t //TODO: *not* a dataset - don't pretend like it is\n\t return $('').addClass('dataset unpaired').append($('').addClass('dataset-name').text(_l('Pair these datasets')));\n\t },\n\t /** a message to display when no unpaired left */\n\t _renderUnpairedEmpty: function () {\n\t //this.debug( '-- renderUnpairedEmpty' );\n\t var $msg = $('').text('(' + _l('no remaining unpaired datasets') + ')');\n\t this.$('.unpaired-columns .paired-column .column-datasets').empty().prepend($msg);\n\t return $msg;\n\t },\n\t /** a message to display when no unpaired can be shown with the current filters */\n\t _renderUnpairedNotShown: function () {\n\t //this.debug( '-- renderUnpairedEmpty' );\n\t var $msg = $('').text('(' + _l('no datasets were found matching the current filters') + ')');\n\t this.$('.unpaired-columns .paired-column .column-datasets').empty().prepend($msg);\n\t return $msg;\n\t },\n\t /** try to detect if the unpaired section has a scrollbar and adjust left column for better centering of all */\n\t _adjUnpairedOnScrollbar: function () {\n\t var $unpairedColumns = this.$('.unpaired-columns').last(),\n\t $firstDataset = this.$('.unpaired-columns .reverse-column .dataset').first();\n\t if (!$firstDataset.length) {\n\t return;\n\t }\n\t var ucRight = $unpairedColumns.offset().left + $unpairedColumns.outerWidth(),\n\t dsRight = $firstDataset.offset().left + $firstDataset.outerWidth(),\n\t rightDiff = Math.floor(ucRight) - Math.floor(dsRight);\n\t //this.debug( 'rightDiff:', ucRight, '-', dsRight, '=', rightDiff );\n\t this.$('.unpaired-columns .forward-column').css('margin-left', rightDiff > 0 ? rightDiff : 0);\n\t },\n\t\n\t /** render the paired section and update counts of paired datasets */\n\t _renderPaired: function (speed, callback) {\n\t //this.debug( '-- _renderPaired' );\n\t this.$('.paired-column-title .title').text([this.paired.length, _l('paired')].join(' '));\n\t // show/hide the unpair all link\n\t this.$('.unpair-all-link').toggle(this.paired.length !== 0);\n\t if (this.paired.length === 0) {\n\t this._renderPairedEmpty();\n\t return;\n\t //TODO: would be best to return here (the $columns)\n\t } else {\n\t // show/hide 'remove extensions link' when any paired and they seem to have extensions\n\t this.$('.remove-extensions-link').show();\n\t }\n\t\n\t this.$('.paired-columns .column-datasets').empty();\n\t var creator = this;\n\t this.paired.forEach(function (pair, i) {\n\t //TODO: cache these?\n\t var pairView = new PairView({ pair: pair });\n\t creator.$('.paired-columns .column-datasets').append(pairView.render().$el).append([''].join(''));\n\t });\n\t },\n\t /** a message to display when none paired */\n\t _renderPairedEmpty: function () {\n\t var $msg = $('').text('(' + _l('no paired datasets yet') + ')');\n\t this.$('.paired-columns .column-datasets').empty().prepend($msg);\n\t return $msg;\n\t },\n\t\n\t footerSettings: {\n\t '.hide-originals': 'hideOriginals',\n\t '.remove-extensions': 'removeExtensions'\n\t },\n\t\n\t /** add any jQuery/bootstrap/custom plugins to elements rendered */\n\t _addPluginComponents: function () {\n\t this._chooseFiltersPopover('.choose-filters-link');\n\t this.$('.help-content i').hoverhighlight('.collection-creator', 'rgba( 64, 255, 255, 1.0 )');\n\t },\n\t\n\t /** build a filter selection popover allowing selection of common filter pairs */\n\t _chooseFiltersPopover: function (selector) {\n\t function filterChoice(val1, val2) {\n\t return [''].join('');\n\t }\n\t var $popoverContent = $(_.template(['
', '
', _l('Choose from the following filters to change which unpaired reads are shown in the display'), ':
'].join(''))({}));\n\t\n\t return this.$(selector).popover({\n\t container: '.collection-creator',\n\t placement: 'bottom',\n\t html: true,\n\t //animation : false,\n\t content: $popoverContent\n\t });\n\t },\n\t\n\t /** add (or clear if clear is truthy) a validation warning to what */\n\t _validationWarning: function (what, clear) {\n\t var VALIDATION_CLASS = 'validation-warning';\n\t if (what === 'name') {\n\t what = this.$('.collection-name').add(this.$('.collection-name-prompt'));\n\t this.$('.collection-name').focus().select();\n\t }\n\t if (clear) {\n\t what = what || this.$('.' + VALIDATION_CLASS);\n\t what.removeClass(VALIDATION_CLASS);\n\t } else {\n\t what.addClass(VALIDATION_CLASS);\n\t }\n\t },\n\t\n\t // ------------------------------------------------------------------------ events\n\t /** set up event handlers on self */\n\t _setUpBehaviors: function () {\n\t this.once('rendered', function () {\n\t this.trigger('rendered:initial', this);\n\t });\n\t\n\t this.on('pair:new', function () {\n\t //TODO: ideally only re-render the columns (or even elements) involved\n\t this._renderUnpaired();\n\t this._renderPaired();\n\t\n\t // scroll to bottom where new pairs are added\n\t //TODO: this doesn't seem to work - innerHeight sticks at 133...\n\t // may have to do with improper flex columns\n\t //var $pairedView = this.$( '.paired-columns' );\n\t //$pairedView.scrollTop( $pairedView.innerHeight() );\n\t //this.debug( $pairedView.height() )\n\t this.$('.paired-columns').scrollTop(8000000);\n\t });\n\t this.on('pair:unpair', function (pairs) {\n\t //TODO: ideally only re-render the columns (or even elements) involved\n\t this._renderUnpaired();\n\t this._renderPaired();\n\t this.splitView();\n\t });\n\t\n\t this.on('filter-change', function () {\n\t this.filters = [this.$('.forward-unpaired-filter input').val(), this.$('.reverse-unpaired-filter input').val()];\n\t this.metric('filter-change', this.filters);\n\t this._renderFilters();\n\t this._renderUnpaired();\n\t });\n\t\n\t this.on('autopair', function () {\n\t this._renderUnpaired();\n\t this._renderPaired();\n\t\n\t var message,\n\t msgClass = null;\n\t if (this.paired.length) {\n\t msgClass = 'alert-success';\n\t message = this.paired.length + ' ' + _l('pairs created');\n\t if (!this.unpaired.length) {\n\t message += ': ' + _l('all datasets have been successfully paired');\n\t this.hideUnpaired();\n\t this.$('.collection-name').focus();\n\t }\n\t } else {\n\t message = _l(['Could not automatically create any pairs from the given dataset names.', 'You may want to choose or enter different filters and try auto-pairing again.', 'Close this message using the X on the right to view more help.'].join(' '));\n\t }\n\t this._showAlert(message, msgClass);\n\t });\n\t\n\t //this.on( 'all', function(){\n\t // this.info( arguments );\n\t //});\n\t return this;\n\t },\n\t\n\t events: {\n\t // header\n\t 'click .more-help': '_clickMoreHelp',\n\t 'click .less-help': '_clickLessHelp',\n\t 'click .main-help': '_toggleHelp',\n\t 'click .header .alert button': '_hideAlert',\n\t 'click .forward-column .column-title': '_clickShowOnlyUnpaired',\n\t 'click .reverse-column .column-title': '_clickShowOnlyUnpaired',\n\t 'click .unpair-all-link': '_clickUnpairAll',\n\t //TODO: this seems kinda backasswards - re-sending jq event as a backbone event, can we listen directly?\n\t 'change .forward-unpaired-filter input': function (ev) {\n\t this.trigger('filter-change');\n\t },\n\t 'focus .forward-unpaired-filter input': function (ev) {\n\t $(ev.currentTarget).select();\n\t },\n\t 'click .autopair-link': '_clickAutopair',\n\t 'click .choose-filters .filter-choice': '_clickFilterChoice',\n\t 'click .clear-filters-link': '_clearFilters',\n\t 'change .reverse-unpaired-filter input': function (ev) {\n\t this.trigger('filter-change');\n\t },\n\t 'focus .reverse-unpaired-filter input': function (ev) {\n\t $(ev.currentTarget).select();\n\t },\n\t // unpaired\n\t 'click .forward-column .dataset.unpaired': '_clickUnpairedDataset',\n\t 'click .reverse-column .dataset.unpaired': '_clickUnpairedDataset',\n\t 'click .paired-column .dataset.unpaired': '_clickPairRow',\n\t 'click .unpaired-columns': 'clearSelectedUnpaired',\n\t 'mousedown .unpaired-columns .dataset': '_mousedownUnpaired',\n\t // divider\n\t 'click .paired-column-title': '_clickShowOnlyPaired',\n\t 'mousedown .flexible-partition-drag': '_startPartitionDrag',\n\t // paired\n\t 'click .paired-columns .dataset.paired': 'selectPair',\n\t 'click .paired-columns': 'clearSelectedPaired',\n\t 'click .paired-columns .pair-name': '_clickPairName',\n\t 'click .unpair-btn': '_clickUnpair',\n\t // paired - drop target\n\t //'dragenter .paired-columns' : '_dragenterPairedColumns',\n\t //'dragleave .paired-columns .column-datasets': '_dragleavePairedColumns',\n\t 'dragover .paired-columns .column-datasets': '_dragoverPairedColumns',\n\t 'drop .paired-columns .column-datasets': '_dropPairedColumns',\n\t\n\t 'pair.dragstart .paired-columns .column-datasets': '_pairDragstart',\n\t 'pair.dragend .paired-columns .column-datasets': '_pairDragend',\n\t\n\t // footer\n\t 'change .remove-extensions': function (ev) {\n\t this.toggleExtensions();\n\t },\n\t 'change .collection-name': '_changeName',\n\t 'keydown .collection-name': '_nameCheckForEnter',\n\t 'change .hide-originals': '_changeHideOriginals',\n\t 'click .cancel-create': '_cancelCreate',\n\t 'click .create-collection': '_clickCreate' //,\n\t },\n\t\n\t /** toggle between showing only unpaired and split view */\n\t _clickShowOnlyUnpaired: function (ev) {\n\t //this.debug( 'click unpaired', ev.currentTarget );\n\t if (this.$('.paired-columns').is(':visible')) {\n\t this.hidePaired();\n\t } else {\n\t this.splitView();\n\t }\n\t },\n\t /** toggle between showing only paired and split view */\n\t _clickShowOnlyPaired: function (ev) {\n\t //this.debug( 'click paired' );\n\t if (this.$('.unpaired-columns').is(':visible')) {\n\t this.hideUnpaired();\n\t } else {\n\t this.splitView();\n\t }\n\t },\n\t\n\t /** hide unpaired, show paired */\n\t hideUnpaired: function (speed, callback) {\n\t this.unpairedPanelHidden = true;\n\t this.pairedPanelHidden = false;\n\t this._renderMiddle(speed, callback);\n\t },\n\t /** hide paired, show unpaired */\n\t hidePaired: function (speed, callback) {\n\t this.unpairedPanelHidden = false;\n\t this.pairedPanelHidden = true;\n\t this._renderMiddle(speed, callback);\n\t },\n\t /** show both paired and unpaired (splitting evenly) */\n\t splitView: function (speed, callback) {\n\t this.unpairedPanelHidden = this.pairedPanelHidden = false;\n\t this._renderMiddle(speed, callback);\n\t return this;\n\t },\n\t\n\t /** unpair all paired and do other super neat stuff which I'm not really sure about yet... */\n\t _clickUnpairAll: function (ev) {\n\t this.metric('unpairAll');\n\t this.unpairAll();\n\t },\n\t\n\t /** attempt to autopair */\n\t _clickAutopair: function (ev) {\n\t var paired = this.autoPair();\n\t this.metric('autopair', paired.length, this.unpaired.length);\n\t this.trigger('autopair');\n\t },\n\t\n\t /** set the filters based on the data attributes of the button click target */\n\t _clickFilterChoice: function (ev) {\n\t var $selected = $(ev.currentTarget);\n\t this.$('.forward-unpaired-filter input').val($selected.data('forward'));\n\t this.$('.reverse-unpaired-filter input').val($selected.data('reverse'));\n\t this._hideChooseFilters();\n\t this.trigger('filter-change');\n\t },\n\t\n\t /** hide the choose filters popover */\n\t _hideChooseFilters: function () {\n\t //TODO: update bootstrap and remove the following hack\n\t // see also: https://github.com/twbs/bootstrap/issues/10260\n\t this.$('.choose-filters-link').popover('hide');\n\t this.$('.popover').css('display', 'none');\n\t },\n\t\n\t /** clear both filters */\n\t _clearFilters: function (ev) {\n\t this.$('.forward-unpaired-filter input').val('');\n\t this.$('.reverse-unpaired-filter input').val('');\n\t this.trigger('filter-change');\n\t },\n\t\n\t // ........................................................................ unpaired\n\t /** select an unpaired dataset */\n\t _clickUnpairedDataset: function (ev) {\n\t ev.stopPropagation();\n\t return this.toggleSelectUnpaired($(ev.currentTarget));\n\t },\n\t\n\t /** Toggle the selection of an unpaired dataset representation.\n\t * @param [jQuery] $dataset the unpaired dataset dom rep to select\n\t * @param [Boolean] options.force if defined, force selection based on T/F; otherwise, toggle\n\t */\n\t toggleSelectUnpaired: function ($dataset, options) {\n\t options = options || {};\n\t var dataset = $dataset.data('dataset'),\n\t select = options.force !== undefined ? options.force : !$dataset.hasClass('selected');\n\t //this.debug( id, options.force, $dataset, dataset );\n\t if (!$dataset.length || dataset === undefined) {\n\t return $dataset;\n\t }\n\t\n\t if (select) {\n\t $dataset.addClass('selected');\n\t if (!options.waitToPair) {\n\t this.pairAllSelected();\n\t }\n\t } else {\n\t $dataset.removeClass('selected');\n\t //delete dataset.selected;\n\t }\n\t return $dataset;\n\t },\n\t\n\t /** pair all the currently selected unpaired datasets */\n\t pairAllSelected: function (options) {\n\t options = options || {};\n\t var creator = this,\n\t fwds = [],\n\t revs = [],\n\t pairs = [];\n\t creator.$('.unpaired-columns .forward-column .dataset.selected').each(function () {\n\t fwds.push($(this).data('dataset'));\n\t });\n\t creator.$('.unpaired-columns .reverse-column .dataset.selected').each(function () {\n\t revs.push($(this).data('dataset'));\n\t });\n\t fwds.length = revs.length = Math.min(fwds.length, revs.length);\n\t //this.debug( fwds );\n\t //this.debug( revs );\n\t fwds.forEach(function (fwd, i) {\n\t try {\n\t pairs.push(creator._pair(fwd, revs[i], { silent: true }));\n\t } catch (err) {\n\t //TODO: preserve selected state of those that couldn't be paired\n\t //TODO: warn that some could not be paired\n\t creator.error(err);\n\t }\n\t });\n\t if (pairs.length && !options.silent) {\n\t this.trigger('pair:new', pairs);\n\t }\n\t return pairs;\n\t },\n\t\n\t /** clear the selection on all unpaired datasets */\n\t clearSelectedUnpaired: function () {\n\t this.$('.unpaired-columns .dataset.selected').removeClass('selected');\n\t },\n\t\n\t /** when holding down the shift key on a click, 'paint' the moused over datasets as selected */\n\t _mousedownUnpaired: function (ev) {\n\t if (ev.shiftKey) {\n\t var creator = this,\n\t $startTarget = $(ev.target).addClass('selected'),\n\t moveListener = function (ev) {\n\t creator.$(ev.target).filter('.dataset').addClass('selected');\n\t };\n\t $startTarget.parent().on('mousemove', moveListener);\n\t\n\t // on any mouseup, stop listening to the move and try to pair any selected\n\t $(document).one('mouseup', function (ev) {\n\t $startTarget.parent().off('mousemove', moveListener);\n\t creator.pairAllSelected();\n\t });\n\t }\n\t },\n\t\n\t /** attempt to pair two datasets directly across from one another */\n\t _clickPairRow: function (ev) {\n\t //if( !ev.currentTarget ){ return true; }\n\t var rowIndex = $(ev.currentTarget).index(),\n\t fwd = $('.unpaired-columns .forward-column .dataset').eq(rowIndex).data('dataset'),\n\t rev = $('.unpaired-columns .reverse-column .dataset').eq(rowIndex).data('dataset');\n\t //this.debug( 'row:', rowIndex, fwd, rev );\n\t this._pair(fwd, rev);\n\t },\n\t\n\t // ........................................................................ divider/partition\n\t /** start dragging the visible divider/partition between unpaired and paired panes */\n\t _startPartitionDrag: function (ev) {\n\t var creator = this,\n\t startingY = ev.pageY;\n\t //this.debug( 'partition drag START:', ev );\n\t $('body').css('cursor', 'ns-resize');\n\t creator.$('.flexible-partition-drag').css('color', 'black');\n\t\n\t function endDrag(ev) {\n\t //creator.debug( 'partition drag STOP:', ev );\n\t // doing this by an added class didn't really work well - kept flashing still\n\t creator.$('.flexible-partition-drag').css('color', '');\n\t $('body').css('cursor', '').unbind('mousemove', trackMouse);\n\t }\n\t function trackMouse(ev) {\n\t var offset = ev.pageY - startingY;\n\t //creator.debug( 'partition:', startingY, offset );\n\t if (!creator.adjPartition(offset)) {\n\t //creator.debug( 'mouseup triggered' );\n\t $('body').trigger('mouseup');\n\t }\n\t creator._adjUnpairedOnScrollbar();\n\t startingY += offset;\n\t }\n\t $('body').mousemove(trackMouse);\n\t $('body').one('mouseup', endDrag);\n\t },\n\t\n\t /** adjust the parition up/down +/-adj pixels */\n\t adjPartition: function (adj) {\n\t var $unpaired = this.$('.unpaired-columns'),\n\t $paired = this.$('.paired-columns'),\n\t unpairedHi = parseInt($unpaired.css('height'), 10),\n\t pairedHi = parseInt($paired.css('height'), 10);\n\t //this.debug( adj, 'hi\\'s:', unpairedHi, pairedHi, unpairedHi + adj, pairedHi - adj );\n\t\n\t unpairedHi = Math.max(10, unpairedHi + adj);\n\t pairedHi = pairedHi - adj;\n\t\n\t var movingUpwards = adj < 0;\n\t // when the divider gets close to the top - lock into hiding the unpaired section\n\t if (movingUpwards) {\n\t if (this.unpairedPanelHidden) {\n\t return false;\n\t } else if (unpairedHi <= 10) {\n\t this.hideUnpaired();\n\t return false;\n\t }\n\t } else {\n\t if (this.unpairedPanelHidden) {\n\t $unpaired.show();\n\t this.unpairedPanelHidden = false;\n\t }\n\t }\n\t\n\t // when the divider gets close to the bottom - lock into hiding the paired section\n\t if (!movingUpwards) {\n\t if (this.pairedPanelHidden) {\n\t return false;\n\t } else if (pairedHi <= 15) {\n\t this.hidePaired();\n\t return false;\n\t }\n\t } else {\n\t if (this.pairedPanelHidden) {\n\t $paired.show();\n\t this.pairedPanelHidden = false;\n\t }\n\t }\n\t\n\t $unpaired.css({\n\t height: unpairedHi + 'px',\n\t flex: '0 0 auto'\n\t });\n\t return true;\n\t },\n\t\n\t // ........................................................................ paired\n\t /** select a pair when clicked */\n\t selectPair: function (ev) {\n\t ev.stopPropagation();\n\t $(ev.currentTarget).toggleClass('selected');\n\t },\n\t\n\t /** deselect all pairs */\n\t clearSelectedPaired: function (ev) {\n\t this.$('.paired-columns .dataset.selected').removeClass('selected');\n\t },\n\t\n\t /** rename a pair when the pair name is clicked */\n\t _clickPairName: function (ev) {\n\t ev.stopPropagation();\n\t var $name = $(ev.currentTarget),\n\t $pair = $name.parent().parent(),\n\t index = $pair.index('.dataset.paired'),\n\t pair = this.paired[index],\n\t response = prompt('Enter a new name for the pair:', pair.name);\n\t if (response) {\n\t pair.name = response;\n\t // set a flag (which won't be passed in json creation) for manual naming so we don't overwrite these\n\t // when adding/removing extensions\n\t //hackish\n\t pair.customizedName = true;\n\t $name.text(pair.name);\n\t }\n\t },\n\t\n\t /** unpair this pair */\n\t _clickUnpair: function (ev) {\n\t //if( !ev.currentTarget ){ return true; }\n\t var pairIndex = Math.floor($(ev.currentTarget).index('.unpair-btn'));\n\t //this.debug( 'pair:', pairIndex );\n\t this._unpair(this.paired[pairIndex]);\n\t },\n\t\n\t // ........................................................................ paired - drag and drop re-ordering\n\t //_dragenterPairedColumns : function( ev ){\n\t // this.debug( '_dragenterPairedColumns:', ev );\n\t //},\n\t //_dragleavePairedColumns : function( ev ){\n\t // //this.debug( '_dragleavePairedColumns:', ev );\n\t //},\n\t /** track the mouse drag over the paired list adding a placeholder to show where the drop would occur */\n\t _dragoverPairedColumns: function (ev) {\n\t //this.debug( '_dragoverPairedColumns:', ev );\n\t ev.preventDefault();\n\t\n\t var $list = this.$('.paired-columns .column-datasets');\n\t this._checkForAutoscroll($list, ev.originalEvent.clientY);\n\t //this.debug( ev.originalEvent.clientX, ev.originalEvent.clientY );\n\t var $nearest = this._getNearestPairedDatasetLi(ev.originalEvent.clientY);\n\t\n\t $('.element-drop-placeholder').remove();\n\t var $placeholder = $('');\n\t if (!$nearest.length) {\n\t $list.append($placeholder);\n\t } else {\n\t $nearest.before($placeholder);\n\t }\n\t },\n\t\n\t /** If the mouse is near enough to the list's top or bottom, scroll the list */\n\t _checkForAutoscroll: function ($element, y) {\n\t var AUTOSCROLL_SPEED = 2;\n\t var offset = $element.offset(),\n\t scrollTop = $element.scrollTop(),\n\t upperDist = y - offset.top,\n\t lowerDist = offset.top + $element.outerHeight() - y;\n\t //this.debug( '_checkForAutoscroll:', scrollTop, upperDist, lowerDist );\n\t if (upperDist >= 0 && upperDist < this.autoscrollDist) {\n\t $element.scrollTop(scrollTop - AUTOSCROLL_SPEED);\n\t } else if (lowerDist >= 0 && lowerDist < this.autoscrollDist) {\n\t $element.scrollTop(scrollTop + AUTOSCROLL_SPEED);\n\t }\n\t },\n\t\n\t /** get the nearest *previous* paired dataset PairView based on the mouse's Y coordinate.\n\t * If the y is at the end of the list, return an empty jQuery object.\n\t */\n\t _getNearestPairedDatasetLi: function (y) {\n\t var WIGGLE = 4,\n\t lis = this.$('.paired-columns .column-datasets li').toArray();\n\t for (var i = 0; i < lis.length; i++) {\n\t var $li = $(lis[i]),\n\t top = $li.offset().top,\n\t halfHeight = Math.floor($li.outerHeight() / 2) + WIGGLE;\n\t if (top + halfHeight > y && top - halfHeight < y) {\n\t //this.debug( y, top + halfHeight, top - halfHeight )\n\t return $li;\n\t }\n\t }\n\t return $();\n\t },\n\t /** drop (dragged/selected PairViews) onto the list, re-ordering both the DOM and the internal array of pairs */\n\t _dropPairedColumns: function (ev) {\n\t // both required for firefox\n\t ev.preventDefault();\n\t ev.dataTransfer.dropEffect = 'move';\n\t\n\t var $nearest = this._getNearestPairedDatasetLi(ev.originalEvent.clientY);\n\t if ($nearest.length) {\n\t this.$dragging.insertBefore($nearest);\n\t } else {\n\t // no nearest before - insert after last element (unpair button)\n\t this.$dragging.insertAfter(this.$('.paired-columns .unpair-btn').last());\n\t }\n\t // resync the creator's list of paired based on the new DOM order\n\t this._syncPairsToDom();\n\t return false;\n\t },\n\t /** resync the creator's list of paired based on the DOM order of pairs */\n\t _syncPairsToDom: function () {\n\t var newPaired = [];\n\t //TODO: doesn't seem wise to use the dom to store these - can't we sync another way?\n\t this.$('.paired-columns .dataset.paired').each(function () {\n\t newPaired.push($(this).data('pair'));\n\t });\n\t //this.debug( newPaired );\n\t this.paired = newPaired;\n\t this._renderPaired();\n\t },\n\t /** drag communication with pair sub-views: dragstart */\n\t _pairDragstart: function (ev, pair) {\n\t //this.debug( '_pairDragstart', ev, pair )\n\t // auto select the pair causing the event and move all selected\n\t pair.$el.addClass('selected');\n\t var $selected = this.$('.paired-columns .dataset.selected');\n\t this.$dragging = $selected;\n\t },\n\t /** drag communication with pair sub-views: dragend - remove the placeholder */\n\t _pairDragend: function (ev, pair) {\n\t //this.debug( '_pairDragend', ev, pair )\n\t $('.element-drop-placeholder').remove();\n\t this.$dragging = null;\n\t },\n\t\n\t // ........................................................................ footer\n\t toggleExtensions: function (force) {\n\t var creator = this;\n\t creator.removeExtensions = force !== undefined ? force : !creator.removeExtensions;\n\t\n\t _.each(creator.paired, function (pair) {\n\t // don't overwrite custom names\n\t if (pair.customizedName) {\n\t return;\n\t }\n\t pair.name = creator._guessNameForPair(pair.forward, pair.reverse);\n\t });\n\t\n\t creator._renderPaired();\n\t creator._renderFooter();\n\t },\n\t\n\t // ------------------------------------------------------------------------ misc\n\t /** debug a dataset list */\n\t _printList: function (list) {\n\t var creator = this;\n\t _.each(list, function (e) {\n\t if (list === creator.paired) {\n\t creator._printPair(e);\n\t } else {\n\t //creator.debug( e );\n\t }\n\t });\n\t },\n\t\n\t /** print a pair Object */\n\t _printPair: function (pair) {\n\t this.debug(pair.forward.name, pair.reverse.name, ': ->', pair.name);\n\t },\n\t\n\t /** string rep */\n\t toString: function () {\n\t return 'PairedCollectionCreator';\n\t },\n\t\n\t templates: _.extend({}, baseCreator.CollectionCreatorMixin._creatorTemplates, {\n\t\n\t /** the header (not including help text) */\n\t header: _.template(['
'].join('')),\n\t\n\t /** the middle: unpaired, divider, and paired */\n\t middle: _.template([\n\t // contains two flex rows (rows that fill available space) and a divider btwn\n\t '
'].join('')),\n\t\n\t /** help content */\n\t helpContent: _.template(['
', _l(['Collections of paired datasets are ordered lists of dataset pairs (often forward and reverse reads). ', 'These collections can be passed to tools and workflows in order to have analyses done on each member of ', 'the entire group. This interface allows you to create a collection, choose which datasets are paired, ', 'and re-order the final collection.'].join('')), '
', '
', _l(['Unpaired datasets are shown in the unpaired section ', '(hover over the underlined words to highlight below). ', 'Paired datasets are shown in the paired section.', '
To pair datasets, you can:', '
Click a dataset in the ', 'forward column ', 'to select it then click a dataset in the ', 'reverse column.', '
', '
Click one of the \"Pair these datasets\" buttons in the ', 'middle column ', 'to pair the datasets in a particular row.', '
', '
Click \"Auto-pair\" ', 'to have your datasets automatically paired based on name.', '
', '
'].join('')), '', '
', _l(['
You can filter what is shown in the unpaired sections by:', '
Entering partial dataset names in either the ', 'forward filter or ', 'reverse filter.', '
', '
Choosing from a list of preset filters by clicking the ', '\"Choose filters\" link.', '
Clearing the filters by clicking the ', '\"Clear filters\" link.', '
', '
'].join('')), '', '
', _l(['To unpair individual dataset pairs, click the ', 'unpair buttons ( ). ', 'Click the \"Unpair all\" link to unpair all pairs.'].join('')), '
', '
', _l(['You can include or remove the file extensions (e.g. \".fastq\") from your pair names by toggling the ', '\"Remove file extensions from pair names?\" control.'].join('')), '
', '
', _l(['Once your collection is complete, enter a name and ', 'click \"Create list\". ', '(Note: you do not have to pair all unpaired datasets to finish.)'].join('')), '
'].join(''))\n\t })\n\t });\n\t\n\t //=============================================================================\n\t /** a modal version of the paired collection creator */\n\t var pairedCollectionCreatorModal = function _pairedCollectionCreatorModal(datasets, options) {\n\t\n\t var deferred = jQuery.Deferred(),\n\t creator;\n\t\n\t options = _.defaults(options || {}, {\n\t datasets: datasets,\n\t oncancel: function () {\n\t Galaxy.modal.hide();\n\t deferred.reject('cancelled');\n\t },\n\t oncreate: function (creator, response) {\n\t Galaxy.modal.hide();\n\t deferred.resolve(response);\n\t }\n\t });\n\t\n\t if (!window.Galaxy || !Galaxy.modal) {\n\t throw new Error('Galaxy or Galaxy.modal not found');\n\t }\n\t\n\t creator = new PairedCollectionCreator(options);\n\t Galaxy.modal.show({\n\t title: 'Create a collection of paired datasets',\n\t body: creator.$el,\n\t width: '80%',\n\t height: '800px',\n\t closing_events: true\n\t });\n\t creator.render();\n\t window.creator = creator;\n\t\n\t //TODO: remove modal header\n\t return deferred;\n\t };\n\t\n\t //=============================================================================\n\t function createListOfPairsCollection(collection, defaultHideSourceItems) {\n\t var elements = collection.toJSON();\n\t //TODO: validate elements\n\t return pairedCollectionCreatorModal(elements, {\n\t historyId: collection.historyId,\n\t defaultHideSourceItems: defaultHideSourceItems\n\t });\n\t }\n\t\n\t //=============================================================================\n\t return {\n\t PairedCollectionCreator: PairedCollectionCreator,\n\t pairedCollectionCreatorModal: pairedCollectionCreatorModal,\n\t createListOfPairsCollection: createListOfPairsCollection\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2), __webpack_require__(1), __webpack_require__(1)))\n\n/***/ }),\n/* 113 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, jQuery) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(37), __webpack_require__(44), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (LIST_CREATOR, HDCA, BASE_MVC, _l) {\n\t\n\t 'use strict';\n\t\n\t var logNamespace = 'collections';\n\t /*==============================================================================\n\t TODO:\n\t the paired creator doesn't really mesh with the list creator as parent\n\t it may be better to make an abstract super class for both\n\t composites may inherit from this (or vis-versa)\n\t PairedDatasetCollectionElementView doesn't make a lot of sense\n\t \n\t ==============================================================================*/\n\t /** */\n\t var PairedDatasetCollectionElementView = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({\n\t _logNamespace: logNamespace,\n\t\n\t //TODO: use proper class (DatasetDCE or NestedDCDCE (or the union of both))\n\t tagName: 'li',\n\t className: 'collection-element',\n\t\n\t initialize: function (attributes) {\n\t this.element = attributes.element || {};\n\t this.identifier = attributes.identifier;\n\t },\n\t\n\t render: function () {\n\t this.$el.attr('data-element-id', this.element.id).html(this.template({ identifier: this.identifier, element: this.element }));\n\t return this;\n\t },\n\t\n\t //TODO: lots of unused space in the element - possibly load details and display them horiz.\n\t template: _.template(['<%- identifier %>', '<%- element.name %>'].join('')),\n\t\n\t /** remove the DOM and any listeners */\n\t destroy: function () {\n\t this.off();\n\t this.$el.remove();\n\t },\n\t\n\t /** string rep */\n\t toString: function () {\n\t return 'DatasetCollectionElementView()';\n\t }\n\t });\n\t\n\t // ============================================================================\n\t var _super = LIST_CREATOR.ListCollectionCreator;\n\t\n\t /** An interface for building collections.\n\t */\n\t var PairCollectionCreator = _super.extend({\n\t\n\t /** the class used to display individual elements */\n\t elementViewClass: PairedDatasetCollectionElementView,\n\t /** the class this creator will create and save */\n\t collectionClass: HDCA.HistoryPairDatasetCollection,\n\t className: 'pair-collection-creator collection-creator flex-row-container',\n\t\n\t /** override to no-op */\n\t _mangleDuplicateNames: function () {},\n\t\n\t // TODO: this whole pattern sucks. There needs to be two classes of problem area:\n\t // bad inital choices and\n\t // when the user has painted his/her self into a corner during creation/use-of-the-creator\n\t /** render the entire interface */\n\t render: function (speed, callback) {\n\t if (this.workingElements.length === 2) {\n\t return _super.prototype.render.call(this, speed, callback);\n\t }\n\t return this._renderInvalid(speed, callback);\n\t },\n\t\n\t // ------------------------------------------------------------------------ rendering elements\n\t /** render forward/reverse */\n\t _renderList: function (speed, callback) {\n\t //this.debug( '-- _renderList' );\n\t //precondition: there are two valid elements in workingElements\n\t var creator = this,\n\t $tmp = jQuery(''),\n\t $list = creator.$list();\n\t\n\t // lose the original views, create the new, append all at once, then call their renders\n\t _.each(this.elementViews, function (view) {\n\t view.destroy();\n\t creator.removeElementView(view);\n\t });\n\t $tmp.append(creator._createForwardElementView().$el);\n\t $tmp.append(creator._createReverseElementView().$el);\n\t $list.empty().append($tmp.children());\n\t _.invoke(creator.elementViews, 'render');\n\t },\n\t\n\t /** create the forward element view */\n\t _createForwardElementView: function () {\n\t return this._createElementView(this.workingElements[0], { identifier: 'forward' });\n\t },\n\t\n\t /** create the forward element view */\n\t _createReverseElementView: function () {\n\t return this._createElementView(this.workingElements[1], { identifier: 'reverse' });\n\t },\n\t\n\t /** create an element view, cache in elementViews, and return */\n\t _createElementView: function (element, options) {\n\t var elementView = new this.elementViewClass(_.extend(options, {\n\t element: element\n\t }));\n\t this.elementViews.push(elementView);\n\t return elementView;\n\t },\n\t\n\t /** swap the forward, reverse elements and re-render */\n\t swap: function () {\n\t this.workingElements = [this.workingElements[1], this.workingElements[0]];\n\t this._renderList();\n\t },\n\t\n\t events: _.extend(_.clone(_super.prototype.events), {\n\t 'click .swap': 'swap'\n\t }),\n\t\n\t // ------------------------------------------------------------------------ templates\n\t //TODO: move to require text plugin and load these as text\n\t //TODO: underscore currently unnecc. bc no vars are used\n\t //TODO: better way of localizing text-nodes in long strings\n\t /** underscore template fns attached to class */\n\t templates: _.extend(_.clone(_super.prototype.templates), {\n\t /** the middle: element list */\n\t middle: _.template(['
'].join('')),\n\t\n\t /** help content */\n\t helpContent: _.template(['
', _l(['Pair collections are permanent collections containing two datasets: one forward and one reverse. ', 'Often these are forward and reverse reads. The pair collections can be passed to tools and ', 'workflows in order to have analyses done on both datasets. This interface allows ', 'you to create a pair, name it, and swap which is forward and which reverse.'].join('')), '
', '
', '
', _l(['Click the \"Swap\" link to make your forward dataset the reverse ', 'and the reverse dataset forward.'].join('')), '
', '
', _l(['Click the \"Cancel\" button to exit the interface.'].join('')), '
', '
', '
', _l(['Once your collection is complete, enter a name and ', 'click \"Create list\".'].join('')), '
'].join('')),\n\t\n\t /** a simplified page communicating what went wrong and why the user needs to reselect something else */\n\t invalidInitial: _.template(['
', '
', '', '<% if( _.size( problems ) ){ %>', _l('The following selections could not be included due to problems'), '
<% _.each( problems, function( problem ){ %>', '
<%- problem.element.name %>: <%- problem.text %>
', '<% }); %>
', '<% } else if( _.size( elements ) === 0 ){ %>', _l('No datasets were selected'), '.', '<% } else if( _.size( elements ) === 1 ){ %>', _l('Only one dataset was selected'), ': <%- elements[0].name %>', '<% } else if( _.size( elements ) > 2 ){ %>', _l('Too many datasets were selected'), ': <%- _.pluck( elements, \"name\" ).join( \", \") %>', '<% } %>', ' ', _l('Two (and only two) elements are needed for the pair'), '. ', _l('You may need to '), '', _l('cancel'), ' ', _l('and reselect new elements'), '.', '', '
', '
', ''].join(''))\n\t }),\n\t\n\t // ------------------------------------------------------------------------ misc\n\t /** string rep */\n\t toString: function () {\n\t return 'PairCollectionCreator';\n\t }\n\t });\n\t\n\t //==============================================================================\n\t /** List collection flavor of collectionCreatorModal. */\n\t var pairCollectionCreatorModal = function _pairCollectionCreatorModal(elements, options) {\n\t options = options || {};\n\t options.title = _l('Create a collection from a pair of datasets');\n\t return LIST_CREATOR.collectionCreatorModal(elements, options, PairCollectionCreator);\n\t };\n\t\n\t //==============================================================================\n\t /** Use a modal to create a pair collection, then add it to the given history contents.\n\t * @returns {Deferred} resolved when the collection is added to the history.\n\t */\n\t function createPairCollection(contents, defaultHideSourceItems) {\n\t var elements = contents.toJSON(),\n\t promise = pairCollectionCreatorModal(elements, {\n\t defaultHideSourceItems: defaultHideSourceItems,\n\t creationFn: function (elements, name, hideSourceItems) {\n\t elements = [{ name: \"forward\", src: \"hda\", id: elements[0].id }, { name: \"reverse\", src: \"hda\", id: elements[1].id }];\n\t return contents.createHDCA(elements, 'paired', name, hideSourceItems);\n\t }\n\t });\n\t return promise;\n\t }\n\t\n\t //==============================================================================\n\t return {\n\t PairCollectionCreator: PairCollectionCreator,\n\t pairCollectionCreatorModal: pairCollectionCreatorModal,\n\t createPairCollection: createPairCollection\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ }),\n/* 114 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_, jQuery, $) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(8), __webpack_require__(83), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (MODAL, ERROR_MODAL, _l) {\n\t\n\t 'use strict';\n\t\n\t //==============================================================================\n\t /**\n\t * A dialog/modal that allows copying a user history or 'importing' from user\n\t * another. Generally called via historyCopyDialog below.\n\t * @type {Object}\n\t */\n\t\n\t var CopyDialog = {\n\t\n\t // language related strings/fns\n\t defaultName: _.template(\"Copy of '<%- name %>'\"),\n\t title: _.template(_l('Copying history') + ' \"<%- name %>\"'),\n\t submitLabel: _l('Copy'),\n\t errorMessage: _l('History could not be copied.'),\n\t progressive: _l('Copying history'),\n\t activeLabel: _l('Copy only the active, non-deleted datasets'),\n\t allLabel: _l('Copy all datasets including deleted ones'),\n\t anonWarning: _l('As an anonymous user, unless you login or register, you will lose your current history ') + _l('after copying this history. '),\n\t\n\t // template for modal body\n\t _template: _.template([\n\t //TODO: remove inline styles\n\t // show a warning message for losing current to anon users\n\t '<% if( isAnon ){ %>', '
', '<% } %>', ''].join('')),\n\t\n\t // empty modal body and let the user know the copy is happening\n\t _showAjaxIndicator: function _showAjaxIndicator() {\n\t var indicator = '
' + this.progressive + '...
';\n\t this.modal.$('.modal-body').empty().append(indicator).css({ 'margin-top': '8px' });\n\t },\n\t\n\t // (sorta) public interface - display the modal, render the form, and potentially copy the history\n\t // returns a jQuery.Deferred done->history copied, fail->user cancelled\n\t dialog: function _dialog(modal, history, options) {\n\t options = options || {};\n\t\n\t var dialog = this,\n\t deferred = jQuery.Deferred(),\n\t\n\t // TODO: getting a little byzantine here\n\t defaultCopyNameFn = options.nameFn || this.defaultName,\n\t defaultCopyName = defaultCopyNameFn({ name: history.get('name') }),\n\t\n\t // TODO: these two might be simpler as one 3 state option (all,active,no-choice)\n\t defaultCopyWhat = options.allDatasets ? 'copy-all' : 'copy-non-deleted',\n\t allowAll = !_.isUndefined(options.allowAll) ? options.allowAll : true,\n\t autoClose = !_.isUndefined(options.autoClose) ? options.autoClose : true;\n\t\n\t this.modal = modal;\n\t\n\t // validate the name and copy if good\n\t function checkNameAndCopy() {\n\t var name = modal.$('#copy-modal-title').val();\n\t if (!name) {\n\t modal.$('.invalid-title').show();\n\t return;\n\t }\n\t // get further settings, shut down and indicate the ajax call, then hide and resolve/reject\n\t var copyAllDatasets = modal.$('input[name=\"copy-what\"]:checked').val() === 'copy-all';\n\t modal.$('button').prop('disabled', true);\n\t dialog._showAjaxIndicator();\n\t history.copy(true, name, copyAllDatasets).done(function (response) {\n\t deferred.resolve(response);\n\t }).fail(function (xhr, status, message) {\n\t var options = { name: name, copyAllDatasets: copyAllDatasets };\n\t ERROR_MODAL.ajaxErrorModal(history, xhr, options, dialog.errorMessage);\n\t deferred.rejectWith(deferred, arguments);\n\t }).done(function () {\n\t if (autoClose) {\n\t modal.hide();\n\t }\n\t });\n\t }\n\t\n\t var originalClosingCallback = options.closing_callback;\n\t modal.show(_.extend(options, {\n\t title: this.title({ name: history.get('name') }),\n\t body: $(dialog._template({\n\t name: defaultCopyName,\n\t isAnon: Galaxy.user.isAnonymous(),\n\t allowAll: allowAll,\n\t copyWhat: defaultCopyWhat,\n\t activeLabel: this.activeLabel,\n\t allLabel: this.allLabel,\n\t anonWarning: this.anonWarning\n\t })),\n\t buttons: _.object([[_l('Cancel'), function () {\n\t modal.hide();\n\t }], [this.submitLabel, checkNameAndCopy]]),\n\t height: 'auto',\n\t closing_events: true,\n\t closing_callback: function _historyCopyClose(cancelled) {\n\t if (cancelled) {\n\t deferred.reject({ cancelled: true });\n\t }\n\t if (originalClosingCallback) {\n\t originalClosingCallback(cancelled);\n\t }\n\t }\n\t }));\n\t\n\t // set the default dataset copy, autofocus the title, and set up for a simple return\n\t modal.$('#copy-modal-title').focus().select();\n\t modal.$('#copy-modal-title').on('keydown', function (ev) {\n\t if (ev.keyCode === 13) {\n\t ev.preventDefault();\n\t checkNameAndCopy();\n\t }\n\t });\n\t\n\t return deferred;\n\t }\n\t };\n\t\n\t //==============================================================================\n\t // maintain the (slight) distinction between copy and import\n\t /**\n\t * Subclass CopyDialog to use the import language.\n\t */\n\t var ImportDialog = _.extend({}, CopyDialog, {\n\t defaultName: _.template(\"imported: <%- name %>\"),\n\t title: _.template(_l('Importing history') + ' \"<%- name %>\"'),\n\t submitLabel: _l('Import'),\n\t errorMessage: _l('History could not be imported.'),\n\t progressive: _l('Importing history'),\n\t activeLabel: _l('Import only the active, non-deleted datasets'),\n\t allLabel: _l('Import all datasets including deleted ones'),\n\t anonWarning: _l('As an anonymous user, unless you login or register, you will lose your current history ') + _l('after importing this history. ')\n\t\n\t });\n\t\n\t //==============================================================================\n\t /**\n\t * Main interface for both history import and history copy dialogs.\n\t * @param {Backbone.Model} history the history to copy\n\t * @param {Object} options a hash\n\t * @return {jQuery.Deferred} promise that fails on close and succeeds on copy\n\t *\n\t * options:\n\t * (this object is also passed to the modal used to display the dialog and accepts modal options)\n\t * {Function} nameFn if defined, use this to build the default name shown to the user\n\t * (the fn is passed: {name: })\n\t * {bool} useImport if true, use the 'import' language (instead of Copy)\n\t * {bool} allowAll if true, allow the user to choose between copying all datasets and\n\t * only non-deleted datasets\n\t * {String} allDatasets default initial checked radio button: 'copy-all' or 'copy-non-deleted',\n\t */\n\t var historyCopyDialog = function (history, options) {\n\t options = options || {};\n\t // create our own modal if Galaxy doesn't have one (mako tab without use_panels)\n\t var modal = window.parent.Galaxy.modal || new MODAL.View({});\n\t return options.useImport ? ImportDialog.dialog(modal, history, options) : CopyDialog.dialog(modal, history, options);\n\t };\n\t\n\t //==============================================================================\n\t return historyCopyDialog;\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(1)))\n\n/***/ }),\n/* 115 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(jQuery, _) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(74), __webpack_require__(76), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (DATASET_LI_EDIT, HDA_LI, BASE_MVC, _l) {\n\t\n\t 'use strict';\n\t\n\t //==============================================================================\n\t\n\t var _super = DATASET_LI_EDIT.DatasetListItemEdit;\n\t /** @class Editing view for HistoryDatasetAssociation.\n\t */\n\t var HDAListItemEdit = _super.extend(\n\t /** @lends HDAListItemEdit.prototype */{\n\t\n\t className: _super.prototype.className + \" history-content\",\n\t\n\t /** In this override, only get details if in the ready state, get rerunnable if in other states.\n\t * Note: fetch with no 'change' event triggering to prevent automatic rendering.\n\t */\n\t _fetchModelDetails: function () {\n\t var view = this;\n\t if (view.model.inReadyState() && !view.model.hasDetails()) {\n\t return view.model.fetch({ silent: true });\n\t\n\t // special case the need for the rerunnable and creating_job attributes\n\t // needed for rendering re-run button on queued, running datasets\n\t } else if (!view.model.has('rerunnable')) {\n\t return view.model.fetch({ silent: true, data: {\n\t // only fetch rerunnable and creating_job to keep overhead down\n\t keys: ['rerunnable', 'creating_job'].join(',')\n\t } });\n\t }\n\t return jQuery.when();\n\t },\n\t\n\t /** event map */\n\t events: _.extend(_.clone(_super.prototype.events), {\n\t 'click .unhide-link': function (ev) {\n\t this.model.unhide();return false;\n\t }\n\t }),\n\t\n\t /** string rep */\n\t toString: function () {\n\t var modelString = this.model ? this.model + '' : '(no model)';\n\t return 'HDAListItemEdit(' + modelString + ')';\n\t }\n\t });\n\t\n\t // ............................................................................ TEMPLATES\n\t /** underscore templates */\n\t HDAListItemEdit.prototype.templates = function () {\n\t\n\t var warnings = _.extend({}, _super.prototype.templates.warnings, {\n\t hidden: BASE_MVC.wrapTemplate(['<% if( !dataset.visible ){ %>',\n\t // add a link to unhide a dataset\n\t '
', '<% } %>'], 'dataset')\n\t });\n\t\n\t return _.extend({}, _super.prototype.templates, {\n\t //NOTE: *steal* the HDAListItemView titleBar\n\t titleBar: HDA_LI.HDAListItemView.prototype.templates.titleBar,\n\t warnings: warnings\n\t });\n\t }();\n\t\n\t //==============================================================================\n\t return {\n\t HDAListItemEdit: HDAListItemEdit\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1), __webpack_require__(2)))\n\n/***/ }),\n/* 116 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(78), __webpack_require__(111), __webpack_require__(17), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (HDCA_LI, DC_VIEW_EDIT, faIconButton, _l) {\n\t\n\t 'use strict';\n\t\n\t //==============================================================================\n\t\n\t var _super = HDCA_LI.HDCAListItemView;\n\t /** @class Editing view for HistoryDatasetCollectionAssociation.\n\t */\n\t var HDCAListItemEdit = _super.extend(\n\t /** @lends HDCAListItemEdit.prototype */{\n\t\n\t /** logger used to record this.log messages, commonly set to console */\n\t //logger : console,\n\t\n\t /** Override to return editable versions of the collection panels */\n\t _getFoldoutPanelClass: function () {\n\t switch (this.model.get('collection_type')) {\n\t case 'list':\n\t return DC_VIEW_EDIT.ListCollectionViewEdit;\n\t case 'paired':\n\t return DC_VIEW_EDIT.PairCollectionViewEdit;\n\t case 'list:paired':\n\t return DC_VIEW_EDIT.ListOfPairsCollectionViewEdit;\n\t case 'list:list':\n\t return DC_VIEW_EDIT.ListOfListsCollectionViewEdit;\n\t }\n\t throw new TypeError('Uknown collection_type: ' + this.model.get('collection_type'));\n\t },\n\t\n\t // ......................................................................... delete\n\t /** In this override, add the delete button. */\n\t _renderPrimaryActions: function () {\n\t this.log(this + '._renderPrimaryActions');\n\t // render the display, edit attr and delete icon-buttons\n\t return _super.prototype._renderPrimaryActions.call(this).concat([this._renderDeleteButton()]);\n\t },\n\t\n\t /** Render icon-button to delete this collection. */\n\t _renderDeleteButton: function () {\n\t var self = this,\n\t deleted = this.model.get('deleted');\n\t return faIconButton({\n\t title: deleted ? _l('Dataset collection is already deleted') : _l('Delete'),\n\t classes: 'delete-btn',\n\t faIcon: 'fa-times',\n\t disabled: deleted,\n\t onclick: function () {\n\t // ...bler... tooltips being left behind in DOM (hover out never called on deletion)\n\t self.$el.find('.icon-btn.delete-btn').trigger('mouseout');\n\t self.model['delete']();\n\t }\n\t });\n\t },\n\t\n\t // ......................................................................... misc\n\t /** string rep */\n\t toString: function () {\n\t var modelString = this.model ? this.model + '' : '(no model)';\n\t return 'HDCAListItemEdit(' + modelString + ')';\n\t }\n\t });\n\t\n\t //==============================================================================\n\t return {\n\t HDCAListItemEdit: HDCAListItemEdit\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\n/***/ }),\n/* 117 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_, $, jQuery) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(80), __webpack_require__(118), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (HISTORY_MODEL, HISTORY_VIEW_EDIT, BASE_MVC, _l) {\n\t\n\t 'use strict';\n\t\n\t // ============================================================================\n\t /** session storage for history panel preferences (and to maintain state)\n\t */\n\t\n\t var HistoryViewPrefs = BASE_MVC.SessionStorageModel.extend(\n\t /** @lends HistoryViewPrefs.prototype */{\n\t defaults: {\n\t /** should the tags editor be shown or hidden initially? */\n\t tagsEditorShown: false,\n\t /** should the annotation editor be shown or hidden initially? */\n\t annotationEditorShown: false,\n\t ///** what is the currently focused content (dataset or collection) in the current history?\n\t // * (the history panel will highlight and scroll to the focused content view)\n\t // */\n\t //focusedContentId : null\n\t /** Current scroll position */\n\t scrollPosition: 0\n\t },\n\t toString: function () {\n\t return 'HistoryViewPrefs(' + JSON.stringify(this.toJSON()) + ')';\n\t }\n\t });\n\t\n\t /** key string to store panel prefs (made accessible on class so you can access sessionStorage directly) */\n\t HistoryViewPrefs.storageKey = function storageKey() {\n\t return 'history-panel';\n\t };\n\t\n\t /* =============================================================================\n\t TODO:\n\t \n\t ============================================================================= */\n\t var _super = HISTORY_VIEW_EDIT.HistoryViewEdit;\n\t // used in root/index.mako\n\t /** @class View/Controller for the user's current history model as used in the history\n\t * panel (current right hand panel) of the analysis page.\n\t *\n\t * The only history panel that:\n\t * will poll for updates.\n\t * displays datasets in reverse hid order.\n\t */\n\t var CurrentHistoryView = _super.extend( /** @lends CurrentHistoryView.prototype */{\n\t\n\t className: _super.prototype.className + ' current-history-panel',\n\t\n\t /** override to use drilldown (and not foldout) for how collections are displayed */\n\t HDCAViewClass: _super.prototype.HDCAViewClass.extend({\n\t foldoutStyle: 'drilldown'\n\t }),\n\t\n\t emptyMsg: [_l('This history is empty'), '. ', _l('You can '), '', _l('load your own data'), '', _l(' or '), '', _l('get data from an external source'), ''].join(''),\n\t\n\t // ......................................................................... SET UP\n\t /** Set up the view, set up storage, bind listeners to HistoryContents events */\n\t initialize: function (attributes) {\n\t attributes = attributes || {};\n\t\n\t // ---- persistent preferences\n\t /** maintain state / preferences over page loads */\n\t this.preferences = new HistoryViewPrefs(_.extend({\n\t id: HistoryViewPrefs.storageKey()\n\t }, _.pick(attributes, _.keys(HistoryViewPrefs.prototype.defaults))));\n\t\n\t _super.prototype.initialize.call(this, attributes);\n\t\n\t /** sub-views that will overlay this panel (collections) */\n\t this.panelStack = [];\n\t\n\t /** id of currently focused content */\n\t this.currentContentId = attributes.currentContentId || null;\n\t //NOTE: purposely not sent to localstorage since panel recreation roughly lines up with a reset of this value\n\t },\n\t\n\t /** Override to cache the current scroll position with a listener */\n\t _setUpListeners: function () {\n\t _super.prototype._setUpListeners.call(this);\n\t\n\t var panel = this;\n\t // reset scroll position when there's a new history\n\t this.on('new-model', function () {\n\t panel.preferences.set('scrollPosition', 0);\n\t });\n\t },\n\t\n\t // ------------------------------------------------------------------------ loading history/item models\n\t // TODO: next three more appropriate moved to the app level\n\t /** (re-)loads the user's current history & contents w/ details */\n\t loadCurrentHistory: function () {\n\t return this.loadHistory(null, { url: Galaxy.root + 'history/current_history_json' });\n\t },\n\t\n\t /** loads a history & contents w/ details and makes them the current history */\n\t switchToHistory: function (historyId, attributes) {\n\t if (Galaxy.user.isAnonymous()) {\n\t this.trigger('error', _l('You must be logged in to switch histories'), _l('Anonymous user'));\n\t return $.when();\n\t }\n\t return this.loadHistory(historyId, { url: Galaxy.root + 'history/set_as_current?id=' + historyId });\n\t },\n\t\n\t /** creates a new history on the server and sets it as the user's current history */\n\t createNewHistory: function (attributes) {\n\t if (Galaxy.user.isAnonymous()) {\n\t this.trigger('error', _l('You must be logged in to create histories'), _l('Anonymous user'));\n\t return $.when();\n\t }\n\t return this.loadHistory(null, { url: Galaxy.root + 'history/create_new_current' });\n\t },\n\t\n\t /** release/free/shutdown old models and set up panel for new models */\n\t setModel: function (model, attributes, render) {\n\t _super.prototype.setModel.call(this, model, attributes, render);\n\t if (this.model && this.model.id) {\n\t this.log('checking for updates');\n\t this.model.checkForUpdates();\n\t }\n\t return this;\n\t },\n\t\n\t // ------------------------------------------------------------------------ history/content event listening\n\t /** listening for history events */\n\t _setUpModelListeners: function () {\n\t _super.prototype._setUpModelListeners.call(this);\n\t // re-broadcast any model change events so that listeners don't have to re-bind to each history\n\t return this.listenTo(this.model, {\n\t 'change:nice_size change:size': function () {\n\t this.trigger('history-size-change', this, this.model, arguments);\n\t },\n\t 'change:id': function () {\n\t this.once('loading-done', function () {\n\t this.model.checkForUpdates();\n\t });\n\t }\n\t });\n\t },\n\t\n\t /** listening for collection events */\n\t _setUpCollectionListeners: function () {\n\t _super.prototype._setUpCollectionListeners.call(this);\n\t // if a hidden item is created (gen. by a workflow), moves thru the updater to the ready state,\n\t // then: remove it from the collection if the panel is set to NOT show hidden datasets\n\t this.listenTo(this.collection, 'state:ready', function (model, newState, oldState) {\n\t if (!model.get('visible') && !this.collection.storage.includeHidden()) {\n\t this.removeItemView(model);\n\t }\n\t });\n\t },\n\t\n\t // ------------------------------------------------------------------------ panel rendering\n\t /** override to add a handler to capture the scroll position when the parent scrolls */\n\t _setUpBehaviors: function ($where) {\n\t $where = $where || this.$el;\n\t // console.log( '_setUpBehaviors', this.$scrollContainer( $where ).get(0), this.$list( $where ) );\n\t // we need to call this in _setUpBehaviors which is called after render since the $el\n\t // may not be attached to $el.parent and $scrollContainer() may not work\n\t var panel = this;\n\t _super.prototype._setUpBehaviors.call(panel, $where);\n\t\n\t // cache the handler to remove and re-add so we don't pile up the handlers\n\t if (!this._debouncedScrollCaptureHandler) {\n\t this._debouncedScrollCaptureHandler = _.debounce(function scrollCapture() {\n\t // cache the scroll position (only if visible)\n\t if (panel.$el.is(':visible')) {\n\t panel.preferences.set('scrollPosition', $(this).scrollTop());\n\t }\n\t }, 40);\n\t }\n\t\n\t panel.$scrollContainer($where).off('scroll', this._debouncedScrollCaptureHandler).on('scroll', this._debouncedScrollCaptureHandler);\n\t return panel;\n\t },\n\t\n\t /** In this override, handle null models and move the search input to the top */\n\t _buildNewRender: function () {\n\t if (!this.model) {\n\t return $();\n\t }\n\t var $newRender = _super.prototype._buildNewRender.call(this);\n\t $newRender.find('.search').prependTo($newRender.find('> .controls'));\n\t this._renderQuotaMessage($newRender);\n\t return $newRender;\n\t },\n\t\n\t /** render the message displayed when a user is over quota and can't run jobs */\n\t _renderQuotaMessage: function ($whereTo) {\n\t $whereTo = $whereTo || this.$el;\n\t return $(this.templates.quotaMsg({}, this)).prependTo($whereTo.find('.messages'));\n\t },\n\t\n\t /** In this override, get and set current panel preferences when editor is used */\n\t _renderTags: function ($where) {\n\t var panel = this;\n\t // render tags and show/hide based on preferences\n\t _super.prototype._renderTags.call(panel, $where);\n\t if (panel.preferences.get('tagsEditorShown')) {\n\t panel.tagsEditor.toggle(true);\n\t }\n\t // store preference when shown or hidden\n\t panel.listenTo(panel.tagsEditor, 'hiddenUntilActivated:shown hiddenUntilActivated:hidden', function (tagsEditor) {\n\t panel.preferences.set('tagsEditorShown', tagsEditor.hidden);\n\t });\n\t },\n\t\n\t /** In this override, get and set current panel preferences when editor is used */\n\t _renderAnnotation: function ($where) {\n\t var panel = this;\n\t // render annotation and show/hide based on preferences\n\t _super.prototype._renderAnnotation.call(panel, $where);\n\t if (panel.preferences.get('annotationEditorShown')) {\n\t panel.annotationEditor.toggle(true);\n\t }\n\t // store preference when shown or hidden\n\t panel.listenTo(panel.annotationEditor, 'hiddenUntilActivated:shown hiddenUntilActivated:hidden', function (annotationEditor) {\n\t panel.preferences.set('annotationEditorShown', annotationEditor.hidden);\n\t });\n\t },\n\t\n\t /** Override to scroll to cached position (in prefs) after swapping */\n\t _swapNewRender: function ($newRender) {\n\t _super.prototype._swapNewRender.call(this, $newRender);\n\t var panel = this;\n\t _.delay(function () {\n\t var pos = panel.preferences.get('scrollPosition');\n\t if (pos) {\n\t panel.scrollTo(pos, 0);\n\t }\n\t }, 10);\n\t //TODO: is this enough of a delay on larger histories?\n\t\n\t return this;\n\t },\n\t\n\t // ------------------------------------------------------------------------ sub-views\n\t /** Override to add the current-content highlight class to currentContentId's view */\n\t _attachItems: function ($whereTo) {\n\t _super.prototype._attachItems.call(this, $whereTo);\n\t var panel = this;\n\t if (panel.currentContentId) {\n\t panel._setCurrentContentById(panel.currentContentId);\n\t }\n\t return this;\n\t },\n\t\n\t /** Override to remove any drill down panels */\n\t addItemView: function (model, collection, options) {\n\t var view = _super.prototype.addItemView.call(this, model, collection, options);\n\t if (!view) {\n\t return view;\n\t }\n\t if (this.panelStack.length) {\n\t return this._collapseDrilldownPanel();\n\t }\n\t return view;\n\t },\n\t\n\t // ------------------------------------------------------------------------ collection sub-views\n\t /** In this override, add/remove expanded/collapsed model ids to/from web storage */\n\t _setUpItemViewListeners: function (view) {\n\t var panel = this;\n\t _super.prototype._setUpItemViewListeners.call(panel, view);\n\t // use pub-sub to: handle drilldown expansion and collapse\n\t return panel.listenTo(view, {\n\t 'expanded:drilldown': function (v, drilldown) {\n\t this._expandDrilldownPanel(drilldown);\n\t },\n\t 'collapsed:drilldown': function (v, drilldown) {\n\t this._collapseDrilldownPanel(drilldown);\n\t }\n\t });\n\t },\n\t\n\t /** display 'current content': add a visible highlight and store the id of a content item */\n\t setCurrentContent: function (view) {\n\t this.$('.history-content.current-content').removeClass('current-content');\n\t if (view) {\n\t view.$el.addClass('current-content');\n\t this.currentContentId = view.model.id;\n\t } else {\n\t this.currentContentId = null;\n\t }\n\t },\n\t\n\t /** find the view with the id and then call setCurrentContent on it */\n\t _setCurrentContentById: function (id) {\n\t var view = this.viewFromModelId(id) || null;\n\t this.setCurrentContent(view);\n\t },\n\t\n\t /** Handle drill down by hiding this panels list and controls and showing the sub-panel */\n\t _expandDrilldownPanel: function (drilldown) {\n\t this.panelStack.push(drilldown);\n\t // hide this panel's controls and list, set the name for back navigation, and attach to the $el\n\t this.$controls().add(this.$list()).hide();\n\t drilldown.parentName = this.model.get('name');\n\t drilldown.delegateEvents().render().$el.appendTo(this.$el);\n\t },\n\t\n\t /** Handle drilldown close by freeing the panel and re-rendering this panel */\n\t _collapseDrilldownPanel: function (drilldown) {\n\t this.panelStack.pop();\n\t //TODO: MEM: free the panel\n\t this.$controls().add(this.$list()).show();\n\t },\n\t\n\t // ........................................................................ panel events\n\t /** event map */\n\t events: _.extend(_.clone(_super.prototype.events), {\n\t // the two links in the empty message\n\t 'click .uploader-link': function (ev) {\n\t Galaxy.upload.show(ev);\n\t },\n\t 'click .get-data-link': function (ev) {\n\t var $toolMenu = $('.toolMenuContainer');\n\t $toolMenu.parent().scrollTop(0);\n\t $toolMenu.find('span:contains(\"Get Data\")').click();\n\t }\n\t }),\n\t\n\t // ........................................................................ external objects/MVC\n\t listenToGalaxy: function (galaxy) {\n\t this.listenTo(galaxy, {\n\t // when the galaxy_main iframe is loaded with a new page,\n\t // compare the url to the following list and if there's a match\n\t // pull the id from url and indicate in the history view that\n\t // the dataset with that id is the 'current'ly active dataset\n\t 'galaxy_main:load': function (data) {\n\t var pathToMatch = data.fullpath;\n\t var hdaId = null;\n\t var useToURLRegexMap = {\n\t 'display': /datasets\\/([a-f0-9]+)\\/display/,\n\t 'edit': /datasets\\/([a-f0-9]+)\\/edit/,\n\t 'report_error': /dataset\\/errors\\?id=([a-f0-9]+)/,\n\t 'rerun': /tool_runner\\/rerun\\?id=([a-f0-9]+)/,\n\t 'show_params': /datasets\\/([a-f0-9]+)\\/show_params/\n\t };\n\t _.find(useToURLRegexMap, function (regex, use) {\n\t // grab the more specific match result (1), save, and use it as the find flag\n\t hdaId = _.result(pathToMatch.match(regex), 1);\n\t return hdaId;\n\t });\n\t // need to type mangle to go from web route to history contents\n\t this._setCurrentContentById(hdaId ? 'dataset-' + hdaId : null);\n\t },\n\t // when the center panel is given a new view, clear the current indicator\n\t 'center-panel:load': function (view) {\n\t this._setCurrentContentById();\n\t }\n\t });\n\t },\n\t\n\t //TODO: remove quota meter from panel and remove this\n\t /** add listeners to an external quota meter (mvc/user/user-quotameter.js) */\n\t connectToQuotaMeter: function (quotaMeter) {\n\t if (!quotaMeter) {\n\t return this;\n\t }\n\t // show/hide the 'over quota message' in the history when the meter tells it to\n\t this.listenTo(quotaMeter, 'quota:over', this.showQuotaMessage);\n\t this.listenTo(quotaMeter, 'quota:under', this.hideQuotaMessage);\n\t\n\t // having to add this to handle re-render of hview while overquota (the above do not fire)\n\t this.on('rendered rendered:initial', function () {\n\t if (quotaMeter && quotaMeter.isOverQuota()) {\n\t this.showQuotaMessage();\n\t }\n\t });\n\t return this;\n\t },\n\t\n\t /** Override to preserve the quota message */\n\t clearMessages: function (ev) {\n\t var $target = !_.isUndefined(ev) ? $(ev.currentTarget) : this.$messages().children('[class$=\"message\"]');\n\t $target = $target.not('.quota-message');\n\t $target.fadeOut(this.fxSpeed, function () {\n\t $(this).remove();\n\t });\n\t return this;\n\t },\n\t\n\t /** Show the over quota message (which happens to be in the history panel).\n\t */\n\t showQuotaMessage: function () {\n\t var $msg = this.$('.quota-message');\n\t if ($msg.is(':hidden')) {\n\t $msg.slideDown(this.fxSpeed);\n\t }\n\t },\n\t\n\t /** Hide the over quota message (which happens to be in the history panel).\n\t */\n\t hideQuotaMessage: function () {\n\t var $msg = this.$('.quota-message');\n\t if (!$msg.is(':hidden')) {\n\t $msg.slideUp(this.fxSpeed);\n\t }\n\t },\n\t\n\t // ........................................................................ options menu\n\t //TODO: remove to batch\n\t /** unhide any hidden datasets */\n\t unhideHidden: function () {\n\t var self = this;\n\t if (confirm(_l('Really unhide all hidden datasets?'))) {\n\t // get all hidden, regardless of deleted/purged\n\t return self.model.contents._filterAndUpdate({ visible: false, deleted: '', purged: '' }, { visible: true }).done(function () {\n\t // TODO: would be better to render these as they're unhidden instead of all at once\n\t if (!self.model.contents.includeHidden) {\n\t self.renderItems();\n\t }\n\t });\n\t }\n\t return jQuery.when();\n\t },\n\t\n\t /** delete any hidden datasets */\n\t deleteHidden: function () {\n\t var self = this;\n\t if (confirm(_l('Really delete all hidden datasets?'))) {\n\t return self.model.contents._filterAndUpdate(\n\t // get all hidden, regardless of deleted/purged\n\t { visible: false, deleted: '', purged: '' },\n\t // both delete *and* unhide them\n\t { deleted: true, visible: true });\n\t }\n\t return jQuery.when();\n\t },\n\t\n\t /** Return a string rep of the history */\n\t toString: function () {\n\t return 'CurrentHistoryView(' + (this.model ? this.model.get('name') : '') + ')';\n\t }\n\t });\n\t\n\t //------------------------------------------------------------------------------ TEMPLATES\n\t CurrentHistoryView.prototype.templates = function () {\n\t\n\t var quotaMsgTemplate = BASE_MVC.wrapTemplate(['
', _l('You are over your disk quota'), '. ', _l('Tool execution is on hold until your disk usage drops below your allocated quota'), '.', '
'], 'history');\n\t return _.extend(_.clone(_super.prototype.templates), {\n\t quotaMsg: quotaMsgTemplate\n\t });\n\t }();\n\t\n\t //==============================================================================\n\t return {\n\t CurrentHistoryView: CurrentHistoryView\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(1)))\n\n/***/ }),\n/* 118 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(jQuery, _, $) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(119), __webpack_require__(45), __webpack_require__(11), __webpack_require__(77), __webpack_require__(115), __webpack_require__(116), __webpack_require__(48), __webpack_require__(70), __webpack_require__(37), __webpack_require__(113), __webpack_require__(112), __webpack_require__(17), __webpack_require__(84), __webpack_require__(6), __webpack_require__(5), __webpack_require__(16)], __WEBPACK_AMD_DEFINE_RESULT__ = function (HISTORY_VIEW, HISTORY_CONTENTS, STATES, HDA_MODEL, HDA_LI_EDIT, HDCA_LI_EDIT, TAGS, ANNOTATIONS, LIST_COLLECTION_CREATOR, PAIR_COLLECTION_CREATOR, LIST_OF_PAIRS_COLLECTION_CREATOR, faIconButton, PopupMenu, BASE_MVC, _l) {\n\t\n\t 'use strict';\n\t\n\t /* =============================================================================\n\t TODO:\n\t \n\t ============================================================================= */\n\t\n\t var _super = HISTORY_VIEW.HistoryView;\n\t // base class for history-view-edit-current and used as-is in history/view.mako\n\t /** @class Editable View/Controller for the history model.\n\t *\n\t * Allows:\n\t * (everything HistoryView allows)\n\t * changing the name\n\t * displaying and editing tags and annotations\n\t * multi-selection and operations on mulitple content items\n\t */\n\t var HistoryViewEdit = _super.extend(\n\t /** @lends HistoryViewEdit.prototype */{\n\t\n\t /** class to use for constructing the HistoryDatasetAssociation views */\n\t HDAViewClass: HDA_LI_EDIT.HDAListItemEdit,\n\t /** class to use for constructing the HistoryDatasetCollectionAssociation views */\n\t HDCAViewClass: HDCA_LI_EDIT.HDCAListItemEdit,\n\t\n\t // ......................................................................... SET UP\n\t /** Set up the view, set up storage, bind listeners to HistoryContents events\n\t * @param {Object} attributes\n\t */\n\t initialize: function (attributes) {\n\t attributes = attributes || {};\n\t _super.prototype.initialize.call(this, attributes);\n\t\n\t // ---- set up instance vars\n\t /** editor for tags - sub-view */\n\t this.tagsEditor = null;\n\t\n\t /** enable drag and drop - sub-view */\n\t this.dragItems = true;\n\t\n\t /** editor for annotations - sub-view */\n\t this.annotationEditor = null;\n\t\n\t /** allow user purge of dataset files? */\n\t this.purgeAllowed = attributes.purgeAllowed || false;\n\t\n\t // states/modes the panel can be in\n\t /** is the panel currently showing the dataset selection controls? */\n\t this.annotationEditorShown = attributes.annotationEditorShown || false;\n\t this.tagsEditorShown = attributes.tagsEditorShown || false;\n\t },\n\t\n\t /** Override to handle history as drag-drop target */\n\t _setUpListeners: function () {\n\t _super.prototype._setUpListeners.call(this);\n\t return this.on({\n\t 'droptarget:drop': function (ev, data) {\n\t // process whatever was dropped and re-hide the drop target\n\t this.dataDropped(data);\n\t this.dropTargetOff();\n\t },\n\t 'view:attached view:removed': function () {\n\t this._renderCounts();\n\t },\n\t 'search:loading-progress': this._renderSearchProgress,\n\t 'search:searching': this._renderSearchFindings\n\t });\n\t },\n\t\n\t // ------------------------------------------------------------------------ listeners\n\t /** listening for history and HDA events */\n\t _setUpModelListeners: function () {\n\t _super.prototype._setUpModelListeners.call(this);\n\t this.listenTo(this.model, 'change:size', this.updateHistoryDiskSize);\n\t return this;\n\t },\n\t\n\t /** listening for collection events */\n\t _setUpCollectionListeners: function () {\n\t _super.prototype._setUpCollectionListeners.call(this);\n\t this.listenTo(this.collection, {\n\t 'change:deleted': this._handleItemDeletedChange,\n\t 'change:visible': this._handleItemVisibleChange,\n\t 'change:purged': function (model) {\n\t // hafta get the new nice-size w/o the purged model\n\t this.model.fetch();\n\t },\n\t // loading indicators for deleted/hidden\n\t 'fetching-deleted': function (collection) {\n\t this.$('> .controls .deleted-count').html('' + _l('loading...') + '');\n\t },\n\t 'fetching-hidden': function (collection) {\n\t this.$('> .controls .hidden-count').html('' + _l('loading...') + '');\n\t },\n\t 'fetching-deleted-done fetching-hidden-done': this._renderCounts\n\t });\n\t return this;\n\t },\n\t\n\t // ------------------------------------------------------------------------ panel rendering\n\t /** In this override, add tag and annotation editors and a btn to toggle the selectors */\n\t _buildNewRender: function () {\n\t // create a new render using a skeleton template, render title buttons, render body, and set up events, etc.\n\t var $newRender = _super.prototype._buildNewRender.call(this);\n\t if (!this.model) {\n\t return $newRender;\n\t }\n\t\n\t if (Galaxy && Galaxy.user && Galaxy.user.id && Galaxy.user.id === this.model.get('user_id')) {\n\t this._renderTags($newRender);\n\t this._renderAnnotation($newRender);\n\t }\n\t return $newRender;\n\t },\n\t\n\t /** Update the history size display (curr. upper right of panel). */\n\t updateHistoryDiskSize: function () {\n\t this.$('.history-size').text(this.model.get('nice_size'));\n\t },\n\t\n\t /** override to render counts when the items are rendered */\n\t renderItems: function ($whereTo) {\n\t var views = _super.prototype.renderItems.call(this, $whereTo);\n\t if (!this.searchFor) {\n\t this._renderCounts($whereTo);\n\t }\n\t return views;\n\t },\n\t\n\t /** override to show counts, what's deleted/hidden, and links to toggle those */\n\t _renderCounts: function ($whereTo) {\n\t $whereTo = $whereTo instanceof jQuery ? $whereTo : this.$el;\n\t var html = this.templates.counts(this.model.toJSON(), this);\n\t return $whereTo.find('> .controls .subtitle').html(html);\n\t },\n\t\n\t /** render the tags sub-view controller */\n\t _renderTags: function ($where) {\n\t var panel = this;\n\t this.tagsEditor = new TAGS.TagsEditor({\n\t model: this.model,\n\t el: $where.find('.controls .tags-display'),\n\t onshowFirstTime: function () {\n\t this.render();\n\t },\n\t // show hide sub-view tag editors when this is shown/hidden\n\t onshow: function () {\n\t panel.toggleHDATagEditors(true, panel.fxSpeed);\n\t },\n\t onhide: function () {\n\t panel.toggleHDATagEditors(false, panel.fxSpeed);\n\t },\n\t $activator: faIconButton({\n\t title: _l('Edit history tags'),\n\t classes: 'history-tag-btn',\n\t faIcon: 'fa-tags'\n\t }).appendTo($where.find('.controls .actions'))\n\t });\n\t },\n\t /** render the annotation sub-view controller */\n\t _renderAnnotation: function ($where) {\n\t var panel = this;\n\t this.annotationEditor = new ANNOTATIONS.AnnotationEditor({\n\t model: this.model,\n\t el: $where.find('.controls .annotation-display'),\n\t onshowFirstTime: function () {\n\t this.render();\n\t },\n\t // show hide sub-view view annotation editors when this is shown/hidden\n\t onshow: function () {\n\t panel.toggleHDAAnnotationEditors(true, panel.fxSpeed);\n\t },\n\t onhide: function () {\n\t panel.toggleHDAAnnotationEditors(false, panel.fxSpeed);\n\t },\n\t $activator: faIconButton({\n\t title: _l('Edit history annotation'),\n\t classes: 'history-annotate-btn',\n\t faIcon: 'fa-comment'\n\t }).appendTo($where.find('.controls .actions'))\n\t });\n\t },\n\t\n\t /** Set up HistoryViewEdit js/widget behaviours\n\t * In this override, make the name editable\n\t */\n\t _setUpBehaviors: function ($where) {\n\t $where = $where || this.$el;\n\t _super.prototype._setUpBehaviors.call(this, $where);\n\t if (!this.model) {\n\t return;\n\t }\n\t\n\t // anon users shouldn't have access to any of the following\n\t if (!Galaxy.user || Galaxy.user.isAnonymous() || Galaxy.user.id !== this.model.get('user_id')) {\n\t return;\n\t }\n\t\n\t var panel = this,\n\t nameSelector = '> .controls .name';\n\t $where.find(nameSelector).attr('title', _l('Click to rename history')).tooltip({ placement: 'bottom' }).make_text_editable({\n\t on_finish: function (newName) {\n\t var previousName = panel.model.get('name');\n\t if (newName && newName !== previousName) {\n\t panel.$el.find(nameSelector).text(newName);\n\t panel.model.save({ name: newName }).fail(function () {\n\t panel.$el.find(nameSelector).text(panel.model.previous('name'));\n\t });\n\t } else {\n\t panel.$el.find(nameSelector).text(previousName);\n\t }\n\t }\n\t });\n\t },\n\t\n\t /** return a new popup menu for choosing a multi selection action\n\t * ajax calls made for multiple datasets are queued\n\t */\n\t multiselectActions: function () {\n\t var panel = this,\n\t actions = [{ html: _l('Hide datasets'), func: function () {\n\t var action = HDA_MODEL.HistoryDatasetAssociation.prototype.hide;\n\t panel.getSelectedModels().ajaxQueue(action);\n\t }\n\t }, { html: _l('Unhide datasets'), func: function () {\n\t var action = HDA_MODEL.HistoryDatasetAssociation.prototype.unhide;\n\t panel.getSelectedModels().ajaxQueue(action);\n\t }\n\t }, { html: _l('Delete datasets'), func: function () {\n\t var action = HDA_MODEL.HistoryDatasetAssociation.prototype['delete'];\n\t panel.getSelectedModels().ajaxQueue(action);\n\t }\n\t }, { html: _l('Undelete datasets'), func: function () {\n\t var action = HDA_MODEL.HistoryDatasetAssociation.prototype.undelete;\n\t panel.getSelectedModels().ajaxQueue(action);\n\t }\n\t }];\n\t if (panel.purgeAllowed) {\n\t actions.push({\n\t html: _l('Permanently delete datasets'), func: function () {\n\t if (confirm(_l('This will permanently remove the data in your datasets. Are you sure?'))) {\n\t var action = HDA_MODEL.HistoryDatasetAssociation.prototype.purge;\n\t panel.getSelectedModels().ajaxQueue(action);\n\t }\n\t }\n\t });\n\t }\n\t actions = actions.concat(panel._collectionActions());\n\t return actions;\n\t },\n\t\n\t /** */\n\t _collectionActions: function () {\n\t var panel = this;\n\t return [{ html: _l('Build Dataset List'), func: function () {\n\t panel.buildCollection(\"list\");\n\t }\n\t },\n\t // TODO: Only show quick pair if two things selected.\n\t { html: _l('Build Dataset Pair'), func: function () {\n\t panel.buildCollection(\"paired\");\n\t }\n\t }, { html: _l('Build List of Dataset Pairs'), func: function () {\n\t panel.buildCollection(\"list:paired\");\n\t }\n\t }];\n\t },\n\t\n\t buildCollection: function (collectionType, selection, hideSourceItems) {\n\t var panel = this;\n\t var selection = selection || panel.getSelectedModels();\n\t var hideSourceItems = hideSourceItems || false;\n\t var createFunc;\n\t if (collectionType == \"list\") {\n\t createFunc = LIST_COLLECTION_CREATOR.createListCollection;\n\t } else if (collectionType == \"paired\") {\n\t createFunc = PAIR_COLLECTION_CREATOR.createPairCollection;\n\t } else if (collectionType == \"list:paired\") {\n\t createFunc = LIST_OF_PAIRS_COLLECTION_CREATOR.createListOfPairsCollection;\n\t } else {\n\t console.warn(\"Unknown collectionType encountered \" + collectionType);\n\t }\n\t createFunc(selection, hideSourceItems).done(function () {\n\t panel.model.refresh();\n\t });\n\t },\n\t\n\t // ------------------------------------------------------------------------ sub-views\n\t /** In this override, add purgeAllowed and whether tags/annotation editors should be shown */\n\t _getItemViewOptions: function (model) {\n\t var options = _super.prototype._getItemViewOptions.call(this, model);\n\t _.extend(options, {\n\t purgeAllowed: this.purgeAllowed,\n\t tagsEditorShown: this.tagsEditor && !this.tagsEditor.hidden,\n\t annotationEditorShown: this.annotationEditor && !this.annotationEditor.hidden\n\t });\n\t return options;\n\t },\n\t\n\t /** If this item is deleted and we're not showing deleted items, remove the view\n\t * @param {Model} the item model to check\n\t */\n\t _handleItemDeletedChange: function (itemModel) {\n\t if (itemModel.get('deleted')) {\n\t this._handleItemDeletion(itemModel);\n\t } else {\n\t this._handleItemUndeletion(itemModel);\n\t }\n\t this._renderCounts();\n\t },\n\t\n\t _handleItemDeletion: function (itemModel) {\n\t var contentsShown = this.model.get('contents_active');\n\t contentsShown.deleted += 1;\n\t contentsShown.active -= 1;\n\t if (!this.model.contents.includeDeleted) {\n\t this.removeItemView(itemModel);\n\t }\n\t this.model.set('contents_active', contentsShown);\n\t },\n\t\n\t _handleItemUndeletion: function (itemModel) {\n\t var contentsShown = this.model.get('contents_active');\n\t contentsShown.deleted -= 1;\n\t if (!this.model.contents.includeDeleted) {\n\t contentsShown.active -= 1;\n\t }\n\t this.model.set('contents_active', contentsShown);\n\t },\n\t\n\t /** If this item is hidden and we're not showing hidden items, remove the view\n\t * @param {Model} the item model to check\n\t */\n\t _handleItemVisibleChange: function (itemModel) {\n\t if (itemModel.hidden()) {\n\t this._handleItemHidden(itemModel);\n\t } else {\n\t this._handleItemUnhidden(itemModel);\n\t }\n\t this._renderCounts();\n\t },\n\t\n\t _handleItemHidden: function (itemModel) {\n\t var contentsShown = this.model.get('contents_active');\n\t contentsShown.hidden += 1;\n\t contentsShown.active -= 1;\n\t if (!this.model.contents.includeHidden) {\n\t this.removeItemView(itemModel);\n\t }\n\t this.model.set('contents_active', contentsShown);\n\t },\n\t\n\t _handleItemUnhidden: function (itemModel) {\n\t var contentsShown = this.model.get('contents_active');\n\t contentsShown.hidden -= 1;\n\t if (!this.model.contents.includeHidden) {\n\t contentsShown.active -= 1;\n\t }\n\t this.model.set('contents_active', contentsShown);\n\t },\n\t\n\t /** toggle the visibility of each content's tagsEditor applying all the args sent to this function */\n\t toggleHDATagEditors: function (showOrHide, speed) {\n\t _.each(this.views, function (view) {\n\t if (view.tagsEditor) {\n\t view.tagsEditor.toggle(showOrHide, speed);\n\t }\n\t });\n\t },\n\t\n\t /** toggle the visibility of each content's annotationEditor applying all the args sent to this function */\n\t toggleHDAAnnotationEditors: function (showOrHide, speed) {\n\t _.each(this.views, function (view) {\n\t if (view.annotationEditor) {\n\t view.annotationEditor.toggle(showOrHide, speed);\n\t }\n\t });\n\t },\n\t\n\t // ------------------------------------------------------------------------ panel events\n\t /** event map */\n\t events: _.extend(_.clone(_super.prototype.events), {\n\t 'click .show-selectors-btn': 'toggleSelectors',\n\t 'click .toggle-deleted-link': function (ev) {\n\t this.toggleShowDeleted();\n\t },\n\t 'click .toggle-hidden-link': function (ev) {\n\t this.toggleShowHidden();\n\t }\n\t }),\n\t\n\t // ------------------------------------------------------------------------ search\n\t _renderSearchProgress: function (limit, offset) {\n\t var stop = limit + offset;\n\t return this.$('> .controls .subtitle').html(['', _l('Searching '), stop, '/', this.model.contentsShown(), ''].join(''));\n\t },\n\t\n\t /** override to display number found in subtitle */\n\t _renderSearchFindings: function () {\n\t this.$('> .controls .subtitle').html([_l('Found'), this.views.length].join(' '));\n\t return this;\n\t },\n\t\n\t // ------------------------------------------------------------------------ as drop target\n\t /** turn all the drag and drop handlers on and add some help text above the drop area */\n\t dropTargetOn: function () {\n\t if (this.dropTarget) {\n\t return this;\n\t }\n\t this.dropTarget = true;\n\t\n\t //TODO: to init\n\t var dropHandlers = {\n\t 'dragenter': _.bind(this.dragenter, this),\n\t 'dragover': _.bind(this.dragover, this),\n\t 'dragleave': _.bind(this.dragleave, this),\n\t 'drop': _.bind(this.drop, this)\n\t };\n\t\n\t var $dropTarget = this._renderDropTarget();\n\t this.$list().before([this._renderDropTargetHelp(), $dropTarget]);\n\t for (var evName in dropHandlers) {\n\t if (dropHandlers.hasOwnProperty(evName)) {\n\t //console.debug( evName, dropHandlers[ evName ] );\n\t $dropTarget.on(evName, dropHandlers[evName]);\n\t }\n\t }\n\t return this;\n\t },\n\t\n\t /** render a box to serve as a 'drop here' area on the history */\n\t _renderDropTarget: function () {\n\t this.$('.history-drop-target').remove();\n\t return $('').addClass('history-drop-target');\n\t },\n\t\n\t /** tell the user how it works */\n\t _renderDropTargetHelp: function () {\n\t this.$('.history-drop-target-help').remove();\n\t return $('').addClass('history-drop-target-help').text(_l('Drag datasets here to copy them to the current history'));\n\t },\n\t\n\t /** shut down drag and drop event handlers and remove drop target */\n\t dropTargetOff: function () {\n\t if (!this.dropTarget) {\n\t return this;\n\t }\n\t //this.log( 'dropTargetOff' );\n\t this.dropTarget = false;\n\t var dropTarget = this.$('.history-drop-target').get(0);\n\t for (var evName in this._dropHandlers) {\n\t if (this._dropHandlers.hasOwnProperty(evName)) {\n\t dropTarget.off(evName, this._dropHandlers[evName]);\n\t }\n\t }\n\t this.$('.history-drop-target').remove();\n\t this.$('.history-drop-target-help').remove();\n\t return this;\n\t },\n\t /** toggle the target on/off */\n\t dropTargetToggle: function () {\n\t if (this.dropTarget) {\n\t this.dropTargetOff();\n\t } else {\n\t this.dropTargetOn();\n\t }\n\t return this;\n\t },\n\t\n\t dragenter: function (ev) {\n\t //console.debug( 'dragenter:', this, ev );\n\t ev.preventDefault();\n\t ev.stopPropagation();\n\t this.$('.history-drop-target').css('border', '2px solid black');\n\t },\n\t dragover: function (ev) {\n\t ev.preventDefault();\n\t ev.stopPropagation();\n\t },\n\t dragleave: function (ev) {\n\t //console.debug( 'dragleave:', this, ev );\n\t ev.preventDefault();\n\t ev.stopPropagation();\n\t this.$('.history-drop-target').css('border', '1px dashed black');\n\t },\n\t /** when (text) is dropped try to parse as json and trigger an event */\n\t drop: function (ev) {\n\t ev.preventDefault();\n\t //ev.stopPropagation();\n\t\n\t var self = this;\n\t var dataTransfer = ev.originalEvent.dataTransfer;\n\t var data = dataTransfer.getData(\"text\");\n\t\n\t dataTransfer.dropEffect = 'move';\n\t try {\n\t data = JSON.parse(data);\n\t } catch (err) {\n\t self.warn('error parsing JSON from drop:', data);\n\t }\n\t\n\t self.trigger('droptarget:drop', ev, data, self);\n\t return false;\n\t },\n\t\n\t /** handler that copies data into the contents */\n\t dataDropped: function (data) {\n\t var self = this;\n\t // HDA: dropping will copy it to the history\n\t if (_.isObject(data) && data.model_class === 'HistoryDatasetAssociation' && data.id) {\n\t if (self.contents.currentPage !== 0) {\n\t return self.contents.fetchPage(0).then(function () {\n\t return self.model.contents.copy(data.id);\n\t });\n\t }\n\t return self.model.contents.copy(data.id);\n\t }\n\t return jQuery.when();\n\t },\n\t\n\t // ........................................................................ misc\n\t /** Return a string rep of the history */\n\t toString: function () {\n\t return 'HistoryViewEdit(' + (this.model ? this.model.get('name') : '') + ')';\n\t }\n\t });\n\t\n\t //------------------------------------------------------------------------------ TEMPLATES\n\t HistoryViewEdit.prototype.templates = function () {\n\t\n\t var countsTemplate = BASE_MVC.wrapTemplate(['<% var shown = Math.max( view.views.length, history.contents_active.active ) %>', '<% if( shown ){ %>', '', '<%- shown %> ', _l('shown'), '', '<% } %>', '<% if( history.contents_active.deleted ){ %>', '', '<% if( view.model.contents.includeDeleted ){ %>', '', _l('hide deleted'), '', '<% } else { %>', '<%- history.contents_active.deleted %> ', '', _l('deleted'), '', '<% } %>', '', '<% } %>', '<% if( history.contents_active.hidden ){ %>', '', '<% if( view.model.contents.includeHidden ){ %>', '', _l('hide hidden'), '', '<% } else { %>', '<%- history.contents_active.hidden %> ', '', _l('hidden'), '', '<% } %>', '', '<% } %>'], 'history');\n\t\n\t return _.extend(_.clone(_super.prototype.templates), {\n\t counts: countsTemplate\n\t });\n\t }();\n\t\n\t //==============================================================================\n\t return {\n\t HistoryViewEdit: HistoryViewEdit\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ }),\n/* 119 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_, $) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(81), __webpack_require__(80), __webpack_require__(45), __webpack_require__(46), __webpack_require__(76), __webpack_require__(78), __webpack_require__(85), __webpack_require__(83), __webpack_require__(17), __webpack_require__(6), __webpack_require__(5), __webpack_require__(88)], __WEBPACK_AMD_DEFINE_RESULT__ = function (LIST_VIEW, HISTORY_MODEL, HISTORY_CONTENTS, HISTORY_PREFS, HDA_LI, HDCA_LI, USER, ERROR_MODAL, faIconButton, BASE_MVC, _l) {\n\t 'use strict';\n\t\n\t /* =============================================================================\n\t TODO:\n\t \n\t ============================================================================= */\n\t /** @class non-editable, read-only View/Controller for a history model.\n\t * Allows:\n\t * changing the loaded history\n\t * displaying data, info, and download\n\t * tracking history attrs: size, tags, annotations, name, etc.\n\t * Does not allow:\n\t * changing the name\n\t */\n\t\n\t var _super = LIST_VIEW.ModelListPanel;\n\t var HistoryView = _super.extend(\n\t /** @lends HistoryView.prototype */{\n\t _logNamespace: 'history',\n\t\n\t /** class to use for constructing the HDA views */\n\t HDAViewClass: HDA_LI.HDAListItemView,\n\t /** class to use for constructing the HDCA views */\n\t HDCAViewClass: HDCA_LI.HDCAListItemView,\n\t /** class to used for constructing collection of sub-view models */\n\t collectionClass: HISTORY_CONTENTS.HistoryContents,\n\t /** key of attribute in model to assign to this.collection */\n\t modelCollectionKey: 'contents',\n\t\n\t tagName: 'div',\n\t className: _super.prototype.className + ' history-panel',\n\t\n\t /** string to display when the collection is empty */\n\t emptyMsg: _l('This history is empty'),\n\t /** displayed when no items match the search terms */\n\t noneFoundMsg: _l('No matching datasets found'),\n\t /** string used for search placeholder */\n\t searchPlaceholder: _l('search datasets'),\n\t\n\t /** @type {Number} ms to wait after history load to fetch/decorate hdcas with element_count */\n\t FETCH_COLLECTION_COUNTS_DELAY: 2000,\n\t\n\t // ......................................................................... SET UP\n\t /** Set up the view, bind listeners.\n\t * @param {Object} attributes optional settings for the panel\n\t */\n\t initialize: function (attributes) {\n\t _super.prototype.initialize.call(this, attributes);\n\t // ---- instance vars\n\t // control contents/behavior based on where (and in what context) the panel is being used\n\t /** where should pages from links be displayed? (default to new tab/window) */\n\t this.linkTarget = attributes.linkTarget || '_blank';\n\t },\n\t\n\t /** create and return a collection for when none is initially passed */\n\t _createDefaultCollection: function () {\n\t // override\n\t return new this.collectionClass([], { history: this.model });\n\t },\n\t\n\t /** In this override, clear the update timer on the model */\n\t freeModel: function () {\n\t _super.prototype.freeModel.call(this);\n\t if (this.model) {\n\t this.model.clearUpdateTimeout();\n\t }\n\t return this;\n\t },\n\t\n\t /** create any event listeners for the panel\n\t * @fires: rendered:initial on the first render\n\t * @fires: empty-history when switching to a history with no contents or creating a new history\n\t */\n\t _setUpListeners: function () {\n\t _super.prototype._setUpListeners.call(this);\n\t this.on({\n\t error: function (model, xhr, options, msg, details) {\n\t this.errorHandler(model, xhr, options, msg, details);\n\t },\n\t 'loading-done': function () {\n\t var self = this;\n\t // after the initial load, decorate with more time consuming fields (like HDCA element_counts)\n\t _.delay(function () {\n\t self.model.contents.fetchCollectionCounts();\n\t }, self.FETCH_COLLECTION_COUNTS_DELAY);\n\t },\n\t 'views:ready view:attached view:removed': function (view) {\n\t this._renderSelectButton();\n\t },\n\t 'view:attached': function (view) {\n\t this.scrollTo(0);\n\t }\n\t });\n\t // this.on( 'all', function(){ console.debug( arguments ); });\n\t },\n\t\n\t // ------------------------------------------------------------------------ loading history/hda models\n\t /** load the history with the given id then it's contents, sending ajax options to both */\n\t loadHistory: function (historyId, options, contentsOptions) {\n\t contentsOptions = _.extend(contentsOptions || { silent: true });\n\t this.info('loadHistory:', historyId, options, contentsOptions);\n\t var self = this;\n\t self.setModel(new HISTORY_MODEL.History({ id: historyId }));\n\t\n\t contentsOptions.silent = true;\n\t self.trigger('loading');\n\t return self.model.fetchWithContents(options, contentsOptions).always(function () {\n\t self.render();\n\t self.trigger('loading-done');\n\t });\n\t },\n\t\n\t /** convenience alias to the model. Updates the item list only (not the history) */\n\t refreshContents: function (options) {\n\t if (this.model) {\n\t return this.model.refresh(options);\n\t }\n\t // may have callbacks - so return an empty promise\n\t return $.when();\n\t },\n\t\n\t /** Override to reset web storage when the id changes (since it needs the id) */\n\t _setUpCollectionListeners: function () {\n\t _super.prototype._setUpCollectionListeners.call(this);\n\t return this.listenTo(this.collection, {\n\t // 'all' : function(){ console.log( this.collection + ':', arguments ); },\n\t 'fetching-more': function () {\n\t this._toggleContentsLoadingIndicator(true);\n\t this.$emptyMessage().hide();\n\t },\n\t 'fetching-more-done': function () {\n\t this._toggleContentsLoadingIndicator(false);\n\t }\n\t });\n\t },\n\t\n\t // ------------------------------------------------------------------------ panel rendering\n\t /** hide the $el and display a loading indicator (in the $el's parent) when loading new data */\n\t _showLoadingIndicator: function (msg, speed, callback) {\n\t var $indicator = $('
');\n\t this.$el.html($indicator.text(msg).slideDown(!_.isUndefined(speed) ? speed : this.fxSpeed));\n\t },\n\t\n\t /** hide the loading indicator */\n\t _hideLoadingIndicator: function (speed) {\n\t // make speed a bit slower to compensate for slow rendering of up to 500 contents\n\t this.$('.loading-indicator').slideUp(!_.isUndefined(speed) ? speed : this.fxSpeed + 200, function () {\n\t $(this).remove();\n\t });\n\t },\n\t\n\t /** In this override, add a btn to toggle the selectors */\n\t _buildNewRender: function () {\n\t var $newRender = _super.prototype._buildNewRender.call(this);\n\t this._renderSelectButton($newRender);\n\t return $newRender;\n\t },\n\t\n\t /** button for starting select mode */\n\t _renderSelectButton: function ($where) {\n\t $where = $where || this.$el;\n\t // do not render selector option if no actions\n\t if (!this.multiselectActions().length) {\n\t return null;\n\t }\n\t // do not render (and remove even) if nothing to select\n\t if (!this.views.length) {\n\t this.hideSelectors();\n\t $where.find('.controls .actions .show-selectors-btn').remove();\n\t return null;\n\t }\n\t // don't bother rendering if there's one already\n\t var $existing = $where.find('.controls .actions .show-selectors-btn');\n\t if ($existing.length) {\n\t return $existing;\n\t }\n\t\n\t return faIconButton({\n\t title: _l('Operations on multiple datasets'),\n\t classes: 'show-selectors-btn',\n\t faIcon: 'fa-check-square-o'\n\t }).prependTo($where.find('.controls .actions'));\n\t },\n\t\n\t /** override to avoid showing intial empty message using contents_active */\n\t _renderEmptyMessage: function ($whereTo) {\n\t var self = this;\n\t var $emptyMsg = self.$emptyMessage($whereTo);\n\t\n\t var empty = self.model.get('contents_active').active <= 0;\n\t if (empty) {\n\t return $emptyMsg.empty().append(self.emptyMsg).show();\n\t } else if (self.searchFor && self.model.contents.haveSearchDetails() && !self.views.length) {\n\t return $emptyMsg.empty().append(self.noneFoundMsg).show();\n\t }\n\t $emptyMsg.hide();\n\t return $();\n\t },\n\t\n\t /** the scroll container for this panel - can be $el, $el.parent(), or grandparent depending on context */\n\t $scrollContainer: function ($where) {\n\t // override or set via attributes.$scrollContainer\n\t return this.$list($where);\n\t },\n\t\n\t // ------------------------------------------------------------------------ subviews\n\t _toggleContentsLoadingIndicator: function (show) {\n\t if (!show) {\n\t this.$list().find('.contents-loading-indicator').remove();\n\t } else {\n\t this.$list().html('
' + '
');\n\t }\n\t },\n\t\n\t /** override to render pagination also */\n\t renderItems: function ($whereTo) {\n\t // console.log( this + '.renderItems-----------------', new Date() );\n\t $whereTo = $whereTo || this.$el;\n\t var self = this;\n\t var $list = self.$list($whereTo);\n\t\n\t // TODO: bootstrap hack to remove orphaned tooltips\n\t $('.tooltip').remove();\n\t\n\t $list.empty();\n\t self.views = [];\n\t\n\t var models = self._filterCollection();\n\t if (models.length) {\n\t self._renderPagination($whereTo);\n\t self.views = self._renderSomeItems(models, $list);\n\t } else {\n\t // TODO: consolidate with _renderPagination above by (???) passing in models/length?\n\t $whereTo.find('> .controls .list-pagination').empty();\n\t }\n\t self._renderEmptyMessage($whereTo).toggle(!models.length);\n\t\n\t self.trigger('views:ready', self.views);\n\t return self.views;\n\t },\n\t\n\t /** render pagination controls if not searching and contents says we're paginating */\n\t _renderPagination: function ($whereTo) {\n\t var $paginationControls = $whereTo.find('> .controls .list-pagination');\n\t if (this.searchFor || !this.model.contents.shouldPaginate()) return $paginationControls.empty();\n\t\n\t $paginationControls.html(this.templates.pagination({\n\t // pagination is 1-based for the user\n\t current: this.model.contents.currentPage + 1,\n\t last: this.model.contents.getLastPage() + 1\n\t }, this));\n\t $paginationControls.find('select.pages').tooltip();\n\t return $paginationControls;\n\t },\n\t\n\t /** render a subset of the entire collection (client-side pagination) */\n\t _renderSomeItems: function (models, $list) {\n\t var self = this;\n\t var views = [];\n\t $list.append(models.map(function (m) {\n\t var view = self._createItemView(m);\n\t views.push(view);\n\t return self._renderItemView$el(view);\n\t }));\n\t return views;\n\t },\n\t\n\t // ------------------------------------------------------------------------ sub-views\n\t /** in this override, check if the contents would also display based on includeDeleted/hidden */\n\t _filterItem: function (model) {\n\t var self = this;\n\t var contents = self.model.contents;\n\t return (contents.includeHidden || !model.hidden()) && (contents.includeDeleted || !model.isDeletedOrPurged()) && _super.prototype._filterItem.call(self, model);\n\t },\n\t\n\t /** In this override, since history contents are mixed,\n\t * get the appropo view class based on history_content_type\n\t */\n\t _getItemViewClass: function (model) {\n\t var contentType = model.get(\"history_content_type\");\n\t switch (contentType) {\n\t case 'dataset':\n\t return this.HDAViewClass;\n\t case 'dataset_collection':\n\t return this.HDCAViewClass;\n\t }\n\t throw new TypeError('Unknown history_content_type: ' + contentType);\n\t },\n\t\n\t /** in this override, add a linktarget, and expand if id is in web storage */\n\t _getItemViewOptions: function (model) {\n\t var options = _super.prototype._getItemViewOptions.call(this, model);\n\t return _.extend(options, {\n\t linkTarget: this.linkTarget,\n\t expanded: this.model.contents.storage.isExpanded(model.id),\n\t hasUser: this.model.ownedByCurrUser()\n\t });\n\t },\n\t\n\t /** In this override, add/remove expanded/collapsed model ids to/from web storage */\n\t _setUpItemViewListeners: function (view) {\n\t var panel = this;\n\t _super.prototype._setUpItemViewListeners.call(panel, view);\n\t //TODO: send from content view: this.model.collection.storage.addExpanded\n\t // maintain a list of items whose bodies are expanded\n\t return panel.listenTo(view, {\n\t 'expanded': function (v) {\n\t panel.model.contents.storage.addExpanded(v.model);\n\t },\n\t 'collapsed': function (v) {\n\t panel.model.contents.storage.removeExpanded(v.model);\n\t }\n\t });\n\t },\n\t\n\t /** override to remove expandedIds from webstorage */\n\t collapseAll: function () {\n\t this.model.contents.storage.clearExpanded();\n\t _super.prototype.collapseAll.call(this);\n\t },\n\t\n\t // ------------------------------------------------------------------------ selection\n\t /** Override to correctly set the historyId of the new collection */\n\t getSelectedModels: function () {\n\t var collection = _super.prototype.getSelectedModels.call(this);\n\t collection.historyId = this.collection.historyId;\n\t return collection;\n\t },\n\t\n\t // ------------------------------------------------------------------------ panel events\n\t /** event map */\n\t events: _.extend(_.clone(_super.prototype.events), {\n\t 'click .show-selectors-btn': 'toggleSelectors',\n\t 'click > .controls .prev': '_clickPrevPage',\n\t 'click > .controls .next': '_clickNextPage',\n\t 'change > .controls .pages': '_changePageSelect',\n\t // allow (error) messages to be clicked away\n\t 'click .messages [class$=message]': 'clearMessages'\n\t }),\n\t\n\t _clickPrevPage: function (ev) {\n\t this.model.clearUpdateTimeout();\n\t this.model.contents.fetchPrevPage();\n\t },\n\t\n\t _clickNextPage: function (ev) {\n\t this.model.clearUpdateTimeout();\n\t this.model.contents.fetchNextPage();\n\t },\n\t\n\t _changePageSelect: function (ev) {\n\t this.model.clearUpdateTimeout();\n\t var page = $(ev.currentTarget).val();\n\t this.model.contents.fetchPage(page);\n\t },\n\t\n\t /** Toggle and store the deleted visibility and re-render items\n\t * @returns {Boolean} new setting\n\t */\n\t toggleShowDeleted: function (show, options) {\n\t show = show !== undefined ? show : !this.model.contents.includeDeleted;\n\t var self = this;\n\t var contents = self.model.contents;\n\t contents.setIncludeDeleted(show, options);\n\t self.trigger('show-deleted', show);\n\t\n\t contents.fetchCurrentPage({ renderAll: true });\n\t return show;\n\t },\n\t\n\t /** Toggle and store whether to render explicity hidden contents\n\t * @returns {Boolean} new setting\n\t */\n\t toggleShowHidden: function (show, store, options) {\n\t // console.log( 'toggleShowHidden', show, store );\n\t show = show !== undefined ? show : !this.model.contents.includeHidden;\n\t var self = this;\n\t var contents = self.model.contents;\n\t contents.setIncludeHidden(show, options);\n\t self.trigger('show-hidden', show);\n\t\n\t contents.fetchCurrentPage({ renderAll: true });\n\t return show;\n\t },\n\t\n\t /** On the first search, if there are no details - load them, then search */\n\t _firstSearch: function (searchFor) {\n\t var self = this;\n\t var inputSelector = '> .controls .search-input';\n\t this.log('onFirstSearch', searchFor);\n\t\n\t // if the contents already have enough details to search, search and return now\n\t if (self.model.contents.haveSearchDetails()) {\n\t self.searchItems(searchFor);\n\t return;\n\t }\n\t\n\t // otherwise, load the details progressively here\n\t self.$(inputSelector).searchInput('toggle-loading');\n\t // set this now so that only results will show during progress\n\t self.searchFor = searchFor;\n\t var xhr = self.model.contents.progressivelyFetchDetails({ silent: true }).progress(function (response, limit, offset) {\n\t self.renderItems();\n\t self.trigger('search:loading-progress', limit, offset);\n\t }).always(function () {\n\t self.$el.find(inputSelector).searchInput('toggle-loading');\n\t }).done(function () {\n\t self.searchItems(searchFor, 'force');\n\t });\n\t },\n\t\n\t /** clear the search filters and show all views that are normally shown */\n\t clearSearch: function (searchFor) {\n\t var self = this;\n\t if (!self.searchFor) return self;\n\t //self.log( 'onSearchClear', self );\n\t self.searchFor = '';\n\t self.trigger('search:clear', self);\n\t self.$('> .controls .search-query').val('');\n\t // NOTE: silent + render prevents collection update event with merge only\n\t // - which causes an empty page due to event handler above\n\t self.model.contents.fetchCurrentPage({ silent: true }).done(function () {\n\t self.renderItems();\n\t });\n\t return self;\n\t },\n\t\n\t // ........................................................................ error handling\n\t /** Event handler for errors (from the panel, the history, or the history's contents)\n\t * Alternately use two strings for model and xhr to use custom message and title (respectively)\n\t * @param {Model or View} model the (Backbone) source of the error\n\t * @param {XMLHTTPRequest} xhr any ajax obj. assoc. with the error\n\t * @param {Object} options the options map commonly used with bbone ajax\n\t */\n\t errorHandler: function (model, xhr, options) {\n\t //TODO: to mixin or base model\n\t // interrupted ajax or no connection\n\t if (xhr && xhr.status === 0 && xhr.readyState === 0) {\n\t // return ERROR_MODAL.offlineErrorModal();\n\t // fail silently\n\t return;\n\t }\n\t // otherwise, leave something to report in the console\n\t this.error(model, xhr, options);\n\t // and feedback to a modal\n\t // if sent two strings (and possibly details as 'options'), use those as message and title\n\t if (_.isString(model) && _.isString(xhr)) {\n\t var message = model;\n\t var title = xhr;\n\t return ERROR_MODAL.errorModal(message, title, options);\n\t }\n\t // bad gateway\n\t // TODO: possibly to global handler\n\t if (xhr && xhr.status === 502) {\n\t return ERROR_MODAL.badGatewayErrorModal();\n\t }\n\t return ERROR_MODAL.ajaxErrorModal(model, xhr, options);\n\t },\n\t\n\t /** Remove all messages from the panel. */\n\t clearMessages: function (ev) {\n\t var $target = !_.isUndefined(ev) ? $(ev.currentTarget) : this.$messages().children('[class$=\"message\"]');\n\t $target.fadeOut(this.fxSpeed, function () {\n\t $(this).remove();\n\t });\n\t return this;\n\t },\n\t\n\t // ........................................................................ scrolling\n\t /** Scrolls the panel to show the content sub-view with the given hid.\n\t * @param {Integer} hid the hid of item to scroll into view\n\t * @returns {HistoryView} the panel\n\t */\n\t scrollToHid: function (hid) {\n\t return this.scrollToItem(_.first(this.viewsWhereModel({ hid: hid })));\n\t },\n\t\n\t // ........................................................................ misc\n\t /** utility for adding -st, -nd, -rd, -th to numbers */\n\t ordinalIndicator: function (number) {\n\t var numStr = number + '';\n\t switch (numStr.charAt(numStr.length - 1)) {\n\t case '1':\n\t return numStr + 'st';\n\t case '2':\n\t return numStr + 'nd';\n\t case '3':\n\t return numStr + 'rd';\n\t default:\n\t return numStr + 'th';\n\t }\n\t },\n\t\n\t /** Return a string rep of the history */\n\t toString: function () {\n\t return 'HistoryView(' + (this.model ? this.model.get('name') : '') + ')';\n\t }\n\t });\n\t\n\t //------------------------------------------------------------------------------ TEMPLATES\n\t HistoryView.prototype.templates = function () {\n\t\n\t var mainTemplate = BASE_MVC.wrapTemplate([\n\t // temp container\n\t '
', '', '
', '', '
']);\n\t\n\t var controlsTemplate = BASE_MVC.wrapTemplate(['
Trackster uses this information to populate the select box for chrom/contig, and' + 'to set the maximum basepair of the track browser. You may either upload a .len file' + 'of this format (Len File option), or directly enter the information into the box ' + '(Len Entry option).
';\n\t },\n\t\n\t _templateFasta: function () {\n\t return '
FASTA format
' + '
' + 'This is a multi-fasta file from your current history that provides the genome' + 'sequences for each chromosome/contig in your build.' + '
' + '
' + 'Here is a snippet from an example multi-fasta file:' + '
' + '';\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1)))\n\n/***/ }),\n/* 131 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/** User Preferences view */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(20), __webpack_require__(7)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Form, Ui) {\n\t\n\t /** Contains descriptive dictionaries describing user forms */\n\t var Model = Backbone.Model.extend({\n\t initialize: function (options) {\n\t options = options || {};\n\t options.user_id = options.user_id || Galaxy.user.id;\n\t this.set({\n\t 'user_id': options.user_id,\n\t 'information': {\n\t title: 'Manage information',\n\t description: 'Edit your email, addresses and custom parameters or change your username.',\n\t url: 'api/users/' + options.user_id + '/information/inputs',\n\t icon: 'fa-user'\n\t },\n\t 'password': {\n\t title: 'Change password',\n\t description: 'Allows you to change your login credentials.',\n\t icon: 'fa-unlock-alt',\n\t url: 'api/users/' + options.user_id + '/password/inputs',\n\t submit_title: 'Save password'\n\t },\n\t 'communication': {\n\t title: 'Change communication settings',\n\t description: 'Enable or disable the communication feature to chat with other users.',\n\t url: 'api/users/' + options.user_id + '/communication/inputs',\n\t icon: 'fa-comments-o'\n\t },\n\t 'permissions': {\n\t title: 'Set dataset permissions for new histories',\n\t description: 'Grant others default access to newly created histories. Changes made here will only affect histories created after these settings have been stored.',\n\t url: 'api/users/' + options.user_id + '/permissions/inputs',\n\t icon: 'fa-users',\n\t submit_title: 'Save permissions'\n\t },\n\t 'api_key': {\n\t title: 'Manage API key',\n\t description: 'Access your current API key or create a new one.',\n\t url: 'api/users/' + options.user_id + '/api_key/inputs',\n\t icon: 'fa-key',\n\t submit_title: 'Create a new key',\n\t submit_icon: 'fa-check'\n\t },\n\t 'toolbox_filters': {\n\t title: 'Manage Toolbox filters',\n\t description: 'Customize your Toolbox by displaying or omitting sets of Tools.',\n\t url: 'api/users/' + options.user_id + '/toolbox_filters/inputs',\n\t icon: 'fa-filter',\n\t submit_title: 'Save filters'\n\t },\n\t 'openids': {\n\t title: 'Manage OpenIDs',\n\t description: 'Associate OpenIDs with your account.',\n\t icon: 'fa-openid',\n\t onclick: function () {\n\t window.location.href = Galaxy.root + 'user/openid_manage?cntrller=user&use_panels=True';\n\t }\n\t },\n\t 'custom_builds': {\n\t title: 'Manage custom builds',\n\t description: 'Add or remove custom builds using history datasets.',\n\t icon: 'fa-cubes',\n\t onclick: function () {\n\t window.location.href = Galaxy.root + 'custom_builds';\n\t }\n\t },\n\t 'logout': {\n\t title: 'Sign out',\n\t description: 'Click here to sign out of all sessions.',\n\t icon: 'fa-sign-out',\n\t onclick: function () {\n\t Galaxy.modal.show({\n\t title: 'Sign out',\n\t body: 'Do you want to continue and sign out of all active sessions?',\n\t buttons: {\n\t 'Cancel': function () {\n\t Galaxy.modal.hide();\n\t },\n\t 'Sign out': function () {\n\t window.location.href = Galaxy.root + 'user/logout';\n\t }\n\t }\n\t });\n\t }\n\t }\n\t });\n\t }\n\t });\n\t\n\t /** View of the main user preference panel with links to individual user forms */\n\t var View = Backbone.View.extend({\n\t\n\t initialize: function () {\n\t this.model = new Model();\n\t this.message = new Ui.Message();\n\t this.setElement('');\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var self = this;\n\t var config = Galaxy.config;\n\t $.getJSON(Galaxy.root + 'api/users/' + Galaxy.user.id, function (data) {\n\t self.$preferences = $('').addClass('ui-panel').append(self.message.$el).append($('').append('User preferences')).append($('').append('You are logged in as ' + _.escape(data.email) + '.')).append(self.$table = $('
').addClass('ui-panel-table'));\n\t if (!config.use_remote_user) {\n\t self._addLink('information');\n\t self._addLink('password');\n\t }\n\t if (config.enable_communication_server) {\n\t self._addLink('communication');\n\t }\n\t self._addLink('custom_builds');\n\t self._addLink('permissions');\n\t self._addLink('api_key');\n\t if (config.has_user_tool_filters) {\n\t self._addLink('toolbox_filters');\n\t }\n\t if (config.enable_openid && !config.use_remote_user) {\n\t self._addLink('openids');\n\t }\n\t self._addLink('logout');\n\t self.$preferences.append(self._templateFooter(data));\n\t self.$el.empty().append(self.$preferences);\n\t });\n\t },\n\t\n\t _addLink: function (action) {\n\t var options = this.model.get(action);\n\t var $row = $(this._templateLink(options));\n\t var $a = $row.find('a');\n\t if (options.onclick) {\n\t $a.on('click', function () {\n\t options.onclick();\n\t });\n\t } else {\n\t $a.attr('href', Galaxy.root + 'user/' + action);\n\t }\n\t this.$table.append($row);\n\t },\n\t\n\t _templateLink: function (options) {\n\t return '
';\n\t },\n\t\n\t _templateFooter: function (options) {\n\t return '
' + 'You are using ' + options.nice_total_disk_usage + ' of disk space in this Galaxy instance. ' + (Galaxy.config.enable_quotas ? 'Your disk quota is: ' + options.quota + '. ' : '') + 'Is your usage more than expected? See the documentation for tips on how to find all of the data in your account.' + '
';\n\t }\n\t });\n\t\n\t /** View of individual user forms */\n\t var Forms = Backbone.View.extend({\n\t\n\t initialize: function (options) {\n\t this.model = new Model(options);\n\t this.page = this.model.get(options.form_id);\n\t this.setElement('');\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var self = this;\n\t $.ajax({\n\t url: Galaxy.root + this.page.url,\n\t type: 'GET'\n\t }).done(function (response) {\n\t var options = $.extend({}, self.page, response);\n\t var form = new Form({\n\t title: options.title,\n\t icon: options.icon,\n\t inputs: options.inputs,\n\t operations: {\n\t 'submit': new Ui.ButtonIcon({\n\t tooltip: options.submit_tooltip,\n\t title: options.submit_title || 'Save settings',\n\t icon: options.submit_icon || 'fa-save',\n\t onclick: function () {\n\t self._submit(form, options);\n\t }\n\t })\n\t }\n\t });\n\t self.$el.empty().append(form.$el);\n\t }).fail(function (response) {\n\t self.$el.empty().append(new Ui.Message({\n\t message: 'Failed to load resource ' + self.page.url + '.',\n\t status: 'danger',\n\t persistent: true\n\t }).$el);\n\t });\n\t },\n\t\n\t _submit: function (form, options) {\n\t var self = this;\n\t $.ajax({\n\t url: Galaxy.root + options.url,\n\t data: JSON.stringify(form.data.create()),\n\t type: 'PUT',\n\t contentType: 'application/json'\n\t }).done(function (response) {\n\t form.data.matchModel(response, function (input, input_id) {\n\t form.field_list[input_id].value(input.value);\n\t });\n\t form.message.update({ message: response.message, status: 'success' });\n\t }).fail(function (response) {\n\t form.message.update({ message: response.responseJSON.err_msg, status: 'danger' });\n\t });\n\t }\n\t });\n\t\n\t return {\n\t View: View,\n\t Forms: Forms\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1), __webpack_require__(2)))\n\n/***/ }),\n/* 132 */,\n/* 133 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/** Configure Workflow Menu View */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t var View = Backbone.View.extend({\n\t\n\t initialize: function (options) {\n\t this.setElement('');\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var self = this;\n\t $.getJSON(Galaxy.root + 'api/workflows/menu/', function (response) {\n\t var workflows = response.workflows,\n\t ids_in_menu = response.ids_in_menu,\n\t $el_config_worflow = null;\n\t\n\t // Add configure workflow header\n\t self.$el.empty().append(self._templateConfigWorkflowHeader());\n\t $el_config_worflow = self.$el.find('.configure-workflows');\n\t $el_config_worflow.append(self._templateActionButtons());\n\t if (workflows.length > 0) {\n\t $el_config_worflow.append(self._templateConfigureWorkflow(self, workflows, ids_in_menu));\n\t self.save_workflow_menu(self);\n\t self.make_checked(self, ids_in_menu);\n\t self.register_check_uncheck_all(self);\n\t } else {\n\t $el_config_worflow.append(self._templateNoWorkflow());\n\t }\n\t });\n\t },\n\t\n\t /** Register check and uncheck all callbacks*/\n\t register_check_uncheck_all: function (self) {\n\t var $el_check_all = self.$el.find('.check-all-wf'),\n\t $el_uncheck_all = self.$el.find('.uncheck-all-wf');\n\t\n\t $el_check_all.click(function (e) {\n\t self.check_uncheck_all(self, true);\n\t });\n\t $el_uncheck_all.click(function (e) {\n\t self.check_uncheck_all(self, false);\n\t });\n\t },\n\t\n\t /** Check or uncheck all workflows */\n\t check_uncheck_all: function (self, checked) {\n\t $.each(self.$el.find('.wf-config-item'), function () {\n\t var wf_checkbox = $(this)[0];\n\t wf_checkbox.checked = checked;\n\t });\n\t },\n\t\n\t /** Make the worflows as checked if present in the menu */\n\t make_checked: function (self, ids_in_menu) {\n\t $.each(self.$el.find('.wf-config-item'), function () {\n\t var wf_checkbox = $(this)[0];\n\t _.each(ids_in_menu, function (id) {\n\t if (parseInt(wf_checkbox.value) === id) {\n\t wf_checkbox.checked = true;\n\t }\n\t });\n\t });\n\t },\n\t\n\t /** Save the changes for workflow menu */\n\t save_workflow_menu: function (self) {\n\t var $el_save_workflow_menu = self.$el.find('.wf-save-menu');\n\t $el_save_workflow_menu.click(function (e) {\n\t var ids = [];\n\t $.each(self.$el.find('.wf-config-item'), function () {\n\t var wf_checkbox = $(this)[0];\n\t if (wf_checkbox.checked || wf_checkbox.checked === 'true') {\n\t ids.push(parseInt(wf_checkbox.value));\n\t }\n\t });\n\t $.ajax({\n\t type: 'PUT',\n\t url: Galaxy.root + 'api/workflows/menu/',\n\t data: JSON.stringify({ 'workflow_ids': ids }),\n\t contentType: 'application/json'\n\t }).done(function (response) {\n\t window.location = Galaxy.root + 'workflow?status=' + response.status + '&message=' + response.message;\n\t });\n\t });\n\t },\n\t\n\t /** Template for actions buttons */\n\t _templateActionButtons: function () {\n\t return '
';\n\t tableHtml = tableHtml + '' + 'Save' + '' + '' + 'Back to workflow' + '';\n\t return tableHtml;\n\t },\n\t\n\t /** Template for no workflow */\n\t _templateNoWorkflow: function () {\n\t return '
You do not have any accessible workflows.
';\n\t },\n\t\n\t /** Template for checkboxes */\n\t _templateInputCheckbox: function (self, wf) {\n\t return '';\n\t },\n\t\n\t /** Template for main config workflow menu */\n\t _templateConfigWorkflowHeader: function () {\n\t return '
' + '
' + '
Configure workflow menu
' + '
' + '
';\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1), __webpack_require__(2)))\n\n/***/ }),\n/* 134 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/** Workflow view */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t\n\t /** View of the main workflow list page */\n\t var View = Backbone.View.extend({\n\t\n\t initialize: function () {\n\t this.setElement('');\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var self = this,\n\t min_query_length = 3;\n\t $.getJSON(Galaxy.root + 'api/workflows/', function (workflows) {\n\t var $el_workflow = null;\n\t // Add workflow header\n\t self.$el.empty().append(self._templateHeader());\n\t // Add user actions message if any\n\t self.build_messages(self);\n\t $el_workflow = self.$el.find('.user-workflows');\n\t // Add the actions buttons\n\t $el_workflow.append(self._templateActionButtons());\n\t if (workflows.length > 0) {\n\t $el_workflow.append(self._templateWorkflowTable(self, workflows));\n\t self.adjust_actiondropdown($el_workflow);\n\t // Register delete and run workflow events\n\t _.each(workflows, function (wf) {\n\t self.confirm_delete(self, wf);\n\t });\n\t // Register search workflow event\n\t self.search_workflow(self, self.$el.find('.search-wf'), self.$el.find('.workflow-search tr'), min_query_length);\n\t } else {\n\t $el_workflow.append(self._templateNoWorkflow());\n\t }\n\t });\n\t },\n\t\n\t /** Build messages after user action */\n\t build_messages: function (self) {\n\t var $el_message = self.$el.find('.response-message'),\n\t status = self.get_querystring('status'),\n\t message = self.get_querystring('message');\n\t\n\t if (message && message !== null && message !== \"\") {\n\t $el_message.addClass(status + 'message');\n\t $el_message.html('
' + _.escape(message) + '
');\n\t } else {\n\t $el_message.html(\"\");\n\t }\n\t },\n\t\n\t /** Add confirm box before removing/unsharing workflow */\n\t confirm_delete: function (self, workflow) {\n\t var $el_wf_link = self.$el.find('.link-confirm-' + workflow.id),\n\t $el_shared_wf_link = self.$el.find('.link-confirm-shared-' + workflow.id);\n\t $el_wf_link.click(function () {\n\t return confirm(\"Are you sure you want to delete workflow '\" + workflow.name + \"'?\");\n\t });\n\t $el_shared_wf_link.click(function () {\n\t return confirm(\"Are you sure you want to remove the shared workflow '\" + workflow.name + \"'?\");\n\t });\n\t },\n\t\n\t /** Implement client side workflow search/filtering */\n\t search_workflow: function (self, $el_searchinput, $el_tabletr, min_querylen) {\n\t $el_searchinput.on('keyup', function () {\n\t var query = $(this).val();\n\t // Filter when query is at least 3 characters\n\t // otherwise show all rows\n\t if (query.length >= min_querylen) {\n\t // Ignore the query's case using 'i'\n\t var regular_expression = new RegExp(query, 'i');\n\t $el_tabletr.hide();\n\t $el_tabletr.filter(function () {\n\t // Apply regular expression on each row's text\n\t // and show when there is a match\n\t return regular_expression.test($(this).text());\n\t }).show();\n\t } else {\n\t $el_tabletr.show();\n\t }\n\t });\n\t },\n\t\n\t /** Get querystrings from url */\n\t get_querystring: function (key) {\n\t return decodeURIComponent(window.location.search.replace(new RegExp(\"^(?:.*[&\\\\?]\" + encodeURIComponent(key).replace(/[\\.\\+\\*]/g, \"\\\\$&\") + \"(?:\\\\=([^&]*))?)?.*$\", \"i\"), \"$1\"));\n\t },\n\t\n\t /** Ajust the position of dropdown with respect to table */\n\t adjust_actiondropdown: function ($el) {\n\t $el.on('show.bs.dropdown', function () {\n\t $el.css(\"overflow\", \"inherit\");\n\t });\n\t\n\t $el.on('hide.bs.dropdown', function () {\n\t $el.css(\"overflow\", \"auto\");\n\t });\n\t },\n\t\n\t /** Template for no workflow */\n\t _templateNoWorkflow: function () {\n\t return '
You have no workflows.
';\n\t },\n\t\n\t /** Template for actions buttons */\n\t _templateActionButtons: function () {\n\t return '
';\n\t },\n\t\n\t /** Template for user actions for workflows */\n\t _templateActions: function (workflow) {\n\t if (workflow.owner === Galaxy.user.attributes.username) {\n\t return '
');\n }\n }\n\n // Render first chunk.\n var self = this,\n first_chunk = this.model.get('first_data_chunk');\n if (first_chunk) {\n // First chunk is bootstrapped, so render now.\n this._renderChunk(first_chunk);\n }\n else {\n // No bootstrapping, so get first chunk and then render.\n $.when(self.model.get_next_chunk()).then(function(result) {\n self._renderChunk(result);\n });\n }\n\n // -- Show new chunks during scrolling. --\n\n // Set up chunk loading when scrolling using the scrolling element.\n this.scroll_elt.scroll(function(){\n self.attempt_to_fetch();\n });\n },\n\n /**\n * Returns true if user has scrolled to the bottom of the view.\n */\n scrolled_to_bottom: function() {\n return false;\n },\n\n // -- Helper functions. --\n\n _renderCell: function(cell_contents, index, colspan) {\n var $cell = $('
').text(cell_contents);\n var column_types = this.model.get_metadata('column_types');\n if (colspan !== undefined) {\n $cell.attr('colspan', colspan).addClass('stringalign');\n } else if (column_types) {\n if (index < column_types.length) {\n if (column_types[index] === 'str' || column_types[index] === 'list') {\n /* Left align all str columns, right align the rest */\n $cell.addClass('stringalign');\n }\n }\n }\n return $cell;\n },\n\n _renderRow: function(line) {\n // Check length of cells to ensure this is a complete row.\n var cells = line.split('\\t'),\n row = $('
'),\n num_columns = this.model.get_metadata('columns');\n\n if (this.row_count % 2 !== 0) {\n row.addClass('dark_row');\n }\n\n if (cells.length === num_columns) {\n _.each(cells, function(cell_contents, index) {\n row.append(this._renderCell(cell_contents, index));\n }, this);\n }\n else if (cells.length > num_columns) {\n // SAM file or like format with optional metadata included.\n _.each(cells.slice(0, num_columns - 1), function(cell_contents, index) {\n row.append(this._renderCell(cell_contents, index));\n }, this);\n row.append(this._renderCell(cells.slice(num_columns - 1).join('\\t'), num_columns - 1));\n }\n else if (cells.length === 1){\n // Comment line, just return the one cell.\n row.append(this._renderCell(line, 0, num_columns));\n }\n else {\n // cells.length is greater than one, but less than num_columns. Render cells and pad tds.\n // Possibly a SAM file or like format with optional metadata missing.\n // Could also be a tabular file with a line with missing columns.\n _.each(cells, function(cell_contents, index) {\n row.append(this._renderCell(cell_contents, index));\n }, this);\n _.each(_.range(num_columns - cells.length), function(){\n row.append($('
'));\n });\n }\n\n this.row_count++;\n return row;\n },\n\n _renderChunk: function(chunk) {\n var data_table = this.$el.find('table');\n _.each(chunk.ck_data.split('\\n'), function(line, index) {\n if (line !== ''){\n data_table.append(this._renderRow(line));\n }\n }, this);\n }\n});\n\n/**\n * Tabular view that is placed at the top level of page. Scrolling occurs\n * view top-level elements outside of view.\n */\nvar TopLevelTabularDatasetChunkedView = TabularDatasetChunkedView.extend({\n\n initialize: function(options) {\n TabularDatasetChunkedView.prototype.initialize.call(this, options);\n\n // Scrolling happens in top-level elements.\n scroll_elt = _.find(this.$el.parents(), function(p) {\n return $(p).css('overflow') === 'auto';\n });\n\n // If no scrolling element found, use window.\n if (!scroll_elt) { scroll_elt = window; }\n\n // Wrap scrolling element for easy access.\n this.scroll_elt = $(scroll_elt);\n },\n\n /**\n * Returns true if user has scrolled to the bottom of the view.\n */\n scrolled_to_bottom: function() {\n return (this.$el.height() - this.scroll_elt.scrollTop() - this.scroll_elt.height() <= 0);\n }\n\n});\n\n/**\n * Tabular view tnat is embedded in a page. Scrolling occurs in view's el.\n */\nvar EmbeddedTabularDatasetChunkedView = TabularDatasetChunkedView.extend({\n\n initialize: function(options) {\n TabularDatasetChunkedView.prototype.initialize.call(this, options);\n\n // Because view is embedded, set up div to do scrolling.\n this.scroll_elt = this.$el.css({\n position: 'relative',\n overflow: 'scroll',\n height: options.height || '500px'\n });\n },\n\n /**\n * Returns true if user has scrolled to the bottom of the view.\n */\n scrolled_to_bottom: function() {\n return this.$el.scrollTop() + this.$el.innerHeight() >= this.el.scrollHeight;\n }\n\n});\n\n// button for trackster visualization\nvar TabularButtonTracksterView = Backbone.View.extend({\n\n // gene region columns\n col: {\n chrom : null,\n start : null,\n end : null\n },\n\n // url for trackster\n url_viz : null,\n\n // dataset id\n dataset_id : null,\n\n // database key\n genome_build: null,\n\n // data type\n file_ext : null,\n\n // backbone initialize\n initialize: function (options) {\n // check if environment is available\n var Galaxy = parent.Galaxy;\n\n // link galaxy modal or create one\n if (Galaxy && Galaxy.modal) {\n this.modal = Galaxy.modal;\n }\n\n // link galaxy frames\n if (Galaxy && Galaxy.frame) {\n this.frame = Galaxy.frame;\n }\n\n // check\n if (!this.modal || !this.frame) {\n return;\n }\n\n // model/metadata\n var model = options.model;\n var metadata = model.get('metadata');\n\n // check for datatype\n if (!model.get('file_ext')) {\n return;\n }\n\n // get data type\n this.file_ext = model.get('file_ext');\n\n // check for bed-file format\n if (this.file_ext == 'bed')\n {\n // verify that metadata exists\n if (metadata.get('chromCol') && metadata.get('startCol') && metadata.get('endCol'))\n {\n // read in columns\n this.col.chrom = metadata.get('chromCol') - 1;\n this.col.start = metadata.get('startCol') - 1;\n this.col.end = metadata.get('endCol') - 1;\n } else {\n console.log('TabularButtonTrackster : Bed-file metadata incomplete.');\n return;\n }\n }\n\n // check for vcf-file format\n if (this.file_ext == 'vcf')\n {\n // search array\n function search (str, array) {\n for (var j = 0; j < array.length; j++)\n if (array[j].match(str)) return j;\n return -1;\n };\n\n // load\n this.col.chrom = search('Chrom', metadata.get('column_names'));\n this.col.start = search('Pos', metadata.get('column_names'));\n this.col.end = null;\n\n // verify that metadata exists\n if (this.col.chrom == -1 || this.col.start == -1) {\n console.log('TabularButtonTrackster : VCF-file metadata incomplete.');\n return;\n }\n }\n\n // check\n if(this.col.chrom === undefined) {\n return;\n }\n\n // get dataset id\n if (model.id) {\n this.dataset_id = model.id;\n } else {\n console.log('TabularButtonTrackster : Dataset identification is missing.');\n return;\n }\n\n // get url\n if (model.get('url_viz')) {\n this.url_viz = model.get('url_viz');\n } else {\n console.log('TabularButtonTrackster : Url for visualization controller is missing.');\n return;\n }\n\n // get genome_build / database key\n if (model.get('genome_build')) {\n this.genome_build = model.get('genome_build');\n }\n\n // create the icon\n var btn_viz = new mod_icon_btn.IconButtonView({\n model : new mod_icon_btn.IconButton({\n title : 'Visualize',\n icon_class : 'chart_curve',\n id : 'btn_viz'\n })\n });\n\n // set element\n this.setElement(options.$el);\n\n // add to element\n this.$el.append(btn_viz.render().$el);\n\n // hide the button\n this.hide();\n },\n\n // backbone events\n events:\n {\n 'mouseover tr' : 'show',\n 'mouseleave' : 'hide'\n },\n\n // show button\n show: function (e) {\n // is numeric\n function is_numeric(n) {\n return !isNaN(parseFloat(n)) && isFinite(n);\n };\n\n // check\n if(this.col.chrom === null)\n return;\n\n // get selected data line\n var row = $(e.target).parent();\n\n // verify that location has been found\n var chrom = row.children().eq(this.col.chrom).html();\n var start = row.children().eq(this.col.start).html();\n\n // end is optional\n var end = this.col.end ? row.children().eq(this.col.end).html() : start;\n\n // double check location\n if (!chrom.match(\"^#\") && chrom !== \"\" && is_numeric(start)) {\n\n // get target gene region\n var btn_viz_pars = {\n dataset_id : this.dataset_id,\n gene_region : chrom + \":\" + start + \"-\" + end\n };\n\n // get button position\n var offset = row.offset();\n var left = offset.left - 10;\n var top = offset.top - $(window).scrollTop() + 3;\n\n // update css\n $('#btn_viz').css({'position': 'fixed', 'top': top + 'px', 'left': left + 'px'});\n $('#btn_viz').off('click');\n $('#btn_viz').click(this.create_trackster_action(this.url_viz, btn_viz_pars, this.genome_build));\n\n // show the button\n $('#btn_viz').show();\n } else {\n // hide the button\n $('#btn_viz').hide();\n }\n },\n\n // hide button\n hide: function () {\n this.$el.find('#btn_viz').hide();\n },\n\n // create action\n create_trackster_action : function (vis_url, dataset_params, dbkey) {\n // link this\n var self = this;\n\n // create function\n return function() {\n var listTracksParams = {};\n if (dbkey) {\n listTracksParams[ 'f-dbkey' ] = dbkey;\n }\n $.ajax({\n url: vis_url + '/list_tracks?' + $.param( listTracksParams ),\n dataType: 'html',\n error: function() {\n // show error message\n self.modal.show({\n title : 'Something went wrong!',\n body : 'Unfortunately we could not add this dataset to the track browser. Please try again or contact us.',\n buttons : {\n 'Cancel': function(){\n self.modal.hide();\n }\n }\n });\n },\n success: function(table_html) {\n self.modal.show({\n title : 'View Data in a New or Saved Visualization',\n buttons :{\n 'Cancel': function(){\n self.modal.hide();\n },\n 'View in saved visualization': function(){\n // show modal with saved visualizations\n self.modal.show(\n {\n title : 'Add Data to Saved Visualization',\n body : table_html,\n buttons : {\n 'Cancel': function(){\n self.modal.hide();\n },\n 'Add to visualization': function(){\n // hide\n self.modal.hide();\n\n // search selected fields\n self.modal.$el.find('input[name=id]:checked').each(function(){\n // get visualization id\n var vis_id = $(this).val();\n dataset_params.id = vis_id;\n\n // add widget\n self.frame.add({\n title : 'Trackster',\n type : 'url',\n content : vis_url + '/trackster?' + $.param(dataset_params)\n });\n });\n }\n }\n });\n },\n 'View in new visualization': function(){\n // hide\n self.modal.hide();\n\n // add widget\n self.frame.add({\n title : 'Trackster',\n type : 'url',\n content : vis_url + '/trackster?' + $.param(dataset_params)\n });\n }\n }\n });\n }\n });\n return false;\n };\n }\n});\n\n// -- Utility functions. --\n\n/**\n * Create a model, attach it to a view, render view, and attach it to a parent element.\n */\nvar createModelAndView = function(model, view, model_config, parent_elt) {\n // Create model, view.\n var a_view = new view({\n model: new model(model_config)\n });\n\n // Render view and add to parent element.\n a_view.render();\n if (parent_elt) {\n parent_elt.append(a_view.$el);\n }\n\n return a_view;\n};\n\n/**\n * Create a tabular dataset chunked view (and requisite tabular dataset model)\n * and appends to parent_elt.\n */\nvar createTabularDatasetChunkedView = function(options) {\n // If no model, create and set model from dataset config.\n if (!options.model) {\n options.model = new TabularDataset(options.dataset_config);\n }\n\n var parent_elt = options.parent_elt;\n var embedded = options.embedded;\n\n // Clean up options so that only needed options are passed to view.\n delete options.embedded;\n delete options.parent_elt;\n delete options.dataset_config;\n\n // Create and set up view.\n var view = (embedded ? new EmbeddedTabularDatasetChunkedView(options) :\n new TopLevelTabularDatasetChunkedView(options));\n view.render();\n\n if (parent_elt) {\n parent_elt.append(view.$el);\n // If we're sticking this in another element, once it's appended check\n // to make sure we've filled enough space.\n // Without this, the scroll elements don't work.\n view.expand_to_container();\n }\n\n return view;\n};\n\nreturn {\n Dataset: Dataset,\n TabularDataset: TabularDataset,\n DatasetCollection: DatasetCollection,\n TabularDatasetChunkedView: TabularDatasetChunkedView,\n createTabularDatasetChunkedView: createTabularDatasetChunkedView\n};\n\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/dataset/data.js","define([\n], function(){\n\n'use strict';\n//==============================================================================\n/** Map of possible HDA/collection/job states to their string equivalents.\n * A port of galaxy.model.Dataset.states.\n */\nvar STATES = {\n // NOT ready states\n /** is uploading and not ready */\n UPLOAD : 'upload',\n /** the job that will produce the dataset queued in the runner */\n QUEUED : 'queued',\n /** the job that will produce the dataset is running */\n RUNNING : 'running',\n /** metadata for the dataset is being discovered/set */\n SETTING_METADATA : 'setting_metadata',\n\n // ready states\n /** was created without a tool */\n NEW : 'new',\n /** has no data */\n EMPTY : 'empty',\n /** has successfully completed running */\n OK : 'ok',\n\n /** the job that will produce the dataset paused */\n PAUSED : 'paused',\n /** metadata discovery/setting failed or errored (but otherwise ok) */\n FAILED_METADATA : 'failed_metadata',\n//TODO: not in trans.app.model.Dataset.states - is in database\n /** not accessible to the current user (i.e. due to permissions) */\n NOT_VIEWABLE : 'noPermission',\n /** deleted while uploading */\n DISCARDED : 'discarded',\n /** the tool producing this dataset failed */\n ERROR : 'error'\n};\n\nSTATES.READY_STATES = [\n STATES.OK,\n STATES.EMPTY,\n STATES.PAUSED,\n STATES.FAILED_METADATA,\n STATES.NOT_VIEWABLE,\n STATES.DISCARDED,\n STATES.ERROR\n];\n\nSTATES.NOT_READY_STATES = [\n STATES.UPLOAD,\n STATES.QUEUED,\n STATES.RUNNING,\n STATES.SETTING_METADATA,\n STATES.NEW\n];\n\n\n//==============================================================================\n return STATES;\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/dataset/states.js","/** This module contains all button views. */\ndefine( [ 'utils/utils' ], function( Utils ) {\n /** This renders the default button which is used e.g. at the bottom of the upload modal. */\n var ButtonDefault = Backbone.View.extend({\n initialize: function( options ) {\n this.model = options && options.model || new Backbone.Model({\n id : Utils.uid(),\n title : '',\n floating : 'right',\n icon : '',\n cls : 'btn btn-default',\n wait : false,\n wait_text : 'Sending...',\n wait_cls : 'btn btn-info',\n disabled : false,\n percentage : -1\n }).set( options );\n this.setElement( $( '' ).attr( 'type', 'button' )\n .append( this.$icon = $( '' ) )\n .append( this.$title = $( '' ) )\n .append( this.$progress = $( '' ).append( this.$progress_bar = $( '' ) ) ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n\n render: function() {\n var self = this;\n var options = this.model.attributes;\n this.$el.removeClass()\n .addClass( 'ui-button-default' )\n .addClass( options.disabled && 'disabled' )\n .attr( 'id', options.id )\n .attr( 'disabled', options.disabled )\n .css( 'float', options.floating )\n .off( 'click' ).on( 'click' , function() {\n $( '.tooltip' ).hide();\n options.onclick && !self.disabled && options.onclick();\n })\n .tooltip( { title: options.tooltip, placement: 'bottom' } );\n this.$progress.addClass( 'progress' ).css( 'display', options.percentage !== -1 ? 'block' : 'none' );\n this.$progress_bar.addClass( 'progress-bar' ).css( { width : options.percentage + '%' } );\n this.$icon.removeClass().addClass( 'icon fa' );\n this.$title.removeClass().addClass( 'title' );\n if ( options.wait ) {\n this.$el.addClass( options.wait_cls ).prop( 'disabled', true );\n this.$icon.addClass( 'fa-spinner fa-spin ui-margin-right' );\n this.$title.html( options.wait_text );\n } else {\n this.$el.addClass( options.cls );\n this.$icon.addClass( options.icon );\n this.$title.html( options.title );\n options.icon && options.title && this.$icon.addClass( 'ui-margin-right' );\n }\n },\n\n /** Show button */\n show: function() {\n this.$el.show();\n },\n\n /** Hide button */\n hide: function() {\n this.$el.hide();\n },\n\n /** Disable button */\n disable: function() {\n this.model.set( 'disabled', true );\n },\n\n /** Enable button */\n enable: function() {\n this.model.set( 'disabled', false );\n },\n\n /** Show spinner to indicate that the button is not ready to be clicked */\n wait: function() {\n this.model.set( 'wait', true );\n },\n\n /** Hide spinner to indicate that the button is ready to be clicked */\n unwait: function() {\n this.model.set( 'wait', false );\n },\n\n /** Change icon */\n setIcon: function( icon ) {\n this.model.set( 'icon', icon );\n }\n });\n\n /** This button allows the right-click/open-in-new-tab feature, its used e.g. for panel buttons. */\n var ButtonLink = ButtonDefault.extend({\n initialize: function( options ) {\n this.model = options && options.model || new Backbone.Model({\n id : Utils.uid(),\n title : '',\n icon : '',\n cls : ''\n }).set( options );\n this.setElement( $( '' ).append( this.$icon = $( '' ) ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n\n render: function() {\n var options = this.model.attributes;\n this.$el.removeClass()\n .addClass( options.cls )\n .attr( { id : options.id,\n href : options.href || 'javascript:void(0)',\n title : options.title,\n target : options.target || '_top',\n disabled : options.disabled } )\n .tooltip( { placement: 'bottom' } )\n .off( 'click' ).on( 'click' , function() {\n options.onclick && !options.disabled && options.onclick();\n });\n this.$icon.removeClass().addClass( options.icon );\n }\n });\n\n /** The check button is used in the tool form and allows to distinguish between multiple states e.g. all, partially and nothing selected. */\n var ButtonCheck = Backbone.View.extend({\n initialize: function( options ) {\n this.model = options && options.model || new Backbone.Model({\n id : Utils.uid(),\n title : 'Select/Unselect all',\n icons : [ 'fa-square-o', 'fa-minus-square-o', 'fa-check-square-o' ],\n value : 0,\n onchange : function(){}\n }).set( options );\n this.setElement( $( '' ).append( this.$icon = $( '' ) )\n .append( this.$title = $( '' ) ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n\n render: function( options ) {\n var self = this;\n var options = this.model.attributes;\n this.$el.addClass( 'ui-button-check' )\n .off( 'click' ).on('click', function() {\n self.model.set( 'value', ( self.model.get( 'value' ) === 0 && 2 ) || 0 );\n options.onclick && options.onclick();\n });\n this.$title.html( options.title );\n this.$icon.removeClass()\n .addClass( 'icon fa ui-margin-right' )\n .addClass( options.icons[ options.value ] );\n },\n\n /* Sets a new value and/or returns the value.\n * @param{Integer} new_val - Set a new value 0=unchecked, 1=partial and 2=checked.\n * OR:\n * @param{Integer} new_val - Number of selected options.\n * @param{Integer} total - Total number of available options.\n */\n value: function ( new_val, total ) {\n if ( new_val !== undefined ) {\n if ( total && new_val !== 0 ) {\n new_val = ( new_val !== total ) && 1 || 2;\n }\n this.model.set( 'value', new_val );\n this.model.get( 'onchange' )( this.model.get( 'value' ) );\n }\n return this.model.get( 'value' );\n }\n });\n\n /** This renders a differently styled, more compact button version. */\n var ButtonIcon = ButtonDefault.extend({\n initialize: function( options ) {\n this.model = options && options.model || new Backbone.Model({\n id : Utils.uid(),\n title : '',\n floating : 'right',\n icon : '',\n cls : 'ui-button-icon',\n disabled : false\n }).set( options );\n this.setElement( $( '' ).append( this.$button = $( '' ).append( this.$icon = $( '' ) )\n .append( this.$title = $( '' ) ) ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n\n render : function( options ) {\n var self = this;\n var options = this.model.attributes;\n this.$el.removeClass()\n .addClass( options.cls )\n .addClass( options.disabled && 'disabled' )\n .attr( 'disabled', options.disabled )\n .attr( 'id', options.id )\n .css( 'float', options.floating )\n .off( 'click' ).on( 'click', function() {\n $( '.tooltip' ).hide();\n !options.disabled && options.onclick && options.onclick();\n });\n this.$button.addClass( 'button' ).tooltip( { title: options.tooltip, placement: 'bottom' } );\n this.$icon.removeClass().addClass( 'icon fa' ).addClass( options.icon );\n this.$title.addClass( 'title' ).html( options.title );\n options.icon && options.title && this.$icon.addClass( 'ui-margin-right' );\n }\n });\n\n /** This class creates a button with dropdown menu. */\n var ButtonMenu = ButtonDefault.extend({\n $menu: null,\n initialize: function ( options ) {\n this.model = options && options.model || new Backbone.Model({\n id : '',\n title : '',\n floating : 'right',\n pull : 'right',\n icon : null,\n onclick : null,\n cls : 'ui-button-icon ui-button-menu',\n tooltip : '',\n target : '',\n href : '',\n onunload : null,\n visible : true,\n tag : ''\n }).set( options );\n this.collection = new Backbone.Collection();\n this.setElement( $( '' ).append( this.$root = $( '' ).append( this.$icon = $( '' ) )\n .append( this.$title = $( '' ) ) ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.listenTo( this.collection, 'change add remove reset', this.render, this );\n this.render();\n },\n\n render: function() {\n var self = this;\n var options = this.model.attributes;\n this.$el.removeClass()\n .addClass( 'dropdown' )\n .addClass( options.cls )\n .attr( 'id', options.id )\n .css( { float : options.floating,\n display : options.visible && this.collection.where( { visible: true } ).length > 0 ? 'block' : 'none' } );\n this.$root.addClass( 'root button dropdown-toggle' )\n .attr( 'data-toggle', 'dropdown' )\n .tooltip( { title: options.tooltip, placement: 'bottom' } )\n .off( 'click' ).on( 'click', function( e ) {\n $( '.tooltip' ).hide();\n e.preventDefault();\n options.onclick && options.onclick();\n } );\n this.$icon.removeClass().addClass( 'icon fa' ).addClass( options.icon );\n this.$title.removeClass().addClass( 'title' ).html( options.title );\n options.icon && options.title && this.$icon.addClass( 'ui-margin-right' );\n this.$menu && this.$menu.remove();\n if ( this.collection.length > 0 ) {\n this.$menu = $( '
' ).addClass( 'menu dropdown-menu' )\n .addClass( 'pull-' + self.model.get( 'pull' ) )\n .attr( 'role', 'menu' );\n this.$el.append( this.$menu );\n }\n this.collection.each( function( submodel ) {\n var suboptions = submodel.attributes;\n if ( suboptions.visible ) {\n var $link = $( '' ).addClass( 'dropdown-item' )\n .attr( { href : suboptions.href, target : suboptions.target } )\n .append( $( '' ).addClass( 'fa' )\n .addClass( suboptions.icon )\n .css( 'display', suboptions.icon ? 'inline-block' : 'none' ) )\n .append( suboptions.title )\n .on( 'click', function( e ) {\n if ( suboptions.onclick ) {\n e.preventDefault();\n suboptions.onclick();\n }\n } );\n self.$menu.append( $( '' ).append( $link ) );\n suboptions.divider && self.$menu.append( $( '' ).addClass( 'divider' ) );\n }\n });\n },\n\n /** Add a new menu item */\n addMenu: function ( options ) {\n this.collection.add( Utils.merge( options, {\n title : '',\n target : '',\n href : '',\n onclick : null,\n divider : false,\n visible : true,\n icon : null,\n cls : 'button-menu btn-group'\n }));\n }\n });\n\n return {\n ButtonDefault : ButtonDefault,\n ButtonLink : ButtonLink,\n ButtonIcon : ButtonIcon,\n ButtonCheck : ButtonCheck,\n ButtonMenu : ButtonMenu\n }\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/ui/ui-buttons.js","define([\n //jquery\n //backbone\n], function(){\n//=============================================================================\n/**\n * backbone model for icon buttons\n */\nvar IconButton = Backbone.Model.extend({\n defaults: {\n title : \"\",\n icon_class : \"\",\n on_click : null,\n menu_options : null,\n is_menu_button : true,\n id : null,\n href : null,\n target : null,\n enabled : true,\n visible : true,\n tooltip_config : {}\n }\n});\n\n/**\n * backbone view for icon buttons\n */\nvar IconButtonView = Backbone.View.extend({\n\n initialize : function(){\n // better rendering this way\n this.model.attributes.tooltip_config = { placement : 'bottom' };\n this.model.bind( 'change', this.render, this );\n },\n\n render : function( ){\n // hide tooltip\n this.$el.tooltip( 'hide' );\n\n var new_elem = this.template( this.model.toJSON() );\n // configure tooltip\n new_elem.tooltip( this.model.get( 'tooltip_config' ));\n this.$el.replaceWith( new_elem );\n this.setElement( new_elem );\n return this;\n },\n\n events : {\n 'click' : 'click'\n },\n\n click : function( event ){\n // if on_click pass to that function\n if( _.isFunction( this.model.get( 'on_click' ) ) ){\n this.model.get( 'on_click' )( event );\n return false;\n }\n // otherwise, bubble up ( to href or whatever )\n return true;\n },\n\n // generate html element\n template: function( options ){\n var buffer = 'title=\"' + options.title + '\" class=\"icon-button';\n\n if( options.is_menu_button ){\n buffer += ' menu-button';\n }\n\n buffer += ' ' + options.icon_class;\n\n if( !options.enabled ){\n buffer += '_disabled';\n }\n\n // close class tag\n buffer += '\"';\n\n if( options.id ){\n buffer += ' id=\"' + options.id + '\"';\n }\n\n buffer += ' href=\"' + options.href + '\"';\n // add target for href\n if( options.target ){\n buffer += ' target=\"' + options.target + '\"';\n }\n // set visibility\n if( !options.visible ){\n buffer += ' style=\"display: none;\"';\n }\n\n // enabled/disabled\n if ( options.enabled ){\n buffer = '';\n } else {\n buffer = '';\n }\n\n // return element\n return $( buffer );\n }\n} );\n\n// define collection\nvar IconButtonCollection = Backbone.Collection.extend({\n model: IconButton\n});\n\n/**\n * menu with multiple icon buttons\n * views are not needed nor used for individual buttons\n */\nvar IconButtonMenuView = Backbone.View.extend({\n\n tagName: 'div',\n\n initialize: function(){\n this.render();\n },\n\n render: function(){\n // initialize icon buttons\n var self = this;\n this.collection.each(function(button){\n // create and add icon button to menu\n var elt = $('')\n .attr('href', 'javascript:void(0)')\n .attr('title', button.attributes.title)\n .addClass('icon-button menu-button')\n .addClass(button.attributes.icon_class)\n .appendTo(self.$el)\n .click(button.attributes.on_click);\n\n // configure tooltip\n if (button.attributes.tooltip_config){\n elt.tooltip(button.attributes.tooltip_config);\n }\n\n // add popup menu to icon\n var menu_options = button.get('options');\n if (menu_options){\n make_popupmenu(elt, menu_options);\n }\n });\n\n // return\n return this;\n }\n});\n\n/**\n * Returns an IconButtonMenuView for the provided configuration.\n * Configuration is a list of dictionaries where each dictionary\n * defines an icon button. Each dictionary must have the following\n * elements: icon_class, title, and on_click.\n */\nvar create_icon_buttons_menu = function(config, global_config)\n{\n // initialize global configuration\n if (!global_config) global_config = {};\n\n // create and initialize menu\n var buttons = new IconButtonCollection(\n _.map(config, function(button_config){\n return new IconButton(_.extend(button_config, global_config));\n })\n );\n\n // return menu\n return new IconButtonMenuView( {collection: buttons} );\n};\n\n\n//=============================================================================\n return {\n IconButton : IconButton,\n IconButtonView : IconButtonView,\n IconButtonCollection : IconButtonCollection,\n IconButtonMenuView : IconButtonMenuView,\n create_icon_buttons_menu: create_icon_buttons_menu\n };\n})\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/ui/icon-button.js","/**\n * Popover wrapper\n*/\ndefine([ 'utils/utils' ], function( Utils ) {\nvar View = Backbone.View.extend({\n optionsDefault: {\n with_close : true,\n title : null,\n placement : 'top',\n container : 'body',\n body : null\n },\n\n initialize: function ( options ) {\n this.setElement( this._template() );\n this.uid = Utils.uid();\n this.options = _.defaults( options || {}, this.optionsDefault );\n this.options.container.parent().append( this.el );\n this.$title = this.$( '.popover-title-label' );\n this.$close = this.$( '.popover-close' );\n this.$body = this.$( '.popover-content' );\n\n // add initial content\n this.options.body && this.append( this.options.body );\n\n // add event to hide if click is outside of popup and not on container\n var self = this;\n $( 'body' ).on( 'mousedown.' + this.uid, function( e ) {\n // the 'is' for buttons that trigger popups\n // the 'has' for icons within a button that triggers a popup\n self.visible && !$( self.options.container ).is( e.target ) && !$( self.el ).is( e.target ) &&\n $( self.el ).has( e.target ).length === 0 && self.hide();\n });\n },\n\n /**\n * Render popover\n */\n render: function() {\n this.$title.html( this.options.title );\n this.$el.removeClass().addClass( 'ui-popover popover fade in' ).addClass( this.options.placement );\n this.$el.css( this._get_placement( this.options.placement ) );\n\n // configure close option\n var self = this;\n if ( this.options.with_close ) {\n this.$close.on( 'click', function() { self.hide() } ).show();\n } else {\n this.$close.off().hide();\n }\n },\n\n /**\n * Set the popover title\n * @params{ String } newTitle - New popover title\n */\n title: function( newTitle ) {\n if ( newTitle !== undefined ) {\n this.options.title = newTitle;\n this.$title.html( newTitle );\n }\n },\n\n /**\n * Show popover\n */\n show: function() {\n this.render();\n this.$el.show();\n this.visible = true;\n },\n\n /**\n * Hide popover\n */\n hide: function() {\n this.$el.hide();\n this.visible = false;\n },\n\n /**\n * Append new content to the popover\n * @params{ Object } $el - Dom element\n */\n append: function( $el ) {\n this.$body.append( $el );\n },\n\n /**\n * Remove all content\n */\n empty: function() {\n this.$body.empty();\n },\n\n /**\n * Remove popover\n */\n remove: function() {\n $( 'body' ).off( 'mousedown.' + this.uid );\n this.$el.remove();\n },\n\n /**\n * Improve popover location/placement\n */\n _get_placement: function( placement ) {\n // get popover dimensions\n var width = this._get_width( this.$el );\n var height = this.$el.height();\n\n // get container details\n var $container = this.options.container;\n var container_width = this._get_width( $container );\n var container_height = this._get_height( $container );\n var container_position = $container.position();\n\n // get position\n var top = left = 0;\n if ([ 'top', 'bottom' ].indexOf( placement ) != -1) {\n left = container_position.left - width + ( container_width + width ) / 2;\n switch ( placement ) {\n case 'top':\n top = container_position.top - height - 5;\n break;\n case 'bottom':\n top = container_position.top + container_height + 5;\n break;\n }\n } else {\n top = container_position.top - height + ( container_height + height ) / 2;\n switch ( placement ) {\n case 'right':\n left = container_position.left + container_width;\n break;\n }\n }\n return { top: top, left: left };\n },\n\n /**\n * Returns padding/margin corrected width\n */\n _get_width: function( $el ) {\n return $el.width() + parseInt( $el.css( 'padding-left' ) ) + parseInt( $el.css( 'margin-left' ) ) +\n parseInt( $el.css( 'padding-right' ) ) + parseInt( $el.css( 'margin-right' ) );\n },\n\n /**\n * Returns padding corrected height\n */\n _get_height: function( $el ) {\n return $el.height() + parseInt( $el.css( 'padding-top' ) ) + parseInt( $el.css( 'padding-bottom' ) );\n },\n\n /**\n * Return the popover template\n */\n _template: function( options ) {\n return '
' +\n '
' +\n '
' +\n '
' +\n '' +\n '
' +\n '
' +\n '
';\n }\n});\n\nreturn {\n View: View\n}\n\n});\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/ui/ui-popover.js","// dependencies\ndefine(['utils/utils'], function(Utils) {\n\n/**\n * A plugin for initializing select2 input items.\n * Make sure the select2 library itself is loaded beforehand.\n * Also the element to which select2 will be appended has to \n * be created before select2 initialization (and passed as option).\n */\nvar View = Backbone.View.extend(\n{\n // options\n optionsDefault: {\n css : '',\n placeholder : 'No data available',\n data : [],\n value : null,\n multiple : false,\n minimumInputLength : 0,\n // example format of initial data: \"id:name,55:anotherrole@role.com,27:role@role.com\"\n initialData : ''\n },\n \n // initialize\n initialize : function(options) {\n // configure options\n this.options = Utils.merge(options, this.optionsDefault);\n \n // create new element\n this.setElement(this._template(this.options));\n \n // check if container exists\n if (!this.options.container) {\n console.log('ui-select::initialize() : container not specified.');\n return;\n }\n \n // add to dom\n this.options.container.append(this.$el);\n \n // link selection dictionary\n this.select_data = this.options.data;\n \n // refresh\n this._refresh();\n \n if (!this.options.multiple){\n // initial value\n if (this.options.value) {\n this._setValue(this.options.value);\n }\n \n // add change event\n var self = this;\n if (this.options.onchange) {\n this.$el.on('change', function() {\n self.options.onchange(self.value());\n });\n }\n }\n },\n \n // value\n value : function (new_value) {\n // get current id/value\n var before = this._getValue();\n \n // check if new_value is defined\n if (new_value !== undefined) {\n this._setValue(new_value);\n }\n \n // get current id/value\n var after = this._getValue();\n \n // fire onchange\n if ((after != before && this.options.onchange)) {\n this.options.onchange(after);\n }\n \n // return current value\n return after;\n },\n \n // label\n text : function () {\n return this.$el.select2('data').text;\n },\n \n // disabled\n disabled: function() {\n return !this.$el.select2('enable');\n },\n\n // enable\n enable: function() {\n this.$el.select2('enable', true);\n },\n \n // disable\n disable: function() {\n this.$el.select2('enable', false);\n },\n \n // add\n add: function(options) {\n // add options\n this.select_data.push({\n id : options.id,\n text : options.text\n });\n \n // refresh\n this._refresh();\n },\n \n // remove\n del: function(id) {\n // search option\n var index = this._getIndex(id);\n \n // check if found\n if (index != -1) {\n // remove options\n this.select_data.splice(index, 1);\n \n // refresh\n this._refresh();\n }\n },\n \n // remove\n remove: function() {\n this.$el.select2('destroy');\n },\n \n // update\n update: function(options) {\n // copy options\n this.select_data = [];\n for (var key in options.data) {\n this.select_data.push(options.data[key]);\n }\n \n // refresh\n this._refresh();\n },\n \n // refresh\n _refresh: function() {\n // add select2 data based on type of input\n if (!this.options.multiple){\n var selected = this._getValue();\n var select_opt = {\n data : this.select_data,\n containerCssClass : this.options.css,\n placeholder : this.options.placeholder,\n dropdownAutoWidth : true\n };\n this.$el.select2(select_opt);\n // select previous value (if exists)\n this._setValue(selected);\n } else {\n var select_opt = {\n multiple : this.options.multiple,\n containerCssClass : this.options.css,\n placeholder : this.options.placeholder,\n minimumInputLength : this.options.minimumInputLength,\n ajax : this.options.ajax,\n dropdownCssClass : this.options.dropdownCssClass,\n escapeMarkup : this.options.escapeMarkup,\n formatResult : this.options.formatResult,\n formatSelection : this.options.formatSelection,\n initSelection : this.options.initSelection,\n initialData : this.options.initialData\n };\n this.$el.select2(select_opt);\n }\n },\n \n // get index\n _getIndex: function(value) {\n // returns the index of the searched value\n _.findIndex(this.select_data, {id: value});\n },\n \n // get value\n _getValue: function() {\n return this.$el.select2('val');\n },\n \n // set value\n _setValue: function(new_value) {\n var index = this._getIndex(new_value);\n if (index == -1) {\n if (this.select_data.length > 0) {\n new_value = this.select_data[0].id;\n }\n }\n this.$el.select2('val', new_value);\n },\n \n // element\n _template: function(options) {\n return '';\n }\n});\n\nreturn {\n View : View\n};\n\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/ui/ui-select.js","// from: https://raw.githubusercontent.com/umdjs/umd/master/jqueryPlugin.js\n// Uses AMD or browser globals to create a jQuery plugin.\n(function (factory) {\n if (typeof define === 'function' && define.amd) {\n //TODO: So...this turns out to be an all or nothing thing. If I load jQuery in the define below, it will\n // (of course) wipe the old jquery *and all the plugins loaded into it*. So the define below *is still\n // relying on jquery being loaded globally* in order to preserve plugins.\n define([ 'jquery' ], factory);\n } else {\n // Browser globals\n factory(jQuery);\n }\n\n}(function ( jQuery ) {\n'use_strict';\n\nvar $ = jQuery;\n\n// ============================================================================\n/**\n * Make an element with text editable: (a) when user clicks on text, a textbox/area\n * is provided for editing; (b) when enter key pressed, element's text is set and on_finish\n * is called.\n */\n$.fn.make_text_editable = function(config_dict) {\n // Get config options.\n var num_cols = (\"num_cols\" in config_dict ? config_dict.num_cols : 30),\n num_rows = (\"num_rows\" in config_dict ? config_dict.num_rows : 4),\n use_textarea = (\"use_textarea\" in config_dict ? config_dict.use_textarea : false),\n on_finish = (\"on_finish\" in config_dict ? config_dict.on_finish : null),\n help_text = (\"help_text\" in config_dict ? config_dict.help_text : null);\n\n // Add element behavior.\n var container = $(this);\n container.addClass(\"editable-text\").click(function(e) {\n // If there's already an input element, editing is active, so do nothing.\n if ($(this).children(\":input\").length > 0) {\n return;\n }\n\n container.removeClass(\"editable-text\");\n\n // Handler for setting element text.\n var set_text = function(new_text) {\n container.find(\":input\").remove();\n\n if (new_text !== \"\") {\n container.text(new_text);\n } else {\n // No text; need a line so that there is a click target.\n container.html(\" \");\n }\n container.addClass(\"editable-text\");\n\n if (on_finish) {\n on_finish(new_text);\n }\n };\n\n // Create input element(s) for editing.\n var cur_text = (\"cur_text\" in config_dict ? config_dict.cur_text : container.text() ),\n input_elt, button_elt;\n\n if (use_textarea) {\n input_elt = $(\"\")\n .attr({ rows: num_rows, cols: num_cols }).text($.trim(cur_text))\n .keyup(function(e) {\n if (e.keyCode === 27) {\n // Escape key.\n set_text(cur_text);\n }\n });\n button_elt = $(\"\").text(\"Done\").click(function() {\n set_text(input_elt.val());\n // Return false so that click does not propogate to container.\n return false;\n });\n }\n else {\n input_elt = $(\"\").attr({ value: $.trim(cur_text), size: num_cols })\n .blur(function() {\n set_text(cur_text);\n }).keyup(function(e) {\n if (e.keyCode === 27) {\n // Escape key.\n $(this).trigger(\"blur\");\n } else if (e.keyCode === 13) {\n // Enter key.\n set_text($(this).val());\n }\n\n // Do not propogate event to avoid unwanted side effects.\n e.stopPropagation();\n });\n }\n\n // Replace text with input object(s) and focus & select.\n container.text(\"\");\n container.append(input_elt);\n if (button_elt) {\n container.append(button_elt);\n }\n input_elt.focus();\n input_elt.select();\n\n // Do not propogate to elements below b/c that blurs input and prevents it from being used.\n e.stopPropagation();\n });\n\n // Add help text if there some.\n if (help_text) {\n container.attr(\"title\", help_text).tooltip();\n }\n\n return container;\n};\n\n// ============================================================================\n}));\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/ui/editable-text.js","(function (root, factory) {\n if (typeof define === 'function' && define.amd) {\n define([], factory);\n } else {\n root.faIconButton = factory();\n }\n\n}(this, function () {\n//============================================================================\n /** Returns a jQuery object containing a clickable font-awesome button.\n * options:\n * tooltipConfig : option map for bootstrap tool tip\n * classes : array of class names (will always be classed as icon-btn)\n * disabled : T/F - add the 'disabled' class?\n * title : tooltip/title string\n * target : optional href target\n * href : optional href\n * faIcon : which font awesome icon to use\n * onclick : function to call when the button is clicked\n */\n var faIconButton = function( options ){\n options = options || {};\n options.tooltipConfig = options.tooltipConfig || { placement: 'bottom' };\n\n options.classes = [ 'icon-btn' ].concat( options.classes || [] );\n if( options.disabled ){\n options.classes.push( 'disabled' );\n }\n\n var html = [\n '',\n // could go with something less specific here - like 'html'\n '',\n ''\n ].join( '' );\n var $button = $( html ).tooltip( options.tooltipConfig );\n if( _.isFunction( options.onclick ) ){\n $button.click( options.onclick );\n }\n return $button;\n };\n\n//============================================================================\n return faIconButton;\n}));\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/ui/fa-icon-button.js","define(function(){\n\n/**\n * Stringifies a number adding commas for digit grouping as per North America.\n */\nfunction commatize( number ) {\n number += ''; // Convert to string\n var rgx = /(\\d+)(\\d{3})/;\n while (rgx.test(number)) {\n number = number.replace(rgx, '$1' + ',' + '$2');\n }\n return number;\n}\n\n/**\n * Helper to determine if object is jQuery deferred.\n */\nvar is_deferred = function ( d ) {\n return ('promise' in d);\n};\n\n/**\n * Implementation of a server-state based deferred. Server is repeatedly polled, and when\n * condition is met, deferred is resolved.\n */\nvar ServerStateDeferred = Backbone.Model.extend({\n defaults: {\n ajax_settings: {},\n interval: 1000,\n success_fn: function(result) { return true; }\n },\n\n /**\n * Returns a deferred that resolves when success function returns true.\n */\n go: function() {\n var deferred = $.Deferred(),\n self = this,\n ajax_settings = self.get('ajax_settings'),\n success_fn = self.get('success_fn'),\n interval = self.get('interval'),\n _go = function() {\n $.ajax(ajax_settings).success(function(result) {\n if (success_fn(result)) {\n // Result is good, so resolve.\n deferred.resolve(result);\n }\n else {\n // Result not good, try again.\n setTimeout(_go, interval);\n }\n });\n };\n _go();\n return deferred;\n }\n});\n\n/**\n * Returns a random color in hexadecimal format that is sufficiently different from a single color\n * or set of colors.\n * @param colors a color or list of colors in the format '#RRGGBB'\n */\nvar get_random_color = function(colors) {\n // Default for colors is white.\n if (!colors) { colors = \"#ffffff\"; }\n\n // If needed, create list of colors.\n if ( typeof(colors) === \"string\" ) {\n colors = [ colors ];\n }\n\n // Convert colors to numbers.\n for (var i = 0; i < colors.length; i++) {\n colors[i] = parseInt( colors[i].slice(1), 16 );\n }\n\n // -- Perceived brightness and difference formulas are from\n // -- http://www.w3.org/WAI/ER/WD-AERT/#color-contrast\n\n // Compute perceived color brightness (based on RGB-YIQ transformation):\n var brightness = function(r, g, b) {\n return ( (r * 299) + (g * 587) + (b * 114) ) / 1000;\n };\n\n // Compute color difference:\n var difference = function(r1, g1, b1, r2, g2, b2) {\n return ( Math.max(r1, r2) - Math.min(r1, r2) ) +\n ( Math.max(g1, g2) - Math.min(g1, g2) ) +\n ( Math.max(b1, b2) - Math.min(b1, b2) );\n };\n\n // Create new random color.\n var new_color, nr, ng, nb,\n other_color, or, og, ob,\n n_brightness, o_brightness,\n diff, ok = false,\n num_tries = 0;\n do {\n // New color is never white b/c random in [0,1)\n new_color = Math.round( Math.random() * 0xffffff );\n nr = ( new_color & 0xff0000 ) >> 16;\n ng = ( new_color & 0x00ff00 ) >> 8;\n nb = new_color & 0x0000ff;\n n_brightness = brightness(nr, ng, nb);\n ok = true;\n for (i = 0; i < colors.length; i++) {\n other_color = colors[i];\n or = ( other_color & 0xff0000 ) >> 16;\n og = ( other_color & 0x00ff00 ) >> 8;\n ob = other_color & 0x0000ff;\n o_brightness = brightness(or, og, ob);\n diff = difference(nr, ng, nb, or, og, ob);\n // These thresholds may need to be adjusted. Brightness difference range is 125;\n // color difference range is 500.\n if ( ( Math.abs(n_brightness - o_brightness) < 40 ) ||\n ( diff < 200 ) ) {\n ok = false;\n break;\n }\n }\n\n num_tries++\n; } while (!ok && num_tries <= 10 );\n\n // Add 0x1000000 to left pad number with 0s.\n return '#' + ( 0x1000000 + new_color ).toString(16).substr(1,6);\n};\n\nreturn {\n commatize: commatize,\n is_deferred: is_deferred,\n ServerStateDeferred : ServerStateDeferred,\n get_random_color : get_random_color\n};\n\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/viz/trackster/util.js","define([\n \"libs/bibtex\",\n \"mvc/base-mvc\",\n \"utils/localization\"\n], function( parseBibtex, baseMVC, _l ){\n/* global Backbone */\n// we use amd here to require, but bibtex uses a global or commonjs pattern.\n// webpack will load via commonjs and plain requirejs will load as global. Check both\nparseBibtex = parseBibtex || window.BibtexParser;\n\nvar logNamespace = 'citation';\n//==============================================================================\n/** @class model for tool citations.\n * @name Citation\n * @augments Backbone.Model\n */\nvar Citation = Backbone.Model.extend( baseMVC.LoggableMixin ).extend({\n _logNamespace : logNamespace,\n\n defaults : {\n content: ''\n },\n\n initialize: function() {\n var parsed;\n try {\n // TODO: to model.parse/.validate\n parsed = parseBibtex( this.attributes.content );\n } catch( err ){\n return;\n }\n // bibtex returns successfully parsed in .entries and any parsing errors in .errors\n if( parsed.errors.length ){\n // the gen. form of these errors seems to be [ line, col, char, error message ]\n var errors = parsed.errors.reduce( function( all, current ){ return all + '; ' + current; });\n // throw new Error( 'Error parsing bibtex: ' + errors );\n this.log( 'Error parsing bibtex: ' + errors );\n }\n\n this._fields = {};\n this.entry = _.first( parsed.entries );\n if( this.entry ){\n var rawFields = this.entry.Fields;\n for( var key in rawFields ){\n var value = rawFields[ key ];\n var lowerKey = key.toLowerCase();\n this._fields[ lowerKey ] = value;\n }\n }\n },\n entryType: function() {\n return this.entry? this.entry.EntryType : undefined;\n },\n fields: function() {\n return this._fields;\n }\n});\n\n\n//==============================================================================\n/** @class Backbone collection of citations.\n */\nvar BaseCitationCollection = Backbone.Collection.extend( baseMVC.LoggableMixin ).extend( {\n _logNamespace : logNamespace,\n\n /** root api url */\n urlRoot : Galaxy.root + 'api',\n partial : true, // Assume some tools in history/workflow may not be properly annotated yet.\n model : Citation,\n} );\n\nvar HistoryCitationCollection = BaseCitationCollection.extend( {\n /** complete api url */\n url : function() {\n return this.urlRoot + '/histories/' + this.history_id + '/citations';\n }\n} );\n\nvar ToolCitationCollection = BaseCitationCollection.extend( {\n /** complete api url */\n url : function() {\n return this.urlRoot + '/tools/' + this.tool_id + '/citations';\n },\n partial : false, // If a tool has citations, assume they are complete.\n} );\n\n\n//==============================================================================\n\nreturn {\n Citation : Citation,\n HistoryCitationCollection : HistoryCitationCollection,\n ToolCitationCollection: ToolCitationCollection\n};\n\n\n});\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/citation/citation-model.js","/**\n This is the main class of the form plugin. It is referenced as 'app' in lower level modules.\n*/\ndefine( [ 'utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'mvc/form/form-section', 'mvc/form/form-data' ],\nfunction( Utils, Portlet, Ui, FormSection, FormData ) {\n return Backbone.View.extend({\n initialize: function( options ) {\n this.model = new Backbone.Model({\n initial_errors : false,\n cls : 'ui-portlet-limited',\n icon : null,\n always_refresh : true,\n message_status : 'warning'\n }).set( options );\n this.setElement( '' );\n this.render();\n },\n\n /** Update available options */\n update: function( new_model ){\n var self = this;\n this.data.matchModel( new_model, function( node, input_id ) {\n var input = self.input_list[ input_id ];\n if ( input && input.options ) {\n if ( !_.isEqual( input.options, node.options ) ) {\n input.options = node.options;\n var field = self.field_list[ input_id ];\n if ( field.update ) {\n var new_options = [];\n if ( ( [ 'data', 'data_collection', 'drill_down' ] ).indexOf( input.type ) != -1 ) {\n new_options = input.options;\n } else {\n for ( var i in node.options ) {\n var opt = node.options[ i ];\n if ( opt.length > 2 ) {\n new_options.push( { label: opt[ 0 ], value: opt[ 1 ] } );\n }\n }\n }\n field.update( new_options );\n field.trigger( 'change' );\n Galaxy.emit.debug( 'form-view::update()', 'Updating options for ' + input_id );\n }\n }\n }\n });\n },\n\n /** Set form into wait mode */\n wait: function( active ) {\n for ( var i in this.input_list ) {\n var field = this.field_list[ i ];\n var input = this.input_list[ i ];\n if ( input.is_dynamic && field.wait && field.unwait ) {\n field[ active ? 'wait' : 'unwait' ]();\n }\n }\n },\n\n /** Highlight and scroll to input element (currently only used for error notifications) */\n highlight: function ( input_id, message, silent ) {\n var input_element = this.element_list[ input_id ];\n if ( input_element ) {\n input_element.error( message || 'Please verify this parameter.' );\n this.portlet.expand();\n this.trigger( 'expand', input_id );\n if ( !silent ) {\n var $panel = this.$el.parents().filter(function() {\n return [ 'auto', 'scroll' ].indexOf( $( this ).css( 'overflow' ) ) != -1;\n }).first();\n $panel.animate( { scrollTop : $panel.scrollTop() + input_element.$el.offset().top - 120 }, 500 );\n }\n }\n },\n\n /** Highlights errors */\n errors: function( options ) {\n this.trigger( 'reset' );\n if ( options && options.errors ) {\n var error_messages = this.data.matchResponse( options.errors );\n for ( var input_id in this.element_list ) {\n var input = this.element_list[ input_id ];\n if ( error_messages[ input_id ] ) {\n this.highlight( input_id, error_messages[ input_id ], true );\n }\n }\n }\n },\n\n /** Render tool form */\n render: function() {\n var self = this;\n this.off('change');\n this.off('reset');\n // contains the dom field elements as created by the parameter factory i.e. form-parameters\n this.field_list = {};\n // contains input definitions/dictionaries as provided by the parameters to_dict() function through the api\n this.input_list = {};\n // contains the dom elements of each input element i.e. form-input which wraps the actual input field\n this.element_list = {};\n // converts the form into a json data structure\n this.data = new FormData.Manager( this );\n this._renderForm();\n this.data.create();\n this.model.get( 'initial_errors' ) && this.errors( this.model.attributes );\n // add listener which triggers on checksum change, and reset the form input wrappers\n var current_check = this.data.checksum();\n this.on( 'change', function( input_id ) {\n var input = self.input_list[ input_id ];\n if ( !input || input.refresh_on_change || self.model.get( 'always_refresh' ) ) {\n var new_check = self.data.checksum();\n if ( new_check != current_check ) {\n current_check = new_check;\n self.model.get( 'onchange' ) && self.model.get( 'onchange' )();\n }\n }\n });\n this.on('reset', function() {\n _.each( self.element_list, function( input_element ) { input_element.reset() } );\n });\n return this;\n },\n\n /** Renders/appends dom elements of the form */\n _renderForm: function() {\n $( '.tooltip' ).remove();\n var options = this.model.attributes;\n this.message = new Ui.UnescapedMessage();\n this.section = new FormSection.View( this, { inputs: options.inputs } );\n this.portlet = new Portlet.View({\n icon : options.icon,\n title : options.title,\n cls : options.cls,\n operations : options.operations,\n buttons : options.buttons,\n collapsible : options.collapsible,\n collapsed : options.collapsed,\n onchange_title : options.onchange_title\n });\n this.portlet.append( this.message.$el );\n this.portlet.append( this.section.$el );\n this.$el.empty();\n options.inputs && this.$el.append( this.portlet.$el );\n options.message && this.message.update( { persistent: true, status: options.message_status, message: options.message } );\n Galaxy.emit.debug( 'form-view::initialize()', 'Completed' );\n }\n });\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/form/form-view.js","// dependencies\ndefine(['utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc'], function(Utils, Portlet, Ui) {\n\n// ui list element\nvar View = Backbone.View.extend({\n // create portlet to keep track of selected list elements\n initialize : function(options) {\n // link this\n var self = this;\n\n // initialize options\n this.options = options;\n this.name = options.name || 'element';\n this.multiple = options.multiple || false;\n\n // create message handler\n this.message = new Ui.Message();\n\n // create portlet\n this.portlet = new Portlet.View({ cls: 'ui-portlet-section' });\n\n // create select field containing the options which can be inserted into the list\n this.select = new Ui.Select.View({ optional : options.optional });\n\n // create insert new list element button\n this.button = new Ui.ButtonIcon({\n icon : 'fa fa-sign-in',\n floating : 'left',\n tooltip : 'Insert new ' + this.name,\n onclick : function() {\n self.add({\n id : self.select.value(),\n name : self.select.text()\n });\n }\n });\n\n // build main element\n this.setElement(this._template(options));\n this.$('.ui-list-message').append(this.message.$el);\n this.$('.ui-list-portlet').append(this.portlet.$el);\n this.$('.ui-list-button').append(this.button.$el);\n this.$('.ui-list-select').append(this.select.$el);\n },\n\n /** Return/Set currently selected list elements */\n value: function(val) {\n // set new value\n if (val !== undefined) {\n this.portlet.empty();\n if ($.isArray(val)) {\n for (var i in val) {\n var v = val[i];\n var v_id = null;\n var v_name = null;\n if ($.type(v) != 'string') {\n v_id = v.id;\n v_name = v.name;\n } else {\n v_id = v_name = v;\n }\n if (v_id != null) {\n this.add({\n id : v_id,\n name : v_name\n });\n }\n }\n }\n this._refresh();\n }\n // get current value\n var lst = [];\n this.$('.ui-list-id').each(function() {\n lst.push({\n id : $(this).prop('id'),\n name : $(this).find('.ui-list-name').html()\n });\n });\n if (lst.length == 0) {\n return null;\n }\n return lst;\n },\n\n /** Add row */\n add: function(options) {\n var self = this;\n if (this.$('[id=\"' + options.id + '\"]').length === 0) {\n if (!Utils.isEmpty(options.id)) {\n var $el = $(this._templateRow({\n id : options.id,\n name : options.name\n }));\n $el.on('click', function() {\n $el.remove();\n self._refresh();\n });\n $el.on('mouseover', function() {\n $el.addClass('portlet-highlight');\n });\n $el.on('mouseout', function() {\n $el.removeClass('portlet-highlight');\n });\n this.portlet.append($el);\n this._refresh();\n } else {\n this.message.update({ message: 'Please select a valid ' + this.name + '.', status: 'danger' });\n }\n } else {\n this.message.update({ message: 'This ' + this.name + ' is already in the list.' });\n }\n },\n\n /** Update available options */\n update: function(options) {\n this.select.update(options);\n },\n\n /** Refresh view */\n _refresh: function() {\n if (this.$('.ui-list-id').length > 0) {\n !this.multiple && this.button.disable();\n this.$('.ui-list-portlet').show();\n } else {\n this.button.enable();\n this.$('.ui-list-portlet').hide();\n }\n this.options.onchange && this.options.onchange();\n },\n\n /** Main Template */\n _template: function(options) {\n return '
',\n 'Warning: This is a experimental feature. Most Galaxy tools will not annotate',\n ' citations explicitly at this time. When writing up your analysis, please manually',\n ' review your histories and find all references',\n ' that should be cited in order to completely describe your work. Also, please remember to',\n ' cite Galaxy.',\n '
'\n ], 'collection' );\n\n // use element identifier\n var subtitleTemplate = BASE_MVC.wrapTemplate([\n '
',\n '<% var countText = collection.element_count? ( collection.element_count + \" \" ) : \"\"; %>',\n '<% if( collection.collection_type === \"list\" ){ %>',\n _l( 'a list of <%- countText %>datasets' ),\n '<% } else if( collection.collection_type === \"paired\" ){ %>',\n _l( 'a pair of datasets' ),\n '<% } else if( collection.collection_type === \"list:paired\" ){ %>',\n _l( 'a list of <%- countText %>dataset pairs' ),\n '<% } else if( collection.collection_type === \"list:list\" ){ %>',\n _l( 'a list of <%- countText %>dataset lists' ),\n '<% } %>',\n '
'\n ], 'collection' );\n\n return _.extend( {}, FoldoutListItemView.prototype.templates, {\n warnings : warnings,\n titleBar : titleBarTemplate,\n subtitle : subtitleTemplate\n });\n}());\n\n\n//==============================================================================\n/** @class Read only view for DatasetCollectionElement.\n */\nvar DCEListItemView = ListItemView.extend(\n/** @lends DCEListItemView.prototype */{\n\n /** add the DCE class to the list item */\n className : ListItemView.prototype.className + \" dataset-collection-element\",\n\n /** set up */\n initialize : function( attributes ){\n if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; }\n this.log( 'DCEListItemView.initialize:', attributes );\n ListItemView.prototype.initialize.call( this, attributes );\n },\n\n // ......................................................................... misc\n /** String representation */\n toString : function(){\n var modelString = ( this.model )?( this.model + '' ):( '(no model)' );\n return 'DCEListItemView(' + modelString + ')';\n }\n});\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nDCEListItemView.prototype.templates = (function(){\n\n // use the element identifier here - since that will persist and the user will need it\n var titleBarTemplate = BASE_MVC.wrapTemplate([\n '
',\n '
',\n '<%- element.element_identifier %>',\n '
',\n '',\n '
'\n ], 'element' );\n\n return _.extend( {}, ListItemView.prototype.templates, {\n titleBar : titleBarTemplate\n });\n}());\n\n\n//==============================================================================\n/** @class Read only view for a DatasetCollectionElement that is also an DatasetAssociation\n * (a dataset contained in a dataset collection).\n */\nvar DatasetDCEListItemView = DATASET_LI.DatasetListItemView.extend(\n/** @lends DatasetDCEListItemView.prototype */{\n\n className : DATASET_LI.DatasetListItemView.prototype.className + \" dataset-collection-element\",\n\n /** set up */\n initialize : function( attributes ){\n if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; }\n this.log( 'DatasetDCEListItemView.initialize:', attributes );\n DATASET_LI.DatasetListItemView.prototype.initialize.call( this, attributes );\n },\n\n /** In this override, only get details if in the ready state.\n * Note: fetch with no 'change' event triggering to prevent automatic rendering.\n */\n _fetchModelDetails : function(){\n var view = this;\n if( view.model.inReadyState() && !view.model.hasDetails() ){\n return view.model.fetch({ silent: true });\n }\n return jQuery.when();\n },\n\n // ......................................................................... misc\n /** String representation */\n toString : function(){\n var modelString = ( this.model )?( this.model + '' ):( '(no model)' );\n return 'DatasetDCEListItemView(' + modelString + ')';\n }\n});\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nDatasetDCEListItemView.prototype.templates = (function(){\n\n // use the element identifier here and not the dataset name\n //TODO:?? can we steal the DCE titlebar?\n var titleBarTemplate = BASE_MVC.wrapTemplate([\n '
',\n '',\n '
',\n '<%- element.element_identifier %>',\n '
',\n '
'\n ], 'element' );\n\n return _.extend( {}, DATASET_LI.DatasetListItemView.prototype.templates, {\n titleBar : titleBarTemplate\n });\n}());\n\n\n//==============================================================================\n/** @class Read only view for a DatasetCollectionElement that is also a DatasetCollection\n * (a nested DC).\n */\nvar NestedDCDCEListItemView = DCListItemView.extend(\n/** @lends NestedDCDCEListItemView.prototype */{\n\n className : DCListItemView.prototype.className + \" dataset-collection-element\",\n\n /** In this override, add the state as a class for use with state-based CSS */\n _swapNewRender : function( $newRender ){\n DCListItemView.prototype._swapNewRender.call( this, $newRender );\n var state = this.model.get( 'state' ) || 'ok';\n this.$el.addClass( 'state-' + state );\n return this.$el;\n },\n\n // ......................................................................... misc\n /** String representation */\n toString : function(){\n var modelString = ( this.model )?( this.model + '' ):( '(no model)' );\n return 'NestedDCDCEListItemView(' + modelString + ')';\n }\n});\n\n\n//==============================================================================\n return {\n DCListItemView : DCListItemView,\n DCEListItemView : DCEListItemView,\n DatasetDCEListItemView : DatasetDCEListItemView,\n NestedDCDCEListItemView : NestedDCDCEListItemView\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/collection/collection-li.js","define([\n \"mvc/dataset/dataset-model\",\n \"mvc/base-mvc\",\n \"utils/localization\"\n], function( DATASET_MODEL, BASE_MVC, _l ){\n'use strict';\n\n//==============================================================================\n/*\nNotes:\n\nTerminology:\n DatasetCollection/DC : a container of datasets or nested DatasetCollections\n Element/DatasetCollectionElement/DCE : an item contained in a DatasetCollection\n HistoryDatasetCollectionAssociation/HDCA: a DatasetCollection contained in a history\n\n\nThis all seems too complex unfortunately:\n\n- Terminology collision between DatasetCollections (DCs) and Backbone Collections.\n- In the DatasetCollections API JSON, DC Elements use a 'Has A' stucture to *contain*\n either a dataset or a nested DC. This would make the hierarchy much taller. I've\n decided to merge the contained JSON with the DC element json - making the 'has a'\n relation into an 'is a' relation. This seems simpler to me and allowed a lot of\n DRY in both models and views, but may make tracking or tracing within these models\n more difficult (since DatasetCollectionElements are now *also* DatasetAssociations\n or DatasetCollections (nested)). This also violates the rule of thumb about\n favoring aggregation over inheritance.\n- Currently, there are three DatasetCollection subclasses: List, Pair, and ListPaired.\n These each should a) be usable on their own, b) be usable in the context of\n nesting within a collection model (at least in the case of ListPaired), and\n c) be usable within the context of other container models (like History or\n LibraryFolder, etc.). I've tried to separate/extract classes in order to\n handle those three situations, but it's proven difficult to do in a simple,\n readable manner.\n- Ideally, histories and libraries would inherit from the same server models as\n dataset collections do since they are (in essence) dataset collections themselves -\n making the whole nested structure simpler. This would be a large, error-prone\n refactoring and migration.\n\nMany of the classes and heirarchy are meant as extension points so, while the\nrelations and flow may be difficult to understand initially, they'll allow us to\nhandle the growth or flux dataset collection in the future (w/o actually implementing\nany YAGNI).\n\n*/\n//_________________________________________________________________________________________________ ELEMENTS\n/** @class mixin for Dataset collection elements.\n * When collection elements are passed from the API, the underlying element is\n * in a sub-object 'object' (IOW, a DCE representing an HDA will have HDA json in element.object).\n * This mixin uses the constructor and parse methods to merge that JSON with the DCE attribtues\n * effectively changing a DCE from a container to a subclass (has a --> is a).\n */\nvar DatasetCollectionElementMixin = {\n\n /** default attributes used by elements in a dataset collection */\n defaults : {\n model_class : 'DatasetCollectionElement',\n element_identifier : null,\n element_index : null,\n element_type : null\n },\n\n /** merge the attributes of the sub-object 'object' into this model */\n _mergeObject : function( attributes ){\n // if we don't preserve and correct ids here, the element id becomes the object id\n // and collision in backbone's _byId will occur and only\n _.extend( attributes, attributes.object, { element_id: attributes.id });\n delete attributes.object;\n return attributes;\n },\n\n /** override to merge this.object into this */\n constructor : function( attributes, options ){\n // console.debug( '\\t DatasetCollectionElement.constructor:', attributes, options );\n attributes = this._mergeObject( attributes );\n this.idAttribute = 'element_id';\n Backbone.Model.apply( this, arguments );\n },\n\n /** when the model is fetched, merge this.object into this */\n parse : function( response, options ){\n var attributes = response;\n attributes = this._mergeObject( attributes );\n return attributes;\n }\n};\n\n/** @class Concrete class of Generic DatasetCollectionElement */\nvar DatasetCollectionElement = Backbone.Model\n .extend( BASE_MVC.LoggableMixin )\n .extend( DatasetCollectionElementMixin )\n .extend({ _logNamespace : 'collections' });\n\n\n//==============================================================================\n/** @class Base/Abstract Backbone collection for Generic DCEs. */\nvar DCECollection = Backbone.Collection.extend( BASE_MVC.LoggableMixin ).extend(\n/** @lends DCECollection.prototype */{\n _logNamespace : 'collections',\n\n model: DatasetCollectionElement,\n\n /** String representation. */\n toString : function(){\n return ([ 'DatasetCollectionElementCollection(', this.length, ')' ].join( '' ));\n }\n});\n\n\n//==============================================================================\n/** @class Backbone model for a dataset collection element that is a dataset (HDA).\n */\nvar DatasetDCE = DATASET_MODEL.DatasetAssociation.extend( BASE_MVC.mixin( DatasetCollectionElementMixin,\n/** @lends DatasetDCE.prototype */{\n\n /** url fn */\n url : function(){\n // won't always be an hda\n if( !this.has( 'history_id' ) ){\n console.warn( 'no endpoint for non-hdas within a collection yet' );\n // (a little silly since this api endpoint *also* points at hdas)\n return Galaxy.root + 'api/datasets';\n }\n return Galaxy.root + 'api/histories/' + this.get( 'history_id' ) + '/contents/' + this.get( 'id' );\n },\n\n defaults : _.extend( {},\n DATASET_MODEL.DatasetAssociation.prototype.defaults,\n DatasetCollectionElementMixin.defaults\n ),\n\n _downloadQueryParameters : function() {\n return '?to_ext=' + this.get( 'file_ext' ) + '&hdca_id=' + this.get( 'parent_hdca_id' ) + '&element_identifier=' + this.get( 'element_identifier' );\n },\n\n // because all objects have constructors (as this hashmap would even if this next line wasn't present)\n // the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model\n // - re-apply manually for now\n /** call the mixin constructor */\n constructor : function( attributes, options ){\n this.debug( '\\t DatasetDCE.constructor:', attributes, options );\n //DATASET_MODEL.DatasetAssociation.prototype.constructor.call( this, attributes, options );\n DatasetCollectionElementMixin.constructor.call( this, attributes, options );\n },\n\n /** Does this model already contain detailed data (as opposed to just summary level data)? */\n hasDetails : function(){\n return this.elements && this.elements.length;\n },\n\n /** String representation. */\n toString : function(){\n var objStr = this.get( 'element_identifier' );\n return ([ 'DatasetDCE(', objStr, ')' ].join( '' ));\n }\n}));\n\n\n//==============================================================================\n/** @class DCECollection of DatasetDCE's (a list of datasets, a pair of datasets).\n */\nvar DatasetDCECollection = DCECollection.extend(\n/** @lends DatasetDCECollection.prototype */{\n model: DatasetDCE,\n\n /** String representation. */\n toString : function(){\n return ([ 'DatasetDCECollection(', this.length, ')' ].join( '' ));\n }\n});\n\n\n//_________________________________________________________________________________________________ COLLECTIONS\n/** @class Backbone model for Dataset Collections.\n * The DC API returns an array of JSON objects under the attribute elements.\n * This model:\n * - removes that array/attribute ('elements') from the model,\n * - creates a bbone collection (of the class defined in the 'collectionClass' attribute),\n * - passes that json onto the bbone collection\n * - caches the bbone collection in this.elements\n */\nvar DatasetCollection = Backbone.Model\n .extend( BASE_MVC.LoggableMixin )\n .extend( BASE_MVC.SearchableModelMixin )\n .extend(/** @lends DatasetCollection.prototype */{\n _logNamespace : 'collections',\n\n /** default attributes for a model */\n defaults : {\n /* 'list', 'paired', or 'list:paired' */\n collection_type : null,\n //??\n deleted : false\n },\n\n /** Which class to use for elements */\n collectionClass : DCECollection,\n\n /** set up: create elements instance var and (on changes to elements) update them */\n initialize : function( model, options ){\n this.debug( this + '(DatasetCollection).initialize:', model, options, this );\n this.elements = this._createElementsModel();\n this.on( 'change:elements', function(){\n this.log( 'change:elements' );\n //TODO: prob. better to update the collection instead of re-creating it\n this.elements = this._createElementsModel();\n });\n },\n\n /** move elements model attribute to full collection */\n _createElementsModel : function(){\n this.debug( this + '._createElementsModel', this.collectionClass, this.get( 'elements' ), this.elements );\n //TODO: same patterns as DatasetCollectionElement _createObjectModel - refactor to BASE_MVC.hasSubModel?\n var elements = this.get( 'elements' ) || [];\n this.unset( 'elements', { silent: true });\n var self = this;\n _.each(elements, function(element, index) {\n _.extend(element, {\"parent_hdca_id\": self.get(\"id\")});\n });\n this.elements = new this.collectionClass( elements );\n //this.debug( 'collectionClass:', this.collectionClass + '', this.elements );\n return this.elements;\n },\n\n // ........................................................................ common queries\n /** pass the elements back within the model json when this is serialized */\n toJSON : function(){\n var json = Backbone.Model.prototype.toJSON.call( this );\n if( this.elements ){\n json.elements = this.elements.toJSON();\n }\n return json;\n },\n\n /** Is this collection in a 'ready' state no processing (for the collection) is left\n * to do on the server.\n */\n inReadyState : function(){\n var populated = this.get( 'populated' );\n return ( this.isDeletedOrPurged() || populated );\n },\n\n //TODO:?? the following are the same interface as DatasetAssociation - can we combine?\n /** Does the DC contain any elements yet? Is a fetch() required? */\n hasDetails : function(){\n return this.elements.length !== 0;\n },\n\n /** Given the filters, what models in this.elements would be returned? */\n getVisibleContents : function( filters ){\n // filters unused for now\n return this.elements;\n },\n\n // ........................................................................ ajax\n /** override to use actual Dates objects for create/update times */\n parse : function( response, options ){\n var parsed = Backbone.Model.prototype.parse.call( this, response, options );\n if( parsed.create_time ){\n parsed.create_time = new Date( parsed.create_time );\n }\n if( parsed.update_time ){\n parsed.update_time = new Date( parsed.update_time );\n }\n return parsed;\n },\n\n /** save this dataset, _Mark_ing it as deleted (just a flag) */\n 'delete' : function( options ){\n if( this.get( 'deleted' ) ){ return jQuery.when(); }\n return this.save( { deleted: true }, options );\n },\n /** save this dataset, _Mark_ing it as undeleted */\n undelete : function( options ){\n if( !this.get( 'deleted' ) || this.get( 'purged' ) ){ return jQuery.when(); }\n return this.save( { deleted: false }, options );\n },\n\n /** Is this collection deleted or purged? */\n isDeletedOrPurged : function(){\n return ( this.get( 'deleted' ) || this.get( 'purged' ) );\n },\n\n // ........................................................................ searchable\n /** searchable attributes for collections */\n searchAttributes : [\n 'name'\n ],\n\n // ........................................................................ misc\n /** String representation */\n toString : function(){\n var idAndName = [ this.get( 'id' ), this.get( 'name' ) || this.get( 'element_identifier' ) ];\n return 'DatasetCollection(' + ( idAndName.join(',') ) + ')';\n }\n});\n\n\n//==============================================================================\n/** Model for a DatasetCollection containing datasets (non-nested).\n */\nvar ListDatasetCollection = DatasetCollection.extend(\n/** @lends ListDatasetCollection.prototype */{\n\n /** override since we know the collection will only contain datasets */\n collectionClass : DatasetDCECollection,\n\n /** String representation. */\n toString : function(){ return 'List' + DatasetCollection.prototype.toString.call( this ); }\n});\n\n\n//==============================================================================\n/** Model for a DatasetCollection containing fwd/rev datasets (a list of 2).\n */\nvar PairDatasetCollection = ListDatasetCollection.extend(\n/** @lends PairDatasetCollection.prototype */{\n\n /** String representation. */\n toString : function(){ return 'Pair' + DatasetCollection.prototype.toString.call( this ); }\n});\n\n\n//_________________________________________________________________________________________________ NESTED COLLECTIONS\n// this is where things get weird, man. Weird.\n//TODO: it might be possible to compact all the following...I think.\n//==============================================================================\n/** @class Backbone model for a Generic DatasetCollectionElement that is also a DatasetCollection\n * (a nested collection). Currently only list:paired.\n */\nvar NestedDCDCE = DatasetCollection.extend( BASE_MVC.mixin( DatasetCollectionElementMixin,\n/** @lends NestedDCDCE.prototype */{\n\n // because all objects have constructors (as this hashmap would even if this next line wasn't present)\n // the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model\n // - re-apply manually it now\n /** call the mixin constructor */\n constructor : function( attributes, options ){\n this.debug( '\\t NestedDCDCE.constructor:', attributes, options );\n DatasetCollectionElementMixin.constructor.call( this, attributes, options );\n },\n\n /** String representation. */\n toString : function(){\n var objStr = ( this.object )?( '' + this.object ):( this.get( 'element_identifier' ) );\n return ([ 'NestedDCDCE(', objStr, ')' ].join( '' ));\n }\n}));\n\n\n//==============================================================================\n/** @class Backbone collection containing Generic NestedDCDCE's (nested dataset collections).\n */\nvar NestedDCDCECollection = DCECollection.extend(\n/** @lends NestedDCDCECollection.prototype */{\n\n /** This is a collection of nested collections */\n model: NestedDCDCE,\n\n /** String representation. */\n toString : function(){\n return ([ 'NestedDCDCECollection(', this.length, ')' ].join( '' ));\n }\n});\n\n\n//==============================================================================\n/** @class Backbone model for a paired dataset collection within a list:paired dataset collection.\n */\nvar NestedPairDCDCE = PairDatasetCollection.extend( BASE_MVC.mixin( DatasetCollectionElementMixin,\n/** @lends NestedPairDCDCE.prototype */{\n//TODO:?? possibly rename to NestedDatasetCollection?\n\n // because all objects have constructors (as this hashmap would even if this next line wasn't present)\n // the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model\n // - re-apply manually it now\n /** This is both a collection and a collection element - call the constructor */\n constructor : function( attributes, options ){\n this.debug( '\\t NestedPairDCDCE.constructor:', attributes, options );\n //DatasetCollection.constructor.call( this, attributes, options );\n DatasetCollectionElementMixin.constructor.call( this, attributes, options );\n },\n\n /** String representation. */\n toString : function(){\n var objStr = ( this.object )?( '' + this.object ):( this.get( 'element_identifier' ) );\n return ([ 'NestedPairDCDCE(', objStr, ')' ].join( '' ));\n }\n}));\n\n\n//==============================================================================\n/** @class Backbone collection for a backbone collection containing paired dataset collections.\n */\nvar NestedPairDCDCECollection = NestedDCDCECollection.extend(\n/** @lends PairDCDCECollection.prototype */{\n\n /** We know this collection is composed of only nested pair collections */\n model: NestedPairDCDCE,\n\n /** String representation. */\n toString : function(){\n return ([ 'NestedPairDCDCECollection(', this.length, ')' ].join( '' ));\n }\n});\n\n\n//==============================================================================\n/** @class Backbone Model for a DatasetCollection (list) that contains DatasetCollections (pairs).\n */\nvar ListPairedDatasetCollection = DatasetCollection.extend(\n/** @lends ListPairedDatasetCollection.prototype */{\n\n /** list:paired is the only collection that itself contains collections */\n collectionClass : NestedPairDCDCECollection,\n\n /** String representation. */\n toString : function(){\n return ([ 'ListPairedDatasetCollection(', this.get( 'name' ), ')' ].join( '' ));\n }\n});\n\n\n//==============================================================================\n/** @class Backbone model for a list dataset collection within a list:list dataset collection. */\nvar NestedListDCDCE = ListDatasetCollection.extend( BASE_MVC.mixin( DatasetCollectionElementMixin,\n/** @lends NestedListDCDCE.prototype */{\n\n /** This is both a collection and a collection element - call the constructor */\n constructor : function( attributes, options ){\n this.debug( '\\t NestedListDCDCE.constructor:', attributes, options );\n DatasetCollectionElementMixin.constructor.call( this, attributes, options );\n },\n\n /** String representation. */\n toString : function(){\n var objStr = ( this.object )?( '' + this.object ):( this.get( 'element_identifier' ) );\n return ([ 'NestedListDCDCE(', objStr, ')' ].join( '' ));\n }\n}));\n\n\n//==============================================================================\n/** @class Backbone collection containing list dataset collections. */\nvar NestedListDCDCECollection = NestedDCDCECollection.extend({\n\n /** We know this collection is composed of only nested pair collections */\n model: NestedListDCDCE,\n\n /** String representation. */\n toString : function(){\n return ([ 'NestedListDCDCECollection(', this.length, ')' ].join( '' ));\n }\n});\n\n\n//==============================================================================\n/** @class Backbone Model for a DatasetCollection (list) that contains other lists. */\nvar ListOfListsDatasetCollection = DatasetCollection.extend({\n\n /** list:paired is the only collection that itself contains collections */\n collectionClass : NestedListDCDCECollection,\n\n /** String representation. */\n toString : function(){\n return ([ 'ListOfListsDatasetCollection(', this.get( 'name' ), ')' ].join( '' ));\n }\n});\n\n\n//==============================================================================\n return {\n ListDatasetCollection : ListDatasetCollection,\n PairDatasetCollection : PairDatasetCollection,\n ListPairedDatasetCollection : ListPairedDatasetCollection,\n ListOfListsDatasetCollection: ListOfListsDatasetCollection\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/collection/collection-model.js","\ndefine([\n \"mvc/history/hdca-model\",\n \"mvc/dataset/states\",\n \"mvc/base-mvc\",\n \"mvc/collection/base-creator\",\n \"mvc/ui/ui-modal\",\n \"utils/natural-sort\",\n \"utils/localization\",\n \"ui/hoverhighlight\"\n], function( HDCA, STATES, BASE_MVC, baseCreator, UI_MODAL, naturalSort, _l ){\n\n'use strict';\n\nvar logNamespace = 'collections';\n\n/*==============================================================================\nTODO:\n use proper Element model and not just json\n straighten out createFn, collection.createHDCA\n possibly stop using modals for this\n It would be neat to do a drag and drop\n\n==============================================================================*/\n/** A view for both DatasetDCEs and NestedDCDCEs\n * (things that implement collection-model:DatasetCollectionElementMixin)\n */\nvar DatasetCollectionElementView = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend({\n _logNamespace : logNamespace,\n\n//TODO: use proper class (DatasetDCE or NestedDCDCE (or the union of both))\n tagName : 'li',\n className : 'collection-element',\n\n initialize : function( attributes ){\n this.element = attributes.element || {};\n this.selected = attributes.selected || false;\n },\n\n render : function(){\n this.$el\n .attr( 'data-element-id', this.element.id )\n .attr( 'draggable', true )\n .html( this.template({ element: this.element }) );\n if( this.selected ){\n this.$el.addClass( 'selected' );\n }\n return this;\n },\n\n //TODO: lots of unused space in the element - possibly load details and display them horiz.\n template : _.template([\n '',\n '<%- element.name %>',\n '',\n '',\n ].join('')),\n\n /** select this element and pub */\n select : function( toggle ){\n this.$el.toggleClass( 'selected', toggle );\n this.trigger( 'select', {\n source : this,\n selected : this.$el.hasClass( 'selected' )\n });\n },\n\n /** animate the removal of this element and pub */\n discard : function(){\n var view = this,\n parentWidth = this.$el.parent().width();\n this.$el.animate({ 'margin-right' : parentWidth }, 'fast', function(){\n view.trigger( 'discard', {\n source : view\n });\n view.destroy();\n });\n },\n\n /** remove the DOM and any listeners */\n destroy : function(){\n this.off();\n this.$el.remove();\n },\n\n events : {\n 'click' : '_click',\n 'click .name' : '_clickName',\n 'click .discard': '_clickDiscard',\n\n 'dragstart' : '_dragstart',\n 'dragend' : '_dragend',\n 'dragover' : '_sendToParent',\n 'drop' : '_sendToParent'\n },\n\n /** select when the li is clicked */\n _click : function( ev ){\n ev.stopPropagation();\n this.select( ev );\n },\n\n /** rename a pair when the name is clicked */\n _clickName : function( ev ){\n ev.stopPropagation();\n ev.preventDefault();\n var promptString = [ _l( 'Enter a new name for the element' ), ':\\n(',\n _l( 'Note that changing the name here will not rename the dataset' ), ')' ].join( '' ),\n response = prompt( _l( 'Enter a new name for the element' ) + ':', this.element.name );\n if( response ){\n this.element.name = response;\n this.render();\n }\n //TODO: cancelling with ESC leads to closure of the creator...\n },\n\n /** discard when the discard button is clicked */\n _clickDiscard : function( ev ){\n ev.stopPropagation();\n this.discard();\n },\n\n /** dragging pairs for re-ordering */\n _dragstart : function( ev ){\n if( ev.originalEvent ){ ev = ev.originalEvent; }\n ev.dataTransfer.effectAllowed = 'move';\n ev.dataTransfer.setData( 'text/plain', JSON.stringify( this.element ) );\n\n this.$el.addClass( 'dragging' );\n this.$el.parent().trigger( 'collection-element.dragstart', [ this ] );\n },\n\n /** dragging for re-ordering */\n _dragend : function( ev ){\n this.$el.removeClass( 'dragging' );\n this.$el.parent().trigger( 'collection-element.dragend', [ this ] );\n },\n\n /** manually bubble up an event to the parent/container */\n _sendToParent : function( ev ){\n this.$el.parent().trigger( ev );\n },\n\n /** string rep */\n toString : function(){\n return 'DatasetCollectionElementView()';\n }\n});\n\n\n// ============================================================================\n/** An interface for building collections.\n */\nvar ListCollectionCreator = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend( baseCreator.CollectionCreatorMixin ).extend({\n _logNamespace : logNamespace,\n\n /** the class used to display individual elements */\n elementViewClass : DatasetCollectionElementView,\n /** the class this creator will create and save */\n collectionClass : HDCA.HistoryListDatasetCollection,\n className : 'list-collection-creator collection-creator flex-row-container',\n\n /** minimum number of valid elements to start with in order to build a collection of this type */\n minElements : 1,\n\n defaultAttributes : {\n//TODO: remove - use new collectionClass().save()\n /** takes elements and creates the proper collection - returns a promise */\n creationFn : function(){ throw new TypeError( 'no creation fn for creator' ); },\n /** fn to call when the collection is created (scoped to this) */\n oncreate : function(){},\n /** fn to call when the cancel button is clicked (scoped to this) - if falsy, no btn is displayed */\n oncancel : function(){},\n /** distance from list edge to begin autoscrolling list */\n autoscrollDist : 24,\n /** Color passed to hoverhighlight */\n highlightClr : 'rgba( 64, 255, 255, 1.0 )'\n },\n\n footerSettings : {\n '.hide-originals': 'hideOriginals'\n },\n\n /** set up initial options, instance vars, behaviors */\n initialize : function( attributes ){\n this.metric( 'ListCollectionCreator.initialize', attributes );\n var creator = this;\n _.each( this.defaultAttributes, function( value, key ){\n value = attributes[ key ] || value;\n creator[ key ] = value;\n });\n\n /** unordered, original list - cache to allow reversal */\n creator.initialElements = attributes.elements || [];\n\n this._setUpCommonSettings( attributes );\n this._instanceSetUp();\n this._elementsSetUp();\n this._setUpBehaviors();\n },\n\n /** set up instance vars */\n _instanceSetUp : function(){\n /** Ids of elements that have been selected by the user - to preserve over renders */\n this.selectedIds = {};\n /** DOM elements currently being dragged */\n this.$dragging = null;\n /** Used for blocking UI events during ajax/operations (don't post twice) */\n this.blocking = false;\n },\n\n // ------------------------------------------------------------------------ process raw list\n /** set up main data */\n _elementsSetUp : function(){\n //this.debug( '-- _dataSetUp' );\n /** a list of invalid elements and the reasons they aren't valid */\n this.invalidElements = [];\n//TODO: handle fundamental problem of syncing DOM, views, and list here\n /** data for list in progress */\n this.workingElements = [];\n /** views for workingElements */\n this.elementViews = [];\n\n // copy initial list, sort, add ids if needed\n this.workingElements = this.initialElements.slice( 0 );\n this._ensureElementIds();\n this._validateElements();\n this._mangleDuplicateNames();\n this._sortElements();\n },\n\n /** add ids to dataset objs in initial list if none */\n _ensureElementIds : function(){\n this.workingElements.forEach( function( element ){\n if( !element.hasOwnProperty( 'id' ) ){\n element.id = _.uniqueId();\n }\n });\n return this.workingElements;\n },\n\n /** separate working list into valid and invalid elements for this collection */\n _validateElements : function(){\n var creator = this,\n existingNames = {};\n creator.invalidElements = [];\n\n this.workingElements = this.workingElements.filter( function( element ){\n var problem = creator._isElementInvalid( element );\n if( problem ){\n creator.invalidElements.push({\n element : element,\n text : problem\n });\n }\n return !problem;\n });\n return this.workingElements;\n },\n\n /** describe what is wrong with a particular element if anything */\n _isElementInvalid : function( element ){\n if( element.history_content_type !== 'dataset' ){\n return _l( \"is not a dataset\" );\n }\n var validState = element.state === STATES.OK || _.contains( STATES.NOT_READY_STATES, element.state );\n if( ! validState ){\n return _l( \"has errored, is paused, or is not accessible\" );\n }\n if( element.deleted || element.purged ){\n return _l( \"has been deleted or purged\" );\n }\n return null;\n },\n\n /** mangle duplicate names using a mac-like '(counter)' addition to any duplicates */\n _mangleDuplicateNames : function(){\n var SAFETY = 900,\n counter = 1,\n existingNames = {};\n this.workingElements.forEach( function( element ){\n var currName = element.name;\n while( existingNames.hasOwnProperty( currName ) ){\n currName = element.name + ' (' + counter + ')';\n counter += 1;\n if( counter >= SAFETY ){\n throw new Error( 'Safety hit in while loop - thats impressive' );\n }\n }\n element.name = currName;\n existingNames[ element.name ] = true;\n });\n },\n\n /** sort a list of elements */\n _sortElements : function( list ){\n // // currently only natural sort by name\n // this.workingElements.sort( function( a, b ){ return naturalSort( a.name, b.name ); });\n // return this.workingElements;\n },\n\n // ------------------------------------------------------------------------ rendering\n // templates : ListCollectionCreator.templates,\n /** render the entire interface */\n render : function( speed, callback ){\n //this.debug( '-- _render' );\n if( this.workingElements.length < this.minElements ){\n return this._renderInvalid( speed, callback );\n }\n\n this.$el.empty().html( this.templates.main() );\n this._renderHeader( speed );\n this._renderMiddle( speed );\n this._renderFooter( speed );\n this._addPluginComponents();\n this.$( '.collection-name' ).focus();\n this.trigger( 'rendered', this );\n return this;\n },\n\n\n /** render a simplified interface aimed at telling the user why they can't move forward */\n _renderInvalid : function( speed, callback ){\n //this.debug( '-- _render' );\n this.$el.empty().html( this.templates.invalidInitial({\n problems: this.invalidElements,\n elements: this.workingElements,\n }));\n if( typeof this.oncancel === 'function' ){\n this.$( '.cancel-create.btn' ).show();\n }\n this.trigger( 'rendered', this );\n return this;\n },\n\n /** render the header section */\n _renderHeader : function( speed, callback ){\n var $header = this.$( '.header' ).empty().html( this.templates.header() )\n .find( '.help-content' ).prepend( $( this.templates.helpContent() ) );\n //TODO: should only show once despite calling _renderHeader again\n if( this.invalidElements.length ){\n this._invalidElementsAlert();\n }\n return $header;\n },\n\n /** render the middle including the elements */\n _renderMiddle : function( speed, callback ){\n var $middle = this.$( '.middle' ).empty().html( this.templates.middle() );\n this._renderList( speed );\n return $middle;\n },\n\n /** add any jQuery/bootstrap/custom plugins to elements rendered */\n _addPluginComponents : function(){\n this.$( '.help-content i' ).hoverhighlight( '.collection-creator', this.highlightClr );\n },\n\n /** build and show an alert describing any elements that could not be included due to problems */\n _invalidElementsAlert : function(){\n this._showAlert( this.templates.invalidElements({ problems: this.invalidElements }), 'alert-warning' );\n },\n\n _disableNameAndCreate : function( disable ){\n disable = !_.isUndefined( disable )? disable : true;\n if( disable ){\n this.$( '.collection-name' ).prop( 'disabled', true );\n this.$( '.create-collection' ).toggleClass( 'disabled', true );\n // } else {\n // this.$( '.collection-name' ).prop( 'disabled', false );\n // this.$( '.create-collection' ).removeClass( 'disable' );\n }\n },\n\n // ------------------------------------------------------------------------ rendering elements\n /** conv. to the main list display DOM */\n $list : function(){\n return this.$( '.collection-elements' );\n },\n\n /** show or hide the clear selected control based on the num of selected elements */\n _renderClearSelected : function(){\n if( _.size( this.selectedIds ) ){\n this.$( '.collection-elements-controls > .clear-selected' ).show();\n } else {\n this.$( '.collection-elements-controls > .clear-selected' ).hide();\n }\n },\n\n /** render the elements in order (or a warning if no elements found) */\n _renderList : function( speed, callback ){\n //this.debug( '-- _renderList' );\n var creator = this,\n $tmp = jQuery( '' ),\n $list = creator.$list();\n\n _.each( this.elementViews, function( view ){\n view.destroy();\n creator.removeElementView( view );\n });\n\n // if( !this.workingElements.length ){\n // this._renderNoValidElements();\n // return;\n // }\n\n creator.workingElements.forEach( function( element ){\n var elementView = creator._createElementView( element );\n $tmp.append( elementView.$el );\n });\n\n creator._renderClearSelected();\n $list.empty().append( $tmp.children() );\n _.invoke( creator.elementViews, 'render' );\n\n if( $list.height() > $list.css( 'max-height' ) ){\n $list.css( 'border-width', '1px 0px 1px 0px' );\n } else {\n $list.css( 'border-width', '0px' );\n }\n },\n\n /** create an element view, cache in elementViews, set up listeners, and return */\n _createElementView : function( element ){\n var elementView = new this.elementViewClass({\n//TODO: use non-generic class or not all\n // model : COLLECTION.DatasetDCE( element )\n element : element,\n selected: _.has( this.selectedIds, element.id )\n });\n this.elementViews.push( elementView );\n this._listenToElementView( elementView );\n return elementView;\n },\n\n /** listen to any element events */\n _listenToElementView : function( view ){\n var creator = this;\n creator.listenTo( view, {\n select : function( data ){\n var element = data.source.element;\n if( data.selected ){\n creator.selectedIds[ element.id ] = true;\n } else {\n delete creator.selectedIds[ element.id ];\n }\n creator.trigger( 'elements:select', data );\n },\n discard : function( data ){\n creator.trigger( 'elements:discard', data );\n }\n });\n },\n\n /** add a new element view based on the json in element */\n addElementView : function( element ){\n//TODO: workingElements is sorted, add element in appropo index\n // add element, sort elements, find element index\n // var view = this._createElementView( element );\n // return view;\n },\n\n /** stop listening to view and remove from caches */\n removeElementView : function( view ){\n delete this.selectedIds[ view.element.id ];\n this._renderClearSelected();\n\n this.elementViews = _.without( this.elementViews, view );\n this.stopListening( view );\n },\n\n /** render a message in the list that no elements remain to create a collection */\n _renderNoElementsLeft : function(){\n this._disableNameAndCreate( true );\n this.$( '.collection-elements' ).append( this.templates.noElementsLeft() );\n },\n\n // /** render a message in the list that no valid elements were found to create a collection */\n // _renderNoValidElements : function(){\n // this._disableNameAndCreate( true );\n // this.$( '.collection-elements' ).append( this.templates.noValidElements() );\n // },\n\n // ------------------------------------------------------------------------ API\n /** convert element into JSON compatible with the collections API */\n _elementToJSON : function( element ){\n // return element.toJSON();\n return element;\n },\n\n /** create the collection via the API\n * @returns {jQuery.xhr Object} the jquery ajax request\n */\n createList : function( name ){\n if( !this.workingElements.length ){\n var message = _l( 'No valid elements for final list' ) + '. ';\n message += '' + _l( 'Cancel' ) + ' ';\n message += _l( 'or' );\n message += ' ' + _l( 'start over' ) + '.';\n this._showAlert( message );\n return;\n }\n\n var creator = this,\n elements = this.workingElements.map( function( element ){\n return creator._elementToJSON( element );\n });\n\n creator.blocking = true;\n return creator.creationFn( elements, name, creator.hideOriginals )\n .always( function(){\n creator.blocking = false;\n })\n .fail( function( xhr, status, message ){\n creator.trigger( 'error', {\n xhr : xhr,\n status : status,\n message : _l( 'An error occurred while creating this collection' )\n });\n })\n .done( function( response, message, xhr ){\n creator.trigger( 'collection:created', response, message, xhr );\n creator.metric( 'collection:created', response );\n if( typeof creator.oncreate === 'function' ){\n creator.oncreate.call( this, response, message, xhr );\n }\n });\n },\n\n // ------------------------------------------------------------------------ events\n /** set up event handlers on self */\n _setUpBehaviors : function(){\n this.on( 'error', this._errorHandler );\n\n this.once( 'rendered', function(){\n this.trigger( 'rendered:initial', this );\n });\n\n this.on( 'elements:select', function( data ){\n this._renderClearSelected();\n });\n\n this.on( 'elements:discard', function( data ){\n var element = data.source.element;\n this.removeElementView( data.source );\n\n this.workingElements = _.without( this.workingElements, element );\n if( !this.workingElements.length ){\n this._renderNoElementsLeft();\n }\n });\n\n //this.on( 'all', function(){\n // this.info( arguments );\n //});\n return this;\n },\n\n /** handle errors with feedback and details to the user (if available) */\n _errorHandler : function( data ){\n this.error( data );\n\n var creator = this;\n content = data.message || _l( 'An error occurred' );\n if( data.xhr ){\n var xhr = data.xhr,\n message = data.message;\n if( xhr.readyState === 0 && xhr.status === 0 ){\n content += ': ' + _l( 'Galaxy could not be reached and may be updating.' ) +\n _l( ' Try again in a few minutes.' );\n } else if( xhr.responseJSON ){\n content += ':
' + JSON.stringify( xhr.responseJSON ) + '
';\n } else {\n content += ': ' + message;\n }\n }\n creator._showAlert( content, 'alert-danger' );\n },\n\n events : {\n // header\n 'click .more-help' : '_clickMoreHelp',\n 'click .less-help' : '_clickLessHelp',\n 'click .main-help' : '_toggleHelp',\n 'click .header .alert button' : '_hideAlert',\n\n 'click .reset' : 'reset',\n 'click .clear-selected' : 'clearSelectedElements',\n\n // elements - selection\n 'click .collection-elements' : 'clearSelectedElements',\n\n // elements - drop target\n // 'dragenter .collection-elements': '_dragenterElements',\n // 'dragleave .collection-elements': '_dragleaveElements',\n 'dragover .collection-elements' : '_dragoverElements',\n 'drop .collection-elements' : '_dropElements',\n\n // these bubble up from the elements as custom events\n 'collection-element.dragstart .collection-elements' : '_elementDragstart',\n 'collection-element.dragend .collection-elements' : '_elementDragend',\n\n // footer\n 'change .collection-name' : '_changeName',\n 'keydown .collection-name' : '_nameCheckForEnter',\n 'change .hide-originals' : '_changeHideOriginals',\n 'click .cancel-create' : '_cancelCreate',\n 'click .create-collection' : '_clickCreate'//,\n },\n\n // ........................................................................ elements\n /** reset all data to the initial state */\n reset : function(){\n this._instanceSetUp();\n this._elementsSetUp();\n this.render();\n },\n\n /** deselect all elements */\n clearSelectedElements : function( ev ){\n this.$( '.collection-elements .collection-element' ).removeClass( 'selected' );\n this.$( '.collection-elements-controls > .clear-selected' ).hide();\n },\n\n //_dragenterElements : function( ev ){\n // //this.debug( '_dragenterElements:', ev );\n //},\n//TODO: if selected are dragged out of the list area - remove the placeholder - cuz it won't work anyway\n // _dragleaveElements : function( ev ){\n // //this.debug( '_dragleaveElements:', ev );\n // },\n\n /** track the mouse drag over the list adding a placeholder to show where the drop would occur */\n _dragoverElements : function( ev ){\n //this.debug( '_dragoverElements:', ev );\n ev.preventDefault();\n\n var $list = this.$list();\n this._checkForAutoscroll( $list, ev.originalEvent.clientY );\n var $nearest = this._getNearestElement( ev.originalEvent.clientY );\n\n //TODO: no need to re-create - move instead\n this.$( '.element-drop-placeholder' ).remove();\n var $placeholder = $( '' );\n if( !$nearest.length ){\n $list.append( $placeholder );\n } else {\n $nearest.before( $placeholder );\n }\n },\n\n /** If the mouse is near enough to the list's top or bottom, scroll the list */\n _checkForAutoscroll : function( $element, y ){\n var AUTOSCROLL_SPEED = 2,\n offset = $element.offset(),\n scrollTop = $element.scrollTop(),\n upperDist = y - offset.top,\n lowerDist = ( offset.top + $element.outerHeight() ) - y;\n if( upperDist >= 0 && upperDist < this.autoscrollDist ){\n $element.scrollTop( scrollTop - AUTOSCROLL_SPEED );\n } else if( lowerDist >= 0 && lowerDist < this.autoscrollDist ){\n $element.scrollTop( scrollTop + AUTOSCROLL_SPEED );\n }\n },\n\n /** get the nearest element based on the mouse's Y coordinate.\n * If the y is at the end of the list, return an empty jQuery object.\n */\n _getNearestElement : function( y ){\n var WIGGLE = 4,\n lis = this.$( '.collection-elements li.collection-element' ).toArray();\n for( var i=0; i y && top - halfHeight < y ){\n return $li;\n }\n }\n return $();\n },\n\n /** drop (dragged/selected elements) onto the list, re-ordering the internal list */\n _dropElements : function( ev ){\n if( ev.originalEvent ){ ev = ev.originalEvent; }\n // both required for firefox\n ev.preventDefault();\n ev.dataTransfer.dropEffect = 'move';\n\n // insert before the nearest element or after the last.\n var $nearest = this._getNearestElement( ev.clientY );\n if( $nearest.length ){\n this.$dragging.insertBefore( $nearest );\n } else {\n // no nearest before - insert after last element\n this.$dragging.insertAfter( this.$( '.collection-elements .collection-element' ).last() );\n }\n // resync the creator's list based on the new DOM order\n this._syncOrderToDom();\n return false;\n },\n\n /** resync the creator's list of elements based on the DOM order */\n _syncOrderToDom : function(){\n var creator = this,\n newElements = [];\n //TODO: doesn't seem wise to use the dom to store these - can't we sync another way?\n this.$( '.collection-elements .collection-element' ).each( function(){\n var id = $( this ).attr( 'data-element-id' ),\n element = _.findWhere( creator.workingElements, { id: id });\n if( element ){\n newElements.push( element );\n } else {\n console.error( 'missing element: ', id );\n }\n });\n this.workingElements = newElements;\n this._renderList();\n },\n\n /** drag communication with element sub-views: dragstart */\n _elementDragstart : function( ev, element ){\n // auto select the element causing the event and move all selected\n element.select( true );\n this.$dragging = this.$( '.collection-elements .collection-element.selected' );\n },\n\n /** drag communication with element sub-views: dragend - remove the placeholder */\n _elementDragend : function( ev, element ){\n $( '.element-drop-placeholder' ).remove();\n this.$dragging = null;\n },\n\n // ------------------------------------------------------------------------ templates\n //TODO: move to require text plugin and load these as text\n //TODO: underscore currently unnecc. bc no vars are used\n //TODO: better way of localizing text-nodes in long strings\n /** underscore template fns attached to class */\n templates : _.extend({}, baseCreator.CollectionCreatorMixin._creatorTemplates, {\n\n /** the header (not including help text) */\n header : _.template([\n '
'\n ].join('')),\n\n /** help content */\n helpContent : _.template([\n '
', _l([\n 'Collections of datasets are permanent, ordered lists of datasets that can be passed to tools and ',\n 'workflows in order to have analyses done on each member of the entire group. This interface allows ',\n 'you to create a collection and re-order the final collection.'\n ].join( '' )), '
',\n '
',\n '
', _l([\n 'Rename elements in the list by clicking on ',\n 'the existing name.'\n ].join( '' )), '
',\n '
', _l([\n 'Discard elements from the final created list by clicking on the ',\n '\"Discard\" button.'\n ].join( '' )), '
',\n '
', _l([\n 'Reorder the list by clicking and dragging elements. Select multiple elements by clicking on ',\n 'them and you can then move those selected by dragging the ',\n 'entire group. Deselect them by clicking them again or by clicking the ',\n 'the \"Clear selected\" link.'\n ].join( '' )), '
',\n '
', _l([\n 'Click the \"Start over\" link to begin again as if you had just opened ',\n 'the interface.'\n ].join( '' )), '
',\n '
', _l([\n 'Click the \"Cancel\" button to exit the interface.'\n ].join( '' )), '
',\n '
',\n '
', _l([\n 'Once your collection is complete, enter a name and ',\n 'click \"Create list\".'\n ].join( '' )), '
'\n ].join('')),\n\n /** shown in list when all elements are discarded */\n invalidElements : _.template([\n _l( 'The following selections could not be included due to problems:' ),\n '
<% _.each( problems, function( problem ){ %>',\n '
<%- problem.element.name %>: <%- problem.text %>
',\n '<% }); %>
'\n ].join('')),\n\n /** shown in list when all elements are discarded */\n noElementsLeft : _.template([\n '
'\n ].join('')),\n\n /** a simplified page communicating what went wrong and why the user needs to reselect something else */\n invalidInitial : _.template([\n '
',\n '
',\n '',\n '<% if( _.size( problems ) ){ %>',\n _l( 'The following selections could not be included due to problems' ), ':',\n '
<% _.each( problems, function( problem ){ %>',\n '
<%- problem.element.name %>: <%- problem.text %>
',\n '<% }); %>
',\n '<% } else if( _.size( elements ) < 1 ){ %>',\n _l( 'No datasets were selected' ), '.',\n '<% } %>',\n ' ',\n _l( 'At least one element is needed for the collection' ), '. ',\n _l( 'You may need to ' ),\n '', _l( 'cancel' ), ' ',\n _l( 'and reselect new elements' ), '.',\n '',\n '
',\n '
',\n ''\n ].join('')),\n }),\n\n // ------------------------------------------------------------------------ misc\n /** string rep */\n toString : function(){ return 'ListCollectionCreator'; }\n});\n\n\n\n//=============================================================================\n/** Create a modal and load its body with the given CreatorClass creator type\n * @returns {Deferred} resolved when creator has built a collection.\n */\nvar collectionCreatorModal = function _collectionCreatorModal( elements, options, CreatorClass ){\n\n var deferred = jQuery.Deferred(),\n modal = Galaxy.modal || ( new UI_MODAL.View() ),\n creator;\n\n options = _.defaults( options || {}, {\n elements : elements,\n oncancel : function(){\n modal.hide();\n deferred.reject( 'cancelled' );\n },\n oncreate : function( creator, response ){\n modal.hide();\n deferred.resolve( response );\n }\n });\n\n creator = new CreatorClass( options );\n modal.show({\n title : options.title || _l( 'Create a collection' ),\n body : creator.$el,\n width : '80%',\n height : '100%',\n closing_events: true\n });\n creator.render();\n window._collectionCreator = creator;\n\n //TODO: remove modal header\n return deferred;\n};\n\n/** List collection flavor of collectionCreatorModal. */\nvar listCollectionCreatorModal = function _listCollectionCreatorModal( elements, options ){\n options = options || {};\n options.title = _l( 'Create a collection from a list of datasets' );\n return collectionCreatorModal( elements, options, ListCollectionCreator );\n};\n\n\n//==============================================================================\n/** Use a modal to create a list collection, then add it to the given history contents.\n * @returns {Deferred} resolved when the collection is added to the history.\n */\nfunction createListCollection( contents, defaultHideSourceItems ){\n var elements = contents.toJSON(),\n promise = listCollectionCreatorModal( elements, {\n defaultHideSourceItems: defaultHideSourceItems,\n creationFn : function( elements, name, hideSourceItems ){\n elements = elements.map( function( element ){\n return {\n id : element.id,\n name : element.name,\n //TODO: this allows for list:list even if the filter above does not - reconcile\n src : ( element.history_content_type === 'dataset'? 'hda' : 'hdca' )\n };\n });\n return contents.createHDCA( elements, 'list', name, hideSourceItems );\n }\n });\n return promise;\n}\n\n//==============================================================================\n return {\n DatasetCollectionElementView: DatasetCollectionElementView,\n ListCollectionCreator : ListCollectionCreator,\n\n collectionCreatorModal : collectionCreatorModal,\n listCollectionCreatorModal : listCollectionCreatorModal,\n createListCollection : createListCollection\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/collection/list-collection-creator.js","define([\n \"mvc/list/list-item\",\n \"mvc/dataset/states\",\n \"ui/fa-icon-button\",\n \"mvc/base-mvc\",\n \"utils/localization\"\n], function( LIST_ITEM, STATES, faIconButton, BASE_MVC, _l ){\n'use strict';\n\nvar logNamespace = 'dataset';\n/*==============================================================================\nTODO:\n straighten out state rendering and templates used\n inaccessible/STATES.NOT_VIEWABLE is a special case\n simplify button rendering\n\n==============================================================================*/\nvar _super = LIST_ITEM.ListItemView;\n/** @class Read only list view for either LDDAs, HDAs, or HDADCEs.\n * Roughly, any DatasetInstance (and not a raw Dataset).\n */\nvar DatasetListItemView = _super.extend(\n/** @lends DatasetListItemView.prototype */{\n _logNamespace : logNamespace,\n\n className : _super.prototype.className + \" dataset\",\n //TODO:?? doesn't exactly match an hda's type_id\n id : function(){\n return [ 'dataset', this.model.get( 'id' ) ].join( '-' );\n },\n\n /** Set up: instance vars, options, and event handlers */\n initialize : function( attributes ){\n if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; }\n this.log( this + '.initialize:', attributes );\n _super.prototype.initialize.call( this, attributes );\n\n /** where should pages from links be displayed? (default to new tab/window) */\n this.linkTarget = attributes.linkTarget || '_blank';\n },\n\n /** event listeners */\n _setUpListeners : function(){\n _super.prototype._setUpListeners.call( this );\n var self = this;\n\n // re-rendering on any model changes\n return self.listenTo( self.model, {\n 'change': function( model ){\n // if the model moved into the ready state and is expanded without details, fetch those details now\n if( self.model.changedAttributes().state &&\n self.model.inReadyState() &&\n self.expanded &&\n !self.model.hasDetails() ){\n // normally, will render automatically (due to fetch -> change),\n // but! setting_metadata sometimes doesn't cause any other changes besides state\n // so, not rendering causes it to seem frozen in setting_metadata state\n self.model.fetch({ silent : true })\n .done( function(){ self.render(); });\n } else {\n if( _.has( model.changed, 'tags' ) && _.keys( model.changed ).length === 1 ){\n // If only the tags have changed, rerender specifically\n // the titlebar region. Otherwise default to the full\n // render.\n self.$( '.nametags' ).html( self._renderNametags() );\n } else {\n self.render();\n }\n }\n }\n });\n },\n\n // ......................................................................... expandable\n /** In this override, only get details if in the ready state, get rerunnable if in other states.\n * Note: fetch with no 'change' event triggering to prevent automatic rendering.\n */\n _fetchModelDetails : function(){\n var view = this;\n if( view.model.inReadyState() && !view.model.hasDetails() ){\n return view.model.fetch({ silent: true });\n }\n return jQuery.when();\n },\n\n // ......................................................................... removal\n /** Remove this view's html from the DOM and remove all event listeners.\n * @param {Number or String} speed jq effect speed\n * @param {Function} callback an optional function called when removal is done (scoped to this view)\n */\n remove : function( speed, callback ){\n var view = this;\n speed = speed || this.fxSpeed;\n this.$el.fadeOut( speed, function(){\n Backbone.View.prototype.remove.call( view );\n if( callback ){ callback.call( view ); }\n });\n },\n\n // ......................................................................... rendering\n /* TODO:\n dataset states are the issue primarily making dataset rendering complex\n each state should have it's own way of displaying/set of details\n often with different actions that can be applied\n throw in deleted/purged/visible and things get complicated easily\n I've considered (a couple of times) - creating a view for each state\n - but recreating the view during an update...seems wrong\n */\n /** In this override, add the dataset state as a class for use with state-based CSS */\n _swapNewRender : function( $newRender ){\n _super.prototype._swapNewRender.call( this, $newRender );\n if( this.model.has( 'state' ) ){\n this.$el.addClass( 'state-' + this.model.get( 'state' ) );\n }\n return this.$el;\n },\n\n // ................................................................................ titlebar\n /** In this override, add the dataset display button. */\n _renderPrimaryActions : function(){\n // render just the display for read-only\n return [ this._renderDisplayButton() ];\n },\n\n /** Render icon-button to display dataset data */\n _renderDisplayButton : function(){\n // don't show display if not viewable or not accessible\n var state = this.model.get( 'state' );\n if( ( state === STATES.NOT_VIEWABLE ) ||\n ( state === STATES.DISCARDED ) ||\n ( !this.model.get( 'accessible' ) ) ){\n return null;\n }\n\n var displayBtnData = {\n target : this.linkTarget,\n classes : 'display-btn'\n };\n\n // show a disabled display if the data's been purged\n if( this.model.get( 'purged' ) ){\n displayBtnData.disabled = true;\n displayBtnData.title = _l( 'Cannot display datasets removed from disk' );\n\n // disable if still uploading\n } else if( state === STATES.UPLOAD ){\n displayBtnData.disabled = true;\n displayBtnData.title = _l( 'This dataset must finish uploading before it can be viewed' );\n\n // disable if still new\n } else if( state === STATES.NEW ){\n displayBtnData.disabled = true;\n displayBtnData.title = _l( 'This dataset is not yet viewable' );\n\n } else {\n displayBtnData.title = _l( 'View data' );\n\n // default link for dataset\n displayBtnData.href = this.model.urls.display;\n\n // add frame manager option onclick event\n var self = this;\n displayBtnData.onclick = function( ev ){\n if (Galaxy.frame && Galaxy.frame.active) {\n // Add dataset to frames.\n Galaxy.frame.addDataset(self.model.get('id'));\n ev.preventDefault();\n }\n };\n }\n displayBtnData.faIcon = 'fa-eye';\n return faIconButton( displayBtnData );\n },\n\n // ......................................................................... rendering details\n /** Render the enclosing div of the hda body and, if expanded, the html in the body\n * @returns {jQuery} rendered DOM\n */\n _renderDetails : function(){\n //TODO: generalize to be allow different details for each state\n\n // no access - render nothing but a message\n if( this.model.get( 'state' ) === STATES.NOT_VIEWABLE ){\n return $( this.templates.noAccess( this.model.toJSON(), this ) );\n }\n\n var $details = _super.prototype._renderDetails.call( this );\n $details.find( '.actions .left' ).empty().append( this._renderSecondaryActions() );\n $details.find( '.summary' ).html( this._renderSummary() )\n .prepend( this._renderDetailMessages() );\n $details.find( '.display-applications' ).html( this._renderDisplayApplications() );\n\n this._setUpBehaviors( $details );\n return $details;\n },\n\n /** Defer to the appropo summary rendering fn based on state */\n _renderSummary : function(){\n var json = this.model.toJSON(),\n summaryRenderFn = this.templates.summaries[ json.state ];\n summaryRenderFn = summaryRenderFn || this.templates.summaries.unknown;\n return summaryRenderFn( json, this );\n },\n\n /** Render messages to be displayed only when the details are shown */\n _renderDetailMessages : function(){\n var view = this,\n $warnings = $( '' ),\n json = view.model.toJSON();\n //TODO:! unordered (map)\n _.each( view.templates.detailMessages, function( templateFn ){\n $warnings.append( $( templateFn( json, view ) ) );\n });\n return $warnings;\n },\n\n /** Render the external display application links */\n _renderDisplayApplications : function(){\n if( this.model.isDeletedOrPurged() ){ return ''; }\n // render both old and new display apps using the same template\n return [\n this.templates.displayApplications( this.model.get( 'display_apps' ), this ),\n this.templates.displayApplications( this.model.get( 'display_types' ), this )\n ].join( '' );\n },\n\n // ......................................................................... secondary/details actions\n /** A series of links/buttons for less commonly used actions: re-run, info, etc. */\n _renderSecondaryActions : function(){\n this.debug( '_renderSecondaryActions' );\n switch( this.model.get( 'state' ) ){\n case STATES.NOT_VIEWABLE:\n return [];\n case STATES.OK:\n case STATES.FAILED_METADATA:\n case STATES.ERROR:\n return [ this._renderDownloadButton(), this._renderShowParamsButton() ];\n }\n return [ this._renderShowParamsButton() ];\n },\n\n /** Render icon-button to show the input and output (stdout/err) for the job that created this.\n * @returns {jQuery} rendered DOM\n */\n _renderShowParamsButton : function(){\n // gen. safe to show in all cases\n return faIconButton({\n title : _l( 'View details' ),\n classes : 'params-btn',\n href : this.model.urls.show_params,\n target : this.linkTarget,\n faIcon : 'fa-info-circle',\n onclick : function( ev ) {\n if ( Galaxy.frame && Galaxy.frame.active ) {\n Galaxy.frame.add( { title: 'Dataset details', url: this.href } );\n ev.preventDefault();\n ev.stopPropagation();\n }\n }\n });\n },\n\n\n /** Render icon-button/popupmenu to download the data (and/or the associated meta files (bai, etc.)) for this.\n * @returns {jQuery} rendered DOM\n */\n _renderDownloadButton : function(){\n // don't show anything if the data's been purged\n if( this.model.get( 'purged' ) || !this.model.hasData() ){ return null; }\n\n // return either: a popupmenu with links to download assoc. meta files (if there are meta files)\n // or a single download icon-button (if there are no meta files)\n if( !_.isEmpty( this.model.get( 'meta_files' ) ) ){\n return this._renderMetaFileDownloadButton();\n }\n\n return $([\n '',\n '',\n ''\n ].join( '' ));\n },\n\n /** Render the download button which opens a dropdown with links to download assoc. meta files (indeces, etc.) */\n _renderMetaFileDownloadButton : function(){\n var urls = this.model.urls;\n return $([\n '
'\n ], 'dataset' );\n\n // messages to be displayed only within the details section ('below the fold')\n var detailMessageTemplates = {\n resubmitted : BASE_MVC.wrapTemplate([\n // deleted not purged\n '<% if( model.resubmitted ){ %>',\n '
',\n _l( 'The job creating this dataset has been resubmitted' ),\n '
',\n '<% } %>'\n ])\n };\n\n // this is applied to both old and new style display apps\n var displayApplicationsTemplate = BASE_MVC.wrapTemplate([\n '<% _.each( apps, function( app ){ %>',\n '
',\n // space for title bar buttons - gen. floated to the right\n '',\n '',\n\n // expandable area for more details\n '',\n '
'\n ]);\n\n var warnings = {};\n\n var titleBarTemplate = BASE_MVC.wrapTemplate([\n // adding a tabindex here allows focusing the title bar and the use of keydown to expand the dataset display\n '
',\n //TODO: prob. belongs in dataset-list-item\n '',\n '
',\n '<%- element.name %>',\n '
',\n '',\n '
'\n ], 'element' );\n\n var subtitleTemplate = BASE_MVC.wrapTemplate([\n // override this\n ''\n ]);\n\n var detailsTemplate = BASE_MVC.wrapTemplate([\n // override this\n ''\n ]);\n\n return {\n el : elTemplato,\n warnings : warnings,\n titleBar : titleBarTemplate,\n subtitle : subtitleTemplate,\n details : detailsTemplate\n };\n}());\n\n\n//==============================================================================\n/** A view that is displayed in some larger list/grid/collection.\n * *AND* can display some sub-list of it's own when expanded (e.g. dataset collections).\n * This list will 'foldout' when the item is expanded depending on this.foldoutStyle:\n * If 'foldout': will expand vertically to show the nested list\n * If 'drilldown': will overlay the parent list\n *\n * Inherits from ListItemView.\n *\n * _renderDetails does the work of creating this.details: a sub-view that shows the nested list\n */\nvar FoldoutListItemView = ListItemView.extend({\n\n /** If 'foldout': show the sub-panel inside the expanded item\n * If 'drilldown': only fire events and handle by pub-sub\n * (allow the panel containing this item to attach it, hide itself, etc.)\n */\n foldoutStyle : 'foldout',\n /** Panel view class to instantiate for the sub-panel */\n foldoutPanelClass : null,\n\n /** override to:\n * add attributes foldoutStyle and foldoutPanelClass for config poly\n * disrespect attributes.expanded if drilldown\n */\n initialize : function( attributes ){\n if( this.foldoutStyle === 'drilldown' ){ this.expanded = false; }\n this.foldoutStyle = attributes.foldoutStyle || this.foldoutStyle;\n this.foldoutPanelClass = attributes.foldoutPanelClass || this.foldoutPanelClass;\n\n ListItemView.prototype.initialize.call( this, attributes );\n this.foldout = this._createFoldoutPanel();\n },\n\n /** in this override, attach the foldout panel when rendering details */\n _renderDetails : function(){\n if( this.foldoutStyle === 'drilldown' ){ return $(); }\n var $newDetails = ListItemView.prototype._renderDetails.call( this );\n return this._attachFoldout( this.foldout, $newDetails );\n },\n\n /** In this override, handle collection expansion. */\n _createFoldoutPanel : function(){\n var model = this.model;\n var FoldoutClass = this._getFoldoutPanelClass( model ),\n options = this._getFoldoutPanelOptions( model ),\n foldout = new FoldoutClass( _.extend( options, {\n model : model\n }));\n return foldout;\n },\n\n /** Stub to return proper foldout panel class */\n _getFoldoutPanelClass : function(){\n // override\n return this.foldoutPanelClass;\n },\n\n /** Stub to return proper foldout panel options */\n _getFoldoutPanelOptions : function(){\n return {\n // propagate foldout style down\n foldoutStyle : this.foldoutStyle,\n fxSpeed : this.fxSpeed\n };\n },\n\n /** Render the foldout panel inside the view, hiding controls */\n _attachFoldout : function( foldout, $whereTo ){\n $whereTo = $whereTo || this.$( '> .details' );\n this.foldout = foldout.render( 0 );\n foldout.$( '> .controls' ).hide();\n return $whereTo.append( foldout.$el );\n },\n\n /** In this override, branch on foldoutStyle to show expanded */\n expand : function(){\n var view = this;\n return view._fetchModelDetails()\n .always(function(){\n if( view.foldoutStyle === 'foldout' ){\n view._expand();\n } else if( view.foldoutStyle === 'drilldown' ){\n view._expandByDrilldown();\n }\n });\n },\n\n /** For drilldown, set up close handler and fire expanded:drilldown\n * containing views can listen to this and handle other things\n * (like hiding themselves) by listening for expanded/collapsed:drilldown\n */\n _expandByDrilldown : function(){\n var view = this;\n // attachment and rendering done by listener\n view.listenTo( view.foldout, 'close', function(){\n view.trigger( 'collapsed:drilldown', view, view.foldout );\n });\n view.trigger( 'expanded:drilldown', view, view.foldout );\n }\n\n});\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nFoldoutListItemView.prototype.templates = (function(){\n\n var detailsTemplate = BASE_MVC.wrapTemplate([\n '
',\n // override with more info (that goes above the panel)\n '
'\n ], 'collection' );\n\n return _.extend( {}, ListItemView.prototype.templates, {\n details : detailsTemplate\n });\n}());\n\n\n//==============================================================================\n return {\n ExpandableView : ExpandableView,\n ListItemView : ListItemView,\n FoldoutListItemView : FoldoutListItemView\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/list/list-item.js","define([\n \"mvc/base-mvc\",\n \"utils/localization\"\n], function( baseMVC, _l ){\n// =============================================================================\n/** A view on any model that has a 'tags' attribute (a list of tag strings)\n * Incorporates the select2 jQuery plugin for tags display/editing:\n * http://ivaynberg.github.io/select2/\n */\nvar TagsEditor = Backbone.View\n .extend( baseMVC.LoggableMixin )\n .extend( baseMVC.HiddenUntilActivatedViewMixin ).extend({\n\n tagName : 'div',\n className : 'tags-display',\n\n /** Set up listeners, parse options */\n initialize : function( options ){\n //console.debug( this, options );\n // only listen to the model only for changes to tags - re-render\n if (options.usePrompt === false) {\n this.label = '';\n } else {\n this.label = '';\n }\n this.hiddenUntilActivated( options.$activator, options );\n },\n\n /** Build the DOM elements, call select to on the created input, and set up behaviors */\n render : function(){\n var self = this;\n this.$el.html( this._template() );\n\n this.$input().select2({\n placeholder : 'Add tags',\n width : '100%',\n tags : function(){\n // initialize possible tags in the dropdown based on all the tags the user has used so far\n return self._getTagsUsed();\n }\n });\n\n this._setUpBehaviors();\n return this;\n },\n\n _hashToName: function(tag){\n if (tag.startsWith('#')){\n return 'name:' + tag.slice(1);\n }\n return tag;\n },\n\n _nameToHash: function(tag){\n if (tag.startsWith('name:')){\n tag = '#' + tag.slice(5);\n }\n return tag;\n },\n\n /** @returns {String} the html text used to build the view's DOM */\n _template : function(){\n return [\n this.label,\n // set up initial tags by adding as CSV to input vals (necc. to init select2)\n ''\n ].join( '' );\n },\n\n /** @returns {String} the sorted, comma-separated tags from the model */\n tagsToCSV : function(){\n var self = this;\n var tagsArray = this.model.get( 'tags' );\n if( !_.isArray( tagsArray ) || _.isEmpty( tagsArray ) ){\n return '';\n }\n return tagsArray.map( function( tag ){\n return _.escape( self._nameToHash( tag ) );\n }).sort().join( ',' );\n },\n\n /** @returns {jQuery} the input for this view */\n $input : function(){\n return this.$el.find( 'input.tags-input' );\n },\n\n /** @returns {String[]} all tags used by the current user */\n _getTagsUsed : function(){\n//TODO: global\n var self = this;\n return _.map(Galaxy.user.get( 'tags_used' ), self._nameToHash);\n },\n\n /** set up any event listeners on the view's DOM (mostly handled by select2) */\n _setUpBehaviors : function(){\n var self = this;\n this.$input().on( 'change', function( event ){\n // Modify any 'hashtag' 'nametags'\n event.val = _.map(event.val, self._hashToName);\n // save the model's tags in either remove or added event\n self.model.save({ tags: event.val });\n // if it's new, add the tag to the users tags\n if( event.added ){\n //??: solve weird behavior in FF on test.galaxyproject.org where\n // event.added.text is string object: 'String{ 0=\"o\", 1=\"n\", 2=\"e\" }'\n self._addNewTagToTagsUsed( event.added.text + '' );\n }\n });\n },\n\n /** add a new tag (if not already there) to the list of all tags used by the user\n * @param {String} newTag the tag to add to the list of used\n */\n _addNewTagToTagsUsed : function( newTag ){\n//TODO: global\n var tagsUsed = Galaxy.user.get( 'tags_used' );\n if( !_.contains( tagsUsed, newTag ) ){\n tagsUsed.push( newTag );\n tagsUsed.sort();\n Galaxy.user.set( 'tags_used', tagsUsed );\n }\n },\n\n /** shut down event listeners and remove this view's DOM */\n remove : function(){\n this.$input.off();\n this.stopListening( this.model );\n Backbone.View.prototype.remove.call( this );\n },\n\n /** string rep */\n toString : function(){ return [ 'TagsEditor(', this.model + '', ')' ].join(''); }\n});\n\n// =============================================================================\nreturn {\n TagsEditor : TagsEditor\n};\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/tag.js","/**\n This is the base class of the tool form plugin. This class is e.g. inherited by the regular and the workflow tool form.\n*/\ndefine( [ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view', 'mvc/citation/citation-model', 'mvc/citation/citation-view' ],\n function( Utils, Deferred, Ui, FormBase, CitationModel, CitationView ) {\n return FormBase.extend({\n initialize: function( options ) {\n var self = this;\n this.deferred = new Deferred();\n FormBase.prototype.initialize.call( this, options );\n if ( this.model.get( 'inputs' ) ) {\n this._buildForm( this.model.attributes );\n } else {\n this.deferred.execute( function( process ) {\n self._buildModel( process, self.model.attributes, true );\n });\n }\n // listen to history panel\n if ( this.model.get( 'listen_to_history' ) && parent.Galaxy && parent.Galaxy.currHistoryPanel ) {\n this.listenTo( parent.Galaxy.currHistoryPanel.collection, 'change', function() {\n self.model.get( 'onchange' )();\n });\n }\n // destroy dom elements\n this.$el.on( 'remove', function() { self.remove() } );\n },\n\n /** Wait for deferred build processes before removal */\n remove: function() {\n var self = this;\n this.$el.hide();\n this.deferred.execute( function() {\n FormBase.prototype.remove.call( self );\n Galaxy.emit.debug( 'tool-form-base::remove()', 'Destroy view.' );\n });\n },\n\n /** Build form */\n _buildForm: function( options ) {\n var self = this;\n this.model.set( options );\n this.model.set({\n title : options.title || '' + options.name + ' ' + options.description + ' (Galaxy Version ' + options.version + ')',\n operations : !this.model.get( 'hide_operations' ) && this._operations(),\n onchange : function() {\n self.deferred.reset();\n self.deferred.execute( function ( process ) {\n self.model.get( 'postchange' )( process, self );\n });\n }\n });\n this.model.get( 'customize' ) && this.model.get( 'customize' )( this );\n this.render();\n if ( !this.model.get( 'collapsible' ) ) {\n this.$el.append( $( '' ).addClass( 'ui-margin-top-large' ).append( this._footer() ) );\n }\n },\n\n /** Builds a new model through api call and recreates the entire form */\n _buildModel: function( process, new_options, hide_message ) {\n var self = this;\n var options = this.model.attributes;\n options.version = new_options.version;\n options.id = new_options.id;\n\n // build request url\n var build_url = '';\n var build_data = {};\n if ( options.job_id ) {\n build_url = Galaxy.root + 'api/jobs/' + options.job_id + '/build_for_rerun';\n } else {\n build_url = Galaxy.root + 'api/tools/' + options.id + '/build';\n if ( Galaxy.params && Galaxy.params.tool_id == options.id ) {\n build_data = $.extend( {}, Galaxy.params );\n options.version && ( build_data[ 'tool_version' ] = options.version );\n }\n }\n\n // get initial model\n Utils.get({\n url : build_url,\n data : build_data,\n success : function( data ) {\n if( !data.display ) {\n window.location = Galaxy.root;\n return;\n }\n self._buildForm( data );\n !hide_message && self.message.update({\n status : 'success',\n message : 'Now you are using \\'' + options.name + '\\' version ' + options.version + ', id \\'' + options.id + '\\'.',\n persistent : false\n });\n Galaxy.emit.debug('tool-form-base::_buildModel()', 'Initial tool model ready.', data);\n process.resolve();\n },\n error : function( response, status ) {\n var error_message = ( response && response.err_msg ) || 'Uncaught error.';\n if ( status == 401 ) {\n window.location = Galaxy.root + 'user/login?' + $.param({ redirect : Galaxy.root + '?tool_id=' + options.id });\n } else if ( self.$el.is( ':empty' ) ) {\n self.$el.prepend( ( new Ui.Message({\n message : error_message,\n status : 'danger',\n persistent : true,\n large : true\n }) ).$el );\n } else {\n Galaxy.modal && Galaxy.modal.show({\n title : 'Tool request failed',\n body : error_message,\n buttons : {\n 'Close' : function() {\n Galaxy.modal.hide();\n }\n }\n });\n }\n Galaxy.emit.debug( 'tool-form-base::_buildModel()', 'Initial tool model request failed.', response );\n process.reject();\n }\n });\n },\n\n /** Create tool operation menu */\n _operations: function() {\n var self = this;\n var options = this.model.attributes;\n\n // button for version selection\n var versions_button = new Ui.ButtonMenu({\n icon : 'fa-cubes',\n title : ( !options.narrow && 'Versions' ) || null,\n tooltip : 'Select another tool version'\n });\n if ( !options.sustain_version && options.versions && options.versions.length > 1 ) {\n for ( var i in options.versions ) {\n var version = options.versions[ i ];\n if ( version != options.version ) {\n versions_button.addMenu({\n title : 'Switch to ' + version,\n version : version,\n icon : 'fa-cube',\n onclick : function() {\n // here we update the tool version (some tools encode the version also in the id)\n var id = options.id.replace( options.version, this.version );\n var version = this.version;\n // queue model request\n self.deferred.reset();\n self.deferred.execute( function( process ) {\n self._buildModel( process, { id : id, version : version } )\n });\n }\n });\n }\n }\n } else {\n versions_button.$el.hide();\n }\n\n // button for options e.g. search, help\n var menu_button = new Ui.ButtonMenu({\n icon : 'fa-caret-down',\n title : ( !options.narrow && 'Options' ) || null,\n tooltip : 'View available options'\n });\n if ( options.biostar_url ) {\n menu_button.addMenu({\n icon : 'fa-question-circle',\n title : 'Question?',\n onclick : function() {\n window.open( options.biostar_url + '/p/new/post/' );\n }\n });\n menu_button.addMenu({\n icon : 'fa-search',\n title : 'Search',\n onclick : function() {\n window.open( options.biostar_url + '/local/search/page/?q=' + options.name );\n }\n });\n };\n menu_button.addMenu({\n icon : 'fa-share',\n title : 'Share',\n onclick : function() {\n prompt( 'Copy to clipboard: Ctrl+C, Enter', window.location.origin + Galaxy.root + 'root?tool_id=' + options.id );\n }\n });\n\n // add admin operations\n if ( Galaxy.user && Galaxy.user.get( 'is_admin' ) ) {\n menu_button.addMenu({\n icon : 'fa-download',\n title : 'Download',\n onclick : function() {\n window.location.href = Galaxy.root + 'api/tools/' + options.id + '/download';\n }\n });\n menu_button.addMenu({\n icon : 'fa-refresh',\n title : 'Reload XML',\n onclick : function() {\n Utils.get({\n url : Galaxy.root + 'api/tools/' + options.id + '/reload',\n success : function( response ) {\n self.message.update( { persistent : false, message : 'Tool XML has been reloaded.', status : 'success' } );\n },\n error : function( response ) {\n self.message.update( { persistent : false, message : response.err_msg, status : 'danger' } );\n }\n });\n }\n });\n }\n\n // button for version selection\n if ( options.requirements && options.requirements.length > 0 ) {\n menu_button.addMenu({\n icon : 'fa-info-circle',\n title : 'Requirements',\n onclick : function() {\n if ( !this.requirements_visible || self.portlet.collapsed ) {\n this.requirements_visible = true;\n self.portlet.expand();\n self.message.update( { persistent : true, message : self._templateRequirements( options ), status : 'info' } );\n } else {\n this.requirements_visible = false;\n self.message.update( { message : '' } );\n }\n }\n });\n }\n\n // add toolshed url\n if ( options.sharable_url ) {\n menu_button.addMenu({\n icon : 'fa-external-link',\n title : 'See in Tool Shed',\n onclick : function() {\n window.open( options.sharable_url );\n }\n });\n }\n\n return {\n menu : menu_button,\n versions : versions_button\n }\n },\n\n /** Create footer */\n _footer: function() {\n var options = this.model.attributes;\n var $el = $( '' ).append( this._templateHelp( options ) );\n if ( options.citations ) {\n var $citations = $( '' );\n var citations = new CitationModel.ToolCitationCollection();\n citations.tool_id = options.id;\n var citation_list_view = new CitationView.CitationListView({ el: $citations, collection: citations });\n citation_list_view.render();\n citations.fetch();\n $el.append( $citations );\n }\n return $el;\n },\n\n /** Templates */\n _templateHelp: function( options ) {\n var $tmpl = $( '' ).addClass( 'ui-form-help' ).append( options.help );\n $tmpl.find( 'a' ).attr( 'target', '_blank' );\n return $tmpl;\n },\n\n _templateRequirements: function( options ) {\n var nreq = options.requirements.length;\n if ( nreq > 0 ) {\n var requirements_message = 'This tool requires ';\n _.each( options.requirements, function( req, i ) {\n requirements_message += req.name + ( req.version ? ' (Version ' + req.version + ')' : '' ) + ( i < nreq - 2 ? ', ' : ( i == nreq - 2 ? ' and ' : '' ) );\n });\n var requirements_link = $( '' ).attr( 'target', '_blank' ).attr( 'href', 'https://galaxyproject.org/tools/requirements/' ).text( 'here' );\n return $( '' ).append( requirements_message + '. Click ' ).append( requirements_link ).append( ' for more information.' );\n }\n return 'No requirements found.';\n }\n });\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/tool/tool-form-base.js","/**\n * Model, view, and controller objects for Galaxy tools and tool panel.\n */\n\n define([\n \"libs/underscore\",\n \"viz/trackster/util\",\n \"mvc/dataset/data\",\n \"mvc/tool/tool-form\"\n\n], function(_, util, data, ToolForm) {\n 'use strict';\n\n/**\n * Mixin for tracking model visibility.\n */\nvar VisibilityMixin = {\n hidden: false,\n\n show: function() {\n this.set(\"hidden\", false);\n },\n\n hide: function() {\n this.set(\"hidden\", true);\n },\n\n toggle: function() {\n this.set(\"hidden\", !this.get(\"hidden\"));\n },\n\n is_visible: function() {\n return !this.attributes.hidden;\n }\n\n};\n\n/**\n * A tool parameter.\n */\nvar ToolParameter = Backbone.Model.extend({\n defaults: {\n name: null,\n label: null,\n type: null,\n value: null,\n html: null,\n num_samples: 5\n },\n\n initialize: function(options) {\n this.attributes.html = unescape(this.attributes.html);\n },\n\n copy: function() {\n return new ToolParameter(this.toJSON());\n },\n\n set_value: function(value) {\n this.set('value', value || '');\n }\n});\n\nvar ToolParameterCollection = Backbone.Collection.extend({\n model: ToolParameter\n});\n\n/**\n * A data tool parameter.\n */\nvar DataToolParameter = ToolParameter.extend({});\n\n/**\n * An integer tool parameter.\n */\nvar IntegerToolParameter = ToolParameter.extend({\n set_value: function(value) {\n this.set('value', parseInt(value, 10));\n },\n\n /**\n * Returns samples from a tool input.\n */\n get_samples: function() {\n return d3.scale.linear()\n .domain([this.get('min'), this.get('max')])\n .ticks(this.get('num_samples'));\n }\n});\n\nvar FloatToolParameter = IntegerToolParameter.extend({\n set_value: function(value) {\n this.set('value', parseFloat(value));\n }\n});\n\n/**\n * A select tool parameter.\n */\nvar SelectToolParameter = ToolParameter.extend({\n /**\n * Returns tool options.\n */\n get_samples: function() {\n return _.map(this.get('options'), function(option) {\n return option[0];\n });\n }\n});\n\n// Set up dictionary of parameter types.\nToolParameter.subModelTypes = {\n 'integer': IntegerToolParameter,\n 'float': FloatToolParameter,\n 'data': DataToolParameter,\n 'select': SelectToolParameter\n};\n\n/**\n * A Galaxy tool.\n */\nvar Tool = Backbone.Model.extend({\n // Default attributes.\n defaults: {\n id: null,\n name: null,\n description: null,\n target: null,\n inputs: [],\n outputs: []\n },\n\n urlRoot: Galaxy.root + 'api/tools',\n\n initialize: function(options) {\n\n // Set parameters.\n this.set('inputs', new ToolParameterCollection(_.map(options.inputs, function(p) {\n var p_class = ToolParameter.subModelTypes[p.type] || ToolParameter;\n return new p_class(p);\n })));\n },\n\n /**\n *\n */\n toJSON: function() {\n var rval = Backbone.Model.prototype.toJSON.call(this);\n\n // Convert inputs to JSON manually.\n rval.inputs = this.get('inputs').map(function(i) { return i.toJSON(); });\n return rval;\n },\n\n /**\n * Removes inputs of a particular type; this is useful because not all inputs can be handled by\n * client and server yet.\n */\n remove_inputs: function(types) {\n var tool = this,\n incompatible_inputs = tool.get('inputs').filter( function(input) {\n return ( types.indexOf( input.get('type') ) !== -1);\n });\n tool.get('inputs').remove(incompatible_inputs);\n },\n\n /**\n * Returns object copy, optionally including only inputs that can be sampled.\n */\n copy: function(only_samplable_inputs) {\n var copy = new Tool(this.toJSON());\n\n // Return only samplable inputs if flag is set.\n if (only_samplable_inputs) {\n var valid_inputs = new Backbone.Collection();\n copy.get('inputs').each(function(input) {\n if (input.get_samples()) {\n valid_inputs.push(input);\n }\n });\n copy.set('inputs', valid_inputs);\n }\n\n return copy;\n },\n\n apply_search_results: function(results) {\n ( _.indexOf(results, this.attributes.id) !== -1 ? this.show() : this.hide() );\n return this.is_visible();\n },\n\n /**\n * Set a tool input's value.\n */\n set_input_value: function(name, value) {\n this.get('inputs').find(function(input) {\n return input.get('name') === name;\n }).set('value', value);\n },\n\n /**\n * Set many input values at once.\n */\n set_input_values: function(inputs_dict) {\n var self = this;\n _.each(_.keys(inputs_dict), function(input_name) {\n self.set_input_value(input_name, inputs_dict[input_name]);\n });\n },\n\n /**\n * Run tool; returns a Deferred that resolves to the tool's output(s).\n */\n run: function() {\n return this._run();\n },\n\n /**\n * Rerun tool using regions and a target dataset.\n */\n rerun: function(target_dataset, regions) {\n return this._run({\n action: 'rerun',\n target_dataset_id: target_dataset.id,\n regions: regions\n });\n },\n\n /**\n * Returns input dict for tool's inputs.\n */\n get_inputs_dict: function() {\n var input_dict = {};\n this.get('inputs').each(function(input) {\n input_dict[input.get('name')] = input.get('value');\n });\n return input_dict;\n },\n\n /**\n * Run tool; returns a Deferred that resolves to the tool's output(s).\n * NOTE: this method is a helper method and should not be called directly.\n */\n _run: function(additional_params) {\n // Create payload.\n var payload = _.extend({\n tool_id: this.id,\n inputs: this.get_inputs_dict()\n }, additional_params);\n\n // Because job may require indexing datasets, use server-side\n // deferred to ensure that job is run. Also use deferred that\n // resolves to outputs from tool.\n var run_deferred = $.Deferred(),\n ss_deferred = new util.ServerStateDeferred({\n ajax_settings: {\n url: this.urlRoot,\n data: JSON.stringify(payload),\n dataType: \"json\",\n contentType: 'application/json',\n type: \"POST\"\n },\n interval: 2000,\n success_fn: function(response) {\n return response !== \"pending\";\n }\n });\n\n // Run job and resolve run_deferred to tool outputs.\n $.when(ss_deferred.go()).then(function(result) {\n run_deferred.resolve(new data.DatasetCollection(result));\n });\n return run_deferred;\n }\n});\n_.extend(Tool.prototype, VisibilityMixin);\n\n/**\n * Tool view.\n */\nvar ToolView = Backbone.View.extend({\n\n});\n\n/**\n * Wrap collection of tools for fast access/manipulation.\n */\nvar ToolCollection = Backbone.Collection.extend({\n model: Tool\n});\n\n/**\n * Label or section header in tool panel.\n */\nvar ToolSectionLabel = Backbone.Model.extend(VisibilityMixin);\n\n/**\n * Section of tool panel with elements (labels and tools).\n */\nvar ToolSection = Backbone.Model.extend({\n defaults: {\n elems: [],\n open: false\n },\n\n clear_search_results: function() {\n _.each(this.attributes.elems, function(elt) {\n elt.show();\n });\n\n this.show();\n this.set(\"open\", false);\n },\n\n apply_search_results: function(results) {\n var all_hidden = true,\n cur_label;\n _.each(this.attributes.elems, function(elt) {\n if (elt instanceof ToolSectionLabel) {\n cur_label = elt;\n cur_label.hide();\n }\n else if (elt instanceof Tool) {\n if (elt.apply_search_results(results)) {\n all_hidden = false;\n if (cur_label) {\n cur_label.show();\n }\n }\n }\n });\n\n if (all_hidden) {\n this.hide();\n }\n else {\n this.show();\n this.set(\"open\", true);\n }\n }\n});\n_.extend(ToolSection.prototype, VisibilityMixin);\n\n/**\n * Tool search that updates results when query is changed. Result value of null\n * indicates that query was not run; if not null, results are from search using\n * query.\n */\nvar ToolSearch = Backbone.Model.extend({\n defaults: {\n search_hint_string: \"search tools\",\n min_chars_for_search: 3,\n clear_btn_url: \"\",\n visible: true,\n query: \"\",\n results: null,\n // ESC (27) will clear the input field and tool search filters\n clear_key: 27\n },\n\n urlRoot: Galaxy.root + 'api/tools',\n\n initialize: function() {\n this.on(\"change:query\", this.do_search);\n },\n\n /**\n * Do the search and update the results.\n */\n do_search: function() {\n var query = this.attributes.query;\n\n // If query is too short, do not search.\n if (query.length < this.attributes.min_chars_for_search) {\n this.set(\"results\", null);\n return;\n }\n\n // Do search via AJAX.\n var q = query;\n // Stop previous ajax-request\n if (this.timer) {\n clearTimeout(this.timer);\n }\n // Start a new ajax-request in X ms\n $(\"#search-clear-btn\").hide();\n $(\"#search-spinner\").show();\n var self = this;\n this.timer = setTimeout(function () {\n // log the search to analytics if present\n if ( typeof ga !== 'undefined' ) {\n ga( 'send', 'pageview', Galaxy.root + '?q=' + q );\n }\n $.get( self.urlRoot, { q: q }, function (data) {\n self.set(\"results\", data);\n $(\"#search-spinner\").hide();\n $(\"#search-clear-btn\").show();\n }, \"json\" );\n }, 400 );\n },\n\n clear_search: function() {\n this.set(\"query\", \"\");\n this.set(\"results\", null);\n }\n\n});\n_.extend(ToolSearch.prototype, VisibilityMixin);\n\n/**\n * Tool Panel.\n */\nvar ToolPanel = Backbone.Model.extend({\n\n initialize: function(options) {\n this.attributes.tool_search = options.tool_search;\n this.attributes.tool_search.on(\"change:results\", this.apply_search_results, this);\n this.attributes.tools = options.tools;\n this.attributes.layout = new Backbone.Collection( this.parse(options.layout) );\n },\n\n /**\n * Parse tool panel dictionary and return collection of tool panel elements.\n */\n parse: function(response) {\n // Recursive function to parse tool panel elements.\n var self = this,\n // Helper to recursively parse tool panel.\n parse_elt = function(elt_dict) {\n var type = elt_dict.model_class;\n // There are many types of tools; for now, anything that ends in 'Tool'\n // is treated as a generic tool.\n if ( type.indexOf('Tool') === type.length - 4 ) {\n return self.attributes.tools.get(elt_dict.id);\n }\n else if (type === 'ToolSection') {\n // Parse elements.\n var elems = _.map(elt_dict.elems, parse_elt);\n elt_dict.elems = elems;\n return new ToolSection(elt_dict);\n }\n else if (type === 'ToolSectionLabel') {\n return new ToolSectionLabel(elt_dict);\n }\n };\n\n return _.map(response, parse_elt);\n },\n\n clear_search_results: function() {\n this.get('layout').each(function(panel_elt) {\n if (panel_elt instanceof ToolSection) {\n panel_elt.clear_search_results();\n }\n else {\n // Label or tool, so just show.\n panel_elt.show();\n }\n });\n },\n\n apply_search_results: function() {\n var results = this.get('tool_search').get('results');\n if (results === null) {\n this.clear_search_results();\n return;\n }\n\n var cur_label = null;\n this.get('layout').each(function(panel_elt) {\n if (panel_elt instanceof ToolSectionLabel) {\n cur_label = panel_elt;\n cur_label.hide();\n }\n else if (panel_elt instanceof Tool) {\n if (panel_elt.apply_search_results(results)) {\n if (cur_label) {\n cur_label.show();\n }\n }\n }\n else {\n // Starting new section, so clear current label.\n cur_label = null;\n panel_elt.apply_search_results(results);\n }\n });\n }\n});\n\n/**\n * View classes for Galaxy tools and tool panel.\n *\n * Views use the templates defined below for rendering. Views update as needed\n * based on (a) model/collection events and (b) user interactions; in this sense,\n * they are controllers are well and the HTML is the real view in the MVC architecture.\n */\n\n/**\n * Base view that handles visibility based on model's hidden attribute.\n */\nvar BaseView = Backbone.View.extend({\n initialize: function() {\n this.model.on(\"change:hidden\", this.update_visible, this);\n this.update_visible();\n },\n update_visible: function() {\n ( this.model.attributes.hidden ? this.$el.hide() : this.$el.show() );\n }\n});\n\n/**\n * Link to a tool.\n */\nvar ToolLinkView = BaseView.extend({\n tagName: 'div',\n\n render: function() {\n // create element\n var $link = $('');\n $link.append(templates.tool_link(this.model.toJSON()));\n\n var formStyle = this.model.get( 'form_style', null );\n // open upload dialog for upload tool\n if (this.model.id === 'upload1') {\n $link.find('a').on('click', function(e) {\n e.preventDefault();\n Galaxy.upload.show();\n });\n }\n else if ( formStyle === 'regular' ) { // regular tools\n var self = this;\n $link.find('a').on('click', function(e) {\n e.preventDefault();\n Galaxy.router.push( '/', { tool_id : self.model.id, version : self.model.get('version') } );\n });\n }\n\n // add element\n this.$el.append($link);\n return this;\n }\n});\n\n/**\n * Panel label/section header.\n */\nvar ToolSectionLabelView = BaseView.extend({\n tagName: 'div',\n className: 'toolPanelLabel',\n\n render: function() {\n this.$el.append( $(\"\").text(this.model.attributes.text) );\n return this;\n }\n});\n\n/**\n * Panel section.\n */\nvar ToolSectionView = BaseView.extend({\n tagName: 'div',\n className: 'toolSectionWrapper',\n\n initialize: function() {\n BaseView.prototype.initialize.call(this);\n this.model.on(\"change:open\", this.update_open, this);\n },\n\n render: function() {\n // Build using template.\n this.$el.append( templates.panel_section(this.model.toJSON()) );\n\n // Add tools to section.\n var section_body = this.$el.find(\".toolSectionBody\");\n _.each(this.model.attributes.elems, function(elt) {\n if (elt instanceof Tool) {\n var tool_view = new ToolLinkView({model: elt, className: \"toolTitle\"});\n tool_view.render();\n section_body.append(tool_view.$el);\n }\n else if (elt instanceof ToolSectionLabel) {\n var label_view = new ToolSectionLabelView({model: elt});\n label_view.render();\n section_body.append(label_view.$el);\n }\n else {\n // TODO: handle nested section bodies?\n }\n });\n return this;\n },\n\n events: {\n 'click .toolSectionTitle > a': 'toggle'\n },\n\n /**\n * Toggle visibility of tool section.\n */\n toggle: function() {\n this.model.set(\"open\", !this.model.attributes.open);\n },\n\n /**\n * Update whether section is open or close.\n */\n update_open: function() {\n (this.model.attributes.open ?\n this.$el.children(\".toolSectionBody\").slideDown(\"fast\") :\n this.$el.children(\".toolSectionBody\").slideUp(\"fast\")\n );\n }\n});\n\nvar ToolSearchView = Backbone.View.extend({\n tagName: 'div',\n id: 'tool-search',\n className: 'bar',\n\n events: {\n 'click': 'focus_and_select',\n 'keyup :input': 'query_changed',\n 'change :input': 'query_changed',\n 'click #search-clear-btn': 'clear'\n },\n\n render: function() {\n this.$el.append( templates.tool_search(this.model.toJSON()) );\n if (!this.model.is_visible()) {\n this.$el.hide();\n }\n\n // Adjust top for issue 2907 depending on whether the messagebox is visible.\n if ($(\"#messagebox\").is(\":visible\")) {\n this.$el.css(\"top\",\"95px\");\n }\n\n this.$el.find('[title]').tooltip();\n return this;\n },\n\n focus_and_select: function() {\n this.$el.find(\":input\").focus().select();\n },\n\n clear: function() {\n this.model.clear_search();\n this.$el.find(\":input\").val('');\n this.focus_and_select();\n return false;\n },\n\n query_changed: function( evData ) {\n // check for the 'clear key' (ESC) first\n if( ( this.model.attributes.clear_key ) &&\n ( this.model.attributes.clear_key === evData.which ) ){\n this.clear();\n return false;\n }\n this.model.set(\"query\", this.$el.find(\":input\").val());\n }\n});\n\n/**\n * Tool panel view. Events triggered include:\n * tool_link_click(click event, tool_model)\n */\nvar ToolPanelView = Backbone.View.extend({\n tagName: 'div',\n className: 'toolMenu',\n\n /**\n * Set up view.\n */\n initialize: function() {\n this.model.get('tool_search').on(\"change:results\", this.handle_search_results, this);\n },\n\n render: function() {\n var self = this;\n\n // Render search.\n var search_view = new ToolSearchView( { model: this.model.get('tool_search') } );\n search_view.render();\n self.$el.append(search_view.$el);\n\n // Render panel.\n this.model.get('layout').each(function(panel_elt) {\n if (panel_elt instanceof ToolSection) {\n var section_title_view = new ToolSectionView({model: panel_elt});\n section_title_view.render();\n self.$el.append(section_title_view.$el);\n }\n else if (panel_elt instanceof Tool) {\n var tool_view = new ToolLinkView({model: panel_elt, className: \"toolTitleNoSection\"});\n tool_view.render();\n self.$el.append(tool_view.$el);\n }\n else if (panel_elt instanceof ToolSectionLabel) {\n var label_view = new ToolSectionLabelView({model: panel_elt});\n label_view.render();\n self.$el.append(label_view.$el);\n }\n });\n\n // Setup tool link click eventing.\n self.$el.find(\"a.tool-link\").click(function(e) {\n // Tool id is always the first class.\n var\n tool_id = $(this).attr('class').split(/\\s+/)[0],\n tool = self.model.get('tools').get(tool_id);\n\n self.trigger(\"tool_link_click\", e, tool);\n });\n\n return this;\n },\n\n handle_search_results: function() {\n var results = this.model.get('tool_search').get('results');\n if (results && results.length === 0) {\n $(\"#search-no-results\").show();\n }\n else {\n $(\"#search-no-results\").hide();\n }\n }\n});\n\n/**\n * View for working with a tool: setting parameters and inputs and executing the tool.\n */\nvar ToolFormView = Backbone.View.extend({\n className: 'toolForm',\n\n render: function() {\n this.$el.children().remove();\n this.$el.append( templates.tool_form(this.model.toJSON()) );\n }\n});\n\n/**\n * Integrated tool menu + tool execution.\n */\nvar IntegratedToolMenuAndView = Backbone.View.extend({\n className: 'toolMenuAndView',\n\n initialize: function() {\n this.tool_panel_view = new ToolPanelView({collection: this.collection});\n this.tool_form_view = new ToolFormView();\n },\n\n render: function() {\n // Render and append tool panel.\n this.tool_panel_view.render();\n this.tool_panel_view.$el.css(\"float\", \"left\");\n this.$el.append(this.tool_panel_view.$el);\n\n // Append tool form view.\n this.tool_form_view.$el.hide();\n this.$el.append(this.tool_form_view.$el);\n\n // On tool link click, show tool.\n var self = this;\n this.tool_panel_view.on(\"tool_link_click\", function(e, tool) {\n // Prevents click from activating link:\n e.preventDefault();\n // Show tool that was clicked on:\n self.show_tool(tool);\n });\n },\n\n /**\n * Fetch and display tool.\n */\n show_tool: function(tool) {\n var self = this;\n tool.fetch().done( function() {\n self.tool_form_view.model = tool;\n self.tool_form_view.render();\n self.tool_form_view.$el.show();\n $('#left').width(\"650px\");\n });\n }\n});\n\n// TODO: move into relevant views\nvar templates = {\n // the search bar at the top of the tool panel\n tool_search : _.template([\n '\" autocomplete=\"off\" type=\"text\" />',\n '',\n //TODO: replace with icon\n '',\n ].join('')),\n\n // the category level container in the tool panel (e.g. 'Get Data', 'Text Manipulation')\n panel_section : _.template([\n '
'\n ].join('')),\n\n // a single tool's link in the tool panel; will load the tool form in the center panel\n tool_link : _.template([\n '',\n '<% _.each( labels, function( label ){ %>',\n '\">',\n '<%- label %>',\n '',\n '<% }); %>',\n '',\n ' tool-link\" href=\"<%= link %>\" target=\"<%- target %>\" minsizehint=\"<%- min_width %>\">',\n '<%- name %>',\n '',\n ' <%- description %>'\n ].join('')),\n\n // the tool form for entering tool parameters, viewing help and executing the tool\n // loaded when a tool link is clicked in the tool panel\n tool_form : _.template([\n '
';\n },\n\n /** Template of info message */\n _templateInfo: function() {\n return '
' +\n 'Your FTP directory does not contain any files.' +\n '
';\n },\n\n /** Template of main view */\n _template: function() {\n return '
' +\n '' +\n '
This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at ' + this.options.ftp_upload_site + ' using your Galaxy credentials (email address and password).
' +\n '
' +\n '
';\n }\n });\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/upload/upload-ftp.js","/** This renders the content of the settings popup, allowing users to specify flags i.e. for space-to-tab conversion **/\ndefine( [ 'utils/utils' ], function( Utils ) {\n return Backbone.View.extend({\n options: {\n class_check : 'fa-check-square-o',\n class_uncheck : 'fa-square-o',\n parameters : [{\n id : 'space_to_tab',\n title : 'Convert spaces to tabs',\n },{\n id : 'to_posix_lines',\n title : 'Use POSIX standard'\n }]\n },\n\n initialize: function( options ) {\n var self = this;\n this.model = options.model;\n this.setElement( $( '' ).addClass( 'upload-settings' ) );\n this.$el.append( $( '' ).addClass( 'upload-settings-cover' ) );\n this.$el.append( $( '
',\n '<% if( collection.collection_type === \"list\" ){ %>',\n _l( 'a list of datasets' ),\n '<% } else if( collection.collection_type === \"paired\" ){ %>',\n _l( 'a pair of datasets' ),\n '<% } else if( collection.collection_type === \"list:paired\" ){ %>',\n _l( 'a list of paired datasets' ),\n '<% } else if( collection.collection_type === \"list:list\" ){ %>',\n _l( 'a list of dataset lists' ),\n '<% } %>',\n '
',\n '
',\n\n '',\n '
'\n ], 'collection' );\n\n return _.extend( _.clone( _super.prototype.templates ), {\n controls : controlsTemplate\n });\n}());\n\n\n\n// =============================================================================\n/** @class non-editable, read-only View/Controller for a dataset collection. */\nvar ListCollectionView = CollectionView.extend(\n/** @lends ListCollectionView.prototype */{\n\n //TODO: not strictly needed - due to switch in CollectionView._getContentClass\n /** sub view class used for datasets */\n DatasetDCEViewClass : DC_LI.DatasetDCEListItemView,\n\n // ........................................................................ misc\n /** string rep */\n toString : function(){\n return 'ListCollectionView(' + (( this.model )?( this.model.get( 'name' )):( '' )) + ')';\n }\n});\n\n\n// =============================================================================\n/** @class non-editable, read-only View/Controller for a dataset collection. */\nvar PairCollectionView = ListCollectionView.extend(\n/** @lends PairCollectionView.prototype */{\n\n // ........................................................................ misc\n /** string rep */\n toString : function(){\n return 'PairCollectionView(' + (( this.model )?( this.model.get( 'name' )):( '' )) + ')';\n }\n});\n\n\n// =============================================================================\n/** @class non-editable, read-only View/Controller for a dataset collection. */\nvar ListOfPairsCollectionView = CollectionView.extend(\n/** @lends ListOfPairsCollectionView.prototype */{\n\n //TODO: not strictly needed - due to switch in CollectionView._getContentClass\n /** sub view class used for nested collections */\n NestedDCDCEViewClass : DC_LI.NestedDCDCEListItemView.extend({\n foldoutPanelClass : PairCollectionView\n }),\n\n // ........................................................................ misc\n /** string rep */\n toString : function(){\n return 'ListOfPairsCollectionView(' + (( this.model )?( this.model.get( 'name' )):( '' )) + ')';\n }\n});\n\n\n// =============================================================================\n/** @class non-editable, read-only View/Controller for a list of lists dataset collection. */\nvar ListOfListsCollectionView = CollectionView.extend({\n\n /** sub view class used for nested collections */\n NestedDCDCEViewClass : DC_LI.NestedDCDCEListItemView.extend({\n foldoutPanelClass : PairCollectionView\n }),\n\n /** string rep */\n toString : function(){\n return 'ListOfListsCollectionView(' + (( this.model )?( this.model.get( 'name' )):( '' )) + ')';\n }\n});\n\n\n//==============================================================================\n return {\n CollectionView : CollectionView,\n ListCollectionView : ListCollectionView,\n PairCollectionView : PairCollectionView,\n ListOfPairsCollectionView : ListOfPairsCollectionView,\n ListOfListsCollectionView : ListOfListsCollectionView\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/collection/collection-view.js","define([\n \"mvc/dataset/states\",\n \"mvc/dataset/dataset-li\",\n \"mvc/tag\",\n \"mvc/annotation\",\n \"ui/fa-icon-button\",\n \"mvc/base-mvc\",\n \"utils/localization\"\n], function( STATES, DATASET_LI, TAGS, ANNOTATIONS, faIconButton, BASE_MVC, _l ){\n\n'use strict';\n//==============================================================================\nvar _super = DATASET_LI.DatasetListItemView;\n/** @class Editing view for DatasetAssociation.\n */\nvar DatasetListItemEdit = _super.extend(\n/** @lends DatasetListItemEdit.prototype */{\n\n /** set up: options */\n initialize : function( attributes ){\n _super.prototype.initialize.call( this, attributes );\n this.hasUser = attributes.hasUser;\n\n /** allow user purge of dataset files? */\n this.purgeAllowed = attributes.purgeAllowed || false;\n\n //TODO: move to HiddenUntilActivatedViewMixin\n /** should the tags editor be shown or hidden initially? */\n this.tagsEditorShown = attributes.tagsEditorShown || false;\n /** should the tags editor be shown or hidden initially? */\n this.annotationEditorShown = attributes.annotationEditorShown || false;\n },\n\n // ......................................................................... titlebar actions\n /** In this override, add the other two primary actions: edit and delete */\n _renderPrimaryActions : function(){\n var actions = _super.prototype._renderPrimaryActions.call( this );\n if( this.model.get( 'state' ) === STATES.NOT_VIEWABLE ){\n return actions;\n }\n // render the display, edit attr and delete icon-buttons\n return _super.prototype._renderPrimaryActions.call( this ).concat([\n this._renderEditButton(),\n this._renderDeleteButton()\n ]);\n },\n\n //TODO: move titleButtons into state renderers, remove state checks in the buttons\n\n /** Render icon-button to edit the attributes (format, permissions, etc.) this dataset. */\n _renderEditButton : function(){\n // don't show edit while uploading, in-accessible\n // DO show if in error (ala previous history panel)\n if( ( this.model.get( 'state' ) === STATES.DISCARDED )\n || ( !this.model.get( 'accessible' ) ) ){\n return null;\n }\n\n var purged = this.model.get( 'purged' ),\n deleted = this.model.get( 'deleted' ),\n editBtnData = {\n title : _l( 'Edit attributes' ),\n href : this.model.urls.edit,\n target : this.linkTarget,\n faIcon : 'fa-pencil',\n classes : 'edit-btn'\n };\n\n // disable if purged or deleted and explain why in the tooltip\n if( deleted || purged ){\n editBtnData.disabled = true;\n if( purged ){\n editBtnData.title = _l( 'Cannot edit attributes of datasets removed from disk' );\n } else if( deleted ){\n editBtnData.title = _l( 'Undelete dataset to edit attributes' );\n }\n\n // disable if still uploading or new\n } else if( _.contains( [ STATES.UPLOAD, STATES.NEW ], this.model.get( 'state' ) ) ){\n editBtnData.disabled = true;\n editBtnData.title = _l( 'This dataset is not yet editable' );\n }\n return faIconButton( editBtnData );\n },\n\n /** Render icon-button to delete this hda. */\n _renderDeleteButton : function(){\n // don't show delete if...\n if( ( !this.model.get( 'accessible' ) ) ){\n return null;\n }\n\n var self = this,\n deletedAlready = this.model.isDeletedOrPurged();\n return faIconButton({\n title : !deletedAlready? _l( 'Delete' ) : _l( 'Dataset is already deleted' ),\n disabled : deletedAlready,\n faIcon : 'fa-times',\n classes : 'delete-btn',\n onclick : function() {\n // ...bler... tooltips being left behind in DOM (hover out never called on deletion)\n self.$el.find( '.icon-btn.delete-btn' ).trigger( 'mouseout' );\n self.model[ 'delete' ]();\n }\n });\n },\n\n // ......................................................................... details\n /** In this override, add tags and annotations controls, make the ? dbkey a link to editing page */\n _renderDetails : function(){\n //TODO: generalize to be allow different details for each state\n var $details = _super.prototype._renderDetails.call( this ),\n state = this.model.get( 'state' );\n\n if( !this.model.isDeletedOrPurged() && _.contains([ STATES.OK, STATES.FAILED_METADATA ], state ) ){\n this._renderTags( $details );\n this._renderAnnotation( $details );\n this._makeDbkeyEditLink( $details );\n }\n\n this._setUpBehaviors( $details );\n return $details;\n },\n\n /**************************************************************************\n * Render help button to show tool help text without rerunning the tool.\n * Issue #2100\n */\n _renderToolHelpButton : function() {\n var datasetID = this.model.attributes.dataset_id;\n var jobID = this.model.attributes.creating_job;\n var self = this;\n\n var parseToolBuild = function(data) {\n var helpString = '
'\n if (data.name && data.help){\n helpString += 'Tool help for ' + data.name + '';\n helpString += data.help;\n } else {\n helpString += 'Tool help is unavailable for this dataset.';\n }\n helpString += '
';\n self.$el.find( '.details' ).append($.parseHTML(helpString));\n };\n var parseToolID = function(data) {\n $.ajax({\n url: Galaxy.root + 'api/tools/' + data.tool_id + '/build'\n }).done(function(data){\n parseToolBuild(data);\n }).fail(function(){\n parseToolBuild({})\n });\n };\n if (Galaxy.user.id === null){\n return null\n }\n return faIconButton({\n title: 'Tool Help',\n classes: 'icon-btn',\n href: '#',\n faIcon: 'fa-question',\n onclick: function() {\n var divString = 'thdiv-' + datasetID;\n if (self.$el.find(\".toolhelp\").length > 0){\n self.$el.find(\".toolhelp\").toggle();\n } else {\n $.ajax({\n url: Galaxy.root + 'api/jobs/' + jobID\n }).done(function(data){\n parseToolID(data);\n }).fail(function(){\n console.log('Failed at recovering job information from the Galaxy API for job id \"' + jobID + '\".');\n });\n }\n }\n });\n },\n //*************************************************************************\n\n /** Add less commonly used actions in the details section based on state */\n _renderSecondaryActions : function(){\n var actions = _super.prototype._renderSecondaryActions.call( this );\n switch( this.model.get( 'state' ) ){\n case STATES.UPLOAD:\n case STATES.NOT_VIEWABLE:\n return actions;\n case STATES.ERROR:\n // error button comes first\n actions.unshift( this._renderErrButton() );\n return actions.concat([ this._renderRerunButton(), this._renderToolHelpButton() ]);\n case STATES.OK:\n case STATES.FAILED_METADATA:\n return actions.concat([ this._renderRerunButton(), this._renderVisualizationsButton(), this._renderToolHelpButton() ]);\n }\n return actions.concat([ this._renderRerunButton(), this._renderToolHelpButton() ]);\n },\n\n /** Render icon-button to report an error on this dataset to the galaxy admin. */\n _renderErrButton : function(){\n return faIconButton({\n title : _l( 'View or report this error' ),\n href : this.model.urls.report_error,\n classes : 'report-error-btn',\n target : this.linkTarget,\n faIcon : 'fa-bug'\n });\n },\n\n /** Render icon-button to re-run the job that created this dataset. */\n _renderRerunButton : function(){\n var creating_job = this.model.get( 'creating_job' );\n if( this.model.get( 'rerunnable' ) ){\n return faIconButton({\n title : _l( 'Run this job again' ),\n href : this.model.urls.rerun,\n classes : 'rerun-btn',\n target : this.linkTarget,\n faIcon : 'fa-refresh',\n onclick : function( ev ) {\n ev.preventDefault();\n Galaxy.router.push( '/', { job_id : creating_job } );\n }\n });\n }\n },\n\n /** Render an icon-button or popupmenu of links based on the applicable visualizations */\n _renderVisualizationsButton : function(){\n //TODO: someday - lazyload visualizations\n var visualizations = this.model.get( 'visualizations' );\n if( ( this.model.isDeletedOrPurged() )\n || ( !this.hasUser )\n || ( !this.model.hasData() )\n || ( _.isEmpty( visualizations ) ) ){\n return null;\n }\n if( !_.isObject( visualizations[0] ) ){\n this.warn( 'Visualizations have been switched off' );\n return null;\n }\n\n var $visualizations = $( this.templates.visualizations( visualizations, this ) );\n //HACK: need to re-write those directed at galaxy_main with linkTarget\n $visualizations.find( '[target=\"galaxy_main\"]').attr( 'target', this.linkTarget );\n // use addBack here to include the root $visualizations elem (for the case of 1 visualization)\n this._addScratchBookFn( $visualizations.find( '.visualization-link' ).addBack( '.visualization-link' ) );\n return $visualizations;\n },\n\n /** add scratchbook functionality to visualization links */\n _addScratchBookFn : function( $links ){\n var li = this;\n $links.click( function( ev ){\n if( Galaxy.frame && Galaxy.frame.active ){\n Galaxy.frame.add({\n title : 'Visualization',\n url : $( this ).attr( 'href' )\n });\n ev.preventDefault();\n ev.stopPropagation();\n }\n });\n },\n\n //TODO: if possible move these to readonly view - but display the owner's tags/annotation (no edit)\n /** Render the tags list/control */\n _renderTags : function( $where ){\n if( !this.hasUser ){ return; }\n var view = this;\n this.tagsEditor = new TAGS.TagsEditor({\n model : this.model,\n el : $where.find( '.tags-display' ),\n onshowFirstTime : function(){ this.render(); },\n // persist state on the hda view (and not the editor) since these are currently re-created each time\n onshow : function(){ view.tagsEditorShown = true; },\n onhide : function(){ view.tagsEditorShown = false; },\n $activator : faIconButton({\n title : _l( 'Edit dataset tags' ),\n classes : 'tag-btn',\n faIcon : 'fa-tags'\n }).appendTo( $where.find( '.actions .right' ) )\n });\n if( this.tagsEditorShown ){ this.tagsEditor.toggle( true ); }\n },\n\n /** Render the annotation display/control */\n _renderAnnotation : function( $where ){\n if( !this.hasUser ){ return; }\n var view = this;\n this.annotationEditor = new ANNOTATIONS.AnnotationEditor({\n model : this.model,\n el : $where.find( '.annotation-display' ),\n onshowFirstTime : function(){ this.render(); },\n // persist state on the hda view (and not the editor) since these are currently re-created each time\n onshow : function(){ view.annotationEditorShown = true; },\n onhide : function(){ view.annotationEditorShown = false; },\n $activator : faIconButton({\n title : _l( 'Edit dataset annotation' ),\n classes : 'annotate-btn',\n faIcon : 'fa-comment'\n }).appendTo( $where.find( '.actions .right' ) )\n });\n if( this.annotationEditorShown ){ this.annotationEditor.toggle( true ); }\n },\n\n /** If the format/dbkey/genome_build isn't set, make the display a link to the edit page */\n _makeDbkeyEditLink : function( $details ){\n // make the dbkey a link to editing\n if( this.model.get( 'metadata_dbkey' ) === '?'\n && !this.model.isDeletedOrPurged() ){\n var editableDbkey = $( '?' )\n .attr( 'href', this.model.urls.edit )\n .attr( 'target', this.linkTarget );\n $details.find( '.dbkey .value' ).replaceWith( editableDbkey );\n }\n },\n\n // ......................................................................... events\n /** event map */\n events : _.extend( _.clone( _super.prototype.events ), {\n 'click .undelete-link' : '_clickUndeleteLink',\n 'click .purge-link' : '_clickPurgeLink',\n\n 'click .edit-btn' : function( ev ){ this.trigger( 'edit', this, ev ); },\n 'click .delete-btn' : function( ev ){ this.trigger( 'delete', this, ev ); },\n 'click .rerun-btn' : function( ev ){ this.trigger( 'rerun', this, ev ); },\n 'click .report-err-btn' : function( ev ){ this.trigger( 'report-err', this, ev ); },\n 'click .visualization-btn' : function( ev ){ this.trigger( 'visualize', this, ev ); },\n 'click .dbkey a' : function( ev ){ this.trigger( 'edit', this, ev ); }\n }),\n\n /** listener for item undelete (in the messages section) */\n _clickUndeleteLink : function( ev ){\n this.model.undelete();\n return false;\n },\n\n /** listener for item purge (in the messages section) */\n _clickPurgeLink : function( ev ){\n if( confirm( _l( 'This will permanently remove the data in your dataset. Are you sure?' ) ) ){\n this.model.purge();\n }\n return false;\n },\n\n // ......................................................................... misc\n /** string rep */\n toString : function(){\n var modelString = ( this.model )?( this.model + '' ):( '(no model)' );\n return 'HDAEditView(' + modelString + ')';\n }\n});\n\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nDatasetListItemEdit.prototype.templates = (function(){\n\n var warnings = _.extend( {}, _super.prototype.templates.warnings, {\n failed_metadata : BASE_MVC.wrapTemplate([\n // in this override, provide a link to the edit page\n '<% if( dataset.state === \"failed_metadata\" ){ %>',\n '
',\n '<% } %>'\n ], 'dataset' ),\n\n deleted : BASE_MVC.wrapTemplate([\n // in this override, provide links to undelete or purge the dataset\n '<% if( dataset.deleted && !dataset.purged ){ %>',\n // deleted not purged\n '
'\n ], 'dataset' );\n\n var warnings = _.extend( {}, _super.prototype.templates.warnings, {\n hidden : BASE_MVC.wrapTemplate([\n // add a warning when hidden\n '<% if( !dataset.visible ){ %>',\n '
',\n _l( 'This dataset has been hidden' ),\n '
',\n '<% } %>'\n ], 'dataset' )\n });\n\n return _.extend( {}, _super.prototype.templates, {\n titleBar : titleBarTemplate,\n warnings : warnings\n });\n}());\n\n\n\n//==============================================================================\n return {\n HDAListItemView : HDAListItemView\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/history/hda-li.js","define([\n \"mvc/dataset/dataset-model\",\n \"mvc/history/history-content-model\",\n \"mvc/base-mvc\",\n \"utils/localization\"\n], function( DATASET, HISTORY_CONTENT, BASE_MVC, _l ){\n'use strict';\n\n//==============================================================================\nvar _super = DATASET.DatasetAssociation,\n hcontentMixin = HISTORY_CONTENT.HistoryContentMixin;\n/** @class (HDA) model for a Galaxy dataset contained in and related to a history.\n */\nvar HistoryDatasetAssociation = _super.extend( BASE_MVC.mixin( hcontentMixin,\n/** @lends HistoryDatasetAssociation.prototype */{\n\n /** default attributes for a model */\n defaults : _.extend( {}, _super.prototype.defaults, hcontentMixin.defaults, {\n history_content_type: 'dataset',\n model_class : 'HistoryDatasetAssociation'\n }),\n}));\n\n//==============================================================================\n return {\n HistoryDatasetAssociation : HistoryDatasetAssociation\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/history/hda-model.js","define([\n \"mvc/dataset/states\",\n \"mvc/collection/collection-li\",\n \"mvc/collection/collection-view\",\n \"mvc/base-mvc\",\n \"utils/localization\"\n], function( STATES, DC_LI, DC_VIEW, BASE_MVC, _l ){\n\n'use strict';\n\n//==============================================================================\nvar _super = DC_LI.DCListItemView;\n/** @class Read only view for HistoryDatasetCollectionAssociation (a dataset collection inside a history).\n */\nvar HDCAListItemView = _super.extend(\n/** @lends HDCAListItemView.prototype */{\n\n className : _super.prototype.className + \" history-content\",\n\n /** event listeners */\n _setUpListeners : function(){\n _super.prototype._setUpListeners.call( this );\n this.listenTo( this.model, {\n 'change:tags change:populated change:visible' : function( model, options ){ this.render(); },\n });\n },\n\n /** Override to provide the proper collections panels as the foldout */\n _getFoldoutPanelClass : function(){\n switch( this.model.get( 'collection_type' ) ){\n case 'list':\n return DC_VIEW.ListCollectionView;\n case 'paired':\n return DC_VIEW.PairCollectionView;\n case 'list:paired':\n return DC_VIEW.ListOfPairsCollectionView;\n case 'list:list':\n return DC_VIEW.ListOfListsCollectionView;\n }\n throw new TypeError( 'Uknown collection_type: ' + this.model.get( 'collection_type' ) );\n },\n\n /** In this override, add the state as a class for use with state-based CSS */\n _swapNewRender : function( $newRender ){\n _super.prototype._swapNewRender.call( this, $newRender );\n //TODO: model currently has no state\n var state = !this.model.get( 'populated' ) ? STATES.RUNNING : STATES.OK;\n //if( this.model.has( 'state' ) ){\n this.$el.addClass( 'state-' + state );\n //}\n return this.$el;\n },\n\n // ......................................................................... misc\n /** String representation */\n toString : function(){\n var modelString = ( this.model )?( this.model + '' ):( '(no model)' );\n return 'HDCAListItemView(' + modelString + ')';\n }\n});\n\n/** underscore templates */\nHDCAListItemView.prototype.templates = (function(){\n\n var warnings = _.extend( {}, _super.prototype.templates.warnings, {\n hidden : BASE_MVC.wrapTemplate([\n // add a warning when hidden\n '<% if( !collection.visible ){ %>',\n '
',\n _l( 'This collection has been hidden' ),\n '
',\n '<% } %>'\n ], 'collection' )\n });\n\n// could steal this from hda-base (or use mixed content)\n var titleBarTemplate = BASE_MVC.wrapTemplate([\n // adding the hid display to the title\n '
',\n '',\n '
',\n //TODO: remove whitespace and use margin-right\n '<%- collection.hid %> ',\n '<%- collection.name %>',\n '
'\n ], 'collection' );\n\n return _.extend( {}, _super.prototype.templates, {\n warnings : warnings,\n titleBar : titleBarTemplate\n });\n}());\n\n\n//==============================================================================\n return {\n HDCAListItemView : HDCAListItemView\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/history/hdca-li.js","define([\n \"mvc/dataset/states\",\n \"mvc/base-mvc\",\n \"utils/localization\"\n], function( STATES, BASE_MVC, _l ){\n'use strict';\n\n//==============================================================================\n/** @class Mixin for HistoryContents content (HDAs, HDCAs).\n */\nvar HistoryContentMixin = {\n\n /** default attributes for a model */\n defaults : {\n /** parent (containing) history */\n history_id : null,\n /** some content_type (HistoryContents can contain mixed model classes) */\n history_content_type: null,\n /** indicating when/what order the content was generated in the context of the history */\n hid : null,\n /** whether the user wants the content shown (visible) */\n visible : true\n },\n\n // ........................................................................ mixed content element\n // In order to be part of a MIXED bbone collection, we can't rely on the id\n // (which may collide btwn models of different classes)\n // Instead, use type_id which prefixes the history_content_type so the bbone collection can differentiate\n idAttribute : 'type_id',\n\n // ........................................................................ common queries\n /** the more common alias of visible */\n hidden : function(){\n return !this.get( 'visible' );\n },\n\n//TODO: remove\n /** based on includeDeleted, includeHidden (gen. from the container control),\n * would this ds show in the list of ds's?\n * @param {Boolean} includeDeleted are we showing deleted hdas?\n * @param {Boolean} includeHidden are we showing hidden hdas?\n */\n isVisible : function( includeDeleted, includeHidden ){\n var isVisible = true;\n if( ( !includeDeleted )\n && ( this.get( 'deleted' ) || this.get( 'purged' ) ) ){\n isVisible = false;\n }\n if( ( !includeHidden )\n && ( !this.get( 'visible' ) ) ){\n isVisible = false;\n }\n return isVisible;\n },\n\n // ........................................................................ ajax\n //TODO?: these are probably better done on the leaf classes\n /** history content goes through the 'api/histories' API */\n urlRoot: Galaxy.root + 'api/histories/',\n\n /** full url spec. for this content */\n url : function(){\n var url = this.urlRoot + this.get( 'history_id' ) + '/contents/'\n + this.get('history_content_type') + 's/' + this.get( 'id' );\n return url;\n },\n\n /** save this content as not visible */\n hide : function( options ){\n if( !this.get( 'visible' ) ){ return jQuery.when(); }\n return this.save( { visible: false }, options );\n },\n /** save this content as visible */\n unhide : function( options ){\n if( this.get( 'visible' ) ){ return jQuery.when(); }\n return this.save( { visible: true }, options );\n },\n\n // ........................................................................ misc\n toString : function(){\n return ([ this.get( 'type_id' ), this.get( 'hid' ), this.get( 'name' ) ].join(':'));\n }\n};\n\n\n//==============================================================================\n return {\n HistoryContentMixin : HistoryContentMixin\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/history/history-content-model.js","\ndefine([\n \"mvc/history/history-contents\",\n \"mvc/history/history-preferences\",\n \"mvc/base/controlled-fetch-collection\",\n \"utils/utils\",\n \"mvc/base-mvc\",\n \"utils/localization\"\n], function( HISTORY_CONTENTS, HISTORY_PREFS, CONTROLLED_FETCH_COLLECTION, UTILS, BASE_MVC, _l ){\n'use strict';\n\n//==============================================================================\n/** @class Model for a Galaxy history resource - both a record of user\n * tool use and a collection of the datasets those tools produced.\n * @name History\n * @augments Backbone.Model\n */\nvar History = Backbone.Model\n .extend( BASE_MVC.LoggableMixin )\n .extend( BASE_MVC.mixin( BASE_MVC.SearchableModelMixin, /** @lends History.prototype */{\n _logNamespace : 'history',\n\n /** ms between fetches when checking running jobs/datasets for updates */\n UPDATE_DELAY : 4000,\n\n // values from api (may need more)\n defaults : {\n model_class : 'History',\n id : null,\n name : 'Unnamed History',\n state : 'new',\n\n deleted : false,\n contents_active : {},\n contents_states : {},\n },\n\n urlRoot: Galaxy.root + 'api/histories',\n\n contentsClass : HISTORY_CONTENTS.HistoryContents,\n\n /** What model fields to search with */\n searchAttributes : [\n 'name', 'annotation', 'tags'\n ],\n\n /** Adding title and singular tag */\n searchAliases : {\n title : 'name',\n tag : 'tags'\n },\n\n // ........................................................................ set up/tear down\n /** Set up the model\n * @param {Object} historyJSON model data for this History\n * @param {Object} options any extra settings including logger\n */\n initialize : function( historyJSON, options ){\n options = options || {};\n this.logger = options.logger || null;\n this.log( this + \".initialize:\", historyJSON, options );\n\n /** HistoryContents collection of the HDAs contained in this history. */\n this.contents = new this.contentsClass( [], {\n history : this,\n historyId : this.get( 'id' ),\n order : options.order,\n });\n\n this._setUpListeners();\n this._setUpCollectionListeners();\n\n /** cached timeout id for the dataset updater */\n this.updateTimeoutId = null;\n },\n\n /** set up any event listeners for this history including those to the contained HDAs\n * events: error:contents if an error occurred with the contents collection\n */\n _setUpListeners : function(){\n // if the model's id changes ('current' or null -> an actual id), update the contents history_id\n return this.on({\n 'error' : function( model, xhr, options, msg, details ){\n this.clearUpdateTimeout();\n },\n 'change:id' : function( model, newId ){\n if( this.contents ){\n this.contents.historyId = newId;\n }\n },\n });\n },\n\n /** event handlers for the contents submodels */\n _setUpCollectionListeners : function(){\n if( !this.contents ){ return this; }\n // bubble up errors\n return this.listenTo( this.contents, {\n 'error' : function(){\n this.trigger.apply( this, jQuery.makeArray( arguments ) );\n },\n });\n },\n\n // ........................................................................ derived attributes\n /** */\n contentsShown : function(){\n var contentsActive = this.get( 'contents_active' );\n var shown = contentsActive.active || 0;\n shown += this.contents.includeDeleted? contentsActive.deleted : 0;\n shown += this.contents.includeHidden? contentsActive.hidden : 0;\n return shown;\n },\n\n /** convert size in bytes to a more human readable version */\n nice_size : function(){\n var size = this.get( 'size' );\n return size? UTILS.bytesToString( size, true, 2 ) : _l( '(empty)' );\n },\n\n /** override to add nice_size */\n toJSON : function(){\n return _.extend( Backbone.Model.prototype.toJSON.call( this ), {\n nice_size : this.nice_size()\n });\n },\n\n /** override to allow getting nice_size */\n get : function( key ){\n if( key === 'nice_size' ){\n return this.nice_size();\n }\n return Backbone.Model.prototype.get.apply( this, arguments );\n },\n\n // ........................................................................ common queries\n /** T/F is this history owned by the current user (Galaxy.user)\n * Note: that this will return false for an anon user even if the history is theirs.\n */\n ownedByCurrUser : function(){\n // no currUser\n if( !Galaxy || !Galaxy.user ){\n return false;\n }\n // user is anon or history isn't owned\n if( Galaxy.user.isAnonymous() || Galaxy.user.id !== this.get( 'user_id' ) ){\n return false;\n }\n return true;\n },\n\n /** Return the number of running jobs assoc with this history (note: unknown === 0) */\n numOfUnfinishedJobs : function(){\n var unfinishedJobIds = this.get( 'non_ready_jobs' );\n return unfinishedJobIds? unfinishedJobIds.length : 0;\n },\n\n /** Return the number of running hda/hdcas in this history (note: unknown === 0) */\n numOfUnfinishedShownContents : function(){\n return this.contents.runningAndActive().length || 0;\n },\n\n // ........................................................................ updates\n _fetchContentRelatedAttributes : function(){\n var contentRelatedAttrs = [ 'size', 'non_ready_jobs', 'contents_active', 'hid_counter' ];\n return this.fetch({ data : $.param({ keys : contentRelatedAttrs.join( ',' ) }) });\n },\n\n /** check for any changes since the last time we updated (or fetch all if ) */\n refresh : function( options ){\n // console.log( this + '.refresh' );\n options = options || {};\n var self = this;\n\n // note if there was no previous update time, all summary contents will be fetched\n var lastUpdateTime = self.lastUpdateTime;\n // if we don't flip this, then a fully-fetched list will not be re-checked via fetch\n this.contents.allFetched = false;\n var fetchFn = self.contents.currentPage !== 0\n ? function(){ return self.contents.fetchPage( self.contents.currentPage ); }\n : function(){ return self.contents.fetchUpdated( lastUpdateTime ); };\n // note: if there was no previous update time, all summary contents will be fetched\n return fetchFn()\n .done( function( response, status, xhr ){\n var serverResponseDatetime;\n try {\n serverResponseDatetime = new Date( xhr.getResponseHeader( 'Date' ) );\n } catch( err ){}\n self.lastUpdateTime = serverResponseDatetime || new Date();\n self.checkForUpdates( options );\n });\n },\n\n /** continuously fetch updated contents every UPDATE_DELAY ms if this history's datasets or jobs are unfinished */\n checkForUpdates : function( options ){\n // console.log( this + '.checkForUpdates' );\n options = options || {};\n var delay = this.UPDATE_DELAY;\n var self = this;\n if( !self.id ){ return; }\n\n function _delayThenUpdate(){\n // prevent buildup of updater timeouts by clearing previous if any, then set new and cache id\n self.clearUpdateTimeout();\n self.updateTimeoutId = setTimeout( function(){\n self.refresh( options );\n }, delay );\n }\n\n // if there are still datasets in the non-ready state, recurse into this function with the new time\n var nonReadyContentCount = this.numOfUnfinishedShownContents();\n // console.log( 'nonReadyContentCount:', nonReadyContentCount );\n if( nonReadyContentCount > 0 ){\n _delayThenUpdate();\n\n } else {\n // no datasets are running, but currently runnning jobs may still produce new datasets\n // see if the history has any running jobs and continue to update if so\n // (also update the size for the user in either case)\n self._fetchContentRelatedAttributes()\n .done( function( historyData ){\n // console.log( 'non_ready_jobs:', historyData.non_ready_jobs );\n if( self.numOfUnfinishedJobs() > 0 ){\n _delayThenUpdate();\n\n } else {\n // otherwise, let listeners know that all updates have stopped\n self.trigger( 'ready' );\n }\n });\n }\n },\n\n /** clear the timeout and the cached timeout id */\n clearUpdateTimeout : function(){\n if( this.updateTimeoutId ){\n clearTimeout( this.updateTimeoutId );\n this.updateTimeoutId = null;\n }\n },\n\n // ........................................................................ ajax\n /** override to use actual Dates objects for create/update times */\n parse : function( response, options ){\n var parsed = Backbone.Model.prototype.parse.call( this, response, options );\n if( parsed.create_time ){\n parsed.create_time = new Date( parsed.create_time );\n }\n if( parsed.update_time ){\n parsed.update_time = new Date( parsed.update_time );\n }\n return parsed;\n },\n\n /** fetch this histories data (using options) then it's contents (using contentsOptions) */\n fetchWithContents : function( options, contentsOptions ){\n options = options || {};\n var self = this;\n\n // console.log( this + '.fetchWithContents' );\n // TODO: push down to a base class\n options.view = 'dev-detailed';\n\n // fetch history then use history data to fetch (paginated) contents\n return this.fetch( options ).then( function getContents( history ){\n self.contents.history = self;\n self.contents.setHistoryId( history.id );\n return self.fetchContents( contentsOptions );\n });\n },\n\n /** fetch this histories contents, adjusting options based on the stored history preferences */\n fetchContents : function( options ){\n options = options || {};\n var self = this;\n\n // we're updating, reset the update time\n self.lastUpdateTime = new Date();\n return self.contents.fetchCurrentPage( options );\n },\n\n /** save this history, _Mark_ing it as deleted (just a flag) */\n _delete : function( options ){\n if( this.get( 'deleted' ) ){ return jQuery.when(); }\n return this.save( { deleted: true }, options );\n },\n /** purge this history, _Mark_ing it as purged and removing all dataset data from the server */\n purge : function( options ){\n if( this.get( 'purged' ) ){ return jQuery.when(); }\n return this.save( { deleted: true, purged: true }, options );\n },\n /** save this history, _Mark_ing it as undeleted */\n undelete : function( options ){\n if( !this.get( 'deleted' ) ){ return jQuery.when(); }\n return this.save( { deleted: false }, options );\n },\n\n /** Make a copy of this history on the server\n * @param {Boolean} current if true, set the copy as the new current history (default: true)\n * @param {String} name name of new history (default: none - server sets to: Copy of )\n * @fires copied passed this history and the response JSON from the copy\n * @returns {xhr}\n */\n copy : function( current, name, allDatasets ){\n current = ( current !== undefined )?( current ):( true );\n if( !this.id ){\n throw new Error( 'You must set the history ID before copying it.' );\n }\n\n var postData = { history_id : this.id };\n if( current ){\n postData.current = true;\n }\n if( name ){\n postData.name = name;\n }\n if( !allDatasets ){\n postData.all_datasets = false;\n }\n postData.view = 'dev-detailed';\n\n var history = this;\n var copy = jQuery.post( this.urlRoot, postData );\n // if current - queue to setAsCurrent before firing 'copied'\n if( current ){\n return copy.then( function( response ){\n var newHistory = new History( response );\n return newHistory.setAsCurrent()\n .done( function(){\n history.trigger( 'copied', history, response );\n });\n });\n }\n return copy.done( function( response ){\n history.trigger( 'copied', history, response );\n });\n },\n\n setAsCurrent : function(){\n var history = this,\n xhr = jQuery.getJSON( Galaxy.root + 'history/set_as_current?id=' + this.id );\n\n xhr.done( function(){\n history.trigger( 'set-as-current', history );\n });\n return xhr;\n },\n\n // ........................................................................ misc\n toString : function(){\n return 'History(' + this.get( 'id' ) + ',' + this.get( 'name' ) + ')';\n }\n}));\n\n\n//==============================================================================\nvar _collectionSuper = CONTROLLED_FETCH_COLLECTION.InfinitelyScrollingCollection;\n/** @class A collection of histories (per user)\n * that maintains the current history as the first in the collection.\n * New or copied histories become the current history.\n */\nvar HistoryCollection = _collectionSuper.extend( BASE_MVC.LoggableMixin ).extend({\n _logNamespace : 'history',\n\n model : History,\n /** @type {String} initial order used by collection */\n order : 'update_time',\n /** @type {Number} limit used for the first fetch (or a reset) */\n limitOnFirstFetch : 10,\n /** @type {Number} limit used for each subsequent fetch */\n limitPerFetch : 10,\n\n initialize : function( models, options ){\n options = options || {};\n this.log( 'HistoryCollection.initialize', models, options );\n _collectionSuper.prototype.initialize.call( this, models, options );\n\n /** @type {boolean} should deleted histories be included */\n this.includeDeleted = options.includeDeleted || false;\n\n /** @type {String} encoded id of the history that's current */\n this.currentHistoryId = options.currentHistoryId;\n\n this.setUpListeners();\n // note: models are sent to reset *after* this fn ends; up to this point\n // the collection *is empty*\n },\n\n urlRoot : Galaxy.root + 'api/histories',\n url : function(){ return this.urlRoot; },\n\n /** set up reflexive event handlers */\n setUpListeners : function setUpListeners(){\n return this.on({\n // when a history is deleted, remove it from the collection (if optionally set to do so)\n 'change:deleted' : function( history ){\n // TODO: this becomes complicated when more filters are used\n this.debug( 'change:deleted', this.includeDeleted, history.get( 'deleted' ) );\n if( !this.includeDeleted && history.get( 'deleted' ) ){\n this.remove( history );\n }\n },\n // listen for a history copy, setting it to current\n 'copied' : function( original, newData ){\n this.setCurrent( new History( newData, [] ) );\n },\n // when a history is made current, track the id in the collection\n 'set-as-current' : function( history ){\n var oldCurrentId = this.currentHistoryId;\n this.trigger( 'no-longer-current', oldCurrentId );\n this.currentHistoryId = history.id;\n }\n });\n },\n\n /** override to change view */\n _buildFetchData : function( options ){\n return _.extend( _collectionSuper.prototype._buildFetchData.call( this, options ), {\n view : 'dev-detailed'\n });\n },\n\n /** override to filter out deleted and purged */\n _buildFetchFilters : function( options ){\n var superFilters = _collectionSuper.prototype._buildFetchFilters.call( this, options ) || {};\n var filters = {};\n if( !this.includeDeleted ){\n filters.deleted = false;\n filters.purged = false;\n } else {\n // force API to return both deleted and non\n //TODO: when the API is updated, remove this\n filters.deleted = null;\n }\n return _.defaults( superFilters, filters );\n },\n\n /** override to fetch current as well (as it may be outside the first 10, etc.) */\n fetchFirst : function( options ){\n var self = this;\n // TODO: batch?\n var xhr = $.when();\n if( this.currentHistoryId ){\n xhr = _collectionSuper.prototype.fetchFirst.call( self, {\n silent: true,\n limit : 1,\n filters: {\n // without these a deleted current history will return [] here and block the other xhr\n 'purged' : '',\n 'deleted' : '',\n 'encoded_id-in' : this.currentHistoryId,\n }\n });\n }\n return xhr.then( function(){\n options = options || {};\n options.offset = 0;\n return self.fetchMore( options );\n });\n },\n\n /** @type {Object} map of collection available sorting orders containing comparator fns */\n comparators : _.extend( _.clone( _collectionSuper.prototype.comparators ), {\n 'name' : BASE_MVC.buildComparator( 'name', { ascending: true }),\n 'name-dsc' : BASE_MVC.buildComparator( 'name', { ascending: false }),\n 'size' : BASE_MVC.buildComparator( 'size', { ascending: false }),\n 'size-asc' : BASE_MVC.buildComparator( 'size', { ascending: true }),\n }),\n\n /** override to always have the current history first */\n sort : function( options ){\n options = options || {};\n var silent = options.silent;\n var currentHistory = this.remove( this.get( this.currentHistoryId ) );\n _collectionSuper.prototype.sort.call( this, _.defaults({ silent: true }, options ) );\n this.unshift( currentHistory, { silent: true });\n if( !silent ){\n this.trigger( 'sort', this, options );\n }\n return this;\n },\n\n /** create a new history and by default set it to be the current history */\n create : function create( data, hdas, historyOptions, xhrOptions ){\n //TODO: .create is actually a collection function that's overridden here\n var collection = this,\n xhr = jQuery.getJSON( Galaxy.root + 'history/create_new_current' );\n return xhr.done( function( newData ){\n collection.setCurrent( new History( newData, [], historyOptions || {} ) );\n });\n },\n\n /** set the current history to the given history, placing it first in the collection.\n * Pass standard bbone options for use in unshift.\n * @triggers new-current passed history and this collection\n */\n setCurrent : function( history, options ){\n options = options || {};\n // new histories go in the front\n this.unshift( history, options );\n this.currentHistoryId = history.get( 'id' );\n if( !options.silent ){\n this.trigger( 'new-current', history, this );\n }\n return this;\n },\n\n toString: function toString(){\n return 'HistoryCollection(' + this.length + ',current:' + this.currentHistoryId + ')';\n }\n});\n\n\n//==============================================================================\nreturn {\n History : History,\n HistoryCollection : HistoryCollection\n};});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/history/history-model.js","define([\n \"mvc/list/list-item\",\n \"ui/loading-indicator\",\n \"mvc/base-mvc\",\n \"utils/localization\",\n \"ui/search-input\"\n], function( LIST_ITEM, LoadingIndicator, BASE_MVC, _l ){\n\n'use strict';\n\nvar logNamespace = 'list';\n/* ============================================================================\nTODO:\n\n============================================================================ */\n/** @class View for a list/collection of models and the sub-views of those models.\n * Sub-views must (at least have the interface if not) inherit from ListItemView.\n * (For a list panel that also includes some 'container' model (History->HistoryContents)\n * use ModelWithListPanel)\n *\n * Allows for:\n * searching collection/sub-views\n * selecting/multi-selecting sub-views\n *\n * Currently used:\n * for dataset/dataset-choice\n * as superclass of ModelListPanel\n */\nvar ListPanel = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend(/** @lends ListPanel.prototype */{\n _logNamespace : logNamespace,\n\n /** class to use for constructing the sub-views */\n viewClass : LIST_ITEM.ListItemView,\n /** class to used for constructing collection of sub-view models */\n collectionClass : Backbone.Collection,\n\n tagName : 'div',\n className : 'list-panel',\n\n /** (in ms) that jquery effects will use */\n fxSpeed : 'fast',\n\n /** string to display when the collection has no contents */\n emptyMsg : _l( 'This list is empty' ),\n /** displayed when no items match the search terms */\n noneFoundMsg : _l( 'No matching items found' ),\n /** string used for search placeholder */\n searchPlaceholder : _l( 'search' ),\n\n // ......................................................................... SET UP\n /** Set up the view, set up storage, bind listeners to HistoryContents events\n * @param {Object} attributes optional settings for the list\n */\n initialize : function( attributes, options ){\n attributes = attributes || {};\n // set the logger if requested\n if( attributes.logger ){\n this.logger = attributes.logger;\n }\n this.log( this + '.initialize:', attributes );\n\n // ---- instance vars\n /** how quickly should jquery fx run? */\n this.fxSpeed = _.has( attributes, 'fxSpeed' )?( attributes.fxSpeed ):( this.fxSpeed );\n\n /** filters for displaying subviews */\n this.filters = [];\n /** current search terms */\n this.searchFor = attributes.searchFor || '';\n\n /** loading indicator */\n // this.indicator = new LoadingIndicator( this.$el );\n\n /** currently showing selectors on items? */\n this.selecting = ( attributes.selecting !== undefined )? attributes.selecting : true;\n //this.selecting = false;\n\n /** cached selected item.model.ids to persist btwn renders */\n this.selected = attributes.selected || [];\n /** the last selected item.model.id */\n this.lastSelected = null;\n\n /** are sub-views draggable */\n this.dragItems = attributes.dragItems || false;\n\n /** list item view class (when passed models) */\n this.viewClass = attributes.viewClass || this.viewClass;\n\n /** list item views */\n this.views = [];\n /** list item models */\n this.collection = attributes.collection || this._createDefaultCollection();\n\n /** filter fns run over collection items to see if they should show in the list */\n this.filters = attributes.filters || [];\n\n /** override $scrollContainer fn via attributes - fn should return jq for elem to call scrollTo on */\n this.$scrollContainer = attributes.$scrollContainer || this.$scrollContainer;\n\n /** @type {String} generic title */\n this.title = attributes.title || '';\n /** @type {String} generic subtitle */\n this.subtitle = attributes.subtitle || '';\n\n this._setUpListeners();\n },\n\n // ------------------------------------------------------------------------ listeners\n /** create any event listeners for the list */\n _setUpListeners : function(){\n this.off();\n\n //TODO: move errorHandler down into list-view from history-view or\n // pass to global error handler (Galaxy)\n this.on({\n error: function( model, xhr, options, msg, details ){\n //this.errorHandler( model, xhr, options, msg, details );\n console.error( model, xhr, options, msg, details );\n },\n // show hide the loading indicator\n loading: function(){\n this._showLoadingIndicator( 'loading...', 40 );\n },\n 'loading-done': function(){\n this._hideLoadingIndicator( 40 );\n },\n });\n\n // throw the first render up as a diff namespace using once (for outside consumption)\n this.once( 'rendered', function(){\n this.trigger( 'rendered:initial', this );\n });\n\n this._setUpCollectionListeners();\n this._setUpViewListeners();\n return this;\n },\n\n /** create and return a collection for when none is initially passed */\n _createDefaultCollection : function(){\n // override\n return new this.collectionClass([]);\n },\n\n /** listening for collection events */\n _setUpCollectionListeners : function(){\n this.log( this + '._setUpCollectionListeners', this.collection );\n this.stopListening( this.collection );\n\n // bubble up error events\n this.listenTo( this.collection, {\n error : function( model, xhr, options, msg, details ){\n this.trigger( 'error', model, xhr, options, msg, details );\n },\n update : function( collection, options ){\n var changes = options.changes;\n // console.info( collection + ', update:', changes, '\\noptions:', options );\n // more than one: render everything\n if( options.renderAll || ( changes.added.length + changes.removed.length > 1 ) ){\n return this.renderItems();\n }\n // otherwise, let the single add/remove handlers do it\n if( changes.added.length === 1 ){\n return this.addItemView( _.first( changes.added ), collection, options );\n }\n if( changes.removed.length === 1 ){\n return this.removeItemView( _.first( changes.removed ), collection, options );\n }\n }\n });\n return this;\n },\n\n /** listening for sub-view events that bubble up with the 'view:' prefix */\n _setUpViewListeners : function(){\n this.log( this + '._setUpViewListeners' );\n\n // shift to select a range\n this.on({\n 'view:selected': function( view, ev ){\n if( ev && ev.shiftKey && this.lastSelected ){\n var lastSelectedView = this.viewFromModelId( this.lastSelected );\n if( lastSelectedView ){\n this.selectRange( view, lastSelectedView );\n }\n } else if( ev && ev.altKey && !this.selecting ){\n this.showSelectors();\n }\n this.selected.push( view.model.id );\n this.lastSelected = view.model.id;\n },\n\n 'view:de-selected': function( view, ev ){\n this.selected = _.without( this.selected, view.model.id );\n }\n });\n },\n\n // ------------------------------------------------------------------------ rendering\n /** Render this content, set up ui.\n * @param {Number or String} speed the speed of the render\n */\n render : function( speed ){\n this.log( this + '.render', speed );\n var $newRender = this._buildNewRender();\n this._setUpBehaviors( $newRender );\n this._queueNewRender( $newRender, speed );\n return this;\n },\n\n /** Build a temp div containing the new children for the view's $el. */\n _buildNewRender : function(){\n this.debug( this + '(ListPanel)._buildNewRender' );\n var $newRender = $( this.templates.el( {}, this ) );\n this._renderControls( $newRender );\n this._renderTitle( $newRender );\n this._renderSubtitle( $newRender );\n this._renderSearch( $newRender );\n this.renderItems( $newRender );\n return $newRender;\n },\n\n /** Build a temp div containing the new children for the view's $el. */\n _renderControls : function( $newRender ){\n this.debug( this + '(ListPanel)._renderControls' );\n var $controls = $( this.templates.controls( {}, this ) );\n $newRender.find( '.controls' ).replaceWith( $controls );\n return $controls;\n },\n\n /** return a jQuery object containing the title DOM */\n _renderTitle : function( $where ){\n //$where = $where || this.$el;\n //$where.find( '.title' ).replaceWith( ... )\n },\n\n /** return a jQuery object containing the subtitle DOM (if any) */\n _renderSubtitle : function( $where ){\n //$where = $where || this.$el;\n //$where.find( '.title' ).replaceWith( ... )\n },\n\n /** Fade out the old el, swap in the new contents, then fade in.\n * @param {Number or String} speed jq speed to use for rendering effects\n * @fires rendered when rendered\n */\n _queueNewRender : function( $newRender, speed ) {\n speed = ( speed === undefined )?( this.fxSpeed ):( speed );\n var panel = this;\n panel.log( '_queueNewRender:', $newRender, speed );\n\n $( panel ).queue( 'fx', [\n function( next ){\n panel.$el.fadeOut( speed, next );\n },\n function( next ){\n panel._swapNewRender( $newRender );\n next();\n },\n function( next ){\n panel.$el.fadeIn( speed, next );\n },\n function( next ){\n panel.trigger( 'rendered', panel );\n next();\n }\n ]);\n },\n\n /** empty out the current el, move the $newRender's children in */\n _swapNewRender : function( $newRender ){\n this.$el.empty().attr( 'class', this.className ).append( $newRender.children() );\n if( this.selecting ){ this.showSelectors( 0 ); }\n return this;\n },\n\n /** Set up any behaviors, handlers (ep. plugins) that need to be called when the entire view has been built but\n * not attached to the page yet.\n */\n _setUpBehaviors : function( $where ){\n $where = $where || this.$el;\n this.$controls( $where ).find('[title]').tooltip();\n // set up the pupup for actions available when multi selecting\n this._renderMultiselectActionMenu( $where );\n return this;\n },\n\n /** render a menu containing the actions available to sets of selected items */\n _renderMultiselectActionMenu : function( $where ){\n $where = $where || this.$el;\n var $menu = $where.find( '.list-action-menu' ),\n actions = this.multiselectActions();\n if( !actions.length ){\n return $menu.empty();\n }\n\n var $newMenu = $([\n '
',\n '',\n '
', '
',\n '
'\n ].join(''));\n var $actions = actions.map( function( action ){\n var html = [ '
'\n ]);\n\n return {\n el : elTemplate,\n controls : controlsTemplate\n };\n}());\n\n\n//=============================================================================\n/** View for a model that has a sub-collection (e.g. History, DatasetCollection)\n * Allows:\n * the model to be reset\n * auto assign panel.collection to panel.model[ panel.modelCollectionKey ]\n *\n */\nvar ModelListPanel = ListPanel.extend({\n\n /** key of attribute in model to assign to this.collection */\n modelCollectionKey : 'contents',\n\n initialize : function( attributes ){\n ListPanel.prototype.initialize.call( this, attributes );\n this.selecting = ( attributes.selecting !== undefined )? attributes.selecting : false;\n\n this.setModel( this.model, attributes );\n },\n\n /** release/free/shutdown old models and set up panel for new models\n * @fires new-model with the panel as parameter\n */\n setModel : function( model, attributes ){\n attributes = attributes || {};\n this.debug( this + '.setModel:', model, attributes );\n\n this.freeModel();\n this.freeViews();\n\n if( model ){\n var oldModelId = this.model? this.model.get( 'id' ): null;\n\n // set up the new model with user, logger, storage, events\n this.model = model;\n if( this.logger ){\n this.model.logger = this.logger;\n }\n this._setUpModelListeners();\n\n //TODO: relation btwn model, collection becoming tangled here\n // free the collection, and assign the new collection to either\n // the model[ modelCollectionKey ], attributes.collection, or an empty vanilla collection\n this.stopListening( this.collection );\n this.collection = this.model[ this.modelCollectionKey ]\n || attributes.collection\n || this._createDefaultCollection();\n this._setUpCollectionListeners();\n\n if( oldModelId && model.get( 'id' ) !== oldModelId ){\n this.trigger( 'new-model', this );\n }\n }\n return this;\n },\n\n /** free the current model and all listeners for it, free any views for the model */\n freeModel : function(){\n // stop/release the previous model, and clear cache to sub-views\n if( this.model ){\n this.stopListening( this.model );\n //TODO: see base-mvc\n //this.model.free();\n //this.model = null;\n }\n return this;\n },\n\n // ------------------------------------------------------------------------ listening\n /** listening for model events */\n _setUpModelListeners : function(){\n // override\n this.log( this + '._setUpModelListeners', this.model );\n // bounce model errors up to the panel\n this.listenTo( this.model, 'error', function(){\n var args = Array.prototype.slice.call( arguments, 0 );\n //args.unshift( 'model:error' );\n args.unshift( 'error' );\n this.trigger.apply( this, args );\n }, this );\n\n // debugging\n if( this.logger ){\n this.listenTo( this.model, 'all', function( event ){\n this.info( this + '(model)', event, arguments );\n });\n }\n return this;\n },\n\n /** Build a temp div containing the new children for the view's $el.\n */\n _renderControls : function( $newRender ){\n this.debug( this + '(ModelListPanel)._renderControls' );\n var json = this.model? this.model.toJSON() : {},\n $controls = $( this.templates.controls( json, this ) );\n $newRender.find( '.controls' ).replaceWith( $controls );\n return $controls;\n },\n\n // ------------------------------------------------------------------------ misc\n /** Return a string rep of the panel */\n toString : function(){\n return 'ModelListPanel(' + this.model + ')';\n }\n});\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nModelListPanel.prototype.templates = (function(){\n\n var controlsTemplate = BASE_MVC.wrapTemplate([\n '
',\n '
',\n //TODO: this is really the only difference - consider factoring titlebar out\n '
<%- model.name %>
',\n '
',\n '
<%- view.subtitle %>
',\n '',\n '',\n\n '
',\n '',\n '
',\n\n '
',\n '
',\n '',\n '',\n '
',\n '
',\n '
',\n '
',\n '
'\n ]);\n\n return _.extend( _.clone( ListPanel.prototype.templates ), {\n controls : controlsTemplate\n });\n}());\n\n\n//=============================================================================\n return {\n ListPanel : ListPanel,\n ModelListPanel : ModelListPanel\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/list/list-view.js","define([\n \"utils/localization\"\n], function( _l ){\n'use strict';\n\n//TODO: toastr is another possibility - I didn't see where I might add details, tho\n\n/* ============================================================================\nError modals meant to replace the o-so-easy alerts.\n\nThese are currently styled as errormessages but use the Galaxy.modal\ninfrastructure to be shown/closed. They're capable of showing details in a\ntogglable dropdown and the details are formatted in a pre.\n\nExample:\n errorModal( 'Heres a message', 'A Title', { some_details: 'here' });\n errorModal( 'Heres a message' ); // no details, title is 'Error'\n\nThere are three specialized forms:\n offlineErrorModal a canned response for when there's no connection\n badGatewayErrorModal canned response for when Galaxy is restarting\n ajaxErrorModal plugable into any Backbone class as an\n error event handler by accepting the error args: model, xhr, options\n\nExamples:\n if( navigator.offLine ){ offlineErrorModal(); }\n if( xhr.status === 502 ){ badGatewayErrorModal(); }\n this.listenTo( this.model, 'error', ajaxErrorModal );\n\n============================================================================ */\n\nvar CONTACT_MSG = _l( 'Please contact a Galaxy administrator if the problem persists.' );\nvar DEFAULT_AJAX_ERR_MSG = _l( 'An error occurred while updating information with the server.' );\nvar DETAILS_MSG = _l( 'The following information can assist the developers in finding the source of the error:' );\n\n/** private helper that builds the modal and handles adding details */\nfunction _errorModal( message, title, details ){\n // create and return the modal, adding details button only if needed\n Galaxy.modal.show({\n title : title,\n body : message,\n closing_events : true,\n buttons : { Ok: function(){ Galaxy.modal.hide(); } },\n });\n Galaxy.modal.$el.addClass( 'error-modal' );\n\n if( details ){\n Galaxy.modal.$( '.error-details' ).add( Galaxy.modal.$( 'button:contains(\"Details\")' ) ).remove();\n $( '' ).addClass( 'error-details' )\n .hide().appendTo( Galaxy.modal.$( '.modal-content' ) )\n .append([\n $( '' ).text( DETAILS_MSG ),\n $( '' ).text( JSON.stringify( details, null, ' ' ) )\n ]);\n\n $( '' )\n .appendTo( Galaxy.modal.$( '.buttons' ) )\n .click( function(){ Galaxy.modal.$( '.error-details' ).toggle(); });\n }\n return Galaxy.modal;\n}\n\n/** Display a modal showing an error message but fallback to alert if there's no modal */\nfunction errorModal( message, title, details ){\n if( !message ){ return; }\n\n message = _l( message );\n title = _l( title ) || _l( 'Error:' );\n if( window.Galaxy && Galaxy.modal ){\n return _errorModal( message, title, details );\n }\n\n alert( title + '\\n\\n' + message );\n console.log( 'error details:', JSON.stringify( details ) );\n}\n\n\n// ----------------------------------------------------------------------------\n/** display a modal when the user may be offline */\nfunction offlineErrorModal(){\n return errorModal(\n _l( 'You appear to be offline. Please check your connection and try again.' ),\n _l( 'Offline?' )\n );\n}\n\n\n// ----------------------------------------------------------------------------\n/** 502 messages that should be displayed when galaxy is restarting */\nfunction badGatewayErrorModal(){\n return errorModal(\n _l( 'Galaxy is currently unreachable. Please try again in a few minutes.' ) + ' ' + CONTACT_MSG,\n _l( 'Cannot connect to Galaxy' )\n );\n}\n\n\n// ----------------------------------------------------------------------------\n/** display a modal (with details) about a failed Backbone ajax operation */\nfunction ajaxErrorModal( model, xhr, options, message, title ){\n message = message || DEFAULT_AJAX_ERR_MSG;\n message += ' ' + CONTACT_MSG;\n title = title || _l( 'An error occurred' );\n var details = _ajaxDetails( model, xhr, options );\n return errorModal( message, title, details );\n}\n\n/** build details which may help debugging the ajax call */\nfunction _ajaxDetails( model, xhr, options ){\n return {\n//TODO: still can't manage Raven id\n raven : _.result( window.Raven, 'lastEventId' ),\n userAgent : navigator.userAgent,\n onLine : navigator.onLine,\n version : _.result( Galaxy.config, 'version_major' ),\n xhr : _.omit( xhr, _.functions( xhr ) ),\n options : _.omit( options, 'xhr' ),\n // add ajax data from Galaxy object cache\n url : _.result( Galaxy.lastAjax, 'url' ),\n data : _.result( Galaxy.lastAjax, 'data' ),\n // backbone stuff (auto-redacting email for user)\n model : _.result( model, 'toJSON' , model + '' ),\n user : _.omit( _.result( Galaxy.user, 'toJSON' ), 'email' ),\n };\n}\n\n\n//=============================================================================\n return {\n errorModal : errorModal,\n offlineErrorModal : offlineErrorModal,\n badGatewayErrorModal: badGatewayErrorModal,\n ajaxErrorModal : ajaxErrorModal\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/ui/error-modal.js","define([\n //jquery\n //backbone\n], function(){\n// =============================================================================\n/**\n * view for a popup menu\n */\nvar PopupMenu = Backbone.View.extend({\n//TODO: maybe better as singleton off the Galaxy obj\n /** Cache the desired button element and options, set up the button click handler\n * NOTE: attaches this view as HTML/jQ data on the button for later use.\n */\n initialize: function( $button, options ){\n // default settings\n this.$button = $button;\n if( !this.$button.length ){\n this.$button = $( '' );\n }\n this.options = options || [];\n this.$button.data( 'popupmenu', this );\n\n // set up button click -> open menu behavior\n var menu = this;\n this.$button.click( function( event ){\n // if there's already a menu open, remove it\n $( '.popmenu-wrapper' ).remove();\n menu._renderAndShow( event );\n return false;\n });\n },\n\n // render the menu, append to the page body at the click position, and set up the 'click-away' handlers, show\n _renderAndShow: function( clickEvent ){\n this.render();\n this.$el.appendTo( 'body' ).css( this._getShownPosition( clickEvent )).show();\n this._setUpCloseBehavior();\n },\n\n // render the menu\n // this menu doesn't attach itself to the DOM ( see _renderAndShow )\n render: function(){\n // render the menu body absolute and hidden, fill with template\n this.$el.addClass( 'popmenu-wrapper' ).hide()\n .css({ position : 'absolute' })\n .html( this.template( this.$button.attr( 'id' ), this.options ));\n\n // set up behavior on each link/anchor elem\n if( this.options.length ){\n var menu = this;\n //precondition: there should be one option per li\n this.$el.find( 'li' ).each( function( i, li ){\n var option = menu.options[i];\n\n // if the option has 'func', call that function when the anchor is clicked\n if( option.func ){\n $( this ).children( 'a.popupmenu-option' ).click( function( event ){\n option.func.call( menu, event, option );\n // We must preventDefault otherwise clicking \"cancel\"\n // on a purge or something still navigates and causes\n // the action.\n event.preventDefault();\n // bubble up so that an option click will call the close behavior\n });\n }\n });\n }\n return this;\n },\n\n template : function( id, options ){\n return [\n '
'\n ].join('')),\n\n /** the middle: unpaired, divider, and paired */\n middle : _.template([\n // contains two flex rows (rows that fill available space) and a divider btwn\n '
'\n ].join('')),\n\n /** help content */\n helpContent : _.template([\n '
', _l([\n 'Collections of paired datasets are ordered lists of dataset pairs (often forward and reverse reads). ',\n 'These collections can be passed to tools and workflows in order to have analyses done on each member of ',\n 'the entire group. This interface allows you to create a collection, choose which datasets are paired, ',\n 'and re-order the final collection.'\n ].join( '' )), '
',\n '
', _l([\n 'Unpaired datasets are shown in the unpaired section ',\n '(hover over the underlined words to highlight below). ',\n 'Paired datasets are shown in the paired section.',\n '
To pair datasets, you can:',\n '
Click a dataset in the ',\n 'forward column ',\n 'to select it then click a dataset in the ',\n 'reverse column.',\n '
',\n '
Click one of the \"Pair these datasets\" buttons in the ',\n 'middle column ',\n 'to pair the datasets in a particular row.',\n '
',\n '
Click \"Auto-pair\" ',\n 'to have your datasets automatically paired based on name.',\n '
',\n '
'\n ].join( '' )), '',\n '
', _l([\n '
You can filter what is shown in the unpaired sections by:',\n '
Entering partial dataset names in either the ',\n 'forward filter or ',\n 'reverse filter.',\n '
',\n '
Choosing from a list of preset filters by clicking the ',\n '\"Choose filters\" link.',\n '
Clearing the filters by clicking the ',\n '\"Clear filters\" link.',\n '
',\n '
'\n ].join( '' )), '',\n '
', _l([\n 'To unpair individual dataset pairs, click the ',\n 'unpair buttons ( ). ',\n 'Click the \"Unpair all\" link to unpair all pairs.'\n ].join( '' )), '
',\n '
', _l([\n 'You can include or remove the file extensions (e.g. \".fastq\") from your pair names by toggling the ',\n '\"Remove file extensions from pair names?\" control.'\n ].join( '' )), '
',\n '
', _l([\n 'Once your collection is complete, enter a name and ',\n 'click \"Create list\". ',\n '(Note: you do not have to pair all unpaired datasets to finish.)'\n ].join( '' )), '
'\n ].join(''))\n })\n});\n\n//=============================================================================\n/** a modal version of the paired collection creator */\nvar pairedCollectionCreatorModal = function _pairedCollectionCreatorModal( datasets, options ){\n\n var deferred = jQuery.Deferred(),\n creator;\n\n options = _.defaults( options || {}, {\n datasets : datasets,\n oncancel : function(){\n Galaxy.modal.hide();\n deferred.reject( 'cancelled' );\n },\n oncreate : function( creator, response ){\n Galaxy.modal.hide();\n deferred.resolve( response );\n }\n });\n\n if( !window.Galaxy || !Galaxy.modal ){\n throw new Error( 'Galaxy or Galaxy.modal not found' );\n }\n\n creator = new PairedCollectionCreator( options );\n Galaxy.modal.show({\n title : 'Create a collection of paired datasets',\n body : creator.$el,\n width : '80%',\n height : '800px',\n closing_events: true\n });\n creator.render();\n window.creator = creator;\n\n //TODO: remove modal header\n return deferred;\n};\n\n\n//=============================================================================\nfunction createListOfPairsCollection( collection, defaultHideSourceItems ){\n var elements = collection.toJSON();\n//TODO: validate elements\n return pairedCollectionCreatorModal( elements, {\n historyId : collection.historyId,\n defaultHideSourceItems: defaultHideSourceItems\n });\n}\n\n\n//=============================================================================\n return {\n PairedCollectionCreator : PairedCollectionCreator,\n pairedCollectionCreatorModal : pairedCollectionCreatorModal,\n createListOfPairsCollection : createListOfPairsCollection\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js","define([\n \"mvc/collection/list-collection-creator\",\n \"mvc/history/hdca-model\",\n \"mvc/base-mvc\",\n \"utils/localization\"\n], function( LIST_CREATOR, HDCA, BASE_MVC, _l ){\n\n'use strict';\n\nvar logNamespace = 'collections';\n/*==============================================================================\nTODO:\n the paired creator doesn't really mesh with the list creator as parent\n it may be better to make an abstract super class for both\n composites may inherit from this (or vis-versa)\n PairedDatasetCollectionElementView doesn't make a lot of sense\n\n==============================================================================*/\n/** */\nvar PairedDatasetCollectionElementView = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend({\n _logNamespace : logNamespace,\n\n//TODO: use proper class (DatasetDCE or NestedDCDCE (or the union of both))\n tagName : 'li',\n className : 'collection-element',\n\n initialize : function( attributes ){\n this.element = attributes.element || {};\n this.identifier = attributes.identifier;\n },\n\n render : function(){\n this.$el\n .attr( 'data-element-id', this.element.id )\n .html( this.template({ identifier: this.identifier, element: this.element }) );\n return this;\n },\n\n //TODO: lots of unused space in the element - possibly load details and display them horiz.\n template : _.template([\n '<%- identifier %>',\n '<%- element.name %>',\n ].join('')),\n\n /** remove the DOM and any listeners */\n destroy : function(){\n this.off();\n this.$el.remove();\n },\n\n /** string rep */\n toString : function(){\n return 'DatasetCollectionElementView()';\n }\n});\n\n\n// ============================================================================\nvar _super = LIST_CREATOR.ListCollectionCreator;\n\n/** An interface for building collections.\n */\nvar PairCollectionCreator = _super.extend({\n\n /** the class used to display individual elements */\n elementViewClass : PairedDatasetCollectionElementView,\n /** the class this creator will create and save */\n collectionClass : HDCA.HistoryPairDatasetCollection,\n className : 'pair-collection-creator collection-creator flex-row-container',\n\n /** override to no-op */\n _mangleDuplicateNames : function(){},\n\n // TODO: this whole pattern sucks. There needs to be two classes of problem area:\n // bad inital choices and\n // when the user has painted his/her self into a corner during creation/use-of-the-creator\n /** render the entire interface */\n render : function( speed, callback ){\n if( this.workingElements.length === 2 ){\n return _super.prototype.render.call( this, speed, callback );\n }\n return this._renderInvalid( speed, callback );\n },\n\n // ------------------------------------------------------------------------ rendering elements\n /** render forward/reverse */\n _renderList : function( speed, callback ){\n //this.debug( '-- _renderList' );\n //precondition: there are two valid elements in workingElements\n var creator = this,\n $tmp = jQuery( '' ),\n $list = creator.$list();\n\n // lose the original views, create the new, append all at once, then call their renders\n _.each( this.elementViews, function( view ){\n view.destroy();\n creator.removeElementView( view );\n });\n $tmp.append( creator._createForwardElementView().$el );\n $tmp.append( creator._createReverseElementView().$el );\n $list.empty().append( $tmp.children() );\n _.invoke( creator.elementViews, 'render' );\n },\n\n /** create the forward element view */\n _createForwardElementView : function(){\n return this._createElementView( this.workingElements[0], { identifier: 'forward' } );\n },\n\n /** create the forward element view */\n _createReverseElementView : function(){\n return this._createElementView( this.workingElements[1], { identifier: 'reverse' } );\n },\n\n /** create an element view, cache in elementViews, and return */\n _createElementView : function( element, options ){\n var elementView = new this.elementViewClass( _.extend( options, {\n element : element,\n }));\n this.elementViews.push( elementView );\n return elementView;\n },\n\n /** swap the forward, reverse elements and re-render */\n swap : function(){\n this.workingElements = [\n this.workingElements[1],\n this.workingElements[0],\n ];\n this._renderList();\n },\n\n events : _.extend( _.clone( _super.prototype.events ), {\n 'click .swap' : 'swap',\n }),\n\n // ------------------------------------------------------------------------ templates\n //TODO: move to require text plugin and load these as text\n //TODO: underscore currently unnecc. bc no vars are used\n //TODO: better way of localizing text-nodes in long strings\n /** underscore template fns attached to class */\n templates : _.extend( _.clone( _super.prototype.templates ), {\n /** the middle: element list */\n middle : _.template([\n '
'\n ].join('')),\n\n /** help content */\n helpContent : _.template([\n '
', _l([\n 'Pair collections are permanent collections containing two datasets: one forward and one reverse. ',\n 'Often these are forward and reverse reads. The pair collections can be passed to tools and ',\n 'workflows in order to have analyses done on both datasets. This interface allows ',\n 'you to create a pair, name it, and swap which is forward and which reverse.'\n ].join( '' )), '
',\n '
',\n '
', _l([\n 'Click the \"Swap\" link to make your forward dataset the reverse ',\n 'and the reverse dataset forward.'\n ].join( '' )), '
',\n '
', _l([\n 'Click the \"Cancel\" button to exit the interface.'\n ].join( '' )), '
',\n '
',\n '
', _l([\n 'Once your collection is complete, enter a name and ',\n 'click \"Create list\".'\n ].join( '' )), '
'\n ].join('')),\n\n /** a simplified page communicating what went wrong and why the user needs to reselect something else */\n invalidInitial : _.template([\n '
',\n '
',\n '',\n '<% if( _.size( problems ) ){ %>',\n _l( 'The following selections could not be included due to problems' ),\n '
<% _.each( problems, function( problem ){ %>',\n '
<%- problem.element.name %>: <%- problem.text %>
',\n '<% }); %>
',\n '<% } else if( _.size( elements ) === 0 ){ %>',\n _l( 'No datasets were selected' ), '.',\n '<% } else if( _.size( elements ) === 1 ){ %>',\n _l( 'Only one dataset was selected' ), ': <%- elements[0].name %>',\n '<% } else if( _.size( elements ) > 2 ){ %>',\n _l( 'Too many datasets were selected' ),\n ': <%- _.pluck( elements, \"name\" ).join( \", \") %>',\n '<% } %>',\n ' ',\n _l( 'Two (and only two) elements are needed for the pair' ), '. ',\n _l( 'You may need to ' ),\n '', _l( 'cancel' ), ' ',\n _l( 'and reselect new elements' ), '.',\n '',\n '
',\n '
',\n ''\n ].join('')),\n }),\n\n // ------------------------------------------------------------------------ misc\n /** string rep */\n toString : function(){ return 'PairCollectionCreator'; }\n});\n\n\n//==============================================================================\n/** List collection flavor of collectionCreatorModal. */\nvar pairCollectionCreatorModal = function _pairCollectionCreatorModal( elements, options ){\n options = options || {};\n options.title = _l( 'Create a collection from a pair of datasets' );\n return LIST_CREATOR.collectionCreatorModal( elements, options, PairCollectionCreator );\n};\n\n\n//==============================================================================\n/** Use a modal to create a pair collection, then add it to the given history contents.\n * @returns {Deferred} resolved when the collection is added to the history.\n */\nfunction createPairCollection( contents, defaultHideSourceItems ){\n var elements = contents.toJSON(),\n promise = pairCollectionCreatorModal( elements, {\n defaultHideSourceItems: defaultHideSourceItems,\n creationFn : function( elements, name, hideSourceItems ){\n elements = [\n { name: \"forward\", src: \"hda\", id: elements[0].id },\n { name: \"reverse\", src: \"hda\", id: elements[1].id }\n ];\n return contents.createHDCA( elements, 'paired', name, hideSourceItems );\n }\n });\n return promise;\n}\n\n//==============================================================================\n return {\n PairCollectionCreator : PairCollectionCreator,\n pairCollectionCreatorModal : pairCollectionCreatorModal,\n createPairCollection : createPairCollection,\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/collection/pair-collection-creator.js","define([\n \"mvc/ui/ui-modal\",\n \"mvc/ui/error-modal\",\n \"utils/localization\"\n], function( MODAL, ERROR_MODAL, _l ){\n\n'use strict';\n\n//==============================================================================\n/**\n * A dialog/modal that allows copying a user history or 'importing' from user\n * another. Generally called via historyCopyDialog below.\n * @type {Object}\n */\nvar CopyDialog = {\n\n // language related strings/fns\n defaultName : _.template( \"Copy of '<%- name %>'\" ),\n title : _.template( _l( 'Copying history' ) + ' \"<%- name %>\"' ),\n submitLabel : _l( 'Copy' ),\n errorMessage : _l( 'History could not be copied.' ),\n progressive : _l( 'Copying history' ),\n activeLabel : _l( 'Copy only the active, non-deleted datasets' ),\n allLabel : _l( 'Copy all datasets including deleted ones' ),\n anonWarning : _l( 'As an anonymous user, unless you login or register, you will lose your current history ' ) +\n _l( 'after copying this history. ' ),\n\n // template for modal body\n _template : _.template([\n //TODO: remove inline styles\n // show a warning message for losing current to anon users\n '<% if( isAnon ){ %>',\n '
',\n '<% } %>',\n ''\n ].join( '' )),\n\n // empty modal body and let the user know the copy is happening\n _showAjaxIndicator : function _showAjaxIndicator(){\n var indicator = '
' + this.progressive + '...
';\n this.modal.$( '.modal-body' ).empty().append( indicator ).css({ 'margin-top': '8px' });\n },\n\n // (sorta) public interface - display the modal, render the form, and potentially copy the history\n // returns a jQuery.Deferred done->history copied, fail->user cancelled\n dialog : function _dialog( modal, history, options ){\n options = options || {};\n\n var dialog = this,\n deferred = jQuery.Deferred(),\n // TODO: getting a little byzantine here\n defaultCopyNameFn = options.nameFn || this.defaultName,\n defaultCopyName = defaultCopyNameFn({ name: history.get( 'name' ) }),\n // TODO: these two might be simpler as one 3 state option (all,active,no-choice)\n defaultCopyWhat = options.allDatasets? 'copy-all' : 'copy-non-deleted',\n allowAll = !_.isUndefined( options.allowAll )? options.allowAll : true,\n autoClose = !_.isUndefined( options.autoClose )? options.autoClose : true;\n\n this.modal = modal;\n\n\n // validate the name and copy if good\n function checkNameAndCopy(){\n var name = modal.$( '#copy-modal-title' ).val();\n if( !name ){\n modal.$( '.invalid-title' ).show();\n return;\n }\n // get further settings, shut down and indicate the ajax call, then hide and resolve/reject\n var copyAllDatasets = modal.$( 'input[name=\"copy-what\"]:checked' ).val() === 'copy-all';\n modal.$( 'button' ).prop( 'disabled', true );\n dialog._showAjaxIndicator();\n history.copy( true, name, copyAllDatasets )\n .done( function( response ){\n deferred.resolve( response );\n })\n .fail( function( xhr, status, message ){\n var options = { name: name, copyAllDatasets: copyAllDatasets };\n ERROR_MODAL.ajaxErrorModal( history, xhr, options, dialog.errorMessage );\n deferred.rejectWith( deferred, arguments );\n })\n .done( function(){\n if( autoClose ){ modal.hide(); }\n });\n }\n\n var originalClosingCallback = options.closing_callback;\n modal.show( _.extend( options, {\n title : this.title({ name: history.get( 'name' ) }),\n body : $( dialog._template({\n name : defaultCopyName,\n isAnon : Galaxy.user.isAnonymous(),\n allowAll : allowAll,\n copyWhat : defaultCopyWhat,\n activeLabel : this.activeLabel,\n allLabel : this.allLabel,\n anonWarning : this.anonWarning,\n })),\n buttons : _.object([\n [ _l( 'Cancel' ), function(){ modal.hide(); } ],\n [ this.submitLabel, checkNameAndCopy ]\n ]),\n height : 'auto',\n closing_events : true,\n closing_callback: function _historyCopyClose( cancelled ){\n if( cancelled ){\n deferred.reject({ cancelled : true });\n }\n if( originalClosingCallback ){\n originalClosingCallback( cancelled );\n }\n }\n }));\n\n // set the default dataset copy, autofocus the title, and set up for a simple return\n modal.$( '#copy-modal-title' ).focus().select();\n modal.$( '#copy-modal-title' ).on( 'keydown', function( ev ){\n if( ev.keyCode === 13 ){\n ev.preventDefault();\n checkNameAndCopy();\n }\n });\n\n return deferred;\n },\n};\n\n//==============================================================================\n// maintain the (slight) distinction between copy and import\n/**\n * Subclass CopyDialog to use the import language.\n */\nvar ImportDialog = _.extend( {}, CopyDialog, {\n defaultName : _.template( \"imported: <%- name %>\" ),\n title : _.template( _l( 'Importing history' ) + ' \"<%- name %>\"' ),\n submitLabel : _l( 'Import' ),\n errorMessage : _l( 'History could not be imported.' ),\n progressive : _l( 'Importing history' ),\n activeLabel : _l( 'Import only the active, non-deleted datasets' ),\n allLabel : _l( 'Import all datasets including deleted ones' ),\n anonWarning : _l( 'As an anonymous user, unless you login or register, you will lose your current history ' ) +\n _l( 'after importing this history. ' ),\n\n});\n\n//==============================================================================\n/**\n * Main interface for both history import and history copy dialogs.\n * @param {Backbone.Model} history the history to copy\n * @param {Object} options a hash\n * @return {jQuery.Deferred} promise that fails on close and succeeds on copy\n *\n * options:\n * (this object is also passed to the modal used to display the dialog and accepts modal options)\n * {Function} nameFn if defined, use this to build the default name shown to the user\n * (the fn is passed: {name: })\n * {bool} useImport if true, use the 'import' language (instead of Copy)\n * {bool} allowAll if true, allow the user to choose between copying all datasets and\n * only non-deleted datasets\n * {String} allDatasets default initial checked radio button: 'copy-all' or 'copy-non-deleted',\n */\nvar historyCopyDialog = function( history, options ){\n options = options || {};\n // create our own modal if Galaxy doesn't have one (mako tab without use_panels)\n var modal = window.parent.Galaxy.modal || new MODAL.View({});\n return options.useImport?\n ImportDialog.dialog( modal, history, options ):\n CopyDialog.dialog( modal, history, options );\n};\n\n\n//==============================================================================\n return historyCopyDialog;\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/history/copy-dialog.js","define([\n \"mvc/dataset/dataset-li-edit\",\n \"mvc/history/hda-li\",\n \"mvc/base-mvc\",\n \"utils/localization\"\n], function( DATASET_LI_EDIT, HDA_LI, BASE_MVC, _l ){\n\n'use strict';\n\n//==============================================================================\nvar _super = DATASET_LI_EDIT.DatasetListItemEdit;\n/** @class Editing view for HistoryDatasetAssociation.\n */\nvar HDAListItemEdit = _super.extend(\n/** @lends HDAListItemEdit.prototype */{\n\n className : _super.prototype.className + \" history-content\",\n\n /** In this override, only get details if in the ready state, get rerunnable if in other states.\n * Note: fetch with no 'change' event triggering to prevent automatic rendering.\n */\n _fetchModelDetails : function(){\n var view = this;\n if( view.model.inReadyState() && !view.model.hasDetails() ){\n return view.model.fetch({ silent: true });\n\n // special case the need for the rerunnable and creating_job attributes\n // needed for rendering re-run button on queued, running datasets\n } else if( !view.model.has( 'rerunnable' ) ){\n return view.model.fetch({ silent: true, data: {\n // only fetch rerunnable and creating_job to keep overhead down\n keys: [ 'rerunnable', 'creating_job' ].join(',')\n }});\n }\n return jQuery.when();\n },\n\n /** event map */\n events : _.extend( _.clone( _super.prototype.events ), {\n 'click .unhide-link' : function( ev ){ this.model.unhide(); return false; }\n }),\n\n /** string rep */\n toString : function(){\n var modelString = ( this.model )?( this.model + '' ):( '(no model)' );\n return 'HDAListItemEdit(' + modelString + ')';\n }\n});\n\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nHDAListItemEdit.prototype.templates = (function(){\n\n var warnings = _.extend( {}, _super.prototype.templates.warnings, {\n hidden : BASE_MVC.wrapTemplate([\n '<% if( !dataset.visible ){ %>',\n // add a link to unhide a dataset\n '
',\n '<% } %>'\n ], 'dataset' )\n });\n\n return _.extend( {}, _super.prototype.templates, {\n //NOTE: *steal* the HDAListItemView titleBar\n titleBar : HDA_LI.HDAListItemView.prototype.templates.titleBar,\n warnings : warnings\n });\n}());\n\n\n//==============================================================================\n return {\n HDAListItemEdit : HDAListItemEdit\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/history/hda-li-edit.js","define([\n \"mvc/history/hdca-li\",\n \"mvc/collection/collection-view-edit\",\n \"ui/fa-icon-button\",\n \"utils/localization\"\n], function( HDCA_LI, DC_VIEW_EDIT, faIconButton, _l ){\n\n'use strict';\n\n//==============================================================================\nvar _super = HDCA_LI.HDCAListItemView;\n/** @class Editing view for HistoryDatasetCollectionAssociation.\n */\nvar HDCAListItemEdit = _super.extend(\n/** @lends HDCAListItemEdit.prototype */{\n\n /** logger used to record this.log messages, commonly set to console */\n //logger : console,\n\n /** Override to return editable versions of the collection panels */\n _getFoldoutPanelClass : function(){\n switch( this.model.get( 'collection_type' ) ){\n case 'list':\n return DC_VIEW_EDIT.ListCollectionViewEdit;\n case 'paired':\n return DC_VIEW_EDIT.PairCollectionViewEdit;\n case 'list:paired':\n return DC_VIEW_EDIT.ListOfPairsCollectionViewEdit;\n case 'list:list':\n return DC_VIEW_EDIT.ListOfListsCollectionViewEdit;\n }\n throw new TypeError( 'Uknown collection_type: ' + this.model.get( 'collection_type' ) );\n },\n\n // ......................................................................... delete\n /** In this override, add the delete button. */\n _renderPrimaryActions : function(){\n this.log( this + '._renderPrimaryActions' );\n // render the display, edit attr and delete icon-buttons\n return _super.prototype._renderPrimaryActions.call( this )\n .concat([\n this._renderDeleteButton()\n ]);\n },\n\n /** Render icon-button to delete this collection. */\n _renderDeleteButton : function(){\n var self = this,\n deleted = this.model.get( 'deleted' );\n return faIconButton({\n title : deleted? _l( 'Dataset collection is already deleted' ): _l( 'Delete' ),\n classes : 'delete-btn',\n faIcon : 'fa-times',\n disabled : deleted,\n onclick : function() {\n // ...bler... tooltips being left behind in DOM (hover out never called on deletion)\n self.$el.find( '.icon-btn.delete-btn' ).trigger( 'mouseout' );\n self.model[ 'delete' ]();\n }\n });\n },\n\n // ......................................................................... misc\n /** string rep */\n toString : function(){\n var modelString = ( this.model )?( this.model + '' ):( '(no model)' );\n return 'HDCAListItemEdit(' + modelString + ')';\n }\n});\n\n//==============================================================================\n return {\n HDCAListItemEdit : HDCAListItemEdit\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/history/hdca-li-edit.js","define([\n \"mvc/history/history-model\",\n \"mvc/history/history-view-edit\",\n \"mvc/base-mvc\",\n \"utils/localization\"\n], function( HISTORY_MODEL, HISTORY_VIEW_EDIT, BASE_MVC, _l ){\n\n'use strict';\n\n// ============================================================================\n/** session storage for history panel preferences (and to maintain state)\n */\nvar HistoryViewPrefs = BASE_MVC.SessionStorageModel.extend(\n/** @lends HistoryViewPrefs.prototype */{\n defaults : {\n /** should the tags editor be shown or hidden initially? */\n tagsEditorShown : false,\n /** should the annotation editor be shown or hidden initially? */\n annotationEditorShown : false,\n ///** what is the currently focused content (dataset or collection) in the current history?\n // * (the history panel will highlight and scroll to the focused content view)\n // */\n //focusedContentId : null\n /** Current scroll position */\n scrollPosition : 0\n },\n toString : function(){\n return 'HistoryViewPrefs(' + JSON.stringify( this.toJSON() ) + ')';\n }\n});\n\n/** key string to store panel prefs (made accessible on class so you can access sessionStorage directly) */\nHistoryViewPrefs.storageKey = function storageKey(){\n return ( 'history-panel' );\n};\n\n/* =============================================================================\nTODO:\n\n============================================================================= */\nvar _super = HISTORY_VIEW_EDIT.HistoryViewEdit;\n// used in root/index.mako\n/** @class View/Controller for the user's current history model as used in the history\n * panel (current right hand panel) of the analysis page.\n *\n * The only history panel that:\n * will poll for updates.\n * displays datasets in reverse hid order.\n */\nvar CurrentHistoryView = _super.extend(/** @lends CurrentHistoryView.prototype */{\n\n className : _super.prototype.className + ' current-history-panel',\n\n /** override to use drilldown (and not foldout) for how collections are displayed */\n HDCAViewClass : _super.prototype.HDCAViewClass.extend({\n foldoutStyle : 'drilldown'\n }),\n\n emptyMsg : [\n _l( 'This history is empty' ), '. ',\n _l( 'You can ' ),\n '',\n _l( 'load your own data' ),\n '',\n _l( ' or ' ),\n '',\n _l( 'get data from an external source' ),\n ''\n ].join(''),\n\n // ......................................................................... SET UP\n /** Set up the view, set up storage, bind listeners to HistoryContents events */\n initialize : function( attributes ){\n attributes = attributes || {};\n\n // ---- persistent preferences\n /** maintain state / preferences over page loads */\n this.preferences = new HistoryViewPrefs( _.extend({\n id : HistoryViewPrefs.storageKey()\n }, _.pick( attributes, _.keys( HistoryViewPrefs.prototype.defaults ) )));\n\n _super.prototype.initialize.call( this, attributes );\n\n /** sub-views that will overlay this panel (collections) */\n this.panelStack = [];\n\n /** id of currently focused content */\n this.currentContentId = attributes.currentContentId || null;\n //NOTE: purposely not sent to localstorage since panel recreation roughly lines up with a reset of this value\n },\n\n /** Override to cache the current scroll position with a listener */\n _setUpListeners : function(){\n _super.prototype._setUpListeners.call( this );\n\n var panel = this;\n // reset scroll position when there's a new history\n this.on( 'new-model', function(){\n panel.preferences.set( 'scrollPosition', 0 );\n });\n },\n\n // ------------------------------------------------------------------------ loading history/item models\n // TODO: next three more appropriate moved to the app level\n /** (re-)loads the user's current history & contents w/ details */\n loadCurrentHistory : function(){\n return this.loadHistory( null, { url : Galaxy.root + 'history/current_history_json' });\n },\n\n /** loads a history & contents w/ details and makes them the current history */\n switchToHistory : function( historyId, attributes ){\n if( Galaxy.user.isAnonymous() ){\n this.trigger( 'error', _l( 'You must be logged in to switch histories' ), _l( 'Anonymous user' ) );\n return $.when();\n }\n return this.loadHistory( historyId, { url : Galaxy.root + 'history/set_as_current?id=' + historyId });\n },\n\n /** creates a new history on the server and sets it as the user's current history */\n createNewHistory : function( attributes ){\n if( Galaxy.user.isAnonymous() ){\n this.trigger( 'error', _l( 'You must be logged in to create histories' ), _l( 'Anonymous user' ) );\n return $.when();\n }\n return this.loadHistory( null, { url : Galaxy.root + 'history/create_new_current' });\n },\n\n /** release/free/shutdown old models and set up panel for new models */\n setModel : function( model, attributes, render ){\n _super.prototype.setModel.call( this, model, attributes, render );\n if( this.model && this.model.id ){\n this.log( 'checking for updates' );\n this.model.checkForUpdates();\n }\n return this;\n },\n\n // ------------------------------------------------------------------------ history/content event listening\n /** listening for history events */\n _setUpModelListeners : function(){\n _super.prototype._setUpModelListeners.call( this );\n // re-broadcast any model change events so that listeners don't have to re-bind to each history\n return this.listenTo( this.model, {\n 'change:nice_size change:size' : function(){\n this.trigger( 'history-size-change', this, this.model, arguments );\n },\n 'change:id' : function(){\n this.once( 'loading-done', function(){ this.model.checkForUpdates(); });\n }\n });\n },\n\n /** listening for collection events */\n _setUpCollectionListeners : function(){\n _super.prototype._setUpCollectionListeners.call( this );\n // if a hidden item is created (gen. by a workflow), moves thru the updater to the ready state,\n // then: remove it from the collection if the panel is set to NOT show hidden datasets\n this.listenTo( this.collection, 'state:ready', function( model, newState, oldState ){\n if( ( !model.get( 'visible' ) )\n && ( !this.collection.storage.includeHidden() ) ){\n this.removeItemView( model );\n }\n });\n },\n\n // ------------------------------------------------------------------------ panel rendering\n /** override to add a handler to capture the scroll position when the parent scrolls */\n _setUpBehaviors : function( $where ){\n $where = $where || this.$el;\n // console.log( '_setUpBehaviors', this.$scrollContainer( $where ).get(0), this.$list( $where ) );\n // we need to call this in _setUpBehaviors which is called after render since the $el\n // may not be attached to $el.parent and $scrollContainer() may not work\n var panel = this;\n _super.prototype._setUpBehaviors.call( panel, $where );\n\n // cache the handler to remove and re-add so we don't pile up the handlers\n if( !this._debouncedScrollCaptureHandler ){\n this._debouncedScrollCaptureHandler = _.debounce( function scrollCapture(){\n // cache the scroll position (only if visible)\n if( panel.$el.is( ':visible' ) ){\n panel.preferences.set( 'scrollPosition', $( this ).scrollTop() );\n }\n }, 40 );\n }\n\n panel.$scrollContainer( $where )\n .off( 'scroll', this._debouncedScrollCaptureHandler )\n .on( 'scroll', this._debouncedScrollCaptureHandler );\n return panel;\n },\n\n /** In this override, handle null models and move the search input to the top */\n _buildNewRender : function(){\n if( !this.model ){ return $(); }\n var $newRender = _super.prototype._buildNewRender.call( this );\n $newRender.find( '.search' ).prependTo( $newRender.find( '> .controls' ) );\n this._renderQuotaMessage( $newRender );\n return $newRender;\n },\n\n /** render the message displayed when a user is over quota and can't run jobs */\n _renderQuotaMessage : function( $whereTo ){\n $whereTo = $whereTo || this.$el;\n return $( this.templates.quotaMsg( {}, this ) ).prependTo( $whereTo.find( '.messages' ) );\n },\n\n /** In this override, get and set current panel preferences when editor is used */\n _renderTags : function( $where ){\n var panel = this;\n // render tags and show/hide based on preferences\n _super.prototype._renderTags.call( panel, $where );\n if( panel.preferences.get( 'tagsEditorShown' ) ){\n panel.tagsEditor.toggle( true );\n }\n // store preference when shown or hidden\n panel.listenTo( panel.tagsEditor, 'hiddenUntilActivated:shown hiddenUntilActivated:hidden',\n function( tagsEditor ){\n panel.preferences.set( 'tagsEditorShown', tagsEditor.hidden );\n }\n );\n },\n\n /** In this override, get and set current panel preferences when editor is used */\n _renderAnnotation : function( $where ){\n var panel = this;\n // render annotation and show/hide based on preferences\n _super.prototype._renderAnnotation.call( panel, $where );\n if( panel.preferences.get( 'annotationEditorShown' ) ){\n panel.annotationEditor.toggle( true );\n }\n // store preference when shown or hidden\n panel.listenTo( panel.annotationEditor, 'hiddenUntilActivated:shown hiddenUntilActivated:hidden',\n function( annotationEditor ){\n panel.preferences.set( 'annotationEditorShown', annotationEditor.hidden );\n }\n );\n },\n\n /** Override to scroll to cached position (in prefs) after swapping */\n _swapNewRender : function( $newRender ){\n _super.prototype._swapNewRender.call( this, $newRender );\n var panel = this;\n _.delay( function(){\n var pos = panel.preferences.get( 'scrollPosition' );\n if( pos ){\n panel.scrollTo( pos, 0 );\n }\n }, 10 );\n //TODO: is this enough of a delay on larger histories?\n\n return this;\n },\n\n // ------------------------------------------------------------------------ sub-views\n /** Override to add the current-content highlight class to currentContentId's view */\n _attachItems : function( $whereTo ){\n _super.prototype._attachItems.call( this, $whereTo );\n var panel = this;\n if( panel.currentContentId ){\n panel._setCurrentContentById( panel.currentContentId );\n }\n return this;\n },\n\n /** Override to remove any drill down panels */\n addItemView : function( model, collection, options ){\n var view = _super.prototype.addItemView.call( this, model, collection, options );\n if( !view ){ return view; }\n if( this.panelStack.length ){ return this._collapseDrilldownPanel(); }\n return view;\n },\n\n // ------------------------------------------------------------------------ collection sub-views\n /** In this override, add/remove expanded/collapsed model ids to/from web storage */\n _setUpItemViewListeners : function( view ){\n var panel = this;\n _super.prototype._setUpItemViewListeners.call( panel, view );\n // use pub-sub to: handle drilldown expansion and collapse\n return panel.listenTo( view, {\n 'expanded:drilldown' : function( v, drilldown ){\n this._expandDrilldownPanel( drilldown );\n },\n 'collapsed:drilldown' : function( v, drilldown ){\n this._collapseDrilldownPanel( drilldown );\n },\n });\n },\n\n /** display 'current content': add a visible highlight and store the id of a content item */\n setCurrentContent : function( view ){\n this.$( '.history-content.current-content' ).removeClass( 'current-content' );\n if( view ){\n view.$el.addClass( 'current-content' );\n this.currentContentId = view.model.id;\n } else {\n this.currentContentId = null;\n }\n },\n\n /** find the view with the id and then call setCurrentContent on it */\n _setCurrentContentById : function( id ){\n var view = this.viewFromModelId( id ) || null;\n this.setCurrentContent( view );\n },\n\n /** Handle drill down by hiding this panels list and controls and showing the sub-panel */\n _expandDrilldownPanel : function( drilldown ){\n this.panelStack.push( drilldown );\n // hide this panel's controls and list, set the name for back navigation, and attach to the $el\n this.$controls().add( this.$list() ).hide();\n drilldown.parentName = this.model.get( 'name' );\n drilldown.delegateEvents().render().$el.appendTo( this.$el );\n },\n\n /** Handle drilldown close by freeing the panel and re-rendering this panel */\n _collapseDrilldownPanel : function( drilldown ){\n this.panelStack.pop();\n //TODO: MEM: free the panel\n this.$controls().add( this.$list() ).show();\n },\n\n // ........................................................................ panel events\n /** event map */\n events : _.extend( _.clone( _super.prototype.events ), {\n // the two links in the empty message\n 'click .uploader-link' : function( ev ){ Galaxy.upload.show( ev ); },\n 'click .get-data-link' : function( ev ){\n var $toolMenu = $( '.toolMenuContainer' );\n $toolMenu.parent().scrollTop( 0 );\n $toolMenu.find( 'span:contains(\"Get Data\")' ).click();\n }\n }),\n\n // ........................................................................ external objects/MVC\n listenToGalaxy : function( galaxy ){\n this.listenTo( galaxy, {\n // when the galaxy_main iframe is loaded with a new page,\n // compare the url to the following list and if there's a match\n // pull the id from url and indicate in the history view that\n // the dataset with that id is the 'current'ly active dataset\n 'galaxy_main:load': function( data ){\n var pathToMatch = data.fullpath;\n var hdaId = null;\n var useToURLRegexMap = {\n 'display' : /datasets\\/([a-f0-9]+)\\/display/,\n 'edit' : /datasets\\/([a-f0-9]+)\\/edit/,\n 'report_error' : /dataset\\/errors\\?id=([a-f0-9]+)/,\n 'rerun' : /tool_runner\\/rerun\\?id=([a-f0-9]+)/,\n 'show_params' : /datasets\\/([a-f0-9]+)\\/show_params/,\n // no great way to do this here? (leave it in the dataset event handlers above?)\n // 'visualization' : 'visualization',\n };\n _.find( useToURLRegexMap, function( regex, use ){\n // grab the more specific match result (1), save, and use it as the find flag\n hdaId = _.result( pathToMatch.match( regex ), 1 );\n return hdaId;\n });\n // need to type mangle to go from web route to history contents\n this._setCurrentContentById( hdaId? ( 'dataset-' + hdaId ) : null );\n },\n // when the center panel is given a new view, clear the current indicator\n 'center-panel:load': function( view ){\n this._setCurrentContentById();\n }\n });\n },\n\n //TODO: remove quota meter from panel and remove this\n /** add listeners to an external quota meter (mvc/user/user-quotameter.js) */\n connectToQuotaMeter : function( quotaMeter ){\n if( !quotaMeter ){\n return this;\n }\n // show/hide the 'over quota message' in the history when the meter tells it to\n this.listenTo( quotaMeter, 'quota:over', this.showQuotaMessage );\n this.listenTo( quotaMeter, 'quota:under', this.hideQuotaMessage );\n\n // having to add this to handle re-render of hview while overquota (the above do not fire)\n this.on( 'rendered rendered:initial', function(){\n if( quotaMeter && quotaMeter.isOverQuota() ){\n this.showQuotaMessage();\n }\n });\n return this;\n },\n\n /** Override to preserve the quota message */\n clearMessages : function( ev ){\n var $target = !_.isUndefined( ev )?\n $( ev.currentTarget )\n :this.$messages().children( '[class$=\"message\"]' );\n $target = $target.not( '.quota-message' );\n $target.fadeOut( this.fxSpeed, function(){\n $( this ).remove();\n });\n return this;\n },\n\n /** Show the over quota message (which happens to be in the history panel).\n */\n showQuotaMessage : function(){\n var $msg = this.$( '.quota-message' );\n if( $msg.is( ':hidden' ) ){ $msg.slideDown( this.fxSpeed ); }\n },\n\n /** Hide the over quota message (which happens to be in the history panel).\n */\n hideQuotaMessage : function(){\n var $msg = this.$( '.quota-message' );\n if( !$msg.is( ':hidden' ) ){ $msg.slideUp( this.fxSpeed ); }\n },\n\n // ........................................................................ options menu\n //TODO: remove to batch\n /** unhide any hidden datasets */\n unhideHidden : function() {\n var self = this;\n if( confirm( _l( 'Really unhide all hidden datasets?' ) ) ){\n // get all hidden, regardless of deleted/purged\n return self.model.contents._filterAndUpdate(\n { visible: false, deleted: '', purged: '' },\n { visible : true }\n ).done( function(){\n // TODO: would be better to render these as they're unhidden instead of all at once\n if( !self.model.contents.includeHidden ){\n self.renderItems();\n }\n });\n }\n return jQuery.when();\n },\n\n /** delete any hidden datasets */\n deleteHidden : function() {\n var self = this;\n if( confirm( _l( 'Really delete all hidden datasets?' ) ) ){\n return self.model.contents._filterAndUpdate(\n // get all hidden, regardless of deleted/purged\n { visible: false, deleted: '', purged: '' },\n // both delete *and* unhide them\n { deleted : true, visible: true }\n );\n }\n return jQuery.when();\n },\n\n /** Return a string rep of the history */\n toString : function(){\n return 'CurrentHistoryView(' + (( this.model )?( this.model.get( 'name' )):( '' )) + ')';\n }\n});\n\n\n//------------------------------------------------------------------------------ TEMPLATES\nCurrentHistoryView.prototype.templates = (function(){\n\n var quotaMsgTemplate = BASE_MVC.wrapTemplate([\n '
',\n _l( 'You are over your disk quota' ), '. ',\n _l( 'Tool execution is on hold until your disk usage drops below your allocated quota' ), '.',\n '
'\n ], 'history' );\n return _.extend( _.clone( _super.prototype.templates ), {\n quotaMsg : quotaMsgTemplate\n });\n\n}());\n\n\n//==============================================================================\n return {\n CurrentHistoryView : CurrentHistoryView\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/history/history-view-edit-current.js","define([\n \"mvc/history/history-view\",\n \"mvc/history/history-contents\",\n \"mvc/dataset/states\",\n \"mvc/history/hda-model\",\n \"mvc/history/hda-li-edit\",\n \"mvc/history/hdca-li-edit\",\n \"mvc/tag\",\n \"mvc/annotation\",\n \"mvc/collection/list-collection-creator\",\n \"mvc/collection/pair-collection-creator\",\n \"mvc/collection/list-of-pairs-collection-creator\",\n \"ui/fa-icon-button\",\n \"mvc/ui/popup-menu\",\n \"mvc/base-mvc\",\n \"utils/localization\",\n \"ui/editable-text\",\n], function(\n HISTORY_VIEW,\n HISTORY_CONTENTS,\n STATES,\n HDA_MODEL,\n HDA_LI_EDIT,\n HDCA_LI_EDIT,\n TAGS,\n ANNOTATIONS,\n LIST_COLLECTION_CREATOR,\n PAIR_COLLECTION_CREATOR,\n LIST_OF_PAIRS_COLLECTION_CREATOR,\n faIconButton,\n PopupMenu,\n BASE_MVC,\n _l\n){\n\n'use strict';\n\n/* =============================================================================\nTODO:\n\n============================================================================= */\nvar _super = HISTORY_VIEW.HistoryView;\n// base class for history-view-edit-current and used as-is in history/view.mako\n/** @class Editable View/Controller for the history model.\n *\n * Allows:\n * (everything HistoryView allows)\n * changing the name\n * displaying and editing tags and annotations\n * multi-selection and operations on mulitple content items\n */\nvar HistoryViewEdit = _super.extend(\n/** @lends HistoryViewEdit.prototype */{\n\n /** class to use for constructing the HistoryDatasetAssociation views */\n HDAViewClass : HDA_LI_EDIT.HDAListItemEdit,\n /** class to use for constructing the HistoryDatasetCollectionAssociation views */\n HDCAViewClass : HDCA_LI_EDIT.HDCAListItemEdit,\n\n // ......................................................................... SET UP\n /** Set up the view, set up storage, bind listeners to HistoryContents events\n * @param {Object} attributes\n */\n initialize : function( attributes ){\n attributes = attributes || {};\n _super.prototype.initialize.call( this, attributes );\n\n // ---- set up instance vars\n /** editor for tags - sub-view */\n this.tagsEditor = null;\n\n /** enable drag and drop - sub-view */\n this.dragItems = true;\n\n /** editor for annotations - sub-view */\n this.annotationEditor = null;\n\n /** allow user purge of dataset files? */\n this.purgeAllowed = attributes.purgeAllowed || false;\n\n // states/modes the panel can be in\n /** is the panel currently showing the dataset selection controls? */\n this.annotationEditorShown = attributes.annotationEditorShown || false;\n this.tagsEditorShown = attributes.tagsEditorShown || false;\n },\n\n /** Override to handle history as drag-drop target */\n _setUpListeners : function(){\n _super.prototype._setUpListeners.call( this );\n return this.on({\n 'droptarget:drop': function( ev, data ){\n // process whatever was dropped and re-hide the drop target\n this.dataDropped( data );\n this.dropTargetOff();\n },\n 'view:attached view:removed': function(){\n this._renderCounts();\n },\n 'search:loading-progress': this._renderSearchProgress,\n 'search:searching': this._renderSearchFindings,\n });\n },\n\n // ------------------------------------------------------------------------ listeners\n /** listening for history and HDA events */\n _setUpModelListeners : function(){\n _super.prototype._setUpModelListeners.call( this );\n this.listenTo( this.model, 'change:size', this.updateHistoryDiskSize );\n return this;\n },\n\n /** listening for collection events */\n _setUpCollectionListeners : function(){\n _super.prototype._setUpCollectionListeners.call( this );\n this.listenTo( this.collection, {\n 'change:deleted': this._handleItemDeletedChange,\n 'change:visible': this._handleItemVisibleChange,\n 'change:purged' : function( model ){\n // hafta get the new nice-size w/o the purged model\n this.model.fetch();\n },\n // loading indicators for deleted/hidden\n 'fetching-deleted' : function( collection ){\n this.$( '> .controls .deleted-count' )\n .html( '' + _l( 'loading...' ) + '' );\n },\n 'fetching-hidden' : function( collection ){\n this.$( '> .controls .hidden-count' )\n .html( '' + _l( 'loading...' ) + '' );\n },\n 'fetching-deleted-done fetching-hidden-done' : this._renderCounts,\n });\n return this;\n },\n\n // ------------------------------------------------------------------------ panel rendering\n /** In this override, add tag and annotation editors and a btn to toggle the selectors */\n _buildNewRender : function(){\n // create a new render using a skeleton template, render title buttons, render body, and set up events, etc.\n var $newRender = _super.prototype._buildNewRender.call( this );\n if( !this.model ){ return $newRender; }\n\n if( Galaxy && Galaxy.user && Galaxy.user.id && Galaxy.user.id === this.model.get( 'user_id' ) ){\n this._renderTags( $newRender );\n this._renderAnnotation( $newRender );\n }\n return $newRender;\n },\n\n /** Update the history size display (curr. upper right of panel). */\n updateHistoryDiskSize : function(){\n this.$( '.history-size' ).text( this.model.get( 'nice_size' ) );\n },\n\n /** override to render counts when the items are rendered */\n renderItems : function( $whereTo ){\n var views = _super.prototype.renderItems.call( this, $whereTo );\n if( !this.searchFor ){ this._renderCounts( $whereTo ); }\n return views;\n },\n\n /** override to show counts, what's deleted/hidden, and links to toggle those */\n _renderCounts : function( $whereTo ){\n $whereTo = $whereTo instanceof jQuery? $whereTo : this.$el;\n var html = this.templates.counts( this.model.toJSON(), this );\n return $whereTo.find( '> .controls .subtitle' ).html( html );\n },\n\n /** render the tags sub-view controller */\n _renderTags : function( $where ){\n var panel = this;\n this.tagsEditor = new TAGS.TagsEditor({\n model : this.model,\n el : $where.find( '.controls .tags-display' ),\n onshowFirstTime : function(){ this.render(); },\n // show hide sub-view tag editors when this is shown/hidden\n onshow : function(){\n panel.toggleHDATagEditors( true, panel.fxSpeed );\n },\n onhide : function(){\n panel.toggleHDATagEditors( false, panel.fxSpeed );\n },\n $activator : faIconButton({\n title : _l( 'Edit history tags' ),\n classes : 'history-tag-btn',\n faIcon : 'fa-tags'\n }).appendTo( $where.find( '.controls .actions' ) )\n });\n },\n /** render the annotation sub-view controller */\n _renderAnnotation : function( $where ){\n var panel = this;\n this.annotationEditor = new ANNOTATIONS.AnnotationEditor({\n model : this.model,\n el : $where.find( '.controls .annotation-display' ),\n onshowFirstTime : function(){ this.render(); },\n // show hide sub-view view annotation editors when this is shown/hidden\n onshow : function(){\n panel.toggleHDAAnnotationEditors( true, panel.fxSpeed );\n },\n onhide : function(){\n panel.toggleHDAAnnotationEditors( false, panel.fxSpeed );\n },\n $activator : faIconButton({\n title : _l( 'Edit history annotation' ),\n classes : 'history-annotate-btn',\n faIcon : 'fa-comment'\n }).appendTo( $where.find( '.controls .actions' ) )\n });\n },\n\n /** Set up HistoryViewEdit js/widget behaviours\n * In this override, make the name editable\n */\n _setUpBehaviors : function( $where ){\n $where = $where || this.$el;\n _super.prototype._setUpBehaviors.call( this, $where );\n if( !this.model ){ return; }\n\n // anon users shouldn't have access to any of the following\n if( ( !Galaxy.user || Galaxy.user.isAnonymous() )\n || ( Galaxy.user.id !== this.model.get( 'user_id' ) ) ){\n return;\n }\n\n var panel = this,\n nameSelector = '> .controls .name';\n $where.find( nameSelector )\n .attr( 'title', _l( 'Click to rename history' ) )\n .tooltip({ placement: 'bottom' })\n .make_text_editable({\n on_finish: function( newName ){\n var previousName = panel.model.get( 'name' );\n if( newName && newName !== previousName ){\n panel.$el.find( nameSelector ).text( newName );\n panel.model.save({ name: newName })\n .fail( function(){\n panel.$el.find( nameSelector ).text( panel.model.previous( 'name' ) );\n });\n } else {\n panel.$el.find( nameSelector ).text( previousName );\n }\n }\n });\n },\n\n /** return a new popup menu for choosing a multi selection action\n * ajax calls made for multiple datasets are queued\n */\n multiselectActions : function(){\n var panel = this,\n actions = [\n { html: _l( 'Hide datasets' ), func: function(){\n var action = HDA_MODEL.HistoryDatasetAssociation.prototype.hide;\n panel.getSelectedModels().ajaxQueue( action );\n }\n },\n { html: _l( 'Unhide datasets' ), func: function(){\n var action = HDA_MODEL.HistoryDatasetAssociation.prototype.unhide;\n panel.getSelectedModels().ajaxQueue( action );\n }\n },\n { html: _l( 'Delete datasets' ), func: function(){\n var action = HDA_MODEL.HistoryDatasetAssociation.prototype['delete'];\n panel.getSelectedModels().ajaxQueue( action );\n }\n },\n { html: _l( 'Undelete datasets' ), func: function(){\n var action = HDA_MODEL.HistoryDatasetAssociation.prototype.undelete;\n panel.getSelectedModels().ajaxQueue( action );\n }\n }\n ];\n if( panel.purgeAllowed ){\n actions.push({\n html: _l( 'Permanently delete datasets' ), func: function(){\n if( confirm( _l( 'This will permanently remove the data in your datasets. Are you sure?' ) ) ){\n var action = HDA_MODEL.HistoryDatasetAssociation.prototype.purge;\n panel.getSelectedModels().ajaxQueue( action );\n }\n }\n });\n }\n actions = actions.concat( panel._collectionActions() );\n return actions;\n },\n\n /** */\n _collectionActions : function(){\n var panel = this;\n return [\n { html: _l( 'Build Dataset List' ), func: function() { panel.buildCollection( \"list\") }\n },\n // TODO: Only show quick pair if two things selected.\n { html: _l( 'Build Dataset Pair' ), func: function() { panel.buildCollection( \"paired\") }\n },\n { html: _l( 'Build List of Dataset Pairs' ), func: function() { panel.buildCollection( \"list:paired\" ) }\n },\n ];\n },\n\n buildCollection : function( collectionType, selection, hideSourceItems ) {\n var panel = this;\n var selection = selection || panel.getSelectedModels();\n var hideSourceItems = hideSourceItems || false;\n var createFunc;\n if( collectionType == \"list\" ) {\n createFunc = LIST_COLLECTION_CREATOR.createListCollection;\n } else if( collectionType == \"paired\" ) {\n createFunc = PAIR_COLLECTION_CREATOR.createPairCollection;\n } else if( collectionType == \"list:paired\" ) {\n createFunc = LIST_OF_PAIRS_COLLECTION_CREATOR.createListOfPairsCollection;\n } else {\n console.warn( \"Unknown collectionType encountered \" + collectionType );\n }\n createFunc( selection, hideSourceItems ).done( function() { panel.model.refresh() } );\n },\n\n // ------------------------------------------------------------------------ sub-views\n /** In this override, add purgeAllowed and whether tags/annotation editors should be shown */\n _getItemViewOptions : function( model ){\n var options = _super.prototype._getItemViewOptions.call( this, model );\n _.extend( options, {\n purgeAllowed : this.purgeAllowed,\n tagsEditorShown : ( this.tagsEditor && !this.tagsEditor.hidden ),\n annotationEditorShown : ( this.annotationEditor && !this.annotationEditor.hidden )\n });\n return options;\n },\n\n /** If this item is deleted and we're not showing deleted items, remove the view\n * @param {Model} the item model to check\n */\n _handleItemDeletedChange : function( itemModel ){\n if( itemModel.get( 'deleted' ) ){\n this._handleItemDeletion( itemModel );\n } else {\n this._handleItemUndeletion( itemModel );\n }\n this._renderCounts();\n },\n\n _handleItemDeletion : function( itemModel ){\n var contentsShown = this.model.get( 'contents_active' );\n contentsShown.deleted += 1;\n contentsShown.active -= 1;\n if( !this.model.contents.includeDeleted ){\n this.removeItemView( itemModel );\n }\n this.model.set( 'contents_active', contentsShown );\n },\n\n _handleItemUndeletion : function( itemModel ){\n var contentsShown = this.model.get( 'contents_active' );\n contentsShown.deleted -= 1;\n if( !this.model.contents.includeDeleted ){\n contentsShown.active -= 1;\n }\n this.model.set( 'contents_active', contentsShown );\n },\n\n /** If this item is hidden and we're not showing hidden items, remove the view\n * @param {Model} the item model to check\n */\n _handleItemVisibleChange : function( itemModel ){\n if( itemModel.hidden() ){\n this._handleItemHidden( itemModel );\n } else {\n this._handleItemUnhidden( itemModel );\n }\n this._renderCounts();\n },\n\n _handleItemHidden : function( itemModel ){\n var contentsShown = this.model.get( 'contents_active' );\n contentsShown.hidden += 1;\n contentsShown.active -= 1;\n if( !this.model.contents.includeHidden ){\n this.removeItemView( itemModel );\n }\n this.model.set( 'contents_active', contentsShown );\n },\n\n _handleItemUnhidden : function( itemModel ){\n var contentsShown = this.model.get( 'contents_active' );\n contentsShown.hidden -= 1;\n if( !this.model.contents.includeHidden ){\n contentsShown.active -= 1;\n }\n this.model.set( 'contents_active', contentsShown );\n },\n\n /** toggle the visibility of each content's tagsEditor applying all the args sent to this function */\n toggleHDATagEditors : function( showOrHide, speed ){\n _.each( this.views, function( view ){\n if( view.tagsEditor ){\n view.tagsEditor.toggle( showOrHide, speed );\n }\n });\n },\n\n /** toggle the visibility of each content's annotationEditor applying all the args sent to this function */\n toggleHDAAnnotationEditors : function( showOrHide, speed ){\n _.each( this.views, function( view ){\n if( view.annotationEditor ){\n view.annotationEditor.toggle( showOrHide, speed );\n }\n });\n },\n\n // ------------------------------------------------------------------------ panel events\n /** event map */\n events : _.extend( _.clone( _super.prototype.events ), {\n 'click .show-selectors-btn' : 'toggleSelectors',\n 'click .toggle-deleted-link' : function( ev ){ this.toggleShowDeleted(); },\n 'click .toggle-hidden-link' : function( ev ){ this.toggleShowHidden(); }\n }),\n\n // ------------------------------------------------------------------------ search\n _renderSearchProgress : function( limit, offset ){\n var stop = limit + offset;\n return this.$( '> .controls .subtitle' ).html([\n '',\n _l( 'Searching ' ), stop, '/', this.model.contentsShown(),\n ''\n ].join(''));\n },\n\n /** override to display number found in subtitle */\n _renderSearchFindings : function(){\n this.$( '> .controls .subtitle' ).html([\n _l( 'Found' ), this.views.length\n ].join(' '));\n return this;\n },\n\n // ------------------------------------------------------------------------ as drop target\n /** turn all the drag and drop handlers on and add some help text above the drop area */\n dropTargetOn : function(){\n if( this.dropTarget ){ return this; }\n this.dropTarget = true;\n\n //TODO: to init\n var dropHandlers = {\n 'dragenter' : _.bind( this.dragenter, this ),\n 'dragover' : _.bind( this.dragover, this ),\n 'dragleave' : _.bind( this.dragleave, this ),\n 'drop' : _.bind( this.drop, this )\n };\n\n var $dropTarget = this._renderDropTarget();\n this.$list().before([ this._renderDropTargetHelp(), $dropTarget ]);\n for( var evName in dropHandlers ){\n if( dropHandlers.hasOwnProperty( evName ) ){\n //console.debug( evName, dropHandlers[ evName ] );\n $dropTarget.on( evName, dropHandlers[ evName ] );\n }\n }\n return this;\n },\n\n /** render a box to serve as a 'drop here' area on the history */\n _renderDropTarget : function(){\n this.$( '.history-drop-target' ).remove();\n return $( '' ).addClass( 'history-drop-target' );\n },\n\n /** tell the user how it works */\n _renderDropTargetHelp : function(){\n this.$( '.history-drop-target-help' ).remove();\n return $( '' ).addClass( 'history-drop-target-help' )\n .text( _l( 'Drag datasets here to copy them to the current history' ) );\n },\n\n /** shut down drag and drop event handlers and remove drop target */\n dropTargetOff : function(){\n if( !this.dropTarget ){ return this; }\n //this.log( 'dropTargetOff' );\n this.dropTarget = false;\n var dropTarget = this.$( '.history-drop-target' ).get(0);\n for( var evName in this._dropHandlers ){\n if( this._dropHandlers.hasOwnProperty( evName ) ){\n dropTarget.off( evName, this._dropHandlers[ evName ] );\n }\n }\n this.$( '.history-drop-target' ).remove();\n this.$( '.history-drop-target-help' ).remove();\n return this;\n },\n /** toggle the target on/off */\n dropTargetToggle : function(){\n if( this.dropTarget ){\n this.dropTargetOff();\n } else {\n this.dropTargetOn();\n }\n return this;\n },\n\n dragenter : function( ev ){\n //console.debug( 'dragenter:', this, ev );\n ev.preventDefault();\n ev.stopPropagation();\n this.$( '.history-drop-target' ).css( 'border', '2px solid black' );\n },\n dragover : function( ev ){\n ev.preventDefault();\n ev.stopPropagation();\n },\n dragleave : function( ev ){\n //console.debug( 'dragleave:', this, ev );\n ev.preventDefault();\n ev.stopPropagation();\n this.$( '.history-drop-target' ).css( 'border', '1px dashed black' );\n },\n /** when (text) is dropped try to parse as json and trigger an event */\n drop : function( ev ){\n ev.preventDefault();\n //ev.stopPropagation();\n\n var self = this;\n var dataTransfer = ev.originalEvent.dataTransfer;\n var data = dataTransfer.getData( \"text\" );\n\n dataTransfer.dropEffect = 'move';\n try {\n data = JSON.parse( data );\n } catch( err ){\n self.warn( 'error parsing JSON from drop:', data );\n }\n\n self.trigger( 'droptarget:drop', ev, data, self );\n return false;\n },\n\n /** handler that copies data into the contents */\n dataDropped : function( data ){\n var self = this;\n // HDA: dropping will copy it to the history\n if( _.isObject( data ) && data.model_class === 'HistoryDatasetAssociation' && data.id ){\n if( self.contents.currentPage !== 0 ){\n return self.contents.fetchPage( 0 )\n .then( function(){\n return self.model.contents.copy( data.id );\n });\n }\n return self.model.contents.copy( data.id );\n }\n return jQuery.when();\n },\n\n // ........................................................................ misc\n /** Return a string rep of the history */\n toString : function(){\n return 'HistoryViewEdit(' + (( this.model )?( this.model.get( 'name' )):( '' )) + ')';\n }\n});\n\n//------------------------------------------------------------------------------ TEMPLATES\nHistoryViewEdit.prototype.templates = (function(){\n\n var countsTemplate = BASE_MVC.wrapTemplate([\n '<% var shown = Math.max( view.views.length, history.contents_active.active ) %>',\n '<% if( shown ){ %>',\n '',\n '<%- shown %> ', _l( 'shown' ),\n '',\n '<% } %>',\n\n '<% if( history.contents_active.deleted ){ %>',\n '',\n '<% if( view.model.contents.includeDeleted ){ %>',\n '',\n _l( 'hide deleted' ),\n '',\n '<% } else { %>',\n '<%- history.contents_active.deleted %> ',\n '',\n _l( 'deleted' ),\n '',\n '<% } %>',\n '',\n '<% } %>',\n\n '<% if( history.contents_active.hidden ){ %>',\n '',\n '<% if( view.model.contents.includeHidden ){ %>',\n '',\n _l( 'hide hidden' ),\n '',\n '<% } else { %>',\n '<%- history.contents_active.hidden %> ',\n '',\n _l( 'hidden' ),\n '',\n '<% } %>',\n '',\n '<% } %>',\n ], 'history' );\n\n return _.extend( _.clone( _super.prototype.templates ), {\n counts : countsTemplate\n });\n}());\n\n\n//==============================================================================\n return {\n HistoryViewEdit : HistoryViewEdit\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/history/history-view-edit.js","define([\n \"mvc/list/list-view\",\n \"mvc/history/history-model\",\n \"mvc/history/history-contents\",\n \"mvc/history/history-preferences\",\n \"mvc/history/hda-li\",\n \"mvc/history/hdca-li\",\n \"mvc/user/user-model\",\n \"mvc/ui/error-modal\",\n \"ui/fa-icon-button\",\n \"mvc/base-mvc\",\n \"utils/localization\",\n \"ui/search-input\"\n], function(\n LIST_VIEW,\n HISTORY_MODEL,\n HISTORY_CONTENTS,\n HISTORY_PREFS,\n HDA_LI,\n HDCA_LI,\n USER,\n ERROR_MODAL,\n faIconButton,\n BASE_MVC,\n _l\n){\n'use strict';\n\n/* =============================================================================\nTODO:\n\n============================================================================= */\n/** @class non-editable, read-only View/Controller for a history model.\n * Allows:\n * changing the loaded history\n * displaying data, info, and download\n * tracking history attrs: size, tags, annotations, name, etc.\n * Does not allow:\n * changing the name\n */\nvar _super = LIST_VIEW.ModelListPanel;\nvar HistoryView = _super.extend(\n/** @lends HistoryView.prototype */{\n _logNamespace : 'history',\n\n /** class to use for constructing the HDA views */\n HDAViewClass : HDA_LI.HDAListItemView,\n /** class to use for constructing the HDCA views */\n HDCAViewClass : HDCA_LI.HDCAListItemView,\n /** class to used for constructing collection of sub-view models */\n collectionClass : HISTORY_CONTENTS.HistoryContents,\n /** key of attribute in model to assign to this.collection */\n modelCollectionKey : 'contents',\n\n tagName : 'div',\n className : _super.prototype.className + ' history-panel',\n\n /** string to display when the collection is empty */\n emptyMsg : _l( 'This history is empty' ),\n /** displayed when no items match the search terms */\n noneFoundMsg : _l( 'No matching datasets found' ),\n /** string used for search placeholder */\n searchPlaceholder : _l( 'search datasets' ),\n\n /** @type {Number} ms to wait after history load to fetch/decorate hdcas with element_count */\n FETCH_COLLECTION_COUNTS_DELAY : 2000,\n\n // ......................................................................... SET UP\n /** Set up the view, bind listeners.\n * @param {Object} attributes optional settings for the panel\n */\n initialize : function( attributes ){\n _super.prototype.initialize.call( this, attributes );\n // ---- instance vars\n // control contents/behavior based on where (and in what context) the panel is being used\n /** where should pages from links be displayed? (default to new tab/window) */\n this.linkTarget = attributes.linkTarget || '_blank';\n },\n\n /** create and return a collection for when none is initially passed */\n _createDefaultCollection : function(){\n // override\n return new this.collectionClass([], { history: this.model });\n },\n\n /** In this override, clear the update timer on the model */\n freeModel : function(){\n _super.prototype.freeModel.call( this );\n if( this.model ){\n this.model.clearUpdateTimeout();\n }\n return this;\n },\n\n /** create any event listeners for the panel\n * @fires: rendered:initial on the first render\n * @fires: empty-history when switching to a history with no contents or creating a new history\n */\n _setUpListeners : function(){\n _super.prototype._setUpListeners.call( this );\n this.on({\n error : function( model, xhr, options, msg, details ){\n this.errorHandler( model, xhr, options, msg, details );\n },\n 'loading-done' : function(){\n var self = this;\n // after the initial load, decorate with more time consuming fields (like HDCA element_counts)\n _.delay( function(){\n self.model.contents.fetchCollectionCounts();\n }, self.FETCH_COLLECTION_COUNTS_DELAY );\n },\n 'views:ready view:attached view:removed' : function( view ){\n this._renderSelectButton();\n },\n 'view:attached' : function( view ){\n this.scrollTo(0);\n },\n });\n // this.on( 'all', function(){ console.debug( arguments ); });\n },\n\n // ------------------------------------------------------------------------ loading history/hda models\n /** load the history with the given id then it's contents, sending ajax options to both */\n loadHistory : function( historyId, options, contentsOptions ){\n contentsOptions = _.extend( contentsOptions || { silent: true });\n this.info( 'loadHistory:', historyId, options, contentsOptions );\n var self = this;\n self.setModel( new HISTORY_MODEL.History({ id : historyId }) );\n\n contentsOptions.silent = true;\n self.trigger( 'loading' );\n return self.model\n .fetchWithContents( options, contentsOptions )\n .always( function(){\n self.render();\n self.trigger( 'loading-done' );\n });\n },\n\n /** convenience alias to the model. Updates the item list only (not the history) */\n refreshContents : function( options ){\n if( this.model ){\n return this.model.refresh( options );\n }\n // may have callbacks - so return an empty promise\n return $.when();\n },\n\n /** Override to reset web storage when the id changes (since it needs the id) */\n _setUpCollectionListeners : function(){\n _super.prototype._setUpCollectionListeners.call( this );\n return this.listenTo( this.collection, {\n // 'all' : function(){ console.log( this.collection + ':', arguments ); },\n 'fetching-more' : function(){\n this._toggleContentsLoadingIndicator( true );\n this.$emptyMessage().hide();\n },\n 'fetching-more-done': function(){ this._toggleContentsLoadingIndicator( false ); },\n });\n },\n\n // ------------------------------------------------------------------------ panel rendering\n /** hide the $el and display a loading indicator (in the $el's parent) when loading new data */\n _showLoadingIndicator : function( msg, speed, callback ){\n var $indicator = $( '
' );\n this.$el.html( $indicator.text( msg ).slideDown( !_.isUndefined( speed )? speed : this.fxSpeed ) );\n },\n\n /** hide the loading indicator */\n _hideLoadingIndicator : function( speed ){\n // make speed a bit slower to compensate for slow rendering of up to 500 contents\n this.$( '.loading-indicator' ).slideUp( !_.isUndefined( speed )? speed : ( this.fxSpeed + 200 ), function(){\n $( this ).remove();\n });\n },\n\n /** In this override, add a btn to toggle the selectors */\n _buildNewRender : function(){\n var $newRender = _super.prototype._buildNewRender.call( this );\n this._renderSelectButton( $newRender );\n return $newRender;\n },\n\n /** button for starting select mode */\n _renderSelectButton : function( $where ){\n $where = $where || this.$el;\n // do not render selector option if no actions\n if( !this.multiselectActions().length ){\n return null;\n }\n // do not render (and remove even) if nothing to select\n if( !this.views.length ){\n this.hideSelectors();\n $where.find( '.controls .actions .show-selectors-btn' ).remove();\n return null;\n }\n // don't bother rendering if there's one already\n var $existing = $where.find( '.controls .actions .show-selectors-btn' );\n if( $existing.length ){\n return $existing;\n }\n\n return faIconButton({\n title : _l( 'Operations on multiple datasets' ),\n classes : 'show-selectors-btn',\n faIcon : 'fa-check-square-o'\n }).prependTo( $where.find( '.controls .actions' ) );\n },\n\n /** override to avoid showing intial empty message using contents_active */\n _renderEmptyMessage : function( $whereTo ){\n var self = this;\n var $emptyMsg = self.$emptyMessage( $whereTo );\n\n var empty = self.model.get( 'contents_active' ).active <= 0;\n if( empty ){\n return $emptyMsg.empty().append( self.emptyMsg ).show();\n\n } else if( self.searchFor && self.model.contents.haveSearchDetails() && !self.views.length ){\n return $emptyMsg.empty().append( self.noneFoundMsg ).show();\n }\n $emptyMsg.hide();\n return $();\n },\n\n /** the scroll container for this panel - can be $el, $el.parent(), or grandparent depending on context */\n $scrollContainer : function( $where ){\n // override or set via attributes.$scrollContainer\n return this.$list( $where );\n },\n\n // ------------------------------------------------------------------------ subviews\n _toggleContentsLoadingIndicator : function( show ){\n if( !show ){\n this.$list().find( '.contents-loading-indicator' ).remove();\n } else {\n this.$list().html( '
'\n + '
' );\n }\n },\n\n /** override to render pagination also */\n renderItems: function( $whereTo ){\n // console.log( this + '.renderItems-----------------', new Date() );\n $whereTo = $whereTo || this.$el;\n var self = this;\n var $list = self.$list( $whereTo );\n\n // TODO: bootstrap hack to remove orphaned tooltips\n $( '.tooltip' ).remove();\n\n $list.empty();\n self.views = [];\n\n var models = self._filterCollection();\n if( models.length ){\n self._renderPagination( $whereTo );\n self.views = self._renderSomeItems( models, $list );\n } else {\n // TODO: consolidate with _renderPagination above by (???) passing in models/length?\n $whereTo.find( '> .controls .list-pagination' ).empty();\n }\n self._renderEmptyMessage( $whereTo ).toggle( !models.length );\n\n self.trigger( 'views:ready', self.views );\n return self.views;\n },\n\n /** render pagination controls if not searching and contents says we're paginating */\n _renderPagination: function( $whereTo ){\n var $paginationControls = $whereTo.find( '> .controls .list-pagination' );\n if( this.searchFor || !this.model.contents.shouldPaginate() ) return $paginationControls.empty();\n\n $paginationControls.html( this.templates.pagination({\n // pagination is 1-based for the user\n current : this.model.contents.currentPage + 1,\n last : this.model.contents.getLastPage() + 1,\n }, this ));\n $paginationControls.find( 'select.pages' ).tooltip();\n return $paginationControls;\n },\n\n /** render a subset of the entire collection (client-side pagination) */\n _renderSomeItems: function( models, $list ){\n var self = this;\n var views = [];\n $list.append( models.map( function( m ){\n var view = self._createItemView( m );\n views.push( view );\n return self._renderItemView$el( view );\n }));\n return views;\n },\n\n // ------------------------------------------------------------------------ sub-views\n /** in this override, check if the contents would also display based on includeDeleted/hidden */\n _filterItem : function( model ){\n var self = this;\n var contents = self.model.contents;\n return ( contents.includeHidden || !model.hidden() )\n && ( contents.includeDeleted || !model.isDeletedOrPurged() )\n && ( _super.prototype._filterItem.call( self, model ) );\n },\n\n /** In this override, since history contents are mixed,\n * get the appropo view class based on history_content_type\n */\n _getItemViewClass : function( model ){\n var contentType = model.get( \"history_content_type\" );\n switch( contentType ){\n case 'dataset':\n return this.HDAViewClass;\n case 'dataset_collection':\n return this.HDCAViewClass;\n }\n throw new TypeError( 'Unknown history_content_type: ' + contentType );\n },\n\n /** in this override, add a linktarget, and expand if id is in web storage */\n _getItemViewOptions : function( model ){\n var options = _super.prototype._getItemViewOptions.call( this, model );\n return _.extend( options, {\n linkTarget : this.linkTarget,\n expanded : this.model.contents.storage.isExpanded( model.id ),\n hasUser : this.model.ownedByCurrUser()\n });\n },\n\n /** In this override, add/remove expanded/collapsed model ids to/from web storage */\n _setUpItemViewListeners : function( view ){\n var panel = this;\n _super.prototype._setUpItemViewListeners.call( panel, view );\n //TODO: send from content view: this.model.collection.storage.addExpanded\n // maintain a list of items whose bodies are expanded\n return panel.listenTo( view, {\n 'expanded': function( v ){\n panel.model.contents.storage.addExpanded( v.model );\n },\n 'collapsed': function( v ){\n panel.model.contents.storage.removeExpanded( v.model );\n }\n });\n },\n\n /** override to remove expandedIds from webstorage */\n collapseAll : function(){\n this.model.contents.storage.clearExpanded();\n _super.prototype.collapseAll.call( this );\n },\n\n // ------------------------------------------------------------------------ selection\n /** Override to correctly set the historyId of the new collection */\n getSelectedModels : function(){\n var collection = _super.prototype.getSelectedModels.call( this );\n collection.historyId = this.collection.historyId;\n return collection;\n },\n\n\n // ------------------------------------------------------------------------ panel events\n /** event map */\n events : _.extend( _.clone( _super.prototype.events ), {\n 'click .show-selectors-btn' : 'toggleSelectors',\n 'click > .controls .prev' : '_clickPrevPage',\n 'click > .controls .next' : '_clickNextPage',\n 'change > .controls .pages' : '_changePageSelect',\n // allow (error) messages to be clicked away\n 'click .messages [class$=message]' : 'clearMessages',\n }),\n\n _clickPrevPage : function( ev ){\n this.model.clearUpdateTimeout();\n this.model.contents.fetchPrevPage();\n },\n\n _clickNextPage : function( ev ){\n this.model.clearUpdateTimeout();\n this.model.contents.fetchNextPage();\n },\n\n _changePageSelect : function( ev ){\n this.model.clearUpdateTimeout();\n var page = $( ev.currentTarget ).val();\n this.model.contents.fetchPage( page );\n },\n\n /** Toggle and store the deleted visibility and re-render items\n * @returns {Boolean} new setting\n */\n toggleShowDeleted : function( show, options ){\n show = ( show !== undefined )?( show ):( !this.model.contents.includeDeleted );\n var self = this;\n var contents = self.model.contents;\n contents.setIncludeDeleted( show, options );\n self.trigger( 'show-deleted', show );\n\n contents.fetchCurrentPage({ renderAll: true });\n return show;\n },\n\n /** Toggle and store whether to render explicity hidden contents\n * @returns {Boolean} new setting\n */\n toggleShowHidden : function( show, store, options ){\n // console.log( 'toggleShowHidden', show, store );\n show = ( show !== undefined )?( show ):( !this.model.contents.includeHidden );\n var self = this;\n var contents = self.model.contents;\n contents.setIncludeHidden( show, options );\n self.trigger( 'show-hidden', show );\n\n contents.fetchCurrentPage({ renderAll: true });\n return show;\n },\n\n /** On the first search, if there are no details - load them, then search */\n _firstSearch : function( searchFor ){\n var self = this;\n var inputSelector = '> .controls .search-input';\n this.log( 'onFirstSearch', searchFor );\n\n // if the contents already have enough details to search, search and return now\n if( self.model.contents.haveSearchDetails() ){\n self.searchItems( searchFor );\n return;\n }\n\n // otherwise, load the details progressively here\n self.$( inputSelector ).searchInput( 'toggle-loading' );\n // set this now so that only results will show during progress\n self.searchFor = searchFor;\n var xhr = self.model.contents.progressivelyFetchDetails({ silent: true })\n .progress( function( response, limit, offset ){\n self.renderItems();\n self.trigger( 'search:loading-progress', limit, offset );\n })\n .always( function(){\n self.$el.find( inputSelector ).searchInput( 'toggle-loading' );\n })\n .done( function(){\n self.searchItems( searchFor, 'force' );\n });\n },\n\n /** clear the search filters and show all views that are normally shown */\n clearSearch : function( searchFor ){\n var self = this;\n if( !self.searchFor ) return self;\n //self.log( 'onSearchClear', self );\n self.searchFor = '';\n self.trigger( 'search:clear', self );\n self.$( '> .controls .search-query' ).val( '' );\n // NOTE: silent + render prevents collection update event with merge only\n // - which causes an empty page due to event handler above\n self.model.contents.fetchCurrentPage({ silent: true })\n .done( function(){\n self.renderItems();\n });\n return self;\n },\n\n // ........................................................................ error handling\n /** Event handler for errors (from the panel, the history, or the history's contents)\n * Alternately use two strings for model and xhr to use custom message and title (respectively)\n * @param {Model or View} model the (Backbone) source of the error\n * @param {XMLHTTPRequest} xhr any ajax obj. assoc. with the error\n * @param {Object} options the options map commonly used with bbone ajax\n */\n errorHandler : function( model, xhr, options ){\n //TODO: to mixin or base model\n // interrupted ajax or no connection\n if( xhr && xhr.status === 0 && xhr.readyState === 0 ){\n // return ERROR_MODAL.offlineErrorModal();\n // fail silently\n return;\n }\n // otherwise, leave something to report in the console\n this.error( model, xhr, options );\n // and feedback to a modal\n // if sent two strings (and possibly details as 'options'), use those as message and title\n if( _.isString( model ) && _.isString( xhr ) ){\n var message = model;\n var title = xhr;\n return ERROR_MODAL.errorModal( message, title, options );\n }\n // bad gateway\n // TODO: possibly to global handler\n if( xhr && xhr.status === 502 ){\n return ERROR_MODAL.badGatewayErrorModal();\n }\n return ERROR_MODAL.ajaxErrorModal( model, xhr, options );\n },\n\n /** Remove all messages from the panel. */\n clearMessages : function( ev ){\n var $target = !_.isUndefined( ev )?\n $( ev.currentTarget )\n :this.$messages().children( '[class$=\"message\"]' );\n $target.fadeOut( this.fxSpeed, function(){\n $( this ).remove();\n });\n return this;\n },\n\n // ........................................................................ scrolling\n /** Scrolls the panel to show the content sub-view with the given hid.\n * @param {Integer} hid the hid of item to scroll into view\n * @returns {HistoryView} the panel\n */\n scrollToHid : function( hid ){\n return this.scrollToItem( _.first( this.viewsWhereModel({ hid: hid }) ) );\n },\n\n // ........................................................................ misc\n /** utility for adding -st, -nd, -rd, -th to numbers */\n ordinalIndicator : function( number ){\n var numStr = number + '';\n switch( numStr.charAt( numStr.length - 1 )){\n case '1': return numStr + 'st';\n case '2': return numStr + 'nd';\n case '3': return numStr + 'rd';\n default : return numStr + 'th';\n }\n },\n\n /** Return a string rep of the history */\n toString : function(){\n return 'HistoryView(' + (( this.model )?( this.model.get( 'name' )):( '' )) + ')';\n }\n});\n\n\n//------------------------------------------------------------------------------ TEMPLATES\nHistoryView.prototype.templates = (function(){\n\n var mainTemplate = BASE_MVC.wrapTemplate([\n // temp container\n '
',\n '',\n '
',\n '',\n '
'\n ]);\n\n var controlsTemplate = BASE_MVC.wrapTemplate([\n '
Trackster uses this information to populate the select box for chrom/contig, and' +\n 'to set the maximum basepair of the track browser. You may either upload a .len file' +\n 'of this format (Len File option), or directly enter the information into the box ' +\n '(Len Entry option).
' +\n 'You are using ' + options.nice_total_disk_usage + ' of disk space in this Galaxy instance. ' +\n ( Galaxy.config.enable_quotas ? 'Your disk quota is: ' + options.quota + '. ' : '' ) +\n 'Is your usage more than expected? See the documentation for tips on how to find all of the data in your account.' +\n '
';\n }\n });\n\n /** View of individual user forms */\n var Forms = Backbone.View.extend({\n\n initialize: function( options ) {\n this.model = new Model( options );\n this.page = this.model.get( options.form_id );\n this.setElement( '' );\n this.render();\n },\n\n render: function() {\n var self = this;\n $.ajax({\n url : Galaxy.root + this.page.url,\n type : 'GET'\n }).done( function( response ) {\n var options = $.extend( {}, self.page, response );\n var form = new Form({\n title : options.title,\n icon : options.icon,\n inputs : options.inputs,\n operations: {\n 'submit': new Ui.ButtonIcon({\n tooltip : options.submit_tooltip,\n title : options.submit_title || 'Save settings',\n icon : options.submit_icon || 'fa-save',\n onclick : function() { self._submit( form, options ) }\n })\n }\n });\n self.$el.empty().append( form.$el );\n }).fail( function( response ) {\n self.$el.empty().append( new Ui.Message({\n message : 'Failed to load resource ' + self.page.url + '.',\n status : 'danger',\n persistent : true\n }).$el );\n });\n },\n\n _submit: function( form, options ) {\n var self = this;\n $.ajax( {\n url : Galaxy.root + options.url,\n data : JSON.stringify( form.data.create() ),\n type : 'PUT',\n contentType : 'application/json'\n }).done( function( response ) {\n form.data.matchModel( response, function ( input, input_id ) {\n form.field_list[ input_id ].value( input.value );\n });\n form.message.update( { message: response.message, status: 'success' } );\n }).fail( function( response ) {\n form.message.update( { message: response.responseJSON.err_msg, status: 'danger' } );\n });\n }\n });\n\n return {\n View : View,\n Forms : Forms\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/user/user-preferences.js","/** Configure Workflow Menu View */\ndefine( [], function() {\n var View = Backbone.View.extend({\n\n initialize: function( options ) {\n this.setElement( '' );\n this.render();\n },\n\n render: function() {\n var self = this;\n $.getJSON( Galaxy.root + 'api/workflows/menu/', function( response ) {\n var workflows = response.workflows,\n ids_in_menu = response.ids_in_menu,\n $el_config_worflow = null;\n\n // Add configure workflow header\n self.$el.empty().append( self._templateConfigWorkflowHeader() );\n $el_config_worflow = self.$el.find( '.configure-workflows' );\n $el_config_worflow.append( self._templateActionButtons() );\n if( workflows.length > 0 ) {\n $el_config_worflow.append( self._templateConfigureWorkflow( self, workflows, ids_in_menu ) );\n self.save_workflow_menu( self );\n self.make_checked( self, ids_in_menu );\n self.register_check_uncheck_all( self );\n }\n else {\n $el_config_worflow.append( self._templateNoWorkflow() );\n }\n });\n },\n\n /** Register check and uncheck all callbacks*/\n register_check_uncheck_all: function( self ) {\n var $el_check_all = self.$el.find( '.check-all-wf' ),\n $el_uncheck_all = self.$el.find( '.uncheck-all-wf' );\n \n $el_check_all.click(function( e ) {\n self.check_uncheck_all( self, true );\n });\n $el_uncheck_all.click(function( e ) {\n self.check_uncheck_all( self, false );\n });\n },\n\n /** Check or uncheck all workflows */\n check_uncheck_all: function( self, checked ) {\n $.each(self.$el.find( '.wf-config-item' ), function() {\n var wf_checkbox = $( this )[0];\n wf_checkbox.checked = checked;\n });\n },\n\n /** Make the worflows as checked if present in the menu */\n make_checked: function( self, ids_in_menu ) {\n $.each(self.$el.find( '.wf-config-item' ), function() {\n var wf_checkbox = $( this )[0];\n _.each( ids_in_menu, function( id ) {\n if ( parseInt( wf_checkbox.value ) === id ) {\n wf_checkbox.checked = true;\n }\n });\n });\n },\n\n /** Save the changes for workflow menu */\n save_workflow_menu: function( self ) {\n var $el_save_workflow_menu = self.$el.find( '.wf-save-menu' );\n $el_save_workflow_menu.click( function( e ) {\n var ids = [];\n $.each(self.$el.find( '.wf-config-item' ), function() {\n var wf_checkbox = $( this )[0];\n if( wf_checkbox.checked || wf_checkbox.checked === 'true' ) {\n ids.push( parseInt( wf_checkbox.value ) );\n }\n });\n $.ajax({\n type: 'PUT',\n url: Galaxy.root + 'api/workflows/menu/',\n data: JSON.stringify( { 'workflow_ids': ids } ),\n contentType : 'application/json'\n }).done( function( response ) {\n window.location = Galaxy.root + 'workflow?status='+ response.status +'&message=' + response.message;\n });\n });\n },\n\n /** Template for actions buttons */\n _templateActionButtons: function() {\n return '
');\n\t }\n\t }\n\t\n\t // Render first chunk.\n\t var self = this,\n\t first_chunk = this.model.get('first_data_chunk');\n\t if (first_chunk) {\n\t // First chunk is bootstrapped, so render now.\n\t this._renderChunk(first_chunk);\n\t } else {\n\t // No bootstrapping, so get first chunk and then render.\n\t $.when(self.model.get_next_chunk()).then(function (result) {\n\t self._renderChunk(result);\n\t });\n\t }\n\t\n\t // -- Show new chunks during scrolling. --\n\t\n\t // Set up chunk loading when scrolling using the scrolling element.\n\t this.scroll_elt.scroll(function () {\n\t self.attempt_to_fetch();\n\t });\n\t },\n\t\n\t /**\n\t * Returns true if user has scrolled to the bottom of the view.\n\t */\n\t scrolled_to_bottom: function () {\n\t return false;\n\t },\n\t\n\t // -- Helper functions. --\n\t\n\t _renderCell: function (cell_contents, index, colspan) {\n\t var $cell = $('
').text(cell_contents);\n\t var column_types = this.model.get_metadata('column_types');\n\t if (colspan !== undefined) {\n\t $cell.attr('colspan', colspan).addClass('stringalign');\n\t } else if (column_types) {\n\t if (index < column_types.length) {\n\t if (column_types[index] === 'str' || column_types[index] === 'list') {\n\t /* Left align all str columns, right align the rest */\n\t $cell.addClass('stringalign');\n\t }\n\t }\n\t }\n\t return $cell;\n\t },\n\t\n\t _renderRow: function (line) {\n\t // Check length of cells to ensure this is a complete row.\n\t var cells = line.split('\\t'),\n\t row = $('
'),\n\t num_columns = this.model.get_metadata('columns');\n\t\n\t if (this.row_count % 2 !== 0) {\n\t row.addClass('dark_row');\n\t }\n\t\n\t if (cells.length === num_columns) {\n\t _.each(cells, function (cell_contents, index) {\n\t row.append(this._renderCell(cell_contents, index));\n\t }, this);\n\t } else if (cells.length > num_columns) {\n\t // SAM file or like format with optional metadata included.\n\t _.each(cells.slice(0, num_columns - 1), function (cell_contents, index) {\n\t row.append(this._renderCell(cell_contents, index));\n\t }, this);\n\t row.append(this._renderCell(cells.slice(num_columns - 1).join('\\t'), num_columns - 1));\n\t } else if (cells.length === 1) {\n\t // Comment line, just return the one cell.\n\t row.append(this._renderCell(line, 0, num_columns));\n\t } else {\n\t // cells.length is greater than one, but less than num_columns. Render cells and pad tds.\n\t // Possibly a SAM file or like format with optional metadata missing.\n\t // Could also be a tabular file with a line with missing columns.\n\t _.each(cells, function (cell_contents, index) {\n\t row.append(this._renderCell(cell_contents, index));\n\t }, this);\n\t _.each(_.range(num_columns - cells.length), function () {\n\t row.append($('
'));\n\t });\n\t }\n\t\n\t this.row_count++;\n\t return row;\n\t },\n\t\n\t _renderChunk: function (chunk) {\n\t var data_table = this.$el.find('table');\n\t _.each(chunk.ck_data.split('\\n'), function (line, index) {\n\t if (line !== '') {\n\t data_table.append(this._renderRow(line));\n\t }\n\t }, this);\n\t }\n\t });\n\t\n\t /**\n\t * Tabular view that is placed at the top level of page. Scrolling occurs\n\t * view top-level elements outside of view.\n\t */\n\t var TopLevelTabularDatasetChunkedView = TabularDatasetChunkedView.extend({\n\t\n\t initialize: function (options) {\n\t TabularDatasetChunkedView.prototype.initialize.call(this, options);\n\t\n\t // Scrolling happens in top-level elements.\n\t scroll_elt = _.find(this.$el.parents(), function (p) {\n\t return $(p).css('overflow') === 'auto';\n\t });\n\t\n\t // If no scrolling element found, use window.\n\t if (!scroll_elt) {\n\t scroll_elt = window;\n\t }\n\t\n\t // Wrap scrolling element for easy access.\n\t this.scroll_elt = $(scroll_elt);\n\t },\n\t\n\t /**\n\t * Returns true if user has scrolled to the bottom of the view.\n\t */\n\t scrolled_to_bottom: function () {\n\t return this.$el.height() - this.scroll_elt.scrollTop() - this.scroll_elt.height() <= 0;\n\t }\n\t\n\t });\n\t\n\t /**\n\t * Tabular view tnat is embedded in a page. Scrolling occurs in view's el.\n\t */\n\t var EmbeddedTabularDatasetChunkedView = TabularDatasetChunkedView.extend({\n\t\n\t initialize: function (options) {\n\t TabularDatasetChunkedView.prototype.initialize.call(this, options);\n\t\n\t // Because view is embedded, set up div to do scrolling.\n\t this.scroll_elt = this.$el.css({\n\t position: 'relative',\n\t overflow: 'scroll',\n\t height: options.height || '500px'\n\t });\n\t },\n\t\n\t /**\n\t * Returns true if user has scrolled to the bottom of the view.\n\t */\n\t scrolled_to_bottom: function () {\n\t return this.$el.scrollTop() + this.$el.innerHeight() >= this.el.scrollHeight;\n\t }\n\t\n\t });\n\t\n\t // button for trackster visualization\n\t var TabularButtonTracksterView = Backbone.View.extend({\n\t\n\t // gene region columns\n\t col: {\n\t chrom: null,\n\t start: null,\n\t end: null\n\t },\n\t\n\t // url for trackster\n\t url_viz: null,\n\t\n\t // dataset id\n\t dataset_id: null,\n\t\n\t // database key\n\t genome_build: null,\n\t\n\t // data type\n\t file_ext: null,\n\t\n\t // backbone initialize\n\t initialize: function (options) {\n\t // check if environment is available\n\t var Galaxy = parent.Galaxy;\n\t\n\t // link galaxy modal or create one\n\t if (Galaxy && Galaxy.modal) {\n\t this.modal = Galaxy.modal;\n\t }\n\t\n\t // link galaxy frames\n\t if (Galaxy && Galaxy.frame) {\n\t this.frame = Galaxy.frame;\n\t }\n\t\n\t // check\n\t if (!this.modal || !this.frame) {\n\t return;\n\t }\n\t\n\t // model/metadata\n\t var model = options.model;\n\t var metadata = model.get('metadata');\n\t\n\t // check for datatype\n\t if (!model.get('file_ext')) {\n\t return;\n\t }\n\t\n\t // get data type\n\t this.file_ext = model.get('file_ext');\n\t\n\t // check for bed-file format\n\t if (this.file_ext == 'bed') {\n\t // verify that metadata exists\n\t if (metadata.get('chromCol') && metadata.get('startCol') && metadata.get('endCol')) {\n\t // read in columns\n\t this.col.chrom = metadata.get('chromCol') - 1;\n\t this.col.start = metadata.get('startCol') - 1;\n\t this.col.end = metadata.get('endCol') - 1;\n\t } else {\n\t console.log('TabularButtonTrackster : Bed-file metadata incomplete.');\n\t return;\n\t }\n\t }\n\t\n\t // check for vcf-file format\n\t if (this.file_ext == 'vcf') {\n\t // search array\n\t function search(str, array) {\n\t for (var j = 0; j < array.length; j++) if (array[j].match(str)) return j;\n\t return -1;\n\t };\n\t\n\t // load\n\t this.col.chrom = search('Chrom', metadata.get('column_names'));\n\t this.col.start = search('Pos', metadata.get('column_names'));\n\t this.col.end = null;\n\t\n\t // verify that metadata exists\n\t if (this.col.chrom == -1 || this.col.start == -1) {\n\t console.log('TabularButtonTrackster : VCF-file metadata incomplete.');\n\t return;\n\t }\n\t }\n\t\n\t // check\n\t if (this.col.chrom === undefined) {\n\t return;\n\t }\n\t\n\t // get dataset id\n\t if (model.id) {\n\t this.dataset_id = model.id;\n\t } else {\n\t console.log('TabularButtonTrackster : Dataset identification is missing.');\n\t return;\n\t }\n\t\n\t // get url\n\t if (model.get('url_viz')) {\n\t this.url_viz = model.get('url_viz');\n\t } else {\n\t console.log('TabularButtonTrackster : Url for visualization controller is missing.');\n\t return;\n\t }\n\t\n\t // get genome_build / database key\n\t if (model.get('genome_build')) {\n\t this.genome_build = model.get('genome_build');\n\t }\n\t\n\t // create the icon\n\t var btn_viz = new mod_icon_btn.IconButtonView({\n\t model: new mod_icon_btn.IconButton({\n\t title: 'Visualize',\n\t icon_class: 'chart_curve',\n\t id: 'btn_viz'\n\t })\n\t });\n\t\n\t // set element\n\t this.setElement(options.$el);\n\t\n\t // add to element\n\t this.$el.append(btn_viz.render().$el);\n\t\n\t // hide the button\n\t this.hide();\n\t },\n\t\n\t // backbone events\n\t events: {\n\t 'mouseover tr': 'show',\n\t 'mouseleave': 'hide'\n\t },\n\t\n\t // show button\n\t show: function (e) {\n\t // is numeric\n\t function is_numeric(n) {\n\t return !isNaN(parseFloat(n)) && isFinite(n);\n\t };\n\t\n\t // check\n\t if (this.col.chrom === null) return;\n\t\n\t // get selected data line\n\t var row = $(e.target).parent();\n\t\n\t // verify that location has been found\n\t var chrom = row.children().eq(this.col.chrom).html();\n\t var start = row.children().eq(this.col.start).html();\n\t\n\t // end is optional\n\t var end = this.col.end ? row.children().eq(this.col.end).html() : start;\n\t\n\t // double check location\n\t if (!chrom.match(\"^#\") && chrom !== \"\" && is_numeric(start)) {\n\t\n\t // get target gene region\n\t var btn_viz_pars = {\n\t dataset_id: this.dataset_id,\n\t gene_region: chrom + \":\" + start + \"-\" + end\n\t };\n\t\n\t // get button position\n\t var offset = row.offset();\n\t var left = offset.left - 10;\n\t var top = offset.top - $(window).scrollTop() + 3;\n\t\n\t // update css\n\t $('#btn_viz').css({ 'position': 'fixed', 'top': top + 'px', 'left': left + 'px' });\n\t $('#btn_viz').off('click');\n\t $('#btn_viz').click(this.create_trackster_action(this.url_viz, btn_viz_pars, this.genome_build));\n\t\n\t // show the button\n\t $('#btn_viz').show();\n\t } else {\n\t // hide the button\n\t $('#btn_viz').hide();\n\t }\n\t },\n\t\n\t // hide button\n\t hide: function () {\n\t this.$el.find('#btn_viz').hide();\n\t },\n\t\n\t // create action\n\t create_trackster_action: function (vis_url, dataset_params, dbkey) {\n\t // link this\n\t var self = this;\n\t\n\t // create function\n\t return function () {\n\t var listTracksParams = {};\n\t if (dbkey) {\n\t listTracksParams['f-dbkey'] = dbkey;\n\t }\n\t $.ajax({\n\t url: vis_url + '/list_tracks?' + $.param(listTracksParams),\n\t dataType: 'html',\n\t error: function () {\n\t // show error message\n\t self.modal.show({\n\t title: 'Something went wrong!',\n\t body: 'Unfortunately we could not add this dataset to the track browser. Please try again or contact us.',\n\t buttons: {\n\t 'Cancel': function () {\n\t self.modal.hide();\n\t }\n\t }\n\t });\n\t },\n\t success: function (table_html) {\n\t self.modal.show({\n\t title: 'View Data in a New or Saved Visualization',\n\t buttons: {\n\t 'Cancel': function () {\n\t self.modal.hide();\n\t },\n\t 'View in saved visualization': function () {\n\t // show modal with saved visualizations\n\t self.modal.show({\n\t title: 'Add Data to Saved Visualization',\n\t body: table_html,\n\t buttons: {\n\t 'Cancel': function () {\n\t self.modal.hide();\n\t },\n\t 'Add to visualization': function () {\n\t // hide\n\t self.modal.hide();\n\t\n\t // search selected fields\n\t self.modal.$el.find('input[name=id]:checked').each(function () {\n\t // get visualization id\n\t var vis_id = $(this).val();\n\t dataset_params.id = vis_id;\n\t\n\t // add widget\n\t self.frame.add({\n\t title: 'Trackster',\n\t type: 'url',\n\t content: vis_url + '/trackster?' + $.param(dataset_params)\n\t });\n\t });\n\t }\n\t }\n\t });\n\t },\n\t 'View in new visualization': function () {\n\t // hide\n\t self.modal.hide();\n\t\n\t // add widget\n\t self.frame.add({\n\t title: 'Trackster',\n\t type: 'url',\n\t content: vis_url + '/trackster?' + $.param(dataset_params)\n\t });\n\t }\n\t }\n\t });\n\t }\n\t });\n\t return false;\n\t };\n\t }\n\t });\n\t\n\t // -- Utility functions. --\n\t\n\t /**\n\t * Create a model, attach it to a view, render view, and attach it to a parent element.\n\t */\n\t var createModelAndView = function (model, view, model_config, parent_elt) {\n\t // Create model, view.\n\t var a_view = new view({\n\t model: new model(model_config)\n\t });\n\t\n\t // Render view and add to parent element.\n\t a_view.render();\n\t if (parent_elt) {\n\t parent_elt.append(a_view.$el);\n\t }\n\t\n\t return a_view;\n\t };\n\t\n\t /**\n\t * Create a tabular dataset chunked view (and requisite tabular dataset model)\n\t * and appends to parent_elt.\n\t */\n\t var createTabularDatasetChunkedView = function (options) {\n\t // If no model, create and set model from dataset config.\n\t if (!options.model) {\n\t options.model = new TabularDataset(options.dataset_config);\n\t }\n\t\n\t var parent_elt = options.parent_elt;\n\t var embedded = options.embedded;\n\t\n\t // Clean up options so that only needed options are passed to view.\n\t delete options.embedded;\n\t delete options.parent_elt;\n\t delete options.dataset_config;\n\t\n\t // Create and set up view.\n\t var view = embedded ? new EmbeddedTabularDatasetChunkedView(options) : new TopLevelTabularDatasetChunkedView(options);\n\t view.render();\n\t\n\t if (parent_elt) {\n\t parent_elt.append(view.$el);\n\t // If we're sticking this in another element, once it's appended check\n\t // to make sure we've filled enough space.\n\t // Without this, the scroll elements don't work.\n\t view.expand_to_container();\n\t }\n\t\n\t return view;\n\t };\n\t\n\t return {\n\t Dataset: Dataset,\n\t TabularDataset: TabularDataset,\n\t DatasetCollection: DatasetCollection,\n\t TabularDatasetChunkedView: TabularDatasetChunkedView,\n\t createTabularDatasetChunkedView: createTabularDatasetChunkedView\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ }),\n/* 11 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;!(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t\n\t 'use strict';\n\t //==============================================================================\n\t /** Map of possible HDA/collection/job states to their string equivalents.\n\t * A port of galaxy.model.Dataset.states.\n\t */\n\t\n\t var STATES = {\n\t // NOT ready states\n\t /** is uploading and not ready */\n\t UPLOAD: 'upload',\n\t /** the job that will produce the dataset queued in the runner */\n\t QUEUED: 'queued',\n\t /** the job that will produce the dataset is running */\n\t RUNNING: 'running',\n\t /** metadata for the dataset is being discovered/set */\n\t SETTING_METADATA: 'setting_metadata',\n\t\n\t // ready states\n\t /** was created without a tool */\n\t NEW: 'new',\n\t /** has no data */\n\t EMPTY: 'empty',\n\t /** has successfully completed running */\n\t OK: 'ok',\n\t\n\t /** the job that will produce the dataset paused */\n\t PAUSED: 'paused',\n\t /** metadata discovery/setting failed or errored (but otherwise ok) */\n\t FAILED_METADATA: 'failed_metadata',\n\t //TODO: not in trans.app.model.Dataset.states - is in database\n\t /** not accessible to the current user (i.e. due to permissions) */\n\t NOT_VIEWABLE: 'noPermission',\n\t /** deleted while uploading */\n\t DISCARDED: 'discarded',\n\t /** the tool producing this dataset failed */\n\t ERROR: 'error'\n\t };\n\t\n\t STATES.READY_STATES = [STATES.OK, STATES.EMPTY, STATES.PAUSED, STATES.FAILED_METADATA, STATES.NOT_VIEWABLE, STATES.DISCARDED, STATES.ERROR];\n\t\n\t STATES.NOT_READY_STATES = [STATES.UPLOAD, STATES.QUEUED, STATES.RUNNING, STATES.SETTING_METADATA, STATES.NEW];\n\t\n\t //==============================================================================\n\t return STATES;\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\n/***/ }),\n/* 12 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {/** This module contains all button views. */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t /** This renders the default button which is used e.g. at the bottom of the upload modal. */\n\t var ButtonDefault = Backbone.View.extend({\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model({\n\t id: Utils.uid(),\n\t title: '',\n\t floating: 'right',\n\t icon: '',\n\t cls: 'btn btn-default',\n\t wait: false,\n\t wait_text: 'Sending...',\n\t wait_cls: 'btn btn-info',\n\t disabled: false,\n\t percentage: -1\n\t }).set(options);\n\t this.setElement($('').attr('type', 'button').append(this.$icon = $('')).append(this.$title = $('')).append(this.$progress = $('').append(this.$progress_bar = $(''))));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var self = this;\n\t var options = this.model.attributes;\n\t this.$el.removeClass().addClass('ui-button-default').addClass(options.disabled && 'disabled').attr('id', options.id).attr('disabled', options.disabled).css('float', options.floating).off('click').on('click', function () {\n\t $('.tooltip').hide();\n\t options.onclick && !self.disabled && options.onclick();\n\t }).tooltip({ title: options.tooltip, placement: 'bottom' });\n\t this.$progress.addClass('progress').css('display', options.percentage !== -1 ? 'block' : 'none');\n\t this.$progress_bar.addClass('progress-bar').css({ width: options.percentage + '%' });\n\t this.$icon.removeClass().addClass('icon fa');\n\t this.$title.removeClass().addClass('title');\n\t if (options.wait) {\n\t this.$el.addClass(options.wait_cls).prop('disabled', true);\n\t this.$icon.addClass('fa-spinner fa-spin ui-margin-right');\n\t this.$title.html(options.wait_text);\n\t } else {\n\t this.$el.addClass(options.cls);\n\t this.$icon.addClass(options.icon);\n\t this.$title.html(options.title);\n\t options.icon && options.title && this.$icon.addClass('ui-margin-right');\n\t }\n\t },\n\t\n\t /** Show button */\n\t show: function () {\n\t this.$el.show();\n\t },\n\t\n\t /** Hide button */\n\t hide: function () {\n\t this.$el.hide();\n\t },\n\t\n\t /** Disable button */\n\t disable: function () {\n\t this.model.set('disabled', true);\n\t },\n\t\n\t /** Enable button */\n\t enable: function () {\n\t this.model.set('disabled', false);\n\t },\n\t\n\t /** Show spinner to indicate that the button is not ready to be clicked */\n\t wait: function () {\n\t this.model.set('wait', true);\n\t },\n\t\n\t /** Hide spinner to indicate that the button is ready to be clicked */\n\t unwait: function () {\n\t this.model.set('wait', false);\n\t },\n\t\n\t /** Change icon */\n\t setIcon: function (icon) {\n\t this.model.set('icon', icon);\n\t }\n\t });\n\t\n\t /** This button allows the right-click/open-in-new-tab feature, its used e.g. for panel buttons. */\n\t var ButtonLink = ButtonDefault.extend({\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model({\n\t id: Utils.uid(),\n\t title: '',\n\t icon: '',\n\t cls: ''\n\t }).set(options);\n\t this.setElement($('').append(this.$icon = $('')));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var options = this.model.attributes;\n\t this.$el.removeClass().addClass(options.cls).attr({ id: options.id,\n\t href: options.href || 'javascript:void(0)',\n\t title: options.title,\n\t target: options.target || '_top',\n\t disabled: options.disabled }).tooltip({ placement: 'bottom' }).off('click').on('click', function () {\n\t options.onclick && !options.disabled && options.onclick();\n\t });\n\t this.$icon.removeClass().addClass(options.icon);\n\t }\n\t });\n\t\n\t /** The check button is used in the tool form and allows to distinguish between multiple states e.g. all, partially and nothing selected. */\n\t var ButtonCheck = Backbone.View.extend({\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model({\n\t id: Utils.uid(),\n\t title: 'Select/Unselect all',\n\t icons: ['fa-square-o', 'fa-minus-square-o', 'fa-check-square-o'],\n\t value: 0,\n\t onchange: function () {}\n\t }).set(options);\n\t this.setElement($('').append(this.$icon = $('')).append(this.$title = $('')));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t\n\t render: function (options) {\n\t var self = this;\n\t var options = this.model.attributes;\n\t this.$el.addClass('ui-button-check').off('click').on('click', function () {\n\t self.model.set('value', self.model.get('value') === 0 && 2 || 0);\n\t options.onclick && options.onclick();\n\t });\n\t this.$title.html(options.title);\n\t this.$icon.removeClass().addClass('icon fa ui-margin-right').addClass(options.icons[options.value]);\n\t },\n\t\n\t /* Sets a new value and/or returns the value.\n\t * @param{Integer} new_val - Set a new value 0=unchecked, 1=partial and 2=checked.\n\t * OR:\n\t * @param{Integer} new_val - Number of selected options.\n\t * @param{Integer} total - Total number of available options.\n\t */\n\t value: function (new_val, total) {\n\t if (new_val !== undefined) {\n\t if (total && new_val !== 0) {\n\t new_val = new_val !== total && 1 || 2;\n\t }\n\t this.model.set('value', new_val);\n\t this.model.get('onchange')(this.model.get('value'));\n\t }\n\t return this.model.get('value');\n\t }\n\t });\n\t\n\t /** This renders a differently styled, more compact button version. */\n\t var ButtonIcon = ButtonDefault.extend({\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model({\n\t id: Utils.uid(),\n\t title: '',\n\t floating: 'right',\n\t icon: '',\n\t cls: 'ui-button-icon',\n\t disabled: false\n\t }).set(options);\n\t this.setElement($('').append(this.$button = $('').append(this.$icon = $('')).append(this.$title = $(''))));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t\n\t render: function (options) {\n\t var self = this;\n\t var options = this.model.attributes;\n\t this.$el.removeClass().addClass(options.cls).addClass(options.disabled && 'disabled').attr('disabled', options.disabled).attr('id', options.id).css('float', options.floating).off('click').on('click', function () {\n\t $('.tooltip').hide();\n\t !options.disabled && options.onclick && options.onclick();\n\t });\n\t this.$button.addClass('button').tooltip({ title: options.tooltip, placement: 'bottom' });\n\t this.$icon.removeClass().addClass('icon fa').addClass(options.icon);\n\t this.$title.addClass('title').html(options.title);\n\t options.icon && options.title && this.$icon.addClass('ui-margin-right');\n\t }\n\t });\n\t\n\t /** This class creates a button with dropdown menu. */\n\t var ButtonMenu = ButtonDefault.extend({\n\t $menu: null,\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model({\n\t id: '',\n\t title: '',\n\t floating: 'right',\n\t pull: 'right',\n\t icon: null,\n\t onclick: null,\n\t cls: 'ui-button-icon ui-button-menu',\n\t tooltip: '',\n\t target: '',\n\t href: '',\n\t onunload: null,\n\t visible: true,\n\t tag: ''\n\t }).set(options);\n\t this.collection = new Backbone.Collection();\n\t this.setElement($('').append(this.$root = $('').append(this.$icon = $('')).append(this.$title = $(''))));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.listenTo(this.collection, 'change add remove reset', this.render, this);\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var self = this;\n\t var options = this.model.attributes;\n\t this.$el.removeClass().addClass('dropdown').addClass(options.cls).attr('id', options.id).css({ float: options.floating,\n\t display: options.visible && this.collection.where({ visible: true }).length > 0 ? 'block' : 'none' });\n\t this.$root.addClass('root button dropdown-toggle').attr('data-toggle', 'dropdown').tooltip({ title: options.tooltip, placement: 'bottom' }).off('click').on('click', function (e) {\n\t $('.tooltip').hide();\n\t e.preventDefault();\n\t options.onclick && options.onclick();\n\t });\n\t this.$icon.removeClass().addClass('icon fa').addClass(options.icon);\n\t this.$title.removeClass().addClass('title').html(options.title);\n\t options.icon && options.title && this.$icon.addClass('ui-margin-right');\n\t this.$menu && this.$menu.remove();\n\t if (this.collection.length > 0) {\n\t this.$menu = $('
').addClass('menu dropdown-menu').addClass('pull-' + self.model.get('pull')).attr('role', 'menu');\n\t this.$el.append(this.$menu);\n\t }\n\t this.collection.each(function (submodel) {\n\t var suboptions = submodel.attributes;\n\t if (suboptions.visible) {\n\t var $link = $('').addClass('dropdown-item').attr({ href: suboptions.href, target: suboptions.target }).append($('').addClass('fa').addClass(suboptions.icon).css('display', suboptions.icon ? 'inline-block' : 'none')).append(suboptions.title).on('click', function (e) {\n\t if (suboptions.onclick) {\n\t e.preventDefault();\n\t suboptions.onclick();\n\t }\n\t });\n\t self.$menu.append($('').append($link));\n\t suboptions.divider && self.$menu.append($('').addClass('divider'));\n\t }\n\t });\n\t },\n\t\n\t /** Add a new menu item */\n\t addMenu: function (options) {\n\t this.collection.add(Utils.merge(options, {\n\t title: '',\n\t target: '',\n\t href: '',\n\t onclick: null,\n\t divider: false,\n\t visible: true,\n\t icon: null,\n\t cls: 'button-menu btn-group'\n\t }));\n\t }\n\t });\n\t\n\t return {\n\t ButtonDefault: ButtonDefault,\n\t ButtonLink: ButtonLink,\n\t ButtonIcon: ButtonIcon,\n\t ButtonCheck: ButtonCheck,\n\t ButtonMenu: ButtonMenu\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1)))\n\n/***/ }),\n/* 13 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, $) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [\n\t //jquery\n\t //backbone\n\t], __WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t //=============================================================================\n\t /**\n\t * backbone model for icon buttons\n\t */\n\t var IconButton = Backbone.Model.extend({\n\t defaults: {\n\t title: \"\",\n\t icon_class: \"\",\n\t on_click: null,\n\t menu_options: null,\n\t is_menu_button: true,\n\t id: null,\n\t href: null,\n\t target: null,\n\t enabled: true,\n\t visible: true,\n\t tooltip_config: {}\n\t }\n\t });\n\t\n\t /**\n\t * backbone view for icon buttons\n\t */\n\t var IconButtonView = Backbone.View.extend({\n\t\n\t initialize: function () {\n\t // better rendering this way\n\t this.model.attributes.tooltip_config = { placement: 'bottom' };\n\t this.model.bind('change', this.render, this);\n\t },\n\t\n\t render: function () {\n\t // hide tooltip\n\t this.$el.tooltip('hide');\n\t\n\t var new_elem = this.template(this.model.toJSON());\n\t // configure tooltip\n\t new_elem.tooltip(this.model.get('tooltip_config'));\n\t this.$el.replaceWith(new_elem);\n\t this.setElement(new_elem);\n\t return this;\n\t },\n\t\n\t events: {\n\t 'click': 'click'\n\t },\n\t\n\t click: function (event) {\n\t // if on_click pass to that function\n\t if (_.isFunction(this.model.get('on_click'))) {\n\t this.model.get('on_click')(event);\n\t return false;\n\t }\n\t // otherwise, bubble up ( to href or whatever )\n\t return true;\n\t },\n\t\n\t // generate html element\n\t template: function (options) {\n\t var buffer = 'title=\"' + options.title + '\" class=\"icon-button';\n\t\n\t if (options.is_menu_button) {\n\t buffer += ' menu-button';\n\t }\n\t\n\t buffer += ' ' + options.icon_class;\n\t\n\t if (!options.enabled) {\n\t buffer += '_disabled';\n\t }\n\t\n\t // close class tag\n\t buffer += '\"';\n\t\n\t if (options.id) {\n\t buffer += ' id=\"' + options.id + '\"';\n\t }\n\t\n\t buffer += ' href=\"' + options.href + '\"';\n\t // add target for href\n\t if (options.target) {\n\t buffer += ' target=\"' + options.target + '\"';\n\t }\n\t // set visibility\n\t if (!options.visible) {\n\t buffer += ' style=\"display: none;\"';\n\t }\n\t\n\t // enabled/disabled\n\t if (options.enabled) {\n\t buffer = '';\n\t } else {\n\t buffer = '';\n\t }\n\t\n\t // return element\n\t return $(buffer);\n\t }\n\t });\n\t\n\t // define collection\n\t var IconButtonCollection = Backbone.Collection.extend({\n\t model: IconButton\n\t });\n\t\n\t /**\n\t * menu with multiple icon buttons\n\t * views are not needed nor used for individual buttons\n\t */\n\t var IconButtonMenuView = Backbone.View.extend({\n\t\n\t tagName: 'div',\n\t\n\t initialize: function () {\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t // initialize icon buttons\n\t var self = this;\n\t this.collection.each(function (button) {\n\t // create and add icon button to menu\n\t var elt = $('').attr('href', 'javascript:void(0)').attr('title', button.attributes.title).addClass('icon-button menu-button').addClass(button.attributes.icon_class).appendTo(self.$el).click(button.attributes.on_click);\n\t\n\t // configure tooltip\n\t if (button.attributes.tooltip_config) {\n\t elt.tooltip(button.attributes.tooltip_config);\n\t }\n\t\n\t // add popup menu to icon\n\t var menu_options = button.get('options');\n\t if (menu_options) {\n\t make_popupmenu(elt, menu_options);\n\t }\n\t });\n\t\n\t // return\n\t return this;\n\t }\n\t });\n\t\n\t /**\n\t * Returns an IconButtonMenuView for the provided configuration.\n\t * Configuration is a list of dictionaries where each dictionary\n\t * defines an icon button. Each dictionary must have the following\n\t * elements: icon_class, title, and on_click.\n\t */\n\t var create_icon_buttons_menu = function (config, global_config) {\n\t // initialize global configuration\n\t if (!global_config) global_config = {};\n\t\n\t // create and initialize menu\n\t var buttons = new IconButtonCollection(_.map(config, function (button_config) {\n\t return new IconButton(_.extend(button_config, global_config));\n\t }));\n\t\n\t // return menu\n\t return new IconButtonMenuView({ collection: buttons });\n\t };\n\t\n\t //=============================================================================\n\t return {\n\t IconButton: IconButton,\n\t IconButtonView: IconButtonView,\n\t IconButtonCollection: IconButtonCollection,\n\t IconButtonMenuView: IconButtonMenuView,\n\t create_icon_buttons_menu: create_icon_buttons_menu\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ }),\n/* 14 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, $) {/**\n\t * Popover wrapper\n\t*/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t var View = Backbone.View.extend({\n\t optionsDefault: {\n\t with_close: true,\n\t title: null,\n\t placement: 'top',\n\t container: 'body',\n\t body: null\n\t },\n\t\n\t initialize: function (options) {\n\t this.setElement(this._template());\n\t this.uid = Utils.uid();\n\t this.options = _.defaults(options || {}, this.optionsDefault);\n\t this.options.container.parent().append(this.el);\n\t this.$title = this.$('.popover-title-label');\n\t this.$close = this.$('.popover-close');\n\t this.$body = this.$('.popover-content');\n\t\n\t // add initial content\n\t this.options.body && this.append(this.options.body);\n\t\n\t // add event to hide if click is outside of popup and not on container\n\t var self = this;\n\t $('body').on('mousedown.' + this.uid, function (e) {\n\t // the 'is' for buttons that trigger popups\n\t // the 'has' for icons within a button that triggers a popup\n\t self.visible && !$(self.options.container).is(e.target) && !$(self.el).is(e.target) && $(self.el).has(e.target).length === 0 && self.hide();\n\t });\n\t },\n\t\n\t /**\n\t * Render popover\n\t */\n\t render: function () {\n\t this.$title.html(this.options.title);\n\t this.$el.removeClass().addClass('ui-popover popover fade in').addClass(this.options.placement);\n\t this.$el.css(this._get_placement(this.options.placement));\n\t\n\t // configure close option\n\t var self = this;\n\t if (this.options.with_close) {\n\t this.$close.on('click', function () {\n\t self.hide();\n\t }).show();\n\t } else {\n\t this.$close.off().hide();\n\t }\n\t },\n\t\n\t /**\n\t * Set the popover title\n\t * @params{ String } newTitle - New popover title\n\t */\n\t title: function (newTitle) {\n\t if (newTitle !== undefined) {\n\t this.options.title = newTitle;\n\t this.$title.html(newTitle);\n\t }\n\t },\n\t\n\t /**\n\t * Show popover\n\t */\n\t show: function () {\n\t this.render();\n\t this.$el.show();\n\t this.visible = true;\n\t },\n\t\n\t /**\n\t * Hide popover\n\t */\n\t hide: function () {\n\t this.$el.hide();\n\t this.visible = false;\n\t },\n\t\n\t /**\n\t * Append new content to the popover\n\t * @params{ Object } $el - Dom element\n\t */\n\t append: function ($el) {\n\t this.$body.append($el);\n\t },\n\t\n\t /**\n\t * Remove all content\n\t */\n\t empty: function () {\n\t this.$body.empty();\n\t },\n\t\n\t /**\n\t * Remove popover\n\t */\n\t remove: function () {\n\t $('body').off('mousedown.' + this.uid);\n\t this.$el.remove();\n\t },\n\t\n\t /**\n\t * Improve popover location/placement\n\t */\n\t _get_placement: function (placement) {\n\t // get popover dimensions\n\t var width = this._get_width(this.$el);\n\t var height = this.$el.height();\n\t\n\t // get container details\n\t var $container = this.options.container;\n\t var container_width = this._get_width($container);\n\t var container_height = this._get_height($container);\n\t var container_position = $container.position();\n\t\n\t // get position\n\t var top = left = 0;\n\t if (['top', 'bottom'].indexOf(placement) != -1) {\n\t left = container_position.left - width + (container_width + width) / 2;\n\t switch (placement) {\n\t case 'top':\n\t top = container_position.top - height - 5;\n\t break;\n\t case 'bottom':\n\t top = container_position.top + container_height + 5;\n\t break;\n\t }\n\t } else {\n\t top = container_position.top - height + (container_height + height) / 2;\n\t switch (placement) {\n\t case 'right':\n\t left = container_position.left + container_width;\n\t break;\n\t }\n\t }\n\t return { top: top, left: left };\n\t },\n\t\n\t /**\n\t * Returns padding/margin corrected width\n\t */\n\t _get_width: function ($el) {\n\t return $el.width() + parseInt($el.css('padding-left')) + parseInt($el.css('margin-left')) + parseInt($el.css('padding-right')) + parseInt($el.css('margin-right'));\n\t },\n\t\n\t /**\n\t * Returns padding corrected height\n\t */\n\t _get_height: function ($el) {\n\t return $el.height() + parseInt($el.css('padding-top')) + parseInt($el.css('padding-bottom'));\n\t },\n\t\n\t /**\n\t * Return the popover template\n\t */\n\t _template: function (options) {\n\t return '
' + '
' + '
' + '
' + '' + '
' + '
' + '
';\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ }),\n/* 15 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _) {// dependencies\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t\n\t /**\n\t * A plugin for initializing select2 input items.\n\t * Make sure the select2 library itself is loaded beforehand.\n\t * Also the element to which select2 will be appended has to \n\t * be created before select2 initialization (and passed as option).\n\t */\n\t var View = Backbone.View.extend({\n\t // options\n\t optionsDefault: {\n\t css: '',\n\t placeholder: 'No data available',\n\t data: [],\n\t value: null,\n\t multiple: false,\n\t minimumInputLength: 0,\n\t // example format of initial data: \"id:name,55:anotherrole@role.com,27:role@role.com\"\n\t initialData: ''\n\t },\n\t\n\t // initialize\n\t initialize: function (options) {\n\t // configure options\n\t this.options = Utils.merge(options, this.optionsDefault);\n\t\n\t // create new element\n\t this.setElement(this._template(this.options));\n\t\n\t // check if container exists\n\t if (!this.options.container) {\n\t console.log('ui-select::initialize() : container not specified.');\n\t return;\n\t }\n\t\n\t // add to dom\n\t this.options.container.append(this.$el);\n\t\n\t // link selection dictionary\n\t this.select_data = this.options.data;\n\t\n\t // refresh\n\t this._refresh();\n\t\n\t if (!this.options.multiple) {\n\t // initial value\n\t if (this.options.value) {\n\t this._setValue(this.options.value);\n\t }\n\t\n\t // add change event\n\t var self = this;\n\t if (this.options.onchange) {\n\t this.$el.on('change', function () {\n\t self.options.onchange(self.value());\n\t });\n\t }\n\t }\n\t },\n\t\n\t // value\n\t value: function (new_value) {\n\t // get current id/value\n\t var before = this._getValue();\n\t\n\t // check if new_value is defined\n\t if (new_value !== undefined) {\n\t this._setValue(new_value);\n\t }\n\t\n\t // get current id/value\n\t var after = this._getValue();\n\t\n\t // fire onchange\n\t if (after != before && this.options.onchange) {\n\t this.options.onchange(after);\n\t }\n\t\n\t // return current value\n\t return after;\n\t },\n\t\n\t // label\n\t text: function () {\n\t return this.$el.select2('data').text;\n\t },\n\t\n\t // disabled\n\t disabled: function () {\n\t return !this.$el.select2('enable');\n\t },\n\t\n\t // enable\n\t enable: function () {\n\t this.$el.select2('enable', true);\n\t },\n\t\n\t // disable\n\t disable: function () {\n\t this.$el.select2('enable', false);\n\t },\n\t\n\t // add\n\t add: function (options) {\n\t // add options\n\t this.select_data.push({\n\t id: options.id,\n\t text: options.text\n\t });\n\t\n\t // refresh\n\t this._refresh();\n\t },\n\t\n\t // remove\n\t del: function (id) {\n\t // search option\n\t var index = this._getIndex(id);\n\t\n\t // check if found\n\t if (index != -1) {\n\t // remove options\n\t this.select_data.splice(index, 1);\n\t\n\t // refresh\n\t this._refresh();\n\t }\n\t },\n\t\n\t // remove\n\t remove: function () {\n\t this.$el.select2('destroy');\n\t },\n\t\n\t // update\n\t update: function (options) {\n\t // copy options\n\t this.select_data = [];\n\t for (var key in options.data) {\n\t this.select_data.push(options.data[key]);\n\t }\n\t\n\t // refresh\n\t this._refresh();\n\t },\n\t\n\t // refresh\n\t _refresh: function () {\n\t // add select2 data based on type of input\n\t if (!this.options.multiple) {\n\t var selected = this._getValue();\n\t var select_opt = {\n\t data: this.select_data,\n\t containerCssClass: this.options.css,\n\t placeholder: this.options.placeholder,\n\t dropdownAutoWidth: true\n\t };\n\t this.$el.select2(select_opt);\n\t // select previous value (if exists)\n\t this._setValue(selected);\n\t } else {\n\t var select_opt = {\n\t multiple: this.options.multiple,\n\t containerCssClass: this.options.css,\n\t placeholder: this.options.placeholder,\n\t minimumInputLength: this.options.minimumInputLength,\n\t ajax: this.options.ajax,\n\t dropdownCssClass: this.options.dropdownCssClass,\n\t escapeMarkup: this.options.escapeMarkup,\n\t formatResult: this.options.formatResult,\n\t formatSelection: this.options.formatSelection,\n\t initSelection: this.options.initSelection,\n\t initialData: this.options.initialData\n\t };\n\t this.$el.select2(select_opt);\n\t }\n\t },\n\t\n\t // get index\n\t _getIndex: function (value) {\n\t // returns the index of the searched value\n\t _.findIndex(this.select_data, { id: value });\n\t },\n\t\n\t // get value\n\t _getValue: function () {\n\t return this.$el.select2('val');\n\t },\n\t\n\t // set value\n\t _setValue: function (new_value) {\n\t var index = this._getIndex(new_value);\n\t if (index == -1) {\n\t if (this.select_data.length > 0) {\n\t new_value = this.select_data[0].id;\n\t }\n\t }\n\t this.$el.select2('val', new_value);\n\t },\n\t\n\t // element\n\t _template: function (options) {\n\t return '';\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2)))\n\n/***/ }),\n/* 16 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_FACTORY__, __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;// from: https://raw.githubusercontent.com/umdjs/umd/master/jqueryPlugin.js\n\t// Uses AMD or browser globals to create a jQuery plugin.\n\t(function (factory) {\n\t if (true) {\n\t //TODO: So...this turns out to be an all or nothing thing. If I load jQuery in the define below, it will\n\t // (of course) wipe the old jquery *and all the plugins loaded into it*. So the define below *is still\n\t // relying on jquery being loaded globally* in order to preserve plugins.\n\t !(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(1)], __WEBPACK_AMD_DEFINE_FACTORY__ = (factory), __WEBPACK_AMD_DEFINE_RESULT__ = (typeof __WEBPACK_AMD_DEFINE_FACTORY__ === 'function' ? (__WEBPACK_AMD_DEFINE_FACTORY__.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__)) : __WEBPACK_AMD_DEFINE_FACTORY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t } else {\n\t // Browser globals\n\t factory(jQuery);\n\t }\n\t})(function (jQuery) {\n\t 'use_strict';\n\t\n\t var $ = jQuery;\n\t\n\t // ============================================================================\n\t /**\n\t * Make an element with text editable: (a) when user clicks on text, a textbox/area\n\t * is provided for editing; (b) when enter key pressed, element's text is set and on_finish\n\t * is called.\n\t */\n\t $.fn.make_text_editable = function (config_dict) {\n\t // Get config options.\n\t var num_cols = \"num_cols\" in config_dict ? config_dict.num_cols : 30,\n\t num_rows = \"num_rows\" in config_dict ? config_dict.num_rows : 4,\n\t use_textarea = \"use_textarea\" in config_dict ? config_dict.use_textarea : false,\n\t on_finish = \"on_finish\" in config_dict ? config_dict.on_finish : null,\n\t help_text = \"help_text\" in config_dict ? config_dict.help_text : null;\n\t\n\t // Add element behavior.\n\t var container = $(this);\n\t container.addClass(\"editable-text\").click(function (e) {\n\t // If there's already an input element, editing is active, so do nothing.\n\t if ($(this).children(\":input\").length > 0) {\n\t return;\n\t }\n\t\n\t container.removeClass(\"editable-text\");\n\t\n\t // Handler for setting element text.\n\t var set_text = function (new_text) {\n\t container.find(\":input\").remove();\n\t\n\t if (new_text !== \"\") {\n\t container.text(new_text);\n\t } else {\n\t // No text; need a line so that there is a click target.\n\t container.html(\" \");\n\t }\n\t container.addClass(\"editable-text\");\n\t\n\t if (on_finish) {\n\t on_finish(new_text);\n\t }\n\t };\n\t\n\t // Create input element(s) for editing.\n\t var cur_text = \"cur_text\" in config_dict ? config_dict.cur_text : container.text(),\n\t input_elt,\n\t button_elt;\n\t\n\t if (use_textarea) {\n\t input_elt = $(\"\").attr({ rows: num_rows, cols: num_cols }).text($.trim(cur_text)).keyup(function (e) {\n\t if (e.keyCode === 27) {\n\t // Escape key.\n\t set_text(cur_text);\n\t }\n\t });\n\t button_elt = $(\"\").text(\"Done\").click(function () {\n\t set_text(input_elt.val());\n\t // Return false so that click does not propogate to container.\n\t return false;\n\t });\n\t } else {\n\t input_elt = $(\"\").attr({ value: $.trim(cur_text), size: num_cols }).blur(function () {\n\t set_text(cur_text);\n\t }).keyup(function (e) {\n\t if (e.keyCode === 27) {\n\t // Escape key.\n\t $(this).trigger(\"blur\");\n\t } else if (e.keyCode === 13) {\n\t // Enter key.\n\t set_text($(this).val());\n\t }\n\t\n\t // Do not propogate event to avoid unwanted side effects.\n\t e.stopPropagation();\n\t });\n\t }\n\t\n\t // Replace text with input object(s) and focus & select.\n\t container.text(\"\");\n\t container.append(input_elt);\n\t if (button_elt) {\n\t container.append(button_elt);\n\t }\n\t input_elt.focus();\n\t input_elt.select();\n\t\n\t // Do not propogate to elements below b/c that blurs input and prevents it from being used.\n\t e.stopPropagation();\n\t });\n\t\n\t // Add help text if there some.\n\t if (help_text) {\n\t container.attr(\"title\", help_text).tooltip();\n\t }\n\t\n\t return container;\n\t };\n\t\n\t // ============================================================================\n\t});\n\n/***/ }),\n/* 17 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_FACTORY__, __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function($, _) {(function (root, factory) {\n\t if (true) {\n\t !(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_FACTORY__ = (factory), __WEBPACK_AMD_DEFINE_RESULT__ = (typeof __WEBPACK_AMD_DEFINE_FACTORY__ === 'function' ? (__WEBPACK_AMD_DEFINE_FACTORY__.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__)) : __WEBPACK_AMD_DEFINE_FACTORY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t } else {\n\t root.faIconButton = factory();\n\t }\n\t})(this, function () {\n\t //============================================================================\n\t /** Returns a jQuery object containing a clickable font-awesome button.\n\t * options:\n\t * tooltipConfig : option map for bootstrap tool tip\n\t * classes : array of class names (will always be classed as icon-btn)\n\t * disabled : T/F - add the 'disabled' class?\n\t * title : tooltip/title string\n\t * target : optional href target\n\t * href : optional href\n\t * faIcon : which font awesome icon to use\n\t * onclick : function to call when the button is clicked\n\t */\n\t var faIconButton = function (options) {\n\t options = options || {};\n\t options.tooltipConfig = options.tooltipConfig || { placement: 'bottom' };\n\t\n\t options.classes = ['icon-btn'].concat(options.classes || []);\n\t if (options.disabled) {\n\t options.classes.push('disabled');\n\t }\n\t\n\t var html = ['',\n\t // could go with something less specific here - like 'html'\n\t '', ''].join('');\n\t var $button = $(html).tooltip(options.tooltipConfig);\n\t if (_.isFunction(options.onclick)) {\n\t $button.click(options.onclick);\n\t }\n\t return $button;\n\t };\n\t\n\t //============================================================================\n\t return faIconButton;\n\t});\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1), __webpack_require__(2)))\n\n/***/ }),\n/* 18 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {!(__WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t\n\t /**\n\t * Stringifies a number adding commas for digit grouping as per North America.\n\t */\n\t function commatize(number) {\n\t number += ''; // Convert to string\n\t var rgx = /(\\d+)(\\d{3})/;\n\t while (rgx.test(number)) {\n\t number = number.replace(rgx, '$1' + ',' + '$2');\n\t }\n\t return number;\n\t }\n\t\n\t /**\n\t * Helper to determine if object is jQuery deferred.\n\t */\n\t var is_deferred = function (d) {\n\t return 'promise' in d;\n\t };\n\t\n\t /**\n\t * Implementation of a server-state based deferred. Server is repeatedly polled, and when\n\t * condition is met, deferred is resolved.\n\t */\n\t var ServerStateDeferred = Backbone.Model.extend({\n\t defaults: {\n\t ajax_settings: {},\n\t interval: 1000,\n\t success_fn: function (result) {\n\t return true;\n\t }\n\t },\n\t\n\t /**\n\t * Returns a deferred that resolves when success function returns true.\n\t */\n\t go: function () {\n\t var deferred = $.Deferred(),\n\t self = this,\n\t ajax_settings = self.get('ajax_settings'),\n\t success_fn = self.get('success_fn'),\n\t interval = self.get('interval'),\n\t _go = function () {\n\t $.ajax(ajax_settings).success(function (result) {\n\t if (success_fn(result)) {\n\t // Result is good, so resolve.\n\t deferred.resolve(result);\n\t } else {\n\t // Result not good, try again.\n\t setTimeout(_go, interval);\n\t }\n\t });\n\t };\n\t _go();\n\t return deferred;\n\t }\n\t });\n\t\n\t /**\n\t * Returns a random color in hexadecimal format that is sufficiently different from a single color\n\t * or set of colors.\n\t * @param colors a color or list of colors in the format '#RRGGBB'\n\t */\n\t var get_random_color = function (colors) {\n\t // Default for colors is white.\n\t if (!colors) {\n\t colors = \"#ffffff\";\n\t }\n\t\n\t // If needed, create list of colors.\n\t if (typeof colors === \"string\") {\n\t colors = [colors];\n\t }\n\t\n\t // Convert colors to numbers.\n\t for (var i = 0; i < colors.length; i++) {\n\t colors[i] = parseInt(colors[i].slice(1), 16);\n\t }\n\t\n\t // -- Perceived brightness and difference formulas are from\n\t // -- http://www.w3.org/WAI/ER/WD-AERT/#color-contrast\n\t\n\t // Compute perceived color brightness (based on RGB-YIQ transformation):\n\t var brightness = function (r, g, b) {\n\t return (r * 299 + g * 587 + b * 114) / 1000;\n\t };\n\t\n\t // Compute color difference:\n\t var difference = function (r1, g1, b1, r2, g2, b2) {\n\t return Math.max(r1, r2) - Math.min(r1, r2) + (Math.max(g1, g2) - Math.min(g1, g2)) + (Math.max(b1, b2) - Math.min(b1, b2));\n\t };\n\t\n\t // Create new random color.\n\t var new_color,\n\t nr,\n\t ng,\n\t nb,\n\t other_color,\n\t or,\n\t og,\n\t ob,\n\t n_brightness,\n\t o_brightness,\n\t diff,\n\t ok = false,\n\t num_tries = 0;\n\t do {\n\t // New color is never white b/c random in [0,1)\n\t new_color = Math.round(Math.random() * 0xffffff);\n\t nr = (new_color & 0xff0000) >> 16;\n\t ng = (new_color & 0x00ff00) >> 8;\n\t nb = new_color & 0x0000ff;\n\t n_brightness = brightness(nr, ng, nb);\n\t ok = true;\n\t for (i = 0; i < colors.length; i++) {\n\t other_color = colors[i];\n\t or = (other_color & 0xff0000) >> 16;\n\t og = (other_color & 0x00ff00) >> 8;\n\t ob = other_color & 0x0000ff;\n\t o_brightness = brightness(or, og, ob);\n\t diff = difference(nr, ng, nb, or, og, ob);\n\t // These thresholds may need to be adjusted. Brightness difference range is 125;\n\t // color difference range is 500.\n\t if (Math.abs(n_brightness - o_brightness) < 40 || diff < 200) {\n\t ok = false;\n\t break;\n\t }\n\t }\n\t\n\t num_tries++;\n\t } while (!ok && num_tries <= 10);\n\t\n\t // Add 0x1000000 to left pad number with 0s.\n\t return '#' + (0x1000000 + new_color).toString(16).substr(1, 6);\n\t };\n\t\n\t return {\n\t commatize: commatize,\n\t is_deferred: is_deferred,\n\t ServerStateDeferred: ServerStateDeferred,\n\t get_random_color: get_random_color\n\t };\n\t}.call(exports, __webpack_require__, exports, module), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1)))\n\n/***/ }),\n/* 19 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(33), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (parseBibtex, baseMVC, _l) {\n\t /* global Backbone */\n\t // we use amd here to require, but bibtex uses a global or commonjs pattern.\n\t // webpack will load via commonjs and plain requirejs will load as global. Check both\n\t parseBibtex = parseBibtex || window.BibtexParser;\n\t\n\t var logNamespace = 'citation';\n\t //==============================================================================\n\t /** @class model for tool citations.\n\t * @name Citation\n\t * @augments Backbone.Model\n\t */\n\t var Citation = Backbone.Model.extend(baseMVC.LoggableMixin).extend({\n\t _logNamespace: logNamespace,\n\t\n\t defaults: {\n\t content: ''\n\t },\n\t\n\t initialize: function () {\n\t var parsed;\n\t try {\n\t // TODO: to model.parse/.validate\n\t parsed = parseBibtex(this.attributes.content);\n\t } catch (err) {\n\t return;\n\t }\n\t // bibtex returns successfully parsed in .entries and any parsing errors in .errors\n\t if (parsed.errors.length) {\n\t // the gen. form of these errors seems to be [ line, col, char, error message ]\n\t var errors = parsed.errors.reduce(function (all, current) {\n\t return all + '; ' + current;\n\t });\n\t // throw new Error( 'Error parsing bibtex: ' + errors );\n\t this.log('Error parsing bibtex: ' + errors);\n\t }\n\t\n\t this._fields = {};\n\t this.entry = _.first(parsed.entries);\n\t if (this.entry) {\n\t var rawFields = this.entry.Fields;\n\t for (var key in rawFields) {\n\t var value = rawFields[key];\n\t var lowerKey = key.toLowerCase();\n\t this._fields[lowerKey] = value;\n\t }\n\t }\n\t },\n\t entryType: function () {\n\t return this.entry ? this.entry.EntryType : undefined;\n\t },\n\t fields: function () {\n\t return this._fields;\n\t }\n\t });\n\t\n\t //==============================================================================\n\t /** @class Backbone collection of citations.\n\t */\n\t var BaseCitationCollection = Backbone.Collection.extend(baseMVC.LoggableMixin).extend({\n\t _logNamespace: logNamespace,\n\t\n\t /** root api url */\n\t urlRoot: Galaxy.root + 'api',\n\t partial: true, // Assume some tools in history/workflow may not be properly annotated yet.\n\t model: Citation\n\t });\n\t\n\t var HistoryCitationCollection = BaseCitationCollection.extend({\n\t /** complete api url */\n\t url: function () {\n\t return this.urlRoot + '/histories/' + this.history_id + '/citations';\n\t }\n\t });\n\t\n\t var ToolCitationCollection = BaseCitationCollection.extend({\n\t /** complete api url */\n\t url: function () {\n\t return this.urlRoot + '/tools/' + this.tool_id + '/citations';\n\t },\n\t partial: false });\n\t\n\t //==============================================================================\n\t\n\t return {\n\t Citation: Citation,\n\t HistoryCitationCollection: HistoryCitationCollection,\n\t ToolCitationCollection: ToolCitationCollection\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2)))\n\n/***/ }),\n/* 20 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, $) {/**\n\t This is the main class of the form plugin. It is referenced as 'app' in lower level modules.\n\t*/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(9), __webpack_require__(7), __webpack_require__(43), __webpack_require__(39)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Portlet, Ui, FormSection, FormData) {\n\t return Backbone.View.extend({\n\t initialize: function (options) {\n\t this.model = new Backbone.Model({\n\t initial_errors: false,\n\t cls: 'ui-portlet-limited',\n\t icon: null,\n\t always_refresh: true,\n\t message_status: 'warning'\n\t }).set(options);\n\t this.setElement('');\n\t this.render();\n\t },\n\t\n\t /** Update available options */\n\t update: function (new_model) {\n\t var self = this;\n\t this.data.matchModel(new_model, function (node, input_id) {\n\t var input = self.input_list[input_id];\n\t if (input && input.options) {\n\t if (!_.isEqual(input.options, node.options)) {\n\t input.options = node.options;\n\t var field = self.field_list[input_id];\n\t if (field.update) {\n\t var new_options = [];\n\t if (['data', 'data_collection', 'drill_down'].indexOf(input.type) != -1) {\n\t new_options = input.options;\n\t } else {\n\t for (var i in node.options) {\n\t var opt = node.options[i];\n\t if (opt.length > 2) {\n\t new_options.push({ label: opt[0], value: opt[1] });\n\t }\n\t }\n\t }\n\t field.update(new_options);\n\t field.trigger('change');\n\t Galaxy.emit.debug('form-view::update()', 'Updating options for ' + input_id);\n\t }\n\t }\n\t }\n\t });\n\t },\n\t\n\t /** Set form into wait mode */\n\t wait: function (active) {\n\t for (var i in this.input_list) {\n\t var field = this.field_list[i];\n\t var input = this.input_list[i];\n\t if (input.is_dynamic && field.wait && field.unwait) {\n\t field[active ? 'wait' : 'unwait']();\n\t }\n\t }\n\t },\n\t\n\t /** Highlight and scroll to input element (currently only used for error notifications) */\n\t highlight: function (input_id, message, silent) {\n\t var input_element = this.element_list[input_id];\n\t if (input_element) {\n\t input_element.error(message || 'Please verify this parameter.');\n\t this.portlet.expand();\n\t this.trigger('expand', input_id);\n\t if (!silent) {\n\t var $panel = this.$el.parents().filter(function () {\n\t return ['auto', 'scroll'].indexOf($(this).css('overflow')) != -1;\n\t }).first();\n\t $panel.animate({ scrollTop: $panel.scrollTop() + input_element.$el.offset().top - 120 }, 500);\n\t }\n\t }\n\t },\n\t\n\t /** Highlights errors */\n\t errors: function (options) {\n\t this.trigger('reset');\n\t if (options && options.errors) {\n\t var error_messages = this.data.matchResponse(options.errors);\n\t for (var input_id in this.element_list) {\n\t var input = this.element_list[input_id];\n\t if (error_messages[input_id]) {\n\t this.highlight(input_id, error_messages[input_id], true);\n\t }\n\t }\n\t }\n\t },\n\t\n\t /** Render tool form */\n\t render: function () {\n\t var self = this;\n\t this.off('change');\n\t this.off('reset');\n\t // contains the dom field elements as created by the parameter factory i.e. form-parameters\n\t this.field_list = {};\n\t // contains input definitions/dictionaries as provided by the parameters to_dict() function through the api\n\t this.input_list = {};\n\t // contains the dom elements of each input element i.e. form-input which wraps the actual input field\n\t this.element_list = {};\n\t // converts the form into a json data structure\n\t this.data = new FormData.Manager(this);\n\t this._renderForm();\n\t this.data.create();\n\t this.model.get('initial_errors') && this.errors(this.model.attributes);\n\t // add listener which triggers on checksum change, and reset the form input wrappers\n\t var current_check = this.data.checksum();\n\t this.on('change', function (input_id) {\n\t var input = self.input_list[input_id];\n\t if (!input || input.refresh_on_change || self.model.get('always_refresh')) {\n\t var new_check = self.data.checksum();\n\t if (new_check != current_check) {\n\t current_check = new_check;\n\t self.model.get('onchange') && self.model.get('onchange')();\n\t }\n\t }\n\t });\n\t this.on('reset', function () {\n\t _.each(self.element_list, function (input_element) {\n\t input_element.reset();\n\t });\n\t });\n\t return this;\n\t },\n\t\n\t /** Renders/appends dom elements of the form */\n\t _renderForm: function () {\n\t $('.tooltip').remove();\n\t var options = this.model.attributes;\n\t this.message = new Ui.UnescapedMessage();\n\t this.section = new FormSection.View(this, { inputs: options.inputs });\n\t this.portlet = new Portlet.View({\n\t icon: options.icon,\n\t title: options.title,\n\t cls: options.cls,\n\t operations: options.operations,\n\t buttons: options.buttons,\n\t collapsible: options.collapsible,\n\t collapsed: options.collapsed,\n\t onchange_title: options.onchange_title\n\t });\n\t this.portlet.append(this.message.$el);\n\t this.portlet.append(this.section.$el);\n\t this.$el.empty();\n\t options.inputs && this.$el.append(this.portlet.$el);\n\t options.message && this.message.update({ persistent: true, status: options.message_status, message: options.message });\n\t Galaxy.emit.debug('form-view::initialize()', 'Completed');\n\t }\n\t });\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ }),\n/* 21 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {// dependencies\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(9), __webpack_require__(7)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Portlet, Ui) {\n\t\n\t // ui list element\n\t var View = Backbone.View.extend({\n\t // create portlet to keep track of selected list elements\n\t initialize: function (options) {\n\t // link this\n\t var self = this;\n\t\n\t // initialize options\n\t this.options = options;\n\t this.name = options.name || 'element';\n\t this.multiple = options.multiple || false;\n\t\n\t // create message handler\n\t this.message = new Ui.Message();\n\t\n\t // create portlet\n\t this.portlet = new Portlet.View({ cls: 'ui-portlet-section' });\n\t\n\t // create select field containing the options which can be inserted into the list\n\t this.select = new Ui.Select.View({ optional: options.optional });\n\t\n\t // create insert new list element button\n\t this.button = new Ui.ButtonIcon({\n\t icon: 'fa fa-sign-in',\n\t floating: 'left',\n\t tooltip: 'Insert new ' + this.name,\n\t onclick: function () {\n\t self.add({\n\t id: self.select.value(),\n\t name: self.select.text()\n\t });\n\t }\n\t });\n\t\n\t // build main element\n\t this.setElement(this._template(options));\n\t this.$('.ui-list-message').append(this.message.$el);\n\t this.$('.ui-list-portlet').append(this.portlet.$el);\n\t this.$('.ui-list-button').append(this.button.$el);\n\t this.$('.ui-list-select').append(this.select.$el);\n\t },\n\t\n\t /** Return/Set currently selected list elements */\n\t value: function (val) {\n\t // set new value\n\t if (val !== undefined) {\n\t this.portlet.empty();\n\t if ($.isArray(val)) {\n\t for (var i in val) {\n\t var v = val[i];\n\t var v_id = null;\n\t var v_name = null;\n\t if ($.type(v) != 'string') {\n\t v_id = v.id;\n\t v_name = v.name;\n\t } else {\n\t v_id = v_name = v;\n\t }\n\t if (v_id != null) {\n\t this.add({\n\t id: v_id,\n\t name: v_name\n\t });\n\t }\n\t }\n\t }\n\t this._refresh();\n\t }\n\t // get current value\n\t var lst = [];\n\t this.$('.ui-list-id').each(function () {\n\t lst.push({\n\t id: $(this).prop('id'),\n\t name: $(this).find('.ui-list-name').html()\n\t });\n\t });\n\t if (lst.length == 0) {\n\t return null;\n\t }\n\t return lst;\n\t },\n\t\n\t /** Add row */\n\t add: function (options) {\n\t var self = this;\n\t if (this.$('[id=\"' + options.id + '\"]').length === 0) {\n\t if (!Utils.isEmpty(options.id)) {\n\t var $el = $(this._templateRow({\n\t id: options.id,\n\t name: options.name\n\t }));\n\t $el.on('click', function () {\n\t $el.remove();\n\t self._refresh();\n\t });\n\t $el.on('mouseover', function () {\n\t $el.addClass('portlet-highlight');\n\t });\n\t $el.on('mouseout', function () {\n\t $el.removeClass('portlet-highlight');\n\t });\n\t this.portlet.append($el);\n\t this._refresh();\n\t } else {\n\t this.message.update({ message: 'Please select a valid ' + this.name + '.', status: 'danger' });\n\t }\n\t } else {\n\t this.message.update({ message: 'This ' + this.name + ' is already in the list.' });\n\t }\n\t },\n\t\n\t /** Update available options */\n\t update: function (options) {\n\t this.select.update(options);\n\t },\n\t\n\t /** Refresh view */\n\t _refresh: function () {\n\t if (this.$('.ui-list-id').length > 0) {\n\t !this.multiple && this.button.disable();\n\t this.$('.ui-list-portlet').show();\n\t } else {\n\t this.button.enable();\n\t this.$('.ui-list-portlet').hide();\n\t }\n\t this.options.onchange && this.options.onchange();\n\t },\n\t\n\t /** Main Template */\n\t _template: function (options) {\n\t return '
\");\n\t return this;\n\t },\n\t formattedReference: function () {\n\t var model = this.model;\n\t var entryType = model.entryType();\n\t var fields = model.fields();\n\t\n\t var ref = \"\";\n\t // Code inspired by...\n\t // https://github.com/vkaravir/bib-publication-list/blob/master/src/bib-publication-list.js\n\t var authorsAndYear = this._asSentence((fields.author ? fields.author : \"\") + (fields.year ? \" (\" + fields.year + \")\" : \"\")) + \" \";\n\t var title = fields.title || \"\";\n\t var pages = fields.pages ? \"pp. \" + fields.pages : \"\";\n\t var address = fields.address;\n\t if (entryType == \"article\") {\n\t var volume = (fields.volume ? fields.volume : \"\") + (fields.number ? \" (\" + fields.number + \")\" : \"\") + (pages ? \", \" + pages : \"\");\n\t ref = authorsAndYear + this._asSentence(title) + (fields.journal ? \"In \" + fields.journal + \", \" : \"\") + this._asSentence(volume) + this._asSentence(fields.address) + \"<\\/em>\";\n\t } else if (entryType == \"inproceedings\" || entryType == \"proceedings\") {\n\t ref = authorsAndYear + this._asSentence(title) + (fields.booktitle ? \"In \" + fields.booktitle + \", \" : \"\") + (pages ? pages : \"\") + (address ? \", \" + address : \"\") + \".<\\/em>\";\n\t } else if (entryType == \"mastersthesis\" || entryType == \"phdthesis\") {\n\t ref = authorsAndYear + this._asSentence(title) + (fields.howpublished ? fields.howpublished + \". \" : \"\") + (fields.note ? fields.note + \".\" : \"\");\n\t } else if (entryType == \"techreport\") {\n\t ref = authorsAndYear + this._asSentence(title) + this._asSentence(fields.institution) + this._asSentence(fields.number) + this._asSentence(fields.type);\n\t } else if (entryType == \"book\" || entryType == \"inbook\" || entryType == \"incollection\") {\n\t ref = authorsAndYear + \" \" + this._formatBookInfo(fields);\n\t } else {\n\t ref = authorsAndYear + \" \" + this._asSentence(title) + this._asSentence(fields.howpublished) + this._asSentence(fields.note);\n\t }\n\t var doiUrl = \"\";\n\t if (fields.doi) {\n\t doiUrl = 'http://dx.doi.org/' + fields.doi;\n\t ref += '[doi:' + fields.doi + \"]\";\n\t }\n\t var url = fields.url || doiUrl;\n\t if (url) {\n\t ref += '[Link]';\n\t }\n\t return ref;\n\t },\n\t _formatBookInfo: function (fields) {\n\t var info = \"\";\n\t if (fields.chapter) {\n\t info += fields.chapter + \" in \";\n\t }\n\t if (fields.title) {\n\t info += \"\" + fields.title + \"<\\/em>\";\n\t }\n\t if (fields.editor) {\n\t info += \", Edited by \" + fields.editor + \", \";\n\t }\n\t if (fields.publisher) {\n\t info += \", \" + fields.publisher;\n\t }\n\t if (fields.pages) {\n\t info += \", pp. \" + fields.pages + \"\";\n\t }\n\t if (fields.series) {\n\t info += \", \" + fields.series + \"<\\/em>\";\n\t }\n\t if (fields.volume) {\n\t info += \", Vol.\" + fields.volume;\n\t }\n\t if (fields.issn) {\n\t info += \", ISBN: \" + fields.issn;\n\t }\n\t return info + \".\";\n\t },\n\t _asSentence: function (str) {\n\t return str && str.trim() ? str + \". \" : \"\";\n\t }\n\t });\n\t\n\t var CitationListView = Backbone.View.extend({\n\t el: '#citations',\n\t /**\n\t * Set up view.\n\t */\n\t initialize: function () {\n\t this.listenTo(this.collection, 'add', this.renderCitation);\n\t },\n\t\n\t events: {\n\t 'click .citations-to-bibtex': 'showBibtex',\n\t 'click .citations-to-formatted': 'showFormatted'\n\t },\n\t\n\t renderCitation: function (citation) {\n\t var citationView = new CitationView({ model: citation });\n\t this.$(\".citations-formatted\").append(citationView.render().el);\n\t var rawTextarea = this.$(\".citations-bibtex-text\");\n\t rawTextarea.val(rawTextarea.val() + \"\\n\\r\" + citation.attributes.content);\n\t },\n\t\n\t render: function () {\n\t this.$el.html(this.citationsElement());\n\t this.collection.each(function (item) {\n\t this.renderCitation(item);\n\t }, this);\n\t this.showFormatted();\n\t },\n\t\n\t showBibtex: function () {\n\t this.$(\".citations-to-formatted\").show();\n\t this.$(\".citations-to-bibtex\").hide();\n\t this.$(\".citations-bibtex\").show();\n\t this.$(\".citations-formatted\").hide();\n\t this.$(\".citations-bibtex-text\").select();\n\t },\n\t\n\t showFormatted: function () {\n\t this.$(\".citations-to-formatted\").hide();\n\t this.$(\".citations-to-bibtex\").show();\n\t this.$(\".citations-bibtex\").hide();\n\t this.$(\".citations-formatted\").show();\n\t },\n\t\n\t partialWarningElement: function () {\n\t if (this.collection.partial) {\n\t return ['
', 'Warning: This is a experimental feature. Most Galaxy tools will not annotate', ' citations explicitly at this time. When writing up your analysis, please manually', ' review your histories and find all references', ' that should be cited in order to completely describe your work. Also, please remember to', ' cite Galaxy.', '
'], 'collection');\n\t\n\t // use element identifier\n\t var subtitleTemplate = BASE_MVC.wrapTemplate(['
', '<% var countText = collection.element_count? ( collection.element_count + \" \" ) : \"\"; %>', '<% if( collection.collection_type === \"list\" ){ %>', _l('a list of <%- countText %>datasets'), '<% } else if( collection.collection_type === \"paired\" ){ %>', _l('a pair of datasets'), '<% } else if( collection.collection_type === \"list:paired\" ){ %>', _l('a list of <%- countText %>dataset pairs'), '<% } else if( collection.collection_type === \"list:list\" ){ %>', _l('a list of <%- countText %>dataset lists'), '<% } %>', '
'], 'collection');\n\t\n\t return _.extend({}, FoldoutListItemView.prototype.templates, {\n\t warnings: warnings,\n\t titleBar: titleBarTemplate,\n\t subtitle: subtitleTemplate\n\t });\n\t }();\n\t\n\t //==============================================================================\n\t /** @class Read only view for DatasetCollectionElement.\n\t */\n\t var DCEListItemView = ListItemView.extend(\n\t /** @lends DCEListItemView.prototype */{\n\t\n\t /** add the DCE class to the list item */\n\t className: ListItemView.prototype.className + \" dataset-collection-element\",\n\t\n\t /** set up */\n\t initialize: function (attributes) {\n\t if (attributes.logger) {\n\t this.logger = this.model.logger = attributes.logger;\n\t }\n\t this.log('DCEListItemView.initialize:', attributes);\n\t ListItemView.prototype.initialize.call(this, attributes);\n\t },\n\t\n\t // ......................................................................... misc\n\t /** String representation */\n\t toString: function () {\n\t var modelString = this.model ? this.model + '' : '(no model)';\n\t return 'DCEListItemView(' + modelString + ')';\n\t }\n\t });\n\t\n\t // ............................................................................ TEMPLATES\n\t /** underscore templates */\n\t DCEListItemView.prototype.templates = function () {\n\t\n\t // use the element identifier here - since that will persist and the user will need it\n\t var titleBarTemplate = BASE_MVC.wrapTemplate(['
', '
', '<%- element.element_identifier %>', '
', '', '
'], 'element');\n\t\n\t return _.extend({}, ListItemView.prototype.templates, {\n\t titleBar: titleBarTemplate\n\t });\n\t }();\n\t\n\t //==============================================================================\n\t /** @class Read only view for a DatasetCollectionElement that is also an DatasetAssociation\n\t * (a dataset contained in a dataset collection).\n\t */\n\t var DatasetDCEListItemView = DATASET_LI.DatasetListItemView.extend(\n\t /** @lends DatasetDCEListItemView.prototype */{\n\t\n\t className: DATASET_LI.DatasetListItemView.prototype.className + \" dataset-collection-element\",\n\t\n\t /** set up */\n\t initialize: function (attributes) {\n\t if (attributes.logger) {\n\t this.logger = this.model.logger = attributes.logger;\n\t }\n\t this.log('DatasetDCEListItemView.initialize:', attributes);\n\t DATASET_LI.DatasetListItemView.prototype.initialize.call(this, attributes);\n\t },\n\t\n\t /** In this override, only get details if in the ready state.\n\t * Note: fetch with no 'change' event triggering to prevent automatic rendering.\n\t */\n\t _fetchModelDetails: function () {\n\t var view = this;\n\t if (view.model.inReadyState() && !view.model.hasDetails()) {\n\t return view.model.fetch({ silent: true });\n\t }\n\t return jQuery.when();\n\t },\n\t\n\t // ......................................................................... misc\n\t /** String representation */\n\t toString: function () {\n\t var modelString = this.model ? this.model + '' : '(no model)';\n\t return 'DatasetDCEListItemView(' + modelString + ')';\n\t }\n\t });\n\t\n\t // ............................................................................ TEMPLATES\n\t /** underscore templates */\n\t DatasetDCEListItemView.prototype.templates = function () {\n\t\n\t // use the element identifier here and not the dataset name\n\t //TODO:?? can we steal the DCE titlebar?\n\t var titleBarTemplate = BASE_MVC.wrapTemplate(['
', '', '
', '<%- element.element_identifier %>', '
', '
'], 'element');\n\t\n\t return _.extend({}, DATASET_LI.DatasetListItemView.prototype.templates, {\n\t titleBar: titleBarTemplate\n\t });\n\t }();\n\t\n\t //==============================================================================\n\t /** @class Read only view for a DatasetCollectionElement that is also a DatasetCollection\n\t * (a nested DC).\n\t */\n\t var NestedDCDCEListItemView = DCListItemView.extend(\n\t /** @lends NestedDCDCEListItemView.prototype */{\n\t\n\t className: DCListItemView.prototype.className + \" dataset-collection-element\",\n\t\n\t /** In this override, add the state as a class for use with state-based CSS */\n\t _swapNewRender: function ($newRender) {\n\t DCListItemView.prototype._swapNewRender.call(this, $newRender);\n\t var state = this.model.get('state') || 'ok';\n\t this.$el.addClass('state-' + state);\n\t return this.$el;\n\t },\n\t\n\t // ......................................................................... misc\n\t /** String representation */\n\t toString: function () {\n\t var modelString = this.model ? this.model + '' : '(no model)';\n\t return 'NestedDCDCEListItemView(' + modelString + ')';\n\t }\n\t });\n\t\n\t //==============================================================================\n\t return {\n\t DCListItemView: DCListItemView,\n\t DCEListItemView: DCEListItemView,\n\t DatasetDCEListItemView: DatasetDCEListItemView,\n\t NestedDCDCEListItemView: NestedDCDCEListItemView\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(1)))\n\n/***/ }),\n/* 36 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_, Backbone, jQuery) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(76), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (DATASET_MODEL, BASE_MVC, _l) {\n\t 'use strict';\n\t\n\t //==============================================================================\n\t /*\n\t Notes:\n\t \n\t Terminology:\n\t DatasetCollection/DC : a container of datasets or nested DatasetCollections\n\t Element/DatasetCollectionElement/DCE : an item contained in a DatasetCollection\n\t HistoryDatasetCollectionAssociation/HDCA: a DatasetCollection contained in a history\n\t \n\t \n\t This all seems too complex unfortunately:\n\t \n\t - Terminology collision between DatasetCollections (DCs) and Backbone Collections.\n\t - In the DatasetCollections API JSON, DC Elements use a 'Has A' stucture to *contain*\n\t either a dataset or a nested DC. This would make the hierarchy much taller. I've\n\t decided to merge the contained JSON with the DC element json - making the 'has a'\n\t relation into an 'is a' relation. This seems simpler to me and allowed a lot of\n\t DRY in both models and views, but may make tracking or tracing within these models\n\t more difficult (since DatasetCollectionElements are now *also* DatasetAssociations\n\t or DatasetCollections (nested)). This also violates the rule of thumb about\n\t favoring aggregation over inheritance.\n\t - Currently, there are three DatasetCollection subclasses: List, Pair, and ListPaired.\n\t These each should a) be usable on their own, b) be usable in the context of\n\t nesting within a collection model (at least in the case of ListPaired), and\n\t c) be usable within the context of other container models (like History or\n\t LibraryFolder, etc.). I've tried to separate/extract classes in order to\n\t handle those three situations, but it's proven difficult to do in a simple,\n\t readable manner.\n\t - Ideally, histories and libraries would inherit from the same server models as\n\t dataset collections do since they are (in essence) dataset collections themselves -\n\t making the whole nested structure simpler. This would be a large, error-prone\n\t refactoring and migration.\n\t \n\t Many of the classes and heirarchy are meant as extension points so, while the\n\t relations and flow may be difficult to understand initially, they'll allow us to\n\t handle the growth or flux dataset collection in the future (w/o actually implementing\n\t any YAGNI).\n\t \n\t */\n\t //_________________________________________________________________________________________________ ELEMENTS\n\t /** @class mixin for Dataset collection elements.\n\t * When collection elements are passed from the API, the underlying element is\n\t * in a sub-object 'object' (IOW, a DCE representing an HDA will have HDA json in element.object).\n\t * This mixin uses the constructor and parse methods to merge that JSON with the DCE attribtues\n\t * effectively changing a DCE from a container to a subclass (has a --> is a).\n\t */\n\t\n\t var DatasetCollectionElementMixin = {\n\t\n\t /** default attributes used by elements in a dataset collection */\n\t defaults: {\n\t model_class: 'DatasetCollectionElement',\n\t element_identifier: null,\n\t element_index: null,\n\t element_type: null\n\t },\n\t\n\t /** merge the attributes of the sub-object 'object' into this model */\n\t _mergeObject: function (attributes) {\n\t // if we don't preserve and correct ids here, the element id becomes the object id\n\t // and collision in backbone's _byId will occur and only\n\t _.extend(attributes, attributes.object, { element_id: attributes.id });\n\t delete attributes.object;\n\t return attributes;\n\t },\n\t\n\t /** override to merge this.object into this */\n\t constructor: function (attributes, options) {\n\t // console.debug( '\\t DatasetCollectionElement.constructor:', attributes, options );\n\t attributes = this._mergeObject(attributes);\n\t this.idAttribute = 'element_id';\n\t Backbone.Model.apply(this, arguments);\n\t },\n\t\n\t /** when the model is fetched, merge this.object into this */\n\t parse: function (response, options) {\n\t var attributes = response;\n\t attributes = this._mergeObject(attributes);\n\t return attributes;\n\t }\n\t };\n\t\n\t /** @class Concrete class of Generic DatasetCollectionElement */\n\t var DatasetCollectionElement = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(DatasetCollectionElementMixin).extend({ _logNamespace: 'collections' });\n\t\n\t //==============================================================================\n\t /** @class Base/Abstract Backbone collection for Generic DCEs. */\n\t var DCECollection = Backbone.Collection.extend(BASE_MVC.LoggableMixin).extend(\n\t /** @lends DCECollection.prototype */{\n\t _logNamespace: 'collections',\n\t\n\t model: DatasetCollectionElement,\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return ['DatasetCollectionElementCollection(', this.length, ')'].join('');\n\t }\n\t });\n\t\n\t //==============================================================================\n\t /** @class Backbone model for a dataset collection element that is a dataset (HDA).\n\t */\n\t var DatasetDCE = DATASET_MODEL.DatasetAssociation.extend(BASE_MVC.mixin(DatasetCollectionElementMixin,\n\t /** @lends DatasetDCE.prototype */{\n\t\n\t /** url fn */\n\t url: function () {\n\t // won't always be an hda\n\t if (!this.has('history_id')) {\n\t console.warn('no endpoint for non-hdas within a collection yet');\n\t // (a little silly since this api endpoint *also* points at hdas)\n\t return Galaxy.root + 'api/datasets';\n\t }\n\t return Galaxy.root + 'api/histories/' + this.get('history_id') + '/contents/' + this.get('id');\n\t },\n\t\n\t defaults: _.extend({}, DATASET_MODEL.DatasetAssociation.prototype.defaults, DatasetCollectionElementMixin.defaults),\n\t\n\t _downloadQueryParameters: function () {\n\t return '?to_ext=' + this.get('file_ext') + '&hdca_id=' + this.get('parent_hdca_id') + '&element_identifier=' + this.get('element_identifier');\n\t },\n\t\n\t // because all objects have constructors (as this hashmap would even if this next line wasn't present)\n\t // the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model\n\t // - re-apply manually for now\n\t /** call the mixin constructor */\n\t constructor: function (attributes, options) {\n\t this.debug('\\t DatasetDCE.constructor:', attributes, options);\n\t //DATASET_MODEL.DatasetAssociation.prototype.constructor.call( this, attributes, options );\n\t DatasetCollectionElementMixin.constructor.call(this, attributes, options);\n\t },\n\t\n\t /** Does this model already contain detailed data (as opposed to just summary level data)? */\n\t hasDetails: function () {\n\t return this.elements && this.elements.length;\n\t },\n\t\n\t /** String representation. */\n\t toString: function () {\n\t var objStr = this.get('element_identifier');\n\t return ['DatasetDCE(', objStr, ')'].join('');\n\t }\n\t }));\n\t\n\t //==============================================================================\n\t /** @class DCECollection of DatasetDCE's (a list of datasets, a pair of datasets).\n\t */\n\t var DatasetDCECollection = DCECollection.extend(\n\t /** @lends DatasetDCECollection.prototype */{\n\t model: DatasetDCE,\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return ['DatasetDCECollection(', this.length, ')'].join('');\n\t }\n\t });\n\t\n\t //_________________________________________________________________________________________________ COLLECTIONS\n\t /** @class Backbone model for Dataset Collections.\n\t * The DC API returns an array of JSON objects under the attribute elements.\n\t * This model:\n\t * - removes that array/attribute ('elements') from the model,\n\t * - creates a bbone collection (of the class defined in the 'collectionClass' attribute),\n\t * - passes that json onto the bbone collection\n\t * - caches the bbone collection in this.elements\n\t */\n\t var DatasetCollection = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(BASE_MVC.SearchableModelMixin).extend( /** @lends DatasetCollection.prototype */{\n\t _logNamespace: 'collections',\n\t\n\t /** default attributes for a model */\n\t defaults: {\n\t /* 'list', 'paired', or 'list:paired' */\n\t collection_type: null,\n\t //??\n\t deleted: false\n\t },\n\t\n\t /** Which class to use for elements */\n\t collectionClass: DCECollection,\n\t\n\t /** set up: create elements instance var and (on changes to elements) update them */\n\t initialize: function (model, options) {\n\t this.debug(this + '(DatasetCollection).initialize:', model, options, this);\n\t this.elements = this._createElementsModel();\n\t this.on('change:elements', function () {\n\t this.log('change:elements');\n\t //TODO: prob. better to update the collection instead of re-creating it\n\t this.elements = this._createElementsModel();\n\t });\n\t },\n\t\n\t /** move elements model attribute to full collection */\n\t _createElementsModel: function () {\n\t this.debug(this + '._createElementsModel', this.collectionClass, this.get('elements'), this.elements);\n\t //TODO: same patterns as DatasetCollectionElement _createObjectModel - refactor to BASE_MVC.hasSubModel?\n\t var elements = this.get('elements') || [];\n\t this.unset('elements', { silent: true });\n\t var self = this;\n\t _.each(elements, function (element, index) {\n\t _.extend(element, { \"parent_hdca_id\": self.get(\"id\") });\n\t });\n\t this.elements = new this.collectionClass(elements);\n\t //this.debug( 'collectionClass:', this.collectionClass + '', this.elements );\n\t return this.elements;\n\t },\n\t\n\t // ........................................................................ common queries\n\t /** pass the elements back within the model json when this is serialized */\n\t toJSON: function () {\n\t var json = Backbone.Model.prototype.toJSON.call(this);\n\t if (this.elements) {\n\t json.elements = this.elements.toJSON();\n\t }\n\t return json;\n\t },\n\t\n\t /** Is this collection in a 'ready' state no processing (for the collection) is left\n\t * to do on the server.\n\t */\n\t inReadyState: function () {\n\t var populated = this.get('populated');\n\t return this.isDeletedOrPurged() || populated;\n\t },\n\t\n\t //TODO:?? the following are the same interface as DatasetAssociation - can we combine?\n\t /** Does the DC contain any elements yet? Is a fetch() required? */\n\t hasDetails: function () {\n\t return this.elements.length !== 0;\n\t },\n\t\n\t /** Given the filters, what models in this.elements would be returned? */\n\t getVisibleContents: function (filters) {\n\t // filters unused for now\n\t return this.elements;\n\t },\n\t\n\t // ........................................................................ ajax\n\t /** override to use actual Dates objects for create/update times */\n\t parse: function (response, options) {\n\t var parsed = Backbone.Model.prototype.parse.call(this, response, options);\n\t if (parsed.create_time) {\n\t parsed.create_time = new Date(parsed.create_time);\n\t }\n\t if (parsed.update_time) {\n\t parsed.update_time = new Date(parsed.update_time);\n\t }\n\t return parsed;\n\t },\n\t\n\t /** save this dataset, _Mark_ing it as deleted (just a flag) */\n\t 'delete': function (options) {\n\t if (this.get('deleted')) {\n\t return jQuery.when();\n\t }\n\t return this.save({ deleted: true }, options);\n\t },\n\t /** save this dataset, _Mark_ing it as undeleted */\n\t undelete: function (options) {\n\t if (!this.get('deleted') || this.get('purged')) {\n\t return jQuery.when();\n\t }\n\t return this.save({ deleted: false }, options);\n\t },\n\t\n\t /** Is this collection deleted or purged? */\n\t isDeletedOrPurged: function () {\n\t return this.get('deleted') || this.get('purged');\n\t },\n\t\n\t // ........................................................................ searchable\n\t /** searchable attributes for collections */\n\t searchAttributes: ['name'],\n\t\n\t // ........................................................................ misc\n\t /** String representation */\n\t toString: function () {\n\t var idAndName = [this.get('id'), this.get('name') || this.get('element_identifier')];\n\t return 'DatasetCollection(' + idAndName.join(',') + ')';\n\t }\n\t });\n\t\n\t //==============================================================================\n\t /** Model for a DatasetCollection containing datasets (non-nested).\n\t */\n\t var ListDatasetCollection = DatasetCollection.extend(\n\t /** @lends ListDatasetCollection.prototype */{\n\t\n\t /** override since we know the collection will only contain datasets */\n\t collectionClass: DatasetDCECollection,\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return 'List' + DatasetCollection.prototype.toString.call(this);\n\t }\n\t });\n\t\n\t //==============================================================================\n\t /** Model for a DatasetCollection containing fwd/rev datasets (a list of 2).\n\t */\n\t var PairDatasetCollection = ListDatasetCollection.extend(\n\t /** @lends PairDatasetCollection.prototype */{\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return 'Pair' + DatasetCollection.prototype.toString.call(this);\n\t }\n\t });\n\t\n\t //_________________________________________________________________________________________________ NESTED COLLECTIONS\n\t // this is where things get weird, man. Weird.\n\t //TODO: it might be possible to compact all the following...I think.\n\t //==============================================================================\n\t /** @class Backbone model for a Generic DatasetCollectionElement that is also a DatasetCollection\n\t * (a nested collection). Currently only list:paired.\n\t */\n\t var NestedDCDCE = DatasetCollection.extend(BASE_MVC.mixin(DatasetCollectionElementMixin,\n\t /** @lends NestedDCDCE.prototype */{\n\t\n\t // because all objects have constructors (as this hashmap would even if this next line wasn't present)\n\t // the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model\n\t // - re-apply manually it now\n\t /** call the mixin constructor */\n\t constructor: function (attributes, options) {\n\t this.debug('\\t NestedDCDCE.constructor:', attributes, options);\n\t DatasetCollectionElementMixin.constructor.call(this, attributes, options);\n\t },\n\t\n\t /** String representation. */\n\t toString: function () {\n\t var objStr = this.object ? '' + this.object : this.get('element_identifier');\n\t return ['NestedDCDCE(', objStr, ')'].join('');\n\t }\n\t }));\n\t\n\t //==============================================================================\n\t /** @class Backbone collection containing Generic NestedDCDCE's (nested dataset collections).\n\t */\n\t var NestedDCDCECollection = DCECollection.extend(\n\t /** @lends NestedDCDCECollection.prototype */{\n\t\n\t /** This is a collection of nested collections */\n\t model: NestedDCDCE,\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return ['NestedDCDCECollection(', this.length, ')'].join('');\n\t }\n\t });\n\t\n\t //==============================================================================\n\t /** @class Backbone model for a paired dataset collection within a list:paired dataset collection.\n\t */\n\t var NestedPairDCDCE = PairDatasetCollection.extend(BASE_MVC.mixin(DatasetCollectionElementMixin,\n\t /** @lends NestedPairDCDCE.prototype */{\n\t //TODO:?? possibly rename to NestedDatasetCollection?\n\t\n\t // because all objects have constructors (as this hashmap would even if this next line wasn't present)\n\t // the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model\n\t // - re-apply manually it now\n\t /** This is both a collection and a collection element - call the constructor */\n\t constructor: function (attributes, options) {\n\t this.debug('\\t NestedPairDCDCE.constructor:', attributes, options);\n\t //DatasetCollection.constructor.call( this, attributes, options );\n\t DatasetCollectionElementMixin.constructor.call(this, attributes, options);\n\t },\n\t\n\t /** String representation. */\n\t toString: function () {\n\t var objStr = this.object ? '' + this.object : this.get('element_identifier');\n\t return ['NestedPairDCDCE(', objStr, ')'].join('');\n\t }\n\t }));\n\t\n\t //==============================================================================\n\t /** @class Backbone collection for a backbone collection containing paired dataset collections.\n\t */\n\t var NestedPairDCDCECollection = NestedDCDCECollection.extend(\n\t /** @lends PairDCDCECollection.prototype */{\n\t\n\t /** We know this collection is composed of only nested pair collections */\n\t model: NestedPairDCDCE,\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return ['NestedPairDCDCECollection(', this.length, ')'].join('');\n\t }\n\t });\n\t\n\t //==============================================================================\n\t /** @class Backbone Model for a DatasetCollection (list) that contains DatasetCollections (pairs).\n\t */\n\t var ListPairedDatasetCollection = DatasetCollection.extend(\n\t /** @lends ListPairedDatasetCollection.prototype */{\n\t\n\t /** list:paired is the only collection that itself contains collections */\n\t collectionClass: NestedPairDCDCECollection,\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return ['ListPairedDatasetCollection(', this.get('name'), ')'].join('');\n\t }\n\t });\n\t\n\t //==============================================================================\n\t /** @class Backbone model for a list dataset collection within a list:list dataset collection. */\n\t var NestedListDCDCE = ListDatasetCollection.extend(BASE_MVC.mixin(DatasetCollectionElementMixin,\n\t /** @lends NestedListDCDCE.prototype */{\n\t\n\t /** This is both a collection and a collection element - call the constructor */\n\t constructor: function (attributes, options) {\n\t this.debug('\\t NestedListDCDCE.constructor:', attributes, options);\n\t DatasetCollectionElementMixin.constructor.call(this, attributes, options);\n\t },\n\t\n\t /** String representation. */\n\t toString: function () {\n\t var objStr = this.object ? '' + this.object : this.get('element_identifier');\n\t return ['NestedListDCDCE(', objStr, ')'].join('');\n\t }\n\t }));\n\t\n\t //==============================================================================\n\t /** @class Backbone collection containing list dataset collections. */\n\t var NestedListDCDCECollection = NestedDCDCECollection.extend({\n\t\n\t /** We know this collection is composed of only nested pair collections */\n\t model: NestedListDCDCE,\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return ['NestedListDCDCECollection(', this.length, ')'].join('');\n\t }\n\t });\n\t\n\t //==============================================================================\n\t /** @class Backbone Model for a DatasetCollection (list) that contains other lists. */\n\t var ListOfListsDatasetCollection = DatasetCollection.extend({\n\t\n\t /** list:paired is the only collection that itself contains collections */\n\t collectionClass: NestedListDCDCECollection,\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return ['ListOfListsDatasetCollection(', this.get('name'), ')'].join('');\n\t }\n\t });\n\t\n\t //==============================================================================\n\t return {\n\t ListDatasetCollection: ListDatasetCollection,\n\t PairDatasetCollection: PairDatasetCollection,\n\t ListPairedDatasetCollection: ListPairedDatasetCollection,\n\t ListOfListsDatasetCollection: ListOfListsDatasetCollection\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(3), __webpack_require__(1)))\n\n/***/ }),\n/* 37 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, $, jQuery) {\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(44), __webpack_require__(11), __webpack_require__(6), __webpack_require__(73), __webpack_require__(8), __webpack_require__(91), __webpack_require__(5), __webpack_require__(88)], __WEBPACK_AMD_DEFINE_RESULT__ = function (HDCA, STATES, BASE_MVC, baseCreator, UI_MODAL, naturalSort, _l) {\n\t\n\t 'use strict';\n\t\n\t var logNamespace = 'collections';\n\t\n\t /*==============================================================================\n\t TODO:\n\t use proper Element model and not just json\n\t straighten out createFn, collection.createHDCA\n\t possibly stop using modals for this\n\t It would be neat to do a drag and drop\n\t \n\t ==============================================================================*/\n\t /** A view for both DatasetDCEs and NestedDCDCEs\n\t * (things that implement collection-model:DatasetCollectionElementMixin)\n\t */\n\t var DatasetCollectionElementView = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({\n\t _logNamespace: logNamespace,\n\t\n\t //TODO: use proper class (DatasetDCE or NestedDCDCE (or the union of both))\n\t tagName: 'li',\n\t className: 'collection-element',\n\t\n\t initialize: function (attributes) {\n\t this.element = attributes.element || {};\n\t this.selected = attributes.selected || false;\n\t },\n\t\n\t render: function () {\n\t this.$el.attr('data-element-id', this.element.id).attr('draggable', true).html(this.template({ element: this.element }));\n\t if (this.selected) {\n\t this.$el.addClass('selected');\n\t }\n\t return this;\n\t },\n\t\n\t //TODO: lots of unused space in the element - possibly load details and display them horiz.\n\t template: _.template(['', '<%- element.name %>', '', ''].join('')),\n\t\n\t /** select this element and pub */\n\t select: function (toggle) {\n\t this.$el.toggleClass('selected', toggle);\n\t this.trigger('select', {\n\t source: this,\n\t selected: this.$el.hasClass('selected')\n\t });\n\t },\n\t\n\t /** animate the removal of this element and pub */\n\t discard: function () {\n\t var view = this,\n\t parentWidth = this.$el.parent().width();\n\t this.$el.animate({ 'margin-right': parentWidth }, 'fast', function () {\n\t view.trigger('discard', {\n\t source: view\n\t });\n\t view.destroy();\n\t });\n\t },\n\t\n\t /** remove the DOM and any listeners */\n\t destroy: function () {\n\t this.off();\n\t this.$el.remove();\n\t },\n\t\n\t events: {\n\t 'click': '_click',\n\t 'click .name': '_clickName',\n\t 'click .discard': '_clickDiscard',\n\t\n\t 'dragstart': '_dragstart',\n\t 'dragend': '_dragend',\n\t 'dragover': '_sendToParent',\n\t 'drop': '_sendToParent'\n\t },\n\t\n\t /** select when the li is clicked */\n\t _click: function (ev) {\n\t ev.stopPropagation();\n\t this.select(ev);\n\t },\n\t\n\t /** rename a pair when the name is clicked */\n\t _clickName: function (ev) {\n\t ev.stopPropagation();\n\t ev.preventDefault();\n\t var promptString = [_l('Enter a new name for the element'), ':\\n(', _l('Note that changing the name here will not rename the dataset'), ')'].join(''),\n\t response = prompt(_l('Enter a new name for the element') + ':', this.element.name);\n\t if (response) {\n\t this.element.name = response;\n\t this.render();\n\t }\n\t //TODO: cancelling with ESC leads to closure of the creator...\n\t },\n\t\n\t /** discard when the discard button is clicked */\n\t _clickDiscard: function (ev) {\n\t ev.stopPropagation();\n\t this.discard();\n\t },\n\t\n\t /** dragging pairs for re-ordering */\n\t _dragstart: function (ev) {\n\t if (ev.originalEvent) {\n\t ev = ev.originalEvent;\n\t }\n\t ev.dataTransfer.effectAllowed = 'move';\n\t ev.dataTransfer.setData('text/plain', JSON.stringify(this.element));\n\t\n\t this.$el.addClass('dragging');\n\t this.$el.parent().trigger('collection-element.dragstart', [this]);\n\t },\n\t\n\t /** dragging for re-ordering */\n\t _dragend: function (ev) {\n\t this.$el.removeClass('dragging');\n\t this.$el.parent().trigger('collection-element.dragend', [this]);\n\t },\n\t\n\t /** manually bubble up an event to the parent/container */\n\t _sendToParent: function (ev) {\n\t this.$el.parent().trigger(ev);\n\t },\n\t\n\t /** string rep */\n\t toString: function () {\n\t return 'DatasetCollectionElementView()';\n\t }\n\t });\n\t\n\t // ============================================================================\n\t /** An interface for building collections.\n\t */\n\t var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(baseCreator.CollectionCreatorMixin).extend({\n\t _logNamespace: logNamespace,\n\t\n\t /** the class used to display individual elements */\n\t elementViewClass: DatasetCollectionElementView,\n\t /** the class this creator will create and save */\n\t collectionClass: HDCA.HistoryListDatasetCollection,\n\t className: 'list-collection-creator collection-creator flex-row-container',\n\t\n\t /** minimum number of valid elements to start with in order to build a collection of this type */\n\t minElements: 1,\n\t\n\t defaultAttributes: {\n\t //TODO: remove - use new collectionClass().save()\n\t /** takes elements and creates the proper collection - returns a promise */\n\t creationFn: function () {\n\t throw new TypeError('no creation fn for creator');\n\t },\n\t /** fn to call when the collection is created (scoped to this) */\n\t oncreate: function () {},\n\t /** fn to call when the cancel button is clicked (scoped to this) - if falsy, no btn is displayed */\n\t oncancel: function () {},\n\t /** distance from list edge to begin autoscrolling list */\n\t autoscrollDist: 24,\n\t /** Color passed to hoverhighlight */\n\t highlightClr: 'rgba( 64, 255, 255, 1.0 )'\n\t },\n\t\n\t footerSettings: {\n\t '.hide-originals': 'hideOriginals'\n\t },\n\t\n\t /** set up initial options, instance vars, behaviors */\n\t initialize: function (attributes) {\n\t this.metric('ListCollectionCreator.initialize', attributes);\n\t var creator = this;\n\t _.each(this.defaultAttributes, function (value, key) {\n\t value = attributes[key] || value;\n\t creator[key] = value;\n\t });\n\t\n\t /** unordered, original list - cache to allow reversal */\n\t creator.initialElements = attributes.elements || [];\n\t\n\t this._setUpCommonSettings(attributes);\n\t this._instanceSetUp();\n\t this._elementsSetUp();\n\t this._setUpBehaviors();\n\t },\n\t\n\t /** set up instance vars */\n\t _instanceSetUp: function () {\n\t /** Ids of elements that have been selected by the user - to preserve over renders */\n\t this.selectedIds = {};\n\t /** DOM elements currently being dragged */\n\t this.$dragging = null;\n\t /** Used for blocking UI events during ajax/operations (don't post twice) */\n\t this.blocking = false;\n\t },\n\t\n\t // ------------------------------------------------------------------------ process raw list\n\t /** set up main data */\n\t _elementsSetUp: function () {\n\t //this.debug( '-- _dataSetUp' );\n\t /** a list of invalid elements and the reasons they aren't valid */\n\t this.invalidElements = [];\n\t //TODO: handle fundamental problem of syncing DOM, views, and list here\n\t /** data for list in progress */\n\t this.workingElements = [];\n\t /** views for workingElements */\n\t this.elementViews = [];\n\t\n\t // copy initial list, sort, add ids if needed\n\t this.workingElements = this.initialElements.slice(0);\n\t this._ensureElementIds();\n\t this._validateElements();\n\t this._mangleDuplicateNames();\n\t this._sortElements();\n\t },\n\t\n\t /** add ids to dataset objs in initial list if none */\n\t _ensureElementIds: function () {\n\t this.workingElements.forEach(function (element) {\n\t if (!element.hasOwnProperty('id')) {\n\t element.id = _.uniqueId();\n\t }\n\t });\n\t return this.workingElements;\n\t },\n\t\n\t /** separate working list into valid and invalid elements for this collection */\n\t _validateElements: function () {\n\t var creator = this,\n\t existingNames = {};\n\t creator.invalidElements = [];\n\t\n\t this.workingElements = this.workingElements.filter(function (element) {\n\t var problem = creator._isElementInvalid(element);\n\t if (problem) {\n\t creator.invalidElements.push({\n\t element: element,\n\t text: problem\n\t });\n\t }\n\t return !problem;\n\t });\n\t return this.workingElements;\n\t },\n\t\n\t /** describe what is wrong with a particular element if anything */\n\t _isElementInvalid: function (element) {\n\t if (element.history_content_type !== 'dataset') {\n\t return _l(\"is not a dataset\");\n\t }\n\t var validState = element.state === STATES.OK || _.contains(STATES.NOT_READY_STATES, element.state);\n\t if (!validState) {\n\t return _l(\"has errored, is paused, or is not accessible\");\n\t }\n\t if (element.deleted || element.purged) {\n\t return _l(\"has been deleted or purged\");\n\t }\n\t return null;\n\t },\n\t\n\t /** mangle duplicate names using a mac-like '(counter)' addition to any duplicates */\n\t _mangleDuplicateNames: function () {\n\t var SAFETY = 900,\n\t counter = 1,\n\t existingNames = {};\n\t this.workingElements.forEach(function (element) {\n\t var currName = element.name;\n\t while (existingNames.hasOwnProperty(currName)) {\n\t currName = element.name + ' (' + counter + ')';\n\t counter += 1;\n\t if (counter >= SAFETY) {\n\t throw new Error('Safety hit in while loop - thats impressive');\n\t }\n\t }\n\t element.name = currName;\n\t existingNames[element.name] = true;\n\t });\n\t },\n\t\n\t /** sort a list of elements */\n\t _sortElements: function (list) {\n\t // // currently only natural sort by name\n\t // this.workingElements.sort( function( a, b ){ return naturalSort( a.name, b.name ); });\n\t // return this.workingElements;\n\t },\n\t\n\t // ------------------------------------------------------------------------ rendering\n\t // templates : ListCollectionCreator.templates,\n\t /** render the entire interface */\n\t render: function (speed, callback) {\n\t //this.debug( '-- _render' );\n\t if (this.workingElements.length < this.minElements) {\n\t return this._renderInvalid(speed, callback);\n\t }\n\t\n\t this.$el.empty().html(this.templates.main());\n\t this._renderHeader(speed);\n\t this._renderMiddle(speed);\n\t this._renderFooter(speed);\n\t this._addPluginComponents();\n\t this.$('.collection-name').focus();\n\t this.trigger('rendered', this);\n\t return this;\n\t },\n\t\n\t /** render a simplified interface aimed at telling the user why they can't move forward */\n\t _renderInvalid: function (speed, callback) {\n\t //this.debug( '-- _render' );\n\t this.$el.empty().html(this.templates.invalidInitial({\n\t problems: this.invalidElements,\n\t elements: this.workingElements\n\t }));\n\t if (typeof this.oncancel === 'function') {\n\t this.$('.cancel-create.btn').show();\n\t }\n\t this.trigger('rendered', this);\n\t return this;\n\t },\n\t\n\t /** render the header section */\n\t _renderHeader: function (speed, callback) {\n\t var $header = this.$('.header').empty().html(this.templates.header()).find('.help-content').prepend($(this.templates.helpContent()));\n\t //TODO: should only show once despite calling _renderHeader again\n\t if (this.invalidElements.length) {\n\t this._invalidElementsAlert();\n\t }\n\t return $header;\n\t },\n\t\n\t /** render the middle including the elements */\n\t _renderMiddle: function (speed, callback) {\n\t var $middle = this.$('.middle').empty().html(this.templates.middle());\n\t this._renderList(speed);\n\t return $middle;\n\t },\n\t\n\t /** add any jQuery/bootstrap/custom plugins to elements rendered */\n\t _addPluginComponents: function () {\n\t this.$('.help-content i').hoverhighlight('.collection-creator', this.highlightClr);\n\t },\n\t\n\t /** build and show an alert describing any elements that could not be included due to problems */\n\t _invalidElementsAlert: function () {\n\t this._showAlert(this.templates.invalidElements({ problems: this.invalidElements }), 'alert-warning');\n\t },\n\t\n\t _disableNameAndCreate: function (disable) {\n\t disable = !_.isUndefined(disable) ? disable : true;\n\t if (disable) {\n\t this.$('.collection-name').prop('disabled', true);\n\t this.$('.create-collection').toggleClass('disabled', true);\n\t // } else {\n\t // this.$( '.collection-name' ).prop( 'disabled', false );\n\t // this.$( '.create-collection' ).removeClass( 'disable' );\n\t }\n\t },\n\t\n\t // ------------------------------------------------------------------------ rendering elements\n\t /** conv. to the main list display DOM */\n\t $list: function () {\n\t return this.$('.collection-elements');\n\t },\n\t\n\t /** show or hide the clear selected control based on the num of selected elements */\n\t _renderClearSelected: function () {\n\t if (_.size(this.selectedIds)) {\n\t this.$('.collection-elements-controls > .clear-selected').show();\n\t } else {\n\t this.$('.collection-elements-controls > .clear-selected').hide();\n\t }\n\t },\n\t\n\t /** render the elements in order (or a warning if no elements found) */\n\t _renderList: function (speed, callback) {\n\t //this.debug( '-- _renderList' );\n\t var creator = this,\n\t $tmp = jQuery(''),\n\t $list = creator.$list();\n\t\n\t _.each(this.elementViews, function (view) {\n\t view.destroy();\n\t creator.removeElementView(view);\n\t });\n\t\n\t // if( !this.workingElements.length ){\n\t // this._renderNoValidElements();\n\t // return;\n\t // }\n\t\n\t creator.workingElements.forEach(function (element) {\n\t var elementView = creator._createElementView(element);\n\t $tmp.append(elementView.$el);\n\t });\n\t\n\t creator._renderClearSelected();\n\t $list.empty().append($tmp.children());\n\t _.invoke(creator.elementViews, 'render');\n\t\n\t if ($list.height() > $list.css('max-height')) {\n\t $list.css('border-width', '1px 0px 1px 0px');\n\t } else {\n\t $list.css('border-width', '0px');\n\t }\n\t },\n\t\n\t /** create an element view, cache in elementViews, set up listeners, and return */\n\t _createElementView: function (element) {\n\t var elementView = new this.elementViewClass({\n\t //TODO: use non-generic class or not all\n\t // model : COLLECTION.DatasetDCE( element )\n\t element: element,\n\t selected: _.has(this.selectedIds, element.id)\n\t });\n\t this.elementViews.push(elementView);\n\t this._listenToElementView(elementView);\n\t return elementView;\n\t },\n\t\n\t /** listen to any element events */\n\t _listenToElementView: function (view) {\n\t var creator = this;\n\t creator.listenTo(view, {\n\t select: function (data) {\n\t var element = data.source.element;\n\t if (data.selected) {\n\t creator.selectedIds[element.id] = true;\n\t } else {\n\t delete creator.selectedIds[element.id];\n\t }\n\t creator.trigger('elements:select', data);\n\t },\n\t discard: function (data) {\n\t creator.trigger('elements:discard', data);\n\t }\n\t });\n\t },\n\t\n\t /** add a new element view based on the json in element */\n\t addElementView: function (element) {\n\t //TODO: workingElements is sorted, add element in appropo index\n\t // add element, sort elements, find element index\n\t // var view = this._createElementView( element );\n\t // return view;\n\t },\n\t\n\t /** stop listening to view and remove from caches */\n\t removeElementView: function (view) {\n\t delete this.selectedIds[view.element.id];\n\t this._renderClearSelected();\n\t\n\t this.elementViews = _.without(this.elementViews, view);\n\t this.stopListening(view);\n\t },\n\t\n\t /** render a message in the list that no elements remain to create a collection */\n\t _renderNoElementsLeft: function () {\n\t this._disableNameAndCreate(true);\n\t this.$('.collection-elements').append(this.templates.noElementsLeft());\n\t },\n\t\n\t // /** render a message in the list that no valid elements were found to create a collection */\n\t // _renderNoValidElements : function(){\n\t // this._disableNameAndCreate( true );\n\t // this.$( '.collection-elements' ).append( this.templates.noValidElements() );\n\t // },\n\t\n\t // ------------------------------------------------------------------------ API\n\t /** convert element into JSON compatible with the collections API */\n\t _elementToJSON: function (element) {\n\t // return element.toJSON();\n\t return element;\n\t },\n\t\n\t /** create the collection via the API\n\t * @returns {jQuery.xhr Object} the jquery ajax request\n\t */\n\t createList: function (name) {\n\t if (!this.workingElements.length) {\n\t var message = _l('No valid elements for final list') + '. ';\n\t message += '' + _l('Cancel') + ' ';\n\t message += _l('or');\n\t message += ' ' + _l('start over') + '.';\n\t this._showAlert(message);\n\t return;\n\t }\n\t\n\t var creator = this,\n\t elements = this.workingElements.map(function (element) {\n\t return creator._elementToJSON(element);\n\t });\n\t\n\t creator.blocking = true;\n\t return creator.creationFn(elements, name, creator.hideOriginals).always(function () {\n\t creator.blocking = false;\n\t }).fail(function (xhr, status, message) {\n\t creator.trigger('error', {\n\t xhr: xhr,\n\t status: status,\n\t message: _l('An error occurred while creating this collection')\n\t });\n\t }).done(function (response, message, xhr) {\n\t creator.trigger('collection:created', response, message, xhr);\n\t creator.metric('collection:created', response);\n\t if (typeof creator.oncreate === 'function') {\n\t creator.oncreate.call(this, response, message, xhr);\n\t }\n\t });\n\t },\n\t\n\t // ------------------------------------------------------------------------ events\n\t /** set up event handlers on self */\n\t _setUpBehaviors: function () {\n\t this.on('error', this._errorHandler);\n\t\n\t this.once('rendered', function () {\n\t this.trigger('rendered:initial', this);\n\t });\n\t\n\t this.on('elements:select', function (data) {\n\t this._renderClearSelected();\n\t });\n\t\n\t this.on('elements:discard', function (data) {\n\t var element = data.source.element;\n\t this.removeElementView(data.source);\n\t\n\t this.workingElements = _.without(this.workingElements, element);\n\t if (!this.workingElements.length) {\n\t this._renderNoElementsLeft();\n\t }\n\t });\n\t\n\t //this.on( 'all', function(){\n\t // this.info( arguments );\n\t //});\n\t return this;\n\t },\n\t\n\t /** handle errors with feedback and details to the user (if available) */\n\t _errorHandler: function (data) {\n\t this.error(data);\n\t\n\t var creator = this;\n\t content = data.message || _l('An error occurred');\n\t if (data.xhr) {\n\t var xhr = data.xhr,\n\t message = data.message;\n\t if (xhr.readyState === 0 && xhr.status === 0) {\n\t content += ': ' + _l('Galaxy could not be reached and may be updating.') + _l(' Try again in a few minutes.');\n\t } else if (xhr.responseJSON) {\n\t content += ':
' + JSON.stringify(xhr.responseJSON) + '
';\n\t } else {\n\t content += ': ' + message;\n\t }\n\t }\n\t creator._showAlert(content, 'alert-danger');\n\t },\n\t\n\t events: {\n\t // header\n\t 'click .more-help': '_clickMoreHelp',\n\t 'click .less-help': '_clickLessHelp',\n\t 'click .main-help': '_toggleHelp',\n\t 'click .header .alert button': '_hideAlert',\n\t\n\t 'click .reset': 'reset',\n\t 'click .clear-selected': 'clearSelectedElements',\n\t\n\t // elements - selection\n\t 'click .collection-elements': 'clearSelectedElements',\n\t\n\t // elements - drop target\n\t // 'dragenter .collection-elements': '_dragenterElements',\n\t // 'dragleave .collection-elements': '_dragleaveElements',\n\t 'dragover .collection-elements': '_dragoverElements',\n\t 'drop .collection-elements': '_dropElements',\n\t\n\t // these bubble up from the elements as custom events\n\t 'collection-element.dragstart .collection-elements': '_elementDragstart',\n\t 'collection-element.dragend .collection-elements': '_elementDragend',\n\t\n\t // footer\n\t 'change .collection-name': '_changeName',\n\t 'keydown .collection-name': '_nameCheckForEnter',\n\t 'change .hide-originals': '_changeHideOriginals',\n\t 'click .cancel-create': '_cancelCreate',\n\t 'click .create-collection': '_clickCreate' //,\n\t },\n\t\n\t // ........................................................................ elements\n\t /** reset all data to the initial state */\n\t reset: function () {\n\t this._instanceSetUp();\n\t this._elementsSetUp();\n\t this.render();\n\t },\n\t\n\t /** deselect all elements */\n\t clearSelectedElements: function (ev) {\n\t this.$('.collection-elements .collection-element').removeClass('selected');\n\t this.$('.collection-elements-controls > .clear-selected').hide();\n\t },\n\t\n\t //_dragenterElements : function( ev ){\n\t // //this.debug( '_dragenterElements:', ev );\n\t //},\n\t //TODO: if selected are dragged out of the list area - remove the placeholder - cuz it won't work anyway\n\t // _dragleaveElements : function( ev ){\n\t // //this.debug( '_dragleaveElements:', ev );\n\t // },\n\t\n\t /** track the mouse drag over the list adding a placeholder to show where the drop would occur */\n\t _dragoverElements: function (ev) {\n\t //this.debug( '_dragoverElements:', ev );\n\t ev.preventDefault();\n\t\n\t var $list = this.$list();\n\t this._checkForAutoscroll($list, ev.originalEvent.clientY);\n\t var $nearest = this._getNearestElement(ev.originalEvent.clientY);\n\t\n\t //TODO: no need to re-create - move instead\n\t this.$('.element-drop-placeholder').remove();\n\t var $placeholder = $('');\n\t if (!$nearest.length) {\n\t $list.append($placeholder);\n\t } else {\n\t $nearest.before($placeholder);\n\t }\n\t },\n\t\n\t /** If the mouse is near enough to the list's top or bottom, scroll the list */\n\t _checkForAutoscroll: function ($element, y) {\n\t var AUTOSCROLL_SPEED = 2,\n\t offset = $element.offset(),\n\t scrollTop = $element.scrollTop(),\n\t upperDist = y - offset.top,\n\t lowerDist = offset.top + $element.outerHeight() - y;\n\t if (upperDist >= 0 && upperDist < this.autoscrollDist) {\n\t $element.scrollTop(scrollTop - AUTOSCROLL_SPEED);\n\t } else if (lowerDist >= 0 && lowerDist < this.autoscrollDist) {\n\t $element.scrollTop(scrollTop + AUTOSCROLL_SPEED);\n\t }\n\t },\n\t\n\t /** get the nearest element based on the mouse's Y coordinate.\n\t * If the y is at the end of the list, return an empty jQuery object.\n\t */\n\t _getNearestElement: function (y) {\n\t var WIGGLE = 4,\n\t lis = this.$('.collection-elements li.collection-element').toArray();\n\t for (var i = 0; i < lis.length; i++) {\n\t var $li = $(lis[i]),\n\t top = $li.offset().top,\n\t halfHeight = Math.floor($li.outerHeight() / 2) + WIGGLE;\n\t if (top + halfHeight > y && top - halfHeight < y) {\n\t return $li;\n\t }\n\t }\n\t return $();\n\t },\n\t\n\t /** drop (dragged/selected elements) onto the list, re-ordering the internal list */\n\t _dropElements: function (ev) {\n\t if (ev.originalEvent) {\n\t ev = ev.originalEvent;\n\t }\n\t // both required for firefox\n\t ev.preventDefault();\n\t ev.dataTransfer.dropEffect = 'move';\n\t\n\t // insert before the nearest element or after the last.\n\t var $nearest = this._getNearestElement(ev.clientY);\n\t if ($nearest.length) {\n\t this.$dragging.insertBefore($nearest);\n\t } else {\n\t // no nearest before - insert after last element\n\t this.$dragging.insertAfter(this.$('.collection-elements .collection-element').last());\n\t }\n\t // resync the creator's list based on the new DOM order\n\t this._syncOrderToDom();\n\t return false;\n\t },\n\t\n\t /** resync the creator's list of elements based on the DOM order */\n\t _syncOrderToDom: function () {\n\t var creator = this,\n\t newElements = [];\n\t //TODO: doesn't seem wise to use the dom to store these - can't we sync another way?\n\t this.$('.collection-elements .collection-element').each(function () {\n\t var id = $(this).attr('data-element-id'),\n\t element = _.findWhere(creator.workingElements, { id: id });\n\t if (element) {\n\t newElements.push(element);\n\t } else {\n\t console.error('missing element: ', id);\n\t }\n\t });\n\t this.workingElements = newElements;\n\t this._renderList();\n\t },\n\t\n\t /** drag communication with element sub-views: dragstart */\n\t _elementDragstart: function (ev, element) {\n\t // auto select the element causing the event and move all selected\n\t element.select(true);\n\t this.$dragging = this.$('.collection-elements .collection-element.selected');\n\t },\n\t\n\t /** drag communication with element sub-views: dragend - remove the placeholder */\n\t _elementDragend: function (ev, element) {\n\t $('.element-drop-placeholder').remove();\n\t this.$dragging = null;\n\t },\n\t\n\t // ------------------------------------------------------------------------ templates\n\t //TODO: move to require text plugin and load these as text\n\t //TODO: underscore currently unnecc. bc no vars are used\n\t //TODO: better way of localizing text-nodes in long strings\n\t /** underscore template fns attached to class */\n\t templates: _.extend({}, baseCreator.CollectionCreatorMixin._creatorTemplates, {\n\t\n\t /** the header (not including help text) */\n\t header: _.template(['
'].join('')),\n\t\n\t /** help content */\n\t helpContent: _.template(['
', _l(['Collections of datasets are permanent, ordered lists of datasets that can be passed to tools and ', 'workflows in order to have analyses done on each member of the entire group. This interface allows ', 'you to create a collection and re-order the final collection.'].join('')), '
', '
', '
', _l(['Rename elements in the list by clicking on ', 'the existing name.'].join('')), '
', '
', _l(['Discard elements from the final created list by clicking on the ', '\"Discard\" button.'].join('')), '
', '
', _l(['Reorder the list by clicking and dragging elements. Select multiple elements by clicking on ', 'them and you can then move those selected by dragging the ', 'entire group. Deselect them by clicking them again or by clicking the ', 'the \"Clear selected\" link.'].join('')), '
', '
', _l(['Click the \"Start over\" link to begin again as if you had just opened ', 'the interface.'].join('')), '
', '
', _l(['Click the \"Cancel\" button to exit the interface.'].join('')), '
', '
', '
', _l(['Once your collection is complete, enter a name and ', 'click \"Create list\".'].join('')), '
'].join('')),\n\t\n\t /** shown in list when all elements are discarded */\n\t invalidElements: _.template([_l('The following selections could not be included due to problems:'), '
<% _.each( problems, function( problem ){ %>', '
<%- problem.element.name %>: <%- problem.text %>
', '<% }); %>
'].join('')),\n\t\n\t /** shown in list when all elements are discarded */\n\t noElementsLeft: _.template(['
'].join('')),\n\t\n\t /** a simplified page communicating what went wrong and why the user needs to reselect something else */\n\t invalidInitial: _.template(['
', '
', '', '<% if( _.size( problems ) ){ %>', _l('The following selections could not be included due to problems'), ':', '
<% _.each( problems, function( problem ){ %>', '
<%- problem.element.name %>: <%- problem.text %>
', '<% }); %>
', '<% } else if( _.size( elements ) < 1 ){ %>', _l('No datasets were selected'), '.', '<% } %>', ' ', _l('At least one element is needed for the collection'), '. ', _l('You may need to '), '', _l('cancel'), ' ', _l('and reselect new elements'), '.', '', '
', '
', ''].join(''))\n\t }),\n\t\n\t // ------------------------------------------------------------------------ misc\n\t /** string rep */\n\t toString: function () {\n\t return 'ListCollectionCreator';\n\t }\n\t });\n\t\n\t //=============================================================================\n\t /** Create a modal and load its body with the given CreatorClass creator type\n\t * @returns {Deferred} resolved when creator has built a collection.\n\t */\n\t var collectionCreatorModal = function _collectionCreatorModal(elements, options, CreatorClass) {\n\t\n\t var deferred = jQuery.Deferred(),\n\t modal = Galaxy.modal || new UI_MODAL.View(),\n\t creator;\n\t\n\t options = _.defaults(options || {}, {\n\t elements: elements,\n\t oncancel: function () {\n\t modal.hide();\n\t deferred.reject('cancelled');\n\t },\n\t oncreate: function (creator, response) {\n\t modal.hide();\n\t deferred.resolve(response);\n\t }\n\t });\n\t\n\t creator = new CreatorClass(options);\n\t modal.show({\n\t title: options.title || _l('Create a collection'),\n\t body: creator.$el,\n\t width: '80%',\n\t height: '100%',\n\t closing_events: true\n\t });\n\t creator.render();\n\t window._collectionCreator = creator;\n\t\n\t //TODO: remove modal header\n\t return deferred;\n\t };\n\t\n\t /** List collection flavor of collectionCreatorModal. */\n\t var listCollectionCreatorModal = function _listCollectionCreatorModal(elements, options) {\n\t options = options || {};\n\t options.title = _l('Create a collection from a list of datasets');\n\t return collectionCreatorModal(elements, options, ListCollectionCreator);\n\t };\n\t\n\t //==============================================================================\n\t /** Use a modal to create a list collection, then add it to the given history contents.\n\t * @returns {Deferred} resolved when the collection is added to the history.\n\t */\n\t function createListCollection(contents, defaultHideSourceItems) {\n\t var elements = contents.toJSON(),\n\t promise = listCollectionCreatorModal(elements, {\n\t defaultHideSourceItems: defaultHideSourceItems,\n\t creationFn: function (elements, name, hideSourceItems) {\n\t elements = elements.map(function (element) {\n\t return {\n\t id: element.id,\n\t name: element.name,\n\t //TODO: this allows for list:list even if the filter above does not - reconcile\n\t src: element.history_content_type === 'dataset' ? 'hda' : 'hdca'\n\t };\n\t });\n\t return contents.createHDCA(elements, 'list', name, hideSourceItems);\n\t }\n\t });\n\t return promise;\n\t }\n\t\n\t //==============================================================================\n\t return {\n\t DatasetCollectionElementView: DatasetCollectionElementView,\n\t ListCollectionCreator: ListCollectionCreator,\n\t\n\t collectionCreatorModal: collectionCreatorModal,\n\t listCollectionCreatorModal: listCollectionCreatorModal,\n\t createListCollection: createListCollection\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2), __webpack_require__(1), __webpack_require__(1)))\n\n/***/ }),\n/* 38 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_, jQuery, Backbone, $) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(47), __webpack_require__(11), __webpack_require__(17), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (LIST_ITEM, STATES, faIconButton, BASE_MVC, _l) {\n\t 'use strict';\n\t\n\t var logNamespace = 'dataset';\n\t /*==============================================================================\n\t TODO:\n\t straighten out state rendering and templates used\n\t inaccessible/STATES.NOT_VIEWABLE is a special case\n\t simplify button rendering\n\t \n\t ==============================================================================*/\n\t var _super = LIST_ITEM.ListItemView;\n\t /** @class Read only list view for either LDDAs, HDAs, or HDADCEs.\n\t * Roughly, any DatasetInstance (and not a raw Dataset).\n\t */\n\t var DatasetListItemView = _super.extend(\n\t /** @lends DatasetListItemView.prototype */{\n\t _logNamespace: logNamespace,\n\t\n\t className: _super.prototype.className + \" dataset\",\n\t //TODO:?? doesn't exactly match an hda's type_id\n\t id: function () {\n\t return ['dataset', this.model.get('id')].join('-');\n\t },\n\t\n\t /** Set up: instance vars, options, and event handlers */\n\t initialize: function (attributes) {\n\t if (attributes.logger) {\n\t this.logger = this.model.logger = attributes.logger;\n\t }\n\t this.log(this + '.initialize:', attributes);\n\t _super.prototype.initialize.call(this, attributes);\n\t\n\t /** where should pages from links be displayed? (default to new tab/window) */\n\t this.linkTarget = attributes.linkTarget || '_blank';\n\t },\n\t\n\t /** event listeners */\n\t _setUpListeners: function () {\n\t _super.prototype._setUpListeners.call(this);\n\t var self = this;\n\t\n\t // re-rendering on any model changes\n\t return self.listenTo(self.model, {\n\t 'change': function (model) {\n\t // if the model moved into the ready state and is expanded without details, fetch those details now\n\t if (self.model.changedAttributes().state && self.model.inReadyState() && self.expanded && !self.model.hasDetails()) {\n\t // normally, will render automatically (due to fetch -> change),\n\t // but! setting_metadata sometimes doesn't cause any other changes besides state\n\t // so, not rendering causes it to seem frozen in setting_metadata state\n\t self.model.fetch({ silent: true }).done(function () {\n\t self.render();\n\t });\n\t } else {\n\t if (_.has(model.changed, 'tags') && _.keys(model.changed).length === 1) {\n\t // If only the tags have changed, rerender specifically\n\t // the titlebar region. Otherwise default to the full\n\t // render.\n\t self.$('.nametags').html(self._renderNametags());\n\t } else {\n\t self.render();\n\t }\n\t }\n\t }\n\t });\n\t },\n\t\n\t // ......................................................................... expandable\n\t /** In this override, only get details if in the ready state, get rerunnable if in other states.\n\t * Note: fetch with no 'change' event triggering to prevent automatic rendering.\n\t */\n\t _fetchModelDetails: function () {\n\t var view = this;\n\t if (view.model.inReadyState() && !view.model.hasDetails()) {\n\t return view.model.fetch({ silent: true });\n\t }\n\t return jQuery.when();\n\t },\n\t\n\t // ......................................................................... removal\n\t /** Remove this view's html from the DOM and remove all event listeners.\n\t * @param {Number or String} speed jq effect speed\n\t * @param {Function} callback an optional function called when removal is done (scoped to this view)\n\t */\n\t remove: function (speed, callback) {\n\t var view = this;\n\t speed = speed || this.fxSpeed;\n\t this.$el.fadeOut(speed, function () {\n\t Backbone.View.prototype.remove.call(view);\n\t if (callback) {\n\t callback.call(view);\n\t }\n\t });\n\t },\n\t\n\t // ......................................................................... rendering\n\t /* TODO:\n\t dataset states are the issue primarily making dataset rendering complex\n\t each state should have it's own way of displaying/set of details\n\t often with different actions that can be applied\n\t throw in deleted/purged/visible and things get complicated easily\n\t I've considered (a couple of times) - creating a view for each state\n\t - but recreating the view during an update...seems wrong\n\t */\n\t /** In this override, add the dataset state as a class for use with state-based CSS */\n\t _swapNewRender: function ($newRender) {\n\t _super.prototype._swapNewRender.call(this, $newRender);\n\t if (this.model.has('state')) {\n\t this.$el.addClass('state-' + this.model.get('state'));\n\t }\n\t return this.$el;\n\t },\n\t\n\t // ................................................................................ titlebar\n\t /** In this override, add the dataset display button. */\n\t _renderPrimaryActions: function () {\n\t // render just the display for read-only\n\t return [this._renderDisplayButton()];\n\t },\n\t\n\t /** Render icon-button to display dataset data */\n\t _renderDisplayButton: function () {\n\t // don't show display if not viewable or not accessible\n\t var state = this.model.get('state');\n\t if (state === STATES.NOT_VIEWABLE || state === STATES.DISCARDED || !this.model.get('accessible')) {\n\t return null;\n\t }\n\t\n\t var displayBtnData = {\n\t target: this.linkTarget,\n\t classes: 'display-btn'\n\t };\n\t\n\t // show a disabled display if the data's been purged\n\t if (this.model.get('purged')) {\n\t displayBtnData.disabled = true;\n\t displayBtnData.title = _l('Cannot display datasets removed from disk');\n\t\n\t // disable if still uploading\n\t } else if (state === STATES.UPLOAD) {\n\t displayBtnData.disabled = true;\n\t displayBtnData.title = _l('This dataset must finish uploading before it can be viewed');\n\t\n\t // disable if still new\n\t } else if (state === STATES.NEW) {\n\t displayBtnData.disabled = true;\n\t displayBtnData.title = _l('This dataset is not yet viewable');\n\t } else {\n\t displayBtnData.title = _l('View data');\n\t\n\t // default link for dataset\n\t displayBtnData.href = this.model.urls.display;\n\t\n\t // add frame manager option onclick event\n\t var self = this;\n\t displayBtnData.onclick = function (ev) {\n\t if (Galaxy.frame && Galaxy.frame.active) {\n\t // Add dataset to frames.\n\t Galaxy.frame.addDataset(self.model.get('id'));\n\t ev.preventDefault();\n\t }\n\t };\n\t }\n\t displayBtnData.faIcon = 'fa-eye';\n\t return faIconButton(displayBtnData);\n\t },\n\t\n\t // ......................................................................... rendering details\n\t /** Render the enclosing div of the hda body and, if expanded, the html in the body\n\t * @returns {jQuery} rendered DOM\n\t */\n\t _renderDetails: function () {\n\t //TODO: generalize to be allow different details for each state\n\t\n\t // no access - render nothing but a message\n\t if (this.model.get('state') === STATES.NOT_VIEWABLE) {\n\t return $(this.templates.noAccess(this.model.toJSON(), this));\n\t }\n\t\n\t var $details = _super.prototype._renderDetails.call(this);\n\t $details.find('.actions .left').empty().append(this._renderSecondaryActions());\n\t $details.find('.summary').html(this._renderSummary()).prepend(this._renderDetailMessages());\n\t $details.find('.display-applications').html(this._renderDisplayApplications());\n\t\n\t this._setUpBehaviors($details);\n\t return $details;\n\t },\n\t\n\t /** Defer to the appropo summary rendering fn based on state */\n\t _renderSummary: function () {\n\t var json = this.model.toJSON(),\n\t summaryRenderFn = this.templates.summaries[json.state];\n\t summaryRenderFn = summaryRenderFn || this.templates.summaries.unknown;\n\t return summaryRenderFn(json, this);\n\t },\n\t\n\t /** Render messages to be displayed only when the details are shown */\n\t _renderDetailMessages: function () {\n\t var view = this,\n\t $warnings = $(''),\n\t json = view.model.toJSON();\n\t //TODO:! unordered (map)\n\t _.each(view.templates.detailMessages, function (templateFn) {\n\t $warnings.append($(templateFn(json, view)));\n\t });\n\t return $warnings;\n\t },\n\t\n\t /** Render the external display application links */\n\t _renderDisplayApplications: function () {\n\t if (this.model.isDeletedOrPurged()) {\n\t return '';\n\t }\n\t // render both old and new display apps using the same template\n\t return [this.templates.displayApplications(this.model.get('display_apps'), this), this.templates.displayApplications(this.model.get('display_types'), this)].join('');\n\t },\n\t\n\t // ......................................................................... secondary/details actions\n\t /** A series of links/buttons for less commonly used actions: re-run, info, etc. */\n\t _renderSecondaryActions: function () {\n\t this.debug('_renderSecondaryActions');\n\t switch (this.model.get('state')) {\n\t case STATES.NOT_VIEWABLE:\n\t return [];\n\t case STATES.OK:\n\t case STATES.FAILED_METADATA:\n\t case STATES.ERROR:\n\t return [this._renderDownloadButton(), this._renderShowParamsButton()];\n\t }\n\t return [this._renderShowParamsButton()];\n\t },\n\t\n\t /** Render icon-button to show the input and output (stdout/err) for the job that created this.\n\t * @returns {jQuery} rendered DOM\n\t */\n\t _renderShowParamsButton: function () {\n\t // gen. safe to show in all cases\n\t return faIconButton({\n\t title: _l('View details'),\n\t classes: 'params-btn',\n\t href: this.model.urls.show_params,\n\t target: this.linkTarget,\n\t faIcon: 'fa-info-circle',\n\t onclick: function (ev) {\n\t if (Galaxy.frame && Galaxy.frame.active) {\n\t Galaxy.frame.add({ title: 'Dataset details', url: this.href });\n\t ev.preventDefault();\n\t ev.stopPropagation();\n\t }\n\t }\n\t });\n\t },\n\t\n\t /** Render icon-button/popupmenu to download the data (and/or the associated meta files (bai, etc.)) for this.\n\t * @returns {jQuery} rendered DOM\n\t */\n\t _renderDownloadButton: function () {\n\t // don't show anything if the data's been purged\n\t if (this.model.get('purged') || !this.model.hasData()) {\n\t return null;\n\t }\n\t\n\t // return either: a popupmenu with links to download assoc. meta files (if there are meta files)\n\t // or a single download icon-button (if there are no meta files)\n\t if (!_.isEmpty(this.model.get('meta_files'))) {\n\t return this._renderMetaFileDownloadButton();\n\t }\n\t\n\t return $(['', '', ''].join(''));\n\t },\n\t\n\t /** Render the download button which opens a dropdown with links to download assoc. meta files (indeces, etc.) */\n\t _renderMetaFileDownloadButton: function () {\n\t var urls = this.model.urls;\n\t return $(['
'], 'dataset');\n\t\n\t // messages to be displayed only within the details section ('below the fold')\n\t var detailMessageTemplates = {\n\t resubmitted: BASE_MVC.wrapTemplate([\n\t // deleted not purged\n\t '<% if( model.resubmitted ){ %>', '
', _l('The job creating this dataset has been resubmitted'), '
', '<% } %>'])\n\t };\n\t\n\t // this is applied to both old and new style display apps\n\t var displayApplicationsTemplate = BASE_MVC.wrapTemplate(['<% _.each( apps, function( app ){ %>', '
', '<% }); %>'], 'apps');\n\t\n\t return _.extend({}, _super.prototype.templates, {\n\t warnings: warnings,\n\t details: detailsTemplate,\n\t noAccess: noAccessTemplate,\n\t summaries: summaryTemplates,\n\t detailMessages: detailMessageTemplates,\n\t displayApplications: displayApplicationsTemplate\n\t });\n\t }();\n\t\n\t // ============================================================================\n\t return {\n\t DatasetListItemView: DatasetListItemView\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3), __webpack_require__(1)))\n\n/***/ }),\n/* 39 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/* This class maps the form dom to an api compatible javascript dictionary. */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t var Manager = Backbone.Model.extend({\n\t initialize: function (app) {\n\t this.app = app;\n\t },\n\t\n\t /** Creates a checksum. */\n\t checksum: function () {\n\t var sum = '';\n\t var self = this;\n\t this.app.section.$el.find('.section-row').each(function () {\n\t var id = $(this).attr('id');\n\t var field = self.app.field_list[id];\n\t if (field) {\n\t sum += id + ':' + JSON.stringify(field.value && field.value()) + ':' + field.collapsed + ';';\n\t }\n\t });\n\t return sum;\n\t },\n\t\n\t /** Convert dom into a dictionary of flat id/value pairs used e.g. on job submission. */\n\t create: function () {\n\t var self = this;\n\t\n\t // get raw dictionary from dom\n\t var dict = {};\n\t this._iterate(this.app.section.$el, dict);\n\t\n\t // add to result dictionary, label elements\n\t var result_dict = {};\n\t this.flat_dict = {};\n\t function add(flat_id, input_id, input_value) {\n\t self.flat_dict[flat_id] = input_id;\n\t result_dict[flat_id] = input_value;\n\t self.app.element_list[input_id] && self.app.element_list[input_id].$el.attr('tour_id', flat_id);\n\t }\n\t // converter between raw dictionary and job dictionary\n\t function convert(identifier, head) {\n\t for (var index in head) {\n\t var node = head[index];\n\t if (node.input) {\n\t var input = node.input;\n\t var flat_id = identifier;\n\t if (identifier != '') {\n\t flat_id += '|';\n\t }\n\t flat_id += input.name;\n\t switch (input.type) {\n\t case 'repeat':\n\t var section_label = 'section-';\n\t var block_indices = [];\n\t var block_prefix = null;\n\t for (var block_label in node) {\n\t var pos = block_label.indexOf(section_label);\n\t if (pos != -1) {\n\t pos += section_label.length;\n\t block_indices.push(parseInt(block_label.substr(pos)));\n\t if (!block_prefix) {\n\t block_prefix = block_label.substr(0, pos);\n\t }\n\t }\n\t }\n\t block_indices.sort(function (a, b) {\n\t return a - b;\n\t });\n\t var index = 0;\n\t for (var i in block_indices) {\n\t convert(flat_id + '_' + index++, node[block_prefix + block_indices[i]]);\n\t }\n\t break;\n\t case 'conditional':\n\t var value = self.app.field_list[input.id].value();\n\t add(flat_id + '|' + input.test_param.name, input.id, value);\n\t var selectedCase = matchCase(input, value);\n\t if (selectedCase != -1) {\n\t convert(flat_id, head[input.id + '-section-' + selectedCase]);\n\t }\n\t break;\n\t case 'section':\n\t convert(!input.flat && flat_id || '', node);\n\t break;\n\t default:\n\t var field = self.app.field_list[input.id];\n\t if (field && field.value) {\n\t var value = field.value();\n\t if (input.ignore === undefined || input.ignore != value) {\n\t if (field.collapsed && input.collapsible_value) {\n\t value = input.collapsible_value;\n\t }\n\t add(flat_id, input.id, value);\n\t if (input.payload) {\n\t for (var p_id in input.payload) {\n\t add(p_id, input.id, input.payload[p_id]);\n\t }\n\t }\n\t }\n\t }\n\t }\n\t }\n\t }\n\t }\n\t convert('', dict);\n\t return result_dict;\n\t },\n\t\n\t /** Matches flat ids to corresponding input element\n\t * @param{string} flat_id - Flat input id to be looked up.\n\t */\n\t match: function (flat_id) {\n\t return this.flat_dict && this.flat_dict[flat_id];\n\t },\n\t\n\t /** Match conditional values to selected cases\n\t */\n\t matchCase: function (input, value) {\n\t return matchCase(input, value);\n\t },\n\t\n\t /** Matches a new tool model to the current input elements e.g. used to update dynamic options\n\t */\n\t matchModel: function (model, callback) {\n\t var self = this;\n\t visitInputs(model.inputs, function (input, name) {\n\t self.flat_dict[name] && callback(input, self.flat_dict[name]);\n\t });\n\t },\n\t\n\t /** Matches identifier from api response to input elements e.g. used to display validation errors\n\t */\n\t matchResponse: function (response) {\n\t var result = {};\n\t var self = this;\n\t function search(id, head) {\n\t if (typeof head === 'string') {\n\t var input_id = self.flat_dict[id];\n\t input_id && (result[input_id] = head);\n\t } else {\n\t for (var i in head) {\n\t var new_id = i;\n\t if (id !== '') {\n\t var separator = '|';\n\t if (head instanceof Array) {\n\t separator = '_';\n\t }\n\t new_id = id + separator + new_id;\n\t }\n\t search(new_id, head[i]);\n\t }\n\t }\n\t }\n\t search('', response);\n\t return result;\n\t },\n\t\n\t /** Map dom tree to dictionary tree with input elements.\n\t */\n\t _iterate: function (parent, dict) {\n\t var self = this;\n\t var children = $(parent).children();\n\t children.each(function () {\n\t var child = this;\n\t var id = $(child).attr('id');\n\t if ($(child).hasClass('section-row')) {\n\t var input = self.app.input_list[id];\n\t dict[id] = input && { input: input } || {};\n\t self._iterate(child, dict[id]);\n\t } else {\n\t self._iterate(child, dict);\n\t }\n\t });\n\t }\n\t });\n\t\n\t /** Match conditional values to selected cases\n\t * @param{dict} input - Definition of conditional input parameter\n\t * @param{dict} value - Current value\n\t */\n\t var matchCase = function (input, value) {\n\t if (input.test_param.type == 'boolean') {\n\t if (value == 'true') {\n\t value = input.test_param.truevalue || 'true';\n\t } else {\n\t value = input.test_param.falsevalue || 'false';\n\t }\n\t }\n\t for (var i in input.cases) {\n\t if (input.cases[i].value == value) {\n\t return i;\n\t }\n\t }\n\t return -1;\n\t };\n\t\n\t /** Visits tool inputs\n\t * @param{dict} inputs - Nested dictionary of input elements\n\t * @param{dict} callback - Called with the mapped dictionary object and corresponding model node\n\t */\n\t var visitInputs = function (inputs, callback, prefix, context) {\n\t context = $.extend(true, {}, context);\n\t _.each(inputs, function (input) {\n\t if (input && input.type && input.name) {\n\t context[input.name] = input;\n\t }\n\t });\n\t for (var key in inputs) {\n\t var node = inputs[key];\n\t node.name = node.name || key;\n\t var name = prefix ? prefix + '|' + node.name : node.name;\n\t switch (node.type) {\n\t case 'repeat':\n\t _.each(node.cache, function (cache, j) {\n\t visitInputs(cache, callback, name + '_' + j, context);\n\t });\n\t break;\n\t case 'conditional':\n\t if (node.test_param) {\n\t callback(node.test_param, name + '|' + node.test_param.name, context);\n\t var selectedCase = matchCase(node, node.test_param.value);\n\t if (selectedCase != -1) {\n\t visitInputs(node.cases[selectedCase].inputs, callback, name, context);\n\t } else {\n\t Galaxy.emit.debug('form-data::visitInputs() - Invalid case for ' + name + '.');\n\t }\n\t } else {\n\t Galaxy.emit.debug('form-data::visitInputs() - Conditional test parameter missing for ' + name + '.');\n\t }\n\t break;\n\t case 'section':\n\t visitInputs(node.inputs, callback, name, context);\n\t break;\n\t default:\n\t callback(node, name, context);\n\t }\n\t }\n\t };\n\t\n\t return {\n\t Manager: Manager,\n\t visitInputs: visitInputs\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1), __webpack_require__(2)))\n\n/***/ }),\n/* 40 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/**\n\t This class creates a form input element wrapper\n\t*/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t return Backbone.View.extend({\n\t initialize: function (app, options) {\n\t this.app = app;\n\t this.app_options = app.model ? app.model.attributes : {};\n\t this.field = options && options.field || new Backbone.View();\n\t this.model = options && options.model || new Backbone.Model({\n\t text_enable: this.app_options.text_enable || 'Enable',\n\t text_disable: this.app_options.text_disable || 'Disable',\n\t cls_enable: this.app_options.cls_enable || 'fa fa-caret-square-o-down',\n\t cls_disable: this.app_options.cls_disable || 'fa fa-caret-square-o-up',\n\t always_refresh: this.app_options.always_refresh\n\t }).set(options);\n\t\n\t // set element and link components\n\t this.setElement(this._template());\n\t this.$field = this.$('.ui-form-field');\n\t this.$info = this.$('.ui-form-info');\n\t this.$preview = this.$('.ui-form-preview');\n\t this.$collapsible = this.$('.ui-form-collapsible');\n\t this.$collapsible_text = this.$('.ui-form-collapsible-text');\n\t this.$collapsible_icon = this.$('.ui-form-collapsible-icon');\n\t this.$title = this.$('.ui-form-title');\n\t this.$title_text = this.$('.ui-form-title-text');\n\t this.$error_text = this.$('.ui-form-error-text');\n\t this.$error = this.$('.ui-form-error');\n\t this.$backdrop = this.$('.ui-form-backdrop');\n\t\n\t // add field element\n\t this.$field.prepend(this.field.$el);\n\t\n\t // decide wether to expand or collapse fields\n\t var collapsible_value = this.model.get('collapsible_value');\n\t this.field.collapsed = collapsible_value !== undefined && JSON.stringify(this.model.get('value')) == JSON.stringify(collapsible_value);\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t\n\t // add click handler\n\t var self = this;\n\t this.$collapsible.on('click', function () {\n\t self.field.collapsed = !self.field.collapsed;\n\t app.trigger && app.trigger('change');\n\t self.render();\n\t });\n\t\n\t // hide error on value change\n\t if (this.field.model && !this.model.get('always_refresh')) {\n\t this.listenTo(this.field.model, 'change:value', function () {\n\t self.reset();\n\t });\n\t }\n\t },\n\t\n\t /** Set backdrop for input element */\n\t backdrop: function () {\n\t this.model.set('backdrop', true);\n\t },\n\t\n\t /** Set error text */\n\t error: function (text) {\n\t this.model.set('error_text', text);\n\t },\n\t\n\t /** Reset this view */\n\t reset: function () {\n\t !this.model.get('fixed') && this.model.set('error_text', null);\n\t },\n\t\n\t render: function () {\n\t // render help\n\t $('.tooltip').hide();\n\t var help_text = this.model.get('help', '');\n\t var help_argument = this.model.get('argument');\n\t if (help_argument && help_text.indexOf('(' + help_argument + ')') == -1) {\n\t help_text += ' (' + help_argument + ')';\n\t }\n\t this.$info.html(help_text);\n\t // render visibility\n\t this.$el[this.model.get('hidden') ? 'hide' : 'show']();\n\t // render preview view for collapsed fields\n\t this.$preview[this.field.collapsed && this.model.get('collapsible_preview') || this.model.get('disabled') ? 'show' : 'hide']().html(_.escape(this.model.get('text_value')));\n\t // render error messages\n\t var error_text = this.model.get('error_text');\n\t this.$error[error_text ? 'show' : 'hide']();\n\t this.$el[error_text ? 'addClass' : 'removeClass']('ui-error');\n\t this.$error_text.html(error_text);\n\t // render backdrop\n\t this.$backdrop[this.model.get('backdrop') ? 'show' : 'hide']();\n\t // render input field\n\t this.field.collapsed || this.model.get('disabled') ? this.$field.hide() : this.$field.show();\n\t // render input field color and style\n\t this.field.model && this.field.model.set({ 'color': this.model.get('color'), 'style': this.model.get('style') });\n\t // render collapsible options\n\t if (!this.model.get('disabled') && this.model.get('collapsible_value') !== undefined) {\n\t var collapsible_state = this.field.collapsed ? 'enable' : 'disable';\n\t this.$title_text.hide();\n\t this.$collapsible.show();\n\t this.$collapsible_text.text(this.model.get('label'));\n\t this.$collapsible_icon.removeClass().addClass('icon').addClass(this.model.get('cls_' + collapsible_state)).attr('data-original-title', this.model.get('text_' + collapsible_state)).tooltip({ placement: 'bottom' });\n\t } else {\n\t this.$title_text.show().text(this.model.get('label'));\n\t this.$collapsible.hide();\n\t }\n\t },\n\t\n\t _template: function () {\n\t return $('').addClass('ui-form-element').append($('').addClass('ui-form-error ui-error').append($('').addClass('fa fa-arrow-down')).append($('').addClass('ui-form-error-text'))).append($('').addClass('ui-form-title').append($('').addClass('ui-form-collapsible').append($('').addClass('ui-form-collapsible-icon')).append($('').addClass('ui-form-collapsible-text'))).append($('').addClass('ui-form-title-text'))).append($('').addClass('ui-form-field').append($('').addClass('ui-form-info')).append($('').addClass('ui-form-backdrop'))).append($('').addClass('ui-form-preview'));\n\t }\n\t });\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1), __webpack_require__(2)))\n\n/***/ }),\n/* 41 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, $) {/**\n\t This class creates input elements. New input parameter types should be added to the types dictionary.\n\t*/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(7), __webpack_require__(54), __webpack_require__(56), __webpack_require__(55), __webpack_require__(52)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Ui, SelectContent, SelectLibrary, SelectFtp, ColorPicker) {\n\t\n\t // create form view\n\t return Backbone.Model.extend({\n\t /** Available parameter types */\n\t types: {\n\t 'text': '_fieldText',\n\t 'password': '_fieldText',\n\t 'select': '_fieldSelect',\n\t 'data_column': '_fieldSelect',\n\t 'genomebuild': '_fieldSelect',\n\t 'data': '_fieldData',\n\t 'data_collection': '_fieldData',\n\t 'integer': '_fieldSlider',\n\t 'float': '_fieldSlider',\n\t 'boolean': '_fieldBoolean',\n\t 'drill_down': '_fieldDrilldown',\n\t 'color': '_fieldColor',\n\t 'hidden': '_fieldHidden',\n\t 'hidden_data': '_fieldHidden',\n\t 'baseurl': '_fieldHidden',\n\t 'library_data': '_fieldLibrary',\n\t 'ftpfile': '_fieldFtp',\n\t 'upload': '_fieldUpload'\n\t },\n\t\n\t /** Returns an input field for a given field type */\n\t create: function (input_def) {\n\t var fieldClass = this.types[input_def.type];\n\t var field = typeof this[fieldClass] === 'function' ? this[fieldClass].call(this, input_def) : null;\n\t if (!field) {\n\t field = input_def.options ? this._fieldSelect(input_def) : this._fieldText(input_def);\n\t Galaxy.emit.debug('form-parameters::_addRow()', 'Auto matched field type (' + input_def.type + ').');\n\t }\n\t input_def.value === undefined && (input_def.value = null);\n\t field.value(input_def.value);\n\t return field;\n\t },\n\t\n\t /** Data input field */\n\t _fieldData: function (input_def) {\n\t return new SelectContent.View({\n\t id: 'field-' + input_def.id,\n\t extensions: input_def.extensions,\n\t optional: input_def.optional,\n\t multiple: input_def.multiple,\n\t type: input_def.type,\n\t flavor: input_def.flavor,\n\t data: input_def.options,\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** Select/Checkbox/Radio options field */\n\t _fieldSelect: function (input_def) {\n\t // show text field e.g. in workflow editor\n\t if (input_def.is_workflow) {\n\t return this._fieldText(input_def);\n\t }\n\t\n\t // customize properties\n\t if (input_def.type == 'data_column') {\n\t input_def.error_text = 'Missing columns in referenced dataset.';\n\t }\n\t\n\t // identify available options\n\t var data = input_def.data;\n\t if (!data) {\n\t data = [];\n\t _.each(input_def.options, function (option) {\n\t data.push({ label: option[0], value: option[1] });\n\t });\n\t }\n\t\n\t // identify display type\n\t var SelectClass = Ui.Select;\n\t switch (input_def.display) {\n\t case 'checkboxes':\n\t SelectClass = Ui.Checkbox;\n\t break;\n\t case 'radio':\n\t SelectClass = Ui.Radio;\n\t break;\n\t case 'radiobutton':\n\t SelectClass = Ui.RadioButton;\n\t break;\n\t }\n\t\n\t // create select field\n\t return new SelectClass.View({\n\t id: 'field-' + input_def.id,\n\t data: data,\n\t error_text: input_def.error_text || 'No options available',\n\t multiple: input_def.multiple,\n\t optional: input_def.optional,\n\t onchange: input_def.onchange,\n\t searchable: input_def.flavor !== 'workflow'\n\t });\n\t },\n\t\n\t /** Drill down options field */\n\t _fieldDrilldown: function (input_def) {\n\t // show text field e.g. in workflow editor\n\t if (input_def.is_workflow) {\n\t return this._fieldText(input_def);\n\t }\n\t\n\t // create drill down field\n\t return new Ui.Drilldown.View({\n\t id: 'field-' + input_def.id,\n\t data: input_def.options,\n\t display: input_def.display,\n\t optional: input_def.optional,\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** Text input field */\n\t _fieldText: function (input_def) {\n\t // field replaces e.g. a select field\n\t if (input_def.options && input_def.data) {\n\t input_def.area = input_def.multiple;\n\t if (Utils.isEmpty(input_def.value)) {\n\t input_def.value = null;\n\t } else {\n\t if ($.isArray(input_def.value)) {\n\t var str_value = '';\n\t for (var i in input_def.value) {\n\t str_value += String(input_def.value[i]);\n\t if (!input_def.multiple) {\n\t break;\n\t }\n\t str_value += '\\n';\n\t }\n\t input_def.value = str_value;\n\t }\n\t }\n\t }\n\t // create input element\n\t return new Ui.Input({\n\t id: 'field-' + input_def.id,\n\t type: input_def.type,\n\t area: input_def.area,\n\t readonly: input_def.readonly,\n\t placeholder: input_def.placeholder,\n\t datalist: input_def.datalist,\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** Slider field */\n\t _fieldSlider: function (input_def) {\n\t return new Ui.Slider.View({\n\t id: 'field-' + input_def.id,\n\t precise: input_def.type == 'float',\n\t is_workflow: input_def.is_workflow,\n\t min: input_def.min,\n\t max: input_def.max,\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** Hidden field */\n\t _fieldHidden: function (input_def) {\n\t return new Ui.Hidden({\n\t id: 'field-' + input_def.id,\n\t info: input_def.info\n\t });\n\t },\n\t\n\t /** Boolean field */\n\t _fieldBoolean: function (input_def) {\n\t return new Ui.RadioButton.View({\n\t id: 'field-' + input_def.id,\n\t data: [{ label: 'Yes', value: 'true' }, { label: 'No', value: 'false' }],\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** Color picker field */\n\t _fieldColor: function (input_def) {\n\t return new ColorPicker({\n\t id: 'field-' + input_def.id,\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** Library dataset field */\n\t _fieldLibrary: function (input_def) {\n\t return new SelectLibrary.View({\n\t id: 'field-' + input_def.id,\n\t optional: input_def.optional,\n\t multiple: input_def.multiple,\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** FTP file field */\n\t _fieldFtp: function (input_def) {\n\t return new SelectFtp.View({\n\t id: 'field-' + input_def.id,\n\t optional: input_def.optional,\n\t multiple: input_def.multiple,\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** Upload file field */\n\t _fieldUpload: function (input_def) {\n\t return new Ui.Upload({\n\t id: 'field-' + input_def.id,\n\t onchange: input_def.onchange\n\t });\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ }),\n/* 42 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/** This class creates a ui component which enables the dynamic creation of portlets */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(9), __webpack_require__(7)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Portlet, Ui) {\n\t var View = Backbone.View.extend({\n\t initialize: function (options) {\n\t this.list = {};\n\t this.options = Utils.merge(options, {\n\t title: 'Repeat',\n\t empty_text: 'Not available.',\n\t max: null,\n\t min: null\n\t });\n\t this.button_new = new Ui.ButtonIcon({\n\t icon: 'fa-plus',\n\t title: 'Insert ' + this.options.title,\n\t tooltip: 'Add new ' + this.options.title + ' block',\n\t floating: 'clear',\n\t cls: 'ui-button-icon form-repeat-add',\n\t onclick: function () {\n\t options.onnew && options.onnew();\n\t }\n\t });\n\t this.setElement($('').append(this.$list = $('')).append($('').append(this.button_new.$el)));\n\t },\n\t\n\t /** Number of repeat blocks */\n\t size: function () {\n\t return _.size(this.list);\n\t },\n\t\n\t /** Add new repeat block */\n\t add: function (options) {\n\t if (!options.id || this.list[options.id]) {\n\t Galaxy.emit.debug('form-repeat::add()', 'Duplicate or invalid repeat block id.');\n\t return;\n\t }\n\t var button_delete = new Ui.ButtonIcon({\n\t icon: 'fa-trash-o',\n\t tooltip: 'Delete this repeat block',\n\t cls: 'ui-button-icon-plain form-repeat-delete',\n\t onclick: function () {\n\t options.ondel && options.ondel();\n\t }\n\t });\n\t var portlet = new Portlet.View({\n\t id: options.id,\n\t title: 'placeholder',\n\t cls: options.cls || 'ui-portlet-repeat',\n\t operations: { button_delete: button_delete }\n\t });\n\t portlet.append(options.$el);\n\t portlet.$el.addClass('section-row').hide();\n\t this.list[options.id] = portlet;\n\t this.$list.append(portlet.$el.fadeIn('fast'));\n\t this.options.max > 0 && this.size() >= this.options.max && this.button_new.disable();\n\t this._refresh();\n\t },\n\t\n\t /** Delete repeat block */\n\t del: function (id) {\n\t if (!this.list[id]) {\n\t Galaxy.emit.debug('form-repeat::del()', 'Invalid repeat block id.');\n\t return;\n\t }\n\t this.$list.find('#' + id).remove();\n\t delete this.list[id];\n\t this.button_new.enable();\n\t this._refresh();\n\t },\n\t\n\t /** Remove all */\n\t delAll: function () {\n\t for (var id in this.list) {\n\t this.del(id);\n\t }\n\t },\n\t\n\t /** Hides add/del options */\n\t hideOptions: function () {\n\t this.button_new.$el.hide();\n\t _.each(this.list, function (portlet) {\n\t portlet.hideOperation('button_delete');\n\t });\n\t _.isEmpty(this.list) && this.$el.append($('').addClass('ui-form-info').html(this.options.empty_text));\n\t },\n\t\n\t /** Refresh view */\n\t _refresh: function () {\n\t var index = 0;\n\t for (var id in this.list) {\n\t var portlet = this.list[id];\n\t portlet.title(++index + ': ' + this.options.title);\n\t portlet[this.size() > this.options.min ? 'showOperation' : 'hideOperation']('button_delete');\n\t }\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1), __webpack_require__(2)))\n\n/***/ }),\n/* 43 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _, jQuery) {/**\n\t This class creates a form section and populates it with input elements. It also handles repeat blocks and conditionals by recursively creating new sub sections.\n\t*/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(7), __webpack_require__(9), __webpack_require__(42), __webpack_require__(40), __webpack_require__(41)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Ui, Portlet, Repeat, InputElement, Parameters) {\n\t var View = Backbone.View.extend({\n\t initialize: function (app, options) {\n\t this.app = app;\n\t this.inputs = options.inputs;\n\t this.parameters = new Parameters();\n\t this.setElement($(''));\n\t this.render();\n\t },\n\t\n\t /** Render section view */\n\t render: function () {\n\t var self = this;\n\t this.$el.empty();\n\t _.each(this.inputs, function (input) {\n\t self.add(input);\n\t });\n\t },\n\t\n\t /** Add a new input element */\n\t add: function (input) {\n\t var input_def = jQuery.extend(true, {}, input);\n\t input_def.id = input.id = Utils.uid();\n\t this.app.input_list[input_def.id] = input_def;\n\t switch (input_def.type) {\n\t case 'conditional':\n\t this._addConditional(input_def);\n\t break;\n\t case 'repeat':\n\t this._addRepeat(input_def);\n\t break;\n\t case 'section':\n\t this._addSection(input_def);\n\t break;\n\t default:\n\t this._addRow(input_def);\n\t }\n\t },\n\t\n\t /** Add a conditional block */\n\t _addConditional: function (input_def) {\n\t var self = this;\n\t input_def.test_param.id = input_def.id;\n\t this.app.model.get('sustain_conditionals') && (input_def.test_param.disabled = true);\n\t var field = this._addRow(input_def.test_param);\n\t\n\t // set onchange event for test parameter\n\t field.model && field.model.set('onchange', function (value) {\n\t var selectedCase = self.app.data.matchCase(input_def, value);\n\t for (var i in input_def.cases) {\n\t var case_def = input_def.cases[i];\n\t var section_row = self.$('#' + input_def.id + '-section-' + i);\n\t var nonhidden = false;\n\t for (var j in case_def.inputs) {\n\t if (!case_def.inputs[j].hidden) {\n\t nonhidden = true;\n\t break;\n\t }\n\t }\n\t if (i == selectedCase && nonhidden) {\n\t section_row.fadeIn('fast');\n\t } else {\n\t section_row.hide();\n\t }\n\t }\n\t self.app.trigger('change');\n\t });\n\t\n\t // add conditional sub sections\n\t for (var i in input_def.cases) {\n\t var sub_section = new View(this.app, { inputs: input_def.cases[i].inputs });\n\t this._append(sub_section.$el.addClass('ui-form-section'), input_def.id + '-section-' + i);\n\t }\n\t\n\t // trigger refresh on conditional input field after all input elements have been created\n\t field.trigger('change');\n\t },\n\t\n\t /** Add a repeat block */\n\t _addRepeat: function (input_def) {\n\t var self = this;\n\t var block_index = 0;\n\t\n\t // create repeat block element\n\t var repeat = new Repeat.View({\n\t title: input_def.title || 'Repeat',\n\t min: input_def.min,\n\t max: input_def.max,\n\t onnew: function () {\n\t create(input_def.inputs);self.app.trigger('change');\n\t }\n\t });\n\t\n\t // helper function to create new repeat blocks\n\t function create(inputs) {\n\t var sub_section_id = input_def.id + '-section-' + block_index++;\n\t var sub_section = new View(self.app, { inputs: inputs });\n\t repeat.add({ id: sub_section_id,\n\t $el: sub_section.$el,\n\t ondel: function () {\n\t repeat.del(sub_section_id);self.app.trigger('change');\n\t } });\n\t }\n\t\n\t //\n\t // add parsed/minimum number of repeat blocks\n\t //\n\t var n_cache = _.size(input_def.cache);\n\t for (var i = 0; i < Math.max(Math.max(n_cache, input_def.min || 0), input_def.default || 0); i++) {\n\t create(i < n_cache ? input_def.cache[i] : input_def.inputs);\n\t }\n\t\n\t // hide options\n\t this.app.model.get('sustain_repeats') && repeat.hideOptions();\n\t\n\t // create input field wrapper\n\t var input_element = new InputElement(this.app, {\n\t label: input_def.title || input_def.name,\n\t help: input_def.help,\n\t field: repeat\n\t });\n\t this._append(input_element.$el, input_def.id);\n\t },\n\t\n\t /** Add a customized section */\n\t _addSection: function (input_def) {\n\t var portlet = new Portlet.View({\n\t title: input_def.title || input_def.name,\n\t cls: 'ui-portlet-section',\n\t collapsible: true,\n\t collapsible_button: true,\n\t collapsed: !input_def.expanded\n\t });\n\t portlet.append(new View(this.app, { inputs: input_def.inputs }).$el);\n\t portlet.append($('').addClass('ui-form-info').html(input_def.help));\n\t this.app.on('expand', function (input_id) {\n\t portlet.$('#' + input_id).length > 0 && portlet.expand();\n\t });\n\t this._append(portlet.$el, input_def.id);\n\t },\n\t\n\t /** Add a single input field element */\n\t _addRow: function (input_def) {\n\t var self = this;\n\t var id = input_def.id;\n\t input_def.onchange = input_def.onchange || function () {\n\t self.app.trigger('change', id);\n\t };\n\t var field = this.parameters.create(input_def);\n\t this.app.field_list[id] = field;\n\t var input_element = new InputElement(this.app, {\n\t name: input_def.name,\n\t label: input_def.hide_label ? '' : input_def.label || input_def.name,\n\t value: input_def.value,\n\t text_value: input_def.text_value,\n\t collapsible_value: input_def.collapsible_value,\n\t collapsible_preview: input_def.collapsible_preview,\n\t help: input_def.help,\n\t argument: input_def.argument,\n\t disabled: input_def.disabled,\n\t color: input_def.color,\n\t style: input_def.style,\n\t backdrop: input_def.backdrop,\n\t hidden: input_def.hidden,\n\t fixed: input_def.fixed,\n\t field: field\n\t });\n\t this.app.element_list[id] = input_element;\n\t this._append(input_element.$el, input_def.id);\n\t return field;\n\t },\n\t\n\t /** Append a new element to the form i.e. input element, repeat block, conditionals etc. */\n\t _append: function ($el, id) {\n\t this.$el.append($el.addClass('section-row').attr('id', id));\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ }),\n/* 44 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(36), __webpack_require__(81), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (DC_MODEL, HISTORY_CONTENT, _l) {\n\t\n\t 'use strict';\n\t\n\t /*==============================================================================\n\t \n\t Models for DatasetCollections contained within a history.\n\t \n\t TODO:\n\t these might be compactable to one class if some duplication with\n\t collection-model is used.\n\t \n\t ==============================================================================*/\n\t\n\t var hcontentMixin = HISTORY_CONTENT.HistoryContentMixin,\n\t ListDC = DC_MODEL.ListDatasetCollection,\n\t PairDC = DC_MODEL.PairDatasetCollection,\n\t ListPairedDC = DC_MODEL.ListPairedDatasetCollection,\n\t ListOfListsDC = DC_MODEL.ListOfListsDatasetCollection;\n\t\n\t //==============================================================================\n\t /** Override to post to contents route w/o id. */\n\t function buildHDCASave(_super) {\n\t return function _save(attributes, options) {\n\t if (this.isNew()) {\n\t options = options || {};\n\t options.url = this.urlRoot + this.get('history_id') + '/contents';\n\t attributes = attributes || {};\n\t attributes.type = 'dataset_collection';\n\t }\n\t return _super.call(this, attributes, options);\n\t };\n\t }\n\t\n\t //==============================================================================\n\t /** @class Backbone model for List Dataset Collection within a History.\n\t */\n\t var HistoryListDatasetCollection = ListDC.extend(hcontentMixin).extend(\n\t /** @lends HistoryListDatasetCollection.prototype */{\n\t\n\t defaults: _.extend(_.clone(ListDC.prototype.defaults), {\n\t history_content_type: 'dataset_collection',\n\t collection_type: 'list',\n\t model_class: 'HistoryDatasetCollectionAssociation'\n\t }),\n\t\n\t /** Override to post to contents route w/o id. */\n\t save: buildHDCASave(ListDC.prototype.save),\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return 'History' + ListDC.prototype.toString.call(this);\n\t }\n\t });\n\t\n\t //==============================================================================\n\t /** @class Backbone model for Pair Dataset Collection within a History.\n\t * @constructs\n\t */\n\t var HistoryPairDatasetCollection = PairDC.extend(hcontentMixin).extend(\n\t /** @lends HistoryPairDatasetCollection.prototype */{\n\t\n\t defaults: _.extend(_.clone(PairDC.prototype.defaults), {\n\t history_content_type: 'dataset_collection',\n\t collection_type: 'paired',\n\t model_class: 'HistoryDatasetCollectionAssociation'\n\t }),\n\t\n\t /** Override to post to contents route w/o id. */\n\t save: buildHDCASave(PairDC.prototype.save),\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return 'History' + PairDC.prototype.toString.call(this);\n\t }\n\t });\n\t\n\t //==============================================================================\n\t /** @class Backbone model for List of Pairs Dataset Collection within a History. */\n\t var HistoryListPairedDatasetCollection = ListPairedDC.extend(hcontentMixin).extend({\n\t\n\t defaults: _.extend(_.clone(ListPairedDC.prototype.defaults), {\n\t history_content_type: 'dataset_collection',\n\t collection_type: 'list:paired',\n\t model_class: 'HistoryDatasetCollectionAssociation'\n\t }),\n\t\n\t /** Override to post to contents route w/o id. */\n\t save: buildHDCASave(ListPairedDC.prototype.save),\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return 'History' + ListPairedDC.prototype.toString.call(this);\n\t }\n\t });\n\t\n\t //==============================================================================\n\t /** @class Backbone model for List of Lists Dataset Collection within a History. */\n\t var HistoryListOfListsDatasetCollection = ListOfListsDC.extend(hcontentMixin).extend({\n\t\n\t defaults: _.extend(_.clone(ListOfListsDC.prototype.defaults), {\n\t history_content_type: 'dataset_collection',\n\t collection_type: 'list:list',\n\t model_class: 'HistoryDatasetCollectionAssociation'\n\t }),\n\t\n\t /** Override to post to contents route w/o id. */\n\t save: buildHDCASave(ListOfListsDC.prototype.save),\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return ['HistoryListOfListsDatasetCollection(', this.get('name'), ')'].join('');\n\t }\n\t });\n\t\n\t //==============================================================================\n\t return {\n\t HistoryListDatasetCollection: HistoryListDatasetCollection,\n\t HistoryPairDatasetCollection: HistoryPairDatasetCollection,\n\t HistoryListPairedDatasetCollection: HistoryListPairedDatasetCollection,\n\t HistoryListOfListsDatasetCollection: HistoryListOfListsDatasetCollection\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2)))\n\n/***/ }),\n/* 45 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_, jQuery, Backbone) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(72), __webpack_require__(79), __webpack_require__(44), __webpack_require__(46), __webpack_require__(6), __webpack_require__(144)], __WEBPACK_AMD_DEFINE_RESULT__ = function (CONTROLLED_FETCH_COLLECTION, HDA_MODEL, HDCA_MODEL, HISTORY_PREFS, BASE_MVC, AJAX_QUEUE) {\n\t 'use strict';\n\t\n\t //==============================================================================\n\t\n\t var _super = CONTROLLED_FETCH_COLLECTION.PaginatedCollection;\n\t /** @class Backbone collection for history content.\n\t * NOTE: history content seems like a dataset collection, but differs in that it is mixed:\n\t * each element can be either an HDA (dataset) or a DatasetCollection and co-exist on\n\t * the same level.\n\t * Dataset collections on the other hand are not mixed and (so far) can only contain either\n\t * HDAs or child dataset collections on one level.\n\t * This is why this does not inherit from any of the DatasetCollections (currently).\n\t */\n\t var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({\n\t _logNamespace: 'history',\n\t\n\t // ........................................................................ composite collection\n\t /** since history content is a mix, override model fn into a factory, creating based on history_content_type */\n\t model: function (attrs, options) {\n\t if (attrs.history_content_type === \"dataset\") {\n\t return new HDA_MODEL.HistoryDatasetAssociation(attrs, options);\n\t } else if (attrs.history_content_type === \"dataset_collection\") {\n\t switch (attrs.collection_type) {\n\t case 'list':\n\t return new HDCA_MODEL.HistoryListDatasetCollection(attrs, options);\n\t case 'paired':\n\t return new HDCA_MODEL.HistoryPairDatasetCollection(attrs, options);\n\t case 'list:paired':\n\t return new HDCA_MODEL.HistoryListPairedDatasetCollection(attrs, options);\n\t case 'list:list':\n\t return new HDCA_MODEL.HistoryListOfListsDatasetCollection(attrs, options);\n\t }\n\t // This is a hack inside a hack:\n\t // Raise a plain object with validationError to fake a model.validationError\n\t // (since we don't have a model to use validate with)\n\t // (the outer hack being the mixed content/model function in this collection)\n\t var msg = 'Unknown collection_type: ' + attrs.collection_type;\n\t console.warn(msg, attrs);\n\t return { validationError: msg };\n\t }\n\t return { validationError: 'Unknown history_content_type: ' + attrs.history_content_type };\n\t },\n\t\n\t // ........................................................................ set up\n\t limitPerPage: 500,\n\t\n\t /** @type {Integer} how many contents per call to fetch when using progressivelyFetchDetails */\n\t limitPerProgressiveFetch: 500,\n\t\n\t /** @type {String} order used here and when fetching from server */\n\t order: 'hid',\n\t\n\t /** root api url */\n\t urlRoot: Galaxy.root + 'api/histories',\n\t\n\t /** complete api url */\n\t url: function () {\n\t return this.urlRoot + '/' + this.historyId + '/contents';\n\t },\n\t\n\t /** Set up */\n\t initialize: function (models, options) {\n\t options = options || {};\n\t _super.prototype.initialize.call(this, models, options);\n\t\n\t this.history = options.history || null;\n\t this.setHistoryId(options.historyId || null);\n\t /** @type {Boolean} does this collection contain and fetch deleted elements */\n\t this.includeDeleted = options.includeDeleted || this.includeDeleted;\n\t /** @type {Boolean} does this collection contain and fetch non-visible elements */\n\t this.includeHidden = options.includeHidden || this.includeHidden;\n\t\n\t // backbonejs uses collection.model.prototype.idAttribute to determine if a model is *already* in a collection\n\t // and either merged or replaced. In this case, our 'model' is a function so we need to add idAttribute\n\t // manually here - if we don't, contents will not merge but be replaced/swapped.\n\t this.model.prototype.idAttribute = 'type_id';\n\t },\n\t\n\t setHistoryId: function (newId) {\n\t this.historyId = newId;\n\t this._setUpWebStorage();\n\t },\n\t\n\t /** Set up client side storage. Currently PersistanStorage keyed under 'history:' */\n\t _setUpWebStorage: function (initialSettings) {\n\t // TODO: use initialSettings\n\t if (!this.historyId) {\n\t return;\n\t }\n\t this.storage = new HISTORY_PREFS.HistoryPrefs({\n\t id: HISTORY_PREFS.HistoryPrefs.historyStorageKey(this.historyId)\n\t });\n\t this.trigger('new-storage', this.storage, this);\n\t\n\t this.on({\n\t 'include-deleted': function (newVal) {\n\t this.storage.includeDeleted(newVal);\n\t },\n\t 'include-hidden': function (newVal) {\n\t this.storage.includeHidden(newVal);\n\t }\n\t });\n\t\n\t this.includeDeleted = this.storage.includeDeleted() || false;\n\t this.includeHidden = this.storage.includeHidden() || false;\n\t return this;\n\t },\n\t\n\t // ........................................................................ common queries\n\t /** @type {Object} map of collection available sorting orders containing comparator fns */\n\t comparators: _.extend(_.clone(_super.prototype.comparators), {\n\t 'name': BASE_MVC.buildComparator('name', { ascending: true }),\n\t 'name-dsc': BASE_MVC.buildComparator('name', { ascending: false }),\n\t 'hid': BASE_MVC.buildComparator('hid', { ascending: false }),\n\t 'hid-asc': BASE_MVC.buildComparator('hid', { ascending: true })\n\t }),\n\t\n\t /** Get every model in this collection not in a 'ready' state (running). */\n\t running: function () {\n\t return this.filter(function (c) {\n\t return !c.inReadyState();\n\t });\n\t },\n\t\n\t /** return contents that are not ready and not deleted/hidden */\n\t runningAndActive: function () {\n\t return this.filter(function (c) {\n\t return !c.inReadyState() && c.get('visible')\n\t // TODO: deletedOrPurged?\n\t && !c.get('deleted');\n\t });\n\t },\n\t\n\t /** Get the model with the given hid\n\t * @param {Int} hid the hid to search for\n\t * @returns {HistoryDatasetAssociation} the model with the given hid or undefined if not found\n\t */\n\t getByHid: function (hid) {\n\t // note: there *can* be more than one content with a given hid, this finds the first based on order\n\t return this.findWhere({ hid: hid });\n\t },\n\t\n\t /** return true if all contents have details */\n\t haveDetails: function () {\n\t return this.all(function (c) {\n\t return c.hasDetails();\n\t });\n\t },\n\t\n\t // ........................................................................ hidden / deleted\n\t /** return a new contents collection of only hidden items */\n\t hidden: function () {\n\t return this.filter(function (c) {\n\t return c.hidden();\n\t });\n\t },\n\t\n\t /** return a new contents collection of only hidden items */\n\t deleted: function () {\n\t return this.filter(function (c) {\n\t return c.get('deleted');\n\t });\n\t },\n\t\n\t /** return a new contents collection of only hidden items */\n\t visibleAndUndeleted: function () {\n\t return this.filter(function (c) {\n\t return c.get('visible') &&\n\t // TODO: deletedOrPurged?\n\t !c.get('deleted');\n\t });\n\t },\n\t\n\t /** create a setter in order to publish the change */\n\t setIncludeDeleted: function (setting, options) {\n\t if (_.isBoolean(setting) && setting !== this.includeDeleted) {\n\t this.includeDeleted = setting;\n\t if (_.result(options, 'silent')) {\n\t return;\n\t }\n\t this.trigger('include-deleted', setting, this);\n\t }\n\t },\n\t\n\t /** create a setter in order to publish the change */\n\t setIncludeHidden: function (setting, options) {\n\t if (_.isBoolean(setting) && setting !== this.includeHidden) {\n\t this.includeHidden = setting;\n\t options = options || {};\n\t if (_.result(options, 'silent')) {\n\t return;\n\t }\n\t this.trigger('include-hidden', setting, this);\n\t }\n\t },\n\t\n\t // ........................................................................ ajax\n\t // ............ controlled fetch collection\n\t /** override to get expanded ids from sessionStorage and pass to API as details */\n\t fetch: function (options) {\n\t options = options || {};\n\t if (this.historyId && !options.details) {\n\t var prefs = HISTORY_PREFS.HistoryPrefs.get(this.historyId).toJSON();\n\t if (!_.isEmpty(prefs.expandedIds)) {\n\t options.details = _.values(prefs.expandedIds).join(',');\n\t }\n\t }\n\t return _super.prototype.fetch.call(this, options);\n\t },\n\t\n\t // ............. ControlledFetch stuff\n\t /** override to include the API versioning flag */\n\t _buildFetchData: function (options) {\n\t return _.extend(_super.prototype._buildFetchData.call(this, options), {\n\t v: 'dev'\n\t });\n\t },\n\t\n\t /** Extend to include details and version */\n\t _fetchParams: _super.prototype._fetchParams.concat([\n\t // TODO: remove (the need for) both\n\t /** version */\n\t 'v',\n\t /** dataset ids to get full details of */\n\t 'details']),\n\t\n\t /** override to add deleted/hidden filters */\n\t _buildFetchFilters: function (options) {\n\t var superFilters = _super.prototype._buildFetchFilters.call(this, options) || {};\n\t var filters = {};\n\t if (!this.includeDeleted) {\n\t filters.deleted = false;\n\t filters.purged = false;\n\t }\n\t if (!this.includeHidden) {\n\t filters.visible = true;\n\t }\n\t return _.defaults(superFilters, filters);\n\t },\n\t\n\t // ............ paginated collection\n\t getTotalItemCount: function () {\n\t return this.history.contentsShown();\n\t },\n\t\n\t // ............ history contents specific ajax\n\t /** override to filter requested contents to those updated after the Date 'since' */\n\t fetchUpdated: function (since, options) {\n\t if (since) {\n\t options = options || { filters: {} };\n\t options.remove = false;\n\t options.filters = {\n\t 'update_time-ge': since.toISOString(),\n\t // workflows will produce hidden datasets (non-output datasets) that still\n\t // need to be updated in the collection or they'll update forever\n\t // we can remove the default visible filter by using an 'empty' value\n\t visible: ''\n\t };\n\t }\n\t return this.fetch(options);\n\t },\n\t\n\t /** fetch all the deleted==true contents of this collection */\n\t fetchDeleted: function (options) {\n\t options = options || {};\n\t var self = this;\n\t options.filters = _.extend(options.filters, {\n\t // all deleted, purged or not\n\t deleted: true,\n\t purged: undefined\n\t });\n\t options.remove = false;\n\t\n\t self.trigger('fetching-deleted', self);\n\t return self.fetch(options).always(function () {\n\t self.trigger('fetching-deleted-done', self);\n\t });\n\t },\n\t\n\t /** fetch all the visible==false contents of this collection */\n\t fetchHidden: function (options) {\n\t options = options || {};\n\t var self = this;\n\t options.filters = _.extend(options.filters, {\n\t visible: false\n\t });\n\t options.remove = false;\n\t\n\t self.trigger('fetching-hidden', self);\n\t return self.fetch(options).always(function () {\n\t self.trigger('fetching-hidden-done', self);\n\t });\n\t },\n\t\n\t /** fetch detailed model data for all contents in this collection */\n\t fetchAllDetails: function (options) {\n\t options = options || {};\n\t var detailsFlag = { details: 'all' };\n\t options.data = _.extend(options.data || {}, detailsFlag);\n\t return this.fetch(options);\n\t },\n\t\n\t /** specialty fetch method for retrieving the element_counts of all hdcas in the history */\n\t fetchCollectionCounts: function (options) {\n\t options = options || {};\n\t options.keys = ['type_id', 'element_count'].join(',');\n\t options.filters = _.extend(options.filters || {}, {\n\t history_content_type: 'dataset_collection'\n\t });\n\t options.remove = false;\n\t return this.fetch(options);\n\t },\n\t\n\t // ............. quasi-batch ops\n\t // TODO: to batch\n\t /** helper that fetches using filterParams then calls save on each fetched using updateWhat as the save params */\n\t _filterAndUpdate: function (filterParams, updateWhat) {\n\t var self = this;\n\t var idAttribute = self.model.prototype.idAttribute;\n\t var updateArgs = [updateWhat];\n\t\n\t return self.fetch({ filters: filterParams, remove: false }).then(function (fetched) {\n\t // convert filtered json array to model array\n\t fetched = fetched.reduce(function (modelArray, currJson, i) {\n\t var model = self.get(currJson[idAttribute]);\n\t return model ? modelArray.concat(model) : modelArray;\n\t }, []);\n\t return self.ajaxQueue('save', updateArgs, fetched);\n\t });\n\t },\n\t\n\t /** using a queue, perform ajaxFn on each of the models in this collection */\n\t ajaxQueue: function (ajaxFn, args, collection) {\n\t collection = collection || this.models;\n\t return new AJAX_QUEUE.AjaxQueue(collection.slice().reverse().map(function (content, i) {\n\t var fn = _.isString(ajaxFn) ? content[ajaxFn] : ajaxFn;\n\t return function () {\n\t return fn.apply(content, args);\n\t };\n\t })).deferred;\n\t },\n\t\n\t /** fetch contents' details in batches of limitPerCall - note: only get searchable details here */\n\t progressivelyFetchDetails: function (options) {\n\t options = options || {};\n\t var deferred = jQuery.Deferred();\n\t var self = this;\n\t var limit = options.limitPerCall || self.limitPerProgressiveFetch;\n\t // TODO: only fetch tags and annotations if specifically requested\n\t var searchAttributes = HDA_MODEL.HistoryDatasetAssociation.prototype.searchAttributes;\n\t var detailKeys = searchAttributes.join(',');\n\t\n\t function _recursivelyFetch(offset) {\n\t offset = offset || 0;\n\t var _options = _.extend(_.clone(options), {\n\t view: 'summary',\n\t keys: detailKeys,\n\t limit: limit,\n\t offset: offset,\n\t reset: offset === 0,\n\t remove: false\n\t });\n\t\n\t _.defer(function () {\n\t self.fetch.call(self, _options).fail(deferred.reject).done(function (response) {\n\t deferred.notify(response, limit, offset);\n\t if (response.length !== limit) {\n\t self.allFetched = true;\n\t deferred.resolve(response, limit, offset);\n\t } else {\n\t _recursivelyFetch(offset + limit);\n\t }\n\t });\n\t });\n\t }\n\t _recursivelyFetch();\n\t return deferred;\n\t },\n\t\n\t /** does some bit of JSON represent something that can be copied into this contents collection */\n\t isCopyable: function (contentsJSON) {\n\t var copyableModelClasses = ['HistoryDatasetAssociation', 'HistoryDatasetCollectionAssociation'];\n\t return _.isObject(contentsJSON) && contentsJSON.id && _.contains(copyableModelClasses, contentsJSON.model_class);\n\t },\n\t\n\t /** copy an existing, accessible hda into this collection */\n\t copy: function (json) {\n\t // TODO: somehow showhorn all this into 'save'\n\t var id, type, contentType;\n\t if (_.isString(json)) {\n\t id = json;\n\t contentType = 'hda';\n\t type = 'dataset';\n\t } else {\n\t id = json.id;\n\t contentType = {\n\t 'HistoryDatasetAssociation': 'hda',\n\t 'LibraryDatasetDatasetAssociation': 'ldda',\n\t 'HistoryDatasetCollectionAssociation': 'hdca'\n\t }[json.model_class] || 'hda';\n\t type = contentType === 'hdca' ? 'dataset_collection' : 'dataset';\n\t }\n\t var collection = this,\n\t xhr = jQuery.ajax(this.url(), {\n\t method: 'POST',\n\t contentType: 'application/json',\n\t data: JSON.stringify({\n\t content: id,\n\t source: contentType,\n\t type: type\n\t })\n\t }).done(function (response) {\n\t collection.add([response], { parse: true });\n\t }).fail(function (error, status, message) {\n\t collection.trigger('error', collection, xhr, {}, 'Error copying contents', { type: type, id: id, source: contentType });\n\t });\n\t return xhr;\n\t },\n\t\n\t /** create a new HDCA in this collection */\n\t createHDCA: function (elementIdentifiers, collectionType, name, hideSourceItems, options) {\n\t // normally collection.create returns the new model, but we need the promise from the ajax, so we fake create\n\t //precondition: elementIdentifiers is an array of plain js objects\n\t // in the proper form to create the collectionType\n\t var hdca = this.model({\n\t history_content_type: 'dataset_collection',\n\t collection_type: collectionType,\n\t history_id: this.historyId,\n\t name: name,\n\t hide_source_items: hideSourceItems || false,\n\t // should probably be able to just send in a bunch of json here and restruct per class\n\t // note: element_identifiers is now (incorrectly) an attribute\n\t element_identifiers: elementIdentifiers\n\t // do not create the model on the client until the ajax returns\n\t });\n\t return hdca.save(options);\n\t },\n\t\n\t // ........................................................................ searching\n\t /** return true if all contents have the searchable attributes */\n\t haveSearchDetails: function () {\n\t return this.allFetched && this.all(function (content) {\n\t // null (which is a valid returned annotation value)\n\t // will return false when using content.has( 'annotation' )\n\t //TODO: a bit hacky - formalize\n\t return _.has(content.attributes, 'annotation');\n\t });\n\t },\n\t\n\t /** return a new collection of contents whose attributes contain the substring matchesWhat */\n\t matches: function (matchesWhat) {\n\t return this.filter(function (content) {\n\t return content.matches(matchesWhat);\n\t });\n\t },\n\t\n\t // ........................................................................ misc\n\t /** In this override, copy the historyId to the clone */\n\t clone: function () {\n\t var clone = Backbone.Collection.prototype.clone.call(this);\n\t clone.historyId = this.historyId;\n\t return clone;\n\t },\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return ['HistoryContents(', [this.historyId, this.length].join(), ')'].join('');\n\t }\n\t });\n\t\n\t //==============================================================================\n\t return {\n\t HistoryContents: HistoryContents\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3)))\n\n/***/ }),\n/* 46 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(6)], __WEBPACK_AMD_DEFINE_RESULT__ = function (BASE_MVC) {\n\t\n\t 'use strict';\n\t\n\t var logNamespace = 'history';\n\t\n\t // ============================================================================\n\t /** session storage for individual history preferences */\n\t var HistoryPrefs = BASE_MVC.SessionStorageModel.extend(\n\t /** @lends HistoryPrefs.prototype */{\n\t //TODO:?? move to user prefs?\n\t defaults: {\n\t //TODO:?? expandedIds to array?\n\t expandedIds: {},\n\t show_deleted: false,\n\t show_hidden: false\n\t },\n\t\n\t /** add an hda id to the hash of expanded hdas */\n\t addExpanded: function (model) {\n\t //TODO: use type_id and not model\n\t var current = this.get('expandedIds');\n\t current[model.id] = model.get('id');\n\t this.save('expandedIds', current);\n\t },\n\t\n\t /** remove an hda id from the hash of expanded hdas */\n\t removeExpanded: function (model) {\n\t var current = this.get('expandedIds');\n\t delete current[model.id];\n\t this.save('expandedIds', current);\n\t },\n\t\n\t isExpanded: function (contentId) {\n\t return _.result(this.get('expandedIds'), contentId, false);\n\t },\n\t\n\t allExpanded: function () {\n\t return _.values(this.get('expandedIds'));\n\t },\n\t\n\t clearExpanded: function () {\n\t this.set('expandedIds', {});\n\t },\n\t\n\t includeDeleted: function (val) {\n\t // moving the invocation here so other components don't need to know the key\n\t // TODO: change this key later\n\t if (!_.isUndefined(val)) {\n\t this.set('show_deleted', val);\n\t }\n\t return this.get('show_deleted');\n\t },\n\t\n\t includeHidden: function (val) {\n\t // TODO: change this key later\n\t if (!_.isUndefined(val)) {\n\t this.set('show_hidden', val);\n\t }\n\t return this.get('show_hidden');\n\t },\n\t\n\t toString: function () {\n\t return 'HistoryPrefs(' + this.id + ')';\n\t }\n\t\n\t }, {\n\t // ........................................................................ class vars\n\t // class lvl for access w/o instantiation\n\t storageKeyPrefix: 'history:',\n\t\n\t /** key string to store each histories settings under */\n\t historyStorageKey: function historyStorageKey(historyId) {\n\t if (!historyId) {\n\t throw new Error('HistoryPrefs.historyStorageKey needs valid id: ' + historyId);\n\t }\n\t // single point of change\n\t return HistoryPrefs.storageKeyPrefix + historyId;\n\t },\n\t\n\t /** return the existing storage for the history with the given id (or create one if it doesn't exist) */\n\t get: function get(historyId) {\n\t return new HistoryPrefs({ id: HistoryPrefs.historyStorageKey(historyId) });\n\t },\n\t\n\t /** clear all history related items in sessionStorage */\n\t clearAll: function clearAll(historyId) {\n\t for (var key in sessionStorage) {\n\t if (key.indexOf(HistoryPrefs.storageKeyPrefix) === 0) {\n\t sessionStorage.removeItem(key);\n\t }\n\t }\n\t }\n\t });\n\t\n\t //==============================================================================\n\t return {\n\t HistoryPrefs: HistoryPrefs\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2)))\n\n/***/ }),\n/* 47 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _, jQuery) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (BASE_MVC, _l) {\n\t\n\t 'use strict';\n\t\n\t var logNamespace = 'list';\n\t //==============================================================================\n\t /** A view which, when first rendered, shows only summary data/attributes, but\n\t * can be expanded to show further details (and optionally fetch those\n\t * details from the server).\n\t */\n\t var ExpandableView = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({\n\t _logNamespace: logNamespace,\n\t\n\t //TODO: Although the reasoning behind them is different, this shares a lot with HiddenUntilActivated above: combine them\n\t //PRECONDITION: model must have method hasDetails\n\t //PRECONDITION: subclasses must have templates.el and templates.details\n\t\n\t initialize: function (attributes) {\n\t /** are the details of this view expanded/shown or not? */\n\t this.expanded = attributes.expanded || false;\n\t this.log('\\t expanded:', this.expanded);\n\t this.fxSpeed = attributes.fxSpeed !== undefined ? attributes.fxSpeed : this.fxSpeed;\n\t },\n\t\n\t // ........................................................................ render main\n\t /** jq fx speed */\n\t fxSpeed: 'fast',\n\t\n\t /** Render this content, set up ui.\n\t * @param {Number or String} speed the speed of the render\n\t */\n\t render: function (speed) {\n\t var $newRender = this._buildNewRender();\n\t this._setUpBehaviors($newRender);\n\t this._queueNewRender($newRender, speed);\n\t return this;\n\t },\n\t\n\t /** Build a temp div containing the new children for the view's $el.\n\t * If the view is already expanded, build the details as well.\n\t */\n\t _buildNewRender: function () {\n\t // create a new render using a skeleton template, render title buttons, render body, and set up events, etc.\n\t var $newRender = $(this.templates.el(this.model.toJSON(), this));\n\t if (this.expanded) {\n\t this.$details($newRender).replaceWith(this._renderDetails().show());\n\t }\n\t return $newRender;\n\t },\n\t\n\t /** Fade out the old el, swap in the new contents, then fade in.\n\t * @param {Number or String} speed jq speed to use for rendering effects\n\t * @fires rendered when rendered\n\t */\n\t _queueNewRender: function ($newRender, speed) {\n\t speed = speed === undefined ? this.fxSpeed : speed;\n\t var view = this;\n\t\n\t if (speed === 0) {\n\t view._swapNewRender($newRender);\n\t view.trigger('rendered', view);\n\t } else {\n\t $(view).queue('fx', [function (next) {\n\t view.$el.fadeOut(speed, next);\n\t }, function (next) {\n\t view._swapNewRender($newRender);\n\t next();\n\t }, function (next) {\n\t view.$el.fadeIn(speed, next);\n\t }, function (next) {\n\t view.trigger('rendered', view);\n\t next();\n\t }]);\n\t }\n\t },\n\t\n\t /** empty out the current el, move the $newRender's children in */\n\t _swapNewRender: function ($newRender) {\n\t return this.$el.empty().attr('class', _.isFunction(this.className) ? this.className() : this.className).append($newRender.children());\n\t },\n\t\n\t /** set up js behaviors, event handlers for elements within the given container\n\t * @param {jQuery} $container jq object that contains the elements to process (defaults to this.$el)\n\t */\n\t _setUpBehaviors: function ($where) {\n\t $where = $where || this.$el;\n\t // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.)\n\t //make_popup_menus( $where );\n\t $where.find('[title]').tooltip({ placement: 'bottom' });\n\t },\n\t\n\t // ......................................................................... details\n\t /** shortcut to details DOM (as jQ) */\n\t $details: function ($where) {\n\t $where = $where || this.$el;\n\t return $where.find('> .details');\n\t },\n\t\n\t /** build the DOM for the details and set up behaviors on it */\n\t _renderDetails: function () {\n\t var $newDetails = $(this.templates.details(this.model.toJSON(), this));\n\t this._setUpBehaviors($newDetails);\n\t return $newDetails;\n\t },\n\t\n\t // ......................................................................... expansion/details\n\t /** Show or hide the details\n\t * @param {Boolean} expand if true, expand; if false, collapse\n\t */\n\t toggleExpanded: function (expand) {\n\t expand = expand === undefined ? !this.expanded : expand;\n\t if (expand) {\n\t this.expand();\n\t } else {\n\t this.collapse();\n\t }\n\t return this;\n\t },\n\t\n\t /** Render and show the full, detailed body of this view including extra data and controls.\n\t * note: if the model does not have detailed data, fetch that data before showing the body\n\t * @fires expanded when a body has been expanded\n\t */\n\t expand: function () {\n\t var view = this;\n\t return view._fetchModelDetails().always(function () {\n\t view._expand();\n\t });\n\t },\n\t\n\t /** Check for model details and, if none, fetch them.\n\t * @returns {jQuery.promise} the model.fetch.xhr if details are being fetched, an empty promise if not\n\t */\n\t _fetchModelDetails: function () {\n\t if (!this.model.hasDetails()) {\n\t return this.model.fetch();\n\t }\n\t return jQuery.when();\n\t },\n\t\n\t /** Inner fn called when expand (public) has fetched the details */\n\t _expand: function () {\n\t var view = this,\n\t $newDetails = view._renderDetails();\n\t view.$details().replaceWith($newDetails);\n\t // needs to be set after the above or the slide will not show\n\t view.expanded = true;\n\t view.$details().slideDown(view.fxSpeed, function () {\n\t view.trigger('expanded', view);\n\t });\n\t },\n\t\n\t /** Hide the body/details of an HDA.\n\t * @fires collapsed when a body has been collapsed\n\t */\n\t collapse: function () {\n\t this.debug(this + '(ExpandableView).collapse');\n\t var view = this;\n\t view.expanded = false;\n\t this.$details().slideUp(view.fxSpeed, function () {\n\t view.trigger('collapsed', view);\n\t });\n\t }\n\t\n\t });\n\t\n\t //==============================================================================\n\t /** A view that is displayed in some larger list/grid/collection.\n\t * Inherits from Expandable, Selectable, Draggable.\n\t * The DOM contains warnings, a title bar, and a series of primary action controls.\n\t * Primary actions are meant to be easily accessible item functions (such as delete)\n\t * that are rendered in the title bar.\n\t *\n\t * Details are rendered when the user clicks the title bar or presses enter/space when\n\t * the title bar is in focus.\n\t *\n\t * Designed as a base class for history panel contents - but usable elsewhere (I hope).\n\t */\n\t var ListItemView = ExpandableView.extend(BASE_MVC.mixin(BASE_MVC.SelectableViewMixin, BASE_MVC.DraggableViewMixin, {\n\t\n\t tagName: 'div',\n\t className: 'list-item',\n\t\n\t /** Set up the base class and all mixins */\n\t initialize: function (attributes) {\n\t ExpandableView.prototype.initialize.call(this, attributes);\n\t BASE_MVC.SelectableViewMixin.initialize.call(this, attributes);\n\t BASE_MVC.DraggableViewMixin.initialize.call(this, attributes);\n\t this._setUpListeners();\n\t },\n\t\n\t /** event listeners */\n\t _setUpListeners: function () {\n\t // hide the primary actions in the title bar when selectable and narrow\n\t this.on('selectable', function (isSelectable) {\n\t if (isSelectable) {\n\t this.$('.primary-actions').hide();\n\t } else {\n\t this.$('.primary-actions').show();\n\t }\n\t }, this);\n\t return this;\n\t },\n\t\n\t // ........................................................................ rendering\n\t /** In this override, call methods to build warnings, titlebar and primary actions */\n\t _buildNewRender: function () {\n\t var $newRender = ExpandableView.prototype._buildNewRender.call(this);\n\t $newRender.children('.warnings').replaceWith(this._renderWarnings());\n\t $newRender.children('.title-bar').replaceWith(this._renderTitleBar());\n\t $newRender.children('.primary-actions').append(this._renderPrimaryActions());\n\t $newRender.find('> .title-bar .subtitle').replaceWith(this._renderSubtitle());\n\t return $newRender;\n\t },\n\t\n\t /** In this override, render the selector controls and set up dragging before the swap */\n\t _swapNewRender: function ($newRender) {\n\t ExpandableView.prototype._swapNewRender.call(this, $newRender);\n\t if (this.selectable) {\n\t this.showSelector(0);\n\t }\n\t if (this.draggable) {\n\t this.draggableOn();\n\t }\n\t return this.$el;\n\t },\n\t\n\t /** Render any warnings the item may need to show (e.g. \"I'm deleted\") */\n\t _renderWarnings: function () {\n\t var view = this,\n\t $warnings = $(''),\n\t json = view.model.toJSON();\n\t //TODO:! unordered (map)\n\t _.each(view.templates.warnings, function (templateFn) {\n\t $warnings.append($(templateFn(json, view)));\n\t });\n\t return $warnings;\n\t },\n\t\n\t /** Render the title bar (the main/exposed SUMMARY dom element) */\n\t _renderTitleBar: function () {\n\t return $(this.templates.titleBar(this.model.toJSON(), this));\n\t },\n\t\n\t /** Return an array of jQ objects containing common/easily-accessible item controls */\n\t _renderPrimaryActions: function () {\n\t // override this\n\t return [];\n\t },\n\t\n\t /** Render the title bar (the main/exposed SUMMARY dom element) */\n\t _renderSubtitle: function () {\n\t return $(this.templates.subtitle(this.model.toJSON(), this));\n\t },\n\t\n\t // ......................................................................... events\n\t /** event map */\n\t events: {\n\t // expand the body when the title is clicked or when in focus and space or enter is pressed\n\t 'click .title-bar': '_clickTitleBar',\n\t 'keydown .title-bar': '_keyDownTitleBar',\n\t 'click .selector': 'toggleSelect'\n\t },\n\t\n\t /** expand when the title bar is clicked */\n\t _clickTitleBar: function (event) {\n\t event.stopPropagation();\n\t if (event.altKey) {\n\t this.toggleSelect(event);\n\t if (!this.selectable) {\n\t this.showSelector();\n\t }\n\t } else {\n\t this.toggleExpanded();\n\t }\n\t },\n\t\n\t /** expand when the title bar is in focus and enter or space is pressed */\n\t _keyDownTitleBar: function (event) {\n\t // bail (with propagation) if keydown and not space or enter\n\t var KEYCODE_SPACE = 32,\n\t KEYCODE_RETURN = 13;\n\t if (event && event.type === 'keydown' && (event.keyCode === KEYCODE_SPACE || event.keyCode === KEYCODE_RETURN)) {\n\t this.toggleExpanded();\n\t event.stopPropagation();\n\t return false;\n\t }\n\t return true;\n\t },\n\t\n\t // ......................................................................... misc\n\t /** String representation */\n\t toString: function () {\n\t var modelString = this.model ? this.model + '' : '(no model)';\n\t return 'ListItemView(' + modelString + ')';\n\t }\n\t }));\n\t\n\t // ............................................................................ TEMPLATES\n\t /** underscore templates */\n\t ListItemView.prototype.templates = function () {\n\t\n\t var elTemplato = BASE_MVC.wrapTemplate(['
',\n\t // space for title bar buttons - gen. floated to the right\n\t '', '',\n\t\n\t // expandable area for more details\n\t '', '
']);\n\t\n\t var warnings = {};\n\t\n\t var titleBarTemplate = BASE_MVC.wrapTemplate([\n\t // adding a tabindex here allows focusing the title bar and the use of keydown to expand the dataset display\n\t '
',\n\t //TODO: prob. belongs in dataset-list-item\n\t '', '
', '<%- element.name %>', '
', '', '
'], 'element');\n\t\n\t var subtitleTemplate = BASE_MVC.wrapTemplate([\n\t // override this\n\t '']);\n\t\n\t var detailsTemplate = BASE_MVC.wrapTemplate([\n\t // override this\n\t '']);\n\t\n\t return {\n\t el: elTemplato,\n\t warnings: warnings,\n\t titleBar: titleBarTemplate,\n\t subtitle: subtitleTemplate,\n\t details: detailsTemplate\n\t };\n\t }();\n\t\n\t //==============================================================================\n\t /** A view that is displayed in some larger list/grid/collection.\n\t * *AND* can display some sub-list of it's own when expanded (e.g. dataset collections).\n\t * This list will 'foldout' when the item is expanded depending on this.foldoutStyle:\n\t * If 'foldout': will expand vertically to show the nested list\n\t * If 'drilldown': will overlay the parent list\n\t *\n\t * Inherits from ListItemView.\n\t *\n\t * _renderDetails does the work of creating this.details: a sub-view that shows the nested list\n\t */\n\t var FoldoutListItemView = ListItemView.extend({\n\t\n\t /** If 'foldout': show the sub-panel inside the expanded item\n\t * If 'drilldown': only fire events and handle by pub-sub\n\t * (allow the panel containing this item to attach it, hide itself, etc.)\n\t */\n\t foldoutStyle: 'foldout',\n\t /** Panel view class to instantiate for the sub-panel */\n\t foldoutPanelClass: null,\n\t\n\t /** override to:\n\t * add attributes foldoutStyle and foldoutPanelClass for config poly\n\t * disrespect attributes.expanded if drilldown\n\t */\n\t initialize: function (attributes) {\n\t if (this.foldoutStyle === 'drilldown') {\n\t this.expanded = false;\n\t }\n\t this.foldoutStyle = attributes.foldoutStyle || this.foldoutStyle;\n\t this.foldoutPanelClass = attributes.foldoutPanelClass || this.foldoutPanelClass;\n\t\n\t ListItemView.prototype.initialize.call(this, attributes);\n\t this.foldout = this._createFoldoutPanel();\n\t },\n\t\n\t /** in this override, attach the foldout panel when rendering details */\n\t _renderDetails: function () {\n\t if (this.foldoutStyle === 'drilldown') {\n\t return $();\n\t }\n\t var $newDetails = ListItemView.prototype._renderDetails.call(this);\n\t return this._attachFoldout(this.foldout, $newDetails);\n\t },\n\t\n\t /** In this override, handle collection expansion. */\n\t _createFoldoutPanel: function () {\n\t var model = this.model;\n\t var FoldoutClass = this._getFoldoutPanelClass(model),\n\t options = this._getFoldoutPanelOptions(model),\n\t foldout = new FoldoutClass(_.extend(options, {\n\t model: model\n\t }));\n\t return foldout;\n\t },\n\t\n\t /** Stub to return proper foldout panel class */\n\t _getFoldoutPanelClass: function () {\n\t // override\n\t return this.foldoutPanelClass;\n\t },\n\t\n\t /** Stub to return proper foldout panel options */\n\t _getFoldoutPanelOptions: function () {\n\t return {\n\t // propagate foldout style down\n\t foldoutStyle: this.foldoutStyle,\n\t fxSpeed: this.fxSpeed\n\t };\n\t },\n\t\n\t /** Render the foldout panel inside the view, hiding controls */\n\t _attachFoldout: function (foldout, $whereTo) {\n\t $whereTo = $whereTo || this.$('> .details');\n\t this.foldout = foldout.render(0);\n\t foldout.$('> .controls').hide();\n\t return $whereTo.append(foldout.$el);\n\t },\n\t\n\t /** In this override, branch on foldoutStyle to show expanded */\n\t expand: function () {\n\t var view = this;\n\t return view._fetchModelDetails().always(function () {\n\t if (view.foldoutStyle === 'foldout') {\n\t view._expand();\n\t } else if (view.foldoutStyle === 'drilldown') {\n\t view._expandByDrilldown();\n\t }\n\t });\n\t },\n\t\n\t /** For drilldown, set up close handler and fire expanded:drilldown\n\t * containing views can listen to this and handle other things\n\t * (like hiding themselves) by listening for expanded/collapsed:drilldown\n\t */\n\t _expandByDrilldown: function () {\n\t var view = this;\n\t // attachment and rendering done by listener\n\t view.listenTo(view.foldout, 'close', function () {\n\t view.trigger('collapsed:drilldown', view, view.foldout);\n\t });\n\t view.trigger('expanded:drilldown', view, view.foldout);\n\t }\n\t\n\t });\n\t\n\t // ............................................................................ TEMPLATES\n\t /** underscore templates */\n\t FoldoutListItemView.prototype.templates = function () {\n\t\n\t var detailsTemplate = BASE_MVC.wrapTemplate(['
',\n\t // override with more info (that goes above the panel)\n\t '
'], 'collection');\n\t\n\t return _.extend({}, ListItemView.prototype.templates, {\n\t details: detailsTemplate\n\t });\n\t }();\n\t\n\t //==============================================================================\n\t return {\n\t ExpandableView: ExpandableView,\n\t ListItemView: ListItemView,\n\t FoldoutListItemView: FoldoutListItemView\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ }),\n/* 48 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (baseMVC, _l) {\n\t // =============================================================================\n\t /** A view on any model that has a 'tags' attribute (a list of tag strings)\n\t * Incorporates the select2 jQuery plugin for tags display/editing:\n\t * http://ivaynberg.github.io/select2/\n\t */\n\t var TagsEditor = Backbone.View.extend(baseMVC.LoggableMixin).extend(baseMVC.HiddenUntilActivatedViewMixin).extend({\n\t\n\t tagName: 'div',\n\t className: 'tags-display',\n\t\n\t /** Set up listeners, parse options */\n\t initialize: function (options) {\n\t //console.debug( this, options );\n\t // only listen to the model only for changes to tags - re-render\n\t if (options.usePrompt === false) {\n\t this.label = '';\n\t } else {\n\t this.label = '';\n\t }\n\t this.hiddenUntilActivated(options.$activator, options);\n\t },\n\t\n\t /** Build the DOM elements, call select to on the created input, and set up behaviors */\n\t render: function () {\n\t var self = this;\n\t this.$el.html(this._template());\n\t\n\t this.$input().select2({\n\t placeholder: 'Add tags',\n\t width: '100%',\n\t tags: function () {\n\t // initialize possible tags in the dropdown based on all the tags the user has used so far\n\t return self._getTagsUsed();\n\t }\n\t });\n\t\n\t this._setUpBehaviors();\n\t return this;\n\t },\n\t\n\t _hashToName: function (tag) {\n\t if (tag.startsWith('#')) {\n\t return 'name:' + tag.slice(1);\n\t }\n\t return tag;\n\t },\n\t\n\t _nameToHash: function (tag) {\n\t if (tag.startsWith('name:')) {\n\t tag = '#' + tag.slice(5);\n\t }\n\t return tag;\n\t },\n\t\n\t /** @returns {String} the html text used to build the view's DOM */\n\t _template: function () {\n\t return [this.label,\n\t // set up initial tags by adding as CSV to input vals (necc. to init select2)\n\t ''].join('');\n\t },\n\t\n\t /** @returns {String} the sorted, comma-separated tags from the model */\n\t tagsToCSV: function () {\n\t var self = this;\n\t var tagsArray = this.model.get('tags');\n\t if (!_.isArray(tagsArray) || _.isEmpty(tagsArray)) {\n\t return '';\n\t }\n\t return tagsArray.map(function (tag) {\n\t return _.escape(self._nameToHash(tag));\n\t }).sort().join(',');\n\t },\n\t\n\t /** @returns {jQuery} the input for this view */\n\t $input: function () {\n\t return this.$el.find('input.tags-input');\n\t },\n\t\n\t /** @returns {String[]} all tags used by the current user */\n\t _getTagsUsed: function () {\n\t //TODO: global\n\t var self = this;\n\t return _.map(Galaxy.user.get('tags_used'), self._nameToHash);\n\t },\n\t\n\t /** set up any event listeners on the view's DOM (mostly handled by select2) */\n\t _setUpBehaviors: function () {\n\t var self = this;\n\t this.$input().on('change', function (event) {\n\t // Modify any 'hashtag' 'nametags'\n\t event.val = _.map(event.val, self._hashToName);\n\t // save the model's tags in either remove or added event\n\t self.model.save({ tags: event.val });\n\t // if it's new, add the tag to the users tags\n\t if (event.added) {\n\t //??: solve weird behavior in FF on test.galaxyproject.org where\n\t // event.added.text is string object: 'String{ 0=\"o\", 1=\"n\", 2=\"e\" }'\n\t self._addNewTagToTagsUsed(event.added.text + '');\n\t }\n\t });\n\t },\n\t\n\t /** add a new tag (if not already there) to the list of all tags used by the user\n\t * @param {String} newTag the tag to add to the list of used\n\t */\n\t _addNewTagToTagsUsed: function (newTag) {\n\t //TODO: global\n\t var tagsUsed = Galaxy.user.get('tags_used');\n\t if (!_.contains(tagsUsed, newTag)) {\n\t tagsUsed.push(newTag);\n\t tagsUsed.sort();\n\t Galaxy.user.set('tags_used', tagsUsed);\n\t }\n\t },\n\t\n\t /** shut down event listeners and remove this view's DOM */\n\t remove: function () {\n\t this.$input.off();\n\t this.stopListening(this.model);\n\t Backbone.View.prototype.remove.call(this);\n\t },\n\t\n\t /** string rep */\n\t toString: function () {\n\t return ['TagsEditor(', this.model + '', ')'].join('');\n\t }\n\t });\n\t\n\t // =============================================================================\n\t return {\n\t TagsEditor: TagsEditor\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2)))\n\n/***/ }),\n/* 49 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function($, _) {/**\n\t This is the base class of the tool form plugin. This class is e.g. inherited by the regular and the workflow tool form.\n\t*/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(61), __webpack_require__(7), __webpack_require__(20), __webpack_require__(19), __webpack_require__(34)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Deferred, Ui, FormBase, CitationModel, CitationView) {\n\t return FormBase.extend({\n\t initialize: function (options) {\n\t var self = this;\n\t this.deferred = new Deferred();\n\t FormBase.prototype.initialize.call(this, options);\n\t if (this.model.get('inputs')) {\n\t this._buildForm(this.model.attributes);\n\t } else {\n\t this.deferred.execute(function (process) {\n\t self._buildModel(process, self.model.attributes, true);\n\t });\n\t }\n\t // listen to history panel\n\t if (this.model.get('listen_to_history') && parent.Galaxy && parent.Galaxy.currHistoryPanel) {\n\t this.listenTo(parent.Galaxy.currHistoryPanel.collection, 'change', function () {\n\t self.model.get('onchange')();\n\t });\n\t }\n\t // destroy dom elements\n\t this.$el.on('remove', function () {\n\t self.remove();\n\t });\n\t },\n\t\n\t /** Wait for deferred build processes before removal */\n\t remove: function () {\n\t var self = this;\n\t this.$el.hide();\n\t this.deferred.execute(function () {\n\t FormBase.prototype.remove.call(self);\n\t Galaxy.emit.debug('tool-form-base::remove()', 'Destroy view.');\n\t });\n\t },\n\t\n\t /** Build form */\n\t _buildForm: function (options) {\n\t var self = this;\n\t this.model.set(options);\n\t this.model.set({\n\t title: options.title || '' + options.name + ' ' + options.description + ' (Galaxy Version ' + options.version + ')',\n\t operations: !this.model.get('hide_operations') && this._operations(),\n\t onchange: function () {\n\t self.deferred.reset();\n\t self.deferred.execute(function (process) {\n\t self.model.get('postchange')(process, self);\n\t });\n\t }\n\t });\n\t this.model.get('customize') && this.model.get('customize')(this);\n\t this.render();\n\t if (!this.model.get('collapsible')) {\n\t this.$el.append($('').addClass('ui-margin-top-large').append(this._footer()));\n\t }\n\t },\n\t\n\t /** Builds a new model through api call and recreates the entire form */\n\t _buildModel: function (process, new_options, hide_message) {\n\t var self = this;\n\t var options = this.model.attributes;\n\t options.version = new_options.version;\n\t options.id = new_options.id;\n\t\n\t // build request url\n\t var build_url = '';\n\t var build_data = {};\n\t if (options.job_id) {\n\t build_url = Galaxy.root + 'api/jobs/' + options.job_id + '/build_for_rerun';\n\t } else {\n\t build_url = Galaxy.root + 'api/tools/' + options.id + '/build';\n\t if (Galaxy.params && Galaxy.params.tool_id == options.id) {\n\t build_data = $.extend({}, Galaxy.params);\n\t options.version && (build_data['tool_version'] = options.version);\n\t }\n\t }\n\t\n\t // get initial model\n\t Utils.get({\n\t url: build_url,\n\t data: build_data,\n\t success: function (data) {\n\t if (!data.display) {\n\t window.location = Galaxy.root;\n\t return;\n\t }\n\t self._buildForm(data);\n\t !hide_message && self.message.update({\n\t status: 'success',\n\t message: 'Now you are using \\'' + options.name + '\\' version ' + options.version + ', id \\'' + options.id + '\\'.',\n\t persistent: false\n\t });\n\t Galaxy.emit.debug('tool-form-base::_buildModel()', 'Initial tool model ready.', data);\n\t process.resolve();\n\t },\n\t error: function (response, status) {\n\t var error_message = response && response.err_msg || 'Uncaught error.';\n\t if (status == 401) {\n\t window.location = Galaxy.root + 'user/login?' + $.param({ redirect: Galaxy.root + '?tool_id=' + options.id });\n\t } else if (self.$el.is(':empty')) {\n\t self.$el.prepend(new Ui.Message({\n\t message: error_message,\n\t status: 'danger',\n\t persistent: true,\n\t large: true\n\t }).$el);\n\t } else {\n\t Galaxy.modal && Galaxy.modal.show({\n\t title: 'Tool request failed',\n\t body: error_message,\n\t buttons: {\n\t 'Close': function () {\n\t Galaxy.modal.hide();\n\t }\n\t }\n\t });\n\t }\n\t Galaxy.emit.debug('tool-form-base::_buildModel()', 'Initial tool model request failed.', response);\n\t process.reject();\n\t }\n\t });\n\t },\n\t\n\t /** Create tool operation menu */\n\t _operations: function () {\n\t var self = this;\n\t var options = this.model.attributes;\n\t\n\t // button for version selection\n\t var versions_button = new Ui.ButtonMenu({\n\t icon: 'fa-cubes',\n\t title: !options.narrow && 'Versions' || null,\n\t tooltip: 'Select another tool version'\n\t });\n\t if (!options.sustain_version && options.versions && options.versions.length > 1) {\n\t for (var i in options.versions) {\n\t var version = options.versions[i];\n\t if (version != options.version) {\n\t versions_button.addMenu({\n\t title: 'Switch to ' + version,\n\t version: version,\n\t icon: 'fa-cube',\n\t onclick: function () {\n\t // here we update the tool version (some tools encode the version also in the id)\n\t var id = options.id.replace(options.version, this.version);\n\t var version = this.version;\n\t // queue model request\n\t self.deferred.reset();\n\t self.deferred.execute(function (process) {\n\t self._buildModel(process, { id: id, version: version });\n\t });\n\t }\n\t });\n\t }\n\t }\n\t } else {\n\t versions_button.$el.hide();\n\t }\n\t\n\t // button for options e.g. search, help\n\t var menu_button = new Ui.ButtonMenu({\n\t icon: 'fa-caret-down',\n\t title: !options.narrow && 'Options' || null,\n\t tooltip: 'View available options'\n\t });\n\t if (options.biostar_url) {\n\t menu_button.addMenu({\n\t icon: 'fa-question-circle',\n\t title: 'Question?',\n\t onclick: function () {\n\t window.open(options.biostar_url + '/p/new/post/');\n\t }\n\t });\n\t menu_button.addMenu({\n\t icon: 'fa-search',\n\t title: 'Search',\n\t onclick: function () {\n\t window.open(options.biostar_url + '/local/search/page/?q=' + options.name);\n\t }\n\t });\n\t };\n\t menu_button.addMenu({\n\t icon: 'fa-share',\n\t title: 'Share',\n\t onclick: function () {\n\t prompt('Copy to clipboard: Ctrl+C, Enter', window.location.origin + Galaxy.root + 'root?tool_id=' + options.id);\n\t }\n\t });\n\t\n\t // add admin operations\n\t if (Galaxy.user && Galaxy.user.get('is_admin')) {\n\t menu_button.addMenu({\n\t icon: 'fa-download',\n\t title: 'Download',\n\t onclick: function () {\n\t window.location.href = Galaxy.root + 'api/tools/' + options.id + '/download';\n\t }\n\t });\n\t menu_button.addMenu({\n\t icon: 'fa-refresh',\n\t title: 'Reload XML',\n\t onclick: function () {\n\t Utils.get({\n\t url: Galaxy.root + 'api/tools/' + options.id + '/reload',\n\t success: function (response) {\n\t self.message.update({ persistent: false, message: 'Tool XML has been reloaded.', status: 'success' });\n\t },\n\t error: function (response) {\n\t self.message.update({ persistent: false, message: response.err_msg, status: 'danger' });\n\t }\n\t });\n\t }\n\t });\n\t }\n\t\n\t // button for version selection\n\t if (options.requirements && options.requirements.length > 0) {\n\t menu_button.addMenu({\n\t icon: 'fa-info-circle',\n\t title: 'Requirements',\n\t onclick: function () {\n\t if (!this.requirements_visible || self.portlet.collapsed) {\n\t this.requirements_visible = true;\n\t self.portlet.expand();\n\t self.message.update({ persistent: true, message: self._templateRequirements(options), status: 'info' });\n\t } else {\n\t this.requirements_visible = false;\n\t self.message.update({ message: '' });\n\t }\n\t }\n\t });\n\t }\n\t\n\t // add toolshed url\n\t if (options.sharable_url) {\n\t menu_button.addMenu({\n\t icon: 'fa-external-link',\n\t title: 'See in Tool Shed',\n\t onclick: function () {\n\t window.open(options.sharable_url);\n\t }\n\t });\n\t }\n\t\n\t // add tool menu webhooks\n\t $.getJSON('/api/webhooks/tool-menu/all', function (webhooks) {\n\t _.each(webhooks, function (webhook) {\n\t if (webhook.activate && webhook.config.function) {\n\t menu_button.addMenu({\n\t icon: webhook.config.icon,\n\t title: webhook.config.title,\n\t onclick: function () {\n\t var func = new Function('options', webhook.config.function);\n\t func(options);\n\t }\n\t });\n\t }\n\t });\n\t });\n\t\n\t return {\n\t menu: menu_button,\n\t versions: versions_button\n\t };\n\t },\n\t\n\t /** Create footer */\n\t _footer: function () {\n\t var options = this.model.attributes;\n\t var $el = $('').append(this._templateHelp(options));\n\t if (options.citations) {\n\t var $citations = $('');\n\t var citations = new CitationModel.ToolCitationCollection();\n\t citations.tool_id = options.id;\n\t var citation_list_view = new CitationView.CitationListView({ el: $citations, collection: citations });\n\t citation_list_view.render();\n\t citations.fetch();\n\t $el.append($citations);\n\t }\n\t return $el;\n\t },\n\t\n\t /** Templates */\n\t _templateHelp: function (options) {\n\t var $tmpl = $('').addClass('ui-form-help').append(options.help);\n\t $tmpl.find('a').attr('target', '_blank');\n\t return $tmpl;\n\t },\n\t\n\t _templateRequirements: function (options) {\n\t var nreq = options.requirements.length;\n\t if (nreq > 0) {\n\t var requirements_message = 'This tool requires ';\n\t _.each(options.requirements, function (req, i) {\n\t requirements_message += req.name + (req.version ? ' (Version ' + req.version + ')' : '') + (i < nreq - 2 ? ', ' : i == nreq - 2 ? ' and ' : '');\n\t });\n\t var requirements_link = $('').attr('target', '_blank').attr('href', 'https://galaxyproject.org/tools/requirements/').text('here');\n\t return $('').append(requirements_message + '. Click ').append(requirements_link).append(' for more information.');\n\t }\n\t return 'No requirements found.';\n\t }\n\t });\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1), __webpack_require__(2)))\n\n/***/ }),\n/* 50 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {/**\n\t * Model, view, and controller objects for Galaxy tools and tool panel.\n\t */\n\t\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(2), __webpack_require__(18), __webpack_require__(10), __webpack_require__(25)], __WEBPACK_AMD_DEFINE_RESULT__ = function (_, util, data, ToolForm) {\n\t 'use strict';\n\t\n\t /**\n\t * Mixin for tracking model visibility.\n\t */\n\t\n\t var VisibilityMixin = {\n\t hidden: false,\n\t\n\t show: function () {\n\t this.set(\"hidden\", false);\n\t },\n\t\n\t hide: function () {\n\t this.set(\"hidden\", true);\n\t },\n\t\n\t toggle: function () {\n\t this.set(\"hidden\", !this.get(\"hidden\"));\n\t },\n\t\n\t is_visible: function () {\n\t return !this.attributes.hidden;\n\t }\n\t\n\t };\n\t\n\t /**\n\t * A tool parameter.\n\t */\n\t var ToolParameter = Backbone.Model.extend({\n\t defaults: {\n\t name: null,\n\t label: null,\n\t type: null,\n\t value: null,\n\t html: null,\n\t num_samples: 5\n\t },\n\t\n\t initialize: function (options) {\n\t this.attributes.html = unescape(this.attributes.html);\n\t },\n\t\n\t copy: function () {\n\t return new ToolParameter(this.toJSON());\n\t },\n\t\n\t set_value: function (value) {\n\t this.set('value', value || '');\n\t }\n\t });\n\t\n\t var ToolParameterCollection = Backbone.Collection.extend({\n\t model: ToolParameter\n\t });\n\t\n\t /**\n\t * A data tool parameter.\n\t */\n\t var DataToolParameter = ToolParameter.extend({});\n\t\n\t /**\n\t * An integer tool parameter.\n\t */\n\t var IntegerToolParameter = ToolParameter.extend({\n\t set_value: function (value) {\n\t this.set('value', parseInt(value, 10));\n\t },\n\t\n\t /**\n\t * Returns samples from a tool input.\n\t */\n\t get_samples: function () {\n\t return d3.scale.linear().domain([this.get('min'), this.get('max')]).ticks(this.get('num_samples'));\n\t }\n\t });\n\t\n\t var FloatToolParameter = IntegerToolParameter.extend({\n\t set_value: function (value) {\n\t this.set('value', parseFloat(value));\n\t }\n\t });\n\t\n\t /**\n\t * A select tool parameter.\n\t */\n\t var SelectToolParameter = ToolParameter.extend({\n\t /**\n\t * Returns tool options.\n\t */\n\t get_samples: function () {\n\t return _.map(this.get('options'), function (option) {\n\t return option[0];\n\t });\n\t }\n\t });\n\t\n\t // Set up dictionary of parameter types.\n\t ToolParameter.subModelTypes = {\n\t 'integer': IntegerToolParameter,\n\t 'float': FloatToolParameter,\n\t 'data': DataToolParameter,\n\t 'select': SelectToolParameter\n\t };\n\t\n\t /**\n\t * A Galaxy tool.\n\t */\n\t var Tool = Backbone.Model.extend({\n\t // Default attributes.\n\t defaults: {\n\t id: null,\n\t name: null,\n\t description: null,\n\t target: null,\n\t inputs: [],\n\t outputs: []\n\t },\n\t\n\t urlRoot: Galaxy.root + 'api/tools',\n\t\n\t initialize: function (options) {\n\t\n\t // Set parameters.\n\t this.set('inputs', new ToolParameterCollection(_.map(options.inputs, function (p) {\n\t var p_class = ToolParameter.subModelTypes[p.type] || ToolParameter;\n\t return new p_class(p);\n\t })));\n\t },\n\t\n\t /**\n\t *\n\t */\n\t toJSON: function () {\n\t var rval = Backbone.Model.prototype.toJSON.call(this);\n\t\n\t // Convert inputs to JSON manually.\n\t rval.inputs = this.get('inputs').map(function (i) {\n\t return i.toJSON();\n\t });\n\t return rval;\n\t },\n\t\n\t /**\n\t * Removes inputs of a particular type; this is useful because not all inputs can be handled by\n\t * client and server yet.\n\t */\n\t remove_inputs: function (types) {\n\t var tool = this,\n\t incompatible_inputs = tool.get('inputs').filter(function (input) {\n\t return types.indexOf(input.get('type')) !== -1;\n\t });\n\t tool.get('inputs').remove(incompatible_inputs);\n\t },\n\t\n\t /**\n\t * Returns object copy, optionally including only inputs that can be sampled.\n\t */\n\t copy: function (only_samplable_inputs) {\n\t var copy = new Tool(this.toJSON());\n\t\n\t // Return only samplable inputs if flag is set.\n\t if (only_samplable_inputs) {\n\t var valid_inputs = new Backbone.Collection();\n\t copy.get('inputs').each(function (input) {\n\t if (input.get_samples()) {\n\t valid_inputs.push(input);\n\t }\n\t });\n\t copy.set('inputs', valid_inputs);\n\t }\n\t\n\t return copy;\n\t },\n\t\n\t apply_search_results: function (results) {\n\t _.indexOf(results, this.attributes.id) !== -1 ? this.show() : this.hide();\n\t return this.is_visible();\n\t },\n\t\n\t /**\n\t * Set a tool input's value.\n\t */\n\t set_input_value: function (name, value) {\n\t this.get('inputs').find(function (input) {\n\t return input.get('name') === name;\n\t }).set('value', value);\n\t },\n\t\n\t /**\n\t * Set many input values at once.\n\t */\n\t set_input_values: function (inputs_dict) {\n\t var self = this;\n\t _.each(_.keys(inputs_dict), function (input_name) {\n\t self.set_input_value(input_name, inputs_dict[input_name]);\n\t });\n\t },\n\t\n\t /**\n\t * Run tool; returns a Deferred that resolves to the tool's output(s).\n\t */\n\t run: function () {\n\t return this._run();\n\t },\n\t\n\t /**\n\t * Rerun tool using regions and a target dataset.\n\t */\n\t rerun: function (target_dataset, regions) {\n\t return this._run({\n\t action: 'rerun',\n\t target_dataset_id: target_dataset.id,\n\t regions: regions\n\t });\n\t },\n\t\n\t /**\n\t * Returns input dict for tool's inputs.\n\t */\n\t get_inputs_dict: function () {\n\t var input_dict = {};\n\t this.get('inputs').each(function (input) {\n\t input_dict[input.get('name')] = input.get('value');\n\t });\n\t return input_dict;\n\t },\n\t\n\t /**\n\t * Run tool; returns a Deferred that resolves to the tool's output(s).\n\t * NOTE: this method is a helper method and should not be called directly.\n\t */\n\t _run: function (additional_params) {\n\t // Create payload.\n\t var payload = _.extend({\n\t tool_id: this.id,\n\t inputs: this.get_inputs_dict()\n\t }, additional_params);\n\t\n\t // Because job may require indexing datasets, use server-side\n\t // deferred to ensure that job is run. Also use deferred that\n\t // resolves to outputs from tool.\n\t var run_deferred = $.Deferred(),\n\t ss_deferred = new util.ServerStateDeferred({\n\t ajax_settings: {\n\t url: this.urlRoot,\n\t data: JSON.stringify(payload),\n\t dataType: \"json\",\n\t contentType: 'application/json',\n\t type: \"POST\"\n\t },\n\t interval: 2000,\n\t success_fn: function (response) {\n\t return response !== \"pending\";\n\t }\n\t });\n\t\n\t // Run job and resolve run_deferred to tool outputs.\n\t $.when(ss_deferred.go()).then(function (result) {\n\t run_deferred.resolve(new data.DatasetCollection(result));\n\t });\n\t return run_deferred;\n\t }\n\t });\n\t _.extend(Tool.prototype, VisibilityMixin);\n\t\n\t /**\n\t * Tool view.\n\t */\n\t var ToolView = Backbone.View.extend({});\n\t\n\t /**\n\t * Wrap collection of tools for fast access/manipulation.\n\t */\n\t var ToolCollection = Backbone.Collection.extend({\n\t model: Tool\n\t });\n\t\n\t /**\n\t * Label or section header in tool panel.\n\t */\n\t var ToolSectionLabel = Backbone.Model.extend(VisibilityMixin);\n\t\n\t /**\n\t * Section of tool panel with elements (labels and tools).\n\t */\n\t var ToolSection = Backbone.Model.extend({\n\t defaults: {\n\t elems: [],\n\t open: false\n\t },\n\t\n\t clear_search_results: function () {\n\t _.each(this.attributes.elems, function (elt) {\n\t elt.show();\n\t });\n\t\n\t this.show();\n\t this.set(\"open\", false);\n\t },\n\t\n\t apply_search_results: function (results) {\n\t var all_hidden = true,\n\t cur_label;\n\t _.each(this.attributes.elems, function (elt) {\n\t if (elt instanceof ToolSectionLabel) {\n\t cur_label = elt;\n\t cur_label.hide();\n\t } else if (elt instanceof Tool) {\n\t if (elt.apply_search_results(results)) {\n\t all_hidden = false;\n\t if (cur_label) {\n\t cur_label.show();\n\t }\n\t }\n\t }\n\t });\n\t\n\t if (all_hidden) {\n\t this.hide();\n\t } else {\n\t this.show();\n\t this.set(\"open\", true);\n\t }\n\t }\n\t });\n\t _.extend(ToolSection.prototype, VisibilityMixin);\n\t\n\t /**\n\t * Tool search that updates results when query is changed. Result value of null\n\t * indicates that query was not run; if not null, results are from search using\n\t * query.\n\t */\n\t var ToolSearch = Backbone.Model.extend({\n\t defaults: {\n\t search_hint_string: \"search tools\",\n\t min_chars_for_search: 3,\n\t clear_btn_url: \"\",\n\t visible: true,\n\t query: \"\",\n\t results: null,\n\t // ESC (27) will clear the input field and tool search filters\n\t clear_key: 27\n\t },\n\t\n\t urlRoot: Galaxy.root + 'api/tools',\n\t\n\t initialize: function () {\n\t this.on(\"change:query\", this.do_search);\n\t },\n\t\n\t /**\n\t * Do the search and update the results.\n\t */\n\t do_search: function () {\n\t var query = this.attributes.query;\n\t\n\t // If query is too short, do not search.\n\t if (query.length < this.attributes.min_chars_for_search) {\n\t this.set(\"results\", null);\n\t return;\n\t }\n\t\n\t // Do search via AJAX.\n\t var q = query;\n\t // Stop previous ajax-request\n\t if (this.timer) {\n\t clearTimeout(this.timer);\n\t }\n\t // Start a new ajax-request in X ms\n\t $(\"#search-clear-btn\").hide();\n\t $(\"#search-spinner\").show();\n\t var self = this;\n\t this.timer = setTimeout(function () {\n\t // log the search to analytics if present\n\t if (typeof ga !== 'undefined') {\n\t ga('send', 'pageview', Galaxy.root + '?q=' + q);\n\t }\n\t $.get(self.urlRoot, { q: q }, function (data) {\n\t self.set(\"results\", data);\n\t $(\"#search-spinner\").hide();\n\t $(\"#search-clear-btn\").show();\n\t }, \"json\");\n\t }, 400);\n\t },\n\t\n\t clear_search: function () {\n\t this.set(\"query\", \"\");\n\t this.set(\"results\", null);\n\t }\n\t\n\t });\n\t _.extend(ToolSearch.prototype, VisibilityMixin);\n\t\n\t /**\n\t * Tool Panel.\n\t */\n\t var ToolPanel = Backbone.Model.extend({\n\t\n\t initialize: function (options) {\n\t this.attributes.tool_search = options.tool_search;\n\t this.attributes.tool_search.on(\"change:results\", this.apply_search_results, this);\n\t this.attributes.tools = options.tools;\n\t this.attributes.layout = new Backbone.Collection(this.parse(options.layout));\n\t },\n\t\n\t /**\n\t * Parse tool panel dictionary and return collection of tool panel elements.\n\t */\n\t parse: function (response) {\n\t // Recursive function to parse tool panel elements.\n\t var self = this,\n\t\n\t // Helper to recursively parse tool panel.\n\t parse_elt = function (elt_dict) {\n\t var type = elt_dict.model_class;\n\t // There are many types of tools; for now, anything that ends in 'Tool'\n\t // is treated as a generic tool.\n\t if (type.indexOf('Tool') === type.length - 4) {\n\t return self.attributes.tools.get(elt_dict.id);\n\t } else if (type === 'ToolSection') {\n\t // Parse elements.\n\t var elems = _.map(elt_dict.elems, parse_elt);\n\t elt_dict.elems = elems;\n\t return new ToolSection(elt_dict);\n\t } else if (type === 'ToolSectionLabel') {\n\t return new ToolSectionLabel(elt_dict);\n\t }\n\t };\n\t\n\t return _.map(response, parse_elt);\n\t },\n\t\n\t clear_search_results: function () {\n\t this.get('layout').each(function (panel_elt) {\n\t if (panel_elt instanceof ToolSection) {\n\t panel_elt.clear_search_results();\n\t } else {\n\t // Label or tool, so just show.\n\t panel_elt.show();\n\t }\n\t });\n\t },\n\t\n\t apply_search_results: function () {\n\t var results = this.get('tool_search').get('results');\n\t if (results === null) {\n\t this.clear_search_results();\n\t return;\n\t }\n\t\n\t var cur_label = null;\n\t this.get('layout').each(function (panel_elt) {\n\t if (panel_elt instanceof ToolSectionLabel) {\n\t cur_label = panel_elt;\n\t cur_label.hide();\n\t } else if (panel_elt instanceof Tool) {\n\t if (panel_elt.apply_search_results(results)) {\n\t if (cur_label) {\n\t cur_label.show();\n\t }\n\t }\n\t } else {\n\t // Starting new section, so clear current label.\n\t cur_label = null;\n\t panel_elt.apply_search_results(results);\n\t }\n\t });\n\t }\n\t });\n\t\n\t /**\n\t * View classes for Galaxy tools and tool panel.\n\t *\n\t * Views use the templates defined below for rendering. Views update as needed\n\t * based on (a) model/collection events and (b) user interactions; in this sense,\n\t * they are controllers are well and the HTML is the real view in the MVC architecture.\n\t */\n\t\n\t /**\n\t * Base view that handles visibility based on model's hidden attribute.\n\t */\n\t var BaseView = Backbone.View.extend({\n\t initialize: function () {\n\t this.model.on(\"change:hidden\", this.update_visible, this);\n\t this.update_visible();\n\t },\n\t update_visible: function () {\n\t this.model.attributes.hidden ? this.$el.hide() : this.$el.show();\n\t }\n\t });\n\t\n\t /**\n\t * Link to a tool.\n\t */\n\t var ToolLinkView = BaseView.extend({\n\t tagName: 'div',\n\t\n\t render: function () {\n\t // create element\n\t var $link = $('');\n\t $link.append(templates.tool_link(this.model.toJSON()));\n\t\n\t var formStyle = this.model.get('form_style', null);\n\t // open upload dialog for upload tool\n\t if (this.model.id === 'upload1') {\n\t $link.find('a').on('click', function (e) {\n\t e.preventDefault();\n\t Galaxy.upload.show();\n\t });\n\t } else if (formStyle === 'regular') {\n\t // regular tools\n\t var self = this;\n\t $link.find('a').on('click', function (e) {\n\t e.preventDefault();\n\t Galaxy.router.push('/', { tool_id: self.model.id, version: self.model.get('version') });\n\t });\n\t }\n\t\n\t // add element\n\t this.$el.append($link);\n\t return this;\n\t }\n\t });\n\t\n\t /**\n\t * Panel label/section header.\n\t */\n\t var ToolSectionLabelView = BaseView.extend({\n\t tagName: 'div',\n\t className: 'toolPanelLabel',\n\t\n\t render: function () {\n\t this.$el.append($(\"\").text(this.model.attributes.text));\n\t return this;\n\t }\n\t });\n\t\n\t /**\n\t * Panel section.\n\t */\n\t var ToolSectionView = BaseView.extend({\n\t tagName: 'div',\n\t className: 'toolSectionWrapper',\n\t\n\t initialize: function () {\n\t BaseView.prototype.initialize.call(this);\n\t this.model.on(\"change:open\", this.update_open, this);\n\t },\n\t\n\t render: function () {\n\t // Build using template.\n\t this.$el.append(templates.panel_section(this.model.toJSON()));\n\t\n\t // Add tools to section.\n\t var section_body = this.$el.find(\".toolSectionBody\");\n\t _.each(this.model.attributes.elems, function (elt) {\n\t if (elt instanceof Tool) {\n\t var tool_view = new ToolLinkView({ model: elt, className: \"toolTitle\" });\n\t tool_view.render();\n\t section_body.append(tool_view.$el);\n\t } else if (elt instanceof ToolSectionLabel) {\n\t var label_view = new ToolSectionLabelView({ model: elt });\n\t label_view.render();\n\t section_body.append(label_view.$el);\n\t } else {\n\t // TODO: handle nested section bodies?\n\t }\n\t });\n\t return this;\n\t },\n\t\n\t events: {\n\t 'click .toolSectionTitle > a': 'toggle'\n\t },\n\t\n\t /**\n\t * Toggle visibility of tool section.\n\t */\n\t toggle: function () {\n\t this.model.set(\"open\", !this.model.attributes.open);\n\t },\n\t\n\t /**\n\t * Update whether section is open or close.\n\t */\n\t update_open: function () {\n\t this.model.attributes.open ? this.$el.children(\".toolSectionBody\").slideDown(\"fast\") : this.$el.children(\".toolSectionBody\").slideUp(\"fast\");\n\t }\n\t });\n\t\n\t var ToolSearchView = Backbone.View.extend({\n\t tagName: 'div',\n\t id: 'tool-search',\n\t className: 'bar',\n\t\n\t events: {\n\t 'click': 'focus_and_select',\n\t 'keyup :input': 'query_changed',\n\t 'change :input': 'query_changed',\n\t 'click #search-clear-btn': 'clear'\n\t },\n\t\n\t render: function () {\n\t this.$el.append(templates.tool_search(this.model.toJSON()));\n\t if (!this.model.is_visible()) {\n\t this.$el.hide();\n\t }\n\t\n\t // Adjust top for issue 2907 depending on whether the messagebox is visible.\n\t if ($(\"#messagebox\").is(\":visible\")) {\n\t this.$el.css(\"top\", \"95px\");\n\t }\n\t\n\t this.$el.find('[title]').tooltip();\n\t return this;\n\t },\n\t\n\t focus_and_select: function () {\n\t this.$el.find(\":input\").focus().select();\n\t },\n\t\n\t clear: function () {\n\t this.model.clear_search();\n\t this.$el.find(\":input\").val('');\n\t this.focus_and_select();\n\t return false;\n\t },\n\t\n\t query_changed: function (evData) {\n\t // check for the 'clear key' (ESC) first\n\t if (this.model.attributes.clear_key && this.model.attributes.clear_key === evData.which) {\n\t this.clear();\n\t return false;\n\t }\n\t this.model.set(\"query\", this.$el.find(\":input\").val());\n\t }\n\t });\n\t\n\t /**\n\t * Tool panel view. Events triggered include:\n\t * tool_link_click(click event, tool_model)\n\t */\n\t var ToolPanelView = Backbone.View.extend({\n\t tagName: 'div',\n\t className: 'toolMenu',\n\t\n\t /**\n\t * Set up view.\n\t */\n\t initialize: function () {\n\t this.model.get('tool_search').on(\"change:results\", this.handle_search_results, this);\n\t },\n\t\n\t render: function () {\n\t var self = this;\n\t\n\t // Render search.\n\t var search_view = new ToolSearchView({ model: this.model.get('tool_search') });\n\t search_view.render();\n\t self.$el.append(search_view.$el);\n\t\n\t // Render panel.\n\t this.model.get('layout').each(function (panel_elt) {\n\t if (panel_elt instanceof ToolSection) {\n\t var section_title_view = new ToolSectionView({ model: panel_elt });\n\t section_title_view.render();\n\t self.$el.append(section_title_view.$el);\n\t } else if (panel_elt instanceof Tool) {\n\t var tool_view = new ToolLinkView({ model: panel_elt, className: \"toolTitleNoSection\" });\n\t tool_view.render();\n\t self.$el.append(tool_view.$el);\n\t } else if (panel_elt instanceof ToolSectionLabel) {\n\t var label_view = new ToolSectionLabelView({ model: panel_elt });\n\t label_view.render();\n\t self.$el.append(label_view.$el);\n\t }\n\t });\n\t\n\t // Setup tool link click eventing.\n\t self.$el.find(\"a.tool-link\").click(function (e) {\n\t // Tool id is always the first class.\n\t var tool_id = $(this).attr('class').split(/\\s+/)[0],\n\t tool = self.model.get('tools').get(tool_id);\n\t\n\t self.trigger(\"tool_link_click\", e, tool);\n\t });\n\t\n\t return this;\n\t },\n\t\n\t handle_search_results: function () {\n\t var results = this.model.get('tool_search').get('results');\n\t if (results && results.length === 0) {\n\t $(\"#search-no-results\").show();\n\t } else {\n\t $(\"#search-no-results\").hide();\n\t }\n\t }\n\t });\n\t\n\t /**\n\t * View for working with a tool: setting parameters and inputs and executing the tool.\n\t */\n\t var ToolFormView = Backbone.View.extend({\n\t className: 'toolForm',\n\t\n\t render: function () {\n\t this.$el.children().remove();\n\t this.$el.append(templates.tool_form(this.model.toJSON()));\n\t }\n\t });\n\t\n\t /**\n\t * Integrated tool menu + tool execution.\n\t */\n\t var IntegratedToolMenuAndView = Backbone.View.extend({\n\t className: 'toolMenuAndView',\n\t\n\t initialize: function () {\n\t this.tool_panel_view = new ToolPanelView({ collection: this.collection });\n\t this.tool_form_view = new ToolFormView();\n\t },\n\t\n\t render: function () {\n\t // Render and append tool panel.\n\t this.tool_panel_view.render();\n\t this.tool_panel_view.$el.css(\"float\", \"left\");\n\t this.$el.append(this.tool_panel_view.$el);\n\t\n\t // Append tool form view.\n\t this.tool_form_view.$el.hide();\n\t this.$el.append(this.tool_form_view.$el);\n\t\n\t // On tool link click, show tool.\n\t var self = this;\n\t this.tool_panel_view.on(\"tool_link_click\", function (e, tool) {\n\t // Prevents click from activating link:\n\t e.preventDefault();\n\t // Show tool that was clicked on:\n\t self.show_tool(tool);\n\t });\n\t },\n\t\n\t /**\n\t * Fetch and display tool.\n\t */\n\t show_tool: function (tool) {\n\t var self = this;\n\t tool.fetch().done(function () {\n\t self.tool_form_view.model = tool;\n\t self.tool_form_view.render();\n\t self.tool_form_view.$el.show();\n\t $('#left').width(\"650px\");\n\t });\n\t }\n\t });\n\t\n\t // TODO: move into relevant views\n\t var templates = {\n\t // the search bar at the top of the tool panel\n\t tool_search: _.template(['\" autocomplete=\"off\" type=\"text\" />', '',\n\t //TODO: replace with icon\n\t ''].join('')),\n\t\n\t // the category level container in the tool panel (e.g. 'Get Data', 'Text Manipulation')\n\t panel_section: _.template(['
'].join('')),\n\t\n\t // a single tool's link in the tool panel; will load the tool form in the center panel\n\t tool_link: _.template(['', '<% _.each( labels, function( label ){ %>', '\">', '<%- label %>', '', '<% }); %>', '', ' tool-link\" href=\"<%= link %>\" target=\"<%- target %>\" minsizehint=\"<%- min_width %>\">', '<%- name %>', '', ' <%- description %>'].join('')),\n\t\n\t // the tool form for entering tool parameters, viewing help and executing the tool\n\t // loaded when a tool link is clicked in the tool panel\n\t tool_form: _.template(['
'].join(''), { variable: 'tool' })\n\t };\n\t\n\t // Exports\n\t return {\n\t ToolParameter: ToolParameter,\n\t IntegerToolParameter: IntegerToolParameter,\n\t SelectToolParameter: SelectToolParameter,\n\t Tool: Tool,\n\t ToolCollection: ToolCollection,\n\t ToolSearch: ToolSearch,\n\t ToolPanel: ToolPanel,\n\t ToolPanelView: ToolPanelView,\n\t ToolFormView: ToolFormView\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1)))\n\n/***/ }),\n/* 51 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _, jQuery) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [\n\t //jquery\n\t //backbone\n\t], __WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t // =============================================================================\n\t /**\n\t * view for a popup menu\n\t */\n\t var PopupMenu = Backbone.View.extend({\n\t //TODO: maybe better as singleton off the Galaxy obj\n\t /** Cache the desired button element and options, set up the button click handler\n\t * NOTE: attaches this view as HTML/jQ data on the button for later use.\n\t */\n\t initialize: function ($button, options) {\n\t // default settings\n\t this.$button = $button;\n\t if (!this.$button.length) {\n\t this.$button = $('');\n\t }\n\t this.options = options || [];\n\t this.$button.data('popupmenu', this);\n\t\n\t // set up button click -> open menu behavior\n\t var menu = this;\n\t this.$button.click(function (event) {\n\t // if there's already a menu open, remove it\n\t $('.popmenu-wrapper').remove();\n\t menu._renderAndShow(event);\n\t return false;\n\t });\n\t },\n\t\n\t // render the menu, append to the page body at the click position, and set up the 'click-away' handlers, show\n\t _renderAndShow: function (clickEvent) {\n\t this.render();\n\t this.$el.appendTo('body').css(this._getShownPosition(clickEvent)).show();\n\t this._setUpCloseBehavior();\n\t },\n\t\n\t // render the menu\n\t // this menu doesn't attach itself to the DOM ( see _renderAndShow )\n\t render: function () {\n\t // render the menu body absolute and hidden, fill with template\n\t this.$el.addClass('popmenu-wrapper').hide().css({ position: 'absolute' }).html(this.template(this.$button.attr('id'), this.options));\n\t\n\t // set up behavior on each link/anchor elem\n\t if (this.options.length) {\n\t var menu = this;\n\t //precondition: there should be one option per li\n\t this.$el.find('li').each(function (i, li) {\n\t var option = menu.options[i];\n\t\n\t // if the option has 'func', call that function when the anchor is clicked\n\t if (option.func) {\n\t $(this).children('a.popupmenu-option').click(function (event) {\n\t option.func.call(menu, event, option);\n\t // We must preventDefault otherwise clicking \"cancel\"\n\t // on a purge or something still navigates and causes\n\t // the action.\n\t event.preventDefault();\n\t // bubble up so that an option click will call the close behavior\n\t });\n\t }\n\t });\n\t }\n\t return this;\n\t },\n\t\n\t template: function (id, options) {\n\t return ['
', this._templateOptions(options), '
'].join('');\n\t },\n\t\n\t _templateOptions: function (options) {\n\t if (!options.length) {\n\t return '
(no options)
';\n\t }\n\t return _.map(options, function (option) {\n\t if (option.divider) {\n\t return '';\n\t } else if (option.header) {\n\t return ['
'].join('');\n\t }).join('');\n\t },\n\t\n\t // get the absolute position/offset for the menu\n\t _getShownPosition: function (clickEvent) {\n\t\n\t // display menu horiz. centered on click...\n\t var menuWidth = this.$el.width();\n\t var x = clickEvent.pageX - menuWidth / 2;\n\t\n\t // adjust to handle horiz. scroll and window dimensions ( draw entirely on visible screen area )\n\t x = Math.min(x, $(document).scrollLeft() + $(window).width() - menuWidth - 5);\n\t x = Math.max(x, $(document).scrollLeft() + 5);\n\t return {\n\t top: clickEvent.pageY,\n\t left: x\n\t };\n\t },\n\t\n\t // bind an event handler to all available frames so that when anything is clicked\n\t // the menu is removed from the DOM and the event handler unbinds itself\n\t _setUpCloseBehavior: function () {\n\t var menu = this;\n\t //TODO: alternately: focus hack, blocking overlay, jquery.blockui\n\t\n\t // function to close popup and unbind itself\n\t function closePopup(event) {\n\t $(document).off('click.close_popup');\n\t if (window && window.parent !== window) {\n\t try {\n\t $(window.parent.document).off(\"click.close_popup\");\n\t } catch (err) {}\n\t } else {\n\t try {\n\t $('iframe#galaxy_main').contents().off(\"click.close_popup\");\n\t } catch (err) {}\n\t }\n\t menu.remove();\n\t }\n\t\n\t $('html').one(\"click.close_popup\", closePopup);\n\t if (window && window.parent !== window) {\n\t try {\n\t $(window.parent.document).find('html').one(\"click.close_popup\", closePopup);\n\t } catch (err) {}\n\t } else {\n\t try {\n\t $('iframe#galaxy_main').contents().one(\"click.close_popup\", closePopup);\n\t } catch (err) {}\n\t }\n\t },\n\t\n\t // add a menu option/item at the given index\n\t addItem: function (item, index) {\n\t // append to end if no index\n\t index = index >= 0 ? index : this.options.length;\n\t this.options.splice(index, 0, item);\n\t return this;\n\t },\n\t\n\t // remove a menu option/item at the given index\n\t removeItem: function (index) {\n\t if (index >= 0) {\n\t this.options.splice(index, 1);\n\t }\n\t return this;\n\t },\n\t\n\t // search for a menu option by its html\n\t findIndexByHtml: function (html) {\n\t for (var i = 0; i < this.options.length; i++) {\n\t if (_.has(this.options[i], 'html') && this.options[i].html === html) {\n\t return i;\n\t }\n\t }\n\t return null;\n\t },\n\t\n\t // search for a menu option by its html\n\t findItemByHtml: function (html) {\n\t return this.options[this.findIndexByHtml(html)];\n\t },\n\t\n\t // string representation\n\t toString: function () {\n\t return 'PopupMenu';\n\t }\n\t });\n\t /** shortcut to new for when you don't need to preserve the ref */\n\t PopupMenu.create = function _create($button, options) {\n\t return new PopupMenu($button, options);\n\t };\n\t\n\t // -----------------------------------------------------------------------------\n\t // the following class functions are bridges from the original make_popupmenu and make_popup_menus\n\t // to the newer backbone.js PopupMenu\n\t\n\t /** Create a PopupMenu from simple map initial_options activated by clicking button_element.\n\t * Converts initial_options to object array used by PopupMenu.\n\t * @param {jQuery|DOMElement} button_element element which, when clicked, activates menu\n\t * @param {Object} initial_options map of key -> values, where\n\t * key is option text, value is fn to call when option is clicked\n\t * @returns {PopupMenu} the PopupMenu created\n\t */\n\t PopupMenu.make_popupmenu = function (button_element, initial_options) {\n\t var convertedOptions = [];\n\t _.each(initial_options, function (optionVal, optionKey) {\n\t var newOption = { html: optionKey };\n\t\n\t // keys with null values indicate: header\n\t if (optionVal === null) {\n\t // !optionVal? (null only?)\n\t newOption.header = true;\n\t\n\t // keys with function values indicate: a menu option\n\t } else if (jQuery.type(optionVal) === 'function') {\n\t newOption.func = optionVal;\n\t }\n\t //TODO:?? any other special optionVals?\n\t // there was no divider option originally\n\t convertedOptions.push(newOption);\n\t });\n\t return new PopupMenu($(button_element), convertedOptions);\n\t };\n\t\n\t /** Find all anchors in $parent (using selector) and covert anchors into a PopupMenu options map.\n\t * @param {jQuery} $parent the element that contains the links to convert to options\n\t * @param {String} selector jq selector string to find links\n\t * @returns {Object[]} the options array to initialize a PopupMenu\n\t */\n\t //TODO: lose parent and selector, pass in array of links, use map to return options\n\t PopupMenu.convertLinksToOptions = function ($parent, selector) {\n\t $parent = $($parent);\n\t selector = selector || 'a';\n\t var options = [];\n\t $parent.find(selector).each(function (elem, i) {\n\t var option = {},\n\t $link = $(elem);\n\t\n\t // convert link text to the option text (html) and the href into the option func\n\t option.html = $link.text();\n\t if ($link.attr('href')) {\n\t var linkHref = $link.attr('href'),\n\t linkTarget = $link.attr('target'),\n\t confirmText = $link.attr('confirm');\n\t\n\t option.func = function () {\n\t // if there's a \"confirm\" attribute, throw up a confirmation dialog, and\n\t // if the user cancels - do nothing\n\t if (confirmText && !confirm(confirmText)) {\n\t return;\n\t }\n\t\n\t // if there's no confirm attribute, or the user accepted the confirm dialog:\n\t switch (linkTarget) {\n\t // relocate the center panel\n\t case '_parent':\n\t window.parent.location = linkHref;\n\t break;\n\t\n\t // relocate the entire window\n\t case '_top':\n\t window.top.location = linkHref;\n\t break;\n\t\n\t // relocate this panel\n\t default:\n\t window.location = linkHref;\n\t }\n\t };\n\t }\n\t options.push(option);\n\t });\n\t return options;\n\t };\n\t\n\t /** Create a single popupmenu from existing DOM button and anchor elements\n\t * @param {jQuery} $buttonElement the element that when clicked will open the menu\n\t * @param {jQuery} $menuElement the element that contains the anchors to convert into a menu\n\t * @param {String} menuElementLinkSelector jq selector string used to find anchors to be made into menu options\n\t * @returns {PopupMenu} the PopupMenu (Backbone View) that can render, control the menu\n\t */\n\t PopupMenu.fromExistingDom = function ($buttonElement, $menuElement, menuElementLinkSelector) {\n\t $buttonElement = $($buttonElement);\n\t $menuElement = $($menuElement);\n\t var options = PopupMenu.convertLinksToOptions($menuElement, menuElementLinkSelector);\n\t // we're done with the menu (having converted it to an options map)\n\t $menuElement.remove();\n\t return new PopupMenu($buttonElement, options);\n\t };\n\t\n\t /** Create all popupmenus within a document or a more specific element\n\t * @param {DOMElement} parent the DOM element in which to search for popupmenus to build (defaults to document)\n\t * @param {String} menuSelector jq selector string to find popupmenu menu elements (defaults to \"div[popupmenu]\")\n\t * @param {Function} buttonSelectorBuildFn the function to build the jq button selector.\n\t * Will be passed $menuElement, parent.\n\t * (Defaults to return '#' + $menuElement.attr( 'popupmenu' ); )\n\t * @returns {PopupMenu[]} array of popupmenus created\n\t */\n\t PopupMenu.make_popup_menus = function (parent, menuSelector, buttonSelectorBuildFn) {\n\t parent = parent || document;\n\t // orig. Glx popupmenu menus have a (non-std) attribute 'popupmenu'\n\t // which contains the id of the button that activates the menu\n\t menuSelector = menuSelector || 'div[popupmenu]';\n\t // default to (orig. Glx) matching button to menu by using the popupmenu attr of the menu as the id of the button\n\t buttonSelectorBuildFn = buttonSelectorBuildFn || function ($menuElement, parent) {\n\t return '#' + $menuElement.attr('popupmenu');\n\t };\n\t\n\t // aggregate and return all PopupMenus\n\t var popupMenusCreated = [];\n\t $(parent).find(menuSelector).each(function () {\n\t var $menuElement = $(this),\n\t $buttonElement = $(parent).find(buttonSelectorBuildFn($menuElement, parent));\n\t popupMenusCreated.push(PopupMenu.fromDom($buttonElement, $menuElement));\n\t $buttonElement.addClass('popup');\n\t });\n\t return popupMenusCreated;\n\t };\n\t\n\t // =============================================================================\n\t return PopupMenu;\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ }),\n/* 52 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {/** Renders the color picker used e.g. in the tool form **/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t return Backbone.View.extend({\n\t colors: {\n\t standard: ['c00000', 'ff0000', 'ffc000', 'ffff00', '92d050', '00b050', '00b0f0', '0070c0', '002060', '7030a0'],\n\t base: ['ffffff', '000000', 'eeece1', '1f497d', '4f81bd', 'c0504d', '9bbb59', '8064a2', '4bacc6', 'f79646'],\n\t theme: [['f2f2f2', '7f7f7f', 'ddd9c3', 'c6d9f0', 'dbe5f1', 'f2dcdb', 'ebf1dd', 'e5e0ec', 'dbeef3', 'fdeada'], ['d8d8d8', '595959', 'c4bd97', '8db3e2', 'b8cce4', 'e5b9b7', 'd7e3bc', 'ccc1d9', 'b7dde8', 'fbd5b5'], ['bfbfbf', '3f3f3f', '938953', '548dd4', '95b3d7', 'd99694', 'c3d69b', 'b2a2c7', '92cddc', 'fac08f'], ['a5a5a5', '262626', '494429', '17365d', '366092', '953734', '76923c', '5f497a', '31859b', 'e36c09'], ['7f7f7e', '0c0c0c', '1d1b10', '0f243e', '244061', '632423', '4f6128', '3f3151', '205867', '974806']]\n\t },\n\t\n\t initialize: function (options) {\n\t this.options = Utils.merge(options, {});\n\t this.setElement(this._template());\n\t this.$panel = this.$('.ui-color-picker-panel');\n\t this.$view = this.$('.ui-color-picker-view');\n\t this.$value = this.$('.ui-color-picker-value');\n\t this.$header = this.$('.ui-color-picker-header');\n\t this._build();\n\t this.visible = false;\n\t this.value(this.options.value);\n\t this.$boxes = this.$('.ui-color-picker-box');\n\t var self = this;\n\t this.$boxes.on('click', function () {\n\t self.value($(this).css('background-color'));\n\t self.$header.trigger('click');\n\t });\n\t this.$header.on('click', function () {\n\t self.visible = !self.visible;\n\t if (self.visible) {\n\t self.$view.fadeIn('fast');\n\t } else {\n\t self.$view.fadeOut('fast');\n\t }\n\t });\n\t },\n\t\n\t /** Get/set value */\n\t value: function (new_val) {\n\t if (new_val !== undefined && new_val !== null) {\n\t this.$value.css('background-color', new_val);\n\t this.$('.ui-color-picker-box').empty();\n\t this.$(this._getValue()).html(this._templateCheck());\n\t this.options.onchange && this.options.onchange(new_val);\n\t }\n\t return this._getValue();\n\t },\n\t\n\t /** Get value from dom */\n\t _getValue: function () {\n\t var rgb = this.$value.css('background-color');\n\t rgb = rgb.match(/^rgb\\((\\d+),\\s*(\\d+),\\s*(\\d+)\\)$/);\n\t if (rgb) {\n\t function hex(x) {\n\t return ('0' + parseInt(x).toString(16)).slice(-2);\n\t }\n\t return '#' + hex(rgb[1]) + hex(rgb[2]) + hex(rgb[3]);\n\t } else {\n\t return null;\n\t }\n\t },\n\t\n\t /** Build color panel */\n\t _build: function () {\n\t this._content({ colors: this.colors.base });\n\t for (var i in this.colors.theme) {\n\t var line_def = {};\n\t if (i == 0) {\n\t line_def['bottom'] = true;\n\t } else if (i != this.colors.theme.length - 1) {\n\t line_def['top'] = true;\n\t line_def['bottom'] = true;\n\t } else {\n\t line_def['top'] = true;\n\t }\n\t line_def['colors'] = this.colors.theme[i];\n\t this._content(line_def);\n\t }\n\t this._content({ colors: this.colors.standard });\n\t },\n\t\n\t /** Create content */\n\t _content: function (options) {\n\t var colors = options.colors;\n\t var $content = $(this._templateContent());\n\t var $line = $content.find('.line');\n\t this.$panel.append($content);\n\t for (var i in colors) {\n\t var $box = $(this._templateBox(colors[i]));\n\t if (options.top) {\n\t $box.css('border-top', 'none');\n\t $box.css('border-top-left-radius', '0px');\n\t $box.css('border-top-right-radius', '0px');\n\t }\n\t if (options.bottom) {\n\t $box.css('border-bottom', 'none');\n\t $box.css('border-bottom-left-radius', '0px');\n\t $box.css('border-bottom-right-radius', '0px');\n\t }\n\t $line.append($box);\n\t }\n\t return $content;\n\t },\n\t\n\t /** Check icon */\n\t _templateCheck: function () {\n\t return '';\n\t },\n\t\n\t /** Content template */\n\t _templateContent: function () {\n\t return '
' + '
' + '
';\n\t },\n\t\n\t /** Box template */\n\t _templateBox: function (color) {\n\t return '';\n\t },\n\t\n\t /** Main template */\n\t _template: function () {\n\t return '
' + '
' + '
' + '
Select a color
' + '
' + '
' + '
' + '
';\n\t '
';\n\t }\n\t });\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1)))\n\n/***/ }),\n/* 53 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function($, _) {/** This class creates/wraps a drill down element. */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(22)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Options) {\n\t\n\t var View = Options.BaseIcons.extend({\n\t initialize: function (options) {\n\t options.type = options.display || 'checkbox';\n\t options.multiple = options.type == 'checkbox';\n\t Options.BaseIcons.prototype.initialize.call(this, options);\n\t },\n\t\n\t /** Set states for selected values */\n\t _setValue: function (new_value) {\n\t Options.BaseIcons.prototype._setValue.call(this, new_value);\n\t if (new_value !== undefined && new_value !== null && this.header_index) {\n\t var self = this;\n\t var values = $.isArray(new_value) ? new_value : [new_value];\n\t _.each(values, function (v) {\n\t var list = self.header_index[v];\n\t _.each(list, function (element) {\n\t self._setState(element, true);\n\t });\n\t });\n\t }\n\t },\n\t\n\t /** Expand/collapse a sub group */\n\t _setState: function (header_id, is_expanded) {\n\t var $button = this.$('.button-' + header_id);\n\t var $subgroup = this.$('.subgroup-' + header_id);\n\t $button.data('is_expanded', is_expanded);\n\t if (is_expanded) {\n\t $subgroup.show();\n\t $button.removeClass('fa-plus-square').addClass('fa-minus-square');\n\t } else {\n\t $subgroup.hide();\n\t $button.removeClass('fa-minus-square').addClass('fa-plus-square');\n\t }\n\t },\n\t\n\t /** Template to create options tree */\n\t _templateOptions: function () {\n\t var self = this;\n\t this.header_index = {};\n\t\n\t // attach event handler\n\t function attach($el, header_id) {\n\t var $button = $el.find('.button-' + header_id);\n\t $button.on('click', function () {\n\t self._setState(header_id, !$button.data('is_expanded'));\n\t });\n\t }\n\t\n\t // recursive function which iterates through options\n\t function iterate($tmpl, options, header) {\n\t header = header || [];\n\t for (i in options) {\n\t var level = options[i];\n\t var has_options = level.options && level.options.length > 0;\n\t var new_header = header.slice(0);\n\t self.header_index[level.value] = new_header.slice(0);\n\t var $group = $('');\n\t if (has_options) {\n\t var header_id = Utils.uid();\n\t var $button = $('').addClass('button-' + header_id).addClass('ui-drilldown-button fa fa-plus-square');\n\t var $subgroup = $('').addClass('subgroup-' + header_id).addClass('ui-drilldown-subgroup');\n\t $group.append($('').append($button).append(self._templateOption({ label: level.name, value: level.value })));\n\t new_header.push(header_id);\n\t iterate($subgroup, level.options, new_header);\n\t $group.append($subgroup);\n\t attach($group, header_id);\n\t } else {\n\t $group.append(self._templateOption({ label: level.name, value: level.value }));\n\t }\n\t $tmpl.append($group);\n\t }\n\t }\n\t\n\t // iterate through options and create dom\n\t var $tmpl = $('');\n\t iterate($tmpl, this.model.get('data'));\n\t return $tmpl;\n\t },\n\t\n\t /** Template for drill down view */\n\t _template: function () {\n\t return $('').addClass('ui-options-list drilldown-container').attr('id', this.model.id);\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1), __webpack_require__(2)))\n\n/***/ }),\n/* 54 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(7), __webpack_require__(23)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Ui, Select) {\n\t\n\t /** Batch mode variations */\n\t var Batch = { DISABLED: 'disabled', ENABLED: 'enabled', LINKED: 'linked' };\n\t\n\t /** List of available content selectors options */\n\t var Configurations = {\n\t data: [{ src: 'hda', icon: 'fa-file-o', tooltip: 'Single dataset', multiple: false, batch: Batch.DISABLED }, { src: 'hda', icon: 'fa-files-o', tooltip: 'Multiple datasets', multiple: true, batch: Batch.LINKED }, { src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection', multiple: false, batch: Batch.LINKED }],\n\t data_multiple: [{ src: 'hda', icon: 'fa-files-o', tooltip: 'Multiple datasets', multiple: true, batch: Batch.DISABLED }, { src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collections', multiple: true, batch: Batch.DISABLED }],\n\t data_collection: [{ src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection', multiple: false, batch: Batch.DISABLED }],\n\t workflow_data: [{ src: 'hda', icon: 'fa-file-o', tooltip: 'Single dataset', multiple: false, batch: Batch.DISABLED }],\n\t workflow_data_multiple: [{ src: 'hda', icon: 'fa-files-o', tooltip: 'Multiple datasets', multiple: true, batch: Batch.DISABLED }],\n\t workflow_data_collection: [{ src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection', multiple: false, batch: Batch.DISABLED }],\n\t module_data: [{ src: 'hda', icon: 'fa-file-o', tooltip: 'Single dataset', multiple: false, batch: Batch.DISABLED }, { src: 'hda', icon: 'fa-files-o', tooltip: 'Multiple datasets', multiple: true, batch: Batch.ENABLED }],\n\t module_data_collection: [{ src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection', multiple: false, batch: Batch.DISABLED }, { src: 'hdca', icon: 'fa-folder', tooltip: 'Multiple collections', multiple: true, batch: Batch.ENABLED }]\n\t };\n\t\n\t /** View for hda and hdca content selector ui elements */\n\t var View = Backbone.View.extend({\n\t initialize: function (options) {\n\t var self = this;\n\t this.model = options && options.model || new Backbone.Model({\n\t src_labels: { 'hda': 'dataset', 'hdca': 'dataset collection' },\n\t pagelimit: 100,\n\t statustimer: 1000\n\t }).set(options);\n\t this.setElement($('').addClass('ui-select-content'));\n\t this.button_product = new Ui.RadioButton.View({\n\t value: 'false',\n\t data: [{ icon: 'fa fa-chain', value: 'false',\n\t tooltip: 'Linked inputs will be run in matched order with other datasets e.g. use this for matching forward and reverse reads.' }, { icon: 'fa fa-chain-broken', value: 'true',\n\t tooltip: 'Unlinked dataset inputs will be run against *all* other inputs.' }] });\n\t var $batch_div = $('').addClass('ui-form-info').append($('').addClass('fa fa-sitemap')).append($('').html('This is a batch mode input field. Separate jobs will be triggered for each dataset selection.'));\n\t this.$batch = {\n\t linked: $batch_div.clone(),\n\t enabled: $batch_div.clone().append($('').append($('').addClass('ui-form-title').html('Batch options:')).append(this.button_product.$el)).append($('').css('clear', 'both'))\n\t };\n\t\n\t // add drag-drop event handlers\n\t this.$el.on('dragenter', function (e) {\n\t this.lastenter = e.target;self.$el.addClass('ui-dragover');\n\t }).on('dragover', function (e) {\n\t e.preventDefault();\n\t }).on('dragleave', function (e) {\n\t this.lastenter === e.target && self.$el.removeClass('ui-dragover');\n\t }).on('drop', function (e) {\n\t self._handleDrop(e);\n\t });\n\t\n\t // track current history elements\n\t this.history = {};\n\t\n\t // add listeners\n\t this.listenTo(this.model, 'change:data', this._changeData, this);\n\t this.listenTo(this.model, 'change:wait', this._changeWait, this);\n\t this.listenTo(this.model, 'change:current', this._changeCurrent, this);\n\t this.listenTo(this.model, 'change:value', this._changeValue, this);\n\t this.listenTo(this.model, 'change:type change:optional change:multiple change:extensions', this._changeType, this);\n\t this.render();\n\t\n\t // add change event\n\t this.on('change', function () {\n\t options.onchange && options.onchange(self.value());\n\t });\n\t },\n\t\n\t render: function () {\n\t this._changeType();\n\t this._changeValue();\n\t this._changeWait();\n\t },\n\t\n\t /** Indicate that select fields are being updated */\n\t wait: function () {\n\t this.model.set('wait', true);\n\t },\n\t\n\t /** Indicate that the options update has been completed */\n\t unwait: function () {\n\t this.model.set('wait', false);\n\t },\n\t\n\t /** Update data representing selectable options */\n\t update: function (options) {\n\t this.model.set('data', options);\n\t },\n\t\n\t /** Return the currently selected dataset values */\n\t value: function (new_value) {\n\t new_value !== undefined && this.model.set('value', new_value);\n\t var current = this.model.get('current');\n\t if (this.config[current]) {\n\t var id_list = this.fields[current].value();\n\t if (id_list !== null) {\n\t id_list = $.isArray(id_list) ? id_list : [id_list];\n\t if (id_list.length > 0) {\n\t var result = this._batch({ values: [] });\n\t for (var i in id_list) {\n\t var details = this.history[id_list[i] + '_' + this.config[current].src];\n\t if (details) {\n\t result.values.push(details);\n\t } else {\n\t Galaxy.emit.debug('ui-select-content::value()', 'Requested details not found for \\'' + id_list[i] + '\\'.');\n\t return null;\n\t }\n\t }\n\t result.values.sort(function (a, b) {\n\t return a.hid - b.hid;\n\t });\n\t return result;\n\t }\n\t }\n\t } else {\n\t Galaxy.emit.debug('ui-select-content::value()', 'Invalid value/source \\'' + new_value + '\\'.');\n\t }\n\t return null;\n\t },\n\t\n\t /** Change of current select field */\n\t _changeCurrent: function () {\n\t var self = this;\n\t _.each(this.fields, function (field, i) {\n\t if (self.model.get('current') == i) {\n\t field.$el.show();\n\t _.each(self.$batch, function ($batchfield, batchmode) {\n\t $batchfield[self.config[i].batch == batchmode ? 'show' : 'hide']();\n\t });\n\t self.button_type.value(i);\n\t } else {\n\t field.$el.hide();\n\t }\n\t });\n\t },\n\t\n\t /** Change of type */\n\t _changeType: function () {\n\t var self = this;\n\t\n\t // identify selector type identifier i.e. [ flavor ]_[ type ]_[ multiple ]\n\t var config_id = (this.model.get('flavor') ? this.model.get('flavor') + '_' : '') + String(this.model.get('type')) + (this.model.get('multiple') ? '_multiple' : '');\n\t if (Configurations[config_id]) {\n\t this.config = Configurations[config_id];\n\t } else {\n\t this.config = Configurations['data'];\n\t Galaxy.emit.debug('ui-select-content::_changeType()', 'Invalid configuration/type id \\'' + config_id + '\\'.');\n\t }\n\t\n\t // prepare extension component of error message\n\t var data = self.model.get('data');\n\t var extensions = Utils.textify(this.model.get('extensions'));\n\t var src_labels = this.model.get('src_labels');\n\t\n\t // build views\n\t this.fields = [];\n\t this.button_data = [];\n\t _.each(this.config, function (c, i) {\n\t self.button_data.push({\n\t value: i,\n\t icon: c.icon,\n\t tooltip: c.tooltip\n\t });\n\t self.fields.push(new Select.View({\n\t optional: self.model.get('optional'),\n\t multiple: c.multiple,\n\t searchable: !c.multiple || data && data[c.src] && data[c.src].length > self.model.get('pagelimit'),\n\t selectall: false,\n\t error_text: 'No ' + (extensions ? extensions + ' ' : '') + (src_labels[c.src] || 'content') + ' available.',\n\t onchange: function () {\n\t self.trigger('change');\n\t }\n\t }));\n\t });\n\t this.button_type = new Ui.RadioButton.View({\n\t value: this.model.get('current'),\n\t data: this.button_data,\n\t onchange: function (value) {\n\t self.model.set('current', value);\n\t self.trigger('change');\n\t }\n\t });\n\t\n\t // append views\n\t this.$el.empty();\n\t var button_width = 0;\n\t if (this.fields.length > 1) {\n\t this.$el.append(this.button_type.$el);\n\t button_width = Math.max(0, this.fields.length * 36) + 'px';\n\t }\n\t _.each(this.fields, function (field) {\n\t self.$el.append(field.$el.css({ 'margin-left': button_width }));\n\t });\n\t _.each(this.$batch, function ($batchfield, batchmode) {\n\t self.$el.append($batchfield.css({ 'margin-left': button_width }));\n\t });\n\t this.model.set('current', 0);\n\t this._changeCurrent();\n\t this._changeData();\n\t },\n\t\n\t /** Change of wait flag */\n\t _changeWait: function () {\n\t var self = this;\n\t _.each(this.fields, function (field) {\n\t field[self.model.get('wait') ? 'wait' : 'unwait']();\n\t });\n\t },\n\t\n\t /** Change of available options */\n\t _changeData: function () {\n\t var options = this.model.get('data');\n\t var self = this;\n\t var select_options = {};\n\t _.each(options, function (items, src) {\n\t select_options[src] = [];\n\t _.each(items, function (item) {\n\t select_options[src].push({\n\t hid: item.hid,\n\t keep: item.keep,\n\t label: item.hid + ': ' + item.name,\n\t value: item.id,\n\t tags: item.tags\n\t });\n\t self.history[item.id + '_' + src] = item;\n\t });\n\t });\n\t _.each(this.config, function (c, i) {\n\t select_options[c.src] && self.fields[i].add(select_options[c.src], function (a, b) {\n\t return b.hid - a.hid;\n\t });\n\t });\n\t },\n\t\n\t /** Change of incoming value */\n\t _changeValue: function () {\n\t var new_value = this.model.get('value');\n\t if (new_value && new_value.values && new_value.values.length > 0) {\n\t // create list with content ids\n\t var list = [];\n\t _.each(new_value.values, function (value) {\n\t list.push(value.id);\n\t });\n\t // sniff first suitable field type from config list\n\t var src = new_value.values[0].src;\n\t var multiple = new_value.values.length > 1;\n\t for (var i = 0; i < this.config.length; i++) {\n\t var field = this.fields[i];\n\t var c = this.config[i];\n\t if (c.src == src && [multiple, true].indexOf(c.multiple) !== -1) {\n\t this.model.set('current', i);\n\t field.value(list);\n\t break;\n\t }\n\t }\n\t } else {\n\t _.each(this.fields, function (field) {\n\t field.value(null);\n\t });\n\t }\n\t },\n\t\n\t /** Handles drop events e.g. from history panel */\n\t _handleDrop: function (ev) {\n\t try {\n\t var data = this.model.get('data');\n\t var current = this.model.get('current');\n\t var config = this.config[current];\n\t var field = this.fields[current];\n\t var drop_data = JSON.parse(ev.originalEvent.dataTransfer.getData('text'))[0];\n\t var new_id = drop_data.id;\n\t var new_src = drop_data.history_content_type == 'dataset' ? 'hda' : 'hdca';\n\t var new_value = { id: new_id, src: new_src };\n\t if (data && _.findWhere(data[new_src], new_value)) {\n\t if (config.src == new_src) {\n\t var current_value = field.value();\n\t if (current_value && config.multiple) {\n\t if (current_value.indexOf(new_id) == -1) {\n\t current_value.push(new_id);\n\t }\n\t } else {\n\t current_value = new_id;\n\t }\n\t field.value(current_value);\n\t } else {\n\t this.model.set('value', { values: [new_value] });\n\t this.model.trigger('change:value');\n\t }\n\t this.trigger('change');\n\t this._handleDropStatus('success');\n\t } else {\n\t this._handleDropStatus('danger');\n\t }\n\t } catch (e) {\n\t this._handleDropStatus('danger');\n\t }\n\t },\n\t\n\t /** Highlight drag result */\n\t _handleDropStatus: function (status) {\n\t var self = this;\n\t this.$el.removeClass('ui-dragover').addClass('ui-dragover-' + status);\n\t setTimeout(function () {\n\t self.$el.removeClass('ui-dragover-' + status);\n\t }, this.model.get('statustimer'));\n\t },\n\t\n\t /** Assists in identifying the batch mode */\n\t _batch: function (result) {\n\t result['batch'] = false;\n\t var current = this.model.get('current');\n\t var config = this.config[current];\n\t if (config.src == 'hdca' && !config.multiple) {\n\t var hdca = this.history[this.fields[current].value() + '_hdca'];\n\t if (hdca && hdca.map_over_type) {\n\t result['batch'] = true;\n\t }\n\t }\n\t if (config.batch == Batch.LINKED || config.batch == Batch.ENABLED) {\n\t result['batch'] = true;\n\t if (config.batch == Batch.ENABLED && this.button_product.value() === 'true') {\n\t result['product'] = true;\n\t }\n\t }\n\t return result;\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1), __webpack_require__(2)))\n\n/***/ }),\n/* 55 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone) {// dependencies\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(21)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, List) {\n\t\n\t /**\n\t * FTP file selector\n\t */\n\t var View = Backbone.View.extend({\n\t // initialize\n\t initialize: function (options) {\n\t // link this\n\t var self = this;\n\t\n\t // create ui-list view to keep track of selected ftp files\n\t this.ftpfile_list = new List.View({\n\t name: 'file',\n\t optional: options.optional,\n\t multiple: options.multiple,\n\t onchange: function () {\n\t options.onchange && options.onchange(self.value());\n\t }\n\t });\n\t\n\t // create elements\n\t this.setElement(this.ftpfile_list.$el);\n\t\n\t // initial fetch of ftps\n\t Utils.get({\n\t url: Galaxy.root + 'api/remote_files',\n\t success: function (response) {\n\t var data = [];\n\t for (var i in response) {\n\t data.push({\n\t value: response[i]['path'],\n\t label: response[i]['path']\n\t });\n\t }\n\t self.ftpfile_list.update(data);\n\t }\n\t });\n\t },\n\t\n\t /** Return/Set currently selected ftp datasets */\n\t value: function (val) {\n\t return this.ftpfile_list.value(val);\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3)))\n\n/***/ }),\n/* 56 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone) {// dependencies\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(7), __webpack_require__(27), __webpack_require__(21)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Ui, Table, List) {\n\t\n\t // collection of libraries\n\t var Libraries = Backbone.Collection.extend({\n\t url: Galaxy.root + 'api/libraries?deleted=false'\n\t });\n\t\n\t // collection of dataset\n\t var LibraryDatasets = Backbone.Collection.extend({\n\t initialize: function () {\n\t var self = this;\n\t this.config = new Backbone.Model({ library_id: null });\n\t this.config.on('change', function () {\n\t self.fetch({ reset: true });\n\t });\n\t },\n\t url: function () {\n\t return Galaxy.root + 'api/libraries/' + this.config.get('library_id') + '/contents';\n\t }\n\t });\n\t\n\t // hda/hdca content selector ui element\n\t var View = Backbone.View.extend({\n\t // initialize\n\t initialize: function (options) {\n\t // link this\n\t var self = this;\n\t\n\t // collections\n\t this.libraries = new Libraries();\n\t this.datasets = new LibraryDatasets();\n\t\n\t // link app and options\n\t this.options = options;\n\t\n\t // select field for the library\n\t // TODO: Remove this once the library API supports searching for library datasets\n\t this.library_select = new Ui.Select.View({\n\t onchange: function (value) {\n\t self.datasets.config.set('library_id', value);\n\t }\n\t });\n\t\n\t // create ui-list view to keep track of selected data libraries\n\t this.dataset_list = new List.View({\n\t name: 'dataset',\n\t optional: options.optional,\n\t multiple: options.multiple,\n\t onchange: function () {\n\t self.trigger('change');\n\t }\n\t });\n\t\n\t // add reset handler for fetched libraries\n\t this.libraries.on('reset', function () {\n\t var data = [];\n\t self.libraries.each(function (model) {\n\t data.push({\n\t value: model.id,\n\t label: model.get('name')\n\t });\n\t });\n\t self.library_select.update(data);\n\t });\n\t\n\t // add reset handler for fetched library datasets\n\t this.datasets.on('reset', function () {\n\t var data = [];\n\t var library_current = self.library_select.text();\n\t if (library_current !== null) {\n\t self.datasets.each(function (model) {\n\t if (model.get('type') === 'file') {\n\t data.push({\n\t value: model.id,\n\t label: model.get('name')\n\t });\n\t }\n\t });\n\t }\n\t self.dataset_list.update(data);\n\t });\n\t\n\t // add change event. fires on trigger\n\t this.on('change', function () {\n\t options.onchange && options.onchange(self.value());\n\t });\n\t\n\t // create elements\n\t this.setElement(this._template());\n\t this.$('.library-select').append(this.library_select.$el);\n\t this.$el.append(this.dataset_list.$el);\n\t\n\t // initial fetch of libraries\n\t this.libraries.fetch({\n\t reset: true,\n\t success: function () {\n\t self.library_select.trigger('change');\n\t if (self.options.value !== undefined) {\n\t self.value(self.options.value);\n\t }\n\t }\n\t });\n\t },\n\t\n\t /** Return/Set currently selected library datasets */\n\t value: function (val) {\n\t return this.dataset_list.value(val);\n\t },\n\t\n\t /** Template */\n\t _template: function () {\n\t return '
' + '
' + 'Select Library' + '' + '
' + '
';\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3)))\n\n/***/ }),\n/* 57 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t var View = Backbone.View.extend({\n\t initialize: function (options) {\n\t var self = this;\n\t this.model = options && options.model || new Backbone.Model({\n\t id: Utils.uid(),\n\t min: null,\n\t max: null,\n\t step: null,\n\t precise: false,\n\t split: 10000,\n\t value: null,\n\t onchange: function () {}\n\t }).set(options);\n\t\n\t // create new element\n\t this.setElement(this._template());\n\t this.$el.attr('id', this.model.id);\n\t this.$text = this.$('.ui-form-slider-text');\n\t this.$slider = this.$('.ui-form-slider-element');\n\t\n\t // add text field event\n\t var pressed = [];\n\t this.$text.on('change', function () {\n\t self.value($(this).val());\n\t }).on('keyup', function (e) {\n\t pressed[e.which] = false;\n\t }).on('keydown', function (e) {\n\t var v = e.which;\n\t pressed[v] = true;\n\t if (self.model.get('is_workflow') && pressed[16] && v == 52) {\n\t self.value('$');\n\t event.preventDefault();\n\t } else if (!(v == 8 || v == 9 || v == 13 || v == 37 || v == 39 || v >= 48 && v <= 57 && !pressed[16] || v >= 96 && v <= 105 || (v == 190 || v == 110) && $(this).val().indexOf('.') == -1 && self.model.get('precise') || (v == 189 || v == 109) && $(this).val().indexOf('-') == -1 || self._isParameter($(this).val()) || pressed[91] || pressed[17])) {\n\t event.preventDefault();\n\t }\n\t });\n\t\n\t // build slider, cannot be rebuild in render\n\t var opts = this.model.attributes;\n\t this.has_slider = opts.max !== null && opts.min !== null && opts.max > opts.min;\n\t var step = opts.step;\n\t if (!step) {\n\t if (opts.precise && this.has_slider) {\n\t step = (opts.max - opts.min) / opts.split;\n\t } else {\n\t step = 1.0;\n\t }\n\t }\n\t if (this.has_slider) {\n\t this.$text.addClass('ui-form-slider-left');\n\t this.$slider.slider({ min: opts.min, max: opts.max, step: step }).on('slide', function (event, ui) {\n\t self.value(ui.value);\n\t });\n\t } else {\n\t this.$slider.hide();\n\t }\n\t\n\t // add listeners\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var value = this.model.get('value');\n\t this.has_slider && this.$slider.slider('value', value);\n\t value !== this.$text.val() && this.$text.val(value);\n\t },\n\t\n\t /** Set and return the current value */\n\t value: function (new_val) {\n\t var options = this.model.attributes;\n\t if (new_val !== undefined) {\n\t if (new_val !== null && new_val !== '' && !this._isParameter(new_val)) {\n\t isNaN(new_val) && (new_val = 0);\n\t !options.precise && (new_val = Math.round(new_val));\n\t options.max !== null && (new_val = Math.min(new_val, options.max));\n\t options.min !== null && (new_val = Math.max(new_val, options.min));\n\t }\n\t this.model.set('value', new_val);\n\t this.model.trigger('change');\n\t options.onchange(new_val);\n\t }\n\t return this.model.get('value');\n\t },\n\t\n\t /** Return true if the field contains a workflow parameter i.e. $('name') */\n\t _isParameter: function (value) {\n\t return this.model.get('is_workflow') && String(value).substring(0, 1) === '$';\n\t },\n\t\n\t /** Slider template */\n\t _template: function () {\n\t return '
' + '' + '
' + '
';\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1)))\n\n/***/ }),\n/* 58 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/** This renders the content of the ftp popup **/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t return Backbone.View.extend({\n\t initialize: function (options) {\n\t var self = this;\n\t this.options = Utils.merge(options, {\n\t class_add: 'upload-icon-button fa fa-square-o',\n\t class_remove: 'upload-icon-button fa fa-check-square-o',\n\t class_partial: 'upload-icon-button fa fa-minus-square-o',\n\t collection: null,\n\t onchange: function () {},\n\t onadd: function () {},\n\t onremove: function () {}\n\t });\n\t this.collection = this.options.collection;\n\t this.setElement(this._template());\n\t this.rows = [];\n\t Utils.get({\n\t url: Galaxy.root + 'api/remote_files',\n\t success: function (ftp_files) {\n\t self._fill(ftp_files);\n\t },\n\t error: function () {\n\t self._fill();\n\t }\n\t });\n\t },\n\t\n\t /** Fill table with ftp entries */\n\t _fill: function (ftp_files) {\n\t if (ftp_files && ftp_files.length > 0) {\n\t this.$('.upload-ftp-content').html($(this._templateTable()));\n\t var size = 0;\n\t for (index in ftp_files) {\n\t this.rows.push(this._add(ftp_files[index]));\n\t size += ftp_files[index].size;\n\t }\n\t this.$('.upload-ftp-number').html(ftp_files.length + ' files');\n\t this.$('.upload-ftp-disk').html(Utils.bytesToString(size, true));\n\t if (this.collection) {\n\t var self = this;\n\t this.$('._has_collection').show();\n\t this.$select_all = this.$('.upload-selectall').addClass(this.options.class_add);\n\t this.$select_all.on('click', function () {\n\t var add = self.$select_all.hasClass(self.options.class_add);\n\t for (index in ftp_files) {\n\t var ftp_file = ftp_files[index];\n\t var model_index = self._find(ftp_file);\n\t if (!model_index && add || model_index && !add) {\n\t self.rows[index].trigger('click');\n\t }\n\t }\n\t });\n\t this._refresh();\n\t }\n\t } else {\n\t this.$('.upload-ftp-content').html($(this._templateInfo()));\n\t }\n\t this.$('.upload-ftp-wait').hide();\n\t },\n\t\n\t /** Add file to table */\n\t _add: function (ftp_file) {\n\t var self = this;\n\t var $it = $(this._templateRow(ftp_file));\n\t var $icon = $it.find('.icon');\n\t this.$('tbody').append($it);\n\t if (this.collection) {\n\t $icon.addClass(this._find(ftp_file) ? this.options.class_remove : this.options.class_add);\n\t $it.on('click', function () {\n\t var model_index = self._find(ftp_file);\n\t $icon.removeClass();\n\t if (!model_index) {\n\t self.options.onadd(ftp_file);\n\t $icon.addClass(self.options.class_remove);\n\t } else {\n\t self.options.onremove(model_index);\n\t $icon.addClass(self.options.class_add);\n\t }\n\t self._refresh();\n\t });\n\t } else {\n\t $it.on('click', function () {\n\t self.options.onchange(ftp_file);\n\t });\n\t }\n\t return $it;\n\t },\n\t\n\t /** Refresh select all button state */\n\t _refresh: function () {\n\t var filtered = this.collection.where({ file_mode: 'ftp', enabled: true });\n\t this.$select_all.removeClass();\n\t if (filtered.length == 0) {\n\t this.$select_all.addClass(this.options.class_add);\n\t } else {\n\t this.$select_all.addClass(filtered.length == this.rows.length ? this.options.class_remove : this.options.class_partial);\n\t }\n\t },\n\t\n\t /** Get model index */\n\t _find: function (ftp_file) {\n\t var item = this.collection.findWhere({\n\t file_path: ftp_file.path,\n\t file_mode: 'ftp',\n\t enabled: true\n\t });\n\t return item && item.get('id');\n\t },\n\t\n\t /** Template of row */\n\t _templateRow: function (options) {\n\t return '
';\n\t },\n\t\n\t /** Template of info message */\n\t _templateInfo: function () {\n\t return '
' + 'Your FTP directory does not contain any files.' + '
';\n\t },\n\t\n\t /** Template of main view */\n\t _template: function () {\n\t return '
' + '' + '
This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at ' + this.options.ftp_upload_site + ' using your Galaxy credentials (email address and password).
' + '
' + '
';\n\t }\n\t });\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1), __webpack_require__(2)))\n\n/***/ }),\n/* 59 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/** This renders the content of the settings popup, allowing users to specify flags i.e. for space-to-tab conversion **/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t return Backbone.View.extend({\n\t options: {\n\t class_check: 'fa-check-square-o',\n\t class_uncheck: 'fa-square-o',\n\t parameters: [{\n\t id: 'space_to_tab',\n\t title: 'Convert spaces to tabs'\n\t }, {\n\t id: 'to_posix_lines',\n\t title: 'Use POSIX standard'\n\t }]\n\t },\n\t\n\t initialize: function (options) {\n\t var self = this;\n\t this.model = options.model;\n\t this.setElement($('').addClass('upload-settings'));\n\t this.$el.append($('').addClass('upload-settings-cover'));\n\t this.$el.append($('
').append(parameter.title)));\n\t });\n\t this.$cover[this.model.get('enabled') && 'hide' || 'show']();\n\t }\n\t });\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1), __webpack_require__(2)))\n\n/***/ }),\n/* 60 */,\n/* 61 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {/**\n\t * This class defines a queue to ensure that multiple deferred callbacks are executed sequentially.\n\t */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t return Backbone.Model.extend({\n\t initialize: function () {\n\t this.active = {};\n\t this.last = null;\n\t },\n\t\n\t /** Adds a callback to the queue. Upon execution a deferred object is parsed to the callback i.e. callback( deferred ).\n\t * If the callback does not take any arguments, the deferred is resolved instantly.\n\t */\n\t execute: function (callback) {\n\t var self = this;\n\t var id = Utils.uid();\n\t var has_deferred = callback.length > 0;\n\t\n\t // register process\n\t this.active[id] = true;\n\t\n\t // deferred process\n\t var process = $.Deferred();\n\t process.promise().always(function () {\n\t delete self.active[id];\n\t has_deferred && Galaxy.emit.debug('deferred::execute()', this.state().charAt(0).toUpperCase() + this.state().slice(1) + ' ' + id);\n\t });\n\t\n\t // deferred queue\n\t $.when(this.last).always(function () {\n\t if (self.active[id]) {\n\t has_deferred && Galaxy.emit.debug('deferred::execute()', 'Running ' + id);\n\t callback(process);\n\t !has_deferred && process.resolve();\n\t } else {\n\t process.reject();\n\t }\n\t });\n\t this.last = process.promise();\n\t },\n\t\n\t /** Resets the promise queue. All currently queued but unexecuted callbacks/promises will be rejected.\n\t */\n\t reset: function () {\n\t Galaxy.emit.debug('deferred::execute()', 'Reset');\n\t for (var i in this.active) {\n\t this.active[i] = false;\n\t }\n\t },\n\t\n\t /** Returns true if all processes are done.\n\t */\n\t ready: function () {\n\t return $.isEmptyObject(this.active);\n\t }\n\t });\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1)))\n\n/***/ }),\n/* 62 */,\n/* 63 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\t/* WEBPACK VAR INJECTION */(function(jQuery, _) {/*\n\t galaxy upload plugins - requires FormData and XMLHttpRequest\n\t*/\n\t;(function ($) {\n\t // add event properties\n\t jQuery.event.props.push(\"dataTransfer\");\n\t\n\t /**\n\t Posts file data to the API\n\t */\n\t $.uploadpost = function (config) {\n\t // parse options\n\t var cnf = $.extend({}, {\n\t data: {},\n\t success: function () {},\n\t error: function () {},\n\t progress: function () {},\n\t url: null,\n\t maxfilesize: 2048,\n\t error_filesize: 'File exceeds 2GB. Please use a FTP client.',\n\t error_default: 'Please make sure the file is available.',\n\t error_server: 'Upload request failed.',\n\t error_login: 'Uploads require you to log in.'\n\t }, config);\n\t\n\t // link data\n\t var data = cnf.data;\n\t\n\t // check errors\n\t if (data.error_message) {\n\t cnf.error(data.error_message);\n\t return;\n\t }\n\t\n\t // construct form data\n\t var form = new FormData();\n\t for (var key in data.payload) {\n\t form.append(key, data.payload[key]);\n\t }\n\t\n\t // add files to submission\n\t var sizes = 0;\n\t for (var key in data.files) {\n\t var d = data.files[key];\n\t form.append(d.name, d.file, d.file.name);\n\t sizes += d.file.size;\n\t }\n\t\n\t // check file size, unless it's an ftp file\n\t if (sizes > 1048576 * cnf.maxfilesize) {\n\t cnf.error(cnf.error_filesize);\n\t return;\n\t }\n\t\n\t // prepare request\n\t xhr = new XMLHttpRequest();\n\t xhr.open('POST', cnf.url, true);\n\t xhr.setRequestHeader('Accept', 'application/json');\n\t xhr.setRequestHeader('Cache-Control', 'no-cache');\n\t xhr.setRequestHeader('X-Requested-With', 'XMLHttpRequest');\n\t\n\t // captures state changes\n\t xhr.onreadystatechange = function () {\n\t // check for request completed, server connection closed\n\t if (xhr.readyState == xhr.DONE) {\n\t // parse response\n\t var response = null;\n\t if (xhr.responseText) {\n\t try {\n\t response = jQuery.parseJSON(xhr.responseText);\n\t } catch (e) {\n\t response = xhr.responseText;\n\t }\n\t }\n\t // pass any error to the error option\n\t if (xhr.status < 200 || xhr.status > 299) {\n\t var text = xhr.statusText;\n\t if (xhr.status == 403) {\n\t text = cnf.error_login;\n\t } else if (xhr.status == 0) {\n\t text = cnf.error_server;\n\t } else if (!text) {\n\t text = cnf.error_default;\n\t }\n\t cnf.error(text + ' (' + xhr.status + ')');\n\t } else {\n\t cnf.success(response);\n\t }\n\t }\n\t };\n\t\n\t // prepare upload progress\n\t xhr.upload.addEventListener('progress', function (e) {\n\t if (e.lengthComputable) {\n\t cnf.progress(Math.round(e.loaded * 100 / e.total));\n\t }\n\t }, false);\n\t\n\t // send request\n\t Galaxy.emit.debug('uploadbox::uploadpost()', 'Posting following data.', cnf);\n\t xhr.send(form);\n\t };\n\t\n\t /**\n\t Handles the upload events drag/drop etc.\n\t */\n\t $.fn.uploadinput = function (options) {\n\t // initialize\n\t var el = this;\n\t var opts = $.extend({}, {\n\t ondragover: function () {},\n\t ondragleave: function () {},\n\t onchange: function () {},\n\t multiple: false\n\t }, options);\n\t\n\t // append hidden upload field\n\t var $input = $('');\n\t el.append($input.change(function (e) {\n\t opts.onchange(e.target.files);\n\t $(this).val('');\n\t }));\n\t\n\t // drag/drop events\n\t el.on('drop', function (e) {\n\t opts.ondragleave(e);\n\t if (e.dataTransfer) {\n\t opts.onchange(e.dataTransfer.files);\n\t e.preventDefault();\n\t }\n\t });\n\t el.on('dragover', function (e) {\n\t e.preventDefault();\n\t opts.ondragover(e);\n\t });\n\t el.on('dragleave', function (e) {\n\t e.stopPropagation();\n\t opts.ondragleave(e);\n\t });\n\t\n\t // exports\n\t return {\n\t dialog: function () {\n\t $input.trigger('click');\n\t }\n\t };\n\t };\n\t\n\t /**\n\t Handles the upload queue and events such as drag/drop etc.\n\t */\n\t $.fn.uploadbox = function (options) {\n\t // parse options\n\t var opts = $.extend({}, {\n\t dragover: function () {},\n\t dragleave: function () {},\n\t announce: function (d) {},\n\t initialize: function (d) {},\n\t progress: function (d, m) {},\n\t success: function (d, m) {},\n\t error: function (d, m) {\n\t alert(m);\n\t },\n\t complete: function () {}\n\t }, options);\n\t\n\t // file queue\n\t var queue = {};\n\t\n\t // queue index/length counter\n\t var queue_index = 0;\n\t var queue_length = 0;\n\t\n\t // indicates if queue is currently running\n\t var queue_running = false;\n\t var queue_stop = false;\n\t\n\t // element\n\t var uploadinput = $(this).uploadinput({\n\t multiple: true,\n\t onchange: function (files) {\n\t add(files);\n\t },\n\t ondragover: options.ondragover,\n\t ondragleave: options.ondragleave\n\t });\n\t\n\t // add new files to upload queue\n\t function add(files) {\n\t if (files && files.length && !queue_running) {\n\t var current_index = queue_index;\n\t _.each(files, function (file, key) {\n\t if (file.mode !== 'new' && _.filter(queue, function (f) {\n\t return f.name === file.name && f.size === file.size;\n\t }).length) {\n\t file.duplicate = true;\n\t }\n\t });\n\t _.each(files, function (file) {\n\t if (!file.duplicate) {\n\t var index = String(queue_index++);\n\t queue[index] = file;\n\t opts.announce(index, queue[index]);\n\t queue_length++;\n\t }\n\t });\n\t return current_index;\n\t }\n\t }\n\t\n\t // remove file from queue\n\t function remove(index) {\n\t if (queue[index]) {\n\t delete queue[index];\n\t queue_length--;\n\t }\n\t }\n\t\n\t // process an upload, recursive\n\t function process() {\n\t // validate\n\t if (queue_length == 0 || queue_stop) {\n\t queue_stop = false;\n\t queue_running = false;\n\t opts.complete();\n\t return;\n\t } else {\n\t queue_running = true;\n\t }\n\t\n\t // get an identifier from the queue\n\t var index = -1;\n\t for (var key in queue) {\n\t index = key;\n\t break;\n\t }\n\t\n\t // get current file from queue\n\t var file = queue[index];\n\t\n\t // remove from queue\n\t remove(index);\n\t\n\t // create and submit data\n\t $.uploadpost({\n\t url: opts.url,\n\t data: opts.initialize(index),\n\t success: function (message) {\n\t opts.success(index, message);process();\n\t },\n\t error: function (message) {\n\t opts.error(index, message);process();\n\t },\n\t progress: function (percentage) {\n\t opts.progress(index, percentage);\n\t }\n\t });\n\t }\n\t\n\t /*\n\t public interface\n\t */\n\t\n\t // open file browser for selection\n\t function select() {\n\t uploadinput.dialog();\n\t }\n\t\n\t // remove all entries from queue\n\t function reset(index) {\n\t for (index in queue) {\n\t remove(index);\n\t }\n\t }\n\t\n\t // initiate upload process\n\t function start() {\n\t if (!queue_running) {\n\t queue_running = true;\n\t process();\n\t }\n\t }\n\t\n\t // stop upload process\n\t function stop() {\n\t queue_stop = true;\n\t }\n\t\n\t // set options\n\t function configure(options) {\n\t opts = $.extend({}, opts, options);\n\t return opts;\n\t }\n\t\n\t // verify browser compatibility\n\t function compatible() {\n\t return window.File && window.FormData && window.XMLHttpRequest && window.FileList;\n\t }\n\t\n\t // export functions\n\t return {\n\t 'select': select,\n\t 'add': add,\n\t 'remove': remove,\n\t 'start': start,\n\t 'stop': stop,\n\t 'reset': reset,\n\t 'configure': configure,\n\t 'compatible': compatible\n\t };\n\t };\n\t})(jQuery);\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1), __webpack_require__(2)))\n\n/***/ }),\n/* 64 */,\n/* 65 */,\n/* 66 */,\n/* 67 */,\n/* 68 */,\n/* 69 */,\n/* 70 */,\n/* 71 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(6), __webpack_require__(5), __webpack_require__(16)], __WEBPACK_AMD_DEFINE_RESULT__ = function (baseMVC, _l) {\n\t // =============================================================================\n\t /** A view on any model that has a 'annotation' attribute\n\t */\n\t var AnnotationEditor = Backbone.View.extend(baseMVC.LoggableMixin).extend(baseMVC.HiddenUntilActivatedViewMixin).extend({\n\t\n\t tagName: 'div',\n\t className: 'annotation-display',\n\t\n\t /** Set up listeners, parse options */\n\t initialize: function (options) {\n\t options = options || {};\n\t this.tooltipConfig = options.tooltipConfig || { placement: 'bottom' };\n\t //console.debug( this, options );\n\t // only listen to the model only for changes to annotations\n\t this.listenTo(this.model, 'change:annotation', function () {\n\t this.render();\n\t });\n\t this.hiddenUntilActivated(options.$activator, options);\n\t },\n\t\n\t /** Build the DOM elements, call select to on the created input, and set up behaviors */\n\t render: function () {\n\t var view = this;\n\t this.$el.html(this._template());\n\t\n\t //TODO: handle empties better\n\t this.$annotation().make_text_editable({\n\t use_textarea: true,\n\t on_finish: function (newAnnotation) {\n\t view.$annotation().text(newAnnotation);\n\t view.model.save({ annotation: newAnnotation }, { silent: true }).fail(function () {\n\t view.$annotation().text(view.model.previous('annotation'));\n\t });\n\t }\n\t });\n\t return this;\n\t },\n\t\n\t /** @returns {String} the html text used to build the view's DOM */\n\t _template: function () {\n\t var annotation = this.model.get('annotation');\n\t return [\n\t //TODO: make prompt optional\n\t '',\n\t // set up initial tags by adding as CSV to input vals (necc. to init select2)\n\t '
', _.escape(annotation), '
'].join('');\n\t },\n\t\n\t /** @returns {jQuery} the main element for this view */\n\t $annotation: function () {\n\t return this.$el.find('.annotation');\n\t },\n\t\n\t /** shut down event listeners and remove this view's DOM */\n\t remove: function () {\n\t this.$annotation.off();\n\t this.stopListening(this.model);\n\t Backbone.View.prototype.remove.call(this);\n\t },\n\t\n\t /** string rep */\n\t toString: function () {\n\t return ['AnnotationEditor(', this.model + '', ')'].join('');\n\t }\n\t });\n\t // =============================================================================\n\t return {\n\t AnnotationEditor: AnnotationEditor\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2)))\n\n/***/ }),\n/* 72 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(jQuery) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(2), __webpack_require__(3), __webpack_require__(6)], __WEBPACK_AMD_DEFINE_RESULT__ = function (_, Backbone, BASE_MVC) {\n\t 'use strict';\n\t\n\t //=============================================================================\n\t /**\n\t * A Collection that can be limited/offset/re-ordered/filtered.\n\t * @type {Backbone.Collection}\n\t */\n\t\n\t var ControlledFetchCollection = Backbone.Collection.extend({\n\t\n\t /** call setOrder on initialization to build the comparator based on options */\n\t initialize: function (models, options) {\n\t Backbone.Collection.prototype.initialize.call(this, models, options);\n\t this.setOrder(options.order || this.order, { silent: true });\n\t },\n\t\n\t /** set up to track order changes and re-sort when changed */\n\t _setUpListeners: function () {\n\t return this.on({\n\t 'changed-order': this.sort\n\t });\n\t },\n\t\n\t /** override to provide order and offsets based on instance vars, set limit if passed,\n\t * and set allFetched/fire 'all-fetched' when xhr returns\n\t */\n\t fetch: function (options) {\n\t options = this._buildFetchOptions(options);\n\t // console.log( 'fetch options:', options );\n\t return Backbone.Collection.prototype.fetch.call(this, options);\n\t },\n\t\n\t /** build ajax data/parameters from options */\n\t _buildFetchOptions: function (options) {\n\t // note: we normally want options passed in to override the defaults built here\n\t // so most of these fns will generate defaults\n\t options = _.clone(options) || {};\n\t var self = this;\n\t\n\t // jquery ajax option; allows multiple q/qv for filters (instead of 'q[]')\n\t options.traditional = true;\n\t\n\t // options.data\n\t // we keep limit, offset, etc. in options *as well as move it into data* because:\n\t // - it makes fetch calling convenient to add it to a single options map (instead of as mult. args)\n\t // - it allows the std. event handlers (for fetch, etc.) to have access\n\t // to the pagination options too\n\t // (i.e. this.on( 'sync', function( options ){ if( options.limit ){ ... } }))\n\t // however, when we send to xhr/jquery we copy them to data also so that they become API query params\n\t options.data = options.data || self._buildFetchData(options);\n\t // console.log( 'data:', options.data );\n\t\n\t // options.data.filters --> options.data.q, options.data.qv\n\t var filters = this._buildFetchFilters(options);\n\t // console.log( 'filters:', filters );\n\t if (!_.isEmpty(filters)) {\n\t _.extend(options.data, this._fetchFiltersToAjaxData(filters));\n\t }\n\t // console.log( 'data:', options.data );\n\t return options;\n\t },\n\t\n\t /** Build the dictionary to send to fetch's XHR as data */\n\t _buildFetchData: function (options) {\n\t var defaults = {};\n\t if (this.order) {\n\t defaults.order = this.order;\n\t }\n\t return _.defaults(_.pick(options, this._fetchParams), defaults);\n\t },\n\t\n\t /** These attribute keys are valid params to fetch/API-index */\n\t _fetchParams: [\n\t /** model dependent string to control the order of models returned */\n\t 'order',\n\t /** limit the number of models returned from a fetch */\n\t 'limit',\n\t /** skip this number of models when fetching */\n\t 'offset',\n\t /** what series of attributes to return (model dependent) */\n\t 'view',\n\t /** individual keys to return for the models (see api/histories.index) */\n\t 'keys'],\n\t\n\t /** add any needed filters here based on collection state */\n\t _buildFetchFilters: function (options) {\n\t // override\n\t return _.clone(options.filters || {});\n\t },\n\t\n\t /** Convert dictionary filters to qqv style arrays */\n\t _fetchFiltersToAjaxData: function (filters) {\n\t // return as a map so ajax.data can extend from it\n\t var filterMap = {\n\t q: [],\n\t qv: []\n\t };\n\t _.each(filters, function (v, k) {\n\t // don't send if filter value is empty\n\t if (v === undefined || v === '') {\n\t return;\n\t }\n\t // json to python\n\t if (v === true) {\n\t v = 'True';\n\t }\n\t if (v === false) {\n\t v = 'False';\n\t }\n\t if (v === null) {\n\t v = 'None';\n\t }\n\t // map to k/v arrays (q/qv)\n\t filterMap.q.push(k);\n\t filterMap.qv.push(v);\n\t });\n\t return filterMap;\n\t },\n\t\n\t /** override to reset allFetched flag to false */\n\t reset: function (models, options) {\n\t this.allFetched = false;\n\t return Backbone.Collection.prototype.reset.call(this, models, options);\n\t },\n\t\n\t // ........................................................................ order\n\t order: null,\n\t\n\t /** @type {Object} map of collection available sorting orders containing comparator fns */\n\t comparators: {\n\t 'update_time': BASE_MVC.buildComparator('update_time', { ascending: false }),\n\t 'update_time-asc': BASE_MVC.buildComparator('update_time', { ascending: true }),\n\t 'create_time': BASE_MVC.buildComparator('create_time', { ascending: false }),\n\t 'create_time-asc': BASE_MVC.buildComparator('create_time', { ascending: true })\n\t },\n\t\n\t /** set the order and comparator for this collection then sort with the new order\n\t * @event 'changed-order' passed the new order and the collection\n\t */\n\t setOrder: function (order, options) {\n\t options = options || {};\n\t var collection = this;\n\t var comparator = collection.comparators[order];\n\t if (_.isUndefined(comparator)) {\n\t throw new Error('unknown order: ' + order);\n\t }\n\t // if( _.isUndefined( comparator ) ){ return; }\n\t if (comparator === collection.comparator) {\n\t return;\n\t }\n\t\n\t var oldOrder = collection.order;\n\t collection.order = order;\n\t collection.comparator = comparator;\n\t\n\t if (!options.silent) {\n\t collection.trigger('changed-order', options);\n\t }\n\t return collection;\n\t }\n\t\n\t });\n\t\n\t //=============================================================================\n\t /**\n\t *\n\t */\n\t var PaginatedCollection = ControlledFetchCollection.extend({\n\t\n\t /** @type {Number} limit used for each page's fetch */\n\t limitPerPage: 500,\n\t\n\t initialize: function (models, options) {\n\t ControlledFetchCollection.prototype.initialize.call(this, models, options);\n\t this.currentPage = options.currentPage || 0;\n\t },\n\t\n\t getTotalItemCount: function () {\n\t return this.length;\n\t },\n\t\n\t shouldPaginate: function () {\n\t return this.getTotalItemCount() >= this.limitPerPage;\n\t },\n\t\n\t getLastPage: function () {\n\t return Math.floor(this.getTotalItemCount() / this.limitPerPage);\n\t },\n\t\n\t getPageCount: function () {\n\t return this.getLastPage() + 1;\n\t },\n\t\n\t getPageLimitOffset: function (pageNum) {\n\t pageNum = this.constrainPageNum(pageNum);\n\t return {\n\t limit: this.limitPerPage,\n\t offset: pageNum * this.limitPerPage\n\t };\n\t },\n\t\n\t constrainPageNum: function (pageNum) {\n\t return Math.max(0, Math.min(pageNum, this.getLastPage()));\n\t },\n\t\n\t /** fetch the next page of data */\n\t fetchPage: function (pageNum, options) {\n\t var self = this;\n\t pageNum = self.constrainPageNum(pageNum);\n\t self.currentPage = pageNum;\n\t options = _.defaults(options || {}, self.getPageLimitOffset(pageNum));\n\t\n\t self.trigger('fetching-more');\n\t return self.fetch(options).always(function () {\n\t self.trigger('fetching-more-done');\n\t });\n\t },\n\t\n\t fetchCurrentPage: function (options) {\n\t return this.fetchPage(this.currentPage, options);\n\t },\n\t\n\t fetchPrevPage: function (options) {\n\t return this.fetchPage(this.currentPage - 1, options);\n\t },\n\t\n\t fetchNextPage: function (options) {\n\t return this.fetchPage(this.currentPage + 1, options);\n\t }\n\t });\n\t\n\t //=============================================================================\n\t /**\n\t * A Collection that will load more elements without reseting.\n\t */\n\t var InfinitelyScrollingCollection = ControlledFetchCollection.extend({\n\t\n\t /** @type {Number} limit used for the first fetch (or a reset) */\n\t limitOnFirstFetch: null,\n\t /** @type {Number} limit used for each subsequent fetch */\n\t limitPerFetch: 100,\n\t\n\t initialize: function (models, options) {\n\t ControlledFetchCollection.prototype.initialize.call(this, models, options);\n\t /** @type {Integer} number of contents to return from the first fetch */\n\t this.limitOnFirstFetch = options.limitOnFirstFetch || this.limitOnFirstFetch;\n\t /** @type {Integer} limit for every fetch after the first */\n\t this.limitPerFetch = options.limitPerFetch || this.limitPerFetch;\n\t /** @type {Boolean} are all contents fetched? */\n\t this.allFetched = false;\n\t /** @type {Integer} what was the offset of the last content returned */\n\t this.lastFetched = options.lastFetched || 0;\n\t },\n\t\n\t /** build ajax data/parameters from options */\n\t _buildFetchOptions: function (options) {\n\t // options (options for backbone.fetch and jquery.ajax generally)\n\t // backbone option; false here to make fetching an addititive process\n\t options.remove = options.remove || false;\n\t return ControlledFetchCollection.prototype._buildFetchOptions.call(this, options);\n\t },\n\t\n\t /** fetch the first 'page' of data */\n\t fetchFirst: function (options) {\n\t // console.log( 'ControlledFetchCollection.fetchFirst:', options );\n\t options = options ? _.clone(options) : {};\n\t this.allFetched = false;\n\t this.lastFetched = 0;\n\t return this.fetchMore(_.defaults(options, {\n\t reset: true,\n\t limit: this.limitOnFirstFetch\n\t }));\n\t },\n\t\n\t /** fetch the next page of data */\n\t fetchMore: function (options) {\n\t // console.log( 'ControlledFetchCollection.fetchMore:', options );\n\t options = _.clone(options || {});\n\t var collection = this;\n\t\n\t // console.log( 'fetchMore, options.reset:', options.reset );\n\t if (!options.reset && collection.allFetched) {\n\t return jQuery.when();\n\t }\n\t\n\t // TODO: this fails in the edge case where\n\t // the first fetch offset === limit (limit 4, offset 4, collection.length 4)\n\t options.offset = options.reset ? 0 : options.offset || collection.lastFetched;\n\t var limit = options.limit = options.limit || collection.limitPerFetch || null;\n\t // console.log( 'fetchMore, limit:', limit, 'offset:', options.offset );\n\t\n\t collection.trigger('fetching-more');\n\t return collection.fetch(options).always(function () {\n\t collection.trigger('fetching-more-done');\n\t })\n\t // maintain allFetched flag and trigger if all were fetched this time\n\t .done(function _postFetchMore(fetchedData) {\n\t var numFetched = _.isArray(fetchedData) ? fetchedData.length : 0;\n\t collection.lastFetched += numFetched;\n\t // console.log( 'fetchMore, lastFetched:', collection.lastFetched );\n\t // anything less than a full page means we got all there is to get\n\t if (!limit || numFetched < limit) {\n\t collection.allFetched = true;\n\t collection.trigger('all-fetched', this);\n\t }\n\t });\n\t },\n\t\n\t /** fetch all the collection */\n\t fetchAll: function (options) {\n\t // whitelist options to prevent allowing limit/offset/filters\n\t // (use vanilla fetch instead)\n\t options = options || {};\n\t var self = this;\n\t options = _.pick(options, 'silent');\n\t options.filters = {};\n\t return self.fetch(options).done(function (fetchData) {\n\t self.allFetched = true;\n\t self.trigger('all-fetched', self);\n\t });\n\t }\n\t });\n\t\n\t //==============================================================================\n\t return {\n\t ControlledFetchCollection: ControlledFetchCollection,\n\t PaginatedCollection: PaginatedCollection,\n\t InfinitelyScrollingCollection: InfinitelyScrollingCollection\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1)))\n\n/***/ }),\n/* 73 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t\n\t /* For presentation-related functionality shared across collection creators.\n\t Particularily overlapping functionality related to name processing and help.\n\t */\n\t var CollectionCreatorMixin = {\n\t\n\t /** add (or clear if clear is truthy) a validation warning to the DOM element described in what */\n\t _validationWarning: function (what, clear) {\n\t var VALIDATION_CLASS = 'validation-warning';\n\t if (what === 'name') {\n\t what = this.$('.collection-name').add(this.$('.collection-name-prompt'));\n\t this.$('.collection-name').focus().select();\n\t }\n\t if (clear) {\n\t what = what || this.$('.' + VALIDATION_CLASS);\n\t what.removeClass(VALIDATION_CLASS);\n\t } else {\n\t what.addClass(VALIDATION_CLASS);\n\t }\n\t },\n\t\n\t _changeHideOriginals: function (ev) {\n\t this.hideOriginals = this.$('.hide-originals').prop(\"checked\");\n\t },\n\t\n\t // ........................................................................ footer\n\t /** handle a collection name change */\n\t _changeName: function (ev) {\n\t this._validationWarning('name', !!this._getName());\n\t },\n\t\n\t /** check for enter key press when in the collection name and submit */\n\t _nameCheckForEnter: function (ev) {\n\t if (ev.keyCode === 13 && !this.blocking) {\n\t this._clickCreate();\n\t }\n\t },\n\t\n\t /** get the current collection name */\n\t _getName: function () {\n\t return _.escape(this.$('.collection-name').val());\n\t },\n\t\n\t // ........................................................................ header\n\t /** expand help */\n\t _clickMoreHelp: function (ev) {\n\t ev.stopPropagation();\n\t this.$('.main-help').addClass('expanded');\n\t this.$('.more-help').hide();\n\t },\n\t /** collapse help */\n\t _clickLessHelp: function (ev) {\n\t ev.stopPropagation();\n\t this.$('.main-help').removeClass('expanded');\n\t this.$('.more-help').show();\n\t },\n\t /** toggle help */\n\t _toggleHelp: function (ev) {\n\t ev.stopPropagation();\n\t this.$('.main-help').toggleClass('expanded');\n\t this.$('.more-help').toggle();\n\t },\n\t\n\t /** show an alert on the top of the interface containing message (alertClass is bootstrap's alert-*) */\n\t _showAlert: function (message, alertClass) {\n\t alertClass = alertClass || 'alert-danger';\n\t this.$('.main-help').hide();\n\t this.$('.header .alert').attr('class', 'alert alert-dismissable').addClass(alertClass).show().find('.alert-message').html(message);\n\t },\n\t /** hide the alerts at the top */\n\t _hideAlert: function (message) {\n\t this.$('.main-help').show();\n\t this.$('.header .alert').hide();\n\t },\n\t\n\t _cancelCreate: function (ev) {\n\t if (typeof this.oncancel === 'function') {\n\t this.oncancel.call(this);\n\t }\n\t },\n\t\n\t /** attempt to create the current collection */\n\t _clickCreate: function (ev) {\n\t var name = this._getName();\n\t if (!name) {\n\t this._validationWarning('name');\n\t } else if (!this.blocking) {\n\t this.createList(name);\n\t }\n\t },\n\t\n\t _setUpCommonSettings: function (attributes) {\n\t this.hideOriginals = attributes.defaultHideSourceItems || false;\n\t },\n\t\n\t /** render the footer, completion controls, and cancel controls */\n\t _renderFooter: function (speed, callback) {\n\t var instance = this;\n\t var $footer = this.$('.footer').empty().html(this.templates.footer());\n\t _.each(this.footerSettings, function (property, selector) {\n\t this.$(selector).prop('checked', instance[property]);\n\t });\n\t if (typeof this.oncancel === 'function') {\n\t this.$('.cancel-create.btn').show();\n\t }\n\t return $footer;\n\t },\n\t\n\t _creatorTemplates: {\n\t main: _.template(['', '', ''].join(''))\n\t }\n\t\n\t };\n\t\n\t //==============================================================================\n\t return {\n\t CollectionCreatorMixin: CollectionCreatorMixin\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2)))\n\n/***/ }),\n/* 74 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(83), __webpack_require__(36), __webpack_require__(35), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (LIST_VIEW, DC_MODEL, DC_LI, BASE_MVC, _l) {\n\t\n\t 'use strict';\n\t\n\t var logNamespace = 'collections';\n\t /* =============================================================================\n\t TODO:\n\t \n\t ============================================================================= */\n\t /** @class non-editable, read-only View/Controller for a dataset collection.\n\t */\n\t var _super = LIST_VIEW.ModelListPanel;\n\t var CollectionView = _super.extend(\n\t /** @lends CollectionView.prototype */{\n\t //MODEL is either a DatasetCollection (or subclass) or a DatasetCollectionElement (list of pairs)\n\t _logNamespace: logNamespace,\n\t\n\t className: _super.prototype.className + ' dataset-collection-panel',\n\t\n\t /** sub view class used for datasets */\n\t DatasetDCEViewClass: DC_LI.DatasetDCEListItemView,\n\t /** sub view class used for nested collections */\n\t NestedDCDCEViewClass: DC_LI.NestedDCDCEListItemView,\n\t /** key of attribute in model to assign to this.collection */\n\t modelCollectionKey: 'elements',\n\t\n\t // ......................................................................... SET UP\n\t /** Set up the view, set up storage, bind listeners to HistoryContents events\n\t * @param {Object} attributes optional settings for the panel\n\t */\n\t initialize: function (attributes) {\n\t _super.prototype.initialize.call(this, attributes);\n\t this.linkTarget = attributes.linkTarget || '_blank';\n\t\n\t this.hasUser = attributes.hasUser;\n\t /** A stack of panels that currently cover or hide this panel */\n\t this.panelStack = [];\n\t /** The text of the link to go back to the panel containing this one */\n\t this.parentName = attributes.parentName;\n\t /** foldout or drilldown */\n\t this.foldoutStyle = attributes.foldoutStyle || 'foldout';\n\t this.downloadUrl = this.model.attributes.url + '/download';\n\t },\n\t\n\t _queueNewRender: function ($newRender, speed) {\n\t speed = speed === undefined ? this.fxSpeed : speed;\n\t var panel = this;\n\t panel.log('_queueNewRender:', $newRender, speed);\n\t\n\t // TODO: jquery@1.12 doesn't change display when the elem has display: flex\n\t // this causes display: block for those elems after the use of show/hide animations\n\t // animations are removed from this view for now until fixed\n\t panel._swapNewRender($newRender);\n\t panel.trigger('rendered', panel);\n\t },\n\t\n\t // ------------------------------------------------------------------------ sub-views\n\t /** In this override, use model.getVisibleContents */\n\t _filterCollection: function () {\n\t //TODO: should *not* be model.getVisibleContents - visibility is not model related\n\t return this.model.getVisibleContents();\n\t },\n\t\n\t /** override to return proper view class based on element_type */\n\t _getItemViewClass: function (model) {\n\t //this.debug( this + '._getItemViewClass:', model );\n\t //TODO: subclasses use DCEViewClass - but are currently unused - decide\n\t switch (model.get('element_type')) {\n\t case 'hda':\n\t return this.DatasetDCEViewClass;\n\t case 'dataset_collection':\n\t return this.NestedDCDCEViewClass;\n\t }\n\t throw new TypeError('Unknown element type:', model.get('element_type'));\n\t },\n\t\n\t /** override to add link target and anon */\n\t _getItemViewOptions: function (model) {\n\t var options = _super.prototype._getItemViewOptions.call(this, model);\n\t return _.extend(options, {\n\t linkTarget: this.linkTarget,\n\t hasUser: this.hasUser,\n\t //TODO: could move to only nested: list:paired\n\t foldoutStyle: this.foldoutStyle\n\t });\n\t },\n\t\n\t // ------------------------------------------------------------------------ collection sub-views\n\t /** In this override, add/remove expanded/collapsed model ids to/from web storage */\n\t _setUpItemViewListeners: function (view) {\n\t var panel = this;\n\t _super.prototype._setUpItemViewListeners.call(panel, view);\n\t\n\t // use pub-sub to: handle drilldown expansion and collapse\n\t panel.listenTo(view, {\n\t 'expanded:drilldown': function (v, drilldown) {\n\t this._expandDrilldownPanel(drilldown);\n\t },\n\t 'collapsed:drilldown': function (v, drilldown) {\n\t this._collapseDrilldownPanel(drilldown);\n\t }\n\t });\n\t return this;\n\t },\n\t\n\t /** Handle drill down by hiding this panels list and controls and showing the sub-panel */\n\t _expandDrilldownPanel: function (drilldown) {\n\t this.panelStack.push(drilldown);\n\t // hide this panel's controls and list, set the name for back navigation, and attach to the $el\n\t this.$('> .controls').add(this.$list()).hide();\n\t drilldown.parentName = this.model.get('name');\n\t this.$el.append(drilldown.render().$el);\n\t },\n\t\n\t /** Handle drilldown close by freeing the panel and re-rendering this panel */\n\t _collapseDrilldownPanel: function (drilldown) {\n\t this.panelStack.pop();\n\t this.render();\n\t },\n\t\n\t // ------------------------------------------------------------------------ panel events\n\t /** event map */\n\t events: {\n\t 'click .navigation .back': 'close'\n\t },\n\t\n\t /** close/remove this collection panel */\n\t close: function (event) {\n\t this.remove();\n\t this.trigger('close');\n\t },\n\t\n\t // ........................................................................ misc\n\t /** string rep */\n\t toString: function () {\n\t return 'CollectionView(' + (this.model ? this.model.get('name') : '') + ')';\n\t }\n\t });\n\t\n\t //------------------------------------------------------------------------------ TEMPLATES\n\t CollectionView.prototype.templates = function () {\n\t\n\t var controlsTemplate = BASE_MVC.wrapTemplate(['
'], 'collection');\n\t\n\t return _.extend(_.clone(_super.prototype.templates), {\n\t controls: controlsTemplate\n\t });\n\t }();\n\t\n\t // =============================================================================\n\t /** @class non-editable, read-only View/Controller for a dataset collection. */\n\t var ListCollectionView = CollectionView.extend(\n\t /** @lends ListCollectionView.prototype */{\n\t\n\t //TODO: not strictly needed - due to switch in CollectionView._getContentClass\n\t /** sub view class used for datasets */\n\t DatasetDCEViewClass: DC_LI.DatasetDCEListItemView,\n\t\n\t // ........................................................................ misc\n\t /** string rep */\n\t toString: function () {\n\t return 'ListCollectionView(' + (this.model ? this.model.get('name') : '') + ')';\n\t }\n\t });\n\t\n\t // =============================================================================\n\t /** @class non-editable, read-only View/Controller for a dataset collection. */\n\t var PairCollectionView = ListCollectionView.extend(\n\t /** @lends PairCollectionView.prototype */{\n\t\n\t // ........................................................................ misc\n\t /** string rep */\n\t toString: function () {\n\t return 'PairCollectionView(' + (this.model ? this.model.get('name') : '') + ')';\n\t }\n\t });\n\t\n\t // =============================================================================\n\t /** @class non-editable, read-only View/Controller for a dataset collection. */\n\t var ListOfPairsCollectionView = CollectionView.extend(\n\t /** @lends ListOfPairsCollectionView.prototype */{\n\t\n\t //TODO: not strictly needed - due to switch in CollectionView._getContentClass\n\t /** sub view class used for nested collections */\n\t NestedDCDCEViewClass: DC_LI.NestedDCDCEListItemView.extend({\n\t foldoutPanelClass: PairCollectionView\n\t }),\n\t\n\t // ........................................................................ misc\n\t /** string rep */\n\t toString: function () {\n\t return 'ListOfPairsCollectionView(' + (this.model ? this.model.get('name') : '') + ')';\n\t }\n\t });\n\t\n\t // =============================================================================\n\t /** @class non-editable, read-only View/Controller for a list of lists dataset collection. */\n\t var ListOfListsCollectionView = CollectionView.extend({\n\t\n\t /** sub view class used for nested collections */\n\t NestedDCDCEViewClass: DC_LI.NestedDCDCEListItemView.extend({\n\t foldoutPanelClass: PairCollectionView\n\t }),\n\t\n\t /** string rep */\n\t toString: function () {\n\t return 'ListOfListsCollectionView(' + (this.model ? this.model.get('name') : '') + ')';\n\t }\n\t });\n\t\n\t //==============================================================================\n\t return {\n\t CollectionView: CollectionView,\n\t ListCollectionView: ListCollectionView,\n\t PairCollectionView: PairCollectionView,\n\t ListOfPairsCollectionView: ListOfPairsCollectionView,\n\t ListOfListsCollectionView: ListOfListsCollectionView\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2)))\n\n/***/ }),\n/* 75 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_, $) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(11), __webpack_require__(38), __webpack_require__(48), __webpack_require__(71), __webpack_require__(17), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (STATES, DATASET_LI, TAGS, ANNOTATIONS, faIconButton, BASE_MVC, _l) {\n\t\n\t 'use strict';\n\t //==============================================================================\n\t\n\t var _super = DATASET_LI.DatasetListItemView;\n\t /** @class Editing view for DatasetAssociation.\n\t */\n\t var DatasetListItemEdit = _super.extend(\n\t /** @lends DatasetListItemEdit.prototype */{\n\t\n\t /** set up: options */\n\t initialize: function (attributes) {\n\t _super.prototype.initialize.call(this, attributes);\n\t this.hasUser = attributes.hasUser;\n\t\n\t /** allow user purge of dataset files? */\n\t this.purgeAllowed = attributes.purgeAllowed || false;\n\t\n\t //TODO: move to HiddenUntilActivatedViewMixin\n\t /** should the tags editor be shown or hidden initially? */\n\t this.tagsEditorShown = attributes.tagsEditorShown || false;\n\t /** should the tags editor be shown or hidden initially? */\n\t this.annotationEditorShown = attributes.annotationEditorShown || false;\n\t },\n\t\n\t // ......................................................................... titlebar actions\n\t /** In this override, add the other two primary actions: edit and delete */\n\t _renderPrimaryActions: function () {\n\t var actions = _super.prototype._renderPrimaryActions.call(this);\n\t if (this.model.get('state') === STATES.NOT_VIEWABLE) {\n\t return actions;\n\t }\n\t // render the display, edit attr and delete icon-buttons\n\t return _super.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(), this._renderDeleteButton()]);\n\t },\n\t\n\t //TODO: move titleButtons into state renderers, remove state checks in the buttons\n\t\n\t /** Render icon-button to edit the attributes (format, permissions, etc.) this dataset. */\n\t _renderEditButton: function () {\n\t // don't show edit while uploading, in-accessible\n\t // DO show if in error (ala previous history panel)\n\t if (this.model.get('state') === STATES.DISCARDED || !this.model.get('accessible')) {\n\t return null;\n\t }\n\t\n\t var purged = this.model.get('purged'),\n\t deleted = this.model.get('deleted'),\n\t editBtnData = {\n\t title: _l('Edit attributes'),\n\t href: this.model.urls.edit,\n\t target: this.linkTarget,\n\t faIcon: 'fa-pencil',\n\t classes: 'edit-btn'\n\t };\n\t\n\t // disable if purged or deleted and explain why in the tooltip\n\t if (deleted || purged) {\n\t editBtnData.disabled = true;\n\t if (purged) {\n\t editBtnData.title = _l('Cannot edit attributes of datasets removed from disk');\n\t } else if (deleted) {\n\t editBtnData.title = _l('Undelete dataset to edit attributes');\n\t }\n\t\n\t // disable if still uploading or new\n\t } else if (_.contains([STATES.UPLOAD, STATES.NEW], this.model.get('state'))) {\n\t editBtnData.disabled = true;\n\t editBtnData.title = _l('This dataset is not yet editable');\n\t }\n\t return faIconButton(editBtnData);\n\t },\n\t\n\t /** Render icon-button to delete this hda. */\n\t _renderDeleteButton: function () {\n\t // don't show delete if...\n\t if (!this.model.get('accessible')) {\n\t return null;\n\t }\n\t\n\t var self = this,\n\t deletedAlready = this.model.isDeletedOrPurged();\n\t return faIconButton({\n\t title: !deletedAlready ? _l('Delete') : _l('Dataset is already deleted'),\n\t disabled: deletedAlready,\n\t faIcon: 'fa-times',\n\t classes: 'delete-btn',\n\t onclick: function () {\n\t // ...bler... tooltips being left behind in DOM (hover out never called on deletion)\n\t self.$el.find('.icon-btn.delete-btn').trigger('mouseout');\n\t self.model['delete']();\n\t }\n\t });\n\t },\n\t\n\t // ......................................................................... details\n\t /** In this override, add tags and annotations controls, make the ? dbkey a link to editing page */\n\t _renderDetails: function () {\n\t //TODO: generalize to be allow different details for each state\n\t var $details = _super.prototype._renderDetails.call(this),\n\t state = this.model.get('state');\n\t\n\t if (!this.model.isDeletedOrPurged() && _.contains([STATES.OK, STATES.FAILED_METADATA], state)) {\n\t this._renderTags($details);\n\t this._renderAnnotation($details);\n\t this._makeDbkeyEditLink($details);\n\t }\n\t\n\t this._setUpBehaviors($details);\n\t return $details;\n\t },\n\t\n\t /**************************************************************************\n\t * Render help button to show tool help text without rerunning the tool.\n\t * Issue #2100\n\t */\n\t _renderToolHelpButton: function () {\n\t var datasetID = this.model.attributes.dataset_id;\n\t var jobID = this.model.attributes.creating_job;\n\t var self = this;\n\t\n\t var parseToolBuild = function (data) {\n\t var helpString = '
';\n\t if (data.name && data.help) {\n\t helpString += 'Tool help for ' + data.name + '';\n\t helpString += data.help;\n\t } else {\n\t helpString += 'Tool help is unavailable for this dataset.';\n\t }\n\t helpString += '
';\n\t self.$el.find('.details').append($.parseHTML(helpString));\n\t };\n\t var parseToolID = function (data) {\n\t $.ajax({\n\t url: Galaxy.root + 'api/tools/' + data.tool_id + '/build'\n\t }).done(function (data) {\n\t parseToolBuild(data);\n\t }).fail(function () {\n\t parseToolBuild({});\n\t });\n\t };\n\t if (Galaxy.user.id === null) {\n\t return null;\n\t }\n\t return faIconButton({\n\t title: 'Tool Help',\n\t classes: 'icon-btn',\n\t href: '#',\n\t faIcon: 'fa-question',\n\t onclick: function () {\n\t var divString = 'thdiv-' + datasetID;\n\t if (self.$el.find(\".toolhelp\").length > 0) {\n\t self.$el.find(\".toolhelp\").toggle();\n\t } else {\n\t $.ajax({\n\t url: Galaxy.root + 'api/jobs/' + jobID\n\t }).done(function (data) {\n\t parseToolID(data);\n\t }).fail(function () {\n\t console.log('Failed at recovering job information from the Galaxy API for job id \"' + jobID + '\".');\n\t });\n\t }\n\t }\n\t });\n\t },\n\t //*************************************************************************\n\t\n\t /** Add less commonly used actions in the details section based on state */\n\t _renderSecondaryActions: function () {\n\t var actions = _super.prototype._renderSecondaryActions.call(this);\n\t switch (this.model.get('state')) {\n\t case STATES.UPLOAD:\n\t case STATES.NOT_VIEWABLE:\n\t return actions;\n\t case STATES.ERROR:\n\t // error button comes first\n\t actions.unshift(this._renderErrButton());\n\t return actions.concat([this._renderRerunButton(), this._renderToolHelpButton()]);\n\t case STATES.OK:\n\t case STATES.FAILED_METADATA:\n\t return actions.concat([this._renderRerunButton(), this._renderVisualizationsButton(), this._renderToolHelpButton()]);\n\t }\n\t return actions.concat([this._renderRerunButton(), this._renderToolHelpButton()]);\n\t },\n\t\n\t /** Render icon-button to report an error on this dataset to the galaxy admin. */\n\t _renderErrButton: function () {\n\t return faIconButton({\n\t title: _l('View or report this error'),\n\t href: this.model.urls.report_error,\n\t classes: 'report-error-btn',\n\t target: this.linkTarget,\n\t faIcon: 'fa-bug'\n\t });\n\t },\n\t\n\t /** Render icon-button to re-run the job that created this dataset. */\n\t _renderRerunButton: function () {\n\t var creating_job = this.model.get('creating_job');\n\t if (this.model.get('rerunnable')) {\n\t return faIconButton({\n\t title: _l('Run this job again'),\n\t href: this.model.urls.rerun,\n\t classes: 'rerun-btn',\n\t target: this.linkTarget,\n\t faIcon: 'fa-refresh',\n\t onclick: function (ev) {\n\t ev.preventDefault();\n\t Galaxy.router.push('/', { job_id: creating_job });\n\t }\n\t });\n\t }\n\t },\n\t\n\t /** Render an icon-button or popupmenu of links based on the applicable visualizations */\n\t _renderVisualizationsButton: function () {\n\t //TODO: someday - lazyload visualizations\n\t var visualizations = this.model.get('visualizations');\n\t if (this.model.isDeletedOrPurged() || !this.hasUser || !this.model.hasData() || _.isEmpty(visualizations)) {\n\t return null;\n\t }\n\t if (!_.isObject(visualizations[0])) {\n\t this.warn('Visualizations have been switched off');\n\t return null;\n\t }\n\t\n\t var $visualizations = $(this.templates.visualizations(visualizations, this));\n\t //HACK: need to re-write those directed at galaxy_main with linkTarget\n\t $visualizations.find('[target=\"galaxy_main\"]').attr('target', this.linkTarget);\n\t // use addBack here to include the root $visualizations elem (for the case of 1 visualization)\n\t this._addScratchBookFn($visualizations.find('.visualization-link').addBack('.visualization-link'));\n\t return $visualizations;\n\t },\n\t\n\t /** add scratchbook functionality to visualization links */\n\t _addScratchBookFn: function ($links) {\n\t var li = this;\n\t $links.click(function (ev) {\n\t if (Galaxy.frame && Galaxy.frame.active) {\n\t Galaxy.frame.add({\n\t title: 'Visualization',\n\t url: $(this).attr('href')\n\t });\n\t ev.preventDefault();\n\t ev.stopPropagation();\n\t }\n\t });\n\t },\n\t\n\t //TODO: if possible move these to readonly view - but display the owner's tags/annotation (no edit)\n\t /** Render the tags list/control */\n\t _renderTags: function ($where) {\n\t if (!this.hasUser) {\n\t return;\n\t }\n\t var view = this;\n\t this.tagsEditor = new TAGS.TagsEditor({\n\t model: this.model,\n\t el: $where.find('.tags-display'),\n\t onshowFirstTime: function () {\n\t this.render();\n\t },\n\t // persist state on the hda view (and not the editor) since these are currently re-created each time\n\t onshow: function () {\n\t view.tagsEditorShown = true;\n\t },\n\t onhide: function () {\n\t view.tagsEditorShown = false;\n\t },\n\t $activator: faIconButton({\n\t title: _l('Edit dataset tags'),\n\t classes: 'tag-btn',\n\t faIcon: 'fa-tags'\n\t }).appendTo($where.find('.actions .right'))\n\t });\n\t if (this.tagsEditorShown) {\n\t this.tagsEditor.toggle(true);\n\t }\n\t },\n\t\n\t /** Render the annotation display/control */\n\t _renderAnnotation: function ($where) {\n\t if (!this.hasUser) {\n\t return;\n\t }\n\t var view = this;\n\t this.annotationEditor = new ANNOTATIONS.AnnotationEditor({\n\t model: this.model,\n\t el: $where.find('.annotation-display'),\n\t onshowFirstTime: function () {\n\t this.render();\n\t },\n\t // persist state on the hda view (and not the editor) since these are currently re-created each time\n\t onshow: function () {\n\t view.annotationEditorShown = true;\n\t },\n\t onhide: function () {\n\t view.annotationEditorShown = false;\n\t },\n\t $activator: faIconButton({\n\t title: _l('Edit dataset annotation'),\n\t classes: 'annotate-btn',\n\t faIcon: 'fa-comment'\n\t }).appendTo($where.find('.actions .right'))\n\t });\n\t if (this.annotationEditorShown) {\n\t this.annotationEditor.toggle(true);\n\t }\n\t },\n\t\n\t /** If the format/dbkey/genome_build isn't set, make the display a link to the edit page */\n\t _makeDbkeyEditLink: function ($details) {\n\t // make the dbkey a link to editing\n\t if (this.model.get('metadata_dbkey') === '?' && !this.model.isDeletedOrPurged()) {\n\t var editableDbkey = $('?').attr('href', this.model.urls.edit).attr('target', this.linkTarget);\n\t $details.find('.dbkey .value').replaceWith(editableDbkey);\n\t }\n\t },\n\t\n\t // ......................................................................... events\n\t /** event map */\n\t events: _.extend(_.clone(_super.prototype.events), {\n\t 'click .undelete-link': '_clickUndeleteLink',\n\t 'click .purge-link': '_clickPurgeLink',\n\t\n\t 'click .edit-btn': function (ev) {\n\t this.trigger('edit', this, ev);\n\t },\n\t 'click .delete-btn': function (ev) {\n\t this.trigger('delete', this, ev);\n\t },\n\t 'click .rerun-btn': function (ev) {\n\t this.trigger('rerun', this, ev);\n\t },\n\t 'click .report-err-btn': function (ev) {\n\t this.trigger('report-err', this, ev);\n\t },\n\t 'click .visualization-btn': function (ev) {\n\t this.trigger('visualize', this, ev);\n\t },\n\t 'click .dbkey a': function (ev) {\n\t this.trigger('edit', this, ev);\n\t }\n\t }),\n\t\n\t /** listener for item undelete (in the messages section) */\n\t _clickUndeleteLink: function (ev) {\n\t this.model.undelete();\n\t return false;\n\t },\n\t\n\t /** listener for item purge (in the messages section) */\n\t _clickPurgeLink: function (ev) {\n\t if (confirm(_l('This will permanently remove the data in your dataset. Are you sure?'))) {\n\t this.model.purge();\n\t }\n\t return false;\n\t },\n\t\n\t // ......................................................................... misc\n\t /** string rep */\n\t toString: function () {\n\t var modelString = this.model ? this.model + '' : '(no model)';\n\t return 'HDAEditView(' + modelString + ')';\n\t }\n\t });\n\t\n\t // ............................................................................ TEMPLATES\n\t /** underscore templates */\n\t DatasetListItemEdit.prototype.templates = function () {\n\t\n\t var warnings = _.extend({}, _super.prototype.templates.warnings, {\n\t failed_metadata: BASE_MVC.wrapTemplate([\n\t // in this override, provide a link to the edit page\n\t '<% if( dataset.state === \"failed_metadata\" ){ %>', '
', '<% } %>'], 'dataset'),\n\t\n\t deleted: BASE_MVC.wrapTemplate([\n\t // in this override, provide links to undelete or purge the dataset\n\t '<% if( dataset.deleted && !dataset.purged ){ %>',\n\t // deleted not purged\n\t '
', '<% } %>'], 'visualizations');\n\t\n\t return _.extend({}, _super.prototype.templates, {\n\t warnings: warnings,\n\t visualizations: visualizationsTemplate\n\t });\n\t }();\n\t\n\t //==============================================================================\n\t return {\n\t DatasetListItemEdit: DatasetListItemEdit\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1)))\n\n/***/ }),\n/* 76 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, jQuery) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(11), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (STATES, BASE_MVC, _l) {\n\t 'use strict';\n\t\n\t var logNamespace = 'dataset';\n\t //==============================================================================\n\t var searchableMixin = BASE_MVC.SearchableModelMixin;\n\t /** @class base model for any DatasetAssociation (HDAs, LDDAs, DatasetCollectionDAs).\n\t * No knowledge of what type (HDA/LDDA/DCDA) should be needed here.\n\t * The DA's are made searchable (by attribute) by mixing in SearchableModelMixin.\n\t */\n\t var DatasetAssociation = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(BASE_MVC.mixin(searchableMixin, /** @lends DatasetAssociation.prototype */{\n\t _logNamespace: logNamespace,\n\t\n\t /** default attributes for a model */\n\t defaults: {\n\t state: STATES.NEW,\n\t deleted: false,\n\t purged: false,\n\t name: '(unnamed dataset)',\n\t accessible: true,\n\t // sniffed datatype (sam, tabular, bed, etc.)\n\t data_type: '',\n\t file_ext: '',\n\t file_size: 0,\n\t\n\t // array of associated file types (eg. [ 'bam_index', ... ])\n\t meta_files: [],\n\t\n\t misc_blurb: '',\n\t misc_info: '',\n\t\n\t tags: []\n\t // do NOT default on annotation, as this default is valid and will be passed on 'save'\n\t // which is incorrect behavior when the model is only partially fetched (annos are not passed in summary data)\n\t //annotation : ''\n\t },\n\t\n\t /** instance vars and listeners */\n\t initialize: function (attributes, options) {\n\t this.debug(this + '(Dataset).initialize', attributes, options);\n\t\n\t //!! this state is not in trans.app.model.Dataset.states - set it here -\n\t if (!this.get('accessible')) {\n\t this.set('state', STATES.NOT_VIEWABLE);\n\t }\n\t\n\t /** Datasets rely/use some web controllers - have the model generate those URLs on startup */\n\t this.urls = this._generateUrls();\n\t\n\t this._setUpListeners();\n\t },\n\t\n\t /** returns misc. web urls for rendering things like re-run, display, etc. */\n\t _generateUrls: function () {\n\t var id = this.get('id');\n\t if (!id) {\n\t return {};\n\t }\n\t var urls = {\n\t 'purge': 'datasets/' + id + '/purge_async',\n\t 'display': 'datasets/' + id + '/display/?preview=True',\n\t 'edit': 'datasets/' + id + '/edit',\n\t 'download': 'datasets/' + id + '/display' + this._downloadQueryParameters(),\n\t 'report_error': 'dataset/errors?id=' + id,\n\t 'rerun': 'tool_runner/rerun?id=' + id,\n\t 'show_params': 'datasets/' + id + '/show_params',\n\t 'visualization': 'visualization',\n\t 'meta_download': 'dataset/get_metadata_file?hda_id=' + id + '&metadata_name='\n\t };\n\t _.each(urls, function (value, key) {\n\t urls[key] = Galaxy.root + value;\n\t });\n\t this.urls = urls;\n\t return urls;\n\t },\n\t\n\t _downloadQueryParameters: function () {\n\t return '?to_ext=' + this.get('file_ext');\n\t },\n\t\n\t /** set up any event listeners\n\t * event: state:ready fired when this DA moves into/is already in a ready state\n\t */\n\t _setUpListeners: function () {\n\t // if the state has changed and the new state is a ready state, fire an event\n\t this.on('change:state', function (currModel, newState) {\n\t this.log(this + ' has changed state:', currModel, newState);\n\t if (this.inReadyState()) {\n\t this.trigger('state:ready', currModel, newState, this.previous('state'));\n\t }\n\t });\n\t // the download url (currently) relies on having a correct file extension\n\t this.on('change:id change:file_ext', function (currModel) {\n\t this._generateUrls();\n\t });\n\t },\n\t\n\t // ........................................................................ common queries\n\t /** override to add urls */\n\t toJSON: function () {\n\t var json = Backbone.Model.prototype.toJSON.call(this);\n\t //console.warn( 'returning json?' );\n\t //return json;\n\t return _.extend(json, {\n\t urls: this.urls\n\t });\n\t },\n\t\n\t /** Is this dataset deleted or purged? */\n\t isDeletedOrPurged: function () {\n\t return this.get('deleted') || this.get('purged');\n\t },\n\t\n\t /** Is this dataset in a 'ready' state; where 'Ready' states are states where no\n\t * processing (for the ds) is left to do on the server.\n\t */\n\t inReadyState: function () {\n\t var ready = _.contains(STATES.READY_STATES, this.get('state'));\n\t return this.isDeletedOrPurged() || ready;\n\t },\n\t\n\t /** Does this model already contain detailed data (as opposed to just summary level data)? */\n\t hasDetails: function () {\n\t // if it's inaccessible assume it has everything it needs\n\t if (!this.get('accessible')) {\n\t return true;\n\t }\n\t return this.has('annotation');\n\t },\n\t\n\t /** Convenience function to match dataset.has_data. */\n\t hasData: function () {\n\t return this.get('file_size') > 0;\n\t },\n\t\n\t // ........................................................................ ajax\n\t fetch: function (options) {\n\t var dataset = this;\n\t return Backbone.Model.prototype.fetch.call(this, options).always(function () {\n\t dataset._generateUrls();\n\t });\n\t },\n\t\n\t /** override to use actual Dates objects for create/update times */\n\t parse: function (response, options) {\n\t var parsed = Backbone.Model.prototype.parse.call(this, response, options);\n\t if (parsed.create_time) {\n\t parsed.create_time = new Date(parsed.create_time);\n\t }\n\t if (parsed.update_time) {\n\t parsed.update_time = new Date(parsed.update_time);\n\t }\n\t return parsed;\n\t },\n\t\n\t /** override to wait by default */\n\t save: function (attrs, options) {\n\t options = options || {};\n\t options.wait = _.isUndefined(options.wait) ? true : options.wait;\n\t return Backbone.Model.prototype.save.call(this, attrs, options);\n\t },\n\t\n\t //NOTE: subclasses of DA's will need to implement url and urlRoot in order to have these work properly\n\t /** save this dataset, _Mark_ing it as deleted (just a flag) */\n\t 'delete': function (options) {\n\t if (this.get('deleted')) {\n\t return jQuery.when();\n\t }\n\t return this.save({ deleted: true }, options);\n\t },\n\t /** save this dataset, _Mark_ing it as undeleted */\n\t undelete: function (options) {\n\t if (!this.get('deleted') || this.get('purged')) {\n\t return jQuery.when();\n\t }\n\t return this.save({ deleted: false }, options);\n\t },\n\t\n\t /** remove the file behind this dataset from the filesystem (if permitted) */\n\t purge: function _purge(options) {\n\t //TODO: use, override model.destroy, HDA.delete({ purge: true })\n\t if (this.get('purged')) {\n\t return jQuery.when();\n\t }\n\t options = options || {};\n\t options.url = this.urls.purge;\n\t\n\t //TODO: ideally this would be a DELETE call to the api\n\t // using purge async for now\n\t var hda = this,\n\t xhr = jQuery.ajax(options);\n\t xhr.done(function (message, status, responseObj) {\n\t hda.set({ deleted: true, purged: true });\n\t });\n\t xhr.fail(function (xhr, status, message) {\n\t // Exception messages are hidden within error page including: '...not allowed in this Galaxy instance.'\n\t // unbury and re-add to xhr\n\t var error = _l(\"Unable to purge dataset\");\n\t var messageBuriedInUnfortunatelyFormattedError = 'Removal of datasets by users ' + 'is not allowed in this Galaxy instance';\n\t if (xhr.responseJSON && xhr.responseJSON.error) {\n\t error = xhr.responseJSON.error;\n\t } else if (xhr.responseText.indexOf(messageBuriedInUnfortunatelyFormattedError) !== -1) {\n\t error = messageBuriedInUnfortunatelyFormattedError;\n\t }\n\t xhr.responseText = error;\n\t hda.trigger('error', hda, xhr, options, _l(error), { error: error });\n\t });\n\t return xhr;\n\t },\n\t\n\t // ........................................................................ searching\n\t /** what attributes of an HDA will be used in a text search */\n\t searchAttributes: ['name', 'file_ext', 'genome_build', 'misc_blurb', 'misc_info', 'annotation', 'tags'],\n\t\n\t /** our attr keys don't often match the labels we display to the user - so, when using\n\t * attribute specifiers ('name=\"bler\"') in a term, allow passing in aliases for the\n\t * following attr keys.\n\t */\n\t searchAliases: {\n\t title: 'name',\n\t format: 'file_ext',\n\t database: 'genome_build',\n\t blurb: 'misc_blurb',\n\t description: 'misc_blurb',\n\t info: 'misc_info',\n\t tag: 'tags'\n\t },\n\t\n\t // ........................................................................ misc\n\t /** String representation */\n\t toString: function () {\n\t var nameAndId = this.get('id') || '';\n\t if (this.get('name')) {\n\t nameAndId = '\"' + this.get('name') + '\",' + nameAndId;\n\t }\n\t return 'Dataset(' + nameAndId + ')';\n\t }\n\t }));\n\t\n\t //==============================================================================\n\t /** @class Backbone collection for dataset associations.\n\t */\n\t var DatasetAssociationCollection = Backbone.Collection.extend(BASE_MVC.LoggableMixin).extend(\n\t /** @lends HistoryContents.prototype */{\n\t _logNamespace: logNamespace,\n\t\n\t model: DatasetAssociation,\n\t\n\t /** root api url */\n\t urlRoot: Galaxy.root + 'api/datasets',\n\t\n\t /** url fn */\n\t url: function () {\n\t return this.urlRoot;\n\t },\n\t\n\t // ........................................................................ common queries\n\t /** Get the ids of every item in this collection\n\t * @returns array of encoded ids\n\t */\n\t ids: function () {\n\t return this.map(function (item) {\n\t return item.get('id');\n\t });\n\t },\n\t\n\t /** Get contents that are not ready\n\t * @returns array of content models\n\t */\n\t notReady: function () {\n\t return this.filter(function (content) {\n\t return !content.inReadyState();\n\t });\n\t },\n\t\n\t /** return true if any datasets don't have details */\n\t haveDetails: function () {\n\t return this.all(function (dataset) {\n\t return dataset.hasDetails();\n\t });\n\t },\n\t\n\t // ........................................................................ ajax\n\t /** using a queue, perform ajaxFn on each of the models in this collection */\n\t ajaxQueue: function (ajaxFn, options) {\n\t var deferred = jQuery.Deferred(),\n\t startingLength = this.length,\n\t responses = [];\n\t\n\t if (!startingLength) {\n\t deferred.resolve([]);\n\t return deferred;\n\t }\n\t\n\t // use reverse order (stylistic choice)\n\t var ajaxFns = this.chain().reverse().map(function (dataset, i) {\n\t return function () {\n\t var xhr = ajaxFn.call(dataset, options);\n\t // if successful, notify using the deferred to allow tracking progress\n\t xhr.done(function (response) {\n\t deferred.notify({ curr: i, total: startingLength, response: response, model: dataset });\n\t });\n\t // (regardless of previous error or success) if not last ajax call, shift and call the next\n\t // if last fn, resolve deferred\n\t xhr.always(function (response) {\n\t responses.push(response);\n\t if (ajaxFns.length) {\n\t ajaxFns.shift()();\n\t } else {\n\t deferred.resolve(responses);\n\t }\n\t });\n\t };\n\t }).value();\n\t // start the queue\n\t ajaxFns.shift()();\n\t\n\t return deferred;\n\t },\n\t\n\t // ........................................................................ sorting/filtering\n\t /** return a new collection of datasets whose attributes contain the substring matchesWhat */\n\t matches: function (matchesWhat) {\n\t return this.filter(function (dataset) {\n\t return dataset.matches(matchesWhat);\n\t });\n\t },\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return ['DatasetAssociationCollection(', this.length, ')'].join('');\n\t }\n\t });\n\t\n\t //==============================================================================\n\t return {\n\t DatasetAssociation: DatasetAssociation,\n\t DatasetAssociationCollection: DatasetAssociationCollection\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ }),\n/* 77 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(jQuery, Backbone, $, _) {// This is necessary so that, when nested arrays are used in ajax/post/get methods, square brackets ('[]') are\n\t// not appended to the identifier of a nested array.\n\tjQuery.ajaxSettings.traditional = true;\n\t\n\t// dependencies\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(116), __webpack_require__(117), __webpack_require__(51)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, GridModel, Templates, PopupMenu) {\n\t\n\t // grid view\n\t return Backbone.View.extend({\n\t\n\t // model\n\t grid: null,\n\t\n\t // Initialize\n\t initialize: function (grid_config) {\n\t this.dict_format = grid_config.dict_format;\n\t var self = this;\n\t window.add_tag_to_grid_filter = function (tag_name, tag_value) {\n\t // Put tag name and value together.\n\t var tag = tag_name + (tag_value !== undefined && tag_value !== \"\" ? \":\" + tag_value : \"\");\n\t var advanced_search = $('#advanced-search').is(\":visible\");\n\t if (!advanced_search) {\n\t $('#standard-search').slideToggle('fast');\n\t $('#advanced-search').slideToggle('fast');\n\t }\n\t self.add_filter_condition(\"tags\", tag);\n\t };\n\t\n\t // set element\n\t if (this.dict_format) {\n\t this.setElement('');\n\t if (grid_config.url_base && !grid_config.items) {\n\t Utils.get({\n\t url: grid_config.url_base,\n\t success: function (response) {\n\t self.init_grid(response);\n\t }\n\t });\n\t } else {\n\t this.init_grid(grid_config);\n\t }\n\t } else {\n\t this.setElement('#grid-container');\n\t this.init_grid(grid_config);\n\t }\n\t\n\t // fix padding\n\t if (grid_config.use_panels) {\n\t $('#center').css({\n\t padding: '10px',\n\t overflow: 'auto'\n\t });\n\t }\n\t },\n\t\n\t // refresh frames\n\t handle_refresh: function (refresh_frames) {\n\t if (refresh_frames) {\n\t if ($.inArray('history', refresh_frames) > -1) {\n\t if (top.Galaxy && top.Galaxy.currHistoryPanel) {\n\t top.Galaxy.currHistoryPanel.loadCurrentHistory();\n\t }\n\t }\n\t }\n\t },\n\t\n\t // Initialize\n\t init_grid: function (grid_config) {\n\t // link grid model\n\t this.grid = new GridModel(grid_config);\n\t\n\t // get options\n\t var options = this.grid.attributes;\n\t\n\t // handle refresh requests\n\t this.handle_refresh(options.refresh_frames);\n\t\n\t // strip protocol and domain\n\t var url = this.grid.get('url_base');\n\t url = url.replace(/^.*\\/\\/[^\\/]+/, '');\n\t this.grid.set('url_base', url);\n\t\n\t // append main template\n\t this.$el.html(Templates.grid(options));\n\t\n\t // update div contents\n\t this.$el.find('#grid-table-header').html(Templates.header(options));\n\t this.$el.find('#grid-table-body').html(Templates.body(options));\n\t this.$el.find('#grid-table-footer').html(Templates.footer(options));\n\t\n\t // update message\n\t if (options.message) {\n\t this.$el.find('#grid-message').html(Templates.message(options));\n\t var self = this;\n\t if (options.use_hide_message) {\n\t setTimeout(function () {\n\t self.$el.find('#grid-message').html('');\n\t }, 5000);\n\t }\n\t }\n\t\n\t // configure elements\n\t this.init_grid_elements();\n\t this.init_grid_controls();\n\t\n\t // attach global event handler\n\t // TODO: redundant (the onload/standard page handlers do this) - but needed because these are constructed after page ready\n\t init_refresh_on_change();\n\t },\n\t\n\t // Initialize grid controls\n\t init_grid_controls: function () {\n\t\n\t // link\n\t var self = this;\n\t\n\t // Initialize grid operation button.\n\t this.$el.find('.operation-button').each(function () {\n\t $(this).off();\n\t $(this).click(function () {\n\t self.submit_operation(this);\n\t return false;\n\t });\n\t });\n\t\n\t // Initialize text filters to select text on click and use normal font when user is typing.\n\t this.$el.find('input[type=text]').each(function () {\n\t $(this).off();\n\t $(this).click(function () {\n\t $(this).select();\n\t }).keyup(function () {\n\t $(this).css('font-style', 'normal');\n\t });\n\t });\n\t\n\t // Initialize sort links.\n\t this.$el.find('.sort-link').each(function () {\n\t $(this).off();\n\t $(this).click(function () {\n\t self.set_sort_condition($(this).attr('sort_key'));\n\t return false;\n\t });\n\t });\n\t\n\t // Initialize text filters.\n\t this.$el.find('.text-filter-form').each(function () {\n\t $(this).off();\n\t $(this).submit(function () {\n\t var column_key = $(this).attr('column_key');\n\t var text_input_obj = $('#input-' + column_key + '-filter');\n\t var text_input = text_input_obj.val();\n\t text_input_obj.val('');\n\t self.add_filter_condition(column_key, text_input);\n\t return false;\n\t });\n\t });\n\t\n\t // Initialize categorical filters.\n\t this.$el.find('.text-filter-val > a').each(function () {\n\t $(this).off();\n\t $(this).click(function () {\n\t // Remove visible element.\n\t $(this).parent().remove();\n\t\n\t // Remove filter condition.\n\t self.remove_filter_condition($(this).attr('filter_key'), $(this).attr('filter_val'));\n\t\n\t // Return\n\t return false;\n\t });\n\t });\n\t\n\t // Initialize categorical filters.\n\t this.$el.find('.categorical-filter > a').each(function () {\n\t $(this).off();\n\t $(this).click(function () {\n\t self.set_categorical_filter($(this).attr('filter_key'), $(this).attr('filter_val'));\n\t return false;\n\t });\n\t });\n\t\n\t // Initialize standard, advanced search toggles.\n\t this.$el.find('.advanced-search-toggle').each(function () {\n\t $(this).off();\n\t $(this).click(function () {\n\t self.$el.find('#standard-search').slideToggle('fast');\n\t self.$el.find('#advanced-search').slideToggle('fast');\n\t return false;\n\t });\n\t });\n\t\n\t // Add event to check all box\n\t this.$el.find('#check_all').off();\n\t this.$el.find('#check_all').on('click', function () {\n\t self.check_all_items();\n\t });\n\t },\n\t\n\t // Initialize grid elements.\n\t init_grid_elements: function () {\n\t // Initialize grid selection checkboxes.\n\t this.$el.find('.grid').each(function () {\n\t var checkboxes = $(this).find(\"input.grid-row-select-checkbox\");\n\t var check_count = $(this).find(\"span.grid-selected-count\");\n\t var update_checked = function () {\n\t check_count.text($(checkboxes).filter(\":checked\").length);\n\t };\n\t\n\t $(checkboxes).each(function () {\n\t $(this).change(update_checked);\n\t });\n\t update_checked();\n\t });\n\t\n\t // Initialize ratings.\n\t if (this.$el.find('.community_rating_star').length !== 0) this.$el.find('.community_rating_star').rating({});\n\t\n\t // get options\n\t var options = this.grid.attributes;\n\t var self = this;\n\t\n\t //\n\t // add page click events\n\t //\n\t this.$el.find('.page-link > a').each(function () {\n\t $(this).click(function () {\n\t self.set_page($(this).attr('page_num'));\n\t return false;\n\t });\n\t });\n\t\n\t //\n\t // add inbound/outbound events\n\t //\n\t this.$el.find('.use-target').each(function () {\n\t $(this).click(function (e) {\n\t self.execute({\n\t href: $(this).attr('href'),\n\t target: $(this).attr('target')\n\t });\n\t return false;\n\t });\n\t });\n\t\n\t // empty grid?\n\t var items_length = options.items.length;\n\t if (items_length == 0) {\n\t return;\n\t }\n\t\n\t //\n\t // add operation popup menus\n\t //\n\t for (var i in options.items) {\n\t // get items\n\t var item = options.items[i];\n\t\n\t // get identifiers\n\t var button = this.$el.find('#grid-' + i + '-popup');\n\t button.off();\n\t var popup = new PopupMenu(button);\n\t\n\t // load details\n\t for (var j in options['operations']) {\n\t // get operation details\n\t var operation = options['operations'][j];\n\t var operation_id = operation['label'];\n\t var operation_settings = item['operation_config'][operation_id];\n\t var encode_id = item['encode_id'];\n\t\n\t // check\n\t if (operation_settings['allowed'] && operation['allow_popup']) {\n\t // popup configuration\n\t var popupConfig = {\n\t html: operation['label'],\n\t href: operation_settings['url_args'],\n\t target: operation_settings['target'],\n\t confirmation_text: operation['confirm']\n\t };\n\t\n\t // add popup function\n\t popupConfig.func = function (e) {\n\t e.preventDefault();\n\t var label = $(e.target).html();\n\t var options = this.findItemByHtml(label);\n\t self.execute(options);\n\t };\n\t\n\t // add item\n\t popup.addItem(popupConfig);\n\t }\n\t }\n\t }\n\t },\n\t\n\t // Add a condition to the grid filter; this adds the condition and refreshes the grid.\n\t add_filter_condition: function (name, value) {\n\t // Do nothing is value is empty.\n\t if (value === \"\") {\n\t return false;\n\t }\n\t\n\t // Add condition to grid.\n\t this.grid.add_filter(name, value, true);\n\t\n\t // Add button that displays filter and provides a button to delete it.\n\t var t = $(Templates.filter_element(name, value));\n\t var self = this;\n\t t.click(function () {\n\t // Remove visible element.\n\t $(this).remove();\n\t\n\t // Remove filter condition.\n\t self.remove_filter_condition(name, value);\n\t });\n\t\n\t // append to container\n\t var container = this.$el.find('#' + name + '-filtering-criteria');\n\t container.append(t);\n\t\n\t // execute\n\t this.go_page_one();\n\t this.execute();\n\t },\n\t\n\t // Remove a condition to the grid filter; this adds the condition and refreshes the grid.\n\t remove_filter_condition: function (name, value) {\n\t // Remove filter condition.\n\t this.grid.remove_filter(name, value);\n\t\n\t // Execute\n\t this.go_page_one();\n\t this.execute();\n\t },\n\t\n\t // Set sort condition for grid.\n\t set_sort_condition: function (col_key) {\n\t // Set new sort condition. New sort is col_key if sorting new column; if reversing sort on\n\t // currently sorted column, sort is reversed.\n\t var cur_sort = this.grid.get('sort_key');\n\t var new_sort = col_key;\n\t if (cur_sort.indexOf(col_key) !== -1) {\n\t // Reverse sort.\n\t if (cur_sort.substring(0, 1) !== '-') {\n\t new_sort = '-' + col_key;\n\t }\n\t }\n\t\n\t // Remove sort arrows elements.\n\t this.$el.find('.sort-arrow').remove();\n\t\n\t // Add sort arrow element to new sort column.\n\t var sort_arrow = new_sort.substring(0, 1) == '-' ? '↑' : '↓';\n\t var t = $('' + sort_arrow + '').addClass('sort-arrow');\n\t\n\t // Add to header\n\t this.$el.find('#' + col_key + '-header').append(t);\n\t\n\t // Update grid.\n\t this.grid.set('sort_key', new_sort);\n\t this.go_page_one();\n\t this.execute();\n\t },\n\t\n\t // Set new value for categorical filter.\n\t set_categorical_filter: function (name, new_value) {\n\t // Update filter hyperlinks to reflect new filter value.\n\t var category_filter = this.grid.get('categorical_filters')[name],\n\t cur_value = this.grid.get('filters')[name];\n\t var self = this;\n\t this.$el.find('.' + name + '-filter').each(function () {\n\t var text = $.trim($(this).text());\n\t var filter = category_filter[text];\n\t var filter_value = filter[name];\n\t if (filter_value == new_value) {\n\t // Remove filter link since grid will be using this filter. It is assumed that\n\t // this element has a single child, a hyperlink/anchor with text.\n\t $(this).empty();\n\t $(this).addClass('current-filter');\n\t $(this).append(text);\n\t } else if (filter_value == cur_value) {\n\t // Add hyperlink for this filter since grid will no longer be using this filter. It is assumed that\n\t // this element has a single child, a hyperlink/anchor.\n\t $(this).empty();\n\t var t = $('' + text + '');\n\t t.click(function () {\n\t self.set_categorical_filter(name, filter_value);\n\t });\n\t $(this).removeClass('current-filter');\n\t $(this).append(t);\n\t }\n\t });\n\t\n\t // Update grid.\n\t this.grid.add_filter(name, new_value);\n\t this.go_page_one();\n\t this.execute();\n\t },\n\t\n\t // Set page to view.\n\t set_page: function (new_page) {\n\t // Update page hyperlink to reflect new page.\n\t var self = this;\n\t this.$el.find('.page-link').each(function () {\n\t var id = $(this).attr('id'),\n\t page_num = parseInt(id.split('-')[2], 10),\n\t // Id has form 'page-link-\n\t cur_page = self.grid.get('cur_page'),\n\t text;\n\t if (page_num === new_page) {\n\t // Remove link to page since grid will be on this page. It is assumed that\n\t // this element has a single child, a hyperlink/anchor with text.\n\t text = $(this).children().text();\n\t $(this).empty();\n\t $(this).addClass('inactive-link');\n\t $(this).text(text);\n\t } else if (page_num === cur_page) {\n\t // Add hyperlink to this page since grid will no longer be on this page. It is assumed that\n\t // this element has a single child, a hyperlink/anchor.\n\t text = $(this).text();\n\t $(this).empty();\n\t $(this).removeClass('inactive-link');\n\t var t = $('' + text + '');\n\t t.click(function () {\n\t self.set_page(page_num);\n\t });\n\t $(this).append(t);\n\t }\n\t });\n\t\n\t if (new_page === 'all') {\n\t this.grid.set('cur_page', new_page);\n\t } else {\n\t this.grid.set('cur_page', parseInt(new_page, 10));\n\t }\n\t this.execute();\n\t },\n\t\n\t // confirmation/submission of operation request\n\t submit_operation: function (operation_button, confirmation_text) {\n\t // identify operation\n\t var operation_name = $(operation_button).val();\n\t\n\t // verify in any item is selected\n\t var number_of_checked_ids = this.$el.find('input[name=\"id\"]:checked').length;\n\t if (!number_of_checked_ids > 0) {\n\t return false;\n\t }\n\t\n\t // Check to see if there's grid confirmation text for this operation\n\t var operation = _.findWhere(this.grid.attributes.operations, { label: operation_name });\n\t if (operation && !confirmation_text) {\n\t confirmation_text = operation.confirm || '';\n\t }\n\t\n\t // collect ids\n\t var item_ids = [];\n\t this.$el.find('input[name=id]:checked').each(function () {\n\t item_ids.push($(this).val());\n\t });\n\t\n\t // execute operation\n\t this.execute({\n\t operation: operation_name,\n\t id: item_ids,\n\t confirmation_text: confirmation_text\n\t });\n\t\n\t // return\n\t return true;\n\t },\n\t\n\t check_all_items: function () {\n\t var chk_all = document.getElementById('check_all'),\n\t checks = document.getElementsByTagName('input'),\n\t total = 0,\n\t i;\n\t if (chk_all.checked === true) {\n\t for (i = 0; i < checks.length; i++) {\n\t if (checks[i].name.indexOf('id') !== -1) {\n\t checks[i].checked = true;\n\t total++;\n\t }\n\t }\n\t } else {\n\t for (i = 0; i < checks.length; i++) {\n\t if (checks[i].name.indexOf('id') !== -1) {\n\t checks[i].checked = false;\n\t }\n\t }\n\t }\n\t this.init_grid_elements();\n\t },\n\t\n\t // Go back to page one; this is useful when a filter is applied.\n\t go_page_one: function () {\n\t // Need to go back to page 1 if not showing all.\n\t var cur_page = this.grid.get('cur_page');\n\t if (cur_page !== null && cur_page !== undefined && cur_page !== 'all') {\n\t this.grid.set('cur_page', 1);\n\t }\n\t },\n\t\n\t //\n\t // execute operations and hyperlink requests\n\t //\n\t execute: function (options) {\n\t // get url\n\t var id = null;\n\t var href = null;\n\t var operation = null;\n\t var confirmation_text = null;\n\t var target = null;\n\t\n\t // check for options\n\t if (options) {\n\t // get options\n\t href = options.href;\n\t operation = options.operation;\n\t id = options.id;\n\t confirmation_text = options.confirmation_text;\n\t target = options.target;\n\t\n\t // check if input contains the operation tag\n\t if (href !== undefined && href.indexOf('operation=') != -1) {\n\t // Get operation, id in hyperlink's href.\n\t var href_parts = href.split(\"?\");\n\t if (href_parts.length > 1) {\n\t var href_parms_str = href_parts[1];\n\t var href_parms = href_parms_str.split(\"&\");\n\t for (var index = 0; index < href_parms.length; index++) {\n\t if (href_parms[index].indexOf('operation') != -1) {\n\t // Found operation parm; get operation value.\n\t operation = href_parms[index].split('=')[1];\n\t operation = operation.replace(/\\+/g, ' ');\n\t } else if (href_parms[index].indexOf('id') != -1) {\n\t // Found id parm; get id value.\n\t id = href_parms[index].split('=')[1];\n\t }\n\t }\n\t }\n\t }\n\t }\n\t\n\t // check for operation details\n\t if (operation && id) {\n\t // show confirmation box\n\t if (confirmation_text && confirmation_text != '' && confirmation_text != 'None' && confirmation_text != 'null') if (!confirm(confirmation_text)) return false;\n\t\n\t // use small characters for operation?!\n\t operation = operation.toLowerCase();\n\t\n\t // Update grid.\n\t this.grid.set({\n\t operation: operation,\n\t item_ids: id\n\t });\n\t\n\t // Do operation. If operation cannot be performed asynchronously, redirect to location.\n\t if (this.grid.can_async_op(operation) || this.dict_format) {\n\t this.update_grid();\n\t } else {\n\t this.go_to(target, href);\n\t }\n\t\n\t // done\n\t return false;\n\t }\n\t\n\t // refresh grid\n\t if (href) {\n\t this.go_to(target, href);\n\t return false;\n\t }\n\t\n\t // refresh grid\n\t if (this.grid.get('async') || this.dict_format) {\n\t this.update_grid();\n\t } else {\n\t this.go_to(target, href);\n\t }\n\t\n\t // done\n\t return false;\n\t },\n\t\n\t // go to url\n\t go_to: function (target, href) {\n\t // get aysnc status\n\t var async = this.grid.get('async');\n\t this.grid.set('async', false);\n\t\n\t // get slide status\n\t advanced_search = this.$el.find('#advanced-search').is(':visible');\n\t this.grid.set('advanced_search', advanced_search);\n\t\n\t // get default url\n\t if (!href) {\n\t href = this.grid.get('url_base') + '?' + $.param(this.grid.get_url_data());\n\t }\n\t\n\t // clear grid of transient request attributes.\n\t this.grid.set({\n\t operation: undefined,\n\t item_ids: undefined,\n\t async: async\n\t });\n\t switch (target) {\n\t case 'inbound':\n\t // this currently assumes that there is only a single grid shown at a time\n\t var $div = $('.grid-header').closest('.inbound');\n\t if ($div.length !== 0) {\n\t $div.load(href);\n\t return;\n\t }\n\t break;\n\t case 'top':\n\t window.top.location = href;\n\t break;\n\t default:\n\t window.location = href;\n\t }\n\t },\n\t\n\t // Update grid.\n\t update_grid: function () {\n\t // If there's an operation, do POST; otherwise, do GET.\n\t var method = this.grid.get('operation') ? 'POST' : 'GET';\n\t\n\t // Show overlay to indicate loading and prevent user actions.\n\t this.$el.find('.loading-elt-overlay').show();\n\t var self = this;\n\t $.ajax({\n\t type: method,\n\t url: self.grid.get('url_base'),\n\t data: self.grid.get_url_data(),\n\t error: function (response) {\n\t alert('Grid refresh failed');\n\t },\n\t success: function (response_text) {\n\t\n\t // backup\n\t var embedded = self.grid.get('embedded');\n\t var insert = self.grid.get('insert');\n\t\n\t // request new configuration\n\t var json = self.dict_format ? response_text : $.parseJSON(response_text);\n\t\n\t // update\n\t json.embedded = embedded;\n\t json.insert = insert;\n\t\n\t // Initialize new grid config\n\t self.init_grid(json);\n\t\n\t // Hide loading overlay.\n\t self.$el.find('.loading-elt-overlay').hide();\n\t },\n\t complete: function () {\n\t // Clear grid of transient request attributes.\n\t self.grid.set({\n\t operation: undefined,\n\t item_ids: undefined\n\t });\n\t }\n\t });\n\t }\n\t });\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1), __webpack_require__(3), __webpack_require__(1), __webpack_require__(2)))\n\n/***/ }),\n/* 78 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(38), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (DATASET_LI, BASE_MVC, _l) {\n\t\n\t 'use strict';\n\t\n\t //==============================================================================\n\t\n\t var _super = DATASET_LI.DatasetListItemView;\n\t /** @class Read only view for HistoryDatasetAssociation.\n\t * Since there are no controls on the HDAView to hide the dataset,\n\t * the primary thing this class does (currently) is override templates\n\t * to render the HID.\n\t */\n\t var HDAListItemView = _super.extend(\n\t /** @lends HDAListItemView.prototype */{\n\t\n\t className: _super.prototype.className + \" history-content\",\n\t\n\t initialize: function (attributes, options) {\n\t _super.prototype.initialize.call(this, attributes, options);\n\t },\n\t\n\t // ......................................................................... misc\n\t /** String representation */\n\t toString: function () {\n\t var modelString = this.model ? this.model + '' : '(no model)';\n\t return 'HDAListItemView(' + modelString + ')';\n\t }\n\t });\n\t\n\t // ............................................................................ TEMPLATES\n\t /** underscore templates */\n\t HDAListItemView.prototype.templates = function () {\n\t\n\t var titleBarTemplate = BASE_MVC.wrapTemplate([\n\t // adding the hid display to the title\n\t '
', '', '
',\n\t //TODO: remove whitespace and use margin-right\n\t '<%- dataset.hid %> ', '<%- dataset.name %>', '
'], 'dataset');\n\t\n\t var warnings = _.extend({}, _super.prototype.templates.warnings, {\n\t hidden: BASE_MVC.wrapTemplate([\n\t // add a warning when hidden\n\t '<% if( !dataset.visible ){ %>', '
', _l('This dataset has been hidden'), '
', '<% } %>'], 'dataset')\n\t });\n\t\n\t return _.extend({}, _super.prototype.templates, {\n\t titleBar: titleBarTemplate,\n\t warnings: warnings\n\t });\n\t }();\n\t\n\t //==============================================================================\n\t return {\n\t HDAListItemView: HDAListItemView\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2)))\n\n/***/ }),\n/* 79 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(76), __webpack_require__(81), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (DATASET, HISTORY_CONTENT, BASE_MVC, _l) {\n\t 'use strict';\n\t\n\t //==============================================================================\n\t\n\t var _super = DATASET.DatasetAssociation,\n\t hcontentMixin = HISTORY_CONTENT.HistoryContentMixin;\n\t /** @class (HDA) model for a Galaxy dataset contained in and related to a history.\n\t */\n\t var HistoryDatasetAssociation = _super.extend(BASE_MVC.mixin(hcontentMixin,\n\t /** @lends HistoryDatasetAssociation.prototype */{\n\t\n\t /** default attributes for a model */\n\t defaults: _.extend({}, _super.prototype.defaults, hcontentMixin.defaults, {\n\t history_content_type: 'dataset',\n\t model_class: 'HistoryDatasetAssociation'\n\t })\n\t }));\n\t\n\t //==============================================================================\n\t return {\n\t HistoryDatasetAssociation: HistoryDatasetAssociation\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2)))\n\n/***/ }),\n/* 80 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(11), __webpack_require__(35), __webpack_require__(74), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (STATES, DC_LI, DC_VIEW, BASE_MVC, _l) {\n\t\n\t 'use strict';\n\t\n\t //==============================================================================\n\t\n\t var _super = DC_LI.DCListItemView;\n\t /** @class Read only view for HistoryDatasetCollectionAssociation (a dataset collection inside a history).\n\t */\n\t var HDCAListItemView = _super.extend(\n\t /** @lends HDCAListItemView.prototype */{\n\t\n\t className: _super.prototype.className + \" history-content\",\n\t\n\t /** event listeners */\n\t _setUpListeners: function () {\n\t _super.prototype._setUpListeners.call(this);\n\t this.listenTo(this.model, {\n\t 'change:tags change:populated change:visible': function (model, options) {\n\t this.render();\n\t }\n\t });\n\t },\n\t\n\t /** Override to provide the proper collections panels as the foldout */\n\t _getFoldoutPanelClass: function () {\n\t switch (this.model.get('collection_type')) {\n\t case 'list':\n\t return DC_VIEW.ListCollectionView;\n\t case 'paired':\n\t return DC_VIEW.PairCollectionView;\n\t case 'list:paired':\n\t return DC_VIEW.ListOfPairsCollectionView;\n\t case 'list:list':\n\t return DC_VIEW.ListOfListsCollectionView;\n\t }\n\t throw new TypeError('Uknown collection_type: ' + this.model.get('collection_type'));\n\t },\n\t\n\t /** In this override, add the state as a class for use with state-based CSS */\n\t _swapNewRender: function ($newRender) {\n\t _super.prototype._swapNewRender.call(this, $newRender);\n\t //TODO: model currently has no state\n\t var state = !this.model.get('populated') ? STATES.RUNNING : STATES.OK;\n\t //if( this.model.has( 'state' ) ){\n\t this.$el.addClass('state-' + state);\n\t //}\n\t return this.$el;\n\t },\n\t\n\t // ......................................................................... misc\n\t /** String representation */\n\t toString: function () {\n\t var modelString = this.model ? this.model + '' : '(no model)';\n\t return 'HDCAListItemView(' + modelString + ')';\n\t }\n\t });\n\t\n\t /** underscore templates */\n\t HDCAListItemView.prototype.templates = function () {\n\t\n\t var warnings = _.extend({}, _super.prototype.templates.warnings, {\n\t hidden: BASE_MVC.wrapTemplate([\n\t // add a warning when hidden\n\t '<% if( !collection.visible ){ %>', '
', _l('This collection has been hidden'), '
', '<% } %>'], 'collection')\n\t });\n\t\n\t // could steal this from hda-base (or use mixed content)\n\t var titleBarTemplate = BASE_MVC.wrapTemplate([\n\t // adding the hid display to the title\n\t '
', '', '
',\n\t //TODO: remove whitespace and use margin-right\n\t '<%- collection.hid %> ', '<%- collection.name %>', '
'], 'collection');\n\t\n\t return _.extend({}, _super.prototype.templates, {\n\t warnings: warnings,\n\t titleBar: titleBarTemplate\n\t });\n\t }();\n\t\n\t //==============================================================================\n\t return {\n\t HDCAListItemView: HDCAListItemView\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2)))\n\n/***/ }),\n/* 81 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(jQuery) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(11), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (STATES, BASE_MVC, _l) {\n\t 'use strict';\n\t\n\t //==============================================================================\n\t /** @class Mixin for HistoryContents content (HDAs, HDCAs).\n\t */\n\t\n\t var HistoryContentMixin = {\n\t\n\t /** default attributes for a model */\n\t defaults: {\n\t /** parent (containing) history */\n\t history_id: null,\n\t /** some content_type (HistoryContents can contain mixed model classes) */\n\t history_content_type: null,\n\t /** indicating when/what order the content was generated in the context of the history */\n\t hid: null,\n\t /** whether the user wants the content shown (visible) */\n\t visible: true\n\t },\n\t\n\t // ........................................................................ mixed content element\n\t // In order to be part of a MIXED bbone collection, we can't rely on the id\n\t // (which may collide btwn models of different classes)\n\t // Instead, use type_id which prefixes the history_content_type so the bbone collection can differentiate\n\t idAttribute: 'type_id',\n\t\n\t // ........................................................................ common queries\n\t /** the more common alias of visible */\n\t hidden: function () {\n\t return !this.get('visible');\n\t },\n\t\n\t //TODO: remove\n\t /** based on includeDeleted, includeHidden (gen. from the container control),\n\t * would this ds show in the list of ds's?\n\t * @param {Boolean} includeDeleted are we showing deleted hdas?\n\t * @param {Boolean} includeHidden are we showing hidden hdas?\n\t */\n\t isVisible: function (includeDeleted, includeHidden) {\n\t var isVisible = true;\n\t if (!includeDeleted && (this.get('deleted') || this.get('purged'))) {\n\t isVisible = false;\n\t }\n\t if (!includeHidden && !this.get('visible')) {\n\t isVisible = false;\n\t }\n\t return isVisible;\n\t },\n\t\n\t // ........................................................................ ajax\n\t //TODO?: these are probably better done on the leaf classes\n\t /** history content goes through the 'api/histories' API */\n\t urlRoot: Galaxy.root + 'api/histories/',\n\t\n\t /** full url spec. for this content */\n\t url: function () {\n\t var url = this.urlRoot + this.get('history_id') + '/contents/' + this.get('history_content_type') + 's/' + this.get('id');\n\t return url;\n\t },\n\t\n\t /** save this content as not visible */\n\t hide: function (options) {\n\t if (!this.get('visible')) {\n\t return jQuery.when();\n\t }\n\t return this.save({ visible: false }, options);\n\t },\n\t /** save this content as visible */\n\t unhide: function (options) {\n\t if (this.get('visible')) {\n\t return jQuery.when();\n\t }\n\t return this.save({ visible: true }, options);\n\t },\n\t\n\t // ........................................................................ misc\n\t toString: function () {\n\t return [this.get('type_id'), this.get('hid'), this.get('name')].join(':');\n\t }\n\t };\n\t\n\t //==============================================================================\n\t return {\n\t HistoryContentMixin: HistoryContentMixin\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1)))\n\n/***/ }),\n/* 82 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, jQuery, _, $) {\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(45), __webpack_require__(46), __webpack_require__(72), __webpack_require__(4), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (HISTORY_CONTENTS, HISTORY_PREFS, CONTROLLED_FETCH_COLLECTION, UTILS, BASE_MVC, _l) {\n\t 'use strict';\n\t\n\t //==============================================================================\n\t /** @class Model for a Galaxy history resource - both a record of user\n\t * tool use and a collection of the datasets those tools produced.\n\t * @name History\n\t * @augments Backbone.Model\n\t */\n\t\n\t var History = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(BASE_MVC.mixin(BASE_MVC.SearchableModelMixin, /** @lends History.prototype */{\n\t _logNamespace: 'history',\n\t\n\t /** ms between fetches when checking running jobs/datasets for updates */\n\t UPDATE_DELAY: 4000,\n\t\n\t // values from api (may need more)\n\t defaults: {\n\t model_class: 'History',\n\t id: null,\n\t name: 'Unnamed History',\n\t state: 'new',\n\t\n\t deleted: false,\n\t contents_active: {},\n\t contents_states: {}\n\t },\n\t\n\t urlRoot: Galaxy.root + 'api/histories',\n\t\n\t contentsClass: HISTORY_CONTENTS.HistoryContents,\n\t\n\t /** What model fields to search with */\n\t searchAttributes: ['name', 'annotation', 'tags'],\n\t\n\t /** Adding title and singular tag */\n\t searchAliases: {\n\t title: 'name',\n\t tag: 'tags'\n\t },\n\t\n\t // ........................................................................ set up/tear down\n\t /** Set up the model\n\t * @param {Object} historyJSON model data for this History\n\t * @param {Object} options any extra settings including logger\n\t */\n\t initialize: function (historyJSON, options) {\n\t options = options || {};\n\t this.logger = options.logger || null;\n\t this.log(this + \".initialize:\", historyJSON, options);\n\t\n\t /** HistoryContents collection of the HDAs contained in this history. */\n\t this.contents = new this.contentsClass([], {\n\t history: this,\n\t historyId: this.get('id'),\n\t order: options.order\n\t });\n\t\n\t this._setUpListeners();\n\t this._setUpCollectionListeners();\n\t\n\t /** cached timeout id for the dataset updater */\n\t this.updateTimeoutId = null;\n\t },\n\t\n\t /** set up any event listeners for this history including those to the contained HDAs\n\t * events: error:contents if an error occurred with the contents collection\n\t */\n\t _setUpListeners: function () {\n\t // if the model's id changes ('current' or null -> an actual id), update the contents history_id\n\t return this.on({\n\t 'error': function (model, xhr, options, msg, details) {\n\t this.clearUpdateTimeout();\n\t },\n\t 'change:id': function (model, newId) {\n\t if (this.contents) {\n\t this.contents.historyId = newId;\n\t }\n\t }\n\t });\n\t },\n\t\n\t /** event handlers for the contents submodels */\n\t _setUpCollectionListeners: function () {\n\t if (!this.contents) {\n\t return this;\n\t }\n\t // bubble up errors\n\t return this.listenTo(this.contents, {\n\t 'error': function () {\n\t this.trigger.apply(this, jQuery.makeArray(arguments));\n\t }\n\t });\n\t },\n\t\n\t // ........................................................................ derived attributes\n\t /** */\n\t contentsShown: function () {\n\t var contentsActive = this.get('contents_active');\n\t var shown = contentsActive.active || 0;\n\t shown += this.contents.includeDeleted ? contentsActive.deleted : 0;\n\t shown += this.contents.includeHidden ? contentsActive.hidden : 0;\n\t return shown;\n\t },\n\t\n\t /** convert size in bytes to a more human readable version */\n\t nice_size: function () {\n\t var size = this.get('size');\n\t return size ? UTILS.bytesToString(size, true, 2) : _l('(empty)');\n\t },\n\t\n\t /** override to add nice_size */\n\t toJSON: function () {\n\t return _.extend(Backbone.Model.prototype.toJSON.call(this), {\n\t nice_size: this.nice_size()\n\t });\n\t },\n\t\n\t /** override to allow getting nice_size */\n\t get: function (key) {\n\t if (key === 'nice_size') {\n\t return this.nice_size();\n\t }\n\t return Backbone.Model.prototype.get.apply(this, arguments);\n\t },\n\t\n\t // ........................................................................ common queries\n\t /** T/F is this history owned by the current user (Galaxy.user)\n\t * Note: that this will return false for an anon user even if the history is theirs.\n\t */\n\t ownedByCurrUser: function () {\n\t // no currUser\n\t if (!Galaxy || !Galaxy.user) {\n\t return false;\n\t }\n\t // user is anon or history isn't owned\n\t if (Galaxy.user.isAnonymous() || Galaxy.user.id !== this.get('user_id')) {\n\t return false;\n\t }\n\t return true;\n\t },\n\t\n\t /** Return the number of running jobs assoc with this history (note: unknown === 0) */\n\t numOfUnfinishedJobs: function () {\n\t var unfinishedJobIds = this.get('non_ready_jobs');\n\t return unfinishedJobIds ? unfinishedJobIds.length : 0;\n\t },\n\t\n\t /** Return the number of running hda/hdcas in this history (note: unknown === 0) */\n\t numOfUnfinishedShownContents: function () {\n\t return this.contents.runningAndActive().length || 0;\n\t },\n\t\n\t // ........................................................................ updates\n\t _fetchContentRelatedAttributes: function () {\n\t var contentRelatedAttrs = ['size', 'non_ready_jobs', 'contents_active', 'hid_counter'];\n\t return this.fetch({ data: $.param({ keys: contentRelatedAttrs.join(',') }) });\n\t },\n\t\n\t /** check for any changes since the last time we updated (or fetch all if ) */\n\t refresh: function (options) {\n\t // console.log( this + '.refresh' );\n\t options = options || {};\n\t var self = this;\n\t\n\t // note if there was no previous update time, all summary contents will be fetched\n\t var lastUpdateTime = self.lastUpdateTime;\n\t // if we don't flip this, then a fully-fetched list will not be re-checked via fetch\n\t this.contents.allFetched = false;\n\t var fetchFn = self.contents.currentPage !== 0 ? function () {\n\t return self.contents.fetchPage(self.contents.currentPage);\n\t } : function () {\n\t return self.contents.fetchUpdated(lastUpdateTime);\n\t };\n\t // note: if there was no previous update time, all summary contents will be fetched\n\t return fetchFn().done(function (response, status, xhr) {\n\t var serverResponseDatetime;\n\t try {\n\t serverResponseDatetime = new Date(xhr.getResponseHeader('Date'));\n\t } catch (err) {}\n\t self.lastUpdateTime = serverResponseDatetime || new Date();\n\t self.checkForUpdates(options);\n\t });\n\t },\n\t\n\t /** continuously fetch updated contents every UPDATE_DELAY ms if this history's datasets or jobs are unfinished */\n\t checkForUpdates: function (options) {\n\t // console.log( this + '.checkForUpdates' );\n\t options = options || {};\n\t var delay = this.UPDATE_DELAY;\n\t var self = this;\n\t if (!self.id) {\n\t return;\n\t }\n\t\n\t function _delayThenUpdate() {\n\t // prevent buildup of updater timeouts by clearing previous if any, then set new and cache id\n\t self.clearUpdateTimeout();\n\t self.updateTimeoutId = setTimeout(function () {\n\t self.refresh(options);\n\t }, delay);\n\t }\n\t\n\t // if there are still datasets in the non-ready state, recurse into this function with the new time\n\t var nonReadyContentCount = this.numOfUnfinishedShownContents();\n\t // console.log( 'nonReadyContentCount:', nonReadyContentCount );\n\t if (nonReadyContentCount > 0) {\n\t _delayThenUpdate();\n\t } else {\n\t // no datasets are running, but currently runnning jobs may still produce new datasets\n\t // see if the history has any running jobs and continue to update if so\n\t // (also update the size for the user in either case)\n\t self._fetchContentRelatedAttributes().done(function (historyData) {\n\t // console.log( 'non_ready_jobs:', historyData.non_ready_jobs );\n\t if (self.numOfUnfinishedJobs() > 0) {\n\t _delayThenUpdate();\n\t } else {\n\t // otherwise, let listeners know that all updates have stopped\n\t self.trigger('ready');\n\t }\n\t });\n\t }\n\t },\n\t\n\t /** clear the timeout and the cached timeout id */\n\t clearUpdateTimeout: function () {\n\t if (this.updateTimeoutId) {\n\t clearTimeout(this.updateTimeoutId);\n\t this.updateTimeoutId = null;\n\t }\n\t },\n\t\n\t // ........................................................................ ajax\n\t /** override to use actual Dates objects for create/update times */\n\t parse: function (response, options) {\n\t var parsed = Backbone.Model.prototype.parse.call(this, response, options);\n\t if (parsed.create_time) {\n\t parsed.create_time = new Date(parsed.create_time);\n\t }\n\t if (parsed.update_time) {\n\t parsed.update_time = new Date(parsed.update_time);\n\t }\n\t return parsed;\n\t },\n\t\n\t /** fetch this histories data (using options) then it's contents (using contentsOptions) */\n\t fetchWithContents: function (options, contentsOptions) {\n\t options = options || {};\n\t var self = this;\n\t\n\t // console.log( this + '.fetchWithContents' );\n\t // TODO: push down to a base class\n\t options.view = 'dev-detailed';\n\t\n\t // fetch history then use history data to fetch (paginated) contents\n\t return this.fetch(options).then(function getContents(history) {\n\t self.contents.history = self;\n\t self.contents.setHistoryId(history.id);\n\t return self.fetchContents(contentsOptions);\n\t });\n\t },\n\t\n\t /** fetch this histories contents, adjusting options based on the stored history preferences */\n\t fetchContents: function (options) {\n\t options = options || {};\n\t var self = this;\n\t\n\t // we're updating, reset the update time\n\t self.lastUpdateTime = new Date();\n\t return self.contents.fetchCurrentPage(options);\n\t },\n\t\n\t /** save this history, _Mark_ing it as deleted (just a flag) */\n\t _delete: function (options) {\n\t if (this.get('deleted')) {\n\t return jQuery.when();\n\t }\n\t return this.save({ deleted: true }, options);\n\t },\n\t /** purge this history, _Mark_ing it as purged and removing all dataset data from the server */\n\t purge: function (options) {\n\t if (this.get('purged')) {\n\t return jQuery.when();\n\t }\n\t return this.save({ deleted: true, purged: true }, options);\n\t },\n\t /** save this history, _Mark_ing it as undeleted */\n\t undelete: function (options) {\n\t if (!this.get('deleted')) {\n\t return jQuery.when();\n\t }\n\t return this.save({ deleted: false }, options);\n\t },\n\t\n\t /** Make a copy of this history on the server\n\t * @param {Boolean} current if true, set the copy as the new current history (default: true)\n\t * @param {String} name name of new history (default: none - server sets to: Copy of )\n\t * @fires copied passed this history and the response JSON from the copy\n\t * @returns {xhr}\n\t */\n\t copy: function (current, name, allDatasets) {\n\t current = current !== undefined ? current : true;\n\t if (!this.id) {\n\t throw new Error('You must set the history ID before copying it.');\n\t }\n\t\n\t var postData = { history_id: this.id };\n\t if (current) {\n\t postData.current = true;\n\t }\n\t if (name) {\n\t postData.name = name;\n\t }\n\t if (!allDatasets) {\n\t postData.all_datasets = false;\n\t }\n\t postData.view = 'dev-detailed';\n\t\n\t var history = this;\n\t var copy = jQuery.post(this.urlRoot, postData);\n\t // if current - queue to setAsCurrent before firing 'copied'\n\t if (current) {\n\t return copy.then(function (response) {\n\t var newHistory = new History(response);\n\t return newHistory.setAsCurrent().done(function () {\n\t history.trigger('copied', history, response);\n\t });\n\t });\n\t }\n\t return copy.done(function (response) {\n\t history.trigger('copied', history, response);\n\t });\n\t },\n\t\n\t setAsCurrent: function () {\n\t var history = this,\n\t xhr = jQuery.getJSON(Galaxy.root + 'history/set_as_current?id=' + this.id);\n\t\n\t xhr.done(function () {\n\t history.trigger('set-as-current', history);\n\t });\n\t return xhr;\n\t },\n\t\n\t // ........................................................................ misc\n\t toString: function () {\n\t return 'History(' + this.get('id') + ',' + this.get('name') + ')';\n\t }\n\t }));\n\t\n\t //==============================================================================\n\t var _collectionSuper = CONTROLLED_FETCH_COLLECTION.InfinitelyScrollingCollection;\n\t /** @class A collection of histories (per user)\n\t * that maintains the current history as the first in the collection.\n\t * New or copied histories become the current history.\n\t */\n\t var HistoryCollection = _collectionSuper.extend(BASE_MVC.LoggableMixin).extend({\n\t _logNamespace: 'history',\n\t\n\t model: History,\n\t /** @type {String} initial order used by collection */\n\t order: 'update_time',\n\t /** @type {Number} limit used for the first fetch (or a reset) */\n\t limitOnFirstFetch: 10,\n\t /** @type {Number} limit used for each subsequent fetch */\n\t limitPerFetch: 10,\n\t\n\t initialize: function (models, options) {\n\t options = options || {};\n\t this.log('HistoryCollection.initialize', models, options);\n\t _collectionSuper.prototype.initialize.call(this, models, options);\n\t\n\t /** @type {boolean} should deleted histories be included */\n\t this.includeDeleted = options.includeDeleted || false;\n\t\n\t /** @type {String} encoded id of the history that's current */\n\t this.currentHistoryId = options.currentHistoryId;\n\t\n\t this.setUpListeners();\n\t // note: models are sent to reset *after* this fn ends; up to this point\n\t // the collection *is empty*\n\t },\n\t\n\t urlRoot: Galaxy.root + 'api/histories',\n\t url: function () {\n\t return this.urlRoot;\n\t },\n\t\n\t /** set up reflexive event handlers */\n\t setUpListeners: function setUpListeners() {\n\t return this.on({\n\t // when a history is deleted, remove it from the collection (if optionally set to do so)\n\t 'change:deleted': function (history) {\n\t // TODO: this becomes complicated when more filters are used\n\t this.debug('change:deleted', this.includeDeleted, history.get('deleted'));\n\t if (!this.includeDeleted && history.get('deleted')) {\n\t this.remove(history);\n\t }\n\t },\n\t // listen for a history copy, setting it to current\n\t 'copied': function (original, newData) {\n\t this.setCurrent(new History(newData, []));\n\t },\n\t // when a history is made current, track the id in the collection\n\t 'set-as-current': function (history) {\n\t var oldCurrentId = this.currentHistoryId;\n\t this.trigger('no-longer-current', oldCurrentId);\n\t this.currentHistoryId = history.id;\n\t }\n\t });\n\t },\n\t\n\t /** override to change view */\n\t _buildFetchData: function (options) {\n\t return _.extend(_collectionSuper.prototype._buildFetchData.call(this, options), {\n\t view: 'dev-detailed'\n\t });\n\t },\n\t\n\t /** override to filter out deleted and purged */\n\t _buildFetchFilters: function (options) {\n\t var superFilters = _collectionSuper.prototype._buildFetchFilters.call(this, options) || {};\n\t var filters = {};\n\t if (!this.includeDeleted) {\n\t filters.deleted = false;\n\t filters.purged = false;\n\t } else {\n\t // force API to return both deleted and non\n\t //TODO: when the API is updated, remove this\n\t filters.deleted = null;\n\t }\n\t return _.defaults(superFilters, filters);\n\t },\n\t\n\t /** override to fetch current as well (as it may be outside the first 10, etc.) */\n\t fetchFirst: function (options) {\n\t var self = this;\n\t // TODO: batch?\n\t var xhr = $.when();\n\t if (this.currentHistoryId) {\n\t xhr = _collectionSuper.prototype.fetchFirst.call(self, {\n\t silent: true,\n\t limit: 1,\n\t filters: {\n\t // without these a deleted current history will return [] here and block the other xhr\n\t 'purged': '',\n\t 'deleted': '',\n\t 'encoded_id-in': this.currentHistoryId\n\t }\n\t });\n\t }\n\t return xhr.then(function () {\n\t options = options || {};\n\t options.offset = 0;\n\t return self.fetchMore(options);\n\t });\n\t },\n\t\n\t /** @type {Object} map of collection available sorting orders containing comparator fns */\n\t comparators: _.extend(_.clone(_collectionSuper.prototype.comparators), {\n\t 'name': BASE_MVC.buildComparator('name', { ascending: true }),\n\t 'name-dsc': BASE_MVC.buildComparator('name', { ascending: false }),\n\t 'size': BASE_MVC.buildComparator('size', { ascending: false }),\n\t 'size-asc': BASE_MVC.buildComparator('size', { ascending: true })\n\t }),\n\t\n\t /** override to always have the current history first */\n\t sort: function (options) {\n\t options = options || {};\n\t var silent = options.silent;\n\t var currentHistory = this.remove(this.get(this.currentHistoryId));\n\t _collectionSuper.prototype.sort.call(this, _.defaults({ silent: true }, options));\n\t this.unshift(currentHistory, { silent: true });\n\t if (!silent) {\n\t this.trigger('sort', this, options);\n\t }\n\t return this;\n\t },\n\t\n\t /** create a new history and by default set it to be the current history */\n\t create: function create(data, hdas, historyOptions, xhrOptions) {\n\t //TODO: .create is actually a collection function that's overridden here\n\t var collection = this,\n\t xhr = jQuery.getJSON(Galaxy.root + 'history/create_new_current');\n\t return xhr.done(function (newData) {\n\t collection.setCurrent(new History(newData, [], historyOptions || {}));\n\t });\n\t },\n\t\n\t /** set the current history to the given history, placing it first in the collection.\n\t * Pass standard bbone options for use in unshift.\n\t * @triggers new-current passed history and this collection\n\t */\n\t setCurrent: function (history, options) {\n\t options = options || {};\n\t // new histories go in the front\n\t this.unshift(history, options);\n\t this.currentHistoryId = history.get('id');\n\t if (!options.silent) {\n\t this.trigger('new-current', history, this);\n\t }\n\t return this;\n\t },\n\t\n\t toString: function toString() {\n\t return 'HistoryCollection(' + this.length + ',current:' + this.currentHistoryId + ')';\n\t }\n\t });\n\t\n\t //==============================================================================\n\t return {\n\t History: History,\n\t HistoryCollection: HistoryCollection\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ }),\n/* 83 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, $) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(47), __webpack_require__(142), __webpack_require__(6), __webpack_require__(5), __webpack_require__(89)], __WEBPACK_AMD_DEFINE_RESULT__ = function (LIST_ITEM, LoadingIndicator, BASE_MVC, _l) {\n\t\n\t 'use strict';\n\t\n\t var logNamespace = 'list';\n\t /* ============================================================================\n\t TODO:\n\t \n\t ============================================================================ */\n\t /** @class View for a list/collection of models and the sub-views of those models.\n\t * Sub-views must (at least have the interface if not) inherit from ListItemView.\n\t * (For a list panel that also includes some 'container' model (History->HistoryContents)\n\t * use ModelWithListPanel)\n\t *\n\t * Allows for:\n\t * searching collection/sub-views\n\t * selecting/multi-selecting sub-views\n\t *\n\t * Currently used:\n\t * for dataset/dataset-choice\n\t * as superclass of ModelListPanel\n\t */\n\t var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend( /** @lends ListPanel.prototype */{\n\t _logNamespace: logNamespace,\n\t\n\t /** class to use for constructing the sub-views */\n\t viewClass: LIST_ITEM.ListItemView,\n\t /** class to used for constructing collection of sub-view models */\n\t collectionClass: Backbone.Collection,\n\t\n\t tagName: 'div',\n\t className: 'list-panel',\n\t\n\t /** (in ms) that jquery effects will use */\n\t fxSpeed: 'fast',\n\t\n\t /** string to display when the collection has no contents */\n\t emptyMsg: _l('This list is empty'),\n\t /** displayed when no items match the search terms */\n\t noneFoundMsg: _l('No matching items found'),\n\t /** string used for search placeholder */\n\t searchPlaceholder: _l('search'),\n\t\n\t // ......................................................................... SET UP\n\t /** Set up the view, set up storage, bind listeners to HistoryContents events\n\t * @param {Object} attributes optional settings for the list\n\t */\n\t initialize: function (attributes, options) {\n\t attributes = attributes || {};\n\t // set the logger if requested\n\t if (attributes.logger) {\n\t this.logger = attributes.logger;\n\t }\n\t this.log(this + '.initialize:', attributes);\n\t\n\t // ---- instance vars\n\t /** how quickly should jquery fx run? */\n\t this.fxSpeed = _.has(attributes, 'fxSpeed') ? attributes.fxSpeed : this.fxSpeed;\n\t\n\t /** filters for displaying subviews */\n\t this.filters = [];\n\t /** current search terms */\n\t this.searchFor = attributes.searchFor || '';\n\t\n\t /** loading indicator */\n\t // this.indicator = new LoadingIndicator( this.$el );\n\t\n\t /** currently showing selectors on items? */\n\t this.selecting = attributes.selecting !== undefined ? attributes.selecting : true;\n\t //this.selecting = false;\n\t\n\t /** cached selected item.model.ids to persist btwn renders */\n\t this.selected = attributes.selected || [];\n\t /** the last selected item.model.id */\n\t this.lastSelected = null;\n\t\n\t /** are sub-views draggable */\n\t this.dragItems = attributes.dragItems || false;\n\t\n\t /** list item view class (when passed models) */\n\t this.viewClass = attributes.viewClass || this.viewClass;\n\t\n\t /** list item views */\n\t this.views = [];\n\t /** list item models */\n\t this.collection = attributes.collection || this._createDefaultCollection();\n\t\n\t /** filter fns run over collection items to see if they should show in the list */\n\t this.filters = attributes.filters || [];\n\t\n\t /** override $scrollContainer fn via attributes - fn should return jq for elem to call scrollTo on */\n\t this.$scrollContainer = attributes.$scrollContainer || this.$scrollContainer;\n\t\n\t /** @type {String} generic title */\n\t this.title = attributes.title || '';\n\t /** @type {String} generic subtitle */\n\t this.subtitle = attributes.subtitle || '';\n\t\n\t this._setUpListeners();\n\t },\n\t\n\t // ------------------------------------------------------------------------ listeners\n\t /** create any event listeners for the list */\n\t _setUpListeners: function () {\n\t this.off();\n\t\n\t //TODO: move errorHandler down into list-view from history-view or\n\t // pass to global error handler (Galaxy)\n\t this.on({\n\t error: function (model, xhr, options, msg, details) {\n\t //this.errorHandler( model, xhr, options, msg, details );\n\t console.error(model, xhr, options, msg, details);\n\t },\n\t // show hide the loading indicator\n\t loading: function () {\n\t this._showLoadingIndicator('loading...', 40);\n\t },\n\t 'loading-done': function () {\n\t this._hideLoadingIndicator(40);\n\t }\n\t });\n\t\n\t // throw the first render up as a diff namespace using once (for outside consumption)\n\t this.once('rendered', function () {\n\t this.trigger('rendered:initial', this);\n\t });\n\t\n\t this._setUpCollectionListeners();\n\t this._setUpViewListeners();\n\t return this;\n\t },\n\t\n\t /** create and return a collection for when none is initially passed */\n\t _createDefaultCollection: function () {\n\t // override\n\t return new this.collectionClass([]);\n\t },\n\t\n\t /** listening for collection events */\n\t _setUpCollectionListeners: function () {\n\t this.log(this + '._setUpCollectionListeners', this.collection);\n\t this.stopListening(this.collection);\n\t\n\t // bubble up error events\n\t this.listenTo(this.collection, {\n\t error: function (model, xhr, options, msg, details) {\n\t this.trigger('error', model, xhr, options, msg, details);\n\t },\n\t update: function (collection, options) {\n\t var changes = options.changes;\n\t // console.info( collection + ', update:', changes, '\\noptions:', options );\n\t // more than one: render everything\n\t if (options.renderAll || changes.added.length + changes.removed.length > 1) {\n\t return this.renderItems();\n\t }\n\t // otherwise, let the single add/remove handlers do it\n\t if (changes.added.length === 1) {\n\t return this.addItemView(_.first(changes.added), collection, options);\n\t }\n\t if (changes.removed.length === 1) {\n\t return this.removeItemView(_.first(changes.removed), collection, options);\n\t }\n\t }\n\t });\n\t return this;\n\t },\n\t\n\t /** listening for sub-view events that bubble up with the 'view:' prefix */\n\t _setUpViewListeners: function () {\n\t this.log(this + '._setUpViewListeners');\n\t\n\t // shift to select a range\n\t this.on({\n\t 'view:selected': function (view, ev) {\n\t if (ev && ev.shiftKey && this.lastSelected) {\n\t var lastSelectedView = this.viewFromModelId(this.lastSelected);\n\t if (lastSelectedView) {\n\t this.selectRange(view, lastSelectedView);\n\t }\n\t } else if (ev && ev.altKey && !this.selecting) {\n\t this.showSelectors();\n\t }\n\t this.selected.push(view.model.id);\n\t this.lastSelected = view.model.id;\n\t },\n\t\n\t 'view:de-selected': function (view, ev) {\n\t this.selected = _.without(this.selected, view.model.id);\n\t }\n\t });\n\t },\n\t\n\t // ------------------------------------------------------------------------ rendering\n\t /** Render this content, set up ui.\n\t * @param {Number or String} speed the speed of the render\n\t */\n\t render: function (speed) {\n\t this.log(this + '.render', speed);\n\t var $newRender = this._buildNewRender();\n\t this._setUpBehaviors($newRender);\n\t this._queueNewRender($newRender, speed);\n\t return this;\n\t },\n\t\n\t /** Build a temp div containing the new children for the view's $el. */\n\t _buildNewRender: function () {\n\t this.debug(this + '(ListPanel)._buildNewRender');\n\t var $newRender = $(this.templates.el({}, this));\n\t this._renderControls($newRender);\n\t this._renderTitle($newRender);\n\t this._renderSubtitle($newRender);\n\t this._renderSearch($newRender);\n\t this.renderItems($newRender);\n\t return $newRender;\n\t },\n\t\n\t /** Build a temp div containing the new children for the view's $el. */\n\t _renderControls: function ($newRender) {\n\t this.debug(this + '(ListPanel)._renderControls');\n\t var $controls = $(this.templates.controls({}, this));\n\t $newRender.find('.controls').replaceWith($controls);\n\t return $controls;\n\t },\n\t\n\t /** return a jQuery object containing the title DOM */\n\t _renderTitle: function ($where) {\n\t //$where = $where || this.$el;\n\t //$where.find( '.title' ).replaceWith( ... )\n\t },\n\t\n\t /** return a jQuery object containing the subtitle DOM (if any) */\n\t _renderSubtitle: function ($where) {\n\t //$where = $where || this.$el;\n\t //$where.find( '.title' ).replaceWith( ... )\n\t },\n\t\n\t /** Fade out the old el, swap in the new contents, then fade in.\n\t * @param {Number or String} speed jq speed to use for rendering effects\n\t * @fires rendered when rendered\n\t */\n\t _queueNewRender: function ($newRender, speed) {\n\t speed = speed === undefined ? this.fxSpeed : speed;\n\t var panel = this;\n\t panel.log('_queueNewRender:', $newRender, speed);\n\t\n\t $(panel).queue('fx', [function (next) {\n\t panel.$el.fadeOut(speed, next);\n\t }, function (next) {\n\t panel._swapNewRender($newRender);\n\t next();\n\t }, function (next) {\n\t panel.$el.fadeIn(speed, next);\n\t }, function (next) {\n\t panel.trigger('rendered', panel);\n\t next();\n\t }]);\n\t },\n\t\n\t /** empty out the current el, move the $newRender's children in */\n\t _swapNewRender: function ($newRender) {\n\t this.$el.empty().attr('class', this.className).append($newRender.children());\n\t if (this.selecting) {\n\t this.showSelectors(0);\n\t }\n\t return this;\n\t },\n\t\n\t /** Set up any behaviors, handlers (ep. plugins) that need to be called when the entire view has been built but\n\t * not attached to the page yet.\n\t */\n\t _setUpBehaviors: function ($where) {\n\t $where = $where || this.$el;\n\t this.$controls($where).find('[title]').tooltip();\n\t // set up the pupup for actions available when multi selecting\n\t this._renderMultiselectActionMenu($where);\n\t return this;\n\t },\n\t\n\t /** render a menu containing the actions available to sets of selected items */\n\t _renderMultiselectActionMenu: function ($where) {\n\t $where = $where || this.$el;\n\t var $menu = $where.find('.list-action-menu'),\n\t actions = this.multiselectActions();\n\t if (!actions.length) {\n\t return $menu.empty();\n\t }\n\t\n\t var $newMenu = $(['
', '', '
', '
', '
'].join(''));\n\t var $actions = actions.map(function (action) {\n\t var html = ['
'].join('');\n\t return $(html).click(function (ev) {\n\t ev.preventDefault();\n\t return action.func(ev);\n\t });\n\t });\n\t $newMenu.find('ul').append($actions);\n\t $menu.replaceWith($newMenu);\n\t return $newMenu;\n\t },\n\t\n\t /** return a list of plain objects used to render multiselect actions menu. Each object should have:\n\t * html: an html string used as the anchor contents\n\t * func: a function called when the anchor is clicked (passed the click event)\n\t */\n\t multiselectActions: function () {\n\t return [];\n\t },\n\t\n\t // ------------------------------------------------------------------------ sub-$element shortcuts\n\t /** the scroll container for this panel - can be $el, $el.parent(), or grandparent depending on context */\n\t $scrollContainer: function ($where) {\n\t // override or set via attributes.$scrollContainer\n\t return ($where || this.$el).parent().parent();\n\t },\n\t /** convenience selector for the section that displays the list controls */\n\t $controls: function ($where) {\n\t return ($where || this.$el).find('> .controls');\n\t },\n\t /** list-items: where the subviews are contained in the view's dom */\n\t $list: function ($where) {\n\t return ($where || this.$el).find('> .list-items');\n\t },\n\t /** container where list messages are attached */\n\t $messages: function ($where) {\n\t //TODO: controls isn't really correct here (only for ModelListPanel)\n\t return ($where || this.$el).find('> .controls .messages');\n\t },\n\t /** the message displayed when no views can be shown (no views, none matching search) */\n\t $emptyMessage: function ($where) {\n\t return ($where || this.$el).find('> .empty-message');\n\t },\n\t\n\t // ------------------------------------------------------------------------ hda sub-views\n\t /** render the subviews for the list's collection */\n\t renderItems: function ($whereTo) {\n\t $whereTo = $whereTo || this.$el;\n\t var panel = this;\n\t panel.log(this + '.renderItems', $whereTo);\n\t\n\t var $list = panel.$list($whereTo);\n\t panel.freeViews();\n\t // console.log( 'views freed' );\n\t //TODO:? cache and re-use views?\n\t var shownModels = panel._filterCollection();\n\t // console.log( 'models filtered:', shownModels );\n\t\n\t panel.views = shownModels.map(function (itemModel) {\n\t var view = panel._createItemView(itemModel);\n\t return view;\n\t });\n\t\n\t $list.empty();\n\t // console.log( 'list emptied' );\n\t if (panel.views.length) {\n\t panel._attachItems($whereTo);\n\t // console.log( 'items attached' );\n\t }\n\t panel._renderEmptyMessage($whereTo).toggle(!panel.views.length);\n\t panel.trigger('views:ready', panel.views);\n\t\n\t // console.log( '------------------------------------------- rendering items' );\n\t return panel.views;\n\t },\n\t\n\t /** Filter the collection to only those models that should be currently viewed */\n\t _filterCollection: function () {\n\t // override this\n\t var panel = this;\n\t return panel.collection.filter(_.bind(panel._filterItem, panel));\n\t },\n\t\n\t /** Should the model be viewable in the current state?\n\t * Checks against this.filters and this.searchFor\n\t */\n\t _filterItem: function (model) {\n\t // override this\n\t var panel = this;\n\t return _.every(panel.filters.map(function (fn) {\n\t return fn.call(model);\n\t })) && (!panel.searchFor || model.matchesAll(panel.searchFor));\n\t },\n\t\n\t /** Create a view for a model and set up it's listeners */\n\t _createItemView: function (model) {\n\t var ViewClass = this._getItemViewClass(model);\n\t var options = _.extend(this._getItemViewOptions(model), {\n\t model: model\n\t });\n\t var view = new ViewClass(options);\n\t this._setUpItemViewListeners(view);\n\t return view;\n\t },\n\t\n\t /** Free a view for a model. Note: does not remove it from the DOM */\n\t _destroyItemView: function (view) {\n\t this.stopListening(view);\n\t this.views = _.without(this.views, view);\n\t },\n\t\n\t _destroyItemViews: function (view) {\n\t var self = this;\n\t self.views.forEach(function (v) {\n\t self.stopListening(v);\n\t });\n\t self.views = [];\n\t return self;\n\t },\n\t\n\t /** free any sub-views the list has */\n\t freeViews: function () {\n\t return this._destroyItemViews();\n\t },\n\t\n\t /** Get the bbone view class based on the model */\n\t _getItemViewClass: function (model) {\n\t // override this\n\t return this.viewClass;\n\t },\n\t\n\t /** Get the options passed to the new view based on the model */\n\t _getItemViewOptions: function (model) {\n\t // override this\n\t return {\n\t //logger : this.logger,\n\t fxSpeed: this.fxSpeed,\n\t expanded: false,\n\t selectable: this.selecting,\n\t selected: _.contains(this.selected, model.id),\n\t draggable: this.dragItems\n\t };\n\t },\n\t\n\t /** Set up listeners for new models */\n\t _setUpItemViewListeners: function (view) {\n\t var panel = this;\n\t // send all events to the panel, re-namspaceing them with the view prefix\n\t this.listenTo(view, 'all', function () {\n\t var args = Array.prototype.slice.call(arguments, 0);\n\t args[0] = 'view:' + args[0];\n\t panel.trigger.apply(panel, args);\n\t });\n\t\n\t // drag multiple - hijack ev.setData to add all selected items\n\t this.listenTo(view, 'draggable:dragstart', function (ev, v) {\n\t //TODO: set multiple drag data here\n\t var json = {},\n\t selected = this.getSelectedModels();\n\t if (selected.length) {\n\t json = selected.toJSON();\n\t } else {\n\t json = [v.model.toJSON()];\n\t }\n\t ev.dataTransfer.setData('text', JSON.stringify(json));\n\t //ev.dataTransfer.setDragImage( v.el, 60, 60 );\n\t }, this);\n\t\n\t return panel;\n\t },\n\t\n\t /** Attach views in this.views to the model based on $whereTo */\n\t _attachItems: function ($whereTo) {\n\t var self = this;\n\t // console.log( '_attachItems:', $whereTo, this.$list( $whereTo ) );\n\t //ASSUMES: $list has been emptied\n\t this.$list($whereTo).append(this.views.map(function (view) {\n\t return self._renderItemView$el(view);\n\t }));\n\t return this;\n\t },\n\t\n\t /** get a given subview's $el (or whatever may wrap it) and return it */\n\t _renderItemView$el: function (view) {\n\t // useful to wrap and override\n\t return view.render(0).$el;\n\t },\n\t\n\t /** render the empty/none-found message */\n\t _renderEmptyMessage: function ($whereTo) {\n\t this.debug('_renderEmptyMessage', $whereTo, this.searchFor);\n\t var text = this.searchFor ? this.noneFoundMsg : this.emptyMsg;\n\t return this.$emptyMessage($whereTo).text(text);\n\t },\n\t\n\t /** expand all item views */\n\t expandAll: function () {\n\t _.each(this.views, function (view) {\n\t view.expand();\n\t });\n\t },\n\t\n\t /** collapse all item views */\n\t collapseAll: function () {\n\t _.each(this.views, function (view) {\n\t view.collapse();\n\t });\n\t },\n\t\n\t // ------------------------------------------------------------------------ collection/views syncing\n\t /** Add a view (if the model should be viewable) to the panel */\n\t addItemView: function (model, collection, options) {\n\t // console.log( this + '.addItemView:', model );\n\t var panel = this;\n\t // get the index of the model in the list of filtered models shown by this list\n\t // in order to insert the view in the proper place\n\t //TODO:? potentially expensive\n\t var modelIndex = panel._filterCollection().indexOf(model);\n\t if (modelIndex === -1) {\n\t return undefined;\n\t }\n\t var view = panel._createItemView(model);\n\t // console.log( 'adding and rendering:', modelIndex, view.toString() );\n\t\n\t $(view).queue('fx', [function (next) {\n\t // hide the empty message first if only view\n\t if (panel.$emptyMessage().is(':visible')) {\n\t panel.$emptyMessage().fadeOut(panel.fxSpeed, next);\n\t } else {\n\t next();\n\t }\n\t }, function (next) {\n\t panel._attachView(view, modelIndex);\n\t next();\n\t }]);\n\t return view;\n\t },\n\t\n\t /** internal fn to add view (to both panel.views and panel.$list) */\n\t _attachView: function (view, modelIndex, useFx) {\n\t // console.log( this + '._attachView:', view, modelIndex, useFx );\n\t useFx = _.isUndefined(useFx) ? true : useFx;\n\t modelIndex = modelIndex || 0;\n\t var panel = this;\n\t\n\t // use the modelIndex to splice into views and insert at the proper index in the DOM\n\t panel.views.splice(modelIndex, 0, view);\n\t panel._insertIntoListAt(modelIndex, panel._renderItemView$el(view).hide());\n\t\n\t panel.trigger('view:attached', view);\n\t if (useFx) {\n\t view.$el.slideDown(panel.fxSpeed, function () {\n\t panel.trigger('view:attached:rendered');\n\t });\n\t } else {\n\t view.$el.show();\n\t panel.trigger('view:attached:rendered');\n\t }\n\t return view;\n\t },\n\t\n\t /** insert a jq object as a child of list-items at the specified *DOM index* */\n\t _insertIntoListAt: function (index, $what) {\n\t // console.log( this + '._insertIntoListAt:', index, $what );\n\t var $list = this.$list();\n\t if (index === 0) {\n\t $list.prepend($what);\n\t } else {\n\t $list.children().eq(index - 1).after($what);\n\t }\n\t return $what;\n\t },\n\t\n\t /** Remove a view from the panel (if found) */\n\t removeItemView: function (model, collection, options) {\n\t var panel = this;\n\t var view = _.find(panel.views, function (v) {\n\t return v.model === model;\n\t });\n\t if (!view) {\n\t return undefined;\n\t }\n\t panel.views = _.without(panel.views, view);\n\t panel.trigger('view:removed', view);\n\t\n\t // potentially show the empty message if no views left\n\t // use anonymous queue here - since remove can happen multiple times\n\t $({}).queue('fx', [function (next) {\n\t view.$el.fadeOut(panel.fxSpeed, next);\n\t }, function (next) {\n\t view.remove();\n\t panel.trigger('view:removed:rendered');\n\t if (!panel.views.length) {\n\t panel._renderEmptyMessage().fadeIn(panel.fxSpeed, next);\n\t } else {\n\t next();\n\t }\n\t }]);\n\t return view;\n\t },\n\t\n\t /** get views based on model.id */\n\t viewFromModelId: function (id) {\n\t return _.find(this.views, function (v) {\n\t return v.model.id === id;\n\t });\n\t },\n\t\n\t /** get views based on model */\n\t viewFromModel: function (model) {\n\t return model ? this.viewFromModelId(model.id) : undefined;\n\t },\n\t\n\t /** get views based on model properties */\n\t viewsWhereModel: function (properties) {\n\t return this.views.filter(function (view) {\n\t return _.isMatch(view.model.attributes, properties);\n\t });\n\t },\n\t\n\t /** A range of views between (and including) viewA and viewB */\n\t viewRange: function (viewA, viewB) {\n\t if (viewA === viewB) {\n\t return viewA ? [viewA] : [];\n\t }\n\t\n\t var indexA = this.views.indexOf(viewA),\n\t indexB = this.views.indexOf(viewB);\n\t\n\t // handle not found\n\t if (indexA === -1 || indexB === -1) {\n\t if (indexA === indexB) {\n\t return [];\n\t }\n\t return indexA === -1 ? [viewB] : [viewA];\n\t }\n\t // reverse if indeces are\n\t //note: end inclusive\n\t return indexA < indexB ? this.views.slice(indexA, indexB + 1) : this.views.slice(indexB, indexA + 1);\n\t },\n\t\n\t // ------------------------------------------------------------------------ searching\n\t /** render a search input for filtering datasets shown\n\t * (see SearchableMixin in base-mvc for implementation of the actual searching)\n\t * return will start the search\n\t * esc will clear the search\n\t * clicking the clear button will clear the search\n\t * uses searchInput in ui.js\n\t */\n\t _renderSearch: function ($where) {\n\t $where.find('.controls .search-input').searchInput({\n\t placeholder: this.searchPlaceholder,\n\t initialVal: this.searchFor,\n\t onfirstsearch: _.bind(this._firstSearch, this),\n\t onsearch: _.bind(this.searchItems, this),\n\t onclear: _.bind(this.clearSearch, this)\n\t });\n\t return $where;\n\t },\n\t\n\t /** What to do on the first search entered */\n\t _firstSearch: function (searchFor) {\n\t // override to load model details if necc.\n\t this.log('onFirstSearch', searchFor);\n\t return this.searchItems(searchFor);\n\t },\n\t\n\t /** filter view list to those that contain the searchFor terms */\n\t searchItems: function (searchFor, force) {\n\t this.log('searchItems', searchFor, this.searchFor, force);\n\t if (!force && this.searchFor === searchFor) {\n\t return this;\n\t }\n\t this.searchFor = searchFor;\n\t this.renderItems();\n\t this.trigger('search:searching', searchFor, this);\n\t var $search = this.$('> .controls .search-query');\n\t if ($search.val() !== searchFor) {\n\t $search.val(searchFor);\n\t }\n\t return this;\n\t },\n\t\n\t /** clear the search filters and show all views that are normally shown */\n\t clearSearch: function (searchFor) {\n\t //this.log( 'onSearchClear', this );\n\t this.searchFor = '';\n\t this.trigger('search:clear', this);\n\t this.$('> .controls .search-query').val('');\n\t this.renderItems();\n\t return this;\n\t },\n\t\n\t // ------------------------------------------------------------------------ selection\n\t /** @type Integer when the number of list item views is >= to this, don't animate selectors */\n\t THROTTLE_SELECTOR_FX_AT: 20,\n\t\n\t /** show selectors on all visible itemViews and associated controls */\n\t showSelectors: function (speed) {\n\t speed = speed !== undefined ? speed : this.fxSpeed;\n\t this.selecting = true;\n\t this.$('.list-actions').slideDown(speed);\n\t speed = this.views.length >= this.THROTTLE_SELECTOR_FX_AT ? 0 : speed;\n\t _.each(this.views, function (view) {\n\t view.showSelector(speed);\n\t });\n\t //this.selected = [];\n\t //this.lastSelected = null;\n\t },\n\t\n\t /** hide selectors on all visible itemViews and associated controls */\n\t hideSelectors: function (speed) {\n\t speed = speed !== undefined ? speed : this.fxSpeed;\n\t this.selecting = false;\n\t this.$('.list-actions').slideUp(speed);\n\t speed = this.views.length >= this.THROTTLE_SELECTOR_FX_AT ? 0 : speed;\n\t _.each(this.views, function (view) {\n\t view.hideSelector(speed);\n\t });\n\t this.selected = [];\n\t this.lastSelected = null;\n\t },\n\t\n\t /** show or hide selectors on all visible itemViews and associated controls */\n\t toggleSelectors: function () {\n\t if (!this.selecting) {\n\t this.showSelectors();\n\t } else {\n\t this.hideSelectors();\n\t }\n\t },\n\t\n\t /** select all visible items */\n\t selectAll: function (event) {\n\t _.each(this.views, function (view) {\n\t view.select(event);\n\t });\n\t },\n\t\n\t /** deselect all visible items */\n\t deselectAll: function (event) {\n\t this.lastSelected = null;\n\t _.each(this.views, function (view) {\n\t view.deselect(event);\n\t });\n\t },\n\t\n\t /** select a range of datasets between A and B */\n\t selectRange: function (viewA, viewB) {\n\t var range = this.viewRange(viewA, viewB);\n\t _.each(range, function (view) {\n\t view.select();\n\t });\n\t return range;\n\t },\n\t\n\t /** return an array of all currently selected itemViews */\n\t getSelectedViews: function () {\n\t return _.filter(this.views, function (v) {\n\t return v.selected;\n\t });\n\t },\n\t\n\t /** return a collection of the models of all currenly selected items */\n\t getSelectedModels: function () {\n\t // console.log( '(getSelectedModels)' );\n\t return new this.collection.constructor(_.map(this.getSelectedViews(), function (view) {\n\t return view.model;\n\t }));\n\t },\n\t\n\t // ------------------------------------------------------------------------ loading indicator\n\t /** hide the $el and display a loading indicator (in the $el's parent) when loading new data */\n\t _showLoadingIndicator: function (msg, speed, callback) {\n\t this.debug('_showLoadingIndicator', this.indicator, msg, speed, callback);\n\t speed = speed !== undefined ? speed : this.fxSpeed;\n\t if (!this.indicator) {\n\t this.indicator = new LoadingIndicator(this.$el);\n\t this.debug('\\t created', this.indicator);\n\t }\n\t if (!this.$el.is(':visible')) {\n\t this.indicator.show(0, callback);\n\t } else {\n\t this.$el.fadeOut(speed);\n\t this.indicator.show(msg, speed, callback);\n\t }\n\t },\n\t\n\t /** hide the loading indicator */\n\t _hideLoadingIndicator: function (speed, callback) {\n\t this.debug('_hideLoadingIndicator', this.indicator, speed, callback);\n\t speed = speed !== undefined ? speed : this.fxSpeed;\n\t if (this.indicator) {\n\t this.indicator.hide(speed, callback);\n\t }\n\t },\n\t\n\t // ------------------------------------------------------------------------ scrolling\n\t /** get the current scroll position of the panel in its parent */\n\t scrollPosition: function () {\n\t return this.$scrollContainer().scrollTop();\n\t },\n\t\n\t /** set the current scroll position of the panel in its parent */\n\t scrollTo: function (pos, speed) {\n\t speed = speed || 0;\n\t this.$scrollContainer().animate({ scrollTop: pos }, speed);\n\t return this;\n\t },\n\t\n\t /** Scrolls the panel to the top. */\n\t scrollToTop: function (speed) {\n\t return this.scrollTo(0, speed);\n\t },\n\t\n\t /** scroll to the given view in list-items */\n\t scrollToItem: function (view, speed) {\n\t if (!view) {\n\t return this;\n\t }\n\t return this;\n\t },\n\t\n\t /** Scrolls the panel to show the content with the given id. */\n\t scrollToId: function (id, speed) {\n\t return this.scrollToItem(this.viewFromModelId(id), speed);\n\t },\n\t\n\t // ------------------------------------------------------------------------ panel events\n\t /** event map */\n\t events: {\n\t 'click .select-all': 'selectAll',\n\t 'click .deselect-all': 'deselectAll'\n\t },\n\t\n\t // ------------------------------------------------------------------------ misc\n\t /** Return a string rep of the panel */\n\t toString: function () {\n\t return 'ListPanel(' + this.collection + ')';\n\t }\n\t });\n\t\n\t // ............................................................................ TEMPLATES\n\t /** underscore templates */\n\t ListPanel.prototype.templates = function () {\n\t\n\t var elTemplate = BASE_MVC.wrapTemplate([\n\t // temp container\n\t '
', '', '', '', '
']);\n\t\n\t var controlsTemplate = BASE_MVC.wrapTemplate(['
']);\n\t\n\t return {\n\t el: elTemplate,\n\t controls: controlsTemplate\n\t };\n\t }();\n\t\n\t //=============================================================================\n\t /** View for a model that has a sub-collection (e.g. History, DatasetCollection)\n\t * Allows:\n\t * the model to be reset\n\t * auto assign panel.collection to panel.model[ panel.modelCollectionKey ]\n\t *\n\t */\n\t var ModelListPanel = ListPanel.extend({\n\t\n\t /** key of attribute in model to assign to this.collection */\n\t modelCollectionKey: 'contents',\n\t\n\t initialize: function (attributes) {\n\t ListPanel.prototype.initialize.call(this, attributes);\n\t this.selecting = attributes.selecting !== undefined ? attributes.selecting : false;\n\t\n\t this.setModel(this.model, attributes);\n\t },\n\t\n\t /** release/free/shutdown old models and set up panel for new models\n\t * @fires new-model with the panel as parameter\n\t */\n\t setModel: function (model, attributes) {\n\t attributes = attributes || {};\n\t this.debug(this + '.setModel:', model, attributes);\n\t\n\t this.freeModel();\n\t this.freeViews();\n\t\n\t if (model) {\n\t var oldModelId = this.model ? this.model.get('id') : null;\n\t\n\t // set up the new model with user, logger, storage, events\n\t this.model = model;\n\t if (this.logger) {\n\t this.model.logger = this.logger;\n\t }\n\t this._setUpModelListeners();\n\t\n\t //TODO: relation btwn model, collection becoming tangled here\n\t // free the collection, and assign the new collection to either\n\t // the model[ modelCollectionKey ], attributes.collection, or an empty vanilla collection\n\t this.stopListening(this.collection);\n\t this.collection = this.model[this.modelCollectionKey] || attributes.collection || this._createDefaultCollection();\n\t this._setUpCollectionListeners();\n\t\n\t if (oldModelId && model.get('id') !== oldModelId) {\n\t this.trigger('new-model', this);\n\t }\n\t }\n\t return this;\n\t },\n\t\n\t /** free the current model and all listeners for it, free any views for the model */\n\t freeModel: function () {\n\t // stop/release the previous model, and clear cache to sub-views\n\t if (this.model) {\n\t this.stopListening(this.model);\n\t //TODO: see base-mvc\n\t //this.model.free();\n\t //this.model = null;\n\t }\n\t return this;\n\t },\n\t\n\t // ------------------------------------------------------------------------ listening\n\t /** listening for model events */\n\t _setUpModelListeners: function () {\n\t // override\n\t this.log(this + '._setUpModelListeners', this.model);\n\t // bounce model errors up to the panel\n\t this.listenTo(this.model, 'error', function () {\n\t var args = Array.prototype.slice.call(arguments, 0);\n\t //args.unshift( 'model:error' );\n\t args.unshift('error');\n\t this.trigger.apply(this, args);\n\t }, this);\n\t\n\t // debugging\n\t if (this.logger) {\n\t this.listenTo(this.model, 'all', function (event) {\n\t this.info(this + '(model)', event, arguments);\n\t });\n\t }\n\t return this;\n\t },\n\t\n\t /** Build a temp div containing the new children for the view's $el.\n\t */\n\t _renderControls: function ($newRender) {\n\t this.debug(this + '(ModelListPanel)._renderControls');\n\t var json = this.model ? this.model.toJSON() : {},\n\t $controls = $(this.templates.controls(json, this));\n\t $newRender.find('.controls').replaceWith($controls);\n\t return $controls;\n\t },\n\t\n\t // ------------------------------------------------------------------------ misc\n\t /** Return a string rep of the panel */\n\t toString: function () {\n\t return 'ModelListPanel(' + this.model + ')';\n\t }\n\t });\n\t\n\t // ............................................................................ TEMPLATES\n\t /** underscore templates */\n\t ModelListPanel.prototype.templates = function () {\n\t\n\t var controlsTemplate = BASE_MVC.wrapTemplate(['
', '
',\n\t //TODO: this is really the only difference - consider factoring titlebar out\n\t '
<%- model.name %>
', '
', '
<%- view.subtitle %>
', '', '', '
', '', '
', '
', '
', '', '', '
', '
', '
', '
', '
']);\n\t\n\t return _.extend(_.clone(ListPanel.prototype.templates), {\n\t controls: controlsTemplate\n\t });\n\t }();\n\t\n\t //=============================================================================\n\t return {\n\t ListPanel: ListPanel,\n\t ModelListPanel: ModelListPanel\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ }),\n/* 84 */,\n/* 85 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function($, _) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (_l) {\n\t 'use strict';\n\t\n\t //TODO: toastr is another possibility - I didn't see where I might add details, tho\n\t\n\t /* ============================================================================\n\t Error modals meant to replace the o-so-easy alerts.\n\t \n\t These are currently styled as errormessages but use the Galaxy.modal\n\t infrastructure to be shown/closed. They're capable of showing details in a\n\t togglable dropdown and the details are formatted in a pre.\n\t \n\t Example:\n\t errorModal( 'Heres a message', 'A Title', { some_details: 'here' });\n\t errorModal( 'Heres a message' ); // no details, title is 'Error'\n\t \n\t There are three specialized forms:\n\t offlineErrorModal a canned response for when there's no connection\n\t badGatewayErrorModal canned response for when Galaxy is restarting\n\t ajaxErrorModal plugable into any Backbone class as an\n\t error event handler by accepting the error args: model, xhr, options\n\t \n\t Examples:\n\t if( navigator.offLine ){ offlineErrorModal(); }\n\t if( xhr.status === 502 ){ badGatewayErrorModal(); }\n\t this.listenTo( this.model, 'error', ajaxErrorModal );\n\t \n\t ============================================================================ */\n\t\n\t var CONTACT_MSG = _l('Please contact a Galaxy administrator if the problem persists.');\n\t var DEFAULT_AJAX_ERR_MSG = _l('An error occurred while updating information with the server.');\n\t var DETAILS_MSG = _l('The following information can assist the developers in finding the source of the error:');\n\t\n\t /** private helper that builds the modal and handles adding details */\n\t function _errorModal(message, title, details) {\n\t // create and return the modal, adding details button only if needed\n\t Galaxy.modal.show({\n\t title: title,\n\t body: message,\n\t closing_events: true,\n\t buttons: { Ok: function () {\n\t Galaxy.modal.hide();\n\t } }\n\t });\n\t Galaxy.modal.$el.addClass('error-modal');\n\t\n\t if (details) {\n\t Galaxy.modal.$('.error-details').add(Galaxy.modal.$('button:contains(\"Details\")')).remove();\n\t $('').addClass('error-details').hide().appendTo(Galaxy.modal.$('.modal-content')).append([$('').text(DETAILS_MSG), $('').text(JSON.stringify(details, null, ' '))]);\n\t\n\t $('').appendTo(Galaxy.modal.$('.buttons')).click(function () {\n\t Galaxy.modal.$('.error-details').toggle();\n\t });\n\t }\n\t return Galaxy.modal;\n\t }\n\t\n\t /** Display a modal showing an error message but fallback to alert if there's no modal */\n\t function errorModal(message, title, details) {\n\t if (!message) {\n\t return;\n\t }\n\t\n\t message = _l(message);\n\t title = _l(title) || _l('Error:');\n\t if (window.Galaxy && Galaxy.modal) {\n\t return _errorModal(message, title, details);\n\t }\n\t\n\t alert(title + '\\n\\n' + message);\n\t console.log('error details:', JSON.stringify(details));\n\t }\n\t\n\t // ----------------------------------------------------------------------------\n\t /** display a modal when the user may be offline */\n\t function offlineErrorModal() {\n\t return errorModal(_l('You appear to be offline. Please check your connection and try again.'), _l('Offline?'));\n\t }\n\t\n\t // ----------------------------------------------------------------------------\n\t /** 502 messages that should be displayed when galaxy is restarting */\n\t function badGatewayErrorModal() {\n\t return errorModal(_l('Galaxy is currently unreachable. Please try again in a few minutes.') + ' ' + CONTACT_MSG, _l('Cannot connect to Galaxy'));\n\t }\n\t\n\t // ----------------------------------------------------------------------------\n\t /** display a modal (with details) about a failed Backbone ajax operation */\n\t function ajaxErrorModal(model, xhr, options, message, title) {\n\t message = message || DEFAULT_AJAX_ERR_MSG;\n\t message += ' ' + CONTACT_MSG;\n\t title = title || _l('An error occurred');\n\t var details = _ajaxDetails(model, xhr, options);\n\t return errorModal(message, title, details);\n\t }\n\t\n\t /** build details which may help debugging the ajax call */\n\t function _ajaxDetails(model, xhr, options) {\n\t return {\n\t //TODO: still can't manage Raven id\n\t raven: _.result(window.Raven, 'lastEventId'),\n\t userAgent: navigator.userAgent,\n\t onLine: navigator.onLine,\n\t version: _.result(Galaxy.config, 'version_major'),\n\t xhr: _.omit(xhr, _.functions(xhr)),\n\t options: _.omit(options, 'xhr'),\n\t // add ajax data from Galaxy object cache\n\t url: _.result(Galaxy.lastAjax, 'url'),\n\t data: _.result(Galaxy.lastAjax, 'data'),\n\t // backbone stuff (auto-redacting email for user)\n\t model: _.result(model, 'toJSON', model + ''),\n\t user: _.omit(_.result(Galaxy.user, 'toJSON'), 'email')\n\t };\n\t }\n\t\n\t //=============================================================================\n\t return {\n\t errorModal: errorModal,\n\t offlineErrorModal: offlineErrorModal,\n\t badGatewayErrorModal: badGatewayErrorModal,\n\t ajaxErrorModal: ajaxErrorModal\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1), __webpack_require__(2)))\n\n/***/ }),\n/* 86 */,\n/* 87 */,\n/* 88 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_FACTORY__, __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(jQuery, $) {(function (factory) {\n\t if (true) {\n\t !(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_FACTORY__ = (factory), __WEBPACK_AMD_DEFINE_RESULT__ = (typeof __WEBPACK_AMD_DEFINE_FACTORY__ === 'function' ? (__WEBPACK_AMD_DEFINE_FACTORY__.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__)) : __WEBPACK_AMD_DEFINE_FACTORY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t } else {\n\t // Browser globals\n\t factory(jQuery);\n\t }\n\t})(function () {\n\t //=============================================================================\n\t\n\t jQuery.fn.extend({\n\t hoverhighlight: function $hoverhighlight(scope, color) {\n\t scope = scope || 'body';\n\t if (!this.length) {\n\t return this;\n\t }\n\t\n\t $(this).each(function () {\n\t var $this = $(this),\n\t targetSelector = $this.data('target');\n\t\n\t if (targetSelector) {\n\t $this.mouseover(function (ev) {\n\t $(targetSelector, scope).css({\n\t background: color\n\t });\n\t }).mouseout(function (ev) {\n\t $(targetSelector).css({\n\t background: ''\n\t });\n\t });\n\t }\n\t });\n\t return this;\n\t }\n\t });\n\t});\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1), __webpack_require__(1)))\n\n/***/ }),\n/* 89 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_FACTORY__, __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function($, jQuery) {// from: https://raw.githubusercontent.com/umdjs/umd/master/jqueryPlugin.js\n\t// Uses AMD or browser globals to create a jQuery plugin.\n\t(function (factory) {\n\t if (true) {\n\t //TODO: So...this turns out to be an all or nothing thing. If I load jQuery in the define below, it will\n\t // (of course) wipe the old jquery *and all the plugins loaded into it*. So the define below *is still\n\t // relying on jquery being loaded globally* in order to preserve plugins.\n\t !(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_FACTORY__ = (factory), __WEBPACK_AMD_DEFINE_RESULT__ = (typeof __WEBPACK_AMD_DEFINE_FACTORY__ === 'function' ? (__WEBPACK_AMD_DEFINE_FACTORY__.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__)) : __WEBPACK_AMD_DEFINE_FACTORY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t } else {\n\t // Browser globals\n\t factory(jQuery);\n\t }\n\t})(function () {\n\t var _l = window._l || function (s) {\n\t return s;\n\t };\n\t\n\t //TODO: consolidate with tool menu functionality, use there\n\t\n\t /** searchInput: (jQuery plugin)\n\t * Creates a search input, a clear button, and loading indicator\n\t * within the selected node.\n\t *\n\t * When the user either presses return or enters some minimal number\n\t * of characters, a callback is called. Pressing ESC when the input\n\t * is focused will clear the input and call a separate callback.\n\t */\n\t function searchInput(parentNode, options) {\n\t var KEYCODE_ESC = 27,\n\t KEYCODE_RETURN = 13,\n\t $parentNode = $(parentNode),\n\t firstSearch = true,\n\t defaults = {\n\t initialVal: '',\n\t name: 'search',\n\t placeholder: 'search',\n\t classes: '',\n\t onclear: function () {},\n\t onfirstsearch: null,\n\t onsearch: function (inputVal) {},\n\t minSearchLen: 0,\n\t escWillClear: true,\n\t oninit: function () {}\n\t };\n\t\n\t // .................................................................... input rendering and events\n\t // visually clear the search, trigger an event, and call the callback\n\t function clearSearchInput(event) {\n\t var $input = $(this).parent().children('input');\n\t $input.val('').trigger('searchInput.clear').blur();\n\t options.onclear();\n\t }\n\t\n\t // search for searchTerms, trigger an event, call the appropo callback (based on whether this is the first)\n\t function search(event, searchTerms) {\n\t if (!searchTerms) {\n\t return clearSearchInput();\n\t }\n\t $(this).trigger('search.search', searchTerms);\n\t if (typeof options.onfirstsearch === 'function' && firstSearch) {\n\t firstSearch = false;\n\t options.onfirstsearch(searchTerms);\n\t } else {\n\t options.onsearch(searchTerms);\n\t }\n\t }\n\t\n\t // .................................................................... input rendering and events\n\t function inputTemplate() {\n\t // class search-query is bootstrap 2.3 style that now lives in base.less\n\t return [''].join('');\n\t }\n\t\n\t // the search input that responds to keyboard events and displays the search value\n\t function $input() {\n\t return $(inputTemplate())\n\t // select all text on a focus\n\t .focus(function (event) {\n\t $(this).select();\n\t })\n\t // attach behaviors to esc, return if desired, search on some min len string\n\t .keyup(function (event) {\n\t event.preventDefault();\n\t event.stopPropagation();\n\t\n\t // esc key will clear if desired\n\t if (event.which === KEYCODE_ESC && options.escWillClear) {\n\t clearSearchInput.call(this, event);\n\t } else {\n\t var searchTerms = $(this).val();\n\t // return key or the search string len > minSearchLen (if not 0) triggers search\n\t if (event.which === KEYCODE_RETURN || options.minSearchLen && searchTerms.length >= options.minSearchLen) {\n\t search.call(this, event, searchTerms);\n\t }\n\t }\n\t }).val(options.initialVal);\n\t }\n\t\n\t // .................................................................... clear button rendering and events\n\t // a button for clearing the search bar, placed on the right hand side\n\t function $clearBtn() {\n\t return $([''].join('')).tooltip({ placement: 'bottom' }).click(function (event) {\n\t clearSearchInput.call(this, event);\n\t });\n\t }\n\t\n\t // .................................................................... loadingIndicator rendering\n\t // a button for clearing the search bar, placed on the right hand side\n\t function $loadingIndicator() {\n\t return $([''].join('')).hide().tooltip({ placement: 'bottom' });\n\t }\n\t\n\t // .................................................................... commands\n\t // visually swap the load, clear buttons\n\t function toggleLoadingIndicator() {\n\t $parentNode.find('.search-loading').toggle();\n\t $parentNode.find('.search-clear').toggle();\n\t }\n\t\n\t // .................................................................... init\n\t // string command (not constructor)\n\t if (jQuery.type(options) === 'string') {\n\t if (options === 'toggle-loading') {\n\t toggleLoadingIndicator();\n\t }\n\t return $parentNode;\n\t }\n\t\n\t // initial render\n\t if (jQuery.type(options) === 'object') {\n\t options = jQuery.extend(true, {}, defaults, options);\n\t }\n\t //NOTE: prepended\n\t return $parentNode.addClass('search-input').prepend([$input(), $clearBtn(), $loadingIndicator()]);\n\t }\n\t\n\t // as jq plugin\n\t jQuery.fn.extend({\n\t searchInput: function $searchInput(options) {\n\t return this.each(function () {\n\t return searchInput(this, options);\n\t });\n\t }\n\t });\n\t});\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1), __webpack_require__(1)))\n\n/***/ }),\n/* 90 */,\n/* 91 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;!(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t // Alphanumeric/natural sort fn\n\t function naturalSort(a, b) {\n\t // setup temp-scope variables for comparison evauluation\n\t var re = /(-?[0-9\\.]+)/g,\n\t x = a.toString().toLowerCase() || '',\n\t y = b.toString().toLowerCase() || '',\n\t nC = String.fromCharCode(0),\n\t xN = x.replace(re, nC + '$1' + nC).split(nC),\n\t yN = y.replace(re, nC + '$1' + nC).split(nC),\n\t xD = new Date(x).getTime(),\n\t yD = xD ? new Date(y).getTime() : null;\n\t // natural sorting of dates\n\t if (yD) {\n\t if (xD < yD) {\n\t return -1;\n\t } else if (xD > yD) {\n\t return 1;\n\t }\n\t }\n\t // natural sorting through split numeric strings and default strings\n\t var oFxNcL, oFyNcL;\n\t for (var cLoc = 0, numS = Math.max(xN.length, yN.length); cLoc < numS; cLoc++) {\n\t oFxNcL = parseFloat(xN[cLoc]) || xN[cLoc];\n\t oFyNcL = parseFloat(yN[cLoc]) || yN[cLoc];\n\t if (oFxNcL < oFyNcL) {\n\t return -1;\n\t } else if (oFxNcL > oFyNcL) {\n\t return 1;\n\t }\n\t }\n\t return 0;\n\t }\n\t\n\t return naturalSort;\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\n/***/ }),\n/* 92 */,\n/* 93 */,\n/* 94 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\t/* WEBPACK VAR INJECTION */(function(Backbone) {var Ui = __webpack_require__(7),\n\t historyOptionsMenu = __webpack_require__(124);\n\tCurrentHistoryView = __webpack_require__(121).CurrentHistoryView, _l = __webpack_require__(5);\n\t\n\t/** the right hand panel in the analysis page that shows the current history */\n\tvar HistoryPanel = Backbone.View.extend({\n\t\n\t initialize: function (page, options) {\n\t var self = this;\n\t this.userIsAnonymous = Galaxy.user.isAnonymous();\n\t this.allow_user_dataset_purge = options.config.allow_user_dataset_purge;\n\t this.root = options.root;\n\t\n\t // view of the current history\n\t this.historyView = new CurrentHistoryView({\n\t className: CurrentHistoryView.prototype.className + ' middle',\n\t purgeAllowed: this.allow_user_dataset_purge,\n\t linkTarget: 'galaxy_main'\n\t });\n\t\n\t // add history panel to Galaxy object\n\t Galaxy.currHistoryPanel = this.historyView;\n\t Galaxy.currHistoryPanel.listenToGalaxy(Galaxy);\n\t\n\t // build buttons\n\t this.buttonRefresh = new Ui.ButtonLink({\n\t id: 'history-refresh-button',\n\t title: 'Refresh history',\n\t cls: 'panel-header-button',\n\t icon: 'fa fa-refresh',\n\t onclick: function () {\n\t self.historyView.loadCurrentHistory();\n\t }\n\t });\n\t this.buttonOptions = new Ui.ButtonLink({\n\t id: 'history-options-button',\n\t title: 'History options',\n\t cls: 'panel-header-button',\n\t target: 'galaxy_main',\n\t icon: 'fa fa-cog',\n\t href: this.root + 'root/history_options'\n\t });\n\t this.buttonViewMulti = new Ui.ButtonLink({\n\t id: 'history-view-multi-button',\n\t title: 'View all histories',\n\t cls: 'panel-header-button',\n\t icon: 'fa fa-columns',\n\t href: this.root + 'history/view_multiple'\n\t });\n\t\n\t // define components\n\t this.model = new Backbone.Model({\n\t cls: 'history-right-panel',\n\t title: _l('History'),\n\t buttons: [this.buttonRefresh, this.buttonOptions, this.buttonViewMulti]\n\t });\n\t\n\t // build body template and connect history view\n\t this.setElement(this._template());\n\t this.historyView.setElement(this.$el);\n\t this.historyView.connectToQuotaMeter(Galaxy.quotaMeter);\n\t this.historyView.loadCurrentHistory();\n\t\n\t // fetch to update the quota meter adding 'current' for any anon-user's id\n\t Galaxy.listenTo(this.historyView, 'history-size-change', function () {\n\t Galaxy.user.fetch({ url: Galaxy.user.urlRoot() + '/' + (Galaxy.user.id || 'current') });\n\t });\n\t },\n\t\n\t render: function () {\n\t this.optionsMenu = historyOptionsMenu(this.buttonOptions.$el, {\n\t anonymous: this.userIsAnonymous,\n\t purgeAllowed: this.allow_user_dataset_purge,\n\t root: this.root\n\t });\n\t this.buttonViewMulti.$el[!this.userIsAnonymous ? 'show' : 'hide']();\n\t },\n\t\n\t /** add history view div */\n\t _template: function (data) {\n\t return [''].join('');\n\t },\n\t\n\t toString: function () {\n\t return 'historyPanel';\n\t }\n\t});\n\t\n\tmodule.exports = HistoryPanel;\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3)))\n\n/***/ }),\n/* 95 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\t/* WEBPACK VAR INJECTION */(function(Backbone, _) {var Tools = __webpack_require__(50),\n\t Upload = __webpack_require__(134),\n\t _l = __webpack_require__(5);\n\t\n\tvar ToolPanel = Backbone.View.extend({\n\t initialize: function (page, options) {\n\t // access configuration options\n\t var config = options.config;\n\t this.root = options.root;\n\t\n\t /** @type {Object[]} descriptions of user's workflows to be shown in the tool menu */\n\t this.stored_workflow_menu_entries = config.stored_workflow_menu_entries || [];\n\t\n\t // create tool search, tool panel, and tool panel view.\n\t var tool_search = new Tools.ToolSearch({\n\t hidden: false\n\t });\n\t var tools = new Tools.ToolCollection(config.toolbox);\n\t this.tool_panel = new Tools.ToolPanel({\n\t tool_search: tool_search,\n\t tools: tools,\n\t layout: config.toolbox_in_panel\n\t });\n\t this.tool_panel_view = new Tools.ToolPanelView({ model: this.tool_panel });\n\t\n\t // add upload modal\n\t this.upload_button = new Upload({\n\t nginx_upload_path: config.nginx_upload_path,\n\t ftp_upload_site: config.ftp_upload_site,\n\t default_genome: config.default_genome,\n\t default_extension: config.default_extension\n\t });\n\t\n\t // add uploader button to Galaxy object\n\t Galaxy.upload = this.upload_button;\n\t\n\t // components for panel definition\n\t this.model = new Backbone.Model({\n\t title: _l('Tools'),\n\t buttons: [this.upload_button]\n\t });\n\t\n\t // build body template\n\t this.setElement(this._template());\n\t },\n\t\n\t render: function () {\n\t // if there are tools, render panel and display everything\n\t var self = this;\n\t if (this.tool_panel.get('layout').size() > 0) {\n\t this.$el.prepend(this.tool_panel_view.$el);\n\t this.tool_panel_view.render();\n\t }\n\t // build the dom for the workflow portion of the tool menu\n\t // add internal workflow list\n\t self.$('#internal-workflows').append(self._templateAllWorkflow({\n\t title: _l('All workflows'),\n\t href: 'workflow'\n\t }));\n\t _.each(this.stored_workflow_menu_entries, function (menu_entry) {\n\t self.$('#internal-workflows').append(self._templateTool({\n\t title: menu_entry.stored_workflow.name,\n\t href: 'workflow/run?id=' + menu_entry.encoded_stored_workflow_id\n\t }));\n\t });\n\t },\n\t\n\t /** build a link to one tool */\n\t _templateTool: function (tool) {\n\t return ['
'].join('');\n\t },\n\t\n\t /** override to include inital menu dom and workflow section */\n\t _template: function () {\n\t return ['
', '
', '
', '', _l('Search did not match any tools.'), '', '
', '
', '
', '
', '
', '', _l('Workflows'), '', '
', '
', '
', '
', '
'].join('');\n\t },\n\t\n\t toString: function () {\n\t return 'toolPanel';\n\t }\n\t});\n\t\n\tmodule.exports = ToolPanel;\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2)))\n\n/***/ }),\n/* 96 */,\n/* 97 */,\n/* 98 */,\n/* 99 */,\n/* 100 */,\n/* 101 */,\n/* 102 */,\n/* 103 */,\n/* 104 */,\n/* 105 */,\n/* 106 */,\n/* 107 */,\n/* 108 */,\n/* 109 */,\n/* 110 */,\n/* 111 */,\n/* 112 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(jQuery, _) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(35), __webpack_require__(75), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (DC_LI, DATASET_LI_EDIT, BASE_MVC, _l) {\n\t\n\t 'use strict';\n\t //==============================================================================\n\t\n\t var DCListItemView = DC_LI.DCListItemView;\n\t /** @class Edit view for DatasetCollection.\n\t */\n\t var DCListItemEdit = DCListItemView.extend(\n\t /** @lends DCListItemEdit.prototype */{\n\t\n\t /** override to add linkTarget */\n\t initialize: function (attributes) {\n\t DCListItemView.prototype.initialize.call(this, attributes);\n\t },\n\t\n\t // ......................................................................... misc\n\t /** String representation */\n\t toString: function () {\n\t var modelString = this.model ? this.model + '' : '(no model)';\n\t return 'DCListItemEdit(' + modelString + ')';\n\t }\n\t });\n\t\n\t //==============================================================================\n\t var DCEListItemView = DC_LI.DCEListItemView;\n\t /** @class Read only view for DatasetCollectionElement.\n\t */\n\t var DCEListItemEdit = DCEListItemView.extend(\n\t /** @lends DCEListItemEdit.prototype */{\n\t //TODO: this might be expendable - compacted with HDAListItemView\n\t\n\t /** set up */\n\t initialize: function (attributes) {\n\t DCEListItemView.prototype.initialize.call(this, attributes);\n\t },\n\t\n\t // ......................................................................... misc\n\t /** String representation */\n\t toString: function () {\n\t var modelString = this.model ? this.model + '' : '(no model)';\n\t return 'DCEListItemEdit(' + modelString + ')';\n\t }\n\t });\n\t\n\t //==============================================================================\n\t // NOTE: this does not inherit from DatasetDCEListItemView as you would expect\n\t //TODO: but should - if we can find something simpler than using diamond\n\t /** @class Editable view for a DatasetCollectionElement that is also an DatasetAssociation\n\t * (a dataset contained in a dataset collection).\n\t */\n\t var DatasetDCEListItemEdit = DATASET_LI_EDIT.DatasetListItemEdit.extend(\n\t /** @lends DatasetDCEListItemEdit.prototype */{\n\t\n\t /** set up */\n\t initialize: function (attributes) {\n\t DATASET_LI_EDIT.DatasetListItemEdit.prototype.initialize.call(this, attributes);\n\t },\n\t\n\t // NOTE: this does not inherit from DatasetDCEListItemView - so we duplicate this here\n\t //TODO: fix\n\t /** In this override, only get details if in the ready state.\n\t * Note: fetch with no 'change' event triggering to prevent automatic rendering.\n\t */\n\t _fetchModelDetails: function () {\n\t var view = this;\n\t if (view.model.inReadyState() && !view.model.hasDetails()) {\n\t return view.model.fetch({ silent: true });\n\t }\n\t return jQuery.when();\n\t },\n\t\n\t /** Override to remove delete button */\n\t _renderDeleteButton: function () {\n\t return null;\n\t },\n\t\n\t // ......................................................................... misc\n\t /** String representation */\n\t toString: function () {\n\t var modelString = this.model ? this.model + '' : '(no model)';\n\t return 'DatasetDCEListItemEdit(' + modelString + ')';\n\t }\n\t });\n\t\n\t // ............................................................................ TEMPLATES\n\t /** underscore templates */\n\t DatasetDCEListItemEdit.prototype.templates = function () {\n\t\n\t return _.extend({}, DATASET_LI_EDIT.DatasetListItemEdit.prototype.templates, {\n\t titleBar: DC_LI.DatasetDCEListItemView.prototype.templates.titleBar\n\t });\n\t }();\n\t\n\t //==============================================================================\n\t /** @class Read only view for a DatasetCollectionElement that is also a DatasetCollection\n\t * (a nested DC).\n\t */\n\t var NestedDCDCEListItemEdit = DC_LI.NestedDCDCEListItemView.extend(\n\t /** @lends NestedDCDCEListItemEdit.prototype */{\n\t\n\t /** String representation */\n\t toString: function () {\n\t var modelString = this.model ? this.model + '' : '(no model)';\n\t return 'NestedDCDCEListItemEdit(' + modelString + ')';\n\t }\n\t });\n\t\n\t //==============================================================================\n\t return {\n\t DCListItemEdit: DCListItemEdit,\n\t DCEListItemEdit: DCEListItemEdit,\n\t DatasetDCEListItemEdit: DatasetDCEListItemEdit,\n\t NestedDCDCEListItemEdit: NestedDCDCEListItemEdit\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1), __webpack_require__(2)))\n\n/***/ }),\n/* 113 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(74), __webpack_require__(36), __webpack_require__(112), __webpack_require__(6), __webpack_require__(48), __webpack_require__(17), __webpack_require__(5), __webpack_require__(16)], __WEBPACK_AMD_DEFINE_RESULT__ = function (DC_VIEW, DC_MODEL, DC_EDIT, BASE_MVC, TAGS, faIconButton, _l) {\n\t\n\t 'use strict';\n\t /* =============================================================================\n\t TODO:\n\t \n\t ============================================================================= */\n\t /** @class editable View/Controller for a dataset collection.\n\t */\n\t\n\t var _super = DC_VIEW.CollectionView;\n\t var CollectionViewEdit = _super.extend(\n\t /** @lends CollectionView.prototype */{\n\t //MODEL is either a DatasetCollection (or subclass) or a DatasetCollectionElement (list of pairs)\n\t\n\t /** logger used to record this.log messages, commonly set to console */\n\t //logger : console,\n\t\n\t /** sub view class used for datasets */\n\t DatasetDCEViewClass: DC_EDIT.DatasetDCEListItemEdit,\n\t /** sub view class used for nested collections */\n\t NestedDCDCEViewClass: DC_EDIT.NestedDCDCEListItemEdit,\n\t\n\t // ......................................................................... SET UP\n\t /** Set up the view, set up storage, bind listeners to HistoryContents events\n\t * @param {Object} attributes optional settings for the panel\n\t */\n\t initialize: function (attributes) {\n\t _super.prototype.initialize.call(this, attributes);\n\t },\n\t\n\t /** In this override, make the collection name editable\n\t */\n\t _setUpBehaviors: function ($where) {\n\t $where = $where || this.$el;\n\t _super.prototype._setUpBehaviors.call(this, $where);\n\t if (!this.model) {\n\t return;\n\t }\n\t\n\t // anon users shouldn't have access to any of the following\n\t if (!Galaxy.user || Galaxy.user.isAnonymous()) {\n\t return;\n\t }\n\t\n\t this.tagsEditorShown = true;\n\t\n\t //TODO: extract\n\t var panel = this,\n\t nameSelector = '> .controls .name';\n\t $where.find(nameSelector).attr('title', _l('Click to rename collection')).tooltip({ placement: 'bottom' }).make_text_editable({\n\t on_finish: function (newName) {\n\t var previousName = panel.model.get('name');\n\t if (newName && newName !== previousName) {\n\t panel.$el.find(nameSelector).text(newName);\n\t panel.model.save({ name: newName }).fail(function () {\n\t panel.$el.find(nameSelector).text(panel.model.previous('name'));\n\t });\n\t } else {\n\t panel.$el.find(nameSelector).text(previousName);\n\t }\n\t }\n\t });\n\t this.tagsEditor = new TAGS.TagsEditor({\n\t model: this.model,\n\t el: $where.find('.tags-display'),\n\t onshowFirstTime: function () {\n\t this.render();\n\t },\n\t usePrompt: false\n\t });\n\t this.tagsEditor.toggle(true);\n\t },\n\t\n\t // ........................................................................ misc\n\t /** string rep */\n\t toString: function () {\n\t return 'CollectionViewEdit(' + (this.model ? this.model.get('name') : '') + ')';\n\t }\n\t });\n\t\n\t // =============================================================================\n\t /** @class non-editable, read-only View/Controller for a dataset collection. */\n\t var ListCollectionViewEdit = CollectionViewEdit.extend(\n\t /** @lends ListCollectionView.prototype */{\n\t\n\t //TODO: not strictly needed - due to switch in CollectionView._getContentClass\n\t /** sub view class used for datasets */\n\t DatasetDCEViewClass: DC_EDIT.DatasetDCEListItemEdit,\n\t\n\t // ........................................................................ misc\n\t /** string rep */\n\t toString: function () {\n\t return 'ListCollectionViewEdit(' + (this.model ? this.model.get('name') : '') + ')';\n\t }\n\t });\n\t\n\t // =============================================================================\n\t /** @class Editable, read-only View/Controller for a dataset collection. */\n\t var PairCollectionViewEdit = ListCollectionViewEdit.extend(\n\t /** @lends PairCollectionViewEdit.prototype */{\n\t\n\t // ........................................................................ misc\n\t /** string rep */\n\t toString: function () {\n\t return 'PairCollectionViewEdit(' + (this.model ? this.model.get('name') : '') + ')';\n\t }\n\t });\n\t\n\t // =============================================================================\n\t /** @class Editable (roughly since these collections are immutable),\n\t * View/Controller for a dataset collection.\n\t */\n\t var NestedPairCollectionViewEdit = PairCollectionViewEdit.extend(\n\t /** @lends NestedPairCollectionViewEdit.prototype */{\n\t\n\t /** Override to remove the editable text from the name/identifier - these collections are considered immutable */\n\t _setUpBehaviors: function ($where) {\n\t _super.prototype._setUpBehaviors.call(this, $where);\n\t },\n\t\n\t // ........................................................................ misc\n\t /** string rep */\n\t toString: function () {\n\t return 'NestedPairCollectionViewEdit(' + (this.model ? this.model.get('name') : '') + ')';\n\t }\n\t });\n\t\n\t // =============================================================================\n\t /** @class editable, View/Controller for a list of pairs dataset collection. */\n\t var ListOfPairsCollectionViewEdit = CollectionViewEdit.extend(\n\t /** @lends ListOfPairsCollectionView.prototype */{\n\t\n\t //TODO: not strictly needed - due to switch in CollectionView._getContentClass\n\t /** sub view class used for nested collections */\n\t NestedDCDCEViewClass: DC_EDIT.NestedDCDCEListItemEdit.extend({\n\t foldoutPanelClass: NestedPairCollectionViewEdit\n\t }),\n\t\n\t // ........................................................................ misc\n\t /** string rep */\n\t toString: function () {\n\t return 'ListOfPairsCollectionViewEdit(' + (this.model ? this.model.get('name') : '') + ')';\n\t }\n\t });\n\t\n\t // =============================================================================\n\t /** @class View/Controller for a list of lists dataset collection. */\n\t var ListOfListsCollectionViewEdit = CollectionViewEdit.extend(\n\t /** @lends ListOfListsCollectionView.prototype */{\n\t\n\t //TODO: not strictly needed - due to switch in CollectionView._getContentClass\n\t /** sub view class used for nested collections */\n\t NestedDCDCEViewClass: DC_EDIT.NestedDCDCEListItemEdit.extend({\n\t foldoutPanelClass: NestedPairCollectionViewEdit\n\t }),\n\t\n\t // ........................................................................ misc\n\t /** string rep */\n\t toString: function () {\n\t return 'ListOfListsCollectionViewEdit(' + (this.model ? this.model.get('name') : '') + ')';\n\t }\n\t });\n\t\n\t //==============================================================================\n\t return {\n\t CollectionViewEdit: CollectionViewEdit,\n\t ListCollectionViewEdit: ListCollectionViewEdit,\n\t PairCollectionViewEdit: PairCollectionViewEdit,\n\t ListOfPairsCollectionViewEdit: ListOfPairsCollectionViewEdit,\n\t ListOfListsCollectionViewEdit: ListOfListsCollectionViewEdit\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\n/***/ }),\n/* 114 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, jQuery, $) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(146), __webpack_require__(91), __webpack_require__(73), __webpack_require__(6), __webpack_require__(5), __webpack_require__(88)], __WEBPACK_AMD_DEFINE_RESULT__ = function (levenshteinDistance, naturalSort, baseCreator, baseMVC, _l) {\n\t\n\t 'use strict';\n\t\n\t var logNamespace = 'collections';\n\t /* ============================================================================\n\t TODO:\n\t \n\t \n\t PROGRAMMATICALLY:\n\t currPanel.once( 'rendered', function(){\n\t currPanel.showSelectors();\n\t currPanel.selectAll();\n\t _.last( currPanel.actionsPopup.options ).func();\n\t });\n\t \n\t ============================================================================ */\n\t /** A view for paired datasets in the collections creator.\n\t */\n\t var PairView = Backbone.View.extend(baseMVC.LoggableMixin).extend({\n\t _logNamespace: logNamespace,\n\t\n\t tagName: 'li',\n\t className: 'dataset paired',\n\t\n\t initialize: function (attributes) {\n\t this.pair = attributes.pair || {};\n\t },\n\t\n\t template: _.template(['<%- pair.forward.name %>', '', '<%- pair.name %>', '', '<%- pair.reverse.name %>'].join('')),\n\t\n\t render: function () {\n\t this.$el.attr('draggable', true).data('pair', this.pair).html(this.template({ pair: this.pair })).addClass('flex-column-container');\n\t return this;\n\t },\n\t\n\t events: {\n\t 'dragstart': '_dragstart',\n\t 'dragend': '_dragend',\n\t 'dragover': '_sendToParent',\n\t 'drop': '_sendToParent'\n\t },\n\t\n\t /** dragging pairs for re-ordering */\n\t _dragstart: function (ev) {\n\t ev.currentTarget.style.opacity = '0.4';\n\t if (ev.originalEvent) {\n\t ev = ev.originalEvent;\n\t }\n\t\n\t ev.dataTransfer.effectAllowed = 'move';\n\t ev.dataTransfer.setData('text/plain', JSON.stringify(this.pair));\n\t\n\t this.$el.parent().trigger('pair.dragstart', [this]);\n\t },\n\t\n\t /** dragging pairs for re-ordering */\n\t _dragend: function (ev) {\n\t ev.currentTarget.style.opacity = '1.0';\n\t this.$el.parent().trigger('pair.dragend', [this]);\n\t },\n\t\n\t /** manually bubble up an event to the parent/container */\n\t _sendToParent: function (ev) {\n\t this.$el.parent().trigger(ev);\n\t },\n\t\n\t /** string rep */\n\t toString: function () {\n\t return 'PairView(' + this.pair.name + ')';\n\t }\n\t });\n\t\n\t // ============================================================================\n\t /** returns an autopair function that uses the provided options.match function */\n\t function autoPairFnBuilder(options) {\n\t options = options || {};\n\t options.createPair = options.createPair || function _defaultCreatePair(params) {\n\t params = params || {};\n\t var a = params.listA.splice(params.indexA, 1)[0],\n\t b = params.listB.splice(params.indexB, 1)[0],\n\t aInBIndex = params.listB.indexOf(a),\n\t bInAIndex = params.listA.indexOf(b);\n\t if (aInBIndex !== -1) {\n\t params.listB.splice(aInBIndex, 1);\n\t }\n\t if (bInAIndex !== -1) {\n\t params.listA.splice(bInAIndex, 1);\n\t }\n\t return this._pair(a, b, { silent: true });\n\t };\n\t // compile these here outside of the loop\n\t var _regexps = [];\n\t function getRegExps() {\n\t if (!_regexps.length) {\n\t _regexps = [new RegExp(this.filters[0]), new RegExp(this.filters[1])];\n\t }\n\t return _regexps;\n\t }\n\t // mangle params as needed\n\t options.preprocessMatch = options.preprocessMatch || function _defaultPreprocessMatch(params) {\n\t var regexps = getRegExps.call(this);\n\t return _.extend(params, {\n\t matchTo: params.matchTo.name.replace(regexps[0], ''),\n\t possible: params.possible.name.replace(regexps[1], '')\n\t });\n\t };\n\t\n\t return function _strategy(params) {\n\t this.debug('autopair _strategy ---------------------------');\n\t params = params || {};\n\t var listA = params.listA,\n\t listB = params.listB,\n\t indexA = 0,\n\t indexB,\n\t bestMatch = {\n\t score: 0.0,\n\t index: null\n\t },\n\t paired = [];\n\t //console.debug( 'params:', JSON.stringify( params, null, ' ' ) );\n\t this.debug('starting list lens:', listA.length, listB.length);\n\t this.debug('bestMatch (starting):', JSON.stringify(bestMatch, null, ' '));\n\t\n\t while (indexA < listA.length) {\n\t var matchTo = listA[indexA];\n\t bestMatch.score = 0.0;\n\t\n\t for (indexB = 0; indexB < listB.length; indexB++) {\n\t var possible = listB[indexB];\n\t this.debug(indexA + ':' + matchTo.name);\n\t this.debug(indexB + ':' + possible.name);\n\t\n\t // no matching with self\n\t if (listA[indexA] !== listB[indexB]) {\n\t bestMatch = options.match.call(this, options.preprocessMatch.call(this, {\n\t matchTo: matchTo,\n\t possible: possible,\n\t index: indexB,\n\t bestMatch: bestMatch\n\t }));\n\t this.debug('bestMatch:', JSON.stringify(bestMatch, null, ' '));\n\t if (bestMatch.score === 1.0) {\n\t this.debug('breaking early due to perfect match');\n\t break;\n\t }\n\t }\n\t }\n\t var scoreThreshold = options.scoreThreshold.call(this);\n\t this.debug('scoreThreshold:', scoreThreshold);\n\t this.debug('bestMatch.score:', bestMatch.score);\n\t\n\t if (bestMatch.score >= scoreThreshold) {\n\t //console.debug( 'autoPairFnBuilder.strategy', listA[ indexA ].name, listB[ bestMatch.index ].name );\n\t paired.push(options.createPair.call(this, {\n\t listA: listA,\n\t indexA: indexA,\n\t listB: listB,\n\t indexB: bestMatch.index\n\t }));\n\t //console.debug( 'list lens now:', listA.length, listB.length );\n\t } else {\n\t indexA += 1;\n\t }\n\t if (!listA.length || !listB.length) {\n\t return paired;\n\t }\n\t }\n\t this.debug('paired:', JSON.stringify(paired, null, ' '));\n\t this.debug('autopair _strategy ---------------------------');\n\t return paired;\n\t };\n\t }\n\t\n\t // ============================================================================\n\t /** An interface for building collections of paired datasets.\n\t */\n\t var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin).extend(baseCreator.CollectionCreatorMixin).extend({\n\t _logNamespace: logNamespace,\n\t\n\t className: 'list-of-pairs-collection-creator collection-creator flex-row-container',\n\t\n\t /** set up initial options, instance vars, behaviors, and autopair (if set to do so) */\n\t initialize: function (attributes) {\n\t this.metric('PairedCollectionCreator.initialize', attributes);\n\t //this.debug( '-- PairedCollectionCreator:', attributes );\n\t\n\t attributes = _.defaults(attributes, {\n\t datasets: [],\n\t filters: this.DEFAULT_FILTERS,\n\t automaticallyPair: true,\n\t strategy: 'lcs',\n\t matchPercentage: 0.9,\n\t twoPassAutopairing: true\n\t });\n\t\n\t /** unordered, original list */\n\t this.initialList = attributes.datasets;\n\t\n\t /** is this from a history? if so, what's its id? */\n\t this.historyId = attributes.historyId;\n\t\n\t /** which filters should be used initially? (String[2] or name in commonFilters) */\n\t this.filters = this.commonFilters[attributes.filters] || this.commonFilters[this.DEFAULT_FILTERS];\n\t if (_.isArray(attributes.filters)) {\n\t this.filters = attributes.filters;\n\t }\n\t\n\t /** try to auto pair the unpaired datasets on load? */\n\t this.automaticallyPair = attributes.automaticallyPair;\n\t\n\t /** what method to use for auto pairing (will be passed aggression level) */\n\t this.strategy = this.strategies[attributes.strategy] || this.strategies[this.DEFAULT_STRATEGY];\n\t if (_.isFunction(attributes.strategy)) {\n\t this.strategy = attributes.strategy;\n\t }\n\t\n\t /** distance/mismatch level allowed for autopairing */\n\t this.matchPercentage = attributes.matchPercentage;\n\t\n\t /** try to autopair using simple first, then this.strategy on the remainder */\n\t this.twoPassAutopairing = attributes.twoPassAutopairing;\n\t\n\t /** remove file extensions (\\.*) from created pair names? */\n\t this.removeExtensions = true;\n\t //this.removeExtensions = false;\n\t\n\t /** fn to call when the cancel button is clicked (scoped to this) - if falsy, no btn is displayed */\n\t this.oncancel = attributes.oncancel;\n\t /** fn to call when the collection is created (scoped to this) */\n\t this.oncreate = attributes.oncreate;\n\t\n\t /** fn to call when the cancel button is clicked (scoped to this) - if falsy, no btn is displayed */\n\t this.autoscrollDist = attributes.autoscrollDist || 24;\n\t\n\t /** is the unpaired panel shown? */\n\t this.unpairedPanelHidden = false;\n\t /** is the paired panel shown? */\n\t this.pairedPanelHidden = false;\n\t\n\t /** DOM elements currently being dragged */\n\t this.$dragging = null;\n\t\n\t /** Used for blocking UI events during ajax/operations (don't post twice) */\n\t this.blocking = false;\n\t\n\t this._setUpCommonSettings(attributes);\n\t this._setUpBehaviors();\n\t this._dataSetUp();\n\t },\n\t\n\t /** map of common filter pairs by name */\n\t commonFilters: {\n\t illumina: ['_1', '_2'],\n\t Rs: ['_R1', '_R2']\n\t },\n\t /** which commonFilter to use by default */\n\t DEFAULT_FILTERS: 'illumina',\n\t\n\t /** map of name->fn for autopairing */\n\t strategies: {\n\t 'simple': 'autopairSimple',\n\t 'lcs': 'autopairLCS',\n\t 'levenshtein': 'autopairLevenshtein'\n\t },\n\t /** default autopair strategy name */\n\t DEFAULT_STRATEGY: 'lcs',\n\t\n\t // ------------------------------------------------------------------------ process raw list\n\t /** set up main data: cache initialList, sort, and autopair */\n\t _dataSetUp: function () {\n\t //this.debug( '-- _dataSetUp' );\n\t\n\t this.paired = [];\n\t this.unpaired = [];\n\t\n\t this.selectedIds = [];\n\t\n\t // sort initial list, add ids if needed, and save new working copy to unpaired\n\t this._sortInitialList();\n\t this._ensureIds();\n\t this.unpaired = this.initialList.slice(0);\n\t\n\t if (this.automaticallyPair) {\n\t this.autoPair();\n\t this.once('rendered:initial', function () {\n\t this.trigger('autopair');\n\t });\n\t }\n\t },\n\t\n\t /** sort initial list */\n\t _sortInitialList: function () {\n\t //this.debug( '-- _sortInitialList' );\n\t this._sortDatasetList(this.initialList);\n\t },\n\t\n\t /** sort a list of datasets */\n\t _sortDatasetList: function (list) {\n\t // currently only natural sort by name\n\t list.sort(function (a, b) {\n\t return naturalSort(a.name, b.name);\n\t });\n\t return list;\n\t },\n\t\n\t /** add ids to dataset objs in initial list if none */\n\t _ensureIds: function () {\n\t this.initialList.forEach(function (dataset) {\n\t if (!dataset.hasOwnProperty('id')) {\n\t dataset.id = _.uniqueId();\n\t }\n\t });\n\t return this.initialList;\n\t },\n\t\n\t /** split initial list into two lists, those that pass forward filters & those passing reverse */\n\t _splitByFilters: function () {\n\t var regexFilters = this.filters.map(function (stringFilter) {\n\t return new RegExp(stringFilter);\n\t }),\n\t split = [[], []];\n\t\n\t function _filter(unpaired, filter) {\n\t return filter.test(unpaired.name);\n\t //return dataset.name.indexOf( filter ) >= 0;\n\t }\n\t this.unpaired.forEach(function _filterEach(unpaired) {\n\t // 90% of the time this seems to work, but:\n\t //TODO: this treats *all* strings as regex which may confuse people - possibly check for // surrounding?\n\t // would need explanation in help as well\n\t regexFilters.forEach(function (filter, i) {\n\t if (_filter(unpaired, filter)) {\n\t split[i].push(unpaired);\n\t }\n\t });\n\t });\n\t return split;\n\t },\n\t\n\t /** add a dataset to the unpaired list in it's proper order */\n\t _addToUnpaired: function (dataset) {\n\t // currently, unpaired is natural sorted by name, use binary search to find insertion point\n\t var binSearchSortedIndex = function (low, hi) {\n\t if (low === hi) {\n\t return low;\n\t }\n\t\n\t var mid = Math.floor((hi - low) / 2) + low,\n\t compared = naturalSort(dataset.name, this.unpaired[mid].name);\n\t\n\t if (compared < 0) {\n\t return binSearchSortedIndex(low, mid);\n\t } else if (compared > 0) {\n\t return binSearchSortedIndex(mid + 1, hi);\n\t }\n\t // walk the equal to find the last\n\t while (this.unpaired[mid] && this.unpaired[mid].name === dataset.name) {\n\t mid++;\n\t }\n\t return mid;\n\t }.bind(this);\n\t\n\t this.unpaired.splice(binSearchSortedIndex(0, this.unpaired.length), 0, dataset);\n\t },\n\t\n\t // ------------------------------------------------------------------------ auto pairing\n\t /** two passes to automatically create pairs:\n\t * use both simpleAutoPair, then the fn mentioned in strategy\n\t */\n\t autoPair: function (strategy) {\n\t // split first using exact matching\n\t var split = this._splitByFilters(),\n\t paired = [];\n\t if (this.twoPassAutopairing) {\n\t paired = this.autopairSimple({\n\t listA: split[0],\n\t listB: split[1]\n\t });\n\t split = this._splitByFilters();\n\t }\n\t\n\t // uncomment to see printlns while running tests\n\t //this.debug = function(){ console.log.apply( console, arguments ); };\n\t\n\t // then try the remainder with something less strict\n\t strategy = strategy || this.strategy;\n\t split = this._splitByFilters();\n\t paired = paired.concat(this[strategy].call(this, {\n\t listA: split[0],\n\t listB: split[1]\n\t }));\n\t return paired;\n\t },\n\t\n\t /** autopair by exact match */\n\t autopairSimple: autoPairFnBuilder({\n\t scoreThreshold: function () {\n\t return 1.0;\n\t },\n\t match: function _match(params) {\n\t params = params || {};\n\t if (params.matchTo === params.possible) {\n\t return {\n\t index: params.index,\n\t score: 1.0\n\t };\n\t }\n\t return params.bestMatch;\n\t }\n\t }),\n\t\n\t /** autopair by levenshtein edit distance scoring */\n\t autopairLevenshtein: autoPairFnBuilder({\n\t scoreThreshold: function () {\n\t return this.matchPercentage;\n\t },\n\t match: function _matches(params) {\n\t params = params || {};\n\t var distance = levenshteinDistance(params.matchTo, params.possible),\n\t score = 1.0 - distance / Math.max(params.matchTo.length, params.possible.length);\n\t if (score > params.bestMatch.score) {\n\t return {\n\t index: params.index,\n\t score: score\n\t };\n\t }\n\t return params.bestMatch;\n\t }\n\t }),\n\t\n\t /** autopair by longest common substrings scoring */\n\t autopairLCS: autoPairFnBuilder({\n\t scoreThreshold: function () {\n\t return this.matchPercentage;\n\t },\n\t match: function _matches(params) {\n\t params = params || {};\n\t var match = this._naiveStartingAndEndingLCS(params.matchTo, params.possible).length,\n\t score = match / Math.max(params.matchTo.length, params.possible.length);\n\t if (score > params.bestMatch.score) {\n\t return {\n\t index: params.index,\n\t score: score\n\t };\n\t }\n\t return params.bestMatch;\n\t }\n\t }),\n\t\n\t /** return the concat'd longest common prefix and suffix from two strings */\n\t _naiveStartingAndEndingLCS: function (s1, s2) {\n\t var fwdLCS = '',\n\t revLCS = '',\n\t i = 0,\n\t j = 0;\n\t while (i < s1.length && i < s2.length) {\n\t if (s1[i] !== s2[i]) {\n\t break;\n\t }\n\t fwdLCS += s1[i];\n\t i += 1;\n\t }\n\t if (i === s1.length) {\n\t return s1;\n\t }\n\t if (i === s2.length) {\n\t return s2;\n\t }\n\t\n\t i = s1.length - 1;\n\t j = s2.length - 1;\n\t while (i >= 0 && j >= 0) {\n\t if (s1[i] !== s2[j]) {\n\t break;\n\t }\n\t revLCS = [s1[i], revLCS].join('');\n\t i -= 1;\n\t j -= 1;\n\t }\n\t return fwdLCS + revLCS;\n\t },\n\t\n\t // ------------------------------------------------------------------------ pairing / unpairing\n\t /** create a pair from fwd and rev, removing them from unpaired, and placing the new pair in paired */\n\t _pair: function (fwd, rev, options) {\n\t options = options || {};\n\t this.debug('_pair:', fwd, rev);\n\t var pair = this._createPair(fwd, rev, options.name);\n\t this.paired.push(pair);\n\t this.unpaired = _.without(this.unpaired, fwd, rev);\n\t if (!options.silent) {\n\t this.trigger('pair:new', pair);\n\t }\n\t return pair;\n\t },\n\t\n\t /** create a pair Object from fwd and rev, adding the name attribute (will guess if not given) */\n\t _createPair: function (fwd, rev, name) {\n\t // ensure existance and don't pair something with itself\n\t if (!(fwd && rev) || fwd === rev) {\n\t throw new Error('Bad pairing: ' + [JSON.stringify(fwd), JSON.stringify(rev)]);\n\t }\n\t name = name || this._guessNameForPair(fwd, rev);\n\t return { forward: fwd, name: name, reverse: rev };\n\t },\n\t\n\t /** try to find a good pair name for the given fwd and rev datasets */\n\t _guessNameForPair: function (fwd, rev, removeExtensions) {\n\t removeExtensions = removeExtensions !== undefined ? removeExtensions : this.removeExtensions;\n\t var fwdName = fwd.name,\n\t revName = rev.name,\n\t lcs = this._naiveStartingAndEndingLCS(fwdName.replace(new RegExp(this.filters[0]), ''), revName.replace(new RegExp(this.filters[1]), ''));\n\t if (removeExtensions) {\n\t var lastDotIndex = lcs.lastIndexOf('.');\n\t if (lastDotIndex > 0) {\n\t var extension = lcs.slice(lastDotIndex, lcs.length);\n\t lcs = lcs.replace(extension, '');\n\t fwdName = fwdName.replace(extension, '');\n\t revName = revName.replace(extension, '');\n\t }\n\t }\n\t return lcs || fwdName + ' & ' + revName;\n\t },\n\t\n\t /** unpair a pair, removing it from paired, and adding the fwd,rev datasets back into unpaired */\n\t _unpair: function (pair, options) {\n\t options = options || {};\n\t if (!pair) {\n\t throw new Error('Bad pair: ' + JSON.stringify(pair));\n\t }\n\t this.paired = _.without(this.paired, pair);\n\t this._addToUnpaired(pair.forward);\n\t this._addToUnpaired(pair.reverse);\n\t\n\t if (!options.silent) {\n\t this.trigger('pair:unpair', [pair]);\n\t }\n\t return pair;\n\t },\n\t\n\t /** unpair all paired datasets */\n\t unpairAll: function () {\n\t var pairs = [];\n\t while (this.paired.length) {\n\t pairs.push(this._unpair(this.paired[0], { silent: true }));\n\t }\n\t this.trigger('pair:unpair', pairs);\n\t },\n\t\n\t // ------------------------------------------------------------------------ API\n\t /** convert a pair into JSON compatible with the collections API */\n\t _pairToJSON: function (pair, src) {\n\t src = src || 'hda';\n\t //TODO: consider making this the pair structure when created instead\n\t return {\n\t collection_type: 'paired',\n\t src: 'new_collection',\n\t name: pair.name,\n\t element_identifiers: [{\n\t name: 'forward',\n\t id: pair.forward.id,\n\t src: src\n\t }, {\n\t name: 'reverse',\n\t id: pair.reverse.id,\n\t src: src\n\t }]\n\t };\n\t },\n\t\n\t /** create the collection via the API\n\t * @returns {jQuery.xhr Object} the jquery ajax request\n\t */\n\t createList: function (name) {\n\t var creator = this,\n\t url = Galaxy.root + 'api/histories/' + this.historyId + '/contents/dataset_collections';\n\t\n\t //TODO: use ListPairedCollection.create()\n\t var ajaxData = {\n\t type: 'dataset_collection',\n\t collection_type: 'list:paired',\n\t hide_source_items: creator.hideOriginals || false,\n\t name: _.escape(name || creator.$('.collection-name').val()),\n\t element_identifiers: creator.paired.map(function (pair) {\n\t return creator._pairToJSON(pair);\n\t })\n\t\n\t };\n\t //this.debug( JSON.stringify( ajaxData ) );\n\t creator.blocking = true;\n\t return jQuery.ajax(url, {\n\t type: 'POST',\n\t contentType: 'application/json',\n\t dataType: 'json',\n\t data: JSON.stringify(ajaxData)\n\t }).always(function () {\n\t creator.blocking = false;\n\t }).fail(function (xhr, status, message) {\n\t creator._ajaxErrHandler(xhr, status, message);\n\t }).done(function (response, message, xhr) {\n\t //this.info( 'ok', response, message, xhr );\n\t creator.trigger('collection:created', response, message, xhr);\n\t creator.metric('collection:created', response);\n\t if (typeof creator.oncreate === 'function') {\n\t creator.oncreate.call(this, response, message, xhr);\n\t }\n\t });\n\t },\n\t\n\t /** handle ajax errors with feedback and details to the user (if available) */\n\t _ajaxErrHandler: function (xhr, status, message) {\n\t this.error(xhr, status, message);\n\t var content = _l('An error occurred while creating this collection');\n\t if (xhr) {\n\t if (xhr.readyState === 0 && xhr.status === 0) {\n\t content += ': ' + _l('Galaxy could not be reached and may be updating.') + _l(' Try again in a few minutes.');\n\t } else if (xhr.responseJSON) {\n\t content += '
' + JSON.stringify(xhr.responseJSON) + '
';\n\t } else {\n\t content += ': ' + message;\n\t }\n\t }\n\t creator._showAlert(content, 'alert-danger');\n\t },\n\t\n\t // ------------------------------------------------------------------------ rendering\n\t /** render the entire interface */\n\t render: function (speed, callback) {\n\t //this.debug( '-- _render' );\n\t //this.$el.empty().html( this.templates.main() );\n\t this.$el.empty().html(this.templates.main());\n\t this._renderHeader(speed);\n\t this._renderMiddle(speed);\n\t this._renderFooter(speed);\n\t this._addPluginComponents();\n\t this.trigger('rendered', this);\n\t return this;\n\t },\n\t\n\t /** render the header section */\n\t _renderHeader: function (speed, callback) {\n\t //this.debug( '-- _renderHeader' );\n\t var $header = this.$('.header').empty().html(this.templates.header()).find('.help-content').prepend($(this.templates.helpContent()));\n\t\n\t this._renderFilters();\n\t return $header;\n\t },\n\t /** fill the filter inputs with the filter values */\n\t _renderFilters: function () {\n\t return this.$('.forward-column .column-header input').val(this.filters[0]).add(this.$('.reverse-column .column-header input').val(this.filters[1]));\n\t },\n\t\n\t /** render the middle including unpaired and paired sections (which may be hidden) */\n\t _renderMiddle: function (speed, callback) {\n\t var $middle = this.$('.middle').empty().html(this.templates.middle());\n\t\n\t // (re-) hide the un/paired panels based on instance vars\n\t if (this.unpairedPanelHidden) {\n\t this.$('.unpaired-columns').hide();\n\t } else if (this.pairedPanelHidden) {\n\t this.$('.paired-columns').hide();\n\t }\n\t\n\t this._renderUnpaired();\n\t this._renderPaired();\n\t return $middle;\n\t },\n\t /** render the unpaired section, showing datasets accrd. to filters, update the unpaired counts */\n\t _renderUnpaired: function (speed, callback) {\n\t //this.debug( '-- _renderUnpaired' );\n\t var creator = this,\n\t $fwd,\n\t $rev,\n\t $prd = [],\n\t split = this._splitByFilters();\n\t // update unpaired counts\n\t this.$('.forward-column .title').text([split[0].length, _l('unpaired forward')].join(' '));\n\t this.$('.forward-column .unpaired-info').text(this._renderUnpairedDisplayStr(this.unpaired.length - split[0].length));\n\t this.$('.reverse-column .title').text([split[1].length, _l('unpaired reverse')].join(' '));\n\t this.$('.reverse-column .unpaired-info').text(this._renderUnpairedDisplayStr(this.unpaired.length - split[1].length));\n\t\n\t this.$('.unpaired-columns .column-datasets').empty();\n\t\n\t // show/hide the auto pair button if any unpaired are left\n\t this.$('.autopair-link').toggle(this.unpaired.length !== 0);\n\t if (this.unpaired.length === 0) {\n\t this._renderUnpairedEmpty();\n\t return;\n\t }\n\t\n\t // create the dataset dom arrays\n\t $rev = split[1].map(function (dataset, i) {\n\t // if there'll be a fwd dataset across the way, add a button to pair the row\n\t if (split[0][i] !== undefined && split[0][i] !== dataset) {\n\t $prd.push(creator._renderPairButton());\n\t }\n\t return creator._renderUnpairedDataset(dataset);\n\t });\n\t $fwd = split[0].map(function (dataset) {\n\t return creator._renderUnpairedDataset(dataset);\n\t });\n\t\n\t if (!$fwd.length && !$rev.length) {\n\t this._renderUnpairedNotShown();\n\t return;\n\t }\n\t // add to appropo cols\n\t //TODO: not the best way to render - consider rendering the entire unpaired-columns section in a fragment\n\t // and swapping out that\n\t this.$('.unpaired-columns .forward-column .column-datasets').append($fwd).add(this.$('.unpaired-columns .paired-column .column-datasets').append($prd)).add(this.$('.unpaired-columns .reverse-column .column-datasets').append($rev));\n\t this._adjUnpairedOnScrollbar();\n\t },\n\t /** return a string to display the count of filtered out datasets */\n\t _renderUnpairedDisplayStr: function (numFiltered) {\n\t return ['(', numFiltered, ' ', _l('filtered out'), ')'].join('');\n\t },\n\t /** return an unattached jQuery DOM element to represent an unpaired dataset */\n\t _renderUnpairedDataset: function (dataset) {\n\t //TODO: to underscore template\n\t return $('').attr('id', 'dataset-' + dataset.id).addClass('dataset unpaired').attr('draggable', true).addClass(dataset.selected ? 'selected' : '').append($('').addClass('dataset-name').text(dataset.name))\n\t //??\n\t .data('dataset', dataset);\n\t },\n\t /** render the button that may go between unpaired datasets, allowing the user to pair a row */\n\t _renderPairButton: function () {\n\t //TODO: *not* a dataset - don't pretend like it is\n\t return $('').addClass('dataset unpaired').append($('').addClass('dataset-name').text(_l('Pair these datasets')));\n\t },\n\t /** a message to display when no unpaired left */\n\t _renderUnpairedEmpty: function () {\n\t //this.debug( '-- renderUnpairedEmpty' );\n\t var $msg = $('').text('(' + _l('no remaining unpaired datasets') + ')');\n\t this.$('.unpaired-columns .paired-column .column-datasets').empty().prepend($msg);\n\t return $msg;\n\t },\n\t /** a message to display when no unpaired can be shown with the current filters */\n\t _renderUnpairedNotShown: function () {\n\t //this.debug( '-- renderUnpairedEmpty' );\n\t var $msg = $('').text('(' + _l('no datasets were found matching the current filters') + ')');\n\t this.$('.unpaired-columns .paired-column .column-datasets').empty().prepend($msg);\n\t return $msg;\n\t },\n\t /** try to detect if the unpaired section has a scrollbar and adjust left column for better centering of all */\n\t _adjUnpairedOnScrollbar: function () {\n\t var $unpairedColumns = this.$('.unpaired-columns').last(),\n\t $firstDataset = this.$('.unpaired-columns .reverse-column .dataset').first();\n\t if (!$firstDataset.length) {\n\t return;\n\t }\n\t var ucRight = $unpairedColumns.offset().left + $unpairedColumns.outerWidth(),\n\t dsRight = $firstDataset.offset().left + $firstDataset.outerWidth(),\n\t rightDiff = Math.floor(ucRight) - Math.floor(dsRight);\n\t //this.debug( 'rightDiff:', ucRight, '-', dsRight, '=', rightDiff );\n\t this.$('.unpaired-columns .forward-column').css('margin-left', rightDiff > 0 ? rightDiff : 0);\n\t },\n\t\n\t /** render the paired section and update counts of paired datasets */\n\t _renderPaired: function (speed, callback) {\n\t //this.debug( '-- _renderPaired' );\n\t this.$('.paired-column-title .title').text([this.paired.length, _l('paired')].join(' '));\n\t // show/hide the unpair all link\n\t this.$('.unpair-all-link').toggle(this.paired.length !== 0);\n\t if (this.paired.length === 0) {\n\t this._renderPairedEmpty();\n\t return;\n\t //TODO: would be best to return here (the $columns)\n\t } else {\n\t // show/hide 'remove extensions link' when any paired and they seem to have extensions\n\t this.$('.remove-extensions-link').show();\n\t }\n\t\n\t this.$('.paired-columns .column-datasets').empty();\n\t var creator = this;\n\t this.paired.forEach(function (pair, i) {\n\t //TODO: cache these?\n\t var pairView = new PairView({ pair: pair });\n\t creator.$('.paired-columns .column-datasets').append(pairView.render().$el).append([''].join(''));\n\t });\n\t },\n\t /** a message to display when none paired */\n\t _renderPairedEmpty: function () {\n\t var $msg = $('').text('(' + _l('no paired datasets yet') + ')');\n\t this.$('.paired-columns .column-datasets').empty().prepend($msg);\n\t return $msg;\n\t },\n\t\n\t footerSettings: {\n\t '.hide-originals': 'hideOriginals',\n\t '.remove-extensions': 'removeExtensions'\n\t },\n\t\n\t /** add any jQuery/bootstrap/custom plugins to elements rendered */\n\t _addPluginComponents: function () {\n\t this._chooseFiltersPopover('.choose-filters-link');\n\t this.$('.help-content i').hoverhighlight('.collection-creator', 'rgba( 64, 255, 255, 1.0 )');\n\t },\n\t\n\t /** build a filter selection popover allowing selection of common filter pairs */\n\t _chooseFiltersPopover: function (selector) {\n\t function filterChoice(val1, val2) {\n\t return [''].join('');\n\t }\n\t var $popoverContent = $(_.template(['
', '
', _l('Choose from the following filters to change which unpaired reads are shown in the display'), ':
'].join(''))({}));\n\t\n\t return this.$(selector).popover({\n\t container: '.collection-creator',\n\t placement: 'bottom',\n\t html: true,\n\t //animation : false,\n\t content: $popoverContent\n\t });\n\t },\n\t\n\t /** add (or clear if clear is truthy) a validation warning to what */\n\t _validationWarning: function (what, clear) {\n\t var VALIDATION_CLASS = 'validation-warning';\n\t if (what === 'name') {\n\t what = this.$('.collection-name').add(this.$('.collection-name-prompt'));\n\t this.$('.collection-name').focus().select();\n\t }\n\t if (clear) {\n\t what = what || this.$('.' + VALIDATION_CLASS);\n\t what.removeClass(VALIDATION_CLASS);\n\t } else {\n\t what.addClass(VALIDATION_CLASS);\n\t }\n\t },\n\t\n\t // ------------------------------------------------------------------------ events\n\t /** set up event handlers on self */\n\t _setUpBehaviors: function () {\n\t this.once('rendered', function () {\n\t this.trigger('rendered:initial', this);\n\t });\n\t\n\t this.on('pair:new', function () {\n\t //TODO: ideally only re-render the columns (or even elements) involved\n\t this._renderUnpaired();\n\t this._renderPaired();\n\t\n\t // scroll to bottom where new pairs are added\n\t //TODO: this doesn't seem to work - innerHeight sticks at 133...\n\t // may have to do with improper flex columns\n\t //var $pairedView = this.$( '.paired-columns' );\n\t //$pairedView.scrollTop( $pairedView.innerHeight() );\n\t //this.debug( $pairedView.height() )\n\t this.$('.paired-columns').scrollTop(8000000);\n\t });\n\t this.on('pair:unpair', function (pairs) {\n\t //TODO: ideally only re-render the columns (or even elements) involved\n\t this._renderUnpaired();\n\t this._renderPaired();\n\t this.splitView();\n\t });\n\t\n\t this.on('filter-change', function () {\n\t this.filters = [this.$('.forward-unpaired-filter input').val(), this.$('.reverse-unpaired-filter input').val()];\n\t this.metric('filter-change', this.filters);\n\t this._renderFilters();\n\t this._renderUnpaired();\n\t });\n\t\n\t this.on('autopair', function () {\n\t this._renderUnpaired();\n\t this._renderPaired();\n\t\n\t var message,\n\t msgClass = null;\n\t if (this.paired.length) {\n\t msgClass = 'alert-success';\n\t message = this.paired.length + ' ' + _l('pairs created');\n\t if (!this.unpaired.length) {\n\t message += ': ' + _l('all datasets have been successfully paired');\n\t this.hideUnpaired();\n\t this.$('.collection-name').focus();\n\t }\n\t } else {\n\t message = _l(['Could not automatically create any pairs from the given dataset names.', 'You may want to choose or enter different filters and try auto-pairing again.', 'Close this message using the X on the right to view more help.'].join(' '));\n\t }\n\t this._showAlert(message, msgClass);\n\t });\n\t\n\t //this.on( 'all', function(){\n\t // this.info( arguments );\n\t //});\n\t return this;\n\t },\n\t\n\t events: {\n\t // header\n\t 'click .more-help': '_clickMoreHelp',\n\t 'click .less-help': '_clickLessHelp',\n\t 'click .main-help': '_toggleHelp',\n\t 'click .header .alert button': '_hideAlert',\n\t 'click .forward-column .column-title': '_clickShowOnlyUnpaired',\n\t 'click .reverse-column .column-title': '_clickShowOnlyUnpaired',\n\t 'click .unpair-all-link': '_clickUnpairAll',\n\t //TODO: this seems kinda backasswards - re-sending jq event as a backbone event, can we listen directly?\n\t 'change .forward-unpaired-filter input': function (ev) {\n\t this.trigger('filter-change');\n\t },\n\t 'focus .forward-unpaired-filter input': function (ev) {\n\t $(ev.currentTarget).select();\n\t },\n\t 'click .autopair-link': '_clickAutopair',\n\t 'click .choose-filters .filter-choice': '_clickFilterChoice',\n\t 'click .clear-filters-link': '_clearFilters',\n\t 'change .reverse-unpaired-filter input': function (ev) {\n\t this.trigger('filter-change');\n\t },\n\t 'focus .reverse-unpaired-filter input': function (ev) {\n\t $(ev.currentTarget).select();\n\t },\n\t // unpaired\n\t 'click .forward-column .dataset.unpaired': '_clickUnpairedDataset',\n\t 'click .reverse-column .dataset.unpaired': '_clickUnpairedDataset',\n\t 'click .paired-column .dataset.unpaired': '_clickPairRow',\n\t 'click .unpaired-columns': 'clearSelectedUnpaired',\n\t 'mousedown .unpaired-columns .dataset': '_mousedownUnpaired',\n\t // divider\n\t 'click .paired-column-title': '_clickShowOnlyPaired',\n\t 'mousedown .flexible-partition-drag': '_startPartitionDrag',\n\t // paired\n\t 'click .paired-columns .dataset.paired': 'selectPair',\n\t 'click .paired-columns': 'clearSelectedPaired',\n\t 'click .paired-columns .pair-name': '_clickPairName',\n\t 'click .unpair-btn': '_clickUnpair',\n\t // paired - drop target\n\t //'dragenter .paired-columns' : '_dragenterPairedColumns',\n\t //'dragleave .paired-columns .column-datasets': '_dragleavePairedColumns',\n\t 'dragover .paired-columns .column-datasets': '_dragoverPairedColumns',\n\t 'drop .paired-columns .column-datasets': '_dropPairedColumns',\n\t\n\t 'pair.dragstart .paired-columns .column-datasets': '_pairDragstart',\n\t 'pair.dragend .paired-columns .column-datasets': '_pairDragend',\n\t\n\t // footer\n\t 'change .remove-extensions': function (ev) {\n\t this.toggleExtensions();\n\t },\n\t 'change .collection-name': '_changeName',\n\t 'keydown .collection-name': '_nameCheckForEnter',\n\t 'change .hide-originals': '_changeHideOriginals',\n\t 'click .cancel-create': '_cancelCreate',\n\t 'click .create-collection': '_clickCreate' //,\n\t },\n\t\n\t /** toggle between showing only unpaired and split view */\n\t _clickShowOnlyUnpaired: function (ev) {\n\t //this.debug( 'click unpaired', ev.currentTarget );\n\t if (this.$('.paired-columns').is(':visible')) {\n\t this.hidePaired();\n\t } else {\n\t this.splitView();\n\t }\n\t },\n\t /** toggle between showing only paired and split view */\n\t _clickShowOnlyPaired: function (ev) {\n\t //this.debug( 'click paired' );\n\t if (this.$('.unpaired-columns').is(':visible')) {\n\t this.hideUnpaired();\n\t } else {\n\t this.splitView();\n\t }\n\t },\n\t\n\t /** hide unpaired, show paired */\n\t hideUnpaired: function (speed, callback) {\n\t this.unpairedPanelHidden = true;\n\t this.pairedPanelHidden = false;\n\t this._renderMiddle(speed, callback);\n\t },\n\t /** hide paired, show unpaired */\n\t hidePaired: function (speed, callback) {\n\t this.unpairedPanelHidden = false;\n\t this.pairedPanelHidden = true;\n\t this._renderMiddle(speed, callback);\n\t },\n\t /** show both paired and unpaired (splitting evenly) */\n\t splitView: function (speed, callback) {\n\t this.unpairedPanelHidden = this.pairedPanelHidden = false;\n\t this._renderMiddle(speed, callback);\n\t return this;\n\t },\n\t\n\t /** unpair all paired and do other super neat stuff which I'm not really sure about yet... */\n\t _clickUnpairAll: function (ev) {\n\t this.metric('unpairAll');\n\t this.unpairAll();\n\t },\n\t\n\t /** attempt to autopair */\n\t _clickAutopair: function (ev) {\n\t var paired = this.autoPair();\n\t this.metric('autopair', paired.length, this.unpaired.length);\n\t this.trigger('autopair');\n\t },\n\t\n\t /** set the filters based on the data attributes of the button click target */\n\t _clickFilterChoice: function (ev) {\n\t var $selected = $(ev.currentTarget);\n\t this.$('.forward-unpaired-filter input').val($selected.data('forward'));\n\t this.$('.reverse-unpaired-filter input').val($selected.data('reverse'));\n\t this._hideChooseFilters();\n\t this.trigger('filter-change');\n\t },\n\t\n\t /** hide the choose filters popover */\n\t _hideChooseFilters: function () {\n\t //TODO: update bootstrap and remove the following hack\n\t // see also: https://github.com/twbs/bootstrap/issues/10260\n\t this.$('.choose-filters-link').popover('hide');\n\t this.$('.popover').css('display', 'none');\n\t },\n\t\n\t /** clear both filters */\n\t _clearFilters: function (ev) {\n\t this.$('.forward-unpaired-filter input').val('');\n\t this.$('.reverse-unpaired-filter input').val('');\n\t this.trigger('filter-change');\n\t },\n\t\n\t // ........................................................................ unpaired\n\t /** select an unpaired dataset */\n\t _clickUnpairedDataset: function (ev) {\n\t ev.stopPropagation();\n\t return this.toggleSelectUnpaired($(ev.currentTarget));\n\t },\n\t\n\t /** Toggle the selection of an unpaired dataset representation.\n\t * @param [jQuery] $dataset the unpaired dataset dom rep to select\n\t * @param [Boolean] options.force if defined, force selection based on T/F; otherwise, toggle\n\t */\n\t toggleSelectUnpaired: function ($dataset, options) {\n\t options = options || {};\n\t var dataset = $dataset.data('dataset'),\n\t select = options.force !== undefined ? options.force : !$dataset.hasClass('selected');\n\t //this.debug( id, options.force, $dataset, dataset );\n\t if (!$dataset.length || dataset === undefined) {\n\t return $dataset;\n\t }\n\t\n\t if (select) {\n\t $dataset.addClass('selected');\n\t if (!options.waitToPair) {\n\t this.pairAllSelected();\n\t }\n\t } else {\n\t $dataset.removeClass('selected');\n\t //delete dataset.selected;\n\t }\n\t return $dataset;\n\t },\n\t\n\t /** pair all the currently selected unpaired datasets */\n\t pairAllSelected: function (options) {\n\t options = options || {};\n\t var creator = this,\n\t fwds = [],\n\t revs = [],\n\t pairs = [];\n\t creator.$('.unpaired-columns .forward-column .dataset.selected').each(function () {\n\t fwds.push($(this).data('dataset'));\n\t });\n\t creator.$('.unpaired-columns .reverse-column .dataset.selected').each(function () {\n\t revs.push($(this).data('dataset'));\n\t });\n\t fwds.length = revs.length = Math.min(fwds.length, revs.length);\n\t //this.debug( fwds );\n\t //this.debug( revs );\n\t fwds.forEach(function (fwd, i) {\n\t try {\n\t pairs.push(creator._pair(fwd, revs[i], { silent: true }));\n\t } catch (err) {\n\t //TODO: preserve selected state of those that couldn't be paired\n\t //TODO: warn that some could not be paired\n\t creator.error(err);\n\t }\n\t });\n\t if (pairs.length && !options.silent) {\n\t this.trigger('pair:new', pairs);\n\t }\n\t return pairs;\n\t },\n\t\n\t /** clear the selection on all unpaired datasets */\n\t clearSelectedUnpaired: function () {\n\t this.$('.unpaired-columns .dataset.selected').removeClass('selected');\n\t },\n\t\n\t /** when holding down the shift key on a click, 'paint' the moused over datasets as selected */\n\t _mousedownUnpaired: function (ev) {\n\t if (ev.shiftKey) {\n\t var creator = this,\n\t $startTarget = $(ev.target).addClass('selected'),\n\t moveListener = function (ev) {\n\t creator.$(ev.target).filter('.dataset').addClass('selected');\n\t };\n\t $startTarget.parent().on('mousemove', moveListener);\n\t\n\t // on any mouseup, stop listening to the move and try to pair any selected\n\t $(document).one('mouseup', function (ev) {\n\t $startTarget.parent().off('mousemove', moveListener);\n\t creator.pairAllSelected();\n\t });\n\t }\n\t },\n\t\n\t /** attempt to pair two datasets directly across from one another */\n\t _clickPairRow: function (ev) {\n\t //if( !ev.currentTarget ){ return true; }\n\t var rowIndex = $(ev.currentTarget).index(),\n\t fwd = $('.unpaired-columns .forward-column .dataset').eq(rowIndex).data('dataset'),\n\t rev = $('.unpaired-columns .reverse-column .dataset').eq(rowIndex).data('dataset');\n\t //this.debug( 'row:', rowIndex, fwd, rev );\n\t this._pair(fwd, rev);\n\t },\n\t\n\t // ........................................................................ divider/partition\n\t /** start dragging the visible divider/partition between unpaired and paired panes */\n\t _startPartitionDrag: function (ev) {\n\t var creator = this,\n\t startingY = ev.pageY;\n\t //this.debug( 'partition drag START:', ev );\n\t $('body').css('cursor', 'ns-resize');\n\t creator.$('.flexible-partition-drag').css('color', 'black');\n\t\n\t function endDrag(ev) {\n\t //creator.debug( 'partition drag STOP:', ev );\n\t // doing this by an added class didn't really work well - kept flashing still\n\t creator.$('.flexible-partition-drag').css('color', '');\n\t $('body').css('cursor', '').unbind('mousemove', trackMouse);\n\t }\n\t function trackMouse(ev) {\n\t var offset = ev.pageY - startingY;\n\t //creator.debug( 'partition:', startingY, offset );\n\t if (!creator.adjPartition(offset)) {\n\t //creator.debug( 'mouseup triggered' );\n\t $('body').trigger('mouseup');\n\t }\n\t creator._adjUnpairedOnScrollbar();\n\t startingY += offset;\n\t }\n\t $('body').mousemove(trackMouse);\n\t $('body').one('mouseup', endDrag);\n\t },\n\t\n\t /** adjust the parition up/down +/-adj pixels */\n\t adjPartition: function (adj) {\n\t var $unpaired = this.$('.unpaired-columns'),\n\t $paired = this.$('.paired-columns'),\n\t unpairedHi = parseInt($unpaired.css('height'), 10),\n\t pairedHi = parseInt($paired.css('height'), 10);\n\t //this.debug( adj, 'hi\\'s:', unpairedHi, pairedHi, unpairedHi + adj, pairedHi - adj );\n\t\n\t unpairedHi = Math.max(10, unpairedHi + adj);\n\t pairedHi = pairedHi - adj;\n\t\n\t var movingUpwards = adj < 0;\n\t // when the divider gets close to the top - lock into hiding the unpaired section\n\t if (movingUpwards) {\n\t if (this.unpairedPanelHidden) {\n\t return false;\n\t } else if (unpairedHi <= 10) {\n\t this.hideUnpaired();\n\t return false;\n\t }\n\t } else {\n\t if (this.unpairedPanelHidden) {\n\t $unpaired.show();\n\t this.unpairedPanelHidden = false;\n\t }\n\t }\n\t\n\t // when the divider gets close to the bottom - lock into hiding the paired section\n\t if (!movingUpwards) {\n\t if (this.pairedPanelHidden) {\n\t return false;\n\t } else if (pairedHi <= 15) {\n\t this.hidePaired();\n\t return false;\n\t }\n\t } else {\n\t if (this.pairedPanelHidden) {\n\t $paired.show();\n\t this.pairedPanelHidden = false;\n\t }\n\t }\n\t\n\t $unpaired.css({\n\t height: unpairedHi + 'px',\n\t flex: '0 0 auto'\n\t });\n\t return true;\n\t },\n\t\n\t // ........................................................................ paired\n\t /** select a pair when clicked */\n\t selectPair: function (ev) {\n\t ev.stopPropagation();\n\t $(ev.currentTarget).toggleClass('selected');\n\t },\n\t\n\t /** deselect all pairs */\n\t clearSelectedPaired: function (ev) {\n\t this.$('.paired-columns .dataset.selected').removeClass('selected');\n\t },\n\t\n\t /** rename a pair when the pair name is clicked */\n\t _clickPairName: function (ev) {\n\t ev.stopPropagation();\n\t var $name = $(ev.currentTarget),\n\t $pair = $name.parent().parent(),\n\t index = $pair.index('.dataset.paired'),\n\t pair = this.paired[index],\n\t response = prompt('Enter a new name for the pair:', pair.name);\n\t if (response) {\n\t pair.name = response;\n\t // set a flag (which won't be passed in json creation) for manual naming so we don't overwrite these\n\t // when adding/removing extensions\n\t //hackish\n\t pair.customizedName = true;\n\t $name.text(pair.name);\n\t }\n\t },\n\t\n\t /** unpair this pair */\n\t _clickUnpair: function (ev) {\n\t //if( !ev.currentTarget ){ return true; }\n\t var pairIndex = Math.floor($(ev.currentTarget).index('.unpair-btn'));\n\t //this.debug( 'pair:', pairIndex );\n\t this._unpair(this.paired[pairIndex]);\n\t },\n\t\n\t // ........................................................................ paired - drag and drop re-ordering\n\t //_dragenterPairedColumns : function( ev ){\n\t // this.debug( '_dragenterPairedColumns:', ev );\n\t //},\n\t //_dragleavePairedColumns : function( ev ){\n\t // //this.debug( '_dragleavePairedColumns:', ev );\n\t //},\n\t /** track the mouse drag over the paired list adding a placeholder to show where the drop would occur */\n\t _dragoverPairedColumns: function (ev) {\n\t //this.debug( '_dragoverPairedColumns:', ev );\n\t ev.preventDefault();\n\t\n\t var $list = this.$('.paired-columns .column-datasets');\n\t this._checkForAutoscroll($list, ev.originalEvent.clientY);\n\t //this.debug( ev.originalEvent.clientX, ev.originalEvent.clientY );\n\t var $nearest = this._getNearestPairedDatasetLi(ev.originalEvent.clientY);\n\t\n\t $('.element-drop-placeholder').remove();\n\t var $placeholder = $('');\n\t if (!$nearest.length) {\n\t $list.append($placeholder);\n\t } else {\n\t $nearest.before($placeholder);\n\t }\n\t },\n\t\n\t /** If the mouse is near enough to the list's top or bottom, scroll the list */\n\t _checkForAutoscroll: function ($element, y) {\n\t var AUTOSCROLL_SPEED = 2;\n\t var offset = $element.offset(),\n\t scrollTop = $element.scrollTop(),\n\t upperDist = y - offset.top,\n\t lowerDist = offset.top + $element.outerHeight() - y;\n\t //this.debug( '_checkForAutoscroll:', scrollTop, upperDist, lowerDist );\n\t if (upperDist >= 0 && upperDist < this.autoscrollDist) {\n\t $element.scrollTop(scrollTop - AUTOSCROLL_SPEED);\n\t } else if (lowerDist >= 0 && lowerDist < this.autoscrollDist) {\n\t $element.scrollTop(scrollTop + AUTOSCROLL_SPEED);\n\t }\n\t },\n\t\n\t /** get the nearest *previous* paired dataset PairView based on the mouse's Y coordinate.\n\t * If the y is at the end of the list, return an empty jQuery object.\n\t */\n\t _getNearestPairedDatasetLi: function (y) {\n\t var WIGGLE = 4,\n\t lis = this.$('.paired-columns .column-datasets li').toArray();\n\t for (var i = 0; i < lis.length; i++) {\n\t var $li = $(lis[i]),\n\t top = $li.offset().top,\n\t halfHeight = Math.floor($li.outerHeight() / 2) + WIGGLE;\n\t if (top + halfHeight > y && top - halfHeight < y) {\n\t //this.debug( y, top + halfHeight, top - halfHeight )\n\t return $li;\n\t }\n\t }\n\t return $();\n\t },\n\t /** drop (dragged/selected PairViews) onto the list, re-ordering both the DOM and the internal array of pairs */\n\t _dropPairedColumns: function (ev) {\n\t // both required for firefox\n\t ev.preventDefault();\n\t ev.dataTransfer.dropEffect = 'move';\n\t\n\t var $nearest = this._getNearestPairedDatasetLi(ev.originalEvent.clientY);\n\t if ($nearest.length) {\n\t this.$dragging.insertBefore($nearest);\n\t } else {\n\t // no nearest before - insert after last element (unpair button)\n\t this.$dragging.insertAfter(this.$('.paired-columns .unpair-btn').last());\n\t }\n\t // resync the creator's list of paired based on the new DOM order\n\t this._syncPairsToDom();\n\t return false;\n\t },\n\t /** resync the creator's list of paired based on the DOM order of pairs */\n\t _syncPairsToDom: function () {\n\t var newPaired = [];\n\t //TODO: doesn't seem wise to use the dom to store these - can't we sync another way?\n\t this.$('.paired-columns .dataset.paired').each(function () {\n\t newPaired.push($(this).data('pair'));\n\t });\n\t //this.debug( newPaired );\n\t this.paired = newPaired;\n\t this._renderPaired();\n\t },\n\t /** drag communication with pair sub-views: dragstart */\n\t _pairDragstart: function (ev, pair) {\n\t //this.debug( '_pairDragstart', ev, pair )\n\t // auto select the pair causing the event and move all selected\n\t pair.$el.addClass('selected');\n\t var $selected = this.$('.paired-columns .dataset.selected');\n\t this.$dragging = $selected;\n\t },\n\t /** drag communication with pair sub-views: dragend - remove the placeholder */\n\t _pairDragend: function (ev, pair) {\n\t //this.debug( '_pairDragend', ev, pair )\n\t $('.element-drop-placeholder').remove();\n\t this.$dragging = null;\n\t },\n\t\n\t // ........................................................................ footer\n\t toggleExtensions: function (force) {\n\t var creator = this;\n\t creator.removeExtensions = force !== undefined ? force : !creator.removeExtensions;\n\t\n\t _.each(creator.paired, function (pair) {\n\t // don't overwrite custom names\n\t if (pair.customizedName) {\n\t return;\n\t }\n\t pair.name = creator._guessNameForPair(pair.forward, pair.reverse);\n\t });\n\t\n\t creator._renderPaired();\n\t creator._renderFooter();\n\t },\n\t\n\t // ------------------------------------------------------------------------ misc\n\t /** debug a dataset list */\n\t _printList: function (list) {\n\t var creator = this;\n\t _.each(list, function (e) {\n\t if (list === creator.paired) {\n\t creator._printPair(e);\n\t } else {\n\t //creator.debug( e );\n\t }\n\t });\n\t },\n\t\n\t /** print a pair Object */\n\t _printPair: function (pair) {\n\t this.debug(pair.forward.name, pair.reverse.name, ': ->', pair.name);\n\t },\n\t\n\t /** string rep */\n\t toString: function () {\n\t return 'PairedCollectionCreator';\n\t },\n\t\n\t templates: _.extend({}, baseCreator.CollectionCreatorMixin._creatorTemplates, {\n\t\n\t /** the header (not including help text) */\n\t header: _.template(['
'].join('')),\n\t\n\t /** the middle: unpaired, divider, and paired */\n\t middle: _.template([\n\t // contains two flex rows (rows that fill available space) and a divider btwn\n\t '
'].join('')),\n\t\n\t /** help content */\n\t helpContent: _.template(['
', _l(['Collections of paired datasets are ordered lists of dataset pairs (often forward and reverse reads). ', 'These collections can be passed to tools and workflows in order to have analyses done on each member of ', 'the entire group. This interface allows you to create a collection, choose which datasets are paired, ', 'and re-order the final collection.'].join('')), '
', '
', _l(['Unpaired datasets are shown in the unpaired section ', '(hover over the underlined words to highlight below). ', 'Paired datasets are shown in the paired section.', '
To pair datasets, you can:', '
Click a dataset in the ', 'forward column ', 'to select it then click a dataset in the ', 'reverse column.', '
', '
Click one of the \"Pair these datasets\" buttons in the ', 'middle column ', 'to pair the datasets in a particular row.', '
', '
Click \"Auto-pair\" ', 'to have your datasets automatically paired based on name.', '
', '
'].join('')), '', '
', _l(['
You can filter what is shown in the unpaired sections by:', '
Entering partial dataset names in either the ', 'forward filter or ', 'reverse filter.', '
', '
Choosing from a list of preset filters by clicking the ', '\"Choose filters\" link.', '
Clearing the filters by clicking the ', '\"Clear filters\" link.', '
', '
'].join('')), '', '
', _l(['To unpair individual dataset pairs, click the ', 'unpair buttons ( ). ', 'Click the \"Unpair all\" link to unpair all pairs.'].join('')), '
', '
', _l(['You can include or remove the file extensions (e.g. \".fastq\") from your pair names by toggling the ', '\"Remove file extensions from pair names?\" control.'].join('')), '
', '
', _l(['Once your collection is complete, enter a name and ', 'click \"Create list\". ', '(Note: you do not have to pair all unpaired datasets to finish.)'].join('')), '
'].join(''))\n\t })\n\t });\n\t\n\t //=============================================================================\n\t /** a modal version of the paired collection creator */\n\t var pairedCollectionCreatorModal = function _pairedCollectionCreatorModal(datasets, options) {\n\t\n\t var deferred = jQuery.Deferred(),\n\t creator;\n\t\n\t options = _.defaults(options || {}, {\n\t datasets: datasets,\n\t oncancel: function () {\n\t Galaxy.modal.hide();\n\t deferred.reject('cancelled');\n\t },\n\t oncreate: function (creator, response) {\n\t Galaxy.modal.hide();\n\t deferred.resolve(response);\n\t }\n\t });\n\t\n\t if (!window.Galaxy || !Galaxy.modal) {\n\t throw new Error('Galaxy or Galaxy.modal not found');\n\t }\n\t\n\t creator = new PairedCollectionCreator(options);\n\t Galaxy.modal.show({\n\t title: 'Create a collection of paired datasets',\n\t body: creator.$el,\n\t width: '80%',\n\t height: '800px',\n\t closing_events: true\n\t });\n\t creator.render();\n\t window.creator = creator;\n\t\n\t //TODO: remove modal header\n\t return deferred;\n\t };\n\t\n\t //=============================================================================\n\t function createListOfPairsCollection(collection, defaultHideSourceItems) {\n\t var elements = collection.toJSON();\n\t //TODO: validate elements\n\t return pairedCollectionCreatorModal(elements, {\n\t historyId: collection.historyId,\n\t defaultHideSourceItems: defaultHideSourceItems\n\t });\n\t }\n\t\n\t //=============================================================================\n\t return {\n\t PairedCollectionCreator: PairedCollectionCreator,\n\t pairedCollectionCreatorModal: pairedCollectionCreatorModal,\n\t createListOfPairsCollection: createListOfPairsCollection\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2), __webpack_require__(1), __webpack_require__(1)))\n\n/***/ }),\n/* 115 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, jQuery) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(37), __webpack_require__(44), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (LIST_CREATOR, HDCA, BASE_MVC, _l) {\n\t\n\t 'use strict';\n\t\n\t var logNamespace = 'collections';\n\t /*==============================================================================\n\t TODO:\n\t the paired creator doesn't really mesh with the list creator as parent\n\t it may be better to make an abstract super class for both\n\t composites may inherit from this (or vis-versa)\n\t PairedDatasetCollectionElementView doesn't make a lot of sense\n\t \n\t ==============================================================================*/\n\t /** */\n\t var PairedDatasetCollectionElementView = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({\n\t _logNamespace: logNamespace,\n\t\n\t //TODO: use proper class (DatasetDCE or NestedDCDCE (or the union of both))\n\t tagName: 'li',\n\t className: 'collection-element',\n\t\n\t initialize: function (attributes) {\n\t this.element = attributes.element || {};\n\t this.identifier = attributes.identifier;\n\t },\n\t\n\t render: function () {\n\t this.$el.attr('data-element-id', this.element.id).html(this.template({ identifier: this.identifier, element: this.element }));\n\t return this;\n\t },\n\t\n\t //TODO: lots of unused space in the element - possibly load details and display them horiz.\n\t template: _.template(['<%- identifier %>', '<%- element.name %>'].join('')),\n\t\n\t /** remove the DOM and any listeners */\n\t destroy: function () {\n\t this.off();\n\t this.$el.remove();\n\t },\n\t\n\t /** string rep */\n\t toString: function () {\n\t return 'DatasetCollectionElementView()';\n\t }\n\t });\n\t\n\t // ============================================================================\n\t var _super = LIST_CREATOR.ListCollectionCreator;\n\t\n\t /** An interface for building collections.\n\t */\n\t var PairCollectionCreator = _super.extend({\n\t\n\t /** the class used to display individual elements */\n\t elementViewClass: PairedDatasetCollectionElementView,\n\t /** the class this creator will create and save */\n\t collectionClass: HDCA.HistoryPairDatasetCollection,\n\t className: 'pair-collection-creator collection-creator flex-row-container',\n\t\n\t /** override to no-op */\n\t _mangleDuplicateNames: function () {},\n\t\n\t // TODO: this whole pattern sucks. There needs to be two classes of problem area:\n\t // bad inital choices and\n\t // when the user has painted his/her self into a corner during creation/use-of-the-creator\n\t /** render the entire interface */\n\t render: function (speed, callback) {\n\t if (this.workingElements.length === 2) {\n\t return _super.prototype.render.call(this, speed, callback);\n\t }\n\t return this._renderInvalid(speed, callback);\n\t },\n\t\n\t // ------------------------------------------------------------------------ rendering elements\n\t /** render forward/reverse */\n\t _renderList: function (speed, callback) {\n\t //this.debug( '-- _renderList' );\n\t //precondition: there are two valid elements in workingElements\n\t var creator = this,\n\t $tmp = jQuery(''),\n\t $list = creator.$list();\n\t\n\t // lose the original views, create the new, append all at once, then call their renders\n\t _.each(this.elementViews, function (view) {\n\t view.destroy();\n\t creator.removeElementView(view);\n\t });\n\t $tmp.append(creator._createForwardElementView().$el);\n\t $tmp.append(creator._createReverseElementView().$el);\n\t $list.empty().append($tmp.children());\n\t _.invoke(creator.elementViews, 'render');\n\t },\n\t\n\t /** create the forward element view */\n\t _createForwardElementView: function () {\n\t return this._createElementView(this.workingElements[0], { identifier: 'forward' });\n\t },\n\t\n\t /** create the forward element view */\n\t _createReverseElementView: function () {\n\t return this._createElementView(this.workingElements[1], { identifier: 'reverse' });\n\t },\n\t\n\t /** create an element view, cache in elementViews, and return */\n\t _createElementView: function (element, options) {\n\t var elementView = new this.elementViewClass(_.extend(options, {\n\t element: element\n\t }));\n\t this.elementViews.push(elementView);\n\t return elementView;\n\t },\n\t\n\t /** swap the forward, reverse elements and re-render */\n\t swap: function () {\n\t this.workingElements = [this.workingElements[1], this.workingElements[0]];\n\t this._renderList();\n\t },\n\t\n\t events: _.extend(_.clone(_super.prototype.events), {\n\t 'click .swap': 'swap'\n\t }),\n\t\n\t // ------------------------------------------------------------------------ templates\n\t //TODO: move to require text plugin and load these as text\n\t //TODO: underscore currently unnecc. bc no vars are used\n\t //TODO: better way of localizing text-nodes in long strings\n\t /** underscore template fns attached to class */\n\t templates: _.extend(_.clone(_super.prototype.templates), {\n\t /** the middle: element list */\n\t middle: _.template(['
'].join('')),\n\t\n\t /** help content */\n\t helpContent: _.template(['
', _l(['Pair collections are permanent collections containing two datasets: one forward and one reverse. ', 'Often these are forward and reverse reads. The pair collections can be passed to tools and ', 'workflows in order to have analyses done on both datasets. This interface allows ', 'you to create a pair, name it, and swap which is forward and which reverse.'].join('')), '
', '
', '
', _l(['Click the \"Swap\" link to make your forward dataset the reverse ', 'and the reverse dataset forward.'].join('')), '
', '
', _l(['Click the \"Cancel\" button to exit the interface.'].join('')), '
', '
', '
', _l(['Once your collection is complete, enter a name and ', 'click \"Create list\".'].join('')), '
'].join('')),\n\t\n\t /** a simplified page communicating what went wrong and why the user needs to reselect something else */\n\t invalidInitial: _.template(['
', '
', '', '<% if( _.size( problems ) ){ %>', _l('The following selections could not be included due to problems'), '
<% _.each( problems, function( problem ){ %>', '
<%- problem.element.name %>: <%- problem.text %>
', '<% }); %>
', '<% } else if( _.size( elements ) === 0 ){ %>', _l('No datasets were selected'), '.', '<% } else if( _.size( elements ) === 1 ){ %>', _l('Only one dataset was selected'), ': <%- elements[0].name %>', '<% } else if( _.size( elements ) > 2 ){ %>', _l('Too many datasets were selected'), ': <%- _.pluck( elements, \"name\" ).join( \", \") %>', '<% } %>', ' ', _l('Two (and only two) elements are needed for the pair'), '. ', _l('You may need to '), '', _l('cancel'), ' ', _l('and reselect new elements'), '.', '', '
', '
', ''].join(''))\n\t }),\n\t\n\t // ------------------------------------------------------------------------ misc\n\t /** string rep */\n\t toString: function () {\n\t return 'PairCollectionCreator';\n\t }\n\t });\n\t\n\t //==============================================================================\n\t /** List collection flavor of collectionCreatorModal. */\n\t var pairCollectionCreatorModal = function _pairCollectionCreatorModal(elements, options) {\n\t options = options || {};\n\t options.title = _l('Create a collection from a pair of datasets');\n\t return LIST_CREATOR.collectionCreatorModal(elements, options, PairCollectionCreator);\n\t };\n\t\n\t //==============================================================================\n\t /** Use a modal to create a pair collection, then add it to the given history contents.\n\t * @returns {Deferred} resolved when the collection is added to the history.\n\t */\n\t function createPairCollection(contents, defaultHideSourceItems) {\n\t var elements = contents.toJSON(),\n\t promise = pairCollectionCreatorModal(elements, {\n\t defaultHideSourceItems: defaultHideSourceItems,\n\t creationFn: function (elements, name, hideSourceItems) {\n\t elements = [{ name: \"forward\", src: \"hda\", id: elements[0].id }, { name: \"reverse\", src: \"hda\", id: elements[1].id }];\n\t return contents.createHDCA(elements, 'paired', name, hideSourceItems);\n\t }\n\t });\n\t return promise;\n\t }\n\t\n\t //==============================================================================\n\t return {\n\t PairCollectionCreator: PairCollectionCreator,\n\t pairCollectionCreatorModal: pairCollectionCreatorModal,\n\t createPairCollection: createPairCollection\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ }),\n/* 116 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, $) {// dependencies\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t\n\t // grid model\n\t return Backbone.Model.extend({\n\t defaults: {\n\t url_base: '',\n\t async: false,\n\t async_ops: [],\n\t categorical_filters: [],\n\t filters: {},\n\t sort_key: null,\n\t show_item_checkboxes: false,\n\t advanced_search: false,\n\t cur_page: 1,\n\t num_pages: 1,\n\t operation: undefined,\n\t item_ids: undefined\n\t },\n\t\n\t /**\n\t * Return true if operation can be done asynchronously.\n\t */\n\t can_async_op: function (op) {\n\t return _.indexOf(this.attributes.async_ops, op) !== -1;\n\t },\n\t\n\t /**\n\t * Add filtering criterion.\n\t */\n\t add_filter: function (key, value, append) {\n\t // Update URL arg with new condition. \n\t if (append) {\n\t // Update or append value.\n\t var cur_val = this.attributes.filters[key],\n\t new_val;\n\t if (cur_val === null || cur_val === undefined) {\n\t new_val = value;\n\t } else if (typeof cur_val == 'string') {\n\t if (cur_val == 'All') {\n\t new_val = value;\n\t } else {\n\t // Replace string with array.\n\t var values = [];\n\t values[0] = cur_val;\n\t values[1] = value;\n\t new_val = values;\n\t }\n\t } else {\n\t // Current value is an array.\n\t new_val = cur_val;\n\t new_val.push(value);\n\t }\n\t this.attributes.filters[key] = new_val;\n\t } else {\n\t // Replace value.\n\t this.attributes.filters[key] = value;\n\t }\n\t },\n\t\n\t /**\n\t * Remove filtering criterion.\n\t */\n\t remove_filter: function (key, condition) {\n\t var cur_val = this.attributes.filters[key];\n\t if (cur_val === null || cur_val === undefined) {\n\t return false;\n\t }\n\t\n\t if (typeof cur_val === 'string') {\n\t // overwrite/remove condition.\n\t this.attributes.filters[key] = '';\n\t } else {\n\t // filter contains an array of conditions.\n\t var condition_index = _.indexOf(cur_val, condition);\n\t if (condition_index !== -1) {\n\t cur_val[condition_index] = '';\n\t }\n\t }\n\t },\n\t\n\t /**\n\t * Returns URL data for obtaining a new grid.\n\t */\n\t get_url_data: function () {\n\t var url_data = {\n\t async: this.attributes.async,\n\t sort: this.attributes.sort_key,\n\t page: this.attributes.cur_page,\n\t show_item_checkboxes: this.attributes.show_item_checkboxes,\n\t advanced_search: this.attributes.advanced_search\n\t };\n\t\n\t // Add operation, item_ids only if they have values.\n\t if (this.attributes.operation) {\n\t url_data.operation = this.attributes.operation;\n\t }\n\t if (this.attributes.item_ids) {\n\t url_data.id = this.attributes.item_ids;\n\t }\n\t\n\t // Add filter arguments to data, placing \"f-\" in front of all arguments.\n\t var self = this;\n\t _.each(_.pairs(self.attributes.filters), function (k) {\n\t url_data['f-' + k[0]] = k[1];\n\t });\n\t\n\t return url_data;\n\t },\n\t\n\t // Return URL for obtaining a new grid\n\t get_url: function (args) {\n\t return this.get('url_base') + \"?\" + $.param(this.get_url_data()) + '&' + $.param(args);\n\t }\n\t\n\t });\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ }),\n/* 117 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(jQuery) {// dependencies\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t\n\t // grid view templates\n\t return {\n\t // template\n\t grid: function (options) {\n\t var tmpl = '';\n\t if (options.embedded) {\n\t tmpl = this.grid_header(options) + this.grid_table(options);\n\t } else {\n\t tmpl = '' + '
' + '
' + '
' + this.grid_header(options) + '
' + '
' + '
' + '
' + '
' + '
' + '
' + '
' + '
' + '
' + this.grid_table(options);\n\t }\n\t\n\t // add info text\n\t if (options.info_text) {\n\t tmpl += '
' + options.info_text + '
';\n\t }\n\t\n\t // return\n\t return tmpl;\n\t },\n\t\n\t // template\n\t grid_table: function (options) {\n\t return '';\n\t },\n\t\n\t // template\n\t grid_header: function (options) {\n\t var tmpl = '
';\n\t if (!options.embedded) {\n\t tmpl += '
' + options.title + '
';\n\t }\n\t if (options.global_actions) {\n\t tmpl += '
';\n\t var show_popup = options.global_actions.length >= 3;\n\t if (show_popup) {\n\t tmpl += '
';\n\t }\n\t\n\t // create header elements\n\t for (var i in options.columns) {\n\t var column = options.columns[i];\n\t if (column.visible) {\n\t tmpl += '
';\n\t\n\t // return template\n\t return tmpl;\n\t },\n\t\n\t // template\n\t body: function (options) {\n\t // initialize\n\t var tmpl = '';\n\t var num_rows_rendered = 0;\n\t var items_length = options.items.length;\n\t\n\t // empty grid?\n\t if (items_length == 0) {\n\t // No results.\n\t tmpl += '
No Items
';\n\t num_rows_rendered = 1;\n\t }\n\t\n\t // create rows\n\t for (var i in options.items) {\n\t\n\t // encode ids\n\t var item = options.items[i];\n\t var encoded_id = item.encode_id;\n\t var popupmenu_id = 'grid-' + i + '-popup';\n\t\n\t // Tag current\n\t tmpl += '
' + '
';\n\t }\n\t\n\t // Data columns\n\t for (j in options.columns) {\n\t var column = options.columns[j];\n\t if (column.visible) {\n\t // Nowrap\n\t var nowrap = '';\n\t if (column.nowrap) {\n\t nowrap = 'style=\"white-space:nowrap;\"';\n\t }\n\t\n\t // get column settings\n\t var column_settings = item.column_config[column.label];\n\t\n\t // load attributes\n\t var link = column_settings.link;\n\t var value = column_settings.value;\n\t var target = column_settings.target;\n\t\n\t // unescape value\n\t if (jQuery.type(value) === 'string') {\n\t value = value.replace(/\\/\\//g, '/');\n\t }\n\t\n\t // Attach popup menu?\n\t var id = '';\n\t var cls = '';\n\t if (column.attach_popup) {\n\t id = 'grid-' + i + '-popup';\n\t cls = 'menubutton';\n\t if (link != '') {\n\t cls += ' split';\n\t }\n\t cls += ' popup';\n\t }\n\t\n\t // Check for row wrapping\n\t tmpl += '
';\n\t\n\t // Link\n\t if (link) {\n\t if (options.operations.length != 0) {\n\t tmpl += '
';\n\t }\n\t tmpl += '' + value + '';\n\t if (options.operations.length != 0) {\n\t tmpl += '
';\n\t num_rows_rendered++;\n\t }\n\t return tmpl;\n\t },\n\t\n\t // template\n\t footer: function (options) {\n\t\n\t // create template string\n\t var tmpl = '';\n\t\n\t // paging\n\t if (options.use_paging && options.num_pages > 1) {\n\t // get configuration\n\t var num_page_links = options.num_page_links;\n\t var cur_page_num = options.cur_page_num;\n\t var num_pages = options.num_pages;\n\t\n\t // First pass on min page.\n\t var page_link_range = num_page_links / 2;\n\t var min_page = cur_page_num - page_link_range;\n\t var min_offset = 0;\n\t if (min_page <= 0) {\n\t // Min page is too low.\n\t min_page = 1;\n\t min_offset = page_link_range - (cur_page_num - min_page);\n\t }\n\t\n\t // Set max page.\n\t var max_range = page_link_range + min_offset;\n\t var max_page = cur_page_num + max_range;\n\t if (max_page <= num_pages) {\n\t // Max page is fine.\n\t max_offset = 0;\n\t } else {\n\t // Max page is too high.\n\t max_page = num_pages;\n\t // +1 to account for the +1 in the loop below.\n\t max_offset = max_range - (max_page + 1 - cur_page_num);\n\t }\n\t\n\t // Second and final pass on min page to add any unused\n\t // offset from max to min.\n\t if (max_offset != 0) {\n\t min_page -= max_offset;\n\t if (min_page < 1) {\n\t min_page = 1;\n\t }\n\t }\n\t\n\t // template header\n\t tmpl += '
';\n\t if (options.show_item_checkboxes) {\n\t tmpl += '
';\n\t }\n\t tmpl += '
' + '' + 'Page:';\n\t\n\t if (min_page > 1) {\n\t tmpl += '1 ...';\n\t }\n\t\n\t // create page urls\n\t for (var page_index = min_page; page_index < max_page + 1; page_index++) {\n\t\n\t if (page_index == options.cur_page_num) {\n\t tmpl += '' + page_index + '';\n\t } else {\n\t tmpl += '' + page_index + '';\n\t }\n\t }\n\t\n\t // show last page\n\t if (max_page < num_pages) {\n\t tmpl += '...' + '' + num_pages + '';\n\t }\n\t tmpl += '';\n\t\n\t // Show all link\n\t tmpl += ' | Show All' + '
' + '
';\n\t }\n\t\n\t // Grid operations for multiple items.\n\t if (options.show_item_checkboxes) {\n\t // start template\n\t tmpl += '
' + '' + '
' + '
' + 'For selected items: ';\n\t\n\t // configure buttons for operations\n\t for (i in options.operations) {\n\t var operation = options.operations[i];\n\t if (operation.allow_multiple) {\n\t tmpl += ' ';\n\t }\n\t }\n\t\n\t // finalize template\n\t tmpl += '
' + '
';\n\t }\n\t\n\t // count global operations\n\t var found_global = false;\n\t for (i in options.operations) {\n\t if (options.operations[i].global_operation) {\n\t found_global = true;\n\t break;\n\t }\n\t }\n\t\n\t // add global operations\n\t if (found_global) {\n\t tmpl += '
' + '
';\n\t for (i in options.operations) {\n\t var operation = options.operations[i];\n\t if (operation.global_operation) {\n\t tmpl += '' + operation.label + '';\n\t }\n\t }\n\t tmpl += '
' + '' + '';\n\t },\n\t\n\t // template\n\t grid_filters: function (options) {\n\t\n\t // get filters\n\t var default_filter_dict = options.default_filter_dict;\n\t var filters = options.filters;\n\t\n\t // show advanced search if flag set or if there are filters for advanced search fields\n\t var advanced_search_display = 'none';\n\t if (options.advanced_search) {\n\t advanced_search_display = 'block';\n\t }\n\t\n\t // identify columns with advanced filtering\n\t var show_advanced_search_link = false;\n\t for (var i in options.columns) {\n\t var column = options.columns[i];\n\t if (column.filterable == 'advanced') {\n\t var column_key = column.key;\n\t var f_key = filters[column_key];\n\t var d_key = default_filter_dict[column_key];\n\t if (f_key && d_key && f_key != d_key) {\n\t advanced_search_display = 'block';\n\t }\n\t show_advanced_search_link = true;\n\t }\n\t }\n\t\n\t // hide standard search if advanced is shown\n\t var standard_search_display = 'block';\n\t if (advanced_search_display == 'block') {\n\t standard_search_display = 'none';\n\t }\n\t\n\t //\n\t // standard search\n\t //\n\t var tmpl = '
' + '
' + '
' + '
' + '
';\n\t\n\t // add standard filters\n\t for (var i in options.columns) {\n\t var column = options.columns[i];\n\t if (column.filterable == 'standard') {\n\t tmpl += this.grid_column_filter(options, column);\n\t }\n\t }\n\t\n\t // finalize standard search\n\t tmpl += '
' + '
' + '
' + '
' + '
';\n\t\n\t // show advanced search link in standard display\n\t if (show_advanced_search_link) {\n\t tmpl += 'Advanced Search';\n\t }\n\t\n\t // finalize standard search display\n\t tmpl += '
';\n\t\n\t // add advanced filters\n\t for (var i in options.columns) {\n\t var column = options.columns[i];\n\t if (column.filterable == 'advanced') {\n\t tmpl += this.grid_column_filter(options, column);\n\t }\n\t }\n\t\n\t // finalize advanced search template\n\t tmpl += '
' + '
';\n\t\n\t // return template\n\t return tmpl;\n\t },\n\t\n\t // template\n\t grid_column_filter: function (options, column) {\n\t\n\t // collect parameters\n\t var default_filter_dict = options.default_filter_dict;\n\t var filters = options.filters;\n\t var column_label = column.label;\n\t var column_key = column.key;\n\t if (column.filterable == 'advanced') {\n\t column_label = column_label.toLowerCase();\n\t }\n\t\n\t // start\n\t var tmpl = '
';\n\t\n\t if (column.filterable == 'advanced') {\n\t tmpl += '
' + column_label + ':
';\n\t }\n\t tmpl += '
';\n\t if (column.is_text) {\n\t tmpl += '';\n\t } else {\n\t // filter criteria\n\t tmpl += '';\n\t\n\t // add category filters\n\t var seperator = false;\n\t for (cf_label in options.categorical_filters[column_key]) {\n\t // get category filter\n\t var cf = options.categorical_filters[column_key][cf_label];\n\t\n\t // each filter will have only a single argument, so get that single argument\n\t var cf_key = '';\n\t var cf_arg = '';\n\t for (key in cf) {\n\t cf_key = key;\n\t cf_arg = cf[key];\n\t }\n\t\n\t // add seperator\n\t if (seperator) {\n\t tmpl += ' | ';\n\t }\n\t seperator = true;\n\t\n\t // add category\n\t var filter = filters[column_key];\n\t if (filter && cf[column_key] && filter == cf_arg) {\n\t tmpl += '' + cf_label + '';\n\t } else {\n\t tmpl += '' + '' + cf_label + '' + '';\n\t }\n\t }\n\t tmpl += '';\n\t }\n\t tmpl += '
' + '
';\n\t\n\t // return template\n\t return tmpl;\n\t },\n\t\n\t // template for filter items\n\t filter_element: function (filter_key, filter_value) {\n\t filter_value = Utils.sanitize(filter_value);\n\t return '' + filter_value + '' + '' + '' + '';\n\t }\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1)))\n\n/***/ }),\n/* 118 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_, jQuery, $) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(8), __webpack_require__(85), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (MODAL, ERROR_MODAL, _l) {\n\t\n\t 'use strict';\n\t\n\t //==============================================================================\n\t /**\n\t * A dialog/modal that allows copying a user history or 'importing' from user\n\t * another. Generally called via historyCopyDialog below.\n\t * @type {Object}\n\t */\n\t\n\t var CopyDialog = {\n\t\n\t // language related strings/fns\n\t defaultName: _.template(\"Copy of '<%- name %>'\"),\n\t title: _.template(_l('Copying history') + ' \"<%- name %>\"'),\n\t submitLabel: _l('Copy'),\n\t errorMessage: _l('History could not be copied.'),\n\t progressive: _l('Copying history'),\n\t activeLabel: _l('Copy only the active, non-deleted datasets'),\n\t allLabel: _l('Copy all datasets including deleted ones'),\n\t anonWarning: _l('As an anonymous user, unless you login or register, you will lose your current history ') + _l('after copying this history. '),\n\t\n\t // template for modal body\n\t _template: _.template([\n\t //TODO: remove inline styles\n\t // show a warning message for losing current to anon users\n\t '<% if( isAnon ){ %>', '
', '<% } %>', ''].join('')),\n\t\n\t // empty modal body and let the user know the copy is happening\n\t _showAjaxIndicator: function _showAjaxIndicator() {\n\t var indicator = '
' + this.progressive + '...
';\n\t this.modal.$('.modal-body').empty().append(indicator).css({ 'margin-top': '8px' });\n\t },\n\t\n\t // (sorta) public interface - display the modal, render the form, and potentially copy the history\n\t // returns a jQuery.Deferred done->history copied, fail->user cancelled\n\t dialog: function _dialog(modal, history, options) {\n\t options = options || {};\n\t\n\t var dialog = this,\n\t deferred = jQuery.Deferred(),\n\t\n\t // TODO: getting a little byzantine here\n\t defaultCopyNameFn = options.nameFn || this.defaultName,\n\t defaultCopyName = defaultCopyNameFn({ name: history.get('name') }),\n\t\n\t // TODO: these two might be simpler as one 3 state option (all,active,no-choice)\n\t defaultCopyWhat = options.allDatasets ? 'copy-all' : 'copy-non-deleted',\n\t allowAll = !_.isUndefined(options.allowAll) ? options.allowAll : true,\n\t autoClose = !_.isUndefined(options.autoClose) ? options.autoClose : true;\n\t\n\t this.modal = modal;\n\t\n\t // validate the name and copy if good\n\t function checkNameAndCopy() {\n\t var name = modal.$('#copy-modal-title').val();\n\t if (!name) {\n\t modal.$('.invalid-title').show();\n\t return;\n\t }\n\t // get further settings, shut down and indicate the ajax call, then hide and resolve/reject\n\t var copyAllDatasets = modal.$('input[name=\"copy-what\"]:checked').val() === 'copy-all';\n\t modal.$('button').prop('disabled', true);\n\t dialog._showAjaxIndicator();\n\t history.copy(true, name, copyAllDatasets).done(function (response) {\n\t deferred.resolve(response);\n\t }).fail(function (xhr, status, message) {\n\t var options = { name: name, copyAllDatasets: copyAllDatasets };\n\t ERROR_MODAL.ajaxErrorModal(history, xhr, options, dialog.errorMessage);\n\t deferred.rejectWith(deferred, arguments);\n\t }).done(function () {\n\t if (autoClose) {\n\t modal.hide();\n\t }\n\t });\n\t }\n\t\n\t var originalClosingCallback = options.closing_callback;\n\t modal.show(_.extend(options, {\n\t title: this.title({ name: history.get('name') }),\n\t body: $(dialog._template({\n\t name: defaultCopyName,\n\t isAnon: Galaxy.user.isAnonymous(),\n\t allowAll: allowAll,\n\t copyWhat: defaultCopyWhat,\n\t activeLabel: this.activeLabel,\n\t allLabel: this.allLabel,\n\t anonWarning: this.anonWarning\n\t })),\n\t buttons: _.object([[_l('Cancel'), function () {\n\t modal.hide();\n\t }], [this.submitLabel, checkNameAndCopy]]),\n\t height: 'auto',\n\t closing_events: true,\n\t closing_callback: function _historyCopyClose(cancelled) {\n\t if (cancelled) {\n\t deferred.reject({ cancelled: true });\n\t }\n\t if (originalClosingCallback) {\n\t originalClosingCallback(cancelled);\n\t }\n\t }\n\t }));\n\t\n\t // set the default dataset copy, autofocus the title, and set up for a simple return\n\t modal.$('#copy-modal-title').focus().select();\n\t modal.$('#copy-modal-title').on('keydown', function (ev) {\n\t if (ev.keyCode === 13) {\n\t ev.preventDefault();\n\t checkNameAndCopy();\n\t }\n\t });\n\t\n\t return deferred;\n\t }\n\t };\n\t\n\t //==============================================================================\n\t // maintain the (slight) distinction between copy and import\n\t /**\n\t * Subclass CopyDialog to use the import language.\n\t */\n\t var ImportDialog = _.extend({}, CopyDialog, {\n\t defaultName: _.template(\"imported: <%- name %>\"),\n\t title: _.template(_l('Importing history') + ' \"<%- name %>\"'),\n\t submitLabel: _l('Import'),\n\t errorMessage: _l('History could not be imported.'),\n\t progressive: _l('Importing history'),\n\t activeLabel: _l('Import only the active, non-deleted datasets'),\n\t allLabel: _l('Import all datasets including deleted ones'),\n\t anonWarning: _l('As an anonymous user, unless you login or register, you will lose your current history ') + _l('after importing this history. ')\n\t\n\t });\n\t\n\t //==============================================================================\n\t /**\n\t * Main interface for both history import and history copy dialogs.\n\t * @param {Backbone.Model} history the history to copy\n\t * @param {Object} options a hash\n\t * @return {jQuery.Deferred} promise that fails on close and succeeds on copy\n\t *\n\t * options:\n\t * (this object is also passed to the modal used to display the dialog and accepts modal options)\n\t * {Function} nameFn if defined, use this to build the default name shown to the user\n\t * (the fn is passed: {name: })\n\t * {bool} useImport if true, use the 'import' language (instead of Copy)\n\t * {bool} allowAll if true, allow the user to choose between copying all datasets and\n\t * only non-deleted datasets\n\t * {String} allDatasets default initial checked radio button: 'copy-all' or 'copy-non-deleted',\n\t */\n\t var historyCopyDialog = function (history, options) {\n\t options = options || {};\n\t // create our own modal if Galaxy doesn't have one (mako tab without use_panels)\n\t var modal = window.parent.Galaxy.modal || new MODAL.View({});\n\t return options.useImport ? ImportDialog.dialog(modal, history, options) : CopyDialog.dialog(modal, history, options);\n\t };\n\t\n\t //==============================================================================\n\t return historyCopyDialog;\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(1)))\n\n/***/ }),\n/* 119 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(jQuery, _) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(75), __webpack_require__(78), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (DATASET_LI_EDIT, HDA_LI, BASE_MVC, _l) {\n\t\n\t 'use strict';\n\t\n\t //==============================================================================\n\t\n\t var _super = DATASET_LI_EDIT.DatasetListItemEdit;\n\t /** @class Editing view for HistoryDatasetAssociation.\n\t */\n\t var HDAListItemEdit = _super.extend(\n\t /** @lends HDAListItemEdit.prototype */{\n\t\n\t className: _super.prototype.className + \" history-content\",\n\t\n\t /** In this override, only get details if in the ready state, get rerunnable if in other states.\n\t * Note: fetch with no 'change' event triggering to prevent automatic rendering.\n\t */\n\t _fetchModelDetails: function () {\n\t var view = this;\n\t if (view.model.inReadyState() && !view.model.hasDetails()) {\n\t return view.model.fetch({ silent: true });\n\t\n\t // special case the need for the rerunnable and creating_job attributes\n\t // needed for rendering re-run button on queued, running datasets\n\t } else if (!view.model.has('rerunnable')) {\n\t return view.model.fetch({ silent: true, data: {\n\t // only fetch rerunnable and creating_job to keep overhead down\n\t keys: ['rerunnable', 'creating_job'].join(',')\n\t } });\n\t }\n\t return jQuery.when();\n\t },\n\t\n\t /** event map */\n\t events: _.extend(_.clone(_super.prototype.events), {\n\t 'click .unhide-link': function (ev) {\n\t this.model.unhide();return false;\n\t }\n\t }),\n\t\n\t /** string rep */\n\t toString: function () {\n\t var modelString = this.model ? this.model + '' : '(no model)';\n\t return 'HDAListItemEdit(' + modelString + ')';\n\t }\n\t });\n\t\n\t // ............................................................................ TEMPLATES\n\t /** underscore templates */\n\t HDAListItemEdit.prototype.templates = function () {\n\t\n\t var warnings = _.extend({}, _super.prototype.templates.warnings, {\n\t hidden: BASE_MVC.wrapTemplate(['<% if( !dataset.visible ){ %>',\n\t // add a link to unhide a dataset\n\t '
', '<% } %>'], 'dataset')\n\t });\n\t\n\t return _.extend({}, _super.prototype.templates, {\n\t //NOTE: *steal* the HDAListItemView titleBar\n\t titleBar: HDA_LI.HDAListItemView.prototype.templates.titleBar,\n\t warnings: warnings\n\t });\n\t }();\n\t\n\t //==============================================================================\n\t return {\n\t HDAListItemEdit: HDAListItemEdit\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1), __webpack_require__(2)))\n\n/***/ }),\n/* 120 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(80), __webpack_require__(113), __webpack_require__(17), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (HDCA_LI, DC_VIEW_EDIT, faIconButton, _l) {\n\t\n\t 'use strict';\n\t\n\t //==============================================================================\n\t\n\t var _super = HDCA_LI.HDCAListItemView;\n\t /** @class Editing view for HistoryDatasetCollectionAssociation.\n\t */\n\t var HDCAListItemEdit = _super.extend(\n\t /** @lends HDCAListItemEdit.prototype */{\n\t\n\t /** logger used to record this.log messages, commonly set to console */\n\t //logger : console,\n\t\n\t /** Override to return editable versions of the collection panels */\n\t _getFoldoutPanelClass: function () {\n\t switch (this.model.get('collection_type')) {\n\t case 'list':\n\t return DC_VIEW_EDIT.ListCollectionViewEdit;\n\t case 'paired':\n\t return DC_VIEW_EDIT.PairCollectionViewEdit;\n\t case 'list:paired':\n\t return DC_VIEW_EDIT.ListOfPairsCollectionViewEdit;\n\t case 'list:list':\n\t return DC_VIEW_EDIT.ListOfListsCollectionViewEdit;\n\t }\n\t throw new TypeError('Uknown collection_type: ' + this.model.get('collection_type'));\n\t },\n\t\n\t // ......................................................................... delete\n\t /** In this override, add the delete button. */\n\t _renderPrimaryActions: function () {\n\t this.log(this + '._renderPrimaryActions');\n\t // render the display, edit attr and delete icon-buttons\n\t return _super.prototype._renderPrimaryActions.call(this).concat([this._renderDeleteButton()]);\n\t },\n\t\n\t /** Render icon-button to delete this collection. */\n\t _renderDeleteButton: function () {\n\t var self = this,\n\t deleted = this.model.get('deleted');\n\t return faIconButton({\n\t title: deleted ? _l('Dataset collection is already deleted') : _l('Delete'),\n\t classes: 'delete-btn',\n\t faIcon: 'fa-times',\n\t disabled: deleted,\n\t onclick: function () {\n\t // ...bler... tooltips being left behind in DOM (hover out never called on deletion)\n\t self.$el.find('.icon-btn.delete-btn').trigger('mouseout');\n\t self.model['delete']();\n\t }\n\t });\n\t },\n\t\n\t // ......................................................................... misc\n\t /** string rep */\n\t toString: function () {\n\t var modelString = this.model ? this.model + '' : '(no model)';\n\t return 'HDCAListItemEdit(' + modelString + ')';\n\t }\n\t });\n\t\n\t //==============================================================================\n\t return {\n\t HDCAListItemEdit: HDCAListItemEdit\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\n/***/ }),\n/* 121 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_, $, jQuery) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(82), __webpack_require__(122), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (HISTORY_MODEL, HISTORY_VIEW_EDIT, BASE_MVC, _l) {\n\t\n\t 'use strict';\n\t\n\t // ============================================================================\n\t /** session storage for history panel preferences (and to maintain state)\n\t */\n\t\n\t var HistoryViewPrefs = BASE_MVC.SessionStorageModel.extend(\n\t /** @lends HistoryViewPrefs.prototype */{\n\t defaults: {\n\t /** should the tags editor be shown or hidden initially? */\n\t tagsEditorShown: false,\n\t /** should the annotation editor be shown or hidden initially? */\n\t annotationEditorShown: false,\n\t ///** what is the currently focused content (dataset or collection) in the current history?\n\t // * (the history panel will highlight and scroll to the focused content view)\n\t // */\n\t //focusedContentId : null\n\t /** Current scroll position */\n\t scrollPosition: 0\n\t },\n\t toString: function () {\n\t return 'HistoryViewPrefs(' + JSON.stringify(this.toJSON()) + ')';\n\t }\n\t });\n\t\n\t /** key string to store panel prefs (made accessible on class so you can access sessionStorage directly) */\n\t HistoryViewPrefs.storageKey = function storageKey() {\n\t return 'history-panel';\n\t };\n\t\n\t /* =============================================================================\n\t TODO:\n\t \n\t ============================================================================= */\n\t var _super = HISTORY_VIEW_EDIT.HistoryViewEdit;\n\t // used in root/index.mako\n\t /** @class View/Controller for the user's current history model as used in the history\n\t * panel (current right hand panel) of the analysis page.\n\t *\n\t * The only history panel that:\n\t * will poll for updates.\n\t * displays datasets in reverse hid order.\n\t */\n\t var CurrentHistoryView = _super.extend( /** @lends CurrentHistoryView.prototype */{\n\t\n\t className: _super.prototype.className + ' current-history-panel',\n\t\n\t /** override to use drilldown (and not foldout) for how collections are displayed */\n\t HDCAViewClass: _super.prototype.HDCAViewClass.extend({\n\t foldoutStyle: 'drilldown'\n\t }),\n\t\n\t emptyMsg: [_l('This history is empty'), '. ', _l('You can '), '', _l('load your own data'), '', _l(' or '), '', _l('get data from an external source'), ''].join(''),\n\t\n\t // ......................................................................... SET UP\n\t /** Set up the view, set up storage, bind listeners to HistoryContents events */\n\t initialize: function (attributes) {\n\t attributes = attributes || {};\n\t\n\t // ---- persistent preferences\n\t /** maintain state / preferences over page loads */\n\t this.preferences = new HistoryViewPrefs(_.extend({\n\t id: HistoryViewPrefs.storageKey()\n\t }, _.pick(attributes, _.keys(HistoryViewPrefs.prototype.defaults))));\n\t\n\t _super.prototype.initialize.call(this, attributes);\n\t\n\t /** sub-views that will overlay this panel (collections) */\n\t this.panelStack = [];\n\t\n\t /** id of currently focused content */\n\t this.currentContentId = attributes.currentContentId || null;\n\t //NOTE: purposely not sent to localstorage since panel recreation roughly lines up with a reset of this value\n\t },\n\t\n\t /** Override to cache the current scroll position with a listener */\n\t _setUpListeners: function () {\n\t _super.prototype._setUpListeners.call(this);\n\t\n\t var panel = this;\n\t // reset scroll position when there's a new history\n\t this.on('new-model', function () {\n\t panel.preferences.set('scrollPosition', 0);\n\t });\n\t },\n\t\n\t // ------------------------------------------------------------------------ loading history/item models\n\t // TODO: next three more appropriate moved to the app level\n\t /** (re-)loads the user's current history & contents w/ details */\n\t loadCurrentHistory: function () {\n\t return this.loadHistory(null, { url: Galaxy.root + 'history/current_history_json' });\n\t },\n\t\n\t /** loads a history & contents w/ details and makes them the current history */\n\t switchToHistory: function (historyId, attributes) {\n\t if (Galaxy.user.isAnonymous()) {\n\t this.trigger('error', _l('You must be logged in to switch histories'), _l('Anonymous user'));\n\t return $.when();\n\t }\n\t return this.loadHistory(historyId, { url: Galaxy.root + 'history/set_as_current?id=' + historyId });\n\t },\n\t\n\t /** creates a new history on the server and sets it as the user's current history */\n\t createNewHistory: function (attributes) {\n\t if (Galaxy.user.isAnonymous()) {\n\t this.trigger('error', _l('You must be logged in to create histories'), _l('Anonymous user'));\n\t return $.when();\n\t }\n\t return this.loadHistory(null, { url: Galaxy.root + 'history/create_new_current' });\n\t },\n\t\n\t /** release/free/shutdown old models and set up panel for new models */\n\t setModel: function (model, attributes, render) {\n\t _super.prototype.setModel.call(this, model, attributes, render);\n\t if (this.model && this.model.id) {\n\t this.log('checking for updates');\n\t this.model.checkForUpdates();\n\t }\n\t return this;\n\t },\n\t\n\t // ------------------------------------------------------------------------ history/content event listening\n\t /** listening for history events */\n\t _setUpModelListeners: function () {\n\t _super.prototype._setUpModelListeners.call(this);\n\t // re-broadcast any model change events so that listeners don't have to re-bind to each history\n\t return this.listenTo(this.model, {\n\t 'change:nice_size change:size': function () {\n\t this.trigger('history-size-change', this, this.model, arguments);\n\t },\n\t 'change:id': function () {\n\t this.once('loading-done', function () {\n\t this.model.checkForUpdates();\n\t });\n\t }\n\t });\n\t },\n\t\n\t /** listening for collection events */\n\t _setUpCollectionListeners: function () {\n\t _super.prototype._setUpCollectionListeners.call(this);\n\t // if a hidden item is created (gen. by a workflow), moves thru the updater to the ready state,\n\t // then: remove it from the collection if the panel is set to NOT show hidden datasets\n\t this.listenTo(this.collection, 'state:ready', function (model, newState, oldState) {\n\t if (!model.get('visible') && !this.collection.storage.includeHidden()) {\n\t this.removeItemView(model);\n\t }\n\t });\n\t },\n\t\n\t // ------------------------------------------------------------------------ panel rendering\n\t /** override to add a handler to capture the scroll position when the parent scrolls */\n\t _setUpBehaviors: function ($where) {\n\t $where = $where || this.$el;\n\t // console.log( '_setUpBehaviors', this.$scrollContainer( $where ).get(0), this.$list( $where ) );\n\t // we need to call this in _setUpBehaviors which is called after render since the $el\n\t // may not be attached to $el.parent and $scrollContainer() may not work\n\t var panel = this;\n\t _super.prototype._setUpBehaviors.call(panel, $where);\n\t\n\t // cache the handler to remove and re-add so we don't pile up the handlers\n\t if (!this._debouncedScrollCaptureHandler) {\n\t this._debouncedScrollCaptureHandler = _.debounce(function scrollCapture() {\n\t // cache the scroll position (only if visible)\n\t if (panel.$el.is(':visible')) {\n\t panel.preferences.set('scrollPosition', $(this).scrollTop());\n\t }\n\t }, 40);\n\t }\n\t\n\t panel.$scrollContainer($where).off('scroll', this._debouncedScrollCaptureHandler).on('scroll', this._debouncedScrollCaptureHandler);\n\t return panel;\n\t },\n\t\n\t /** In this override, handle null models and move the search input to the top */\n\t _buildNewRender: function () {\n\t if (!this.model) {\n\t return $();\n\t }\n\t var $newRender = _super.prototype._buildNewRender.call(this);\n\t $newRender.find('.search').prependTo($newRender.find('> .controls'));\n\t this._renderQuotaMessage($newRender);\n\t return $newRender;\n\t },\n\t\n\t /** render the message displayed when a user is over quota and can't run jobs */\n\t _renderQuotaMessage: function ($whereTo) {\n\t $whereTo = $whereTo || this.$el;\n\t return $(this.templates.quotaMsg({}, this)).prependTo($whereTo.find('.messages'));\n\t },\n\t\n\t /** In this override, get and set current panel preferences when editor is used */\n\t _renderTags: function ($where) {\n\t var panel = this;\n\t // render tags and show/hide based on preferences\n\t _super.prototype._renderTags.call(panel, $where);\n\t if (panel.preferences.get('tagsEditorShown')) {\n\t panel.tagsEditor.toggle(true);\n\t }\n\t // store preference when shown or hidden\n\t panel.listenTo(panel.tagsEditor, 'hiddenUntilActivated:shown hiddenUntilActivated:hidden', function (tagsEditor) {\n\t panel.preferences.set('tagsEditorShown', tagsEditor.hidden);\n\t });\n\t },\n\t\n\t /** In this override, get and set current panel preferences when editor is used */\n\t _renderAnnotation: function ($where) {\n\t var panel = this;\n\t // render annotation and show/hide based on preferences\n\t _super.prototype._renderAnnotation.call(panel, $where);\n\t if (panel.preferences.get('annotationEditorShown')) {\n\t panel.annotationEditor.toggle(true);\n\t }\n\t // store preference when shown or hidden\n\t panel.listenTo(panel.annotationEditor, 'hiddenUntilActivated:shown hiddenUntilActivated:hidden', function (annotationEditor) {\n\t panel.preferences.set('annotationEditorShown', annotationEditor.hidden);\n\t });\n\t },\n\t\n\t /** Override to scroll to cached position (in prefs) after swapping */\n\t _swapNewRender: function ($newRender) {\n\t _super.prototype._swapNewRender.call(this, $newRender);\n\t var panel = this;\n\t _.delay(function () {\n\t var pos = panel.preferences.get('scrollPosition');\n\t if (pos) {\n\t panel.scrollTo(pos, 0);\n\t }\n\t }, 10);\n\t //TODO: is this enough of a delay on larger histories?\n\t\n\t return this;\n\t },\n\t\n\t // ------------------------------------------------------------------------ sub-views\n\t /** Override to add the current-content highlight class to currentContentId's view */\n\t _attachItems: function ($whereTo) {\n\t _super.prototype._attachItems.call(this, $whereTo);\n\t var panel = this;\n\t if (panel.currentContentId) {\n\t panel._setCurrentContentById(panel.currentContentId);\n\t }\n\t return this;\n\t },\n\t\n\t /** Override to remove any drill down panels */\n\t addItemView: function (model, collection, options) {\n\t var view = _super.prototype.addItemView.call(this, model, collection, options);\n\t if (!view) {\n\t return view;\n\t }\n\t if (this.panelStack.length) {\n\t return this._collapseDrilldownPanel();\n\t }\n\t return view;\n\t },\n\t\n\t // ------------------------------------------------------------------------ collection sub-views\n\t /** In this override, add/remove expanded/collapsed model ids to/from web storage */\n\t _setUpItemViewListeners: function (view) {\n\t var panel = this;\n\t _super.prototype._setUpItemViewListeners.call(panel, view);\n\t // use pub-sub to: handle drilldown expansion and collapse\n\t return panel.listenTo(view, {\n\t 'expanded:drilldown': function (v, drilldown) {\n\t this._expandDrilldownPanel(drilldown);\n\t },\n\t 'collapsed:drilldown': function (v, drilldown) {\n\t this._collapseDrilldownPanel(drilldown);\n\t }\n\t });\n\t },\n\t\n\t /** display 'current content': add a visible highlight and store the id of a content item */\n\t setCurrentContent: function (view) {\n\t this.$('.history-content.current-content').removeClass('current-content');\n\t if (view) {\n\t view.$el.addClass('current-content');\n\t this.currentContentId = view.model.id;\n\t } else {\n\t this.currentContentId = null;\n\t }\n\t },\n\t\n\t /** find the view with the id and then call setCurrentContent on it */\n\t _setCurrentContentById: function (id) {\n\t var view = this.viewFromModelId(id) || null;\n\t this.setCurrentContent(view);\n\t },\n\t\n\t /** Handle drill down by hiding this panels list and controls and showing the sub-panel */\n\t _expandDrilldownPanel: function (drilldown) {\n\t this.panelStack.push(drilldown);\n\t // hide this panel's controls and list, set the name for back navigation, and attach to the $el\n\t this.$controls().add(this.$list()).hide();\n\t drilldown.parentName = this.model.get('name');\n\t drilldown.delegateEvents().render().$el.appendTo(this.$el);\n\t },\n\t\n\t /** Handle drilldown close by freeing the panel and re-rendering this panel */\n\t _collapseDrilldownPanel: function (drilldown) {\n\t this.panelStack.pop();\n\t //TODO: MEM: free the panel\n\t this.$controls().add(this.$list()).show();\n\t },\n\t\n\t // ........................................................................ panel events\n\t /** event map */\n\t events: _.extend(_.clone(_super.prototype.events), {\n\t // the two links in the empty message\n\t 'click .uploader-link': function (ev) {\n\t Galaxy.upload.show(ev);\n\t },\n\t 'click .get-data-link': function (ev) {\n\t var $toolMenu = $('.toolMenuContainer');\n\t $toolMenu.parent().scrollTop(0);\n\t $toolMenu.find('span:contains(\"Get Data\")').click();\n\t }\n\t }),\n\t\n\t // ........................................................................ external objects/MVC\n\t listenToGalaxy: function (galaxy) {\n\t this.listenTo(galaxy, {\n\t // when the galaxy_main iframe is loaded with a new page,\n\t // compare the url to the following list and if there's a match\n\t // pull the id from url and indicate in the history view that\n\t // the dataset with that id is the 'current'ly active dataset\n\t 'galaxy_main:load': function (data) {\n\t var pathToMatch = data.fullpath;\n\t var hdaId = null;\n\t var useToURLRegexMap = {\n\t 'display': /datasets\\/([a-f0-9]+)\\/display/,\n\t 'edit': /datasets\\/([a-f0-9]+)\\/edit/,\n\t 'report_error': /dataset\\/errors\\?id=([a-f0-9]+)/,\n\t 'rerun': /tool_runner\\/rerun\\?id=([a-f0-9]+)/,\n\t 'show_params': /datasets\\/([a-f0-9]+)\\/show_params/\n\t };\n\t _.find(useToURLRegexMap, function (regex, use) {\n\t // grab the more specific match result (1), save, and use it as the find flag\n\t hdaId = _.result(pathToMatch.match(regex), 1);\n\t return hdaId;\n\t });\n\t // need to type mangle to go from web route to history contents\n\t this._setCurrentContentById(hdaId ? 'dataset-' + hdaId : null);\n\t },\n\t // when the center panel is given a new view, clear the current indicator\n\t 'center-panel:load': function (view) {\n\t this._setCurrentContentById();\n\t }\n\t });\n\t },\n\t\n\t //TODO: remove quota meter from panel and remove this\n\t /** add listeners to an external quota meter (mvc/user/user-quotameter.js) */\n\t connectToQuotaMeter: function (quotaMeter) {\n\t if (!quotaMeter) {\n\t return this;\n\t }\n\t // show/hide the 'over quota message' in the history when the meter tells it to\n\t this.listenTo(quotaMeter, 'quota:over', this.showQuotaMessage);\n\t this.listenTo(quotaMeter, 'quota:under', this.hideQuotaMessage);\n\t\n\t // having to add this to handle re-render of hview while overquota (the above do not fire)\n\t this.on('rendered rendered:initial', function () {\n\t if (quotaMeter && quotaMeter.isOverQuota()) {\n\t this.showQuotaMessage();\n\t }\n\t });\n\t return this;\n\t },\n\t\n\t /** Override to preserve the quota message */\n\t clearMessages: function (ev) {\n\t var $target = !_.isUndefined(ev) ? $(ev.currentTarget) : this.$messages().children('[class$=\"message\"]');\n\t $target = $target.not('.quota-message');\n\t $target.fadeOut(this.fxSpeed, function () {\n\t $(this).remove();\n\t });\n\t return this;\n\t },\n\t\n\t /** Show the over quota message (which happens to be in the history panel).\n\t */\n\t showQuotaMessage: function () {\n\t var $msg = this.$('.quota-message');\n\t if ($msg.is(':hidden')) {\n\t $msg.slideDown(this.fxSpeed);\n\t }\n\t },\n\t\n\t /** Hide the over quota message (which happens to be in the history panel).\n\t */\n\t hideQuotaMessage: function () {\n\t var $msg = this.$('.quota-message');\n\t if (!$msg.is(':hidden')) {\n\t $msg.slideUp(this.fxSpeed);\n\t }\n\t },\n\t\n\t // ........................................................................ options menu\n\t //TODO: remove to batch\n\t /** unhide any hidden datasets */\n\t unhideHidden: function () {\n\t var self = this;\n\t if (confirm(_l('Really unhide all hidden datasets?'))) {\n\t // get all hidden, regardless of deleted/purged\n\t return self.model.contents._filterAndUpdate({ visible: false, deleted: '', purged: '' }, { visible: true }).done(function () {\n\t // TODO: would be better to render these as they're unhidden instead of all at once\n\t if (!self.model.contents.includeHidden) {\n\t self.renderItems();\n\t }\n\t });\n\t }\n\t return jQuery.when();\n\t },\n\t\n\t /** delete any hidden datasets */\n\t deleteHidden: function () {\n\t var self = this;\n\t if (confirm(_l('Really delete all hidden datasets?'))) {\n\t return self.model.contents._filterAndUpdate(\n\t // get all hidden, regardless of deleted/purged\n\t { visible: false, deleted: '', purged: '' },\n\t // both delete *and* unhide them\n\t { deleted: true, visible: true });\n\t }\n\t return jQuery.when();\n\t },\n\t\n\t /** Return a string rep of the history */\n\t toString: function () {\n\t return 'CurrentHistoryView(' + (this.model ? this.model.get('name') : '') + ')';\n\t }\n\t });\n\t\n\t //------------------------------------------------------------------------------ TEMPLATES\n\t CurrentHistoryView.prototype.templates = function () {\n\t\n\t var quotaMsgTemplate = BASE_MVC.wrapTemplate(['
', _l('You are over your disk quota'), '. ', _l('Tool execution is on hold until your disk usage drops below your allocated quota'), '.', '
'], 'history');\n\t return _.extend(_.clone(_super.prototype.templates), {\n\t quotaMsg: quotaMsgTemplate\n\t });\n\t }();\n\t\n\t //==============================================================================\n\t return {\n\t CurrentHistoryView: CurrentHistoryView\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(1)))\n\n/***/ }),\n/* 122 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(jQuery, _, $) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(123), __webpack_require__(45), __webpack_require__(11), __webpack_require__(79), __webpack_require__(119), __webpack_require__(120), __webpack_require__(48), __webpack_require__(71), __webpack_require__(37), __webpack_require__(115), __webpack_require__(114), __webpack_require__(17), __webpack_require__(51), __webpack_require__(6), __webpack_require__(5), __webpack_require__(16)], __WEBPACK_AMD_DEFINE_RESULT__ = function (HISTORY_VIEW, HISTORY_CONTENTS, STATES, HDA_MODEL, HDA_LI_EDIT, HDCA_LI_EDIT, TAGS, ANNOTATIONS, LIST_COLLECTION_CREATOR, PAIR_COLLECTION_CREATOR, LIST_OF_PAIRS_COLLECTION_CREATOR, faIconButton, PopupMenu, BASE_MVC, _l) {\n\t\n\t 'use strict';\n\t\n\t /* =============================================================================\n\t TODO:\n\t \n\t ============================================================================= */\n\t\n\t var _super = HISTORY_VIEW.HistoryView;\n\t // base class for history-view-edit-current and used as-is in history/view.mako\n\t /** @class Editable View/Controller for the history model.\n\t *\n\t * Allows:\n\t * (everything HistoryView allows)\n\t * changing the name\n\t * displaying and editing tags and annotations\n\t * multi-selection and operations on mulitple content items\n\t */\n\t var HistoryViewEdit = _super.extend(\n\t /** @lends HistoryViewEdit.prototype */{\n\t\n\t /** class to use for constructing the HistoryDatasetAssociation views */\n\t HDAViewClass: HDA_LI_EDIT.HDAListItemEdit,\n\t /** class to use for constructing the HistoryDatasetCollectionAssociation views */\n\t HDCAViewClass: HDCA_LI_EDIT.HDCAListItemEdit,\n\t\n\t // ......................................................................... SET UP\n\t /** Set up the view, set up storage, bind listeners to HistoryContents events\n\t * @param {Object} attributes\n\t */\n\t initialize: function (attributes) {\n\t attributes = attributes || {};\n\t _super.prototype.initialize.call(this, attributes);\n\t\n\t // ---- set up instance vars\n\t /** editor for tags - sub-view */\n\t this.tagsEditor = null;\n\t\n\t /** enable drag and drop - sub-view */\n\t this.dragItems = true;\n\t\n\t /** editor for annotations - sub-view */\n\t this.annotationEditor = null;\n\t\n\t /** allow user purge of dataset files? */\n\t this.purgeAllowed = attributes.purgeAllowed || false;\n\t\n\t // states/modes the panel can be in\n\t /** is the panel currently showing the dataset selection controls? */\n\t this.annotationEditorShown = attributes.annotationEditorShown || false;\n\t this.tagsEditorShown = attributes.tagsEditorShown || false;\n\t },\n\t\n\t /** Override to handle history as drag-drop target */\n\t _setUpListeners: function () {\n\t _super.prototype._setUpListeners.call(this);\n\t return this.on({\n\t 'droptarget:drop': function (ev, data) {\n\t // process whatever was dropped and re-hide the drop target\n\t this.dataDropped(data);\n\t this.dropTargetOff();\n\t },\n\t 'view:attached view:removed': function () {\n\t this._renderCounts();\n\t },\n\t 'search:loading-progress': this._renderSearchProgress,\n\t 'search:searching': this._renderSearchFindings\n\t });\n\t },\n\t\n\t // ------------------------------------------------------------------------ listeners\n\t /** listening for history and HDA events */\n\t _setUpModelListeners: function () {\n\t _super.prototype._setUpModelListeners.call(this);\n\t this.listenTo(this.model, 'change:size', this.updateHistoryDiskSize);\n\t return this;\n\t },\n\t\n\t /** listening for collection events */\n\t _setUpCollectionListeners: function () {\n\t _super.prototype._setUpCollectionListeners.call(this);\n\t this.listenTo(this.collection, {\n\t 'change:deleted': this._handleItemDeletedChange,\n\t 'change:visible': this._handleItemVisibleChange,\n\t 'change:purged': function (model) {\n\t // hafta get the new nice-size w/o the purged model\n\t this.model.fetch();\n\t },\n\t // loading indicators for deleted/hidden\n\t 'fetching-deleted': function (collection) {\n\t this.$('> .controls .deleted-count').html('' + _l('loading...') + '');\n\t },\n\t 'fetching-hidden': function (collection) {\n\t this.$('> .controls .hidden-count').html('' + _l('loading...') + '');\n\t },\n\t 'fetching-deleted-done fetching-hidden-done': this._renderCounts\n\t });\n\t return this;\n\t },\n\t\n\t // ------------------------------------------------------------------------ panel rendering\n\t /** In this override, add tag and annotation editors and a btn to toggle the selectors */\n\t _buildNewRender: function () {\n\t // create a new render using a skeleton template, render title buttons, render body, and set up events, etc.\n\t var $newRender = _super.prototype._buildNewRender.call(this);\n\t if (!this.model) {\n\t return $newRender;\n\t }\n\t\n\t if (Galaxy && Galaxy.user && Galaxy.user.id && Galaxy.user.id === this.model.get('user_id')) {\n\t this._renderTags($newRender);\n\t this._renderAnnotation($newRender);\n\t }\n\t return $newRender;\n\t },\n\t\n\t /** Update the history size display (curr. upper right of panel). */\n\t updateHistoryDiskSize: function () {\n\t this.$('.history-size').text(this.model.get('nice_size'));\n\t },\n\t\n\t /** override to render counts when the items are rendered */\n\t renderItems: function ($whereTo) {\n\t var views = _super.prototype.renderItems.call(this, $whereTo);\n\t if (!this.searchFor) {\n\t this._renderCounts($whereTo);\n\t }\n\t return views;\n\t },\n\t\n\t /** override to show counts, what's deleted/hidden, and links to toggle those */\n\t _renderCounts: function ($whereTo) {\n\t $whereTo = $whereTo instanceof jQuery ? $whereTo : this.$el;\n\t var html = this.templates.counts(this.model.toJSON(), this);\n\t return $whereTo.find('> .controls .subtitle').html(html);\n\t },\n\t\n\t /** render the tags sub-view controller */\n\t _renderTags: function ($where) {\n\t var panel = this;\n\t this.tagsEditor = new TAGS.TagsEditor({\n\t model: this.model,\n\t el: $where.find('.controls .tags-display'),\n\t onshowFirstTime: function () {\n\t this.render();\n\t },\n\t // show hide sub-view tag editors when this is shown/hidden\n\t onshow: function () {\n\t panel.toggleHDATagEditors(true, panel.fxSpeed);\n\t },\n\t onhide: function () {\n\t panel.toggleHDATagEditors(false, panel.fxSpeed);\n\t },\n\t $activator: faIconButton({\n\t title: _l('Edit history tags'),\n\t classes: 'history-tag-btn',\n\t faIcon: 'fa-tags'\n\t }).appendTo($where.find('.controls .actions'))\n\t });\n\t },\n\t /** render the annotation sub-view controller */\n\t _renderAnnotation: function ($where) {\n\t var panel = this;\n\t this.annotationEditor = new ANNOTATIONS.AnnotationEditor({\n\t model: this.model,\n\t el: $where.find('.controls .annotation-display'),\n\t onshowFirstTime: function () {\n\t this.render();\n\t },\n\t // show hide sub-view view annotation editors when this is shown/hidden\n\t onshow: function () {\n\t panel.toggleHDAAnnotationEditors(true, panel.fxSpeed);\n\t },\n\t onhide: function () {\n\t panel.toggleHDAAnnotationEditors(false, panel.fxSpeed);\n\t },\n\t $activator: faIconButton({\n\t title: _l('Edit history annotation'),\n\t classes: 'history-annotate-btn',\n\t faIcon: 'fa-comment'\n\t }).appendTo($where.find('.controls .actions'))\n\t });\n\t },\n\t\n\t /** Set up HistoryViewEdit js/widget behaviours\n\t * In this override, make the name editable\n\t */\n\t _setUpBehaviors: function ($where) {\n\t $where = $where || this.$el;\n\t _super.prototype._setUpBehaviors.call(this, $where);\n\t if (!this.model) {\n\t return;\n\t }\n\t\n\t // anon users shouldn't have access to any of the following\n\t if (!Galaxy.user || Galaxy.user.isAnonymous() || Galaxy.user.id !== this.model.get('user_id')) {\n\t return;\n\t }\n\t\n\t var panel = this,\n\t nameSelector = '> .controls .name';\n\t $where.find(nameSelector).attr('title', _l('Click to rename history')).tooltip({ placement: 'bottom' }).make_text_editable({\n\t on_finish: function (newName) {\n\t var previousName = panel.model.get('name');\n\t if (newName && newName !== previousName) {\n\t panel.$el.find(nameSelector).text(newName);\n\t panel.model.save({ name: newName }).fail(function () {\n\t panel.$el.find(nameSelector).text(panel.model.previous('name'));\n\t });\n\t } else {\n\t panel.$el.find(nameSelector).text(previousName);\n\t }\n\t }\n\t });\n\t },\n\t\n\t /** return a new popup menu for choosing a multi selection action\n\t * ajax calls made for multiple datasets are queued\n\t */\n\t multiselectActions: function () {\n\t var panel = this,\n\t actions = [{ html: _l('Hide datasets'), func: function () {\n\t var action = HDA_MODEL.HistoryDatasetAssociation.prototype.hide;\n\t panel.getSelectedModels().ajaxQueue(action);\n\t }\n\t }, { html: _l('Unhide datasets'), func: function () {\n\t var action = HDA_MODEL.HistoryDatasetAssociation.prototype.unhide;\n\t panel.getSelectedModels().ajaxQueue(action);\n\t }\n\t }, { html: _l('Delete datasets'), func: function () {\n\t var action = HDA_MODEL.HistoryDatasetAssociation.prototype['delete'];\n\t panel.getSelectedModels().ajaxQueue(action);\n\t }\n\t }, { html: _l('Undelete datasets'), func: function () {\n\t var action = HDA_MODEL.HistoryDatasetAssociation.prototype.undelete;\n\t panel.getSelectedModels().ajaxQueue(action);\n\t }\n\t }];\n\t if (panel.purgeAllowed) {\n\t actions.push({\n\t html: _l('Permanently delete datasets'), func: function () {\n\t if (confirm(_l('This will permanently remove the data in your datasets. Are you sure?'))) {\n\t var action = HDA_MODEL.HistoryDatasetAssociation.prototype.purge;\n\t panel.getSelectedModels().ajaxQueue(action);\n\t }\n\t }\n\t });\n\t }\n\t actions = actions.concat(panel._collectionActions());\n\t return actions;\n\t },\n\t\n\t /** */\n\t _collectionActions: function () {\n\t var panel = this;\n\t return [{ html: _l('Build Dataset List'), func: function () {\n\t panel.buildCollection(\"list\");\n\t }\n\t },\n\t // TODO: Only show quick pair if two things selected.\n\t { html: _l('Build Dataset Pair'), func: function () {\n\t panel.buildCollection(\"paired\");\n\t }\n\t }, { html: _l('Build List of Dataset Pairs'), func: function () {\n\t panel.buildCollection(\"list:paired\");\n\t }\n\t }];\n\t },\n\t\n\t buildCollection: function (collectionType, selection, hideSourceItems) {\n\t var panel = this;\n\t var selection = selection || panel.getSelectedModels();\n\t var hideSourceItems = hideSourceItems || false;\n\t var createFunc;\n\t if (collectionType == \"list\") {\n\t createFunc = LIST_COLLECTION_CREATOR.createListCollection;\n\t } else if (collectionType == \"paired\") {\n\t createFunc = PAIR_COLLECTION_CREATOR.createPairCollection;\n\t } else if (collectionType == \"list:paired\") {\n\t createFunc = LIST_OF_PAIRS_COLLECTION_CREATOR.createListOfPairsCollection;\n\t } else {\n\t console.warn(\"Unknown collectionType encountered \" + collectionType);\n\t }\n\t createFunc(selection, hideSourceItems).done(function () {\n\t panel.model.refresh();\n\t });\n\t },\n\t\n\t // ------------------------------------------------------------------------ sub-views\n\t /** In this override, add purgeAllowed and whether tags/annotation editors should be shown */\n\t _getItemViewOptions: function (model) {\n\t var options = _super.prototype._getItemViewOptions.call(this, model);\n\t _.extend(options, {\n\t purgeAllowed: this.purgeAllowed,\n\t tagsEditorShown: this.tagsEditor && !this.tagsEditor.hidden,\n\t annotationEditorShown: this.annotationEditor && !this.annotationEditor.hidden\n\t });\n\t return options;\n\t },\n\t\n\t /** If this item is deleted and we're not showing deleted items, remove the view\n\t * @param {Model} the item model to check\n\t */\n\t _handleItemDeletedChange: function (itemModel) {\n\t if (itemModel.get('deleted')) {\n\t this._handleItemDeletion(itemModel);\n\t } else {\n\t this._handleItemUndeletion(itemModel);\n\t }\n\t this._renderCounts();\n\t },\n\t\n\t _handleItemDeletion: function (itemModel) {\n\t var contentsShown = this.model.get('contents_active');\n\t contentsShown.deleted += 1;\n\t contentsShown.active -= 1;\n\t if (!this.model.contents.includeDeleted) {\n\t this.removeItemView(itemModel);\n\t }\n\t this.model.set('contents_active', contentsShown);\n\t },\n\t\n\t _handleItemUndeletion: function (itemModel) {\n\t var contentsShown = this.model.get('contents_active');\n\t contentsShown.deleted -= 1;\n\t if (!this.model.contents.includeDeleted) {\n\t contentsShown.active -= 1;\n\t }\n\t this.model.set('contents_active', contentsShown);\n\t },\n\t\n\t /** If this item is hidden and we're not showing hidden items, remove the view\n\t * @param {Model} the item model to check\n\t */\n\t _handleItemVisibleChange: function (itemModel) {\n\t if (itemModel.hidden()) {\n\t this._handleItemHidden(itemModel);\n\t } else {\n\t this._handleItemUnhidden(itemModel);\n\t }\n\t this._renderCounts();\n\t },\n\t\n\t _handleItemHidden: function (itemModel) {\n\t var contentsShown = this.model.get('contents_active');\n\t contentsShown.hidden += 1;\n\t contentsShown.active -= 1;\n\t if (!this.model.contents.includeHidden) {\n\t this.removeItemView(itemModel);\n\t }\n\t this.model.set('contents_active', contentsShown);\n\t },\n\t\n\t _handleItemUnhidden: function (itemModel) {\n\t var contentsShown = this.model.get('contents_active');\n\t contentsShown.hidden -= 1;\n\t if (!this.model.contents.includeHidden) {\n\t contentsShown.active -= 1;\n\t }\n\t this.model.set('contents_active', contentsShown);\n\t },\n\t\n\t /** toggle the visibility of each content's tagsEditor applying all the args sent to this function */\n\t toggleHDATagEditors: function (showOrHide, speed) {\n\t _.each(this.views, function (view) {\n\t if (view.tagsEditor) {\n\t view.tagsEditor.toggle(showOrHide, speed);\n\t }\n\t });\n\t },\n\t\n\t /** toggle the visibility of each content's annotationEditor applying all the args sent to this function */\n\t toggleHDAAnnotationEditors: function (showOrHide, speed) {\n\t _.each(this.views, function (view) {\n\t if (view.annotationEditor) {\n\t view.annotationEditor.toggle(showOrHide, speed);\n\t }\n\t });\n\t },\n\t\n\t // ------------------------------------------------------------------------ panel events\n\t /** event map */\n\t events: _.extend(_.clone(_super.prototype.events), {\n\t 'click .show-selectors-btn': 'toggleSelectors',\n\t 'click .toggle-deleted-link': function (ev) {\n\t this.toggleShowDeleted();\n\t },\n\t 'click .toggle-hidden-link': function (ev) {\n\t this.toggleShowHidden();\n\t }\n\t }),\n\t\n\t // ------------------------------------------------------------------------ search\n\t _renderSearchProgress: function (limit, offset) {\n\t var stop = limit + offset;\n\t return this.$('> .controls .subtitle').html(['', _l('Searching '), stop, '/', this.model.contentsShown(), ''].join(''));\n\t },\n\t\n\t /** override to display number found in subtitle */\n\t _renderSearchFindings: function () {\n\t this.$('> .controls .subtitle').html([_l('Found'), this.views.length].join(' '));\n\t return this;\n\t },\n\t\n\t // ------------------------------------------------------------------------ as drop target\n\t /** turn all the drag and drop handlers on and add some help text above the drop area */\n\t dropTargetOn: function () {\n\t if (this.dropTarget) {\n\t return this;\n\t }\n\t this.dropTarget = true;\n\t\n\t //TODO: to init\n\t var dropHandlers = {\n\t 'dragenter': _.bind(this.dragenter, this),\n\t 'dragover': _.bind(this.dragover, this),\n\t 'dragleave': _.bind(this.dragleave, this),\n\t 'drop': _.bind(this.drop, this)\n\t };\n\t\n\t var $dropTarget = this._renderDropTarget();\n\t this.$list().before([this._renderDropTargetHelp(), $dropTarget]);\n\t for (var evName in dropHandlers) {\n\t if (dropHandlers.hasOwnProperty(evName)) {\n\t //console.debug( evName, dropHandlers[ evName ] );\n\t $dropTarget.on(evName, dropHandlers[evName]);\n\t }\n\t }\n\t return this;\n\t },\n\t\n\t /** render a box to serve as a 'drop here' area on the history */\n\t _renderDropTarget: function () {\n\t this.$('.history-drop-target').remove();\n\t return $('').addClass('history-drop-target');\n\t },\n\t\n\t /** tell the user how it works */\n\t _renderDropTargetHelp: function () {\n\t this.$('.history-drop-target-help').remove();\n\t return $('').addClass('history-drop-target-help').text(_l('Drag datasets here to copy them to the current history'));\n\t },\n\t\n\t /** shut down drag and drop event handlers and remove drop target */\n\t dropTargetOff: function () {\n\t if (!this.dropTarget) {\n\t return this;\n\t }\n\t //this.log( 'dropTargetOff' );\n\t this.dropTarget = false;\n\t var dropTarget = this.$('.history-drop-target').get(0);\n\t for (var evName in this._dropHandlers) {\n\t if (this._dropHandlers.hasOwnProperty(evName)) {\n\t dropTarget.off(evName, this._dropHandlers[evName]);\n\t }\n\t }\n\t this.$('.history-drop-target').remove();\n\t this.$('.history-drop-target-help').remove();\n\t return this;\n\t },\n\t /** toggle the target on/off */\n\t dropTargetToggle: function () {\n\t if (this.dropTarget) {\n\t this.dropTargetOff();\n\t } else {\n\t this.dropTargetOn();\n\t }\n\t return this;\n\t },\n\t\n\t dragenter: function (ev) {\n\t //console.debug( 'dragenter:', this, ev );\n\t ev.preventDefault();\n\t ev.stopPropagation();\n\t this.$('.history-drop-target').css('border', '2px solid black');\n\t },\n\t dragover: function (ev) {\n\t ev.preventDefault();\n\t ev.stopPropagation();\n\t },\n\t dragleave: function (ev) {\n\t //console.debug( 'dragleave:', this, ev );\n\t ev.preventDefault();\n\t ev.stopPropagation();\n\t this.$('.history-drop-target').css('border', '1px dashed black');\n\t },\n\t /** when (text) is dropped try to parse as json and trigger an event */\n\t drop: function (ev) {\n\t ev.preventDefault();\n\t //ev.stopPropagation();\n\t\n\t var self = this;\n\t var dataTransfer = ev.originalEvent.dataTransfer;\n\t var data = dataTransfer.getData(\"text\");\n\t\n\t dataTransfer.dropEffect = 'move';\n\t try {\n\t data = JSON.parse(data);\n\t } catch (err) {\n\t self.warn('error parsing JSON from drop:', data);\n\t }\n\t\n\t self.trigger('droptarget:drop', ev, data, self);\n\t return false;\n\t },\n\t\n\t /** handler that copies data into the contents */\n\t dataDropped: function (data) {\n\t var self = this;\n\t // HDA: dropping will copy it to the history\n\t if (_.isObject(data) && data.model_class === 'HistoryDatasetAssociation' && data.id) {\n\t if (self.contents.currentPage !== 0) {\n\t return self.contents.fetchPage(0).then(function () {\n\t return self.model.contents.copy(data.id);\n\t });\n\t }\n\t return self.model.contents.copy(data.id);\n\t }\n\t return jQuery.when();\n\t },\n\t\n\t // ........................................................................ misc\n\t /** Return a string rep of the history */\n\t toString: function () {\n\t return 'HistoryViewEdit(' + (this.model ? this.model.get('name') : '') + ')';\n\t }\n\t });\n\t\n\t //------------------------------------------------------------------------------ TEMPLATES\n\t HistoryViewEdit.prototype.templates = function () {\n\t\n\t var countsTemplate = BASE_MVC.wrapTemplate(['<% var shown = Math.max( view.views.length, history.contents_active.active ) %>', '<% if( shown ){ %>', '', '<%- shown %> ', _l('shown'), '', '<% } %>', '<% if( history.contents_active.deleted ){ %>', '', '<% if( view.model.contents.includeDeleted ){ %>', '', _l('hide deleted'), '', '<% } else { %>', '<%- history.contents_active.deleted %> ', '', _l('deleted'), '', '<% } %>', '', '<% } %>', '<% if( history.contents_active.hidden ){ %>', '', '<% if( view.model.contents.includeHidden ){ %>', '', _l('hide hidden'), '', '<% } else { %>', '<%- history.contents_active.hidden %> ', '', _l('hidden'), '', '<% } %>', '', '<% } %>'], 'history');\n\t\n\t return _.extend(_.clone(_super.prototype.templates), {\n\t counts: countsTemplate\n\t });\n\t }();\n\t\n\t //==============================================================================\n\t return {\n\t HistoryViewEdit: HistoryViewEdit\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ }),\n/* 123 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_, $) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(83), __webpack_require__(82), __webpack_require__(45), __webpack_require__(46), __webpack_require__(78), __webpack_require__(80), __webpack_require__(86), __webpack_require__(85), __webpack_require__(17), __webpack_require__(6), __webpack_require__(5), __webpack_require__(89)], __WEBPACK_AMD_DEFINE_RESULT__ = function (LIST_VIEW, HISTORY_MODEL, HISTORY_CONTENTS, HISTORY_PREFS, HDA_LI, HDCA_LI, USER, ERROR_MODAL, faIconButton, BASE_MVC, _l) {\n\t 'use strict';\n\t\n\t /* =============================================================================\n\t TODO:\n\t \n\t ============================================================================= */\n\t /** @class non-editable, read-only View/Controller for a history model.\n\t * Allows:\n\t * changing the loaded history\n\t * displaying data, info, and download\n\t * tracking history attrs: size, tags, annotations, name, etc.\n\t * Does not allow:\n\t * changing the name\n\t */\n\t\n\t var _super = LIST_VIEW.ModelListPanel;\n\t var HistoryView = _super.extend(\n\t /** @lends HistoryView.prototype */{\n\t _logNamespace: 'history',\n\t\n\t /** class to use for constructing the HDA views */\n\t HDAViewClass: HDA_LI.HDAListItemView,\n\t /** class to use for constructing the HDCA views */\n\t HDCAViewClass: HDCA_LI.HDCAListItemView,\n\t /** class to used for constructing collection of sub-view models */\n\t collectionClass: HISTORY_CONTENTS.HistoryContents,\n\t /** key of attribute in model to assign to this.collection */\n\t modelCollectionKey: 'contents',\n\t\n\t tagName: 'div',\n\t className: _super.prototype.className + ' history-panel',\n\t\n\t /** string to display when the collection is empty */\n\t emptyMsg: _l('This history is empty'),\n\t /** displayed when no items match the search terms */\n\t noneFoundMsg: _l('No matching datasets found'),\n\t /** string used for search placeholder */\n\t searchPlaceholder: _l('search datasets'),\n\t\n\t /** @type {Number} ms to wait after history load to fetch/decorate hdcas with element_count */\n\t FETCH_COLLECTION_COUNTS_DELAY: 2000,\n\t\n\t // ......................................................................... SET UP\n\t /** Set up the view, bind listeners.\n\t * @param {Object} attributes optional settings for the panel\n\t */\n\t initialize: function (attributes) {\n\t _super.prototype.initialize.call(this, attributes);\n\t // ---- instance vars\n\t // control contents/behavior based on where (and in what context) the panel is being used\n\t /** where should pages from links be displayed? (default to new tab/window) */\n\t this.linkTarget = attributes.linkTarget || '_blank';\n\t },\n\t\n\t /** create and return a collection for when none is initially passed */\n\t _createDefaultCollection: function () {\n\t // override\n\t return new this.collectionClass([], { history: this.model });\n\t },\n\t\n\t /** In this override, clear the update timer on the model */\n\t freeModel: function () {\n\t _super.prototype.freeModel.call(this);\n\t if (this.model) {\n\t this.model.clearUpdateTimeout();\n\t }\n\t return this;\n\t },\n\t\n\t /** create any event listeners for the panel\n\t * @fires: rendered:initial on the first render\n\t * @fires: empty-history when switching to a history with no contents or creating a new history\n\t */\n\t _setUpListeners: function () {\n\t _super.prototype._setUpListeners.call(this);\n\t this.on({\n\t error: function (model, xhr, options, msg, details) {\n\t this.errorHandler(model, xhr, options, msg, details);\n\t },\n\t 'loading-done': function () {\n\t var self = this;\n\t // after the initial load, decorate with more time consuming fields (like HDCA element_counts)\n\t _.delay(function () {\n\t self.model.contents.fetchCollectionCounts();\n\t }, self.FETCH_COLLECTION_COUNTS_DELAY);\n\t },\n\t 'views:ready view:attached view:removed': function (view) {\n\t this._renderSelectButton();\n\t },\n\t 'view:attached': function (view) {\n\t this.scrollTo(0);\n\t }\n\t });\n\t // this.on( 'all', function(){ console.debug( arguments ); });\n\t },\n\t\n\t // ------------------------------------------------------------------------ loading history/hda models\n\t /** load the history with the given id then it's contents, sending ajax options to both */\n\t loadHistory: function (historyId, options, contentsOptions) {\n\t contentsOptions = _.extend(contentsOptions || { silent: true });\n\t this.info('loadHistory:', historyId, options, contentsOptions);\n\t var self = this;\n\t self.setModel(new HISTORY_MODEL.History({ id: historyId }));\n\t\n\t contentsOptions.silent = true;\n\t self.trigger('loading');\n\t return self.model.fetchWithContents(options, contentsOptions).always(function () {\n\t self.render();\n\t self.trigger('loading-done');\n\t });\n\t },\n\t\n\t /** convenience alias to the model. Updates the item list only (not the history) */\n\t refreshContents: function (options) {\n\t if (this.model) {\n\t return this.model.refresh(options);\n\t }\n\t // may have callbacks - so return an empty promise\n\t return $.when();\n\t },\n\t\n\t /** Override to reset web storage when the id changes (since it needs the id) */\n\t _setUpCollectionListeners: function () {\n\t _super.prototype._setUpCollectionListeners.call(this);\n\t return this.listenTo(this.collection, {\n\t // 'all' : function(){ console.log( this.collection + ':', arguments ); },\n\t 'fetching-more': function () {\n\t this._toggleContentsLoadingIndicator(true);\n\t this.$emptyMessage().hide();\n\t },\n\t 'fetching-more-done': function () {\n\t this._toggleContentsLoadingIndicator(false);\n\t }\n\t });\n\t },\n\t\n\t // ------------------------------------------------------------------------ panel rendering\n\t /** hide the $el and display a loading indicator (in the $el's parent) when loading new data */\n\t _showLoadingIndicator: function (msg, speed, callback) {\n\t var $indicator = $('
');\n\t this.$el.html($indicator.text(msg).slideDown(!_.isUndefined(speed) ? speed : this.fxSpeed));\n\t },\n\t\n\t /** hide the loading indicator */\n\t _hideLoadingIndicator: function (speed) {\n\t // make speed a bit slower to compensate for slow rendering of up to 500 contents\n\t this.$('.loading-indicator').slideUp(!_.isUndefined(speed) ? speed : this.fxSpeed + 200, function () {\n\t $(this).remove();\n\t });\n\t },\n\t\n\t /** In this override, add a btn to toggle the selectors */\n\t _buildNewRender: function () {\n\t var $newRender = _super.prototype._buildNewRender.call(this);\n\t this._renderSelectButton($newRender);\n\t return $newRender;\n\t },\n\t\n\t /** button for starting select mode */\n\t _renderSelectButton: function ($where) {\n\t $where = $where || this.$el;\n\t // do not render selector option if no actions\n\t if (!this.multiselectActions().length) {\n\t return null;\n\t }\n\t // do not render (and remove even) if nothing to select\n\t if (!this.views.length) {\n\t this.hideSelectors();\n\t $where.find('.controls .actions .show-selectors-btn').remove();\n\t return null;\n\t }\n\t // don't bother rendering if there's one already\n\t var $existing = $where.find('.controls .actions .show-selectors-btn');\n\t if ($existing.length) {\n\t return $existing;\n\t }\n\t\n\t return faIconButton({\n\t title: _l('Operations on multiple datasets'),\n\t classes: 'show-selectors-btn',\n\t faIcon: 'fa-check-square-o'\n\t }).prependTo($where.find('.controls .actions'));\n\t },\n\t\n\t /** override to avoid showing intial empty message using contents_active */\n\t _renderEmptyMessage: function ($whereTo) {\n\t var self = this;\n\t var $emptyMsg = self.$emptyMessage($whereTo);\n\t\n\t var empty = self.model.get('contents_active').active <= 0;\n\t if (empty) {\n\t return $emptyMsg.empty().append(self.emptyMsg).show();\n\t } else if (self.searchFor && self.model.contents.haveSearchDetails() && !self.views.length) {\n\t return $emptyMsg.empty().append(self.noneFoundMsg).show();\n\t }\n\t $emptyMsg.hide();\n\t return $();\n\t },\n\t\n\t /** the scroll container for this panel - can be $el, $el.parent(), or grandparent depending on context */\n\t $scrollContainer: function ($where) {\n\t // override or set via attributes.$scrollContainer\n\t return this.$list($where);\n\t },\n\t\n\t // ------------------------------------------------------------------------ subviews\n\t _toggleContentsLoadingIndicator: function (show) {\n\t if (!show) {\n\t this.$list().find('.contents-loading-indicator').remove();\n\t } else {\n\t this.$list().html('
' + '
');\n\t }\n\t },\n\t\n\t /** override to render pagination also */\n\t renderItems: function ($whereTo) {\n\t // console.log( this + '.renderItems-----------------', new Date() );\n\t $whereTo = $whereTo || this.$el;\n\t var self = this;\n\t var $list = self.$list($whereTo);\n\t\n\t // TODO: bootstrap hack to remove orphaned tooltips\n\t $('.tooltip').remove();\n\t\n\t $list.empty();\n\t self.views = [];\n\t\n\t var models = self._filterCollection();\n\t if (models.length) {\n\t self._renderPagination($whereTo);\n\t self.views = self._renderSomeItems(models, $list);\n\t } else {\n\t // TODO: consolidate with _renderPagination above by (???) passing in models/length?\n\t $whereTo.find('> .controls .list-pagination').empty();\n\t }\n\t self._renderEmptyMessage($whereTo).toggle(!models.length);\n\t\n\t self.trigger('views:ready', self.views);\n\t return self.views;\n\t },\n\t\n\t /** render pagination controls if not searching and contents says we're paginating */\n\t _renderPagination: function ($whereTo) {\n\t var $paginationControls = $whereTo.find('> .controls .list-pagination');\n\t if (this.searchFor || !this.model.contents.shouldPaginate()) return $paginationControls.empty();\n\t\n\t $paginationControls.html(this.templates.pagination({\n\t // pagination is 1-based for the user\n\t current: this.model.contents.currentPage + 1,\n\t last: this.model.contents.getLastPage() + 1\n\t }, this));\n\t $paginationControls.find('select.pages').tooltip();\n\t return $paginationControls;\n\t },\n\t\n\t /** render a subset of the entire collection (client-side pagination) */\n\t _renderSomeItems: function (models, $list) {\n\t var self = this;\n\t var views = [];\n\t $list.append(models.map(function (m) {\n\t var view = self._createItemView(m);\n\t views.push(view);\n\t return self._renderItemView$el(view);\n\t }));\n\t return views;\n\t },\n\t\n\t // ------------------------------------------------------------------------ sub-views\n\t /** in this override, check if the contents would also display based on includeDeleted/hidden */\n\t _filterItem: function (model) {\n\t var self = this;\n\t var contents = self.model.contents;\n\t return (contents.includeHidden || !model.hidden()) && (contents.includeDeleted || !model.isDeletedOrPurged()) && _super.prototype._filterItem.call(self, model);\n\t },\n\t\n\t /** In this override, since history contents are mixed,\n\t * get the appropo view class based on history_content_type\n\t */\n\t _getItemViewClass: function (model) {\n\t var contentType = model.get(\"history_content_type\");\n\t switch (contentType) {\n\t case 'dataset':\n\t return this.HDAViewClass;\n\t case 'dataset_collection':\n\t return this.HDCAViewClass;\n\t }\n\t throw new TypeError('Unknown history_content_type: ' + contentType);\n\t },\n\t\n\t /** in this override, add a linktarget, and expand if id is in web storage */\n\t _getItemViewOptions: function (model) {\n\t var options = _super.prototype._getItemViewOptions.call(this, model);\n\t return _.extend(options, {\n\t linkTarget: this.linkTarget,\n\t expanded: this.model.contents.storage.isExpanded(model.id),\n\t hasUser: this.model.ownedByCurrUser()\n\t });\n\t },\n\t\n\t /** In this override, add/remove expanded/collapsed model ids to/from web storage */\n\t _setUpItemViewListeners: function (view) {\n\t var panel = this;\n\t _super.prototype._setUpItemViewListeners.call(panel, view);\n\t //TODO: send from content view: this.model.collection.storage.addExpanded\n\t // maintain a list of items whose bodies are expanded\n\t return panel.listenTo(view, {\n\t 'expanded': function (v) {\n\t panel.model.contents.storage.addExpanded(v.model);\n\t },\n\t 'collapsed': function (v) {\n\t panel.model.contents.storage.removeExpanded(v.model);\n\t }\n\t });\n\t },\n\t\n\t /** override to remove expandedIds from webstorage */\n\t collapseAll: function () {\n\t this.model.contents.storage.clearExpanded();\n\t _super.prototype.collapseAll.call(this);\n\t },\n\t\n\t // ------------------------------------------------------------------------ selection\n\t /** Override to correctly set the historyId of the new collection */\n\t getSelectedModels: function () {\n\t var collection = _super.prototype.getSelectedModels.call(this);\n\t collection.historyId = this.collection.historyId;\n\t return collection;\n\t },\n\t\n\t // ------------------------------------------------------------------------ panel events\n\t /** event map */\n\t events: _.extend(_.clone(_super.prototype.events), {\n\t 'click .show-selectors-btn': 'toggleSelectors',\n\t 'click > .controls .prev': '_clickPrevPage',\n\t 'click > .controls .next': '_clickNextPage',\n\t 'change > .controls .pages': '_changePageSelect',\n\t // allow (error) messages to be clicked away\n\t 'click .messages [class$=message]': 'clearMessages'\n\t }),\n\t\n\t _clickPrevPage: function (ev) {\n\t this.model.clearUpdateTimeout();\n\t this.model.contents.fetchPrevPage();\n\t },\n\t\n\t _clickNextPage: function (ev) {\n\t this.model.clearUpdateTimeout();\n\t this.model.contents.fetchNextPage();\n\t },\n\t\n\t _changePageSelect: function (ev) {\n\t this.model.clearUpdateTimeout();\n\t var page = $(ev.currentTarget).val();\n\t this.model.contents.fetchPage(page);\n\t },\n\t\n\t /** Toggle and store the deleted visibility and re-render items\n\t * @returns {Boolean} new setting\n\t */\n\t toggleShowDeleted: function (show, options) {\n\t show = show !== undefined ? show : !this.model.contents.includeDeleted;\n\t var self = this;\n\t var contents = self.model.contents;\n\t contents.setIncludeDeleted(show, options);\n\t self.trigger('show-deleted', show);\n\t\n\t contents.fetchCurrentPage({ renderAll: true });\n\t return show;\n\t },\n\t\n\t /** Toggle and store whether to render explicity hidden contents\n\t * @returns {Boolean} new setting\n\t */\n\t toggleShowHidden: function (show, store, options) {\n\t // console.log( 'toggleShowHidden', show, store );\n\t show = show !== undefined ? show : !this.model.contents.includeHidden;\n\t var self = this;\n\t var contents = self.model.contents;\n\t contents.setIncludeHidden(show, options);\n\t self.trigger('show-hidden', show);\n\t\n\t contents.fetchCurrentPage({ renderAll: true });\n\t return show;\n\t },\n\t\n\t /** On the first search, if there are no details - load them, then search */\n\t _firstSearch: function (searchFor) {\n\t var self = this;\n\t var inputSelector = '> .controls .search-input';\n\t this.log('onFirstSearch', searchFor);\n\t\n\t // if the contents already have enough details to search, search and return now\n\t if (self.model.contents.haveSearchDetails()) {\n\t self.searchItems(searchFor);\n\t return;\n\t }\n\t\n\t // otherwise, load the details progressively here\n\t self.$(inputSelector).searchInput('toggle-loading');\n\t // set this now so that only results will show during progress\n\t self.searchFor = searchFor;\n\t var xhr = self.model.contents.progressivelyFetchDetails({ silent: true }).progress(function (response, limit, offset) {\n\t self.renderItems();\n\t self.trigger('search:loading-progress', limit, offset);\n\t }).always(function () {\n\t self.$el.find(inputSelector).searchInput('toggle-loading');\n\t }).done(function () {\n\t self.searchItems(searchFor, 'force');\n\t });\n\t },\n\t\n\t /** clear the search filters and show all views that are normally shown */\n\t clearSearch: function (searchFor) {\n\t var self = this;\n\t if (!self.searchFor) return self;\n\t //self.log( 'onSearchClear', self );\n\t self.searchFor = '';\n\t self.trigger('search:clear', self);\n\t self.$('> .controls .search-query').val('');\n\t // NOTE: silent + render prevents collection update event with merge only\n\t // - which causes an empty page due to event handler above\n\t self.model.contents.fetchCurrentPage({ silent: true }).done(function () {\n\t self.renderItems();\n\t });\n\t return self;\n\t },\n\t\n\t // ........................................................................ error handling\n\t /** Event handler for errors (from the panel, the history, or the history's contents)\n\t * Alternately use two strings for model and xhr to use custom message and title (respectively)\n\t * @param {Model or View} model the (Backbone) source of the error\n\t * @param {XMLHTTPRequest} xhr any ajax obj. assoc. with the error\n\t * @param {Object} options the options map commonly used with bbone ajax\n\t */\n\t errorHandler: function (model, xhr, options) {\n\t //TODO: to mixin or base model\n\t // interrupted ajax or no connection\n\t if (xhr && xhr.status === 0 && xhr.readyState === 0) {\n\t // return ERROR_MODAL.offlineErrorModal();\n\t // fail silently\n\t return;\n\t }\n\t // otherwise, leave something to report in the console\n\t this.error(model, xhr, options);\n\t // and feedback to a modal\n\t // if sent two strings (and possibly details as 'options'), use those as message and title\n\t if (_.isString(model) && _.isString(xhr)) {\n\t var message = model;\n\t var title = xhr;\n\t return ERROR_MODAL.errorModal(message, title, options);\n\t }\n\t // bad gateway\n\t // TODO: possibly to global handler\n\t if (xhr && xhr.status === 502) {\n\t return ERROR_MODAL.badGatewayErrorModal();\n\t }\n\t return ERROR_MODAL.ajaxErrorModal(model, xhr, options);\n\t },\n\t\n\t /** Remove all messages from the panel. */\n\t clearMessages: function (ev) {\n\t var $target = !_.isUndefined(ev) ? $(ev.currentTarget) : this.$messages().children('[class$=\"message\"]');\n\t $target.fadeOut(this.fxSpeed, function () {\n\t $(this).remove();\n\t });\n\t return this;\n\t },\n\t\n\t // ........................................................................ scrolling\n\t /** Scrolls the panel to show the content sub-view with the given hid.\n\t * @param {Integer} hid the hid of item to scroll into view\n\t * @returns {HistoryView} the panel\n\t */\n\t scrollToHid: function (hid) {\n\t return this.scrollToItem(_.first(this.viewsWhereModel({ hid: hid })));\n\t },\n\t\n\t // ........................................................................ misc\n\t /** utility for adding -st, -nd, -rd, -th to numbers */\n\t ordinalIndicator: function (number) {\n\t var numStr = number + '';\n\t switch (numStr.charAt(numStr.length - 1)) {\n\t case '1':\n\t return numStr + 'st';\n\t case '2':\n\t return numStr + 'nd';\n\t case '3':\n\t return numStr + 'rd';\n\t default:\n\t return numStr + 'th';\n\t }\n\t },\n\t\n\t /** Return a string rep of the history */\n\t toString: function () {\n\t return 'HistoryView(' + (this.model ? this.model.get('name') : '') + ')';\n\t }\n\t });\n\t\n\t //------------------------------------------------------------------------------ TEMPLATES\n\t HistoryView.prototype.templates = function () {\n\t\n\t var mainTemplate = BASE_MVC.wrapTemplate([\n\t // temp container\n\t '
', '', '
', '', '
']);\n\t\n\t var controlsTemplate = BASE_MVC.wrapTemplate(['
Trackster uses this information to populate the select box for chrom/contig, and' + 'to set the maximum basepair of the track browser. You may either upload a .len file' + 'of this format (Len File option), or directly enter the information into the box ' + '(Len Entry option).
';\n\t },\n\t\n\t _templateFasta: function () {\n\t return '
FASTA format
' + '
' + 'This is a multi-fasta file from your current history that provides the genome' + 'sequences for each chromosome/contig in your build.' + '
' + '
' + 'Here is a snippet from an example multi-fasta file:' + '
' + '';\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1)))\n\n/***/ }),\n/* 136 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/** User Preferences view */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(20), __webpack_require__(7)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Form, Ui) {\n\t\n\t /** Contains descriptive dictionaries describing user forms */\n\t var Model = Backbone.Model.extend({\n\t initialize: function (options) {\n\t options = options || {};\n\t options.user_id = options.user_id || Galaxy.user.id;\n\t this.set({\n\t 'user_id': options.user_id,\n\t 'information': {\n\t title: 'Manage information',\n\t description: 'Edit your email, addresses and custom parameters or change your username.',\n\t url: 'api/users/' + options.user_id + '/information/inputs',\n\t icon: 'fa-user'\n\t },\n\t 'password': {\n\t title: 'Change password',\n\t description: 'Allows you to change your login credentials.',\n\t icon: 'fa-unlock-alt',\n\t url: 'api/users/' + options.user_id + '/password/inputs',\n\t submit_title: 'Save password'\n\t },\n\t 'communication': {\n\t title: 'Change communication settings',\n\t description: 'Enable or disable the communication feature to chat with other users.',\n\t url: 'api/users/' + options.user_id + '/communication/inputs',\n\t icon: 'fa-comments-o'\n\t },\n\t 'permissions': {\n\t title: 'Set dataset permissions for new histories',\n\t description: 'Grant others default access to newly created histories. Changes made here will only affect histories created after these settings have been stored.',\n\t url: 'api/users/' + options.user_id + '/permissions/inputs',\n\t icon: 'fa-users',\n\t submit_title: 'Save permissions'\n\t },\n\t 'api_key': {\n\t title: 'Manage API key',\n\t description: 'Access your current API key or create a new one.',\n\t url: 'api/users/' + options.user_id + '/api_key/inputs',\n\t icon: 'fa-key',\n\t submit_title: 'Create a new key',\n\t submit_icon: 'fa-check'\n\t },\n\t 'toolbox_filters': {\n\t title: 'Manage Toolbox filters',\n\t description: 'Customize your Toolbox by displaying or omitting sets of Tools.',\n\t url: 'api/users/' + options.user_id + '/toolbox_filters/inputs',\n\t icon: 'fa-filter',\n\t submit_title: 'Save filters'\n\t },\n\t 'openids': {\n\t title: 'Manage OpenIDs',\n\t description: 'Associate OpenIDs with your account.',\n\t icon: 'fa-openid',\n\t onclick: function () {\n\t window.location.href = Galaxy.root + 'user/openid_manage?cntrller=user&use_panels=True';\n\t }\n\t },\n\t 'custom_builds': {\n\t title: 'Manage custom builds',\n\t description: 'Add or remove custom builds using history datasets.',\n\t icon: 'fa-cubes',\n\t onclick: function () {\n\t window.location.href = Galaxy.root + 'custom_builds';\n\t }\n\t },\n\t 'logout': {\n\t title: 'Sign out',\n\t description: 'Click here to sign out of all sessions.',\n\t icon: 'fa-sign-out',\n\t onclick: function () {\n\t Galaxy.modal.show({\n\t title: 'Sign out',\n\t body: 'Do you want to continue and sign out of all active sessions?',\n\t buttons: {\n\t 'Cancel': function () {\n\t Galaxy.modal.hide();\n\t },\n\t 'Sign out': function () {\n\t window.location.href = Galaxy.root + 'user/logout';\n\t }\n\t }\n\t });\n\t }\n\t }\n\t });\n\t }\n\t });\n\t\n\t /** View of the main user preference panel with links to individual user forms */\n\t var View = Backbone.View.extend({\n\t\n\t initialize: function () {\n\t this.model = new Model();\n\t this.message = new Ui.Message();\n\t this.setElement('');\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var self = this;\n\t var config = Galaxy.config;\n\t $.getJSON(Galaxy.root + 'api/users/' + Galaxy.user.id, function (data) {\n\t self.$preferences = $('').addClass('ui-panel').append(self.message.$el).append($('').append('User preferences')).append($('').append('You are logged in as ' + _.escape(data.email) + '.')).append(self.$table = $('
').addClass('ui-panel-table'));\n\t if (!config.use_remote_user) {\n\t self._addLink('information');\n\t self._addLink('password');\n\t }\n\t if (config.enable_communication_server) {\n\t self._addLink('communication');\n\t }\n\t self._addLink('custom_builds');\n\t self._addLink('permissions');\n\t self._addLink('api_key');\n\t if (config.has_user_tool_filters) {\n\t self._addLink('toolbox_filters');\n\t }\n\t if (config.enable_openid && !config.use_remote_user) {\n\t self._addLink('openids');\n\t }\n\t self._addLink('logout');\n\t self.$preferences.append(self._templateFooter(data));\n\t self.$el.empty().append(self.$preferences);\n\t });\n\t },\n\t\n\t _addLink: function (action) {\n\t var options = this.model.get(action);\n\t var $row = $(this._templateLink(options));\n\t var $a = $row.find('a');\n\t if (options.onclick) {\n\t $a.on('click', function () {\n\t options.onclick();\n\t });\n\t } else {\n\t $a.attr('href', Galaxy.root + 'user/' + action);\n\t }\n\t this.$table.append($row);\n\t },\n\t\n\t _templateLink: function (options) {\n\t return '
';\n\t },\n\t\n\t _templateFooter: function (options) {\n\t return '
' + 'You are using ' + options.nice_total_disk_usage + ' of disk space in this Galaxy instance. ' + (Galaxy.config.enable_quotas ? 'Your disk quota is: ' + options.quota + '. ' : '') + 'Is your usage more than expected? See the documentation for tips on how to find all of the data in your account.' + '
';\n\t }\n\t });\n\t\n\t /** View of individual user forms */\n\t var Forms = Backbone.View.extend({\n\t\n\t initialize: function (options) {\n\t this.model = new Model(options);\n\t this.page = this.model.get(options.form_id);\n\t this.setElement('');\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var self = this;\n\t $.ajax({\n\t url: Galaxy.root + this.page.url,\n\t type: 'GET'\n\t }).done(function (response) {\n\t var options = $.extend({}, self.page, response);\n\t var form = new Form({\n\t title: options.title,\n\t icon: options.icon,\n\t inputs: options.inputs,\n\t operations: {\n\t 'submit': new Ui.ButtonIcon({\n\t tooltip: options.submit_tooltip,\n\t title: options.submit_title || 'Save settings',\n\t icon: options.submit_icon || 'fa-save',\n\t onclick: function () {\n\t self._submit(form, options);\n\t }\n\t })\n\t }\n\t });\n\t self.$el.empty().append(form.$el);\n\t }).fail(function (response) {\n\t self.$el.empty().append(new Ui.Message({\n\t message: 'Failed to load resource ' + self.page.url + '.',\n\t status: 'danger',\n\t persistent: true\n\t }).$el);\n\t });\n\t },\n\t\n\t _submit: function (form, options) {\n\t var self = this;\n\t $.ajax({\n\t url: Galaxy.root + options.url,\n\t data: JSON.stringify(form.data.create()),\n\t type: 'PUT',\n\t contentType: 'application/json'\n\t }).done(function (response) {\n\t form.data.matchModel(response, function (input, input_id) {\n\t form.field_list[input_id].value(input.value);\n\t });\n\t form.message.update({ message: response.message, status: 'success' });\n\t }).fail(function (response) {\n\t form.message.update({ message: response.responseJSON.err_msg, status: 'danger' });\n\t });\n\t }\n\t });\n\t\n\t return {\n\t View: View,\n\t Forms: Forms\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1), __webpack_require__(2)))\n\n/***/ }),\n/* 137 */,\n/* 138 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/** Configure Workflow Menu View */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t var View = Backbone.View.extend({\n\t\n\t initialize: function (options) {\n\t this.setElement('');\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var self = this;\n\t $.getJSON(Galaxy.root + 'api/workflows/menu/', function (response) {\n\t var workflows = response.workflows,\n\t ids_in_menu = response.ids_in_menu,\n\t $el_config_worflow = null;\n\t\n\t // Add configure workflow header\n\t self.$el.empty().append(self._templateConfigWorkflowHeader());\n\t $el_config_worflow = self.$el.find('.configure-workflows');\n\t $el_config_worflow.append(self._templateActionButtons());\n\t if (workflows.length > 0) {\n\t $el_config_worflow.append(self._templateConfigureWorkflow(self, workflows, ids_in_menu));\n\t self.save_workflow_menu(self);\n\t self.make_checked(self, ids_in_menu);\n\t self.register_check_uncheck_all(self);\n\t } else {\n\t $el_config_worflow.append(self._templateNoWorkflow());\n\t }\n\t });\n\t },\n\t\n\t /** Register check and uncheck all callbacks*/\n\t register_check_uncheck_all: function (self) {\n\t var $el_check_all = self.$el.find('.check-all-wf'),\n\t $el_uncheck_all = self.$el.find('.uncheck-all-wf');\n\t\n\t $el_check_all.click(function (e) {\n\t self.check_uncheck_all(self, true);\n\t });\n\t $el_uncheck_all.click(function (e) {\n\t self.check_uncheck_all(self, false);\n\t });\n\t },\n\t\n\t /** Check or uncheck all workflows */\n\t check_uncheck_all: function (self, checked) {\n\t $.each(self.$el.find('.wf-config-item'), function () {\n\t var wf_checkbox = $(this)[0];\n\t wf_checkbox.checked = checked;\n\t });\n\t },\n\t\n\t /** Make the worflows as checked if present in the menu */\n\t make_checked: function (self, ids_in_menu) {\n\t $.each(self.$el.find('.wf-config-item'), function () {\n\t var wf_checkbox = $(this)[0];\n\t _.each(ids_in_menu, function (id) {\n\t if (parseInt(wf_checkbox.value) === id) {\n\t wf_checkbox.checked = true;\n\t }\n\t });\n\t });\n\t },\n\t\n\t /** Save the changes for workflow menu */\n\t save_workflow_menu: function (self) {\n\t var $el_save_workflow_menu = self.$el.find('.wf-save-menu');\n\t $el_save_workflow_menu.click(function (e) {\n\t var ids = [];\n\t $.each(self.$el.find('.wf-config-item'), function () {\n\t var wf_checkbox = $(this)[0];\n\t if (wf_checkbox.checked || wf_checkbox.checked === 'true') {\n\t ids.push(parseInt(wf_checkbox.value));\n\t }\n\t });\n\t $.ajax({\n\t type: 'PUT',\n\t url: Galaxy.root + 'api/workflows/menu/',\n\t data: JSON.stringify({ 'workflow_ids': ids }),\n\t contentType: 'application/json'\n\t }).done(function (response) {\n\t window.location = Galaxy.root + 'workflow?status=' + response.status + '&message=' + response.message;\n\t });\n\t });\n\t },\n\t\n\t /** Template for actions buttons */\n\t _templateActionButtons: function () {\n\t return '
';\n\t tableHtml = tableHtml + '' + 'Save' + '' + '' + 'Back to workflow' + '';\n\t return tableHtml;\n\t },\n\t\n\t /** Template for no workflow */\n\t _templateNoWorkflow: function () {\n\t return '
You do not have any accessible workflows.
';\n\t },\n\t\n\t /** Template for checkboxes */\n\t _templateInputCheckbox: function (self, wf) {\n\t return '';\n\t },\n\t\n\t /** Template for main config workflow menu */\n\t _templateConfigWorkflowHeader: function () {\n\t return '
' + '
' + '
Configure workflow menu
' + '
' + '
';\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1), __webpack_require__(2)))\n\n/***/ }),\n/* 139 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/** Workflow view */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t\n\t /** View of the main workflow list page */\n\t var View = Backbone.View.extend({\n\t\n\t initialize: function () {\n\t this.setElement('');\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var self = this,\n\t min_query_length = 3;\n\t $.getJSON(Galaxy.root + 'api/workflows/', function (workflows) {\n\t var $el_workflow = null;\n\t // Add workflow header\n\t self.$el.empty().append(self._templateHeader());\n\t // Add user actions message if any\n\t self.build_messages(self);\n\t $el_workflow = self.$el.find('.user-workflows');\n\t // Add the actions buttons\n\t $el_workflow.append(self._templateActionButtons());\n\t if (workflows.length > 0) {\n\t $el_workflow.append(self._templateWorkflowTable(self, workflows));\n\t self.adjust_actiondropdown($el_workflow);\n\t // Register delete and run workflow events\n\t _.each(workflows, function (wf) {\n\t self.confirm_delete(self, wf);\n\t });\n\t // Register search workflow event\n\t self.search_workflow(self, self.$el.find('.search-wf'), self.$el.find('.workflow-search tr'), min_query_length);\n\t } else {\n\t $el_workflow.append(self._templateNoWorkflow());\n\t }\n\t });\n\t },\n\t\n\t /** Build messages after user action */\n\t build_messages: function (self) {\n\t var $el_message = self.$el.find('.response-message'),\n\t status = self.get_querystring('status'),\n\t message = self.get_querystring('message');\n\t\n\t if (message && message !== null && message !== \"\") {\n\t $el_message.addClass(status + 'message');\n\t $el_message.html('
' + _.escape(message) + '
');\n\t } else {\n\t $el_message.html(\"\");\n\t }\n\t },\n\t\n\t /** Add confirm box before removing/unsharing workflow */\n\t confirm_delete: function (self, workflow) {\n\t var $el_wf_link = self.$el.find('.link-confirm-' + workflow.id),\n\t $el_shared_wf_link = self.$el.find('.link-confirm-shared-' + workflow.id);\n\t $el_wf_link.click(function () {\n\t return confirm(\"Are you sure you want to delete workflow '\" + workflow.name + \"'?\");\n\t });\n\t $el_shared_wf_link.click(function () {\n\t return confirm(\"Are you sure you want to remove the shared workflow '\" + workflow.name + \"'?\");\n\t });\n\t },\n\t\n\t /** Implement client side workflow search/filtering */\n\t search_workflow: function (self, $el_searchinput, $el_tabletr, min_querylen) {\n\t $el_searchinput.on('keyup', function () {\n\t var query = $(this).val();\n\t // Filter when query is at least 3 characters\n\t // otherwise show all rows\n\t if (query.length >= min_querylen) {\n\t // Ignore the query's case using 'i'\n\t var regular_expression = new RegExp(query, 'i');\n\t $el_tabletr.hide();\n\t $el_tabletr.filter(function () {\n\t // Apply regular expression on each row's text\n\t // and show when there is a match\n\t return regular_expression.test($(this).text());\n\t }).show();\n\t } else {\n\t $el_tabletr.show();\n\t }\n\t });\n\t },\n\t\n\t /** Get querystrings from url */\n\t get_querystring: function (key) {\n\t return decodeURIComponent(window.location.search.replace(new RegExp(\"^(?:.*[&\\\\?]\" + encodeURIComponent(key).replace(/[\\.\\+\\*]/g, \"\\\\$&\") + \"(?:\\\\=([^&]*))?)?.*$\", \"i\"), \"$1\"));\n\t },\n\t\n\t /** Ajust the position of dropdown with respect to table */\n\t adjust_actiondropdown: function ($el) {\n\t $el.on('show.bs.dropdown', function () {\n\t $el.css(\"overflow\", \"inherit\");\n\t });\n\t\n\t $el.on('hide.bs.dropdown', function () {\n\t $el.css(\"overflow\", \"auto\");\n\t });\n\t },\n\t\n\t /** Template for no workflow */\n\t _templateNoWorkflow: function () {\n\t return '
You have no workflows.
';\n\t },\n\t\n\t /** Template for actions buttons */\n\t _templateActionButtons: function () {\n\t return '
';\n\t },\n\t\n\t /** Template for user actions for workflows */\n\t _templateActions: function (workflow) {\n\t if (workflow.owner === Galaxy.user.attributes.username) {\n\t return '
');\n }\n }\n\n // Render first chunk.\n var self = this,\n first_chunk = this.model.get('first_data_chunk');\n if (first_chunk) {\n // First chunk is bootstrapped, so render now.\n this._renderChunk(first_chunk);\n }\n else {\n // No bootstrapping, so get first chunk and then render.\n $.when(self.model.get_next_chunk()).then(function(result) {\n self._renderChunk(result);\n });\n }\n\n // -- Show new chunks during scrolling. --\n\n // Set up chunk loading when scrolling using the scrolling element.\n this.scroll_elt.scroll(function(){\n self.attempt_to_fetch();\n });\n },\n\n /**\n * Returns true if user has scrolled to the bottom of the view.\n */\n scrolled_to_bottom: function() {\n return false;\n },\n\n // -- Helper functions. --\n\n _renderCell: function(cell_contents, index, colspan) {\n var $cell = $('
').text(cell_contents);\n var column_types = this.model.get_metadata('column_types');\n if (colspan !== undefined) {\n $cell.attr('colspan', colspan).addClass('stringalign');\n } else if (column_types) {\n if (index < column_types.length) {\n if (column_types[index] === 'str' || column_types[index] === 'list') {\n /* Left align all str columns, right align the rest */\n $cell.addClass('stringalign');\n }\n }\n }\n return $cell;\n },\n\n _renderRow: function(line) {\n // Check length of cells to ensure this is a complete row.\n var cells = line.split('\\t'),\n row = $('
'),\n num_columns = this.model.get_metadata('columns');\n\n if (this.row_count % 2 !== 0) {\n row.addClass('dark_row');\n }\n\n if (cells.length === num_columns) {\n _.each(cells, function(cell_contents, index) {\n row.append(this._renderCell(cell_contents, index));\n }, this);\n }\n else if (cells.length > num_columns) {\n // SAM file or like format with optional metadata included.\n _.each(cells.slice(0, num_columns - 1), function(cell_contents, index) {\n row.append(this._renderCell(cell_contents, index));\n }, this);\n row.append(this._renderCell(cells.slice(num_columns - 1).join('\\t'), num_columns - 1));\n }\n else if (cells.length === 1){\n // Comment line, just return the one cell.\n row.append(this._renderCell(line, 0, num_columns));\n }\n else {\n // cells.length is greater than one, but less than num_columns. Render cells and pad tds.\n // Possibly a SAM file or like format with optional metadata missing.\n // Could also be a tabular file with a line with missing columns.\n _.each(cells, function(cell_contents, index) {\n row.append(this._renderCell(cell_contents, index));\n }, this);\n _.each(_.range(num_columns - cells.length), function(){\n row.append($('
'));\n });\n }\n\n this.row_count++;\n return row;\n },\n\n _renderChunk: function(chunk) {\n var data_table = this.$el.find('table');\n _.each(chunk.ck_data.split('\\n'), function(line, index) {\n if (line !== ''){\n data_table.append(this._renderRow(line));\n }\n }, this);\n }\n});\n\n/**\n * Tabular view that is placed at the top level of page. Scrolling occurs\n * view top-level elements outside of view.\n */\nvar TopLevelTabularDatasetChunkedView = TabularDatasetChunkedView.extend({\n\n initialize: function(options) {\n TabularDatasetChunkedView.prototype.initialize.call(this, options);\n\n // Scrolling happens in top-level elements.\n scroll_elt = _.find(this.$el.parents(), function(p) {\n return $(p).css('overflow') === 'auto';\n });\n\n // If no scrolling element found, use window.\n if (!scroll_elt) { scroll_elt = window; }\n\n // Wrap scrolling element for easy access.\n this.scroll_elt = $(scroll_elt);\n },\n\n /**\n * Returns true if user has scrolled to the bottom of the view.\n */\n scrolled_to_bottom: function() {\n return (this.$el.height() - this.scroll_elt.scrollTop() - this.scroll_elt.height() <= 0);\n }\n\n});\n\n/**\n * Tabular view tnat is embedded in a page. Scrolling occurs in view's el.\n */\nvar EmbeddedTabularDatasetChunkedView = TabularDatasetChunkedView.extend({\n\n initialize: function(options) {\n TabularDatasetChunkedView.prototype.initialize.call(this, options);\n\n // Because view is embedded, set up div to do scrolling.\n this.scroll_elt = this.$el.css({\n position: 'relative',\n overflow: 'scroll',\n height: options.height || '500px'\n });\n },\n\n /**\n * Returns true if user has scrolled to the bottom of the view.\n */\n scrolled_to_bottom: function() {\n return this.$el.scrollTop() + this.$el.innerHeight() >= this.el.scrollHeight;\n }\n\n});\n\n// button for trackster visualization\nvar TabularButtonTracksterView = Backbone.View.extend({\n\n // gene region columns\n col: {\n chrom : null,\n start : null,\n end : null\n },\n\n // url for trackster\n url_viz : null,\n\n // dataset id\n dataset_id : null,\n\n // database key\n genome_build: null,\n\n // data type\n file_ext : null,\n\n // backbone initialize\n initialize: function (options) {\n // check if environment is available\n var Galaxy = parent.Galaxy;\n\n // link galaxy modal or create one\n if (Galaxy && Galaxy.modal) {\n this.modal = Galaxy.modal;\n }\n\n // link galaxy frames\n if (Galaxy && Galaxy.frame) {\n this.frame = Galaxy.frame;\n }\n\n // check\n if (!this.modal || !this.frame) {\n return;\n }\n\n // model/metadata\n var model = options.model;\n var metadata = model.get('metadata');\n\n // check for datatype\n if (!model.get('file_ext')) {\n return;\n }\n\n // get data type\n this.file_ext = model.get('file_ext');\n\n // check for bed-file format\n if (this.file_ext == 'bed')\n {\n // verify that metadata exists\n if (metadata.get('chromCol') && metadata.get('startCol') && metadata.get('endCol'))\n {\n // read in columns\n this.col.chrom = metadata.get('chromCol') - 1;\n this.col.start = metadata.get('startCol') - 1;\n this.col.end = metadata.get('endCol') - 1;\n } else {\n console.log('TabularButtonTrackster : Bed-file metadata incomplete.');\n return;\n }\n }\n\n // check for vcf-file format\n if (this.file_ext == 'vcf')\n {\n // search array\n function search (str, array) {\n for (var j = 0; j < array.length; j++)\n if (array[j].match(str)) return j;\n return -1;\n };\n\n // load\n this.col.chrom = search('Chrom', metadata.get('column_names'));\n this.col.start = search('Pos', metadata.get('column_names'));\n this.col.end = null;\n\n // verify that metadata exists\n if (this.col.chrom == -1 || this.col.start == -1) {\n console.log('TabularButtonTrackster : VCF-file metadata incomplete.');\n return;\n }\n }\n\n // check\n if(this.col.chrom === undefined) {\n return;\n }\n\n // get dataset id\n if (model.id) {\n this.dataset_id = model.id;\n } else {\n console.log('TabularButtonTrackster : Dataset identification is missing.');\n return;\n }\n\n // get url\n if (model.get('url_viz')) {\n this.url_viz = model.get('url_viz');\n } else {\n console.log('TabularButtonTrackster : Url for visualization controller is missing.');\n return;\n }\n\n // get genome_build / database key\n if (model.get('genome_build')) {\n this.genome_build = model.get('genome_build');\n }\n\n // create the icon\n var btn_viz = new mod_icon_btn.IconButtonView({\n model : new mod_icon_btn.IconButton({\n title : 'Visualize',\n icon_class : 'chart_curve',\n id : 'btn_viz'\n })\n });\n\n // set element\n this.setElement(options.$el);\n\n // add to element\n this.$el.append(btn_viz.render().$el);\n\n // hide the button\n this.hide();\n },\n\n // backbone events\n events:\n {\n 'mouseover tr' : 'show',\n 'mouseleave' : 'hide'\n },\n\n // show button\n show: function (e) {\n // is numeric\n function is_numeric(n) {\n return !isNaN(parseFloat(n)) && isFinite(n);\n };\n\n // check\n if(this.col.chrom === null)\n return;\n\n // get selected data line\n var row = $(e.target).parent();\n\n // verify that location has been found\n var chrom = row.children().eq(this.col.chrom).html();\n var start = row.children().eq(this.col.start).html();\n\n // end is optional\n var end = this.col.end ? row.children().eq(this.col.end).html() : start;\n\n // double check location\n if (!chrom.match(\"^#\") && chrom !== \"\" && is_numeric(start)) {\n\n // get target gene region\n var btn_viz_pars = {\n dataset_id : this.dataset_id,\n gene_region : chrom + \":\" + start + \"-\" + end\n };\n\n // get button position\n var offset = row.offset();\n var left = offset.left - 10;\n var top = offset.top - $(window).scrollTop() + 3;\n\n // update css\n $('#btn_viz').css({'position': 'fixed', 'top': top + 'px', 'left': left + 'px'});\n $('#btn_viz').off('click');\n $('#btn_viz').click(this.create_trackster_action(this.url_viz, btn_viz_pars, this.genome_build));\n\n // show the button\n $('#btn_viz').show();\n } else {\n // hide the button\n $('#btn_viz').hide();\n }\n },\n\n // hide button\n hide: function () {\n this.$el.find('#btn_viz').hide();\n },\n\n // create action\n create_trackster_action : function (vis_url, dataset_params, dbkey) {\n // link this\n var self = this;\n\n // create function\n return function() {\n var listTracksParams = {};\n if (dbkey) {\n listTracksParams[ 'f-dbkey' ] = dbkey;\n }\n $.ajax({\n url: vis_url + '/list_tracks?' + $.param( listTracksParams ),\n dataType: 'html',\n error: function() {\n // show error message\n self.modal.show({\n title : 'Something went wrong!',\n body : 'Unfortunately we could not add this dataset to the track browser. Please try again or contact us.',\n buttons : {\n 'Cancel': function(){\n self.modal.hide();\n }\n }\n });\n },\n success: function(table_html) {\n self.modal.show({\n title : 'View Data in a New or Saved Visualization',\n buttons :{\n 'Cancel': function(){\n self.modal.hide();\n },\n 'View in saved visualization': function(){\n // show modal with saved visualizations\n self.modal.show(\n {\n title : 'Add Data to Saved Visualization',\n body : table_html,\n buttons : {\n 'Cancel': function(){\n self.modal.hide();\n },\n 'Add to visualization': function(){\n // hide\n self.modal.hide();\n\n // search selected fields\n self.modal.$el.find('input[name=id]:checked').each(function(){\n // get visualization id\n var vis_id = $(this).val();\n dataset_params.id = vis_id;\n\n // add widget\n self.frame.add({\n title : 'Trackster',\n type : 'url',\n content : vis_url + '/trackster?' + $.param(dataset_params)\n });\n });\n }\n }\n });\n },\n 'View in new visualization': function(){\n // hide\n self.modal.hide();\n\n // add widget\n self.frame.add({\n title : 'Trackster',\n type : 'url',\n content : vis_url + '/trackster?' + $.param(dataset_params)\n });\n }\n }\n });\n }\n });\n return false;\n };\n }\n});\n\n// -- Utility functions. --\n\n/**\n * Create a model, attach it to a view, render view, and attach it to a parent element.\n */\nvar createModelAndView = function(model, view, model_config, parent_elt) {\n // Create model, view.\n var a_view = new view({\n model: new model(model_config)\n });\n\n // Render view and add to parent element.\n a_view.render();\n if (parent_elt) {\n parent_elt.append(a_view.$el);\n }\n\n return a_view;\n};\n\n/**\n * Create a tabular dataset chunked view (and requisite tabular dataset model)\n * and appends to parent_elt.\n */\nvar createTabularDatasetChunkedView = function(options) {\n // If no model, create and set model from dataset config.\n if (!options.model) {\n options.model = new TabularDataset(options.dataset_config);\n }\n\n var parent_elt = options.parent_elt;\n var embedded = options.embedded;\n\n // Clean up options so that only needed options are passed to view.\n delete options.embedded;\n delete options.parent_elt;\n delete options.dataset_config;\n\n // Create and set up view.\n var view = (embedded ? new EmbeddedTabularDatasetChunkedView(options) :\n new TopLevelTabularDatasetChunkedView(options));\n view.render();\n\n if (parent_elt) {\n parent_elt.append(view.$el);\n // If we're sticking this in another element, once it's appended check\n // to make sure we've filled enough space.\n // Without this, the scroll elements don't work.\n view.expand_to_container();\n }\n\n return view;\n};\n\nreturn {\n Dataset: Dataset,\n TabularDataset: TabularDataset,\n DatasetCollection: DatasetCollection,\n TabularDatasetChunkedView: TabularDatasetChunkedView,\n createTabularDatasetChunkedView: createTabularDatasetChunkedView\n};\n\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/dataset/data.js","define([\n], function(){\n\n'use strict';\n//==============================================================================\n/** Map of possible HDA/collection/job states to their string equivalents.\n * A port of galaxy.model.Dataset.states.\n */\nvar STATES = {\n // NOT ready states\n /** is uploading and not ready */\n UPLOAD : 'upload',\n /** the job that will produce the dataset queued in the runner */\n QUEUED : 'queued',\n /** the job that will produce the dataset is running */\n RUNNING : 'running',\n /** metadata for the dataset is being discovered/set */\n SETTING_METADATA : 'setting_metadata',\n\n // ready states\n /** was created without a tool */\n NEW : 'new',\n /** has no data */\n EMPTY : 'empty',\n /** has successfully completed running */\n OK : 'ok',\n\n /** the job that will produce the dataset paused */\n PAUSED : 'paused',\n /** metadata discovery/setting failed or errored (but otherwise ok) */\n FAILED_METADATA : 'failed_metadata',\n//TODO: not in trans.app.model.Dataset.states - is in database\n /** not accessible to the current user (i.e. due to permissions) */\n NOT_VIEWABLE : 'noPermission',\n /** deleted while uploading */\n DISCARDED : 'discarded',\n /** the tool producing this dataset failed */\n ERROR : 'error'\n};\n\nSTATES.READY_STATES = [\n STATES.OK,\n STATES.EMPTY,\n STATES.PAUSED,\n STATES.FAILED_METADATA,\n STATES.NOT_VIEWABLE,\n STATES.DISCARDED,\n STATES.ERROR\n];\n\nSTATES.NOT_READY_STATES = [\n STATES.UPLOAD,\n STATES.QUEUED,\n STATES.RUNNING,\n STATES.SETTING_METADATA,\n STATES.NEW\n];\n\n\n//==============================================================================\n return STATES;\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/dataset/states.js","/** This module contains all button views. */\ndefine( [ 'utils/utils' ], function( Utils ) {\n /** This renders the default button which is used e.g. at the bottom of the upload modal. */\n var ButtonDefault = Backbone.View.extend({\n initialize: function( options ) {\n this.model = options && options.model || new Backbone.Model({\n id : Utils.uid(),\n title : '',\n floating : 'right',\n icon : '',\n cls : 'btn btn-default',\n wait : false,\n wait_text : 'Sending...',\n wait_cls : 'btn btn-info',\n disabled : false,\n percentage : -1\n }).set( options );\n this.setElement( $( '' ).attr( 'type', 'button' )\n .append( this.$icon = $( '' ) )\n .append( this.$title = $( '' ) )\n .append( this.$progress = $( '' ).append( this.$progress_bar = $( '' ) ) ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n\n render: function() {\n var self = this;\n var options = this.model.attributes;\n this.$el.removeClass()\n .addClass( 'ui-button-default' )\n .addClass( options.disabled && 'disabled' )\n .attr( 'id', options.id )\n .attr( 'disabled', options.disabled )\n .css( 'float', options.floating )\n .off( 'click' ).on( 'click' , function() {\n $( '.tooltip' ).hide();\n options.onclick && !self.disabled && options.onclick();\n })\n .tooltip( { title: options.tooltip, placement: 'bottom' } );\n this.$progress.addClass( 'progress' ).css( 'display', options.percentage !== -1 ? 'block' : 'none' );\n this.$progress_bar.addClass( 'progress-bar' ).css( { width : options.percentage + '%' } );\n this.$icon.removeClass().addClass( 'icon fa' );\n this.$title.removeClass().addClass( 'title' );\n if ( options.wait ) {\n this.$el.addClass( options.wait_cls ).prop( 'disabled', true );\n this.$icon.addClass( 'fa-spinner fa-spin ui-margin-right' );\n this.$title.html( options.wait_text );\n } else {\n this.$el.addClass( options.cls );\n this.$icon.addClass( options.icon );\n this.$title.html( options.title );\n options.icon && options.title && this.$icon.addClass( 'ui-margin-right' );\n }\n },\n\n /** Show button */\n show: function() {\n this.$el.show();\n },\n\n /** Hide button */\n hide: function() {\n this.$el.hide();\n },\n\n /** Disable button */\n disable: function() {\n this.model.set( 'disabled', true );\n },\n\n /** Enable button */\n enable: function() {\n this.model.set( 'disabled', false );\n },\n\n /** Show spinner to indicate that the button is not ready to be clicked */\n wait: function() {\n this.model.set( 'wait', true );\n },\n\n /** Hide spinner to indicate that the button is ready to be clicked */\n unwait: function() {\n this.model.set( 'wait', false );\n },\n\n /** Change icon */\n setIcon: function( icon ) {\n this.model.set( 'icon', icon );\n }\n });\n\n /** This button allows the right-click/open-in-new-tab feature, its used e.g. for panel buttons. */\n var ButtonLink = ButtonDefault.extend({\n initialize: function( options ) {\n this.model = options && options.model || new Backbone.Model({\n id : Utils.uid(),\n title : '',\n icon : '',\n cls : ''\n }).set( options );\n this.setElement( $( '' ).append( this.$icon = $( '' ) ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n\n render: function() {\n var options = this.model.attributes;\n this.$el.removeClass()\n .addClass( options.cls )\n .attr( { id : options.id,\n href : options.href || 'javascript:void(0)',\n title : options.title,\n target : options.target || '_top',\n disabled : options.disabled } )\n .tooltip( { placement: 'bottom' } )\n .off( 'click' ).on( 'click' , function() {\n options.onclick && !options.disabled && options.onclick();\n });\n this.$icon.removeClass().addClass( options.icon );\n }\n });\n\n /** The check button is used in the tool form and allows to distinguish between multiple states e.g. all, partially and nothing selected. */\n var ButtonCheck = Backbone.View.extend({\n initialize: function( options ) {\n this.model = options && options.model || new Backbone.Model({\n id : Utils.uid(),\n title : 'Select/Unselect all',\n icons : [ 'fa-square-o', 'fa-minus-square-o', 'fa-check-square-o' ],\n value : 0,\n onchange : function(){}\n }).set( options );\n this.setElement( $( '' ).append( this.$icon = $( '' ) )\n .append( this.$title = $( '' ) ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n\n render: function( options ) {\n var self = this;\n var options = this.model.attributes;\n this.$el.addClass( 'ui-button-check' )\n .off( 'click' ).on('click', function() {\n self.model.set( 'value', ( self.model.get( 'value' ) === 0 && 2 ) || 0 );\n options.onclick && options.onclick();\n });\n this.$title.html( options.title );\n this.$icon.removeClass()\n .addClass( 'icon fa ui-margin-right' )\n .addClass( options.icons[ options.value ] );\n },\n\n /* Sets a new value and/or returns the value.\n * @param{Integer} new_val - Set a new value 0=unchecked, 1=partial and 2=checked.\n * OR:\n * @param{Integer} new_val - Number of selected options.\n * @param{Integer} total - Total number of available options.\n */\n value: function ( new_val, total ) {\n if ( new_val !== undefined ) {\n if ( total && new_val !== 0 ) {\n new_val = ( new_val !== total ) && 1 || 2;\n }\n this.model.set( 'value', new_val );\n this.model.get( 'onchange' )( this.model.get( 'value' ) );\n }\n return this.model.get( 'value' );\n }\n });\n\n /** This renders a differently styled, more compact button version. */\n var ButtonIcon = ButtonDefault.extend({\n initialize: function( options ) {\n this.model = options && options.model || new Backbone.Model({\n id : Utils.uid(),\n title : '',\n floating : 'right',\n icon : '',\n cls : 'ui-button-icon',\n disabled : false\n }).set( options );\n this.setElement( $( '' ).append( this.$button = $( '' ).append( this.$icon = $( '' ) )\n .append( this.$title = $( '' ) ) ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n\n render : function( options ) {\n var self = this;\n var options = this.model.attributes;\n this.$el.removeClass()\n .addClass( options.cls )\n .addClass( options.disabled && 'disabled' )\n .attr( 'disabled', options.disabled )\n .attr( 'id', options.id )\n .css( 'float', options.floating )\n .off( 'click' ).on( 'click', function() {\n $( '.tooltip' ).hide();\n !options.disabled && options.onclick && options.onclick();\n });\n this.$button.addClass( 'button' ).tooltip( { title: options.tooltip, placement: 'bottom' } );\n this.$icon.removeClass().addClass( 'icon fa' ).addClass( options.icon );\n this.$title.addClass( 'title' ).html( options.title );\n options.icon && options.title && this.$icon.addClass( 'ui-margin-right' );\n }\n });\n\n /** This class creates a button with dropdown menu. */\n var ButtonMenu = ButtonDefault.extend({\n $menu: null,\n initialize: function ( options ) {\n this.model = options && options.model || new Backbone.Model({\n id : '',\n title : '',\n floating : 'right',\n pull : 'right',\n icon : null,\n onclick : null,\n cls : 'ui-button-icon ui-button-menu',\n tooltip : '',\n target : '',\n href : '',\n onunload : null,\n visible : true,\n tag : ''\n }).set( options );\n this.collection = new Backbone.Collection();\n this.setElement( $( '' ).append( this.$root = $( '' ).append( this.$icon = $( '' ) )\n .append( this.$title = $( '' ) ) ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.listenTo( this.collection, 'change add remove reset', this.render, this );\n this.render();\n },\n\n render: function() {\n var self = this;\n var options = this.model.attributes;\n this.$el.removeClass()\n .addClass( 'dropdown' )\n .addClass( options.cls )\n .attr( 'id', options.id )\n .css( { float : options.floating,\n display : options.visible && this.collection.where( { visible: true } ).length > 0 ? 'block' : 'none' } );\n this.$root.addClass( 'root button dropdown-toggle' )\n .attr( 'data-toggle', 'dropdown' )\n .tooltip( { title: options.tooltip, placement: 'bottom' } )\n .off( 'click' ).on( 'click', function( e ) {\n $( '.tooltip' ).hide();\n e.preventDefault();\n options.onclick && options.onclick();\n } );\n this.$icon.removeClass().addClass( 'icon fa' ).addClass( options.icon );\n this.$title.removeClass().addClass( 'title' ).html( options.title );\n options.icon && options.title && this.$icon.addClass( 'ui-margin-right' );\n this.$menu && this.$menu.remove();\n if ( this.collection.length > 0 ) {\n this.$menu = $( '
' ).addClass( 'menu dropdown-menu' )\n .addClass( 'pull-' + self.model.get( 'pull' ) )\n .attr( 'role', 'menu' );\n this.$el.append( this.$menu );\n }\n this.collection.each( function( submodel ) {\n var suboptions = submodel.attributes;\n if ( suboptions.visible ) {\n var $link = $( '' ).addClass( 'dropdown-item' )\n .attr( { href : suboptions.href, target : suboptions.target } )\n .append( $( '' ).addClass( 'fa' )\n .addClass( suboptions.icon )\n .css( 'display', suboptions.icon ? 'inline-block' : 'none' ) )\n .append( suboptions.title )\n .on( 'click', function( e ) {\n if ( suboptions.onclick ) {\n e.preventDefault();\n suboptions.onclick();\n }\n } );\n self.$menu.append( $( '' ).append( $link ) );\n suboptions.divider && self.$menu.append( $( '' ).addClass( 'divider' ) );\n }\n });\n },\n\n /** Add a new menu item */\n addMenu: function ( options ) {\n this.collection.add( Utils.merge( options, {\n title : '',\n target : '',\n href : '',\n onclick : null,\n divider : false,\n visible : true,\n icon : null,\n cls : 'button-menu btn-group'\n }));\n }\n });\n\n return {\n ButtonDefault : ButtonDefault,\n ButtonLink : ButtonLink,\n ButtonIcon : ButtonIcon,\n ButtonCheck : ButtonCheck,\n ButtonMenu : ButtonMenu\n }\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/ui/ui-buttons.js","define([\n //jquery\n //backbone\n], function(){\n//=============================================================================\n/**\n * backbone model for icon buttons\n */\nvar IconButton = Backbone.Model.extend({\n defaults: {\n title : \"\",\n icon_class : \"\",\n on_click : null,\n menu_options : null,\n is_menu_button : true,\n id : null,\n href : null,\n target : null,\n enabled : true,\n visible : true,\n tooltip_config : {}\n }\n});\n\n/**\n * backbone view for icon buttons\n */\nvar IconButtonView = Backbone.View.extend({\n\n initialize : function(){\n // better rendering this way\n this.model.attributes.tooltip_config = { placement : 'bottom' };\n this.model.bind( 'change', this.render, this );\n },\n\n render : function( ){\n // hide tooltip\n this.$el.tooltip( 'hide' );\n\n var new_elem = this.template( this.model.toJSON() );\n // configure tooltip\n new_elem.tooltip( this.model.get( 'tooltip_config' ));\n this.$el.replaceWith( new_elem );\n this.setElement( new_elem );\n return this;\n },\n\n events : {\n 'click' : 'click'\n },\n\n click : function( event ){\n // if on_click pass to that function\n if( _.isFunction( this.model.get( 'on_click' ) ) ){\n this.model.get( 'on_click' )( event );\n return false;\n }\n // otherwise, bubble up ( to href or whatever )\n return true;\n },\n\n // generate html element\n template: function( options ){\n var buffer = 'title=\"' + options.title + '\" class=\"icon-button';\n\n if( options.is_menu_button ){\n buffer += ' menu-button';\n }\n\n buffer += ' ' + options.icon_class;\n\n if( !options.enabled ){\n buffer += '_disabled';\n }\n\n // close class tag\n buffer += '\"';\n\n if( options.id ){\n buffer += ' id=\"' + options.id + '\"';\n }\n\n buffer += ' href=\"' + options.href + '\"';\n // add target for href\n if( options.target ){\n buffer += ' target=\"' + options.target + '\"';\n }\n // set visibility\n if( !options.visible ){\n buffer += ' style=\"display: none;\"';\n }\n\n // enabled/disabled\n if ( options.enabled ){\n buffer = '';\n } else {\n buffer = '';\n }\n\n // return element\n return $( buffer );\n }\n} );\n\n// define collection\nvar IconButtonCollection = Backbone.Collection.extend({\n model: IconButton\n});\n\n/**\n * menu with multiple icon buttons\n * views are not needed nor used for individual buttons\n */\nvar IconButtonMenuView = Backbone.View.extend({\n\n tagName: 'div',\n\n initialize: function(){\n this.render();\n },\n\n render: function(){\n // initialize icon buttons\n var self = this;\n this.collection.each(function(button){\n // create and add icon button to menu\n var elt = $('')\n .attr('href', 'javascript:void(0)')\n .attr('title', button.attributes.title)\n .addClass('icon-button menu-button')\n .addClass(button.attributes.icon_class)\n .appendTo(self.$el)\n .click(button.attributes.on_click);\n\n // configure tooltip\n if (button.attributes.tooltip_config){\n elt.tooltip(button.attributes.tooltip_config);\n }\n\n // add popup menu to icon\n var menu_options = button.get('options');\n if (menu_options){\n make_popupmenu(elt, menu_options);\n }\n });\n\n // return\n return this;\n }\n});\n\n/**\n * Returns an IconButtonMenuView for the provided configuration.\n * Configuration is a list of dictionaries where each dictionary\n * defines an icon button. Each dictionary must have the following\n * elements: icon_class, title, and on_click.\n */\nvar create_icon_buttons_menu = function(config, global_config)\n{\n // initialize global configuration\n if (!global_config) global_config = {};\n\n // create and initialize menu\n var buttons = new IconButtonCollection(\n _.map(config, function(button_config){\n return new IconButton(_.extend(button_config, global_config));\n })\n );\n\n // return menu\n return new IconButtonMenuView( {collection: buttons} );\n};\n\n\n//=============================================================================\n return {\n IconButton : IconButton,\n IconButtonView : IconButtonView,\n IconButtonCollection : IconButtonCollection,\n IconButtonMenuView : IconButtonMenuView,\n create_icon_buttons_menu: create_icon_buttons_menu\n };\n})\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/ui/icon-button.js","/**\n * Popover wrapper\n*/\ndefine([ 'utils/utils' ], function( Utils ) {\nvar View = Backbone.View.extend({\n optionsDefault: {\n with_close : true,\n title : null,\n placement : 'top',\n container : 'body',\n body : null\n },\n\n initialize: function ( options ) {\n this.setElement( this._template() );\n this.uid = Utils.uid();\n this.options = _.defaults( options || {}, this.optionsDefault );\n this.options.container.parent().append( this.el );\n this.$title = this.$( '.popover-title-label' );\n this.$close = this.$( '.popover-close' );\n this.$body = this.$( '.popover-content' );\n\n // add initial content\n this.options.body && this.append( this.options.body );\n\n // add event to hide if click is outside of popup and not on container\n var self = this;\n $( 'body' ).on( 'mousedown.' + this.uid, function( e ) {\n // the 'is' for buttons that trigger popups\n // the 'has' for icons within a button that triggers a popup\n self.visible && !$( self.options.container ).is( e.target ) && !$( self.el ).is( e.target ) &&\n $( self.el ).has( e.target ).length === 0 && self.hide();\n });\n },\n\n /**\n * Render popover\n */\n render: function() {\n this.$title.html( this.options.title );\n this.$el.removeClass().addClass( 'ui-popover popover fade in' ).addClass( this.options.placement );\n this.$el.css( this._get_placement( this.options.placement ) );\n\n // configure close option\n var self = this;\n if ( this.options.with_close ) {\n this.$close.on( 'click', function() { self.hide() } ).show();\n } else {\n this.$close.off().hide();\n }\n },\n\n /**\n * Set the popover title\n * @params{ String } newTitle - New popover title\n */\n title: function( newTitle ) {\n if ( newTitle !== undefined ) {\n this.options.title = newTitle;\n this.$title.html( newTitle );\n }\n },\n\n /**\n * Show popover\n */\n show: function() {\n this.render();\n this.$el.show();\n this.visible = true;\n },\n\n /**\n * Hide popover\n */\n hide: function() {\n this.$el.hide();\n this.visible = false;\n },\n\n /**\n * Append new content to the popover\n * @params{ Object } $el - Dom element\n */\n append: function( $el ) {\n this.$body.append( $el );\n },\n\n /**\n * Remove all content\n */\n empty: function() {\n this.$body.empty();\n },\n\n /**\n * Remove popover\n */\n remove: function() {\n $( 'body' ).off( 'mousedown.' + this.uid );\n this.$el.remove();\n },\n\n /**\n * Improve popover location/placement\n */\n _get_placement: function( placement ) {\n // get popover dimensions\n var width = this._get_width( this.$el );\n var height = this.$el.height();\n\n // get container details\n var $container = this.options.container;\n var container_width = this._get_width( $container );\n var container_height = this._get_height( $container );\n var container_position = $container.position();\n\n // get position\n var top = left = 0;\n if ([ 'top', 'bottom' ].indexOf( placement ) != -1) {\n left = container_position.left - width + ( container_width + width ) / 2;\n switch ( placement ) {\n case 'top':\n top = container_position.top - height - 5;\n break;\n case 'bottom':\n top = container_position.top + container_height + 5;\n break;\n }\n } else {\n top = container_position.top - height + ( container_height + height ) / 2;\n switch ( placement ) {\n case 'right':\n left = container_position.left + container_width;\n break;\n }\n }\n return { top: top, left: left };\n },\n\n /**\n * Returns padding/margin corrected width\n */\n _get_width: function( $el ) {\n return $el.width() + parseInt( $el.css( 'padding-left' ) ) + parseInt( $el.css( 'margin-left' ) ) +\n parseInt( $el.css( 'padding-right' ) ) + parseInt( $el.css( 'margin-right' ) );\n },\n\n /**\n * Returns padding corrected height\n */\n _get_height: function( $el ) {\n return $el.height() + parseInt( $el.css( 'padding-top' ) ) + parseInt( $el.css( 'padding-bottom' ) );\n },\n\n /**\n * Return the popover template\n */\n _template: function( options ) {\n return '
' +\n '
' +\n '
' +\n '
' +\n '' +\n '
' +\n '
' +\n '
';\n }\n});\n\nreturn {\n View: View\n}\n\n});\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/ui/ui-popover.js","// dependencies\ndefine(['utils/utils'], function(Utils) {\n\n/**\n * A plugin for initializing select2 input items.\n * Make sure the select2 library itself is loaded beforehand.\n * Also the element to which select2 will be appended has to \n * be created before select2 initialization (and passed as option).\n */\nvar View = Backbone.View.extend(\n{\n // options\n optionsDefault: {\n css : '',\n placeholder : 'No data available',\n data : [],\n value : null,\n multiple : false,\n minimumInputLength : 0,\n // example format of initial data: \"id:name,55:anotherrole@role.com,27:role@role.com\"\n initialData : ''\n },\n \n // initialize\n initialize : function(options) {\n // configure options\n this.options = Utils.merge(options, this.optionsDefault);\n \n // create new element\n this.setElement(this._template(this.options));\n \n // check if container exists\n if (!this.options.container) {\n console.log('ui-select::initialize() : container not specified.');\n return;\n }\n \n // add to dom\n this.options.container.append(this.$el);\n \n // link selection dictionary\n this.select_data = this.options.data;\n \n // refresh\n this._refresh();\n \n if (!this.options.multiple){\n // initial value\n if (this.options.value) {\n this._setValue(this.options.value);\n }\n \n // add change event\n var self = this;\n if (this.options.onchange) {\n this.$el.on('change', function() {\n self.options.onchange(self.value());\n });\n }\n }\n },\n \n // value\n value : function (new_value) {\n // get current id/value\n var before = this._getValue();\n \n // check if new_value is defined\n if (new_value !== undefined) {\n this._setValue(new_value);\n }\n \n // get current id/value\n var after = this._getValue();\n \n // fire onchange\n if ((after != before && this.options.onchange)) {\n this.options.onchange(after);\n }\n \n // return current value\n return after;\n },\n \n // label\n text : function () {\n return this.$el.select2('data').text;\n },\n \n // disabled\n disabled: function() {\n return !this.$el.select2('enable');\n },\n\n // enable\n enable: function() {\n this.$el.select2('enable', true);\n },\n \n // disable\n disable: function() {\n this.$el.select2('enable', false);\n },\n \n // add\n add: function(options) {\n // add options\n this.select_data.push({\n id : options.id,\n text : options.text\n });\n \n // refresh\n this._refresh();\n },\n \n // remove\n del: function(id) {\n // search option\n var index = this._getIndex(id);\n \n // check if found\n if (index != -1) {\n // remove options\n this.select_data.splice(index, 1);\n \n // refresh\n this._refresh();\n }\n },\n \n // remove\n remove: function() {\n this.$el.select2('destroy');\n },\n \n // update\n update: function(options) {\n // copy options\n this.select_data = [];\n for (var key in options.data) {\n this.select_data.push(options.data[key]);\n }\n \n // refresh\n this._refresh();\n },\n \n // refresh\n _refresh: function() {\n // add select2 data based on type of input\n if (!this.options.multiple){\n var selected = this._getValue();\n var select_opt = {\n data : this.select_data,\n containerCssClass : this.options.css,\n placeholder : this.options.placeholder,\n dropdownAutoWidth : true\n };\n this.$el.select2(select_opt);\n // select previous value (if exists)\n this._setValue(selected);\n } else {\n var select_opt = {\n multiple : this.options.multiple,\n containerCssClass : this.options.css,\n placeholder : this.options.placeholder,\n minimumInputLength : this.options.minimumInputLength,\n ajax : this.options.ajax,\n dropdownCssClass : this.options.dropdownCssClass,\n escapeMarkup : this.options.escapeMarkup,\n formatResult : this.options.formatResult,\n formatSelection : this.options.formatSelection,\n initSelection : this.options.initSelection,\n initialData : this.options.initialData\n };\n this.$el.select2(select_opt);\n }\n },\n \n // get index\n _getIndex: function(value) {\n // returns the index of the searched value\n _.findIndex(this.select_data, {id: value});\n },\n \n // get value\n _getValue: function() {\n return this.$el.select2('val');\n },\n \n // set value\n _setValue: function(new_value) {\n var index = this._getIndex(new_value);\n if (index == -1) {\n if (this.select_data.length > 0) {\n new_value = this.select_data[0].id;\n }\n }\n this.$el.select2('val', new_value);\n },\n \n // element\n _template: function(options) {\n return '';\n }\n});\n\nreturn {\n View : View\n};\n\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/ui/ui-select.js","// from: https://raw.githubusercontent.com/umdjs/umd/master/jqueryPlugin.js\n// Uses AMD or browser globals to create a jQuery plugin.\n(function (factory) {\n if (typeof define === 'function' && define.amd) {\n //TODO: So...this turns out to be an all or nothing thing. If I load jQuery in the define below, it will\n // (of course) wipe the old jquery *and all the plugins loaded into it*. So the define below *is still\n // relying on jquery being loaded globally* in order to preserve plugins.\n define([ 'jquery' ], factory);\n } else {\n // Browser globals\n factory(jQuery);\n }\n\n}(function ( jQuery ) {\n'use_strict';\n\nvar $ = jQuery;\n\n// ============================================================================\n/**\n * Make an element with text editable: (a) when user clicks on text, a textbox/area\n * is provided for editing; (b) when enter key pressed, element's text is set and on_finish\n * is called.\n */\n$.fn.make_text_editable = function(config_dict) {\n // Get config options.\n var num_cols = (\"num_cols\" in config_dict ? config_dict.num_cols : 30),\n num_rows = (\"num_rows\" in config_dict ? config_dict.num_rows : 4),\n use_textarea = (\"use_textarea\" in config_dict ? config_dict.use_textarea : false),\n on_finish = (\"on_finish\" in config_dict ? config_dict.on_finish : null),\n help_text = (\"help_text\" in config_dict ? config_dict.help_text : null);\n\n // Add element behavior.\n var container = $(this);\n container.addClass(\"editable-text\").click(function(e) {\n // If there's already an input element, editing is active, so do nothing.\n if ($(this).children(\":input\").length > 0) {\n return;\n }\n\n container.removeClass(\"editable-text\");\n\n // Handler for setting element text.\n var set_text = function(new_text) {\n container.find(\":input\").remove();\n\n if (new_text !== \"\") {\n container.text(new_text);\n } else {\n // No text; need a line so that there is a click target.\n container.html(\" \");\n }\n container.addClass(\"editable-text\");\n\n if (on_finish) {\n on_finish(new_text);\n }\n };\n\n // Create input element(s) for editing.\n var cur_text = (\"cur_text\" in config_dict ? config_dict.cur_text : container.text() ),\n input_elt, button_elt;\n\n if (use_textarea) {\n input_elt = $(\"\")\n .attr({ rows: num_rows, cols: num_cols }).text($.trim(cur_text))\n .keyup(function(e) {\n if (e.keyCode === 27) {\n // Escape key.\n set_text(cur_text);\n }\n });\n button_elt = $(\"\").text(\"Done\").click(function() {\n set_text(input_elt.val());\n // Return false so that click does not propogate to container.\n return false;\n });\n }\n else {\n input_elt = $(\"\").attr({ value: $.trim(cur_text), size: num_cols })\n .blur(function() {\n set_text(cur_text);\n }).keyup(function(e) {\n if (e.keyCode === 27) {\n // Escape key.\n $(this).trigger(\"blur\");\n } else if (e.keyCode === 13) {\n // Enter key.\n set_text($(this).val());\n }\n\n // Do not propogate event to avoid unwanted side effects.\n e.stopPropagation();\n });\n }\n\n // Replace text with input object(s) and focus & select.\n container.text(\"\");\n container.append(input_elt);\n if (button_elt) {\n container.append(button_elt);\n }\n input_elt.focus();\n input_elt.select();\n\n // Do not propogate to elements below b/c that blurs input and prevents it from being used.\n e.stopPropagation();\n });\n\n // Add help text if there some.\n if (help_text) {\n container.attr(\"title\", help_text).tooltip();\n }\n\n return container;\n};\n\n// ============================================================================\n}));\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/ui/editable-text.js","(function (root, factory) {\n if (typeof define === 'function' && define.amd) {\n define([], factory);\n } else {\n root.faIconButton = factory();\n }\n\n}(this, function () {\n//============================================================================\n /** Returns a jQuery object containing a clickable font-awesome button.\n * options:\n * tooltipConfig : option map for bootstrap tool tip\n * classes : array of class names (will always be classed as icon-btn)\n * disabled : T/F - add the 'disabled' class?\n * title : tooltip/title string\n * target : optional href target\n * href : optional href\n * faIcon : which font awesome icon to use\n * onclick : function to call when the button is clicked\n */\n var faIconButton = function( options ){\n options = options || {};\n options.tooltipConfig = options.tooltipConfig || { placement: 'bottom' };\n\n options.classes = [ 'icon-btn' ].concat( options.classes || [] );\n if( options.disabled ){\n options.classes.push( 'disabled' );\n }\n\n var html = [\n '',\n // could go with something less specific here - like 'html'\n '',\n ''\n ].join( '' );\n var $button = $( html ).tooltip( options.tooltipConfig );\n if( _.isFunction( options.onclick ) ){\n $button.click( options.onclick );\n }\n return $button;\n };\n\n//============================================================================\n return faIconButton;\n}));\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/ui/fa-icon-button.js","define(function(){\n\n/**\n * Stringifies a number adding commas for digit grouping as per North America.\n */\nfunction commatize( number ) {\n number += ''; // Convert to string\n var rgx = /(\\d+)(\\d{3})/;\n while (rgx.test(number)) {\n number = number.replace(rgx, '$1' + ',' + '$2');\n }\n return number;\n}\n\n/**\n * Helper to determine if object is jQuery deferred.\n */\nvar is_deferred = function ( d ) {\n return ('promise' in d);\n};\n\n/**\n * Implementation of a server-state based deferred. Server is repeatedly polled, and when\n * condition is met, deferred is resolved.\n */\nvar ServerStateDeferred = Backbone.Model.extend({\n defaults: {\n ajax_settings: {},\n interval: 1000,\n success_fn: function(result) { return true; }\n },\n\n /**\n * Returns a deferred that resolves when success function returns true.\n */\n go: function() {\n var deferred = $.Deferred(),\n self = this,\n ajax_settings = self.get('ajax_settings'),\n success_fn = self.get('success_fn'),\n interval = self.get('interval'),\n _go = function() {\n $.ajax(ajax_settings).success(function(result) {\n if (success_fn(result)) {\n // Result is good, so resolve.\n deferred.resolve(result);\n }\n else {\n // Result not good, try again.\n setTimeout(_go, interval);\n }\n });\n };\n _go();\n return deferred;\n }\n});\n\n/**\n * Returns a random color in hexadecimal format that is sufficiently different from a single color\n * or set of colors.\n * @param colors a color or list of colors in the format '#RRGGBB'\n */\nvar get_random_color = function(colors) {\n // Default for colors is white.\n if (!colors) { colors = \"#ffffff\"; }\n\n // If needed, create list of colors.\n if ( typeof(colors) === \"string\" ) {\n colors = [ colors ];\n }\n\n // Convert colors to numbers.\n for (var i = 0; i < colors.length; i++) {\n colors[i] = parseInt( colors[i].slice(1), 16 );\n }\n\n // -- Perceived brightness and difference formulas are from\n // -- http://www.w3.org/WAI/ER/WD-AERT/#color-contrast\n\n // Compute perceived color brightness (based on RGB-YIQ transformation):\n var brightness = function(r, g, b) {\n return ( (r * 299) + (g * 587) + (b * 114) ) / 1000;\n };\n\n // Compute color difference:\n var difference = function(r1, g1, b1, r2, g2, b2) {\n return ( Math.max(r1, r2) - Math.min(r1, r2) ) +\n ( Math.max(g1, g2) - Math.min(g1, g2) ) +\n ( Math.max(b1, b2) - Math.min(b1, b2) );\n };\n\n // Create new random color.\n var new_color, nr, ng, nb,\n other_color, or, og, ob,\n n_brightness, o_brightness,\n diff, ok = false,\n num_tries = 0;\n do {\n // New color is never white b/c random in [0,1)\n new_color = Math.round( Math.random() * 0xffffff );\n nr = ( new_color & 0xff0000 ) >> 16;\n ng = ( new_color & 0x00ff00 ) >> 8;\n nb = new_color & 0x0000ff;\n n_brightness = brightness(nr, ng, nb);\n ok = true;\n for (i = 0; i < colors.length; i++) {\n other_color = colors[i];\n or = ( other_color & 0xff0000 ) >> 16;\n og = ( other_color & 0x00ff00 ) >> 8;\n ob = other_color & 0x0000ff;\n o_brightness = brightness(or, og, ob);\n diff = difference(nr, ng, nb, or, og, ob);\n // These thresholds may need to be adjusted. Brightness difference range is 125;\n // color difference range is 500.\n if ( ( Math.abs(n_brightness - o_brightness) < 40 ) ||\n ( diff < 200 ) ) {\n ok = false;\n break;\n }\n }\n\n num_tries++\n; } while (!ok && num_tries <= 10 );\n\n // Add 0x1000000 to left pad number with 0s.\n return '#' + ( 0x1000000 + new_color ).toString(16).substr(1,6);\n};\n\nreturn {\n commatize: commatize,\n is_deferred: is_deferred,\n ServerStateDeferred : ServerStateDeferred,\n get_random_color : get_random_color\n};\n\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/viz/trackster/util.js","define([\n \"libs/bibtex\",\n \"mvc/base-mvc\",\n \"utils/localization\"\n], function( parseBibtex, baseMVC, _l ){\n/* global Backbone */\n// we use amd here to require, but bibtex uses a global or commonjs pattern.\n// webpack will load via commonjs and plain requirejs will load as global. Check both\nparseBibtex = parseBibtex || window.BibtexParser;\n\nvar logNamespace = 'citation';\n//==============================================================================\n/** @class model for tool citations.\n * @name Citation\n * @augments Backbone.Model\n */\nvar Citation = Backbone.Model.extend( baseMVC.LoggableMixin ).extend({\n _logNamespace : logNamespace,\n\n defaults : {\n content: ''\n },\n\n initialize: function() {\n var parsed;\n try {\n // TODO: to model.parse/.validate\n parsed = parseBibtex( this.attributes.content );\n } catch( err ){\n return;\n }\n // bibtex returns successfully parsed in .entries and any parsing errors in .errors\n if( parsed.errors.length ){\n // the gen. form of these errors seems to be [ line, col, char, error message ]\n var errors = parsed.errors.reduce( function( all, current ){ return all + '; ' + current; });\n // throw new Error( 'Error parsing bibtex: ' + errors );\n this.log( 'Error parsing bibtex: ' + errors );\n }\n\n this._fields = {};\n this.entry = _.first( parsed.entries );\n if( this.entry ){\n var rawFields = this.entry.Fields;\n for( var key in rawFields ){\n var value = rawFields[ key ];\n var lowerKey = key.toLowerCase();\n this._fields[ lowerKey ] = value;\n }\n }\n },\n entryType: function() {\n return this.entry? this.entry.EntryType : undefined;\n },\n fields: function() {\n return this._fields;\n }\n});\n\n\n//==============================================================================\n/** @class Backbone collection of citations.\n */\nvar BaseCitationCollection = Backbone.Collection.extend( baseMVC.LoggableMixin ).extend( {\n _logNamespace : logNamespace,\n\n /** root api url */\n urlRoot : Galaxy.root + 'api',\n partial : true, // Assume some tools in history/workflow may not be properly annotated yet.\n model : Citation,\n} );\n\nvar HistoryCitationCollection = BaseCitationCollection.extend( {\n /** complete api url */\n url : function() {\n return this.urlRoot + '/histories/' + this.history_id + '/citations';\n }\n} );\n\nvar ToolCitationCollection = BaseCitationCollection.extend( {\n /** complete api url */\n url : function() {\n return this.urlRoot + '/tools/' + this.tool_id + '/citations';\n },\n partial : false, // If a tool has citations, assume they are complete.\n} );\n\n\n//==============================================================================\n\nreturn {\n Citation : Citation,\n HistoryCitationCollection : HistoryCitationCollection,\n ToolCitationCollection: ToolCitationCollection\n};\n\n\n});\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/citation/citation-model.js","/**\n This is the main class of the form plugin. It is referenced as 'app' in lower level modules.\n*/\ndefine( [ 'utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'mvc/form/form-section', 'mvc/form/form-data' ],\nfunction( Utils, Portlet, Ui, FormSection, FormData ) {\n return Backbone.View.extend({\n initialize: function( options ) {\n this.model = new Backbone.Model({\n initial_errors : false,\n cls : 'ui-portlet-limited',\n icon : null,\n always_refresh : true,\n message_status : 'warning'\n }).set( options );\n this.setElement( '' );\n this.render();\n },\n\n /** Update available options */\n update: function( new_model ){\n var self = this;\n this.data.matchModel( new_model, function( node, input_id ) {\n var input = self.input_list[ input_id ];\n if ( input && input.options ) {\n if ( !_.isEqual( input.options, node.options ) ) {\n input.options = node.options;\n var field = self.field_list[ input_id ];\n if ( field.update ) {\n var new_options = [];\n if ( ( [ 'data', 'data_collection', 'drill_down' ] ).indexOf( input.type ) != -1 ) {\n new_options = input.options;\n } else {\n for ( var i in node.options ) {\n var opt = node.options[ i ];\n if ( opt.length > 2 ) {\n new_options.push( { label: opt[ 0 ], value: opt[ 1 ] } );\n }\n }\n }\n field.update( new_options );\n field.trigger( 'change' );\n Galaxy.emit.debug( 'form-view::update()', 'Updating options for ' + input_id );\n }\n }\n }\n });\n },\n\n /** Set form into wait mode */\n wait: function( active ) {\n for ( var i in this.input_list ) {\n var field = this.field_list[ i ];\n var input = this.input_list[ i ];\n if ( input.is_dynamic && field.wait && field.unwait ) {\n field[ active ? 'wait' : 'unwait' ]();\n }\n }\n },\n\n /** Highlight and scroll to input element (currently only used for error notifications) */\n highlight: function ( input_id, message, silent ) {\n var input_element = this.element_list[ input_id ];\n if ( input_element ) {\n input_element.error( message || 'Please verify this parameter.' );\n this.portlet.expand();\n this.trigger( 'expand', input_id );\n if ( !silent ) {\n var $panel = this.$el.parents().filter(function() {\n return [ 'auto', 'scroll' ].indexOf( $( this ).css( 'overflow' ) ) != -1;\n }).first();\n $panel.animate( { scrollTop : $panel.scrollTop() + input_element.$el.offset().top - 120 }, 500 );\n }\n }\n },\n\n /** Highlights errors */\n errors: function( options ) {\n this.trigger( 'reset' );\n if ( options && options.errors ) {\n var error_messages = this.data.matchResponse( options.errors );\n for ( var input_id in this.element_list ) {\n var input = this.element_list[ input_id ];\n if ( error_messages[ input_id ] ) {\n this.highlight( input_id, error_messages[ input_id ], true );\n }\n }\n }\n },\n\n /** Render tool form */\n render: function() {\n var self = this;\n this.off('change');\n this.off('reset');\n // contains the dom field elements as created by the parameter factory i.e. form-parameters\n this.field_list = {};\n // contains input definitions/dictionaries as provided by the parameters to_dict() function through the api\n this.input_list = {};\n // contains the dom elements of each input element i.e. form-input which wraps the actual input field\n this.element_list = {};\n // converts the form into a json data structure\n this.data = new FormData.Manager( this );\n this._renderForm();\n this.data.create();\n this.model.get( 'initial_errors' ) && this.errors( this.model.attributes );\n // add listener which triggers on checksum change, and reset the form input wrappers\n var current_check = this.data.checksum();\n this.on( 'change', function( input_id ) {\n var input = self.input_list[ input_id ];\n if ( !input || input.refresh_on_change || self.model.get( 'always_refresh' ) ) {\n var new_check = self.data.checksum();\n if ( new_check != current_check ) {\n current_check = new_check;\n self.model.get( 'onchange' ) && self.model.get( 'onchange' )();\n }\n }\n });\n this.on('reset', function() {\n _.each( self.element_list, function( input_element ) { input_element.reset() } );\n });\n return this;\n },\n\n /** Renders/appends dom elements of the form */\n _renderForm: function() {\n $( '.tooltip' ).remove();\n var options = this.model.attributes;\n this.message = new Ui.UnescapedMessage();\n this.section = new FormSection.View( this, { inputs: options.inputs } );\n this.portlet = new Portlet.View({\n icon : options.icon,\n title : options.title,\n cls : options.cls,\n operations : options.operations,\n buttons : options.buttons,\n collapsible : options.collapsible,\n collapsed : options.collapsed,\n onchange_title : options.onchange_title\n });\n this.portlet.append( this.message.$el );\n this.portlet.append( this.section.$el );\n this.$el.empty();\n options.inputs && this.$el.append( this.portlet.$el );\n options.message && this.message.update( { persistent: true, status: options.message_status, message: options.message } );\n Galaxy.emit.debug( 'form-view::initialize()', 'Completed' );\n }\n });\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/form/form-view.js","// dependencies\ndefine(['utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc'], function(Utils, Portlet, Ui) {\n\n// ui list element\nvar View = Backbone.View.extend({\n // create portlet to keep track of selected list elements\n initialize : function(options) {\n // link this\n var self = this;\n\n // initialize options\n this.options = options;\n this.name = options.name || 'element';\n this.multiple = options.multiple || false;\n\n // create message handler\n this.message = new Ui.Message();\n\n // create portlet\n this.portlet = new Portlet.View({ cls: 'ui-portlet-section' });\n\n // create select field containing the options which can be inserted into the list\n this.select = new Ui.Select.View({ optional : options.optional });\n\n // create insert new list element button\n this.button = new Ui.ButtonIcon({\n icon : 'fa fa-sign-in',\n floating : 'left',\n tooltip : 'Insert new ' + this.name,\n onclick : function() {\n self.add({\n id : self.select.value(),\n name : self.select.text()\n });\n }\n });\n\n // build main element\n this.setElement(this._template(options));\n this.$('.ui-list-message').append(this.message.$el);\n this.$('.ui-list-portlet').append(this.portlet.$el);\n this.$('.ui-list-button').append(this.button.$el);\n this.$('.ui-list-select').append(this.select.$el);\n },\n\n /** Return/Set currently selected list elements */\n value: function(val) {\n // set new value\n if (val !== undefined) {\n this.portlet.empty();\n if ($.isArray(val)) {\n for (var i in val) {\n var v = val[i];\n var v_id = null;\n var v_name = null;\n if ($.type(v) != 'string') {\n v_id = v.id;\n v_name = v.name;\n } else {\n v_id = v_name = v;\n }\n if (v_id != null) {\n this.add({\n id : v_id,\n name : v_name\n });\n }\n }\n }\n this._refresh();\n }\n // get current value\n var lst = [];\n this.$('.ui-list-id').each(function() {\n lst.push({\n id : $(this).prop('id'),\n name : $(this).find('.ui-list-name').html()\n });\n });\n if (lst.length == 0) {\n return null;\n }\n return lst;\n },\n\n /** Add row */\n add: function(options) {\n var self = this;\n if (this.$('[id=\"' + options.id + '\"]').length === 0) {\n if (!Utils.isEmpty(options.id)) {\n var $el = $(this._templateRow({\n id : options.id,\n name : options.name\n }));\n $el.on('click', function() {\n $el.remove();\n self._refresh();\n });\n $el.on('mouseover', function() {\n $el.addClass('portlet-highlight');\n });\n $el.on('mouseout', function() {\n $el.removeClass('portlet-highlight');\n });\n this.portlet.append($el);\n this._refresh();\n } else {\n this.message.update({ message: 'Please select a valid ' + this.name + '.', status: 'danger' });\n }\n } else {\n this.message.update({ message: 'This ' + this.name + ' is already in the list.' });\n }\n },\n\n /** Update available options */\n update: function(options) {\n this.select.update(options);\n },\n\n /** Refresh view */\n _refresh: function() {\n if (this.$('.ui-list-id').length > 0) {\n !this.multiple && this.button.disable();\n this.$('.ui-list-portlet').show();\n } else {\n this.button.enable();\n this.$('.ui-list-portlet').hide();\n }\n this.options.onchange && this.options.onchange();\n },\n\n /** Main Template */\n _template: function(options) {\n return '
',\n 'Warning: This is a experimental feature. Most Galaxy tools will not annotate',\n ' citations explicitly at this time. When writing up your analysis, please manually',\n ' review your histories and find all references',\n ' that should be cited in order to completely describe your work. Also, please remember to',\n ' cite Galaxy.',\n '
'\n ], 'collection' );\n\n // use element identifier\n var subtitleTemplate = BASE_MVC.wrapTemplate([\n '
',\n '<% var countText = collection.element_count? ( collection.element_count + \" \" ) : \"\"; %>',\n '<% if( collection.collection_type === \"list\" ){ %>',\n _l( 'a list of <%- countText %>datasets' ),\n '<% } else if( collection.collection_type === \"paired\" ){ %>',\n _l( 'a pair of datasets' ),\n '<% } else if( collection.collection_type === \"list:paired\" ){ %>',\n _l( 'a list of <%- countText %>dataset pairs' ),\n '<% } else if( collection.collection_type === \"list:list\" ){ %>',\n _l( 'a list of <%- countText %>dataset lists' ),\n '<% } %>',\n '
'\n ], 'collection' );\n\n return _.extend( {}, FoldoutListItemView.prototype.templates, {\n warnings : warnings,\n titleBar : titleBarTemplate,\n subtitle : subtitleTemplate\n });\n}());\n\n\n//==============================================================================\n/** @class Read only view for DatasetCollectionElement.\n */\nvar DCEListItemView = ListItemView.extend(\n/** @lends DCEListItemView.prototype */{\n\n /** add the DCE class to the list item */\n className : ListItemView.prototype.className + \" dataset-collection-element\",\n\n /** set up */\n initialize : function( attributes ){\n if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; }\n this.log( 'DCEListItemView.initialize:', attributes );\n ListItemView.prototype.initialize.call( this, attributes );\n },\n\n // ......................................................................... misc\n /** String representation */\n toString : function(){\n var modelString = ( this.model )?( this.model + '' ):( '(no model)' );\n return 'DCEListItemView(' + modelString + ')';\n }\n});\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nDCEListItemView.prototype.templates = (function(){\n\n // use the element identifier here - since that will persist and the user will need it\n var titleBarTemplate = BASE_MVC.wrapTemplate([\n '
',\n '
',\n '<%- element.element_identifier %>',\n '
',\n '',\n '
'\n ], 'element' );\n\n return _.extend( {}, ListItemView.prototype.templates, {\n titleBar : titleBarTemplate\n });\n}());\n\n\n//==============================================================================\n/** @class Read only view for a DatasetCollectionElement that is also an DatasetAssociation\n * (a dataset contained in a dataset collection).\n */\nvar DatasetDCEListItemView = DATASET_LI.DatasetListItemView.extend(\n/** @lends DatasetDCEListItemView.prototype */{\n\n className : DATASET_LI.DatasetListItemView.prototype.className + \" dataset-collection-element\",\n\n /** set up */\n initialize : function( attributes ){\n if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; }\n this.log( 'DatasetDCEListItemView.initialize:', attributes );\n DATASET_LI.DatasetListItemView.prototype.initialize.call( this, attributes );\n },\n\n /** In this override, only get details if in the ready state.\n * Note: fetch with no 'change' event triggering to prevent automatic rendering.\n */\n _fetchModelDetails : function(){\n var view = this;\n if( view.model.inReadyState() && !view.model.hasDetails() ){\n return view.model.fetch({ silent: true });\n }\n return jQuery.when();\n },\n\n // ......................................................................... misc\n /** String representation */\n toString : function(){\n var modelString = ( this.model )?( this.model + '' ):( '(no model)' );\n return 'DatasetDCEListItemView(' + modelString + ')';\n }\n});\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nDatasetDCEListItemView.prototype.templates = (function(){\n\n // use the element identifier here and not the dataset name\n //TODO:?? can we steal the DCE titlebar?\n var titleBarTemplate = BASE_MVC.wrapTemplate([\n '
',\n '',\n '
',\n '<%- element.element_identifier %>',\n '
',\n '
'\n ], 'element' );\n\n return _.extend( {}, DATASET_LI.DatasetListItemView.prototype.templates, {\n titleBar : titleBarTemplate\n });\n}());\n\n\n//==============================================================================\n/** @class Read only view for a DatasetCollectionElement that is also a DatasetCollection\n * (a nested DC).\n */\nvar NestedDCDCEListItemView = DCListItemView.extend(\n/** @lends NestedDCDCEListItemView.prototype */{\n\n className : DCListItemView.prototype.className + \" dataset-collection-element\",\n\n /** In this override, add the state as a class for use with state-based CSS */\n _swapNewRender : function( $newRender ){\n DCListItemView.prototype._swapNewRender.call( this, $newRender );\n var state = this.model.get( 'state' ) || 'ok';\n this.$el.addClass( 'state-' + state );\n return this.$el;\n },\n\n // ......................................................................... misc\n /** String representation */\n toString : function(){\n var modelString = ( this.model )?( this.model + '' ):( '(no model)' );\n return 'NestedDCDCEListItemView(' + modelString + ')';\n }\n});\n\n\n//==============================================================================\n return {\n DCListItemView : DCListItemView,\n DCEListItemView : DCEListItemView,\n DatasetDCEListItemView : DatasetDCEListItemView,\n NestedDCDCEListItemView : NestedDCDCEListItemView\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/collection/collection-li.js","define([\n \"mvc/dataset/dataset-model\",\n \"mvc/base-mvc\",\n \"utils/localization\"\n], function( DATASET_MODEL, BASE_MVC, _l ){\n'use strict';\n\n//==============================================================================\n/*\nNotes:\n\nTerminology:\n DatasetCollection/DC : a container of datasets or nested DatasetCollections\n Element/DatasetCollectionElement/DCE : an item contained in a DatasetCollection\n HistoryDatasetCollectionAssociation/HDCA: a DatasetCollection contained in a history\n\n\nThis all seems too complex unfortunately:\n\n- Terminology collision between DatasetCollections (DCs) and Backbone Collections.\n- In the DatasetCollections API JSON, DC Elements use a 'Has A' stucture to *contain*\n either a dataset or a nested DC. This would make the hierarchy much taller. I've\n decided to merge the contained JSON with the DC element json - making the 'has a'\n relation into an 'is a' relation. This seems simpler to me and allowed a lot of\n DRY in both models and views, but may make tracking or tracing within these models\n more difficult (since DatasetCollectionElements are now *also* DatasetAssociations\n or DatasetCollections (nested)). This also violates the rule of thumb about\n favoring aggregation over inheritance.\n- Currently, there are three DatasetCollection subclasses: List, Pair, and ListPaired.\n These each should a) be usable on their own, b) be usable in the context of\n nesting within a collection model (at least in the case of ListPaired), and\n c) be usable within the context of other container models (like History or\n LibraryFolder, etc.). I've tried to separate/extract classes in order to\n handle those three situations, but it's proven difficult to do in a simple,\n readable manner.\n- Ideally, histories and libraries would inherit from the same server models as\n dataset collections do since they are (in essence) dataset collections themselves -\n making the whole nested structure simpler. This would be a large, error-prone\n refactoring and migration.\n\nMany of the classes and heirarchy are meant as extension points so, while the\nrelations and flow may be difficult to understand initially, they'll allow us to\nhandle the growth or flux dataset collection in the future (w/o actually implementing\nany YAGNI).\n\n*/\n//_________________________________________________________________________________________________ ELEMENTS\n/** @class mixin for Dataset collection elements.\n * When collection elements are passed from the API, the underlying element is\n * in a sub-object 'object' (IOW, a DCE representing an HDA will have HDA json in element.object).\n * This mixin uses the constructor and parse methods to merge that JSON with the DCE attribtues\n * effectively changing a DCE from a container to a subclass (has a --> is a).\n */\nvar DatasetCollectionElementMixin = {\n\n /** default attributes used by elements in a dataset collection */\n defaults : {\n model_class : 'DatasetCollectionElement',\n element_identifier : null,\n element_index : null,\n element_type : null\n },\n\n /** merge the attributes of the sub-object 'object' into this model */\n _mergeObject : function( attributes ){\n // if we don't preserve and correct ids here, the element id becomes the object id\n // and collision in backbone's _byId will occur and only\n _.extend( attributes, attributes.object, { element_id: attributes.id });\n delete attributes.object;\n return attributes;\n },\n\n /** override to merge this.object into this */\n constructor : function( attributes, options ){\n // console.debug( '\\t DatasetCollectionElement.constructor:', attributes, options );\n attributes = this._mergeObject( attributes );\n this.idAttribute = 'element_id';\n Backbone.Model.apply( this, arguments );\n },\n\n /** when the model is fetched, merge this.object into this */\n parse : function( response, options ){\n var attributes = response;\n attributes = this._mergeObject( attributes );\n return attributes;\n }\n};\n\n/** @class Concrete class of Generic DatasetCollectionElement */\nvar DatasetCollectionElement = Backbone.Model\n .extend( BASE_MVC.LoggableMixin )\n .extend( DatasetCollectionElementMixin )\n .extend({ _logNamespace : 'collections' });\n\n\n//==============================================================================\n/** @class Base/Abstract Backbone collection for Generic DCEs. */\nvar DCECollection = Backbone.Collection.extend( BASE_MVC.LoggableMixin ).extend(\n/** @lends DCECollection.prototype */{\n _logNamespace : 'collections',\n\n model: DatasetCollectionElement,\n\n /** String representation. */\n toString : function(){\n return ([ 'DatasetCollectionElementCollection(', this.length, ')' ].join( '' ));\n }\n});\n\n\n//==============================================================================\n/** @class Backbone model for a dataset collection element that is a dataset (HDA).\n */\nvar DatasetDCE = DATASET_MODEL.DatasetAssociation.extend( BASE_MVC.mixin( DatasetCollectionElementMixin,\n/** @lends DatasetDCE.prototype */{\n\n /** url fn */\n url : function(){\n // won't always be an hda\n if( !this.has( 'history_id' ) ){\n console.warn( 'no endpoint for non-hdas within a collection yet' );\n // (a little silly since this api endpoint *also* points at hdas)\n return Galaxy.root + 'api/datasets';\n }\n return Galaxy.root + 'api/histories/' + this.get( 'history_id' ) + '/contents/' + this.get( 'id' );\n },\n\n defaults : _.extend( {},\n DATASET_MODEL.DatasetAssociation.prototype.defaults,\n DatasetCollectionElementMixin.defaults\n ),\n\n _downloadQueryParameters : function() {\n return '?to_ext=' + this.get( 'file_ext' ) + '&hdca_id=' + this.get( 'parent_hdca_id' ) + '&element_identifier=' + this.get( 'element_identifier' );\n },\n\n // because all objects have constructors (as this hashmap would even if this next line wasn't present)\n // the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model\n // - re-apply manually for now\n /** call the mixin constructor */\n constructor : function( attributes, options ){\n this.debug( '\\t DatasetDCE.constructor:', attributes, options );\n //DATASET_MODEL.DatasetAssociation.prototype.constructor.call( this, attributes, options );\n DatasetCollectionElementMixin.constructor.call( this, attributes, options );\n },\n\n /** Does this model already contain detailed data (as opposed to just summary level data)? */\n hasDetails : function(){\n return this.elements && this.elements.length;\n },\n\n /** String representation. */\n toString : function(){\n var objStr = this.get( 'element_identifier' );\n return ([ 'DatasetDCE(', objStr, ')' ].join( '' ));\n }\n}));\n\n\n//==============================================================================\n/** @class DCECollection of DatasetDCE's (a list of datasets, a pair of datasets).\n */\nvar DatasetDCECollection = DCECollection.extend(\n/** @lends DatasetDCECollection.prototype */{\n model: DatasetDCE,\n\n /** String representation. */\n toString : function(){\n return ([ 'DatasetDCECollection(', this.length, ')' ].join( '' ));\n }\n});\n\n\n//_________________________________________________________________________________________________ COLLECTIONS\n/** @class Backbone model for Dataset Collections.\n * The DC API returns an array of JSON objects under the attribute elements.\n * This model:\n * - removes that array/attribute ('elements') from the model,\n * - creates a bbone collection (of the class defined in the 'collectionClass' attribute),\n * - passes that json onto the bbone collection\n * - caches the bbone collection in this.elements\n */\nvar DatasetCollection = Backbone.Model\n .extend( BASE_MVC.LoggableMixin )\n .extend( BASE_MVC.SearchableModelMixin )\n .extend(/** @lends DatasetCollection.prototype */{\n _logNamespace : 'collections',\n\n /** default attributes for a model */\n defaults : {\n /* 'list', 'paired', or 'list:paired' */\n collection_type : null,\n //??\n deleted : false\n },\n\n /** Which class to use for elements */\n collectionClass : DCECollection,\n\n /** set up: create elements instance var and (on changes to elements) update them */\n initialize : function( model, options ){\n this.debug( this + '(DatasetCollection).initialize:', model, options, this );\n this.elements = this._createElementsModel();\n this.on( 'change:elements', function(){\n this.log( 'change:elements' );\n //TODO: prob. better to update the collection instead of re-creating it\n this.elements = this._createElementsModel();\n });\n },\n\n /** move elements model attribute to full collection */\n _createElementsModel : function(){\n this.debug( this + '._createElementsModel', this.collectionClass, this.get( 'elements' ), this.elements );\n //TODO: same patterns as DatasetCollectionElement _createObjectModel - refactor to BASE_MVC.hasSubModel?\n var elements = this.get( 'elements' ) || [];\n this.unset( 'elements', { silent: true });\n var self = this;\n _.each(elements, function(element, index) {\n _.extend(element, {\"parent_hdca_id\": self.get(\"id\")});\n });\n this.elements = new this.collectionClass( elements );\n //this.debug( 'collectionClass:', this.collectionClass + '', this.elements );\n return this.elements;\n },\n\n // ........................................................................ common queries\n /** pass the elements back within the model json when this is serialized */\n toJSON : function(){\n var json = Backbone.Model.prototype.toJSON.call( this );\n if( this.elements ){\n json.elements = this.elements.toJSON();\n }\n return json;\n },\n\n /** Is this collection in a 'ready' state no processing (for the collection) is left\n * to do on the server.\n */\n inReadyState : function(){\n var populated = this.get( 'populated' );\n return ( this.isDeletedOrPurged() || populated );\n },\n\n //TODO:?? the following are the same interface as DatasetAssociation - can we combine?\n /** Does the DC contain any elements yet? Is a fetch() required? */\n hasDetails : function(){\n return this.elements.length !== 0;\n },\n\n /** Given the filters, what models in this.elements would be returned? */\n getVisibleContents : function( filters ){\n // filters unused for now\n return this.elements;\n },\n\n // ........................................................................ ajax\n /** override to use actual Dates objects for create/update times */\n parse : function( response, options ){\n var parsed = Backbone.Model.prototype.parse.call( this, response, options );\n if( parsed.create_time ){\n parsed.create_time = new Date( parsed.create_time );\n }\n if( parsed.update_time ){\n parsed.update_time = new Date( parsed.update_time );\n }\n return parsed;\n },\n\n /** save this dataset, _Mark_ing it as deleted (just a flag) */\n 'delete' : function( options ){\n if( this.get( 'deleted' ) ){ return jQuery.when(); }\n return this.save( { deleted: true }, options );\n },\n /** save this dataset, _Mark_ing it as undeleted */\n undelete : function( options ){\n if( !this.get( 'deleted' ) || this.get( 'purged' ) ){ return jQuery.when(); }\n return this.save( { deleted: false }, options );\n },\n\n /** Is this collection deleted or purged? */\n isDeletedOrPurged : function(){\n return ( this.get( 'deleted' ) || this.get( 'purged' ) );\n },\n\n // ........................................................................ searchable\n /** searchable attributes for collections */\n searchAttributes : [\n 'name'\n ],\n\n // ........................................................................ misc\n /** String representation */\n toString : function(){\n var idAndName = [ this.get( 'id' ), this.get( 'name' ) || this.get( 'element_identifier' ) ];\n return 'DatasetCollection(' + ( idAndName.join(',') ) + ')';\n }\n});\n\n\n//==============================================================================\n/** Model for a DatasetCollection containing datasets (non-nested).\n */\nvar ListDatasetCollection = DatasetCollection.extend(\n/** @lends ListDatasetCollection.prototype */{\n\n /** override since we know the collection will only contain datasets */\n collectionClass : DatasetDCECollection,\n\n /** String representation. */\n toString : function(){ return 'List' + DatasetCollection.prototype.toString.call( this ); }\n});\n\n\n//==============================================================================\n/** Model for a DatasetCollection containing fwd/rev datasets (a list of 2).\n */\nvar PairDatasetCollection = ListDatasetCollection.extend(\n/** @lends PairDatasetCollection.prototype */{\n\n /** String representation. */\n toString : function(){ return 'Pair' + DatasetCollection.prototype.toString.call( this ); }\n});\n\n\n//_________________________________________________________________________________________________ NESTED COLLECTIONS\n// this is where things get weird, man. Weird.\n//TODO: it might be possible to compact all the following...I think.\n//==============================================================================\n/** @class Backbone model for a Generic DatasetCollectionElement that is also a DatasetCollection\n * (a nested collection). Currently only list:paired.\n */\nvar NestedDCDCE = DatasetCollection.extend( BASE_MVC.mixin( DatasetCollectionElementMixin,\n/** @lends NestedDCDCE.prototype */{\n\n // because all objects have constructors (as this hashmap would even if this next line wasn't present)\n // the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model\n // - re-apply manually it now\n /** call the mixin constructor */\n constructor : function( attributes, options ){\n this.debug( '\\t NestedDCDCE.constructor:', attributes, options );\n DatasetCollectionElementMixin.constructor.call( this, attributes, options );\n },\n\n /** String representation. */\n toString : function(){\n var objStr = ( this.object )?( '' + this.object ):( this.get( 'element_identifier' ) );\n return ([ 'NestedDCDCE(', objStr, ')' ].join( '' ));\n }\n}));\n\n\n//==============================================================================\n/** @class Backbone collection containing Generic NestedDCDCE's (nested dataset collections).\n */\nvar NestedDCDCECollection = DCECollection.extend(\n/** @lends NestedDCDCECollection.prototype */{\n\n /** This is a collection of nested collections */\n model: NestedDCDCE,\n\n /** String representation. */\n toString : function(){\n return ([ 'NestedDCDCECollection(', this.length, ')' ].join( '' ));\n }\n});\n\n\n//==============================================================================\n/** @class Backbone model for a paired dataset collection within a list:paired dataset collection.\n */\nvar NestedPairDCDCE = PairDatasetCollection.extend( BASE_MVC.mixin( DatasetCollectionElementMixin,\n/** @lends NestedPairDCDCE.prototype */{\n//TODO:?? possibly rename to NestedDatasetCollection?\n\n // because all objects have constructors (as this hashmap would even if this next line wasn't present)\n // the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model\n // - re-apply manually it now\n /** This is both a collection and a collection element - call the constructor */\n constructor : function( attributes, options ){\n this.debug( '\\t NestedPairDCDCE.constructor:', attributes, options );\n //DatasetCollection.constructor.call( this, attributes, options );\n DatasetCollectionElementMixin.constructor.call( this, attributes, options );\n },\n\n /** String representation. */\n toString : function(){\n var objStr = ( this.object )?( '' + this.object ):( this.get( 'element_identifier' ) );\n return ([ 'NestedPairDCDCE(', objStr, ')' ].join( '' ));\n }\n}));\n\n\n//==============================================================================\n/** @class Backbone collection for a backbone collection containing paired dataset collections.\n */\nvar NestedPairDCDCECollection = NestedDCDCECollection.extend(\n/** @lends PairDCDCECollection.prototype */{\n\n /** We know this collection is composed of only nested pair collections */\n model: NestedPairDCDCE,\n\n /** String representation. */\n toString : function(){\n return ([ 'NestedPairDCDCECollection(', this.length, ')' ].join( '' ));\n }\n});\n\n\n//==============================================================================\n/** @class Backbone Model for a DatasetCollection (list) that contains DatasetCollections (pairs).\n */\nvar ListPairedDatasetCollection = DatasetCollection.extend(\n/** @lends ListPairedDatasetCollection.prototype */{\n\n /** list:paired is the only collection that itself contains collections */\n collectionClass : NestedPairDCDCECollection,\n\n /** String representation. */\n toString : function(){\n return ([ 'ListPairedDatasetCollection(', this.get( 'name' ), ')' ].join( '' ));\n }\n});\n\n\n//==============================================================================\n/** @class Backbone model for a list dataset collection within a list:list dataset collection. */\nvar NestedListDCDCE = ListDatasetCollection.extend( BASE_MVC.mixin( DatasetCollectionElementMixin,\n/** @lends NestedListDCDCE.prototype */{\n\n /** This is both a collection and a collection element - call the constructor */\n constructor : function( attributes, options ){\n this.debug( '\\t NestedListDCDCE.constructor:', attributes, options );\n DatasetCollectionElementMixin.constructor.call( this, attributes, options );\n },\n\n /** String representation. */\n toString : function(){\n var objStr = ( this.object )?( '' + this.object ):( this.get( 'element_identifier' ) );\n return ([ 'NestedListDCDCE(', objStr, ')' ].join( '' ));\n }\n}));\n\n\n//==============================================================================\n/** @class Backbone collection containing list dataset collections. */\nvar NestedListDCDCECollection = NestedDCDCECollection.extend({\n\n /** We know this collection is composed of only nested pair collections */\n model: NestedListDCDCE,\n\n /** String representation. */\n toString : function(){\n return ([ 'NestedListDCDCECollection(', this.length, ')' ].join( '' ));\n }\n});\n\n\n//==============================================================================\n/** @class Backbone Model for a DatasetCollection (list) that contains other lists. */\nvar ListOfListsDatasetCollection = DatasetCollection.extend({\n\n /** list:paired is the only collection that itself contains collections */\n collectionClass : NestedListDCDCECollection,\n\n /** String representation. */\n toString : function(){\n return ([ 'ListOfListsDatasetCollection(', this.get( 'name' ), ')' ].join( '' ));\n }\n});\n\n\n//==============================================================================\n return {\n ListDatasetCollection : ListDatasetCollection,\n PairDatasetCollection : PairDatasetCollection,\n ListPairedDatasetCollection : ListPairedDatasetCollection,\n ListOfListsDatasetCollection: ListOfListsDatasetCollection\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/collection/collection-model.js","\ndefine([\n \"mvc/history/hdca-model\",\n \"mvc/dataset/states\",\n \"mvc/base-mvc\",\n \"mvc/collection/base-creator\",\n \"mvc/ui/ui-modal\",\n \"utils/natural-sort\",\n \"utils/localization\",\n \"ui/hoverhighlight\"\n], function( HDCA, STATES, BASE_MVC, baseCreator, UI_MODAL, naturalSort, _l ){\n\n'use strict';\n\nvar logNamespace = 'collections';\n\n/*==============================================================================\nTODO:\n use proper Element model and not just json\n straighten out createFn, collection.createHDCA\n possibly stop using modals for this\n It would be neat to do a drag and drop\n\n==============================================================================*/\n/** A view for both DatasetDCEs and NestedDCDCEs\n * (things that implement collection-model:DatasetCollectionElementMixin)\n */\nvar DatasetCollectionElementView = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend({\n _logNamespace : logNamespace,\n\n//TODO: use proper class (DatasetDCE or NestedDCDCE (or the union of both))\n tagName : 'li',\n className : 'collection-element',\n\n initialize : function( attributes ){\n this.element = attributes.element || {};\n this.selected = attributes.selected || false;\n },\n\n render : function(){\n this.$el\n .attr( 'data-element-id', this.element.id )\n .attr( 'draggable', true )\n .html( this.template({ element: this.element }) );\n if( this.selected ){\n this.$el.addClass( 'selected' );\n }\n return this;\n },\n\n //TODO: lots of unused space in the element - possibly load details and display them horiz.\n template : _.template([\n '',\n '<%- element.name %>',\n '',\n '',\n ].join('')),\n\n /** select this element and pub */\n select : function( toggle ){\n this.$el.toggleClass( 'selected', toggle );\n this.trigger( 'select', {\n source : this,\n selected : this.$el.hasClass( 'selected' )\n });\n },\n\n /** animate the removal of this element and pub */\n discard : function(){\n var view = this,\n parentWidth = this.$el.parent().width();\n this.$el.animate({ 'margin-right' : parentWidth }, 'fast', function(){\n view.trigger( 'discard', {\n source : view\n });\n view.destroy();\n });\n },\n\n /** remove the DOM and any listeners */\n destroy : function(){\n this.off();\n this.$el.remove();\n },\n\n events : {\n 'click' : '_click',\n 'click .name' : '_clickName',\n 'click .discard': '_clickDiscard',\n\n 'dragstart' : '_dragstart',\n 'dragend' : '_dragend',\n 'dragover' : '_sendToParent',\n 'drop' : '_sendToParent'\n },\n\n /** select when the li is clicked */\n _click : function( ev ){\n ev.stopPropagation();\n this.select( ev );\n },\n\n /** rename a pair when the name is clicked */\n _clickName : function( ev ){\n ev.stopPropagation();\n ev.preventDefault();\n var promptString = [ _l( 'Enter a new name for the element' ), ':\\n(',\n _l( 'Note that changing the name here will not rename the dataset' ), ')' ].join( '' ),\n response = prompt( _l( 'Enter a new name for the element' ) + ':', this.element.name );\n if( response ){\n this.element.name = response;\n this.render();\n }\n //TODO: cancelling with ESC leads to closure of the creator...\n },\n\n /** discard when the discard button is clicked */\n _clickDiscard : function( ev ){\n ev.stopPropagation();\n this.discard();\n },\n\n /** dragging pairs for re-ordering */\n _dragstart : function( ev ){\n if( ev.originalEvent ){ ev = ev.originalEvent; }\n ev.dataTransfer.effectAllowed = 'move';\n ev.dataTransfer.setData( 'text/plain', JSON.stringify( this.element ) );\n\n this.$el.addClass( 'dragging' );\n this.$el.parent().trigger( 'collection-element.dragstart', [ this ] );\n },\n\n /** dragging for re-ordering */\n _dragend : function( ev ){\n this.$el.removeClass( 'dragging' );\n this.$el.parent().trigger( 'collection-element.dragend', [ this ] );\n },\n\n /** manually bubble up an event to the parent/container */\n _sendToParent : function( ev ){\n this.$el.parent().trigger( ev );\n },\n\n /** string rep */\n toString : function(){\n return 'DatasetCollectionElementView()';\n }\n});\n\n\n// ============================================================================\n/** An interface for building collections.\n */\nvar ListCollectionCreator = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend( baseCreator.CollectionCreatorMixin ).extend({\n _logNamespace : logNamespace,\n\n /** the class used to display individual elements */\n elementViewClass : DatasetCollectionElementView,\n /** the class this creator will create and save */\n collectionClass : HDCA.HistoryListDatasetCollection,\n className : 'list-collection-creator collection-creator flex-row-container',\n\n /** minimum number of valid elements to start with in order to build a collection of this type */\n minElements : 1,\n\n defaultAttributes : {\n//TODO: remove - use new collectionClass().save()\n /** takes elements and creates the proper collection - returns a promise */\n creationFn : function(){ throw new TypeError( 'no creation fn for creator' ); },\n /** fn to call when the collection is created (scoped to this) */\n oncreate : function(){},\n /** fn to call when the cancel button is clicked (scoped to this) - if falsy, no btn is displayed */\n oncancel : function(){},\n /** distance from list edge to begin autoscrolling list */\n autoscrollDist : 24,\n /** Color passed to hoverhighlight */\n highlightClr : 'rgba( 64, 255, 255, 1.0 )'\n },\n\n footerSettings : {\n '.hide-originals': 'hideOriginals'\n },\n\n /** set up initial options, instance vars, behaviors */\n initialize : function( attributes ){\n this.metric( 'ListCollectionCreator.initialize', attributes );\n var creator = this;\n _.each( this.defaultAttributes, function( value, key ){\n value = attributes[ key ] || value;\n creator[ key ] = value;\n });\n\n /** unordered, original list - cache to allow reversal */\n creator.initialElements = attributes.elements || [];\n\n this._setUpCommonSettings( attributes );\n this._instanceSetUp();\n this._elementsSetUp();\n this._setUpBehaviors();\n },\n\n /** set up instance vars */\n _instanceSetUp : function(){\n /** Ids of elements that have been selected by the user - to preserve over renders */\n this.selectedIds = {};\n /** DOM elements currently being dragged */\n this.$dragging = null;\n /** Used for blocking UI events during ajax/operations (don't post twice) */\n this.blocking = false;\n },\n\n // ------------------------------------------------------------------------ process raw list\n /** set up main data */\n _elementsSetUp : function(){\n //this.debug( '-- _dataSetUp' );\n /** a list of invalid elements and the reasons they aren't valid */\n this.invalidElements = [];\n//TODO: handle fundamental problem of syncing DOM, views, and list here\n /** data for list in progress */\n this.workingElements = [];\n /** views for workingElements */\n this.elementViews = [];\n\n // copy initial list, sort, add ids if needed\n this.workingElements = this.initialElements.slice( 0 );\n this._ensureElementIds();\n this._validateElements();\n this._mangleDuplicateNames();\n this._sortElements();\n },\n\n /** add ids to dataset objs in initial list if none */\n _ensureElementIds : function(){\n this.workingElements.forEach( function( element ){\n if( !element.hasOwnProperty( 'id' ) ){\n element.id = _.uniqueId();\n }\n });\n return this.workingElements;\n },\n\n /** separate working list into valid and invalid elements for this collection */\n _validateElements : function(){\n var creator = this,\n existingNames = {};\n creator.invalidElements = [];\n\n this.workingElements = this.workingElements.filter( function( element ){\n var problem = creator._isElementInvalid( element );\n if( problem ){\n creator.invalidElements.push({\n element : element,\n text : problem\n });\n }\n return !problem;\n });\n return this.workingElements;\n },\n\n /** describe what is wrong with a particular element if anything */\n _isElementInvalid : function( element ){\n if( element.history_content_type !== 'dataset' ){\n return _l( \"is not a dataset\" );\n }\n var validState = element.state === STATES.OK || _.contains( STATES.NOT_READY_STATES, element.state );\n if( ! validState ){\n return _l( \"has errored, is paused, or is not accessible\" );\n }\n if( element.deleted || element.purged ){\n return _l( \"has been deleted or purged\" );\n }\n return null;\n },\n\n /** mangle duplicate names using a mac-like '(counter)' addition to any duplicates */\n _mangleDuplicateNames : function(){\n var SAFETY = 900,\n counter = 1,\n existingNames = {};\n this.workingElements.forEach( function( element ){\n var currName = element.name;\n while( existingNames.hasOwnProperty( currName ) ){\n currName = element.name + ' (' + counter + ')';\n counter += 1;\n if( counter >= SAFETY ){\n throw new Error( 'Safety hit in while loop - thats impressive' );\n }\n }\n element.name = currName;\n existingNames[ element.name ] = true;\n });\n },\n\n /** sort a list of elements */\n _sortElements : function( list ){\n // // currently only natural sort by name\n // this.workingElements.sort( function( a, b ){ return naturalSort( a.name, b.name ); });\n // return this.workingElements;\n },\n\n // ------------------------------------------------------------------------ rendering\n // templates : ListCollectionCreator.templates,\n /** render the entire interface */\n render : function( speed, callback ){\n //this.debug( '-- _render' );\n if( this.workingElements.length < this.minElements ){\n return this._renderInvalid( speed, callback );\n }\n\n this.$el.empty().html( this.templates.main() );\n this._renderHeader( speed );\n this._renderMiddle( speed );\n this._renderFooter( speed );\n this._addPluginComponents();\n this.$( '.collection-name' ).focus();\n this.trigger( 'rendered', this );\n return this;\n },\n\n\n /** render a simplified interface aimed at telling the user why they can't move forward */\n _renderInvalid : function( speed, callback ){\n //this.debug( '-- _render' );\n this.$el.empty().html( this.templates.invalidInitial({\n problems: this.invalidElements,\n elements: this.workingElements,\n }));\n if( typeof this.oncancel === 'function' ){\n this.$( '.cancel-create.btn' ).show();\n }\n this.trigger( 'rendered', this );\n return this;\n },\n\n /** render the header section */\n _renderHeader : function( speed, callback ){\n var $header = this.$( '.header' ).empty().html( this.templates.header() )\n .find( '.help-content' ).prepend( $( this.templates.helpContent() ) );\n //TODO: should only show once despite calling _renderHeader again\n if( this.invalidElements.length ){\n this._invalidElementsAlert();\n }\n return $header;\n },\n\n /** render the middle including the elements */\n _renderMiddle : function( speed, callback ){\n var $middle = this.$( '.middle' ).empty().html( this.templates.middle() );\n this._renderList( speed );\n return $middle;\n },\n\n /** add any jQuery/bootstrap/custom plugins to elements rendered */\n _addPluginComponents : function(){\n this.$( '.help-content i' ).hoverhighlight( '.collection-creator', this.highlightClr );\n },\n\n /** build and show an alert describing any elements that could not be included due to problems */\n _invalidElementsAlert : function(){\n this._showAlert( this.templates.invalidElements({ problems: this.invalidElements }), 'alert-warning' );\n },\n\n _disableNameAndCreate : function( disable ){\n disable = !_.isUndefined( disable )? disable : true;\n if( disable ){\n this.$( '.collection-name' ).prop( 'disabled', true );\n this.$( '.create-collection' ).toggleClass( 'disabled', true );\n // } else {\n // this.$( '.collection-name' ).prop( 'disabled', false );\n // this.$( '.create-collection' ).removeClass( 'disable' );\n }\n },\n\n // ------------------------------------------------------------------------ rendering elements\n /** conv. to the main list display DOM */\n $list : function(){\n return this.$( '.collection-elements' );\n },\n\n /** show or hide the clear selected control based on the num of selected elements */\n _renderClearSelected : function(){\n if( _.size( this.selectedIds ) ){\n this.$( '.collection-elements-controls > .clear-selected' ).show();\n } else {\n this.$( '.collection-elements-controls > .clear-selected' ).hide();\n }\n },\n\n /** render the elements in order (or a warning if no elements found) */\n _renderList : function( speed, callback ){\n //this.debug( '-- _renderList' );\n var creator = this,\n $tmp = jQuery( '' ),\n $list = creator.$list();\n\n _.each( this.elementViews, function( view ){\n view.destroy();\n creator.removeElementView( view );\n });\n\n // if( !this.workingElements.length ){\n // this._renderNoValidElements();\n // return;\n // }\n\n creator.workingElements.forEach( function( element ){\n var elementView = creator._createElementView( element );\n $tmp.append( elementView.$el );\n });\n\n creator._renderClearSelected();\n $list.empty().append( $tmp.children() );\n _.invoke( creator.elementViews, 'render' );\n\n if( $list.height() > $list.css( 'max-height' ) ){\n $list.css( 'border-width', '1px 0px 1px 0px' );\n } else {\n $list.css( 'border-width', '0px' );\n }\n },\n\n /** create an element view, cache in elementViews, set up listeners, and return */\n _createElementView : function( element ){\n var elementView = new this.elementViewClass({\n//TODO: use non-generic class or not all\n // model : COLLECTION.DatasetDCE( element )\n element : element,\n selected: _.has( this.selectedIds, element.id )\n });\n this.elementViews.push( elementView );\n this._listenToElementView( elementView );\n return elementView;\n },\n\n /** listen to any element events */\n _listenToElementView : function( view ){\n var creator = this;\n creator.listenTo( view, {\n select : function( data ){\n var element = data.source.element;\n if( data.selected ){\n creator.selectedIds[ element.id ] = true;\n } else {\n delete creator.selectedIds[ element.id ];\n }\n creator.trigger( 'elements:select', data );\n },\n discard : function( data ){\n creator.trigger( 'elements:discard', data );\n }\n });\n },\n\n /** add a new element view based on the json in element */\n addElementView : function( element ){\n//TODO: workingElements is sorted, add element in appropo index\n // add element, sort elements, find element index\n // var view = this._createElementView( element );\n // return view;\n },\n\n /** stop listening to view and remove from caches */\n removeElementView : function( view ){\n delete this.selectedIds[ view.element.id ];\n this._renderClearSelected();\n\n this.elementViews = _.without( this.elementViews, view );\n this.stopListening( view );\n },\n\n /** render a message in the list that no elements remain to create a collection */\n _renderNoElementsLeft : function(){\n this._disableNameAndCreate( true );\n this.$( '.collection-elements' ).append( this.templates.noElementsLeft() );\n },\n\n // /** render a message in the list that no valid elements were found to create a collection */\n // _renderNoValidElements : function(){\n // this._disableNameAndCreate( true );\n // this.$( '.collection-elements' ).append( this.templates.noValidElements() );\n // },\n\n // ------------------------------------------------------------------------ API\n /** convert element into JSON compatible with the collections API */\n _elementToJSON : function( element ){\n // return element.toJSON();\n return element;\n },\n\n /** create the collection via the API\n * @returns {jQuery.xhr Object} the jquery ajax request\n */\n createList : function( name ){\n if( !this.workingElements.length ){\n var message = _l( 'No valid elements for final list' ) + '. ';\n message += '' + _l( 'Cancel' ) + ' ';\n message += _l( 'or' );\n message += ' ' + _l( 'start over' ) + '.';\n this._showAlert( message );\n return;\n }\n\n var creator = this,\n elements = this.workingElements.map( function( element ){\n return creator._elementToJSON( element );\n });\n\n creator.blocking = true;\n return creator.creationFn( elements, name, creator.hideOriginals )\n .always( function(){\n creator.blocking = false;\n })\n .fail( function( xhr, status, message ){\n creator.trigger( 'error', {\n xhr : xhr,\n status : status,\n message : _l( 'An error occurred while creating this collection' )\n });\n })\n .done( function( response, message, xhr ){\n creator.trigger( 'collection:created', response, message, xhr );\n creator.metric( 'collection:created', response );\n if( typeof creator.oncreate === 'function' ){\n creator.oncreate.call( this, response, message, xhr );\n }\n });\n },\n\n // ------------------------------------------------------------------------ events\n /** set up event handlers on self */\n _setUpBehaviors : function(){\n this.on( 'error', this._errorHandler );\n\n this.once( 'rendered', function(){\n this.trigger( 'rendered:initial', this );\n });\n\n this.on( 'elements:select', function( data ){\n this._renderClearSelected();\n });\n\n this.on( 'elements:discard', function( data ){\n var element = data.source.element;\n this.removeElementView( data.source );\n\n this.workingElements = _.without( this.workingElements, element );\n if( !this.workingElements.length ){\n this._renderNoElementsLeft();\n }\n });\n\n //this.on( 'all', function(){\n // this.info( arguments );\n //});\n return this;\n },\n\n /** handle errors with feedback and details to the user (if available) */\n _errorHandler : function( data ){\n this.error( data );\n\n var creator = this;\n content = data.message || _l( 'An error occurred' );\n if( data.xhr ){\n var xhr = data.xhr,\n message = data.message;\n if( xhr.readyState === 0 && xhr.status === 0 ){\n content += ': ' + _l( 'Galaxy could not be reached and may be updating.' ) +\n _l( ' Try again in a few minutes.' );\n } else if( xhr.responseJSON ){\n content += ':
' + JSON.stringify( xhr.responseJSON ) + '
';\n } else {\n content += ': ' + message;\n }\n }\n creator._showAlert( content, 'alert-danger' );\n },\n\n events : {\n // header\n 'click .more-help' : '_clickMoreHelp',\n 'click .less-help' : '_clickLessHelp',\n 'click .main-help' : '_toggleHelp',\n 'click .header .alert button' : '_hideAlert',\n\n 'click .reset' : 'reset',\n 'click .clear-selected' : 'clearSelectedElements',\n\n // elements - selection\n 'click .collection-elements' : 'clearSelectedElements',\n\n // elements - drop target\n // 'dragenter .collection-elements': '_dragenterElements',\n // 'dragleave .collection-elements': '_dragleaveElements',\n 'dragover .collection-elements' : '_dragoverElements',\n 'drop .collection-elements' : '_dropElements',\n\n // these bubble up from the elements as custom events\n 'collection-element.dragstart .collection-elements' : '_elementDragstart',\n 'collection-element.dragend .collection-elements' : '_elementDragend',\n\n // footer\n 'change .collection-name' : '_changeName',\n 'keydown .collection-name' : '_nameCheckForEnter',\n 'change .hide-originals' : '_changeHideOriginals',\n 'click .cancel-create' : '_cancelCreate',\n 'click .create-collection' : '_clickCreate'//,\n },\n\n // ........................................................................ elements\n /** reset all data to the initial state */\n reset : function(){\n this._instanceSetUp();\n this._elementsSetUp();\n this.render();\n },\n\n /** deselect all elements */\n clearSelectedElements : function( ev ){\n this.$( '.collection-elements .collection-element' ).removeClass( 'selected' );\n this.$( '.collection-elements-controls > .clear-selected' ).hide();\n },\n\n //_dragenterElements : function( ev ){\n // //this.debug( '_dragenterElements:', ev );\n //},\n//TODO: if selected are dragged out of the list area - remove the placeholder - cuz it won't work anyway\n // _dragleaveElements : function( ev ){\n // //this.debug( '_dragleaveElements:', ev );\n // },\n\n /** track the mouse drag over the list adding a placeholder to show where the drop would occur */\n _dragoverElements : function( ev ){\n //this.debug( '_dragoverElements:', ev );\n ev.preventDefault();\n\n var $list = this.$list();\n this._checkForAutoscroll( $list, ev.originalEvent.clientY );\n var $nearest = this._getNearestElement( ev.originalEvent.clientY );\n\n //TODO: no need to re-create - move instead\n this.$( '.element-drop-placeholder' ).remove();\n var $placeholder = $( '' );\n if( !$nearest.length ){\n $list.append( $placeholder );\n } else {\n $nearest.before( $placeholder );\n }\n },\n\n /** If the mouse is near enough to the list's top or bottom, scroll the list */\n _checkForAutoscroll : function( $element, y ){\n var AUTOSCROLL_SPEED = 2,\n offset = $element.offset(),\n scrollTop = $element.scrollTop(),\n upperDist = y - offset.top,\n lowerDist = ( offset.top + $element.outerHeight() ) - y;\n if( upperDist >= 0 && upperDist < this.autoscrollDist ){\n $element.scrollTop( scrollTop - AUTOSCROLL_SPEED );\n } else if( lowerDist >= 0 && lowerDist < this.autoscrollDist ){\n $element.scrollTop( scrollTop + AUTOSCROLL_SPEED );\n }\n },\n\n /** get the nearest element based on the mouse's Y coordinate.\n * If the y is at the end of the list, return an empty jQuery object.\n */\n _getNearestElement : function( y ){\n var WIGGLE = 4,\n lis = this.$( '.collection-elements li.collection-element' ).toArray();\n for( var i=0; i y && top - halfHeight < y ){\n return $li;\n }\n }\n return $();\n },\n\n /** drop (dragged/selected elements) onto the list, re-ordering the internal list */\n _dropElements : function( ev ){\n if( ev.originalEvent ){ ev = ev.originalEvent; }\n // both required for firefox\n ev.preventDefault();\n ev.dataTransfer.dropEffect = 'move';\n\n // insert before the nearest element or after the last.\n var $nearest = this._getNearestElement( ev.clientY );\n if( $nearest.length ){\n this.$dragging.insertBefore( $nearest );\n } else {\n // no nearest before - insert after last element\n this.$dragging.insertAfter( this.$( '.collection-elements .collection-element' ).last() );\n }\n // resync the creator's list based on the new DOM order\n this._syncOrderToDom();\n return false;\n },\n\n /** resync the creator's list of elements based on the DOM order */\n _syncOrderToDom : function(){\n var creator = this,\n newElements = [];\n //TODO: doesn't seem wise to use the dom to store these - can't we sync another way?\n this.$( '.collection-elements .collection-element' ).each( function(){\n var id = $( this ).attr( 'data-element-id' ),\n element = _.findWhere( creator.workingElements, { id: id });\n if( element ){\n newElements.push( element );\n } else {\n console.error( 'missing element: ', id );\n }\n });\n this.workingElements = newElements;\n this._renderList();\n },\n\n /** drag communication with element sub-views: dragstart */\n _elementDragstart : function( ev, element ){\n // auto select the element causing the event and move all selected\n element.select( true );\n this.$dragging = this.$( '.collection-elements .collection-element.selected' );\n },\n\n /** drag communication with element sub-views: dragend - remove the placeholder */\n _elementDragend : function( ev, element ){\n $( '.element-drop-placeholder' ).remove();\n this.$dragging = null;\n },\n\n // ------------------------------------------------------------------------ templates\n //TODO: move to require text plugin and load these as text\n //TODO: underscore currently unnecc. bc no vars are used\n //TODO: better way of localizing text-nodes in long strings\n /** underscore template fns attached to class */\n templates : _.extend({}, baseCreator.CollectionCreatorMixin._creatorTemplates, {\n\n /** the header (not including help text) */\n header : _.template([\n '
'\n ].join('')),\n\n /** help content */\n helpContent : _.template([\n '
', _l([\n 'Collections of datasets are permanent, ordered lists of datasets that can be passed to tools and ',\n 'workflows in order to have analyses done on each member of the entire group. This interface allows ',\n 'you to create a collection and re-order the final collection.'\n ].join( '' )), '
',\n '
',\n '
', _l([\n 'Rename elements in the list by clicking on ',\n 'the existing name.'\n ].join( '' )), '
',\n '
', _l([\n 'Discard elements from the final created list by clicking on the ',\n '\"Discard\" button.'\n ].join( '' )), '
',\n '
', _l([\n 'Reorder the list by clicking and dragging elements. Select multiple elements by clicking on ',\n 'them and you can then move those selected by dragging the ',\n 'entire group. Deselect them by clicking them again or by clicking the ',\n 'the \"Clear selected\" link.'\n ].join( '' )), '
',\n '
', _l([\n 'Click the \"Start over\" link to begin again as if you had just opened ',\n 'the interface.'\n ].join( '' )), '
',\n '
', _l([\n 'Click the \"Cancel\" button to exit the interface.'\n ].join( '' )), '
',\n '
',\n '
', _l([\n 'Once your collection is complete, enter a name and ',\n 'click \"Create list\".'\n ].join( '' )), '
'\n ].join('')),\n\n /** shown in list when all elements are discarded */\n invalidElements : _.template([\n _l( 'The following selections could not be included due to problems:' ),\n '
<% _.each( problems, function( problem ){ %>',\n '
<%- problem.element.name %>: <%- problem.text %>
',\n '<% }); %>
'\n ].join('')),\n\n /** shown in list when all elements are discarded */\n noElementsLeft : _.template([\n '
'\n ].join('')),\n\n /** a simplified page communicating what went wrong and why the user needs to reselect something else */\n invalidInitial : _.template([\n '
',\n '
',\n '',\n '<% if( _.size( problems ) ){ %>',\n _l( 'The following selections could not be included due to problems' ), ':',\n '
<% _.each( problems, function( problem ){ %>',\n '
<%- problem.element.name %>: <%- problem.text %>
',\n '<% }); %>
',\n '<% } else if( _.size( elements ) < 1 ){ %>',\n _l( 'No datasets were selected' ), '.',\n '<% } %>',\n ' ',\n _l( 'At least one element is needed for the collection' ), '. ',\n _l( 'You may need to ' ),\n '', _l( 'cancel' ), ' ',\n _l( 'and reselect new elements' ), '.',\n '',\n '
',\n '
',\n ''\n ].join('')),\n }),\n\n // ------------------------------------------------------------------------ misc\n /** string rep */\n toString : function(){ return 'ListCollectionCreator'; }\n});\n\n\n\n//=============================================================================\n/** Create a modal and load its body with the given CreatorClass creator type\n * @returns {Deferred} resolved when creator has built a collection.\n */\nvar collectionCreatorModal = function _collectionCreatorModal( elements, options, CreatorClass ){\n\n var deferred = jQuery.Deferred(),\n modal = Galaxy.modal || ( new UI_MODAL.View() ),\n creator;\n\n options = _.defaults( options || {}, {\n elements : elements,\n oncancel : function(){\n modal.hide();\n deferred.reject( 'cancelled' );\n },\n oncreate : function( creator, response ){\n modal.hide();\n deferred.resolve( response );\n }\n });\n\n creator = new CreatorClass( options );\n modal.show({\n title : options.title || _l( 'Create a collection' ),\n body : creator.$el,\n width : '80%',\n height : '100%',\n closing_events: true\n });\n creator.render();\n window._collectionCreator = creator;\n\n //TODO: remove modal header\n return deferred;\n};\n\n/** List collection flavor of collectionCreatorModal. */\nvar listCollectionCreatorModal = function _listCollectionCreatorModal( elements, options ){\n options = options || {};\n options.title = _l( 'Create a collection from a list of datasets' );\n return collectionCreatorModal( elements, options, ListCollectionCreator );\n};\n\n\n//==============================================================================\n/** Use a modal to create a list collection, then add it to the given history contents.\n * @returns {Deferred} resolved when the collection is added to the history.\n */\nfunction createListCollection( contents, defaultHideSourceItems ){\n var elements = contents.toJSON(),\n promise = listCollectionCreatorModal( elements, {\n defaultHideSourceItems: defaultHideSourceItems,\n creationFn : function( elements, name, hideSourceItems ){\n elements = elements.map( function( element ){\n return {\n id : element.id,\n name : element.name,\n //TODO: this allows for list:list even if the filter above does not - reconcile\n src : ( element.history_content_type === 'dataset'? 'hda' : 'hdca' )\n };\n });\n return contents.createHDCA( elements, 'list', name, hideSourceItems );\n }\n });\n return promise;\n}\n\n//==============================================================================\n return {\n DatasetCollectionElementView: DatasetCollectionElementView,\n ListCollectionCreator : ListCollectionCreator,\n\n collectionCreatorModal : collectionCreatorModal,\n listCollectionCreatorModal : listCollectionCreatorModal,\n createListCollection : createListCollection\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/collection/list-collection-creator.js","define([\n \"mvc/list/list-item\",\n \"mvc/dataset/states\",\n \"ui/fa-icon-button\",\n \"mvc/base-mvc\",\n \"utils/localization\"\n], function( LIST_ITEM, STATES, faIconButton, BASE_MVC, _l ){\n'use strict';\n\nvar logNamespace = 'dataset';\n/*==============================================================================\nTODO:\n straighten out state rendering and templates used\n inaccessible/STATES.NOT_VIEWABLE is a special case\n simplify button rendering\n\n==============================================================================*/\nvar _super = LIST_ITEM.ListItemView;\n/** @class Read only list view for either LDDAs, HDAs, or HDADCEs.\n * Roughly, any DatasetInstance (and not a raw Dataset).\n */\nvar DatasetListItemView = _super.extend(\n/** @lends DatasetListItemView.prototype */{\n _logNamespace : logNamespace,\n\n className : _super.prototype.className + \" dataset\",\n //TODO:?? doesn't exactly match an hda's type_id\n id : function(){\n return [ 'dataset', this.model.get( 'id' ) ].join( '-' );\n },\n\n /** Set up: instance vars, options, and event handlers */\n initialize : function( attributes ){\n if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; }\n this.log( this + '.initialize:', attributes );\n _super.prototype.initialize.call( this, attributes );\n\n /** where should pages from links be displayed? (default to new tab/window) */\n this.linkTarget = attributes.linkTarget || '_blank';\n },\n\n /** event listeners */\n _setUpListeners : function(){\n _super.prototype._setUpListeners.call( this );\n var self = this;\n\n // re-rendering on any model changes\n return self.listenTo( self.model, {\n 'change': function( model ){\n // if the model moved into the ready state and is expanded without details, fetch those details now\n if( self.model.changedAttributes().state &&\n self.model.inReadyState() &&\n self.expanded &&\n !self.model.hasDetails() ){\n // normally, will render automatically (due to fetch -> change),\n // but! setting_metadata sometimes doesn't cause any other changes besides state\n // so, not rendering causes it to seem frozen in setting_metadata state\n self.model.fetch({ silent : true })\n .done( function(){ self.render(); });\n } else {\n if( _.has( model.changed, 'tags' ) && _.keys( model.changed ).length === 1 ){\n // If only the tags have changed, rerender specifically\n // the titlebar region. Otherwise default to the full\n // render.\n self.$( '.nametags' ).html( self._renderNametags() );\n } else {\n self.render();\n }\n }\n }\n });\n },\n\n // ......................................................................... expandable\n /** In this override, only get details if in the ready state, get rerunnable if in other states.\n * Note: fetch with no 'change' event triggering to prevent automatic rendering.\n */\n _fetchModelDetails : function(){\n var view = this;\n if( view.model.inReadyState() && !view.model.hasDetails() ){\n return view.model.fetch({ silent: true });\n }\n return jQuery.when();\n },\n\n // ......................................................................... removal\n /** Remove this view's html from the DOM and remove all event listeners.\n * @param {Number or String} speed jq effect speed\n * @param {Function} callback an optional function called when removal is done (scoped to this view)\n */\n remove : function( speed, callback ){\n var view = this;\n speed = speed || this.fxSpeed;\n this.$el.fadeOut( speed, function(){\n Backbone.View.prototype.remove.call( view );\n if( callback ){ callback.call( view ); }\n });\n },\n\n // ......................................................................... rendering\n /* TODO:\n dataset states are the issue primarily making dataset rendering complex\n each state should have it's own way of displaying/set of details\n often with different actions that can be applied\n throw in deleted/purged/visible and things get complicated easily\n I've considered (a couple of times) - creating a view for each state\n - but recreating the view during an update...seems wrong\n */\n /** In this override, add the dataset state as a class for use with state-based CSS */\n _swapNewRender : function( $newRender ){\n _super.prototype._swapNewRender.call( this, $newRender );\n if( this.model.has( 'state' ) ){\n this.$el.addClass( 'state-' + this.model.get( 'state' ) );\n }\n return this.$el;\n },\n\n // ................................................................................ titlebar\n /** In this override, add the dataset display button. */\n _renderPrimaryActions : function(){\n // render just the display for read-only\n return [ this._renderDisplayButton() ];\n },\n\n /** Render icon-button to display dataset data */\n _renderDisplayButton : function(){\n // don't show display if not viewable or not accessible\n var state = this.model.get( 'state' );\n if( ( state === STATES.NOT_VIEWABLE ) ||\n ( state === STATES.DISCARDED ) ||\n ( !this.model.get( 'accessible' ) ) ){\n return null;\n }\n\n var displayBtnData = {\n target : this.linkTarget,\n classes : 'display-btn'\n };\n\n // show a disabled display if the data's been purged\n if( this.model.get( 'purged' ) ){\n displayBtnData.disabled = true;\n displayBtnData.title = _l( 'Cannot display datasets removed from disk' );\n\n // disable if still uploading\n } else if( state === STATES.UPLOAD ){\n displayBtnData.disabled = true;\n displayBtnData.title = _l( 'This dataset must finish uploading before it can be viewed' );\n\n // disable if still new\n } else if( state === STATES.NEW ){\n displayBtnData.disabled = true;\n displayBtnData.title = _l( 'This dataset is not yet viewable' );\n\n } else {\n displayBtnData.title = _l( 'View data' );\n\n // default link for dataset\n displayBtnData.href = this.model.urls.display;\n\n // add frame manager option onclick event\n var self = this;\n displayBtnData.onclick = function( ev ){\n if (Galaxy.frame && Galaxy.frame.active) {\n // Add dataset to frames.\n Galaxy.frame.addDataset(self.model.get('id'));\n ev.preventDefault();\n }\n };\n }\n displayBtnData.faIcon = 'fa-eye';\n return faIconButton( displayBtnData );\n },\n\n // ......................................................................... rendering details\n /** Render the enclosing div of the hda body and, if expanded, the html in the body\n * @returns {jQuery} rendered DOM\n */\n _renderDetails : function(){\n //TODO: generalize to be allow different details for each state\n\n // no access - render nothing but a message\n if( this.model.get( 'state' ) === STATES.NOT_VIEWABLE ){\n return $( this.templates.noAccess( this.model.toJSON(), this ) );\n }\n\n var $details = _super.prototype._renderDetails.call( this );\n $details.find( '.actions .left' ).empty().append( this._renderSecondaryActions() );\n $details.find( '.summary' ).html( this._renderSummary() )\n .prepend( this._renderDetailMessages() );\n $details.find( '.display-applications' ).html( this._renderDisplayApplications() );\n\n this._setUpBehaviors( $details );\n return $details;\n },\n\n /** Defer to the appropo summary rendering fn based on state */\n _renderSummary : function(){\n var json = this.model.toJSON(),\n summaryRenderFn = this.templates.summaries[ json.state ];\n summaryRenderFn = summaryRenderFn || this.templates.summaries.unknown;\n return summaryRenderFn( json, this );\n },\n\n /** Render messages to be displayed only when the details are shown */\n _renderDetailMessages : function(){\n var view = this,\n $warnings = $( '' ),\n json = view.model.toJSON();\n //TODO:! unordered (map)\n _.each( view.templates.detailMessages, function( templateFn ){\n $warnings.append( $( templateFn( json, view ) ) );\n });\n return $warnings;\n },\n\n /** Render the external display application links */\n _renderDisplayApplications : function(){\n if( this.model.isDeletedOrPurged() ){ return ''; }\n // render both old and new display apps using the same template\n return [\n this.templates.displayApplications( this.model.get( 'display_apps' ), this ),\n this.templates.displayApplications( this.model.get( 'display_types' ), this )\n ].join( '' );\n },\n\n // ......................................................................... secondary/details actions\n /** A series of links/buttons for less commonly used actions: re-run, info, etc. */\n _renderSecondaryActions : function(){\n this.debug( '_renderSecondaryActions' );\n switch( this.model.get( 'state' ) ){\n case STATES.NOT_VIEWABLE:\n return [];\n case STATES.OK:\n case STATES.FAILED_METADATA:\n case STATES.ERROR:\n return [ this._renderDownloadButton(), this._renderShowParamsButton() ];\n }\n return [ this._renderShowParamsButton() ];\n },\n\n /** Render icon-button to show the input and output (stdout/err) for the job that created this.\n * @returns {jQuery} rendered DOM\n */\n _renderShowParamsButton : function(){\n // gen. safe to show in all cases\n return faIconButton({\n title : _l( 'View details' ),\n classes : 'params-btn',\n href : this.model.urls.show_params,\n target : this.linkTarget,\n faIcon : 'fa-info-circle',\n onclick : function( ev ) {\n if ( Galaxy.frame && Galaxy.frame.active ) {\n Galaxy.frame.add( { title: 'Dataset details', url: this.href } );\n ev.preventDefault();\n ev.stopPropagation();\n }\n }\n });\n },\n\n\n /** Render icon-button/popupmenu to download the data (and/or the associated meta files (bai, etc.)) for this.\n * @returns {jQuery} rendered DOM\n */\n _renderDownloadButton : function(){\n // don't show anything if the data's been purged\n if( this.model.get( 'purged' ) || !this.model.hasData() ){ return null; }\n\n // return either: a popupmenu with links to download assoc. meta files (if there are meta files)\n // or a single download icon-button (if there are no meta files)\n if( !_.isEmpty( this.model.get( 'meta_files' ) ) ){\n return this._renderMetaFileDownloadButton();\n }\n\n return $([\n '',\n '',\n ''\n ].join( '' ));\n },\n\n /** Render the download button which opens a dropdown with links to download assoc. meta files (indeces, etc.) */\n _renderMetaFileDownloadButton : function(){\n var urls = this.model.urls;\n return $([\n '
'\n ], 'dataset' );\n\n // messages to be displayed only within the details section ('below the fold')\n var detailMessageTemplates = {\n resubmitted : BASE_MVC.wrapTemplate([\n // deleted not purged\n '<% if( model.resubmitted ){ %>',\n '
',\n _l( 'The job creating this dataset has been resubmitted' ),\n '
',\n '<% } %>'\n ])\n };\n\n // this is applied to both old and new style display apps\n var displayApplicationsTemplate = BASE_MVC.wrapTemplate([\n '<% _.each( apps, function( app ){ %>',\n '
',\n // space for title bar buttons - gen. floated to the right\n '',\n '',\n\n // expandable area for more details\n '',\n '
'\n ]);\n\n var warnings = {};\n\n var titleBarTemplate = BASE_MVC.wrapTemplate([\n // adding a tabindex here allows focusing the title bar and the use of keydown to expand the dataset display\n '
',\n //TODO: prob. belongs in dataset-list-item\n '',\n '
',\n '<%- element.name %>',\n '
',\n '',\n '
'\n ], 'element' );\n\n var subtitleTemplate = BASE_MVC.wrapTemplate([\n // override this\n ''\n ]);\n\n var detailsTemplate = BASE_MVC.wrapTemplate([\n // override this\n ''\n ]);\n\n return {\n el : elTemplato,\n warnings : warnings,\n titleBar : titleBarTemplate,\n subtitle : subtitleTemplate,\n details : detailsTemplate\n };\n}());\n\n\n//==============================================================================\n/** A view that is displayed in some larger list/grid/collection.\n * *AND* can display some sub-list of it's own when expanded (e.g. dataset collections).\n * This list will 'foldout' when the item is expanded depending on this.foldoutStyle:\n * If 'foldout': will expand vertically to show the nested list\n * If 'drilldown': will overlay the parent list\n *\n * Inherits from ListItemView.\n *\n * _renderDetails does the work of creating this.details: a sub-view that shows the nested list\n */\nvar FoldoutListItemView = ListItemView.extend({\n\n /** If 'foldout': show the sub-panel inside the expanded item\n * If 'drilldown': only fire events and handle by pub-sub\n * (allow the panel containing this item to attach it, hide itself, etc.)\n */\n foldoutStyle : 'foldout',\n /** Panel view class to instantiate for the sub-panel */\n foldoutPanelClass : null,\n\n /** override to:\n * add attributes foldoutStyle and foldoutPanelClass for config poly\n * disrespect attributes.expanded if drilldown\n */\n initialize : function( attributes ){\n if( this.foldoutStyle === 'drilldown' ){ this.expanded = false; }\n this.foldoutStyle = attributes.foldoutStyle || this.foldoutStyle;\n this.foldoutPanelClass = attributes.foldoutPanelClass || this.foldoutPanelClass;\n\n ListItemView.prototype.initialize.call( this, attributes );\n this.foldout = this._createFoldoutPanel();\n },\n\n /** in this override, attach the foldout panel when rendering details */\n _renderDetails : function(){\n if( this.foldoutStyle === 'drilldown' ){ return $(); }\n var $newDetails = ListItemView.prototype._renderDetails.call( this );\n return this._attachFoldout( this.foldout, $newDetails );\n },\n\n /** In this override, handle collection expansion. */\n _createFoldoutPanel : function(){\n var model = this.model;\n var FoldoutClass = this._getFoldoutPanelClass( model ),\n options = this._getFoldoutPanelOptions( model ),\n foldout = new FoldoutClass( _.extend( options, {\n model : model\n }));\n return foldout;\n },\n\n /** Stub to return proper foldout panel class */\n _getFoldoutPanelClass : function(){\n // override\n return this.foldoutPanelClass;\n },\n\n /** Stub to return proper foldout panel options */\n _getFoldoutPanelOptions : function(){\n return {\n // propagate foldout style down\n foldoutStyle : this.foldoutStyle,\n fxSpeed : this.fxSpeed\n };\n },\n\n /** Render the foldout panel inside the view, hiding controls */\n _attachFoldout : function( foldout, $whereTo ){\n $whereTo = $whereTo || this.$( '> .details' );\n this.foldout = foldout.render( 0 );\n foldout.$( '> .controls' ).hide();\n return $whereTo.append( foldout.$el );\n },\n\n /** In this override, branch on foldoutStyle to show expanded */\n expand : function(){\n var view = this;\n return view._fetchModelDetails()\n .always(function(){\n if( view.foldoutStyle === 'foldout' ){\n view._expand();\n } else if( view.foldoutStyle === 'drilldown' ){\n view._expandByDrilldown();\n }\n });\n },\n\n /** For drilldown, set up close handler and fire expanded:drilldown\n * containing views can listen to this and handle other things\n * (like hiding themselves) by listening for expanded/collapsed:drilldown\n */\n _expandByDrilldown : function(){\n var view = this;\n // attachment and rendering done by listener\n view.listenTo( view.foldout, 'close', function(){\n view.trigger( 'collapsed:drilldown', view, view.foldout );\n });\n view.trigger( 'expanded:drilldown', view, view.foldout );\n }\n\n});\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nFoldoutListItemView.prototype.templates = (function(){\n\n var detailsTemplate = BASE_MVC.wrapTemplate([\n '
',\n // override with more info (that goes above the panel)\n '
'\n ], 'collection' );\n\n return _.extend( {}, ListItemView.prototype.templates, {\n details : detailsTemplate\n });\n}());\n\n\n//==============================================================================\n return {\n ExpandableView : ExpandableView,\n ListItemView : ListItemView,\n FoldoutListItemView : FoldoutListItemView\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/list/list-item.js","define([\n \"mvc/base-mvc\",\n \"utils/localization\"\n], function( baseMVC, _l ){\n// =============================================================================\n/** A view on any model that has a 'tags' attribute (a list of tag strings)\n * Incorporates the select2 jQuery plugin for tags display/editing:\n * http://ivaynberg.github.io/select2/\n */\nvar TagsEditor = Backbone.View\n .extend( baseMVC.LoggableMixin )\n .extend( baseMVC.HiddenUntilActivatedViewMixin ).extend({\n\n tagName : 'div',\n className : 'tags-display',\n\n /** Set up listeners, parse options */\n initialize : function( options ){\n //console.debug( this, options );\n // only listen to the model only for changes to tags - re-render\n if (options.usePrompt === false) {\n this.label = '';\n } else {\n this.label = '';\n }\n this.hiddenUntilActivated( options.$activator, options );\n },\n\n /** Build the DOM elements, call select to on the created input, and set up behaviors */\n render : function(){\n var self = this;\n this.$el.html( this._template() );\n\n this.$input().select2({\n placeholder : 'Add tags',\n width : '100%',\n tags : function(){\n // initialize possible tags in the dropdown based on all the tags the user has used so far\n return self._getTagsUsed();\n }\n });\n\n this._setUpBehaviors();\n return this;\n },\n\n _hashToName: function(tag){\n if (tag.startsWith('#')){\n return 'name:' + tag.slice(1);\n }\n return tag;\n },\n\n _nameToHash: function(tag){\n if (tag.startsWith('name:')){\n tag = '#' + tag.slice(5);\n }\n return tag;\n },\n\n /** @returns {String} the html text used to build the view's DOM */\n _template : function(){\n return [\n this.label,\n // set up initial tags by adding as CSV to input vals (necc. to init select2)\n ''\n ].join( '' );\n },\n\n /** @returns {String} the sorted, comma-separated tags from the model */\n tagsToCSV : function(){\n var self = this;\n var tagsArray = this.model.get( 'tags' );\n if( !_.isArray( tagsArray ) || _.isEmpty( tagsArray ) ){\n return '';\n }\n return tagsArray.map( function( tag ){\n return _.escape( self._nameToHash( tag ) );\n }).sort().join( ',' );\n },\n\n /** @returns {jQuery} the input for this view */\n $input : function(){\n return this.$el.find( 'input.tags-input' );\n },\n\n /** @returns {String[]} all tags used by the current user */\n _getTagsUsed : function(){\n//TODO: global\n var self = this;\n return _.map(Galaxy.user.get( 'tags_used' ), self._nameToHash);\n },\n\n /** set up any event listeners on the view's DOM (mostly handled by select2) */\n _setUpBehaviors : function(){\n var self = this;\n this.$input().on( 'change', function( event ){\n // Modify any 'hashtag' 'nametags'\n event.val = _.map(event.val, self._hashToName);\n // save the model's tags in either remove or added event\n self.model.save({ tags: event.val });\n // if it's new, add the tag to the users tags\n if( event.added ){\n //??: solve weird behavior in FF on test.galaxyproject.org where\n // event.added.text is string object: 'String{ 0=\"o\", 1=\"n\", 2=\"e\" }'\n self._addNewTagToTagsUsed( event.added.text + '' );\n }\n });\n },\n\n /** add a new tag (if not already there) to the list of all tags used by the user\n * @param {String} newTag the tag to add to the list of used\n */\n _addNewTagToTagsUsed : function( newTag ){\n//TODO: global\n var tagsUsed = Galaxy.user.get( 'tags_used' );\n if( !_.contains( tagsUsed, newTag ) ){\n tagsUsed.push( newTag );\n tagsUsed.sort();\n Galaxy.user.set( 'tags_used', tagsUsed );\n }\n },\n\n /** shut down event listeners and remove this view's DOM */\n remove : function(){\n this.$input.off();\n this.stopListening( this.model );\n Backbone.View.prototype.remove.call( this );\n },\n\n /** string rep */\n toString : function(){ return [ 'TagsEditor(', this.model + '', ')' ].join(''); }\n});\n\n// =============================================================================\nreturn {\n TagsEditor : TagsEditor\n};\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/tag.js","/**\n This is the base class of the tool form plugin. This class is e.g. inherited by the regular and the workflow tool form.\n*/\ndefine( [ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view', 'mvc/citation/citation-model', 'mvc/citation/citation-view' ],\n function( Utils, Deferred, Ui, FormBase, CitationModel, CitationView ) {\n return FormBase.extend({\n initialize: function( options ) {\n var self = this;\n this.deferred = new Deferred();\n FormBase.prototype.initialize.call( this, options );\n if ( this.model.get( 'inputs' ) ) {\n this._buildForm( this.model.attributes );\n } else {\n this.deferred.execute( function( process ) {\n self._buildModel( process, self.model.attributes, true );\n });\n }\n // listen to history panel\n if ( this.model.get( 'listen_to_history' ) && parent.Galaxy && parent.Galaxy.currHistoryPanel ) {\n this.listenTo( parent.Galaxy.currHistoryPanel.collection, 'change', function() {\n self.model.get( 'onchange' )();\n });\n }\n // destroy dom elements\n this.$el.on( 'remove', function() { self.remove() } );\n },\n\n /** Wait for deferred build processes before removal */\n remove: function() {\n var self = this;\n this.$el.hide();\n this.deferred.execute( function() {\n FormBase.prototype.remove.call( self );\n Galaxy.emit.debug( 'tool-form-base::remove()', 'Destroy view.' );\n });\n },\n\n /** Build form */\n _buildForm: function( options ) {\n var self = this;\n this.model.set( options );\n this.model.set({\n title : options.title || '' + options.name + ' ' + options.description + ' (Galaxy Version ' + options.version + ')',\n operations : !this.model.get( 'hide_operations' ) && this._operations(),\n onchange : function() {\n self.deferred.reset();\n self.deferred.execute( function ( process ) {\n self.model.get( 'postchange' )( process, self );\n });\n }\n });\n this.model.get( 'customize' ) && this.model.get( 'customize' )( this );\n this.render();\n if ( !this.model.get( 'collapsible' ) ) {\n this.$el.append( $( '' ).addClass( 'ui-margin-top-large' ).append( this._footer() ) );\n }\n },\n\n /** Builds a new model through api call and recreates the entire form */\n _buildModel: function( process, new_options, hide_message ) {\n var self = this;\n var options = this.model.attributes;\n options.version = new_options.version;\n options.id = new_options.id;\n\n // build request url\n var build_url = '';\n var build_data = {};\n if ( options.job_id ) {\n build_url = Galaxy.root + 'api/jobs/' + options.job_id + '/build_for_rerun';\n } else {\n build_url = Galaxy.root + 'api/tools/' + options.id + '/build';\n if ( Galaxy.params && Galaxy.params.tool_id == options.id ) {\n build_data = $.extend( {}, Galaxy.params );\n options.version && ( build_data[ 'tool_version' ] = options.version );\n }\n }\n\n // get initial model\n Utils.get({\n url : build_url,\n data : build_data,\n success : function( data ) {\n if( !data.display ) {\n window.location = Galaxy.root;\n return;\n }\n self._buildForm( data );\n !hide_message && self.message.update({\n status : 'success',\n message : 'Now you are using \\'' + options.name + '\\' version ' + options.version + ', id \\'' + options.id + '\\'.',\n persistent : false\n });\n Galaxy.emit.debug('tool-form-base::_buildModel()', 'Initial tool model ready.', data);\n process.resolve();\n },\n error : function( response, status ) {\n var error_message = ( response && response.err_msg ) || 'Uncaught error.';\n if ( status == 401 ) {\n window.location = Galaxy.root + 'user/login?' + $.param({ redirect : Galaxy.root + '?tool_id=' + options.id });\n } else if ( self.$el.is( ':empty' ) ) {\n self.$el.prepend( ( new Ui.Message({\n message : error_message,\n status : 'danger',\n persistent : true,\n large : true\n }) ).$el );\n } else {\n Galaxy.modal && Galaxy.modal.show({\n title : 'Tool request failed',\n body : error_message,\n buttons : {\n 'Close' : function() {\n Galaxy.modal.hide();\n }\n }\n });\n }\n Galaxy.emit.debug( 'tool-form-base::_buildModel()', 'Initial tool model request failed.', response );\n process.reject();\n }\n });\n },\n\n /** Create tool operation menu */\n _operations: function() {\n var self = this;\n var options = this.model.attributes;\n\n // button for version selection\n var versions_button = new Ui.ButtonMenu({\n icon : 'fa-cubes',\n title : ( !options.narrow && 'Versions' ) || null,\n tooltip : 'Select another tool version'\n });\n if ( !options.sustain_version && options.versions && options.versions.length > 1 ) {\n for ( var i in options.versions ) {\n var version = options.versions[ i ];\n if ( version != options.version ) {\n versions_button.addMenu({\n title : 'Switch to ' + version,\n version : version,\n icon : 'fa-cube',\n onclick : function() {\n // here we update the tool version (some tools encode the version also in the id)\n var id = options.id.replace( options.version, this.version );\n var version = this.version;\n // queue model request\n self.deferred.reset();\n self.deferred.execute( function( process ) {\n self._buildModel( process, { id : id, version : version } )\n });\n }\n });\n }\n }\n } else {\n versions_button.$el.hide();\n }\n\n // button for options e.g. search, help\n var menu_button = new Ui.ButtonMenu({\n icon : 'fa-caret-down',\n title : ( !options.narrow && 'Options' ) || null,\n tooltip : 'View available options'\n });\n if ( options.biostar_url ) {\n menu_button.addMenu({\n icon : 'fa-question-circle',\n title : 'Question?',\n onclick : function() {\n window.open( options.biostar_url + '/p/new/post/' );\n }\n });\n menu_button.addMenu({\n icon : 'fa-search',\n title : 'Search',\n onclick : function() {\n window.open( options.biostar_url + '/local/search/page/?q=' + options.name );\n }\n });\n };\n menu_button.addMenu({\n icon : 'fa-share',\n title : 'Share',\n onclick : function() {\n prompt( 'Copy to clipboard: Ctrl+C, Enter', window.location.origin + Galaxy.root + 'root?tool_id=' + options.id );\n }\n });\n\n // add admin operations\n if ( Galaxy.user && Galaxy.user.get( 'is_admin' ) ) {\n menu_button.addMenu({\n icon : 'fa-download',\n title : 'Download',\n onclick : function() {\n window.location.href = Galaxy.root + 'api/tools/' + options.id + '/download';\n }\n });\n menu_button.addMenu({\n icon : 'fa-refresh',\n title : 'Reload XML',\n onclick : function() {\n Utils.get({\n url : Galaxy.root + 'api/tools/' + options.id + '/reload',\n success : function( response ) {\n self.message.update( { persistent : false, message : 'Tool XML has been reloaded.', status : 'success' } );\n },\n error : function( response ) {\n self.message.update( { persistent : false, message : response.err_msg, status : 'danger' } );\n }\n });\n }\n });\n }\n\n // button for version selection\n if ( options.requirements && options.requirements.length > 0 ) {\n menu_button.addMenu({\n icon : 'fa-info-circle',\n title : 'Requirements',\n onclick : function() {\n if ( !this.requirements_visible || self.portlet.collapsed ) {\n this.requirements_visible = true;\n self.portlet.expand();\n self.message.update( { persistent : true, message : self._templateRequirements( options ), status : 'info' } );\n } else {\n this.requirements_visible = false;\n self.message.update( { message : '' } );\n }\n }\n });\n }\n\n // add toolshed url\n if ( options.sharable_url ) {\n menu_button.addMenu({\n icon : 'fa-external-link',\n title : 'See in Tool Shed',\n onclick : function() {\n window.open( options.sharable_url );\n }\n });\n }\n\n // add tool menu webhooks\n $.getJSON('/api/webhooks/tool-menu/all', function(webhooks) {\n _.each(webhooks, function(webhook) {\n if (webhook.activate && webhook.config.function) {\n menu_button.addMenu({\n icon : webhook.config.icon,\n title : webhook.config.title,\n onclick : function() {\n var func = new Function('options', webhook.config.function);\n func(options);\n }\n });\n }\n });\n });\n\n return {\n menu : menu_button,\n versions : versions_button\n }\n },\n\n /** Create footer */\n _footer: function() {\n var options = this.model.attributes;\n var $el = $( '' ).append( this._templateHelp( options ) );\n if ( options.citations ) {\n var $citations = $( '' );\n var citations = new CitationModel.ToolCitationCollection();\n citations.tool_id = options.id;\n var citation_list_view = new CitationView.CitationListView({ el: $citations, collection: citations });\n citation_list_view.render();\n citations.fetch();\n $el.append( $citations );\n }\n return $el;\n },\n\n /** Templates */\n _templateHelp: function( options ) {\n var $tmpl = $( '' ).addClass( 'ui-form-help' ).append( options.help );\n $tmpl.find( 'a' ).attr( 'target', '_blank' );\n return $tmpl;\n },\n\n _templateRequirements: function( options ) {\n var nreq = options.requirements.length;\n if ( nreq > 0 ) {\n var requirements_message = 'This tool requires ';\n _.each( options.requirements, function( req, i ) {\n requirements_message += req.name + ( req.version ? ' (Version ' + req.version + ')' : '' ) + ( i < nreq - 2 ? ', ' : ( i == nreq - 2 ? ' and ' : '' ) );\n });\n var requirements_link = $( '' ).attr( 'target', '_blank' ).attr( 'href', 'https://galaxyproject.org/tools/requirements/' ).text( 'here' );\n return $( '' ).append( requirements_message + '. Click ' ).append( requirements_link ).append( ' for more information.' );\n }\n return 'No requirements found.';\n }\n });\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/tool/tool-form-base.js","/**\n * Model, view, and controller objects for Galaxy tools and tool panel.\n */\n\n define([\n \"libs/underscore\",\n \"viz/trackster/util\",\n \"mvc/dataset/data\",\n \"mvc/tool/tool-form\"\n\n], function(_, util, data, ToolForm) {\n 'use strict';\n\n/**\n * Mixin for tracking model visibility.\n */\nvar VisibilityMixin = {\n hidden: false,\n\n show: function() {\n this.set(\"hidden\", false);\n },\n\n hide: function() {\n this.set(\"hidden\", true);\n },\n\n toggle: function() {\n this.set(\"hidden\", !this.get(\"hidden\"));\n },\n\n is_visible: function() {\n return !this.attributes.hidden;\n }\n\n};\n\n/**\n * A tool parameter.\n */\nvar ToolParameter = Backbone.Model.extend({\n defaults: {\n name: null,\n label: null,\n type: null,\n value: null,\n html: null,\n num_samples: 5\n },\n\n initialize: function(options) {\n this.attributes.html = unescape(this.attributes.html);\n },\n\n copy: function() {\n return new ToolParameter(this.toJSON());\n },\n\n set_value: function(value) {\n this.set('value', value || '');\n }\n});\n\nvar ToolParameterCollection = Backbone.Collection.extend({\n model: ToolParameter\n});\n\n/**\n * A data tool parameter.\n */\nvar DataToolParameter = ToolParameter.extend({});\n\n/**\n * An integer tool parameter.\n */\nvar IntegerToolParameter = ToolParameter.extend({\n set_value: function(value) {\n this.set('value', parseInt(value, 10));\n },\n\n /**\n * Returns samples from a tool input.\n */\n get_samples: function() {\n return d3.scale.linear()\n .domain([this.get('min'), this.get('max')])\n .ticks(this.get('num_samples'));\n }\n});\n\nvar FloatToolParameter = IntegerToolParameter.extend({\n set_value: function(value) {\n this.set('value', parseFloat(value));\n }\n});\n\n/**\n * A select tool parameter.\n */\nvar SelectToolParameter = ToolParameter.extend({\n /**\n * Returns tool options.\n */\n get_samples: function() {\n return _.map(this.get('options'), function(option) {\n return option[0];\n });\n }\n});\n\n// Set up dictionary of parameter types.\nToolParameter.subModelTypes = {\n 'integer': IntegerToolParameter,\n 'float': FloatToolParameter,\n 'data': DataToolParameter,\n 'select': SelectToolParameter\n};\n\n/**\n * A Galaxy tool.\n */\nvar Tool = Backbone.Model.extend({\n // Default attributes.\n defaults: {\n id: null,\n name: null,\n description: null,\n target: null,\n inputs: [],\n outputs: []\n },\n\n urlRoot: Galaxy.root + 'api/tools',\n\n initialize: function(options) {\n\n // Set parameters.\n this.set('inputs', new ToolParameterCollection(_.map(options.inputs, function(p) {\n var p_class = ToolParameter.subModelTypes[p.type] || ToolParameter;\n return new p_class(p);\n })));\n },\n\n /**\n *\n */\n toJSON: function() {\n var rval = Backbone.Model.prototype.toJSON.call(this);\n\n // Convert inputs to JSON manually.\n rval.inputs = this.get('inputs').map(function(i) { return i.toJSON(); });\n return rval;\n },\n\n /**\n * Removes inputs of a particular type; this is useful because not all inputs can be handled by\n * client and server yet.\n */\n remove_inputs: function(types) {\n var tool = this,\n incompatible_inputs = tool.get('inputs').filter( function(input) {\n return ( types.indexOf( input.get('type') ) !== -1);\n });\n tool.get('inputs').remove(incompatible_inputs);\n },\n\n /**\n * Returns object copy, optionally including only inputs that can be sampled.\n */\n copy: function(only_samplable_inputs) {\n var copy = new Tool(this.toJSON());\n\n // Return only samplable inputs if flag is set.\n if (only_samplable_inputs) {\n var valid_inputs = new Backbone.Collection();\n copy.get('inputs').each(function(input) {\n if (input.get_samples()) {\n valid_inputs.push(input);\n }\n });\n copy.set('inputs', valid_inputs);\n }\n\n return copy;\n },\n\n apply_search_results: function(results) {\n ( _.indexOf(results, this.attributes.id) !== -1 ? this.show() : this.hide() );\n return this.is_visible();\n },\n\n /**\n * Set a tool input's value.\n */\n set_input_value: function(name, value) {\n this.get('inputs').find(function(input) {\n return input.get('name') === name;\n }).set('value', value);\n },\n\n /**\n * Set many input values at once.\n */\n set_input_values: function(inputs_dict) {\n var self = this;\n _.each(_.keys(inputs_dict), function(input_name) {\n self.set_input_value(input_name, inputs_dict[input_name]);\n });\n },\n\n /**\n * Run tool; returns a Deferred that resolves to the tool's output(s).\n */\n run: function() {\n return this._run();\n },\n\n /**\n * Rerun tool using regions and a target dataset.\n */\n rerun: function(target_dataset, regions) {\n return this._run({\n action: 'rerun',\n target_dataset_id: target_dataset.id,\n regions: regions\n });\n },\n\n /**\n * Returns input dict for tool's inputs.\n */\n get_inputs_dict: function() {\n var input_dict = {};\n this.get('inputs').each(function(input) {\n input_dict[input.get('name')] = input.get('value');\n });\n return input_dict;\n },\n\n /**\n * Run tool; returns a Deferred that resolves to the tool's output(s).\n * NOTE: this method is a helper method and should not be called directly.\n */\n _run: function(additional_params) {\n // Create payload.\n var payload = _.extend({\n tool_id: this.id,\n inputs: this.get_inputs_dict()\n }, additional_params);\n\n // Because job may require indexing datasets, use server-side\n // deferred to ensure that job is run. Also use deferred that\n // resolves to outputs from tool.\n var run_deferred = $.Deferred(),\n ss_deferred = new util.ServerStateDeferred({\n ajax_settings: {\n url: this.urlRoot,\n data: JSON.stringify(payload),\n dataType: \"json\",\n contentType: 'application/json',\n type: \"POST\"\n },\n interval: 2000,\n success_fn: function(response) {\n return response !== \"pending\";\n }\n });\n\n // Run job and resolve run_deferred to tool outputs.\n $.when(ss_deferred.go()).then(function(result) {\n run_deferred.resolve(new data.DatasetCollection(result));\n });\n return run_deferred;\n }\n});\n_.extend(Tool.prototype, VisibilityMixin);\n\n/**\n * Tool view.\n */\nvar ToolView = Backbone.View.extend({\n\n});\n\n/**\n * Wrap collection of tools for fast access/manipulation.\n */\nvar ToolCollection = Backbone.Collection.extend({\n model: Tool\n});\n\n/**\n * Label or section header in tool panel.\n */\nvar ToolSectionLabel = Backbone.Model.extend(VisibilityMixin);\n\n/**\n * Section of tool panel with elements (labels and tools).\n */\nvar ToolSection = Backbone.Model.extend({\n defaults: {\n elems: [],\n open: false\n },\n\n clear_search_results: function() {\n _.each(this.attributes.elems, function(elt) {\n elt.show();\n });\n\n this.show();\n this.set(\"open\", false);\n },\n\n apply_search_results: function(results) {\n var all_hidden = true,\n cur_label;\n _.each(this.attributes.elems, function(elt) {\n if (elt instanceof ToolSectionLabel) {\n cur_label = elt;\n cur_label.hide();\n }\n else if (elt instanceof Tool) {\n if (elt.apply_search_results(results)) {\n all_hidden = false;\n if (cur_label) {\n cur_label.show();\n }\n }\n }\n });\n\n if (all_hidden) {\n this.hide();\n }\n else {\n this.show();\n this.set(\"open\", true);\n }\n }\n});\n_.extend(ToolSection.prototype, VisibilityMixin);\n\n/**\n * Tool search that updates results when query is changed. Result value of null\n * indicates that query was not run; if not null, results are from search using\n * query.\n */\nvar ToolSearch = Backbone.Model.extend({\n defaults: {\n search_hint_string: \"search tools\",\n min_chars_for_search: 3,\n clear_btn_url: \"\",\n visible: true,\n query: \"\",\n results: null,\n // ESC (27) will clear the input field and tool search filters\n clear_key: 27\n },\n\n urlRoot: Galaxy.root + 'api/tools',\n\n initialize: function() {\n this.on(\"change:query\", this.do_search);\n },\n\n /**\n * Do the search and update the results.\n */\n do_search: function() {\n var query = this.attributes.query;\n\n // If query is too short, do not search.\n if (query.length < this.attributes.min_chars_for_search) {\n this.set(\"results\", null);\n return;\n }\n\n // Do search via AJAX.\n var q = query;\n // Stop previous ajax-request\n if (this.timer) {\n clearTimeout(this.timer);\n }\n // Start a new ajax-request in X ms\n $(\"#search-clear-btn\").hide();\n $(\"#search-spinner\").show();\n var self = this;\n this.timer = setTimeout(function () {\n // log the search to analytics if present\n if ( typeof ga !== 'undefined' ) {\n ga( 'send', 'pageview', Galaxy.root + '?q=' + q );\n }\n $.get( self.urlRoot, { q: q }, function (data) {\n self.set(\"results\", data);\n $(\"#search-spinner\").hide();\n $(\"#search-clear-btn\").show();\n }, \"json\" );\n }, 400 );\n },\n\n clear_search: function() {\n this.set(\"query\", \"\");\n this.set(\"results\", null);\n }\n\n});\n_.extend(ToolSearch.prototype, VisibilityMixin);\n\n/**\n * Tool Panel.\n */\nvar ToolPanel = Backbone.Model.extend({\n\n initialize: function(options) {\n this.attributes.tool_search = options.tool_search;\n this.attributes.tool_search.on(\"change:results\", this.apply_search_results, this);\n this.attributes.tools = options.tools;\n this.attributes.layout = new Backbone.Collection( this.parse(options.layout) );\n },\n\n /**\n * Parse tool panel dictionary and return collection of tool panel elements.\n */\n parse: function(response) {\n // Recursive function to parse tool panel elements.\n var self = this,\n // Helper to recursively parse tool panel.\n parse_elt = function(elt_dict) {\n var type = elt_dict.model_class;\n // There are many types of tools; for now, anything that ends in 'Tool'\n // is treated as a generic tool.\n if ( type.indexOf('Tool') === type.length - 4 ) {\n return self.attributes.tools.get(elt_dict.id);\n }\n else if (type === 'ToolSection') {\n // Parse elements.\n var elems = _.map(elt_dict.elems, parse_elt);\n elt_dict.elems = elems;\n return new ToolSection(elt_dict);\n }\n else if (type === 'ToolSectionLabel') {\n return new ToolSectionLabel(elt_dict);\n }\n };\n\n return _.map(response, parse_elt);\n },\n\n clear_search_results: function() {\n this.get('layout').each(function(panel_elt) {\n if (panel_elt instanceof ToolSection) {\n panel_elt.clear_search_results();\n }\n else {\n // Label or tool, so just show.\n panel_elt.show();\n }\n });\n },\n\n apply_search_results: function() {\n var results = this.get('tool_search').get('results');\n if (results === null) {\n this.clear_search_results();\n return;\n }\n\n var cur_label = null;\n this.get('layout').each(function(panel_elt) {\n if (panel_elt instanceof ToolSectionLabel) {\n cur_label = panel_elt;\n cur_label.hide();\n }\n else if (panel_elt instanceof Tool) {\n if (panel_elt.apply_search_results(results)) {\n if (cur_label) {\n cur_label.show();\n }\n }\n }\n else {\n // Starting new section, so clear current label.\n cur_label = null;\n panel_elt.apply_search_results(results);\n }\n });\n }\n});\n\n/**\n * View classes for Galaxy tools and tool panel.\n *\n * Views use the templates defined below for rendering. Views update as needed\n * based on (a) model/collection events and (b) user interactions; in this sense,\n * they are controllers are well and the HTML is the real view in the MVC architecture.\n */\n\n/**\n * Base view that handles visibility based on model's hidden attribute.\n */\nvar BaseView = Backbone.View.extend({\n initialize: function() {\n this.model.on(\"change:hidden\", this.update_visible, this);\n this.update_visible();\n },\n update_visible: function() {\n ( this.model.attributes.hidden ? this.$el.hide() : this.$el.show() );\n }\n});\n\n/**\n * Link to a tool.\n */\nvar ToolLinkView = BaseView.extend({\n tagName: 'div',\n\n render: function() {\n // create element\n var $link = $('');\n $link.append(templates.tool_link(this.model.toJSON()));\n\n var formStyle = this.model.get( 'form_style', null );\n // open upload dialog for upload tool\n if (this.model.id === 'upload1') {\n $link.find('a').on('click', function(e) {\n e.preventDefault();\n Galaxy.upload.show();\n });\n }\n else if ( formStyle === 'regular' ) { // regular tools\n var self = this;\n $link.find('a').on('click', function(e) {\n e.preventDefault();\n Galaxy.router.push( '/', { tool_id : self.model.id, version : self.model.get('version') } );\n });\n }\n\n // add element\n this.$el.append($link);\n return this;\n }\n});\n\n/**\n * Panel label/section header.\n */\nvar ToolSectionLabelView = BaseView.extend({\n tagName: 'div',\n className: 'toolPanelLabel',\n\n render: function() {\n this.$el.append( $(\"\").text(this.model.attributes.text) );\n return this;\n }\n});\n\n/**\n * Panel section.\n */\nvar ToolSectionView = BaseView.extend({\n tagName: 'div',\n className: 'toolSectionWrapper',\n\n initialize: function() {\n BaseView.prototype.initialize.call(this);\n this.model.on(\"change:open\", this.update_open, this);\n },\n\n render: function() {\n // Build using template.\n this.$el.append( templates.panel_section(this.model.toJSON()) );\n\n // Add tools to section.\n var section_body = this.$el.find(\".toolSectionBody\");\n _.each(this.model.attributes.elems, function(elt) {\n if (elt instanceof Tool) {\n var tool_view = new ToolLinkView({model: elt, className: \"toolTitle\"});\n tool_view.render();\n section_body.append(tool_view.$el);\n }\n else if (elt instanceof ToolSectionLabel) {\n var label_view = new ToolSectionLabelView({model: elt});\n label_view.render();\n section_body.append(label_view.$el);\n }\n else {\n // TODO: handle nested section bodies?\n }\n });\n return this;\n },\n\n events: {\n 'click .toolSectionTitle > a': 'toggle'\n },\n\n /**\n * Toggle visibility of tool section.\n */\n toggle: function() {\n this.model.set(\"open\", !this.model.attributes.open);\n },\n\n /**\n * Update whether section is open or close.\n */\n update_open: function() {\n (this.model.attributes.open ?\n this.$el.children(\".toolSectionBody\").slideDown(\"fast\") :\n this.$el.children(\".toolSectionBody\").slideUp(\"fast\")\n );\n }\n});\n\nvar ToolSearchView = Backbone.View.extend({\n tagName: 'div',\n id: 'tool-search',\n className: 'bar',\n\n events: {\n 'click': 'focus_and_select',\n 'keyup :input': 'query_changed',\n 'change :input': 'query_changed',\n 'click #search-clear-btn': 'clear'\n },\n\n render: function() {\n this.$el.append( templates.tool_search(this.model.toJSON()) );\n if (!this.model.is_visible()) {\n this.$el.hide();\n }\n\n // Adjust top for issue 2907 depending on whether the messagebox is visible.\n if ($(\"#messagebox\").is(\":visible\")) {\n this.$el.css(\"top\",\"95px\");\n }\n\n this.$el.find('[title]').tooltip();\n return this;\n },\n\n focus_and_select: function() {\n this.$el.find(\":input\").focus().select();\n },\n\n clear: function() {\n this.model.clear_search();\n this.$el.find(\":input\").val('');\n this.focus_and_select();\n return false;\n },\n\n query_changed: function( evData ) {\n // check for the 'clear key' (ESC) first\n if( ( this.model.attributes.clear_key ) &&\n ( this.model.attributes.clear_key === evData.which ) ){\n this.clear();\n return false;\n }\n this.model.set(\"query\", this.$el.find(\":input\").val());\n }\n});\n\n/**\n * Tool panel view. Events triggered include:\n * tool_link_click(click event, tool_model)\n */\nvar ToolPanelView = Backbone.View.extend({\n tagName: 'div',\n className: 'toolMenu',\n\n /**\n * Set up view.\n */\n initialize: function() {\n this.model.get('tool_search').on(\"change:results\", this.handle_search_results, this);\n },\n\n render: function() {\n var self = this;\n\n // Render search.\n var search_view = new ToolSearchView( { model: this.model.get('tool_search') } );\n search_view.render();\n self.$el.append(search_view.$el);\n\n // Render panel.\n this.model.get('layout').each(function(panel_elt) {\n if (panel_elt instanceof ToolSection) {\n var section_title_view = new ToolSectionView({model: panel_elt});\n section_title_view.render();\n self.$el.append(section_title_view.$el);\n }\n else if (panel_elt instanceof Tool) {\n var tool_view = new ToolLinkView({model: panel_elt, className: \"toolTitleNoSection\"});\n tool_view.render();\n self.$el.append(tool_view.$el);\n }\n else if (panel_elt instanceof ToolSectionLabel) {\n var label_view = new ToolSectionLabelView({model: panel_elt});\n label_view.render();\n self.$el.append(label_view.$el);\n }\n });\n\n // Setup tool link click eventing.\n self.$el.find(\"a.tool-link\").click(function(e) {\n // Tool id is always the first class.\n var\n tool_id = $(this).attr('class').split(/\\s+/)[0],\n tool = self.model.get('tools').get(tool_id);\n\n self.trigger(\"tool_link_click\", e, tool);\n });\n\n return this;\n },\n\n handle_search_results: function() {\n var results = this.model.get('tool_search').get('results');\n if (results && results.length === 0) {\n $(\"#search-no-results\").show();\n }\n else {\n $(\"#search-no-results\").hide();\n }\n }\n});\n\n/**\n * View for working with a tool: setting parameters and inputs and executing the tool.\n */\nvar ToolFormView = Backbone.View.extend({\n className: 'toolForm',\n\n render: function() {\n this.$el.children().remove();\n this.$el.append( templates.tool_form(this.model.toJSON()) );\n }\n});\n\n/**\n * Integrated tool menu + tool execution.\n */\nvar IntegratedToolMenuAndView = Backbone.View.extend({\n className: 'toolMenuAndView',\n\n initialize: function() {\n this.tool_panel_view = new ToolPanelView({collection: this.collection});\n this.tool_form_view = new ToolFormView();\n },\n\n render: function() {\n // Render and append tool panel.\n this.tool_panel_view.render();\n this.tool_panel_view.$el.css(\"float\", \"left\");\n this.$el.append(this.tool_panel_view.$el);\n\n // Append tool form view.\n this.tool_form_view.$el.hide();\n this.$el.append(this.tool_form_view.$el);\n\n // On tool link click, show tool.\n var self = this;\n this.tool_panel_view.on(\"tool_link_click\", function(e, tool) {\n // Prevents click from activating link:\n e.preventDefault();\n // Show tool that was clicked on:\n self.show_tool(tool);\n });\n },\n\n /**\n * Fetch and display tool.\n */\n show_tool: function(tool) {\n var self = this;\n tool.fetch().done( function() {\n self.tool_form_view.model = tool;\n self.tool_form_view.render();\n self.tool_form_view.$el.show();\n $('#left').width(\"650px\");\n });\n }\n});\n\n// TODO: move into relevant views\nvar templates = {\n // the search bar at the top of the tool panel\n tool_search : _.template([\n '\" autocomplete=\"off\" type=\"text\" />',\n '',\n //TODO: replace with icon\n '',\n ].join('')),\n\n // the category level container in the tool panel (e.g. 'Get Data', 'Text Manipulation')\n panel_section : _.template([\n '
'\n ].join('')),\n\n // a single tool's link in the tool panel; will load the tool form in the center panel\n tool_link : _.template([\n '',\n '<% _.each( labels, function( label ){ %>',\n '\">',\n '<%- label %>',\n '',\n '<% }); %>',\n '',\n ' tool-link\" href=\"<%= link %>\" target=\"<%- target %>\" minsizehint=\"<%- min_width %>\">',\n '<%- name %>',\n '',\n ' <%- description %>'\n ].join('')),\n\n // the tool form for entering tool parameters, viewing help and executing the tool\n // loaded when a tool link is clicked in the tool panel\n tool_form : _.template([\n '
',\n // TODO: we need scoping here because 'help' is the dom for the help menu in the masthead\n // which implies a leaky variable that I can't find\n ].join(''), { variable: 'tool' }),\n};\n\n\n// Exports\nreturn {\n ToolParameter: ToolParameter,\n IntegerToolParameter: IntegerToolParameter,\n SelectToolParameter: SelectToolParameter,\n Tool: Tool,\n ToolCollection: ToolCollection,\n ToolSearch: ToolSearch,\n ToolPanel: ToolPanel,\n ToolPanelView: ToolPanelView,\n ToolFormView: ToolFormView\n};\n\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/tool/tools.js","define([\n //jquery\n //backbone\n], function(){\n// =============================================================================\n/**\n * view for a popup menu\n */\nvar PopupMenu = Backbone.View.extend({\n//TODO: maybe better as singleton off the Galaxy obj\n /** Cache the desired button element and options, set up the button click handler\n * NOTE: attaches this view as HTML/jQ data on the button for later use.\n */\n initialize: function( $button, options ){\n // default settings\n this.$button = $button;\n if( !this.$button.length ){\n this.$button = $( '' );\n }\n this.options = options || [];\n this.$button.data( 'popupmenu', this );\n\n // set up button click -> open menu behavior\n var menu = this;\n this.$button.click( function( event ){\n // if there's already a menu open, remove it\n $( '.popmenu-wrapper' ).remove();\n menu._renderAndShow( event );\n return false;\n });\n },\n\n // render the menu, append to the page body at the click position, and set up the 'click-away' handlers, show\n _renderAndShow: function( clickEvent ){\n this.render();\n this.$el.appendTo( 'body' ).css( this._getShownPosition( clickEvent )).show();\n this._setUpCloseBehavior();\n },\n\n // render the menu\n // this menu doesn't attach itself to the DOM ( see _renderAndShow )\n render: function(){\n // render the menu body absolute and hidden, fill with template\n this.$el.addClass( 'popmenu-wrapper' ).hide()\n .css({ position : 'absolute' })\n .html( this.template( this.$button.attr( 'id' ), this.options ));\n\n // set up behavior on each link/anchor elem\n if( this.options.length ){\n var menu = this;\n //precondition: there should be one option per li\n this.$el.find( 'li' ).each( function( i, li ){\n var option = menu.options[i];\n\n // if the option has 'func', call that function when the anchor is clicked\n if( option.func ){\n $( this ).children( 'a.popupmenu-option' ).click( function( event ){\n option.func.call( menu, event, option );\n // We must preventDefault otherwise clicking \"cancel\"\n // on a purge or something still navigates and causes\n // the action.\n event.preventDefault();\n // bubble up so that an option click will call the close behavior\n });\n }\n });\n }\n return this;\n },\n\n template : function( id, options ){\n return [\n '
'\n ].join( '' );\n }).join( '' );\n },\n\n // get the absolute position/offset for the menu\n _getShownPosition : function( clickEvent ){\n\n // display menu horiz. centered on click...\n var menuWidth = this.$el.width();\n var x = clickEvent.pageX - menuWidth / 2 ;\n\n // adjust to handle horiz. scroll and window dimensions ( draw entirely on visible screen area )\n x = Math.min( x, $( document ).scrollLeft() + $( window ).width() - menuWidth - 5 );\n x = Math.max( x, $( document ).scrollLeft() + 5 );\n return {\n top: clickEvent.pageY,\n left: x\n };\n },\n\n // bind an event handler to all available frames so that when anything is clicked\n // the menu is removed from the DOM and the event handler unbinds itself\n _setUpCloseBehavior: function(){\n var menu = this;\n//TODO: alternately: focus hack, blocking overlay, jquery.blockui\n\n // function to close popup and unbind itself\n function closePopup( event ){\n $( document ).off( 'click.close_popup' );\n if( window && window.parent !== window ){\n try {\n $( window.parent.document ).off( \"click.close_popup\" );\n } catch( err ){}\n } else {\n try {\n $( 'iframe#galaxy_main' ).contents().off( \"click.close_popup\" );\n } catch( err ){}\n }\n menu.remove();\n }\n\n $( 'html' ).one( \"click.close_popup\", closePopup );\n if( window && window.parent !== window ){\n try {\n $( window.parent.document ).find( 'html' ).one( \"click.close_popup\", closePopup );\n } catch( err ){}\n } else {\n try {\n $( 'iframe#galaxy_main' ).contents().one( \"click.close_popup\", closePopup );\n } catch( err ){}\n }\n },\n\n // add a menu option/item at the given index\n addItem: function( item, index ){\n // append to end if no index\n index = ( index >= 0 ) ? index : this.options.length;\n this.options.splice( index, 0, item );\n return this;\n },\n\n // remove a menu option/item at the given index\n removeItem: function( index ){\n if( index >=0 ){\n this.options.splice( index, 1 );\n }\n return this;\n },\n\n // search for a menu option by its html\n findIndexByHtml: function( html ){\n for( var i = 0; i < this.options.length; i++ ){\n if( _.has( this.options[i], 'html' ) && ( this.options[i].html === html )){\n return i;\n }\n }\n return null;\n },\n\n // search for a menu option by its html\n findItemByHtml: function( html ){\n return this.options[( this.findIndexByHtml( html ))];\n },\n\n // string representation\n toString: function(){\n return 'PopupMenu';\n }\n});\n/** shortcut to new for when you don't need to preserve the ref */\nPopupMenu.create = function _create( $button, options ){\n return new PopupMenu( $button, options );\n};\n\n// -----------------------------------------------------------------------------\n// the following class functions are bridges from the original make_popupmenu and make_popup_menus\n// to the newer backbone.js PopupMenu\n\n/** Create a PopupMenu from simple map initial_options activated by clicking button_element.\n * Converts initial_options to object array used by PopupMenu.\n * @param {jQuery|DOMElement} button_element element which, when clicked, activates menu\n * @param {Object} initial_options map of key -> values, where\n * key is option text, value is fn to call when option is clicked\n * @returns {PopupMenu} the PopupMenu created\n */\nPopupMenu.make_popupmenu = function( button_element, initial_options ){\n var convertedOptions = [];\n _.each( initial_options, function( optionVal, optionKey ){\n var newOption = { html: optionKey };\n\n // keys with null values indicate: header\n if( optionVal === null ){ // !optionVal? (null only?)\n newOption.header = true;\n\n // keys with function values indicate: a menu option\n } else if( jQuery.type( optionVal ) === 'function' ){\n newOption.func = optionVal;\n }\n //TODO:?? any other special optionVals?\n // there was no divider option originally\n convertedOptions.push( newOption );\n });\n return new PopupMenu( $( button_element ), convertedOptions );\n};\n\n/** Find all anchors in $parent (using selector) and covert anchors into a PopupMenu options map.\n * @param {jQuery} $parent the element that contains the links to convert to options\n * @param {String} selector jq selector string to find links\n * @returns {Object[]} the options array to initialize a PopupMenu\n */\n//TODO: lose parent and selector, pass in array of links, use map to return options\nPopupMenu.convertLinksToOptions = function( $parent, selector ){\n $parent = $( $parent );\n selector = selector || 'a';\n var options = [];\n $parent.find( selector ).each( function( elem, i ){\n var option = {}, $link = $( elem );\n\n // convert link text to the option text (html) and the href into the option func\n option.html = $link.text();\n if( $link.attr( 'href' ) ){\n var linkHref = $link.attr( 'href' ),\n linkTarget = $link.attr( 'target' ),\n confirmText = $link.attr( 'confirm' );\n\n option.func = function(){\n // if there's a \"confirm\" attribute, throw up a confirmation dialog, and\n // if the user cancels - do nothing\n if( ( confirmText ) && ( !confirm( confirmText ) ) ){ return; }\n\n // if there's no confirm attribute, or the user accepted the confirm dialog:\n switch( linkTarget ){\n // relocate the center panel\n case '_parent':\n window.parent.location = linkHref;\n break;\n\n // relocate the entire window\n case '_top':\n window.top.location = linkHref;\n break;\n\n // relocate this panel\n default:\n window.location = linkHref;\n }\n };\n }\n options.push( option );\n });\n return options;\n};\n\n/** Create a single popupmenu from existing DOM button and anchor elements\n * @param {jQuery} $buttonElement the element that when clicked will open the menu\n * @param {jQuery} $menuElement the element that contains the anchors to convert into a menu\n * @param {String} menuElementLinkSelector jq selector string used to find anchors to be made into menu options\n * @returns {PopupMenu} the PopupMenu (Backbone View) that can render, control the menu\n */\nPopupMenu.fromExistingDom = function( $buttonElement, $menuElement, menuElementLinkSelector ){\n $buttonElement = $( $buttonElement );\n $menuElement = $( $menuElement );\n var options = PopupMenu.convertLinksToOptions( $menuElement, menuElementLinkSelector );\n // we're done with the menu (having converted it to an options map)\n $menuElement.remove();\n return new PopupMenu( $buttonElement, options );\n};\n\n/** Create all popupmenus within a document or a more specific element\n * @param {DOMElement} parent the DOM element in which to search for popupmenus to build (defaults to document)\n * @param {String} menuSelector jq selector string to find popupmenu menu elements (defaults to \"div[popupmenu]\")\n * @param {Function} buttonSelectorBuildFn the function to build the jq button selector.\n * Will be passed $menuElement, parent.\n * (Defaults to return '#' + $menuElement.attr( 'popupmenu' ); )\n * @returns {PopupMenu[]} array of popupmenus created\n */\nPopupMenu.make_popup_menus = function( parent, menuSelector, buttonSelectorBuildFn ){\n parent = parent || document;\n // orig. Glx popupmenu menus have a (non-std) attribute 'popupmenu'\n // which contains the id of the button that activates the menu\n menuSelector = menuSelector || 'div[popupmenu]';\n // default to (orig. Glx) matching button to menu by using the popupmenu attr of the menu as the id of the button\n buttonSelectorBuildFn = buttonSelectorBuildFn || function( $menuElement, parent ){\n return '#' + $menuElement.attr( 'popupmenu' );\n };\n\n // aggregate and return all PopupMenus\n var popupMenusCreated = [];\n $( parent ).find( menuSelector ).each( function(){\n var $menuElement = $( this ),\n $buttonElement = $( parent ).find( buttonSelectorBuildFn( $menuElement, parent ) );\n popupMenusCreated.push( PopupMenu.fromDom( $buttonElement, $menuElement ) );\n $buttonElement.addClass( 'popup' );\n });\n return popupMenusCreated;\n};\n\n\n// =============================================================================\n return PopupMenu;\n});\n\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/ui/popup-menu.js","/** Renders the color picker used e.g. in the tool form **/\ndefine(['utils/utils'], function( Utils ) {\n return Backbone.View.extend({\n colors: {\n standard: ['c00000','ff0000','ffc000','ffff00','92d050','00b050','00b0f0','0070c0','002060','7030a0'],\n base : ['ffffff','000000','eeece1','1f497d','4f81bd','c0504d','9bbb59','8064a2','4bacc6','f79646'],\n theme :[['f2f2f2','7f7f7f','ddd9c3','c6d9f0','dbe5f1','f2dcdb','ebf1dd','e5e0ec','dbeef3','fdeada'],\n ['d8d8d8','595959','c4bd97','8db3e2','b8cce4','e5b9b7','d7e3bc','ccc1d9','b7dde8','fbd5b5'],\n ['bfbfbf','3f3f3f','938953','548dd4','95b3d7','d99694','c3d69b','b2a2c7','92cddc','fac08f'],\n ['a5a5a5','262626','494429','17365d','366092','953734','76923c','5f497a','31859b','e36c09'],\n ['7f7f7e','0c0c0c','1d1b10','0f243e','244061','632423','4f6128','3f3151','205867','974806']]\n },\n\n initialize : function( options ) {\n this.options = Utils.merge( options, {} );\n this.setElement( this._template() );\n this.$panel = this.$( '.ui-color-picker-panel' );\n this.$view = this.$( '.ui-color-picker-view' );\n this.$value = this.$( '.ui-color-picker-value' );\n this.$header = this.$( '.ui-color-picker-header' );\n this._build();\n this.visible = false;\n this.value( this.options.value );\n this.$boxes = this.$( '.ui-color-picker-box' );\n var self = this;\n this.$boxes.on( 'click', function() {\n self.value( $( this ).css( 'background-color' ) );\n self.$header.trigger( 'click' );\n } );\n this.$header.on( 'click', function() {\n self.visible = !self.visible;\n if ( self.visible ) {\n self.$view.fadeIn( 'fast' );\n } else {\n self.$view.fadeOut( 'fast' );\n }\n } );\n },\n\n /** Get/set value */\n value : function ( new_val ) {\n if ( new_val !== undefined && new_val !== null ) {\n this.$value.css( 'background-color', new_val );\n this.$( '.ui-color-picker-box' ).empty();\n this.$( this._getValue() ).html( this._templateCheck() );\n this.options.onchange && this.options.onchange( new_val );\n }\n return this._getValue();\n },\n\n /** Get value from dom */\n _getValue: function() {\n var rgb = this.$value.css( 'background-color' );\n rgb = rgb.match(/^rgb\\((\\d+),\\s*(\\d+),\\s*(\\d+)\\)$/);\n if ( rgb ) {\n function hex( x ) {\n return ( '0' + parseInt( x ).toString( 16 ) ).slice( -2 );\n }\n return '#' + hex( rgb[ 1] ) + hex( rgb[ 2 ] ) + hex( rgb[ 3 ] );\n } else {\n return null;\n }\n },\n\n /** Build color panel */\n _build: function() {\n this._content( { colors : this.colors.base } );\n for ( var i in this.colors.theme ) {\n var line_def = {};\n if ( i == 0 ) {\n line_def[ 'bottom' ] = true;\n } else if ( i != this.colors.theme.length - 1 ) {\n line_def[ 'top' ] = true;\n line_def[ 'bottom' ] = true;\n } else {\n line_def[ 'top' ] = true;\n }\n line_def[ 'colors' ] = this.colors.theme[ i ];\n this._content( line_def );\n }\n this._content( { colors : this.colors.standard } );\n },\n\n /** Create content */\n _content: function( options ) {\n var colors = options.colors;\n var $content = $( this._templateContent() );\n var $line = $content.find( '.line' );\n this.$panel.append( $content );\n for ( var i in colors ) {\n var $box = $( this._templateBox( colors[ i ] ) );\n if ( options.top ) {\n $box.css( 'border-top', 'none' );\n $box.css( 'border-top-left-radius', '0px' );\n $box.css( 'border-top-right-radius', '0px' );\n }\n if ( options.bottom ) {\n $box.css( 'border-bottom', 'none' );\n $box.css( 'border-bottom-left-radius', '0px' );\n $box.css( 'border-bottom-right-radius', '0px' );\n }\n $line.append( $box );\n }\n return $content;\n },\n\n /** Check icon */\n _templateCheck: function() {\n return '';\n },\n\n /** Content template */\n _templateContent: function() {\n return '
';\n },\n\n /** Template of info message */\n _templateInfo: function() {\n return '
' +\n 'Your FTP directory does not contain any files.' +\n '
';\n },\n\n /** Template of main view */\n _template: function() {\n return '
' +\n '' +\n '
This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at ' + this.options.ftp_upload_site + ' using your Galaxy credentials (email address and password).
' +\n '
' +\n '
';\n }\n });\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/upload/upload-ftp.js","/** This renders the content of the settings popup, allowing users to specify flags i.e. for space-to-tab conversion **/\ndefine( [ 'utils/utils' ], function( Utils ) {\n return Backbone.View.extend({\n options: {\n class_check : 'fa-check-square-o',\n class_uncheck : 'fa-square-o',\n parameters : [{\n id : 'space_to_tab',\n title : 'Convert spaces to tabs',\n },{\n id : 'to_posix_lines',\n title : 'Use POSIX standard'\n }]\n },\n\n initialize: function( options ) {\n var self = this;\n this.model = options.model;\n this.setElement( $( '' ).addClass( 'upload-settings' ) );\n this.$el.append( $( '' ).addClass( 'upload-settings-cover' ) );\n this.$el.append( $( '
',\n ], 'collection' );\n\n return _.extend( _.clone( _super.prototype.templates ), {\n controls : controlsTemplate\n });\n}());\n\n\n\n// =============================================================================\n/** @class non-editable, read-only View/Controller for a dataset collection. */\nvar ListCollectionView = CollectionView.extend(\n/** @lends ListCollectionView.prototype */{\n\n //TODO: not strictly needed - due to switch in CollectionView._getContentClass\n /** sub view class used for datasets */\n DatasetDCEViewClass : DC_LI.DatasetDCEListItemView,\n\n // ........................................................................ misc\n /** string rep */\n toString : function(){\n return 'ListCollectionView(' + (( this.model )?( this.model.get( 'name' )):( '' )) + ')';\n }\n});\n\n\n// =============================================================================\n/** @class non-editable, read-only View/Controller for a dataset collection. */\nvar PairCollectionView = ListCollectionView.extend(\n/** @lends PairCollectionView.prototype */{\n\n // ........................................................................ misc\n /** string rep */\n toString : function(){\n return 'PairCollectionView(' + (( this.model )?( this.model.get( 'name' )):( '' )) + ')';\n }\n});\n\n\n// =============================================================================\n/** @class non-editable, read-only View/Controller for a dataset collection. */\nvar ListOfPairsCollectionView = CollectionView.extend(\n/** @lends ListOfPairsCollectionView.prototype */{\n\n //TODO: not strictly needed - due to switch in CollectionView._getContentClass\n /** sub view class used for nested collections */\n NestedDCDCEViewClass : DC_LI.NestedDCDCEListItemView.extend({\n foldoutPanelClass : PairCollectionView\n }),\n\n // ........................................................................ misc\n /** string rep */\n toString : function(){\n return 'ListOfPairsCollectionView(' + (( this.model )?( this.model.get( 'name' )):( '' )) + ')';\n }\n});\n\n\n// =============================================================================\n/** @class non-editable, read-only View/Controller for a list of lists dataset collection. */\nvar ListOfListsCollectionView = CollectionView.extend({\n\n /** sub view class used for nested collections */\n NestedDCDCEViewClass : DC_LI.NestedDCDCEListItemView.extend({\n foldoutPanelClass : PairCollectionView\n }),\n\n /** string rep */\n toString : function(){\n return 'ListOfListsCollectionView(' + (( this.model )?( this.model.get( 'name' )):( '' )) + ')';\n }\n});\n\n\n//==============================================================================\n return {\n CollectionView : CollectionView,\n ListCollectionView : ListCollectionView,\n PairCollectionView : PairCollectionView,\n ListOfPairsCollectionView : ListOfPairsCollectionView,\n ListOfListsCollectionView : ListOfListsCollectionView\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/collection/collection-view.js","define([\n \"mvc/dataset/states\",\n \"mvc/dataset/dataset-li\",\n \"mvc/tag\",\n \"mvc/annotation\",\n \"ui/fa-icon-button\",\n \"mvc/base-mvc\",\n \"utils/localization\"\n], function( STATES, DATASET_LI, TAGS, ANNOTATIONS, faIconButton, BASE_MVC, _l ){\n\n'use strict';\n//==============================================================================\nvar _super = DATASET_LI.DatasetListItemView;\n/** @class Editing view for DatasetAssociation.\n */\nvar DatasetListItemEdit = _super.extend(\n/** @lends DatasetListItemEdit.prototype */{\n\n /** set up: options */\n initialize : function( attributes ){\n _super.prototype.initialize.call( this, attributes );\n this.hasUser = attributes.hasUser;\n\n /** allow user purge of dataset files? */\n this.purgeAllowed = attributes.purgeAllowed || false;\n\n //TODO: move to HiddenUntilActivatedViewMixin\n /** should the tags editor be shown or hidden initially? */\n this.tagsEditorShown = attributes.tagsEditorShown || false;\n /** should the tags editor be shown or hidden initially? */\n this.annotationEditorShown = attributes.annotationEditorShown || false;\n },\n\n // ......................................................................... titlebar actions\n /** In this override, add the other two primary actions: edit and delete */\n _renderPrimaryActions : function(){\n var actions = _super.prototype._renderPrimaryActions.call( this );\n if( this.model.get( 'state' ) === STATES.NOT_VIEWABLE ){\n return actions;\n }\n // render the display, edit attr and delete icon-buttons\n return _super.prototype._renderPrimaryActions.call( this ).concat([\n this._renderEditButton(),\n this._renderDeleteButton()\n ]);\n },\n\n //TODO: move titleButtons into state renderers, remove state checks in the buttons\n\n /** Render icon-button to edit the attributes (format, permissions, etc.) this dataset. */\n _renderEditButton : function(){\n // don't show edit while uploading, in-accessible\n // DO show if in error (ala previous history panel)\n if( ( this.model.get( 'state' ) === STATES.DISCARDED )\n || ( !this.model.get( 'accessible' ) ) ){\n return null;\n }\n\n var purged = this.model.get( 'purged' ),\n deleted = this.model.get( 'deleted' ),\n editBtnData = {\n title : _l( 'Edit attributes' ),\n href : this.model.urls.edit,\n target : this.linkTarget,\n faIcon : 'fa-pencil',\n classes : 'edit-btn'\n };\n\n // disable if purged or deleted and explain why in the tooltip\n if( deleted || purged ){\n editBtnData.disabled = true;\n if( purged ){\n editBtnData.title = _l( 'Cannot edit attributes of datasets removed from disk' );\n } else if( deleted ){\n editBtnData.title = _l( 'Undelete dataset to edit attributes' );\n }\n\n // disable if still uploading or new\n } else if( _.contains( [ STATES.UPLOAD, STATES.NEW ], this.model.get( 'state' ) ) ){\n editBtnData.disabled = true;\n editBtnData.title = _l( 'This dataset is not yet editable' );\n }\n return faIconButton( editBtnData );\n },\n\n /** Render icon-button to delete this hda. */\n _renderDeleteButton : function(){\n // don't show delete if...\n if( ( !this.model.get( 'accessible' ) ) ){\n return null;\n }\n\n var self = this,\n deletedAlready = this.model.isDeletedOrPurged();\n return faIconButton({\n title : !deletedAlready? _l( 'Delete' ) : _l( 'Dataset is already deleted' ),\n disabled : deletedAlready,\n faIcon : 'fa-times',\n classes : 'delete-btn',\n onclick : function() {\n // ...bler... tooltips being left behind in DOM (hover out never called on deletion)\n self.$el.find( '.icon-btn.delete-btn' ).trigger( 'mouseout' );\n self.model[ 'delete' ]();\n }\n });\n },\n\n // ......................................................................... details\n /** In this override, add tags and annotations controls, make the ? dbkey a link to editing page */\n _renderDetails : function(){\n //TODO: generalize to be allow different details for each state\n var $details = _super.prototype._renderDetails.call( this ),\n state = this.model.get( 'state' );\n\n if( !this.model.isDeletedOrPurged() && _.contains([ STATES.OK, STATES.FAILED_METADATA ], state ) ){\n this._renderTags( $details );\n this._renderAnnotation( $details );\n this._makeDbkeyEditLink( $details );\n }\n\n this._setUpBehaviors( $details );\n return $details;\n },\n\n /**************************************************************************\n * Render help button to show tool help text without rerunning the tool.\n * Issue #2100\n */\n _renderToolHelpButton : function() {\n var datasetID = this.model.attributes.dataset_id;\n var jobID = this.model.attributes.creating_job;\n var self = this;\n\n var parseToolBuild = function(data) {\n var helpString = '
'\n if (data.name && data.help){\n helpString += 'Tool help for ' + data.name + '';\n helpString += data.help;\n } else {\n helpString += 'Tool help is unavailable for this dataset.';\n }\n helpString += '
';\n self.$el.find( '.details' ).append($.parseHTML(helpString));\n };\n var parseToolID = function(data) {\n $.ajax({\n url: Galaxy.root + 'api/tools/' + data.tool_id + '/build'\n }).done(function(data){\n parseToolBuild(data);\n }).fail(function(){\n parseToolBuild({})\n });\n };\n if (Galaxy.user.id === null){\n return null\n }\n return faIconButton({\n title: 'Tool Help',\n classes: 'icon-btn',\n href: '#',\n faIcon: 'fa-question',\n onclick: function() {\n var divString = 'thdiv-' + datasetID;\n if (self.$el.find(\".toolhelp\").length > 0){\n self.$el.find(\".toolhelp\").toggle();\n } else {\n $.ajax({\n url: Galaxy.root + 'api/jobs/' + jobID\n }).done(function(data){\n parseToolID(data);\n }).fail(function(){\n console.log('Failed at recovering job information from the Galaxy API for job id \"' + jobID + '\".');\n });\n }\n }\n });\n },\n //*************************************************************************\n\n /** Add less commonly used actions in the details section based on state */\n _renderSecondaryActions : function(){\n var actions = _super.prototype._renderSecondaryActions.call( this );\n switch( this.model.get( 'state' ) ){\n case STATES.UPLOAD:\n case STATES.NOT_VIEWABLE:\n return actions;\n case STATES.ERROR:\n // error button comes first\n actions.unshift( this._renderErrButton() );\n return actions.concat([ this._renderRerunButton(), this._renderToolHelpButton() ]);\n case STATES.OK:\n case STATES.FAILED_METADATA:\n return actions.concat([ this._renderRerunButton(), this._renderVisualizationsButton(), this._renderToolHelpButton() ]);\n }\n return actions.concat([ this._renderRerunButton(), this._renderToolHelpButton() ]);\n },\n\n /** Render icon-button to report an error on this dataset to the galaxy admin. */\n _renderErrButton : function(){\n return faIconButton({\n title : _l( 'View or report this error' ),\n href : this.model.urls.report_error,\n classes : 'report-error-btn',\n target : this.linkTarget,\n faIcon : 'fa-bug'\n });\n },\n\n /** Render icon-button to re-run the job that created this dataset. */\n _renderRerunButton : function(){\n var creating_job = this.model.get( 'creating_job' );\n if( this.model.get( 'rerunnable' ) ){\n return faIconButton({\n title : _l( 'Run this job again' ),\n href : this.model.urls.rerun,\n classes : 'rerun-btn',\n target : this.linkTarget,\n faIcon : 'fa-refresh',\n onclick : function( ev ) {\n ev.preventDefault();\n Galaxy.router.push( '/', { job_id : creating_job } );\n }\n });\n }\n },\n\n /** Render an icon-button or popupmenu of links based on the applicable visualizations */\n _renderVisualizationsButton : function(){\n //TODO: someday - lazyload visualizations\n var visualizations = this.model.get( 'visualizations' );\n if( ( this.model.isDeletedOrPurged() )\n || ( !this.hasUser )\n || ( !this.model.hasData() )\n || ( _.isEmpty( visualizations ) ) ){\n return null;\n }\n if( !_.isObject( visualizations[0] ) ){\n this.warn( 'Visualizations have been switched off' );\n return null;\n }\n\n var $visualizations = $( this.templates.visualizations( visualizations, this ) );\n //HACK: need to re-write those directed at galaxy_main with linkTarget\n $visualizations.find( '[target=\"galaxy_main\"]').attr( 'target', this.linkTarget );\n // use addBack here to include the root $visualizations elem (for the case of 1 visualization)\n this._addScratchBookFn( $visualizations.find( '.visualization-link' ).addBack( '.visualization-link' ) );\n return $visualizations;\n },\n\n /** add scratchbook functionality to visualization links */\n _addScratchBookFn : function( $links ){\n var li = this;\n $links.click( function( ev ){\n if( Galaxy.frame && Galaxy.frame.active ){\n Galaxy.frame.add({\n title : 'Visualization',\n url : $( this ).attr( 'href' )\n });\n ev.preventDefault();\n ev.stopPropagation();\n }\n });\n },\n\n //TODO: if possible move these to readonly view - but display the owner's tags/annotation (no edit)\n /** Render the tags list/control */\n _renderTags : function( $where ){\n if( !this.hasUser ){ return; }\n var view = this;\n this.tagsEditor = new TAGS.TagsEditor({\n model : this.model,\n el : $where.find( '.tags-display' ),\n onshowFirstTime : function(){ this.render(); },\n // persist state on the hda view (and not the editor) since these are currently re-created each time\n onshow : function(){ view.tagsEditorShown = true; },\n onhide : function(){ view.tagsEditorShown = false; },\n $activator : faIconButton({\n title : _l( 'Edit dataset tags' ),\n classes : 'tag-btn',\n faIcon : 'fa-tags'\n }).appendTo( $where.find( '.actions .right' ) )\n });\n if( this.tagsEditorShown ){ this.tagsEditor.toggle( true ); }\n },\n\n /** Render the annotation display/control */\n _renderAnnotation : function( $where ){\n if( !this.hasUser ){ return; }\n var view = this;\n this.annotationEditor = new ANNOTATIONS.AnnotationEditor({\n model : this.model,\n el : $where.find( '.annotation-display' ),\n onshowFirstTime : function(){ this.render(); },\n // persist state on the hda view (and not the editor) since these are currently re-created each time\n onshow : function(){ view.annotationEditorShown = true; },\n onhide : function(){ view.annotationEditorShown = false; },\n $activator : faIconButton({\n title : _l( 'Edit dataset annotation' ),\n classes : 'annotate-btn',\n faIcon : 'fa-comment'\n }).appendTo( $where.find( '.actions .right' ) )\n });\n if( this.annotationEditorShown ){ this.annotationEditor.toggle( true ); }\n },\n\n /** If the format/dbkey/genome_build isn't set, make the display a link to the edit page */\n _makeDbkeyEditLink : function( $details ){\n // make the dbkey a link to editing\n if( this.model.get( 'metadata_dbkey' ) === '?'\n && !this.model.isDeletedOrPurged() ){\n var editableDbkey = $( '?' )\n .attr( 'href', this.model.urls.edit )\n .attr( 'target', this.linkTarget );\n $details.find( '.dbkey .value' ).replaceWith( editableDbkey );\n }\n },\n\n // ......................................................................... events\n /** event map */\n events : _.extend( _.clone( _super.prototype.events ), {\n 'click .undelete-link' : '_clickUndeleteLink',\n 'click .purge-link' : '_clickPurgeLink',\n\n 'click .edit-btn' : function( ev ){ this.trigger( 'edit', this, ev ); },\n 'click .delete-btn' : function( ev ){ this.trigger( 'delete', this, ev ); },\n 'click .rerun-btn' : function( ev ){ this.trigger( 'rerun', this, ev ); },\n 'click .report-err-btn' : function( ev ){ this.trigger( 'report-err', this, ev ); },\n 'click .visualization-btn' : function( ev ){ this.trigger( 'visualize', this, ev ); },\n 'click .dbkey a' : function( ev ){ this.trigger( 'edit', this, ev ); }\n }),\n\n /** listener for item undelete (in the messages section) */\n _clickUndeleteLink : function( ev ){\n this.model.undelete();\n return false;\n },\n\n /** listener for item purge (in the messages section) */\n _clickPurgeLink : function( ev ){\n if( confirm( _l( 'This will permanently remove the data in your dataset. Are you sure?' ) ) ){\n this.model.purge();\n }\n return false;\n },\n\n // ......................................................................... misc\n /** string rep */\n toString : function(){\n var modelString = ( this.model )?( this.model + '' ):( '(no model)' );\n return 'HDAEditView(' + modelString + ')';\n }\n});\n\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nDatasetListItemEdit.prototype.templates = (function(){\n\n var warnings = _.extend( {}, _super.prototype.templates.warnings, {\n failed_metadata : BASE_MVC.wrapTemplate([\n // in this override, provide a link to the edit page\n '<% if( dataset.state === \"failed_metadata\" ){ %>',\n '
',\n '<% } %>'\n ], 'dataset' ),\n\n deleted : BASE_MVC.wrapTemplate([\n // in this override, provide links to undelete or purge the dataset\n '<% if( dataset.deleted && !dataset.purged ){ %>',\n // deleted not purged\n '
'\n ], 'dataset' );\n\n var warnings = _.extend( {}, _super.prototype.templates.warnings, {\n hidden : BASE_MVC.wrapTemplate([\n // add a warning when hidden\n '<% if( !dataset.visible ){ %>',\n '
',\n _l( 'This dataset has been hidden' ),\n '
',\n '<% } %>'\n ], 'dataset' )\n });\n\n return _.extend( {}, _super.prototype.templates, {\n titleBar : titleBarTemplate,\n warnings : warnings\n });\n}());\n\n\n\n//==============================================================================\n return {\n HDAListItemView : HDAListItemView\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/history/hda-li.js","define([\n \"mvc/dataset/dataset-model\",\n \"mvc/history/history-content-model\",\n \"mvc/base-mvc\",\n \"utils/localization\"\n], function( DATASET, HISTORY_CONTENT, BASE_MVC, _l ){\n'use strict';\n\n//==============================================================================\nvar _super = DATASET.DatasetAssociation,\n hcontentMixin = HISTORY_CONTENT.HistoryContentMixin;\n/** @class (HDA) model for a Galaxy dataset contained in and related to a history.\n */\nvar HistoryDatasetAssociation = _super.extend( BASE_MVC.mixin( hcontentMixin,\n/** @lends HistoryDatasetAssociation.prototype */{\n\n /** default attributes for a model */\n defaults : _.extend( {}, _super.prototype.defaults, hcontentMixin.defaults, {\n history_content_type: 'dataset',\n model_class : 'HistoryDatasetAssociation'\n }),\n}));\n\n//==============================================================================\n return {\n HistoryDatasetAssociation : HistoryDatasetAssociation\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/history/hda-model.js","define([\n \"mvc/dataset/states\",\n \"mvc/collection/collection-li\",\n \"mvc/collection/collection-view\",\n \"mvc/base-mvc\",\n \"utils/localization\"\n], function( STATES, DC_LI, DC_VIEW, BASE_MVC, _l ){\n\n'use strict';\n\n//==============================================================================\nvar _super = DC_LI.DCListItemView;\n/** @class Read only view for HistoryDatasetCollectionAssociation (a dataset collection inside a history).\n */\nvar HDCAListItemView = _super.extend(\n/** @lends HDCAListItemView.prototype */{\n\n className : _super.prototype.className + \" history-content\",\n\n /** event listeners */\n _setUpListeners : function(){\n _super.prototype._setUpListeners.call( this );\n this.listenTo( this.model, {\n 'change:tags change:populated change:visible' : function( model, options ){ this.render(); },\n });\n },\n\n /** Override to provide the proper collections panels as the foldout */\n _getFoldoutPanelClass : function(){\n switch( this.model.get( 'collection_type' ) ){\n case 'list':\n return DC_VIEW.ListCollectionView;\n case 'paired':\n return DC_VIEW.PairCollectionView;\n case 'list:paired':\n return DC_VIEW.ListOfPairsCollectionView;\n case 'list:list':\n return DC_VIEW.ListOfListsCollectionView;\n }\n throw new TypeError( 'Uknown collection_type: ' + this.model.get( 'collection_type' ) );\n },\n\n /** In this override, add the state as a class for use with state-based CSS */\n _swapNewRender : function( $newRender ){\n _super.prototype._swapNewRender.call( this, $newRender );\n //TODO: model currently has no state\n var state = !this.model.get( 'populated' ) ? STATES.RUNNING : STATES.OK;\n //if( this.model.has( 'state' ) ){\n this.$el.addClass( 'state-' + state );\n //}\n return this.$el;\n },\n\n // ......................................................................... misc\n /** String representation */\n toString : function(){\n var modelString = ( this.model )?( this.model + '' ):( '(no model)' );\n return 'HDCAListItemView(' + modelString + ')';\n }\n});\n\n/** underscore templates */\nHDCAListItemView.prototype.templates = (function(){\n\n var warnings = _.extend( {}, _super.prototype.templates.warnings, {\n hidden : BASE_MVC.wrapTemplate([\n // add a warning when hidden\n '<% if( !collection.visible ){ %>',\n '
',\n _l( 'This collection has been hidden' ),\n '
',\n '<% } %>'\n ], 'collection' )\n });\n\n// could steal this from hda-base (or use mixed content)\n var titleBarTemplate = BASE_MVC.wrapTemplate([\n // adding the hid display to the title\n '
',\n '',\n '
',\n //TODO: remove whitespace and use margin-right\n '<%- collection.hid %> ',\n '<%- collection.name %>',\n '
'\n ], 'collection' );\n\n return _.extend( {}, _super.prototype.templates, {\n warnings : warnings,\n titleBar : titleBarTemplate\n });\n}());\n\n\n//==============================================================================\n return {\n HDCAListItemView : HDCAListItemView\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/history/hdca-li.js","define([\n \"mvc/dataset/states\",\n \"mvc/base-mvc\",\n \"utils/localization\"\n], function( STATES, BASE_MVC, _l ){\n'use strict';\n\n//==============================================================================\n/** @class Mixin for HistoryContents content (HDAs, HDCAs).\n */\nvar HistoryContentMixin = {\n\n /** default attributes for a model */\n defaults : {\n /** parent (containing) history */\n history_id : null,\n /** some content_type (HistoryContents can contain mixed model classes) */\n history_content_type: null,\n /** indicating when/what order the content was generated in the context of the history */\n hid : null,\n /** whether the user wants the content shown (visible) */\n visible : true\n },\n\n // ........................................................................ mixed content element\n // In order to be part of a MIXED bbone collection, we can't rely on the id\n // (which may collide btwn models of different classes)\n // Instead, use type_id which prefixes the history_content_type so the bbone collection can differentiate\n idAttribute : 'type_id',\n\n // ........................................................................ common queries\n /** the more common alias of visible */\n hidden : function(){\n return !this.get( 'visible' );\n },\n\n//TODO: remove\n /** based on includeDeleted, includeHidden (gen. from the container control),\n * would this ds show in the list of ds's?\n * @param {Boolean} includeDeleted are we showing deleted hdas?\n * @param {Boolean} includeHidden are we showing hidden hdas?\n */\n isVisible : function( includeDeleted, includeHidden ){\n var isVisible = true;\n if( ( !includeDeleted )\n && ( this.get( 'deleted' ) || this.get( 'purged' ) ) ){\n isVisible = false;\n }\n if( ( !includeHidden )\n && ( !this.get( 'visible' ) ) ){\n isVisible = false;\n }\n return isVisible;\n },\n\n // ........................................................................ ajax\n //TODO?: these are probably better done on the leaf classes\n /** history content goes through the 'api/histories' API */\n urlRoot: Galaxy.root + 'api/histories/',\n\n /** full url spec. for this content */\n url : function(){\n var url = this.urlRoot + this.get( 'history_id' ) + '/contents/'\n + this.get('history_content_type') + 's/' + this.get( 'id' );\n return url;\n },\n\n /** save this content as not visible */\n hide : function( options ){\n if( !this.get( 'visible' ) ){ return jQuery.when(); }\n return this.save( { visible: false }, options );\n },\n /** save this content as visible */\n unhide : function( options ){\n if( this.get( 'visible' ) ){ return jQuery.when(); }\n return this.save( { visible: true }, options );\n },\n\n // ........................................................................ misc\n toString : function(){\n return ([ this.get( 'type_id' ), this.get( 'hid' ), this.get( 'name' ) ].join(':'));\n }\n};\n\n\n//==============================================================================\n return {\n HistoryContentMixin : HistoryContentMixin\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/history/history-content-model.js","\ndefine([\n \"mvc/history/history-contents\",\n \"mvc/history/history-preferences\",\n \"mvc/base/controlled-fetch-collection\",\n \"utils/utils\",\n \"mvc/base-mvc\",\n \"utils/localization\"\n], function( HISTORY_CONTENTS, HISTORY_PREFS, CONTROLLED_FETCH_COLLECTION, UTILS, BASE_MVC, _l ){\n'use strict';\n\n//==============================================================================\n/** @class Model for a Galaxy history resource - both a record of user\n * tool use and a collection of the datasets those tools produced.\n * @name History\n * @augments Backbone.Model\n */\nvar History = Backbone.Model\n .extend( BASE_MVC.LoggableMixin )\n .extend( BASE_MVC.mixin( BASE_MVC.SearchableModelMixin, /** @lends History.prototype */{\n _logNamespace : 'history',\n\n /** ms between fetches when checking running jobs/datasets for updates */\n UPDATE_DELAY : 4000,\n\n // values from api (may need more)\n defaults : {\n model_class : 'History',\n id : null,\n name : 'Unnamed History',\n state : 'new',\n\n deleted : false,\n contents_active : {},\n contents_states : {},\n },\n\n urlRoot: Galaxy.root + 'api/histories',\n\n contentsClass : HISTORY_CONTENTS.HistoryContents,\n\n /** What model fields to search with */\n searchAttributes : [\n 'name', 'annotation', 'tags'\n ],\n\n /** Adding title and singular tag */\n searchAliases : {\n title : 'name',\n tag : 'tags'\n },\n\n // ........................................................................ set up/tear down\n /** Set up the model\n * @param {Object} historyJSON model data for this History\n * @param {Object} options any extra settings including logger\n */\n initialize : function( historyJSON, options ){\n options = options || {};\n this.logger = options.logger || null;\n this.log( this + \".initialize:\", historyJSON, options );\n\n /** HistoryContents collection of the HDAs contained in this history. */\n this.contents = new this.contentsClass( [], {\n history : this,\n historyId : this.get( 'id' ),\n order : options.order,\n });\n\n this._setUpListeners();\n this._setUpCollectionListeners();\n\n /** cached timeout id for the dataset updater */\n this.updateTimeoutId = null;\n },\n\n /** set up any event listeners for this history including those to the contained HDAs\n * events: error:contents if an error occurred with the contents collection\n */\n _setUpListeners : function(){\n // if the model's id changes ('current' or null -> an actual id), update the contents history_id\n return this.on({\n 'error' : function( model, xhr, options, msg, details ){\n this.clearUpdateTimeout();\n },\n 'change:id' : function( model, newId ){\n if( this.contents ){\n this.contents.historyId = newId;\n }\n },\n });\n },\n\n /** event handlers for the contents submodels */\n _setUpCollectionListeners : function(){\n if( !this.contents ){ return this; }\n // bubble up errors\n return this.listenTo( this.contents, {\n 'error' : function(){\n this.trigger.apply( this, jQuery.makeArray( arguments ) );\n },\n });\n },\n\n // ........................................................................ derived attributes\n /** */\n contentsShown : function(){\n var contentsActive = this.get( 'contents_active' );\n var shown = contentsActive.active || 0;\n shown += this.contents.includeDeleted? contentsActive.deleted : 0;\n shown += this.contents.includeHidden? contentsActive.hidden : 0;\n return shown;\n },\n\n /** convert size in bytes to a more human readable version */\n nice_size : function(){\n var size = this.get( 'size' );\n return size? UTILS.bytesToString( size, true, 2 ) : _l( '(empty)' );\n },\n\n /** override to add nice_size */\n toJSON : function(){\n return _.extend( Backbone.Model.prototype.toJSON.call( this ), {\n nice_size : this.nice_size()\n });\n },\n\n /** override to allow getting nice_size */\n get : function( key ){\n if( key === 'nice_size' ){\n return this.nice_size();\n }\n return Backbone.Model.prototype.get.apply( this, arguments );\n },\n\n // ........................................................................ common queries\n /** T/F is this history owned by the current user (Galaxy.user)\n * Note: that this will return false for an anon user even if the history is theirs.\n */\n ownedByCurrUser : function(){\n // no currUser\n if( !Galaxy || !Galaxy.user ){\n return false;\n }\n // user is anon or history isn't owned\n if( Galaxy.user.isAnonymous() || Galaxy.user.id !== this.get( 'user_id' ) ){\n return false;\n }\n return true;\n },\n\n /** Return the number of running jobs assoc with this history (note: unknown === 0) */\n numOfUnfinishedJobs : function(){\n var unfinishedJobIds = this.get( 'non_ready_jobs' );\n return unfinishedJobIds? unfinishedJobIds.length : 0;\n },\n\n /** Return the number of running hda/hdcas in this history (note: unknown === 0) */\n numOfUnfinishedShownContents : function(){\n return this.contents.runningAndActive().length || 0;\n },\n\n // ........................................................................ updates\n _fetchContentRelatedAttributes : function(){\n var contentRelatedAttrs = [ 'size', 'non_ready_jobs', 'contents_active', 'hid_counter' ];\n return this.fetch({ data : $.param({ keys : contentRelatedAttrs.join( ',' ) }) });\n },\n\n /** check for any changes since the last time we updated (or fetch all if ) */\n refresh : function( options ){\n // console.log( this + '.refresh' );\n options = options || {};\n var self = this;\n\n // note if there was no previous update time, all summary contents will be fetched\n var lastUpdateTime = self.lastUpdateTime;\n // if we don't flip this, then a fully-fetched list will not be re-checked via fetch\n this.contents.allFetched = false;\n var fetchFn = self.contents.currentPage !== 0\n ? function(){ return self.contents.fetchPage( self.contents.currentPage ); }\n : function(){ return self.contents.fetchUpdated( lastUpdateTime ); };\n // note: if there was no previous update time, all summary contents will be fetched\n return fetchFn()\n .done( function( response, status, xhr ){\n var serverResponseDatetime;\n try {\n serverResponseDatetime = new Date( xhr.getResponseHeader( 'Date' ) );\n } catch( err ){}\n self.lastUpdateTime = serverResponseDatetime || new Date();\n self.checkForUpdates( options );\n });\n },\n\n /** continuously fetch updated contents every UPDATE_DELAY ms if this history's datasets or jobs are unfinished */\n checkForUpdates : function( options ){\n // console.log( this + '.checkForUpdates' );\n options = options || {};\n var delay = this.UPDATE_DELAY;\n var self = this;\n if( !self.id ){ return; }\n\n function _delayThenUpdate(){\n // prevent buildup of updater timeouts by clearing previous if any, then set new and cache id\n self.clearUpdateTimeout();\n self.updateTimeoutId = setTimeout( function(){\n self.refresh( options );\n }, delay );\n }\n\n // if there are still datasets in the non-ready state, recurse into this function with the new time\n var nonReadyContentCount = this.numOfUnfinishedShownContents();\n // console.log( 'nonReadyContentCount:', nonReadyContentCount );\n if( nonReadyContentCount > 0 ){\n _delayThenUpdate();\n\n } else {\n // no datasets are running, but currently runnning jobs may still produce new datasets\n // see if the history has any running jobs and continue to update if so\n // (also update the size for the user in either case)\n self._fetchContentRelatedAttributes()\n .done( function( historyData ){\n // console.log( 'non_ready_jobs:', historyData.non_ready_jobs );\n if( self.numOfUnfinishedJobs() > 0 ){\n _delayThenUpdate();\n\n } else {\n // otherwise, let listeners know that all updates have stopped\n self.trigger( 'ready' );\n }\n });\n }\n },\n\n /** clear the timeout and the cached timeout id */\n clearUpdateTimeout : function(){\n if( this.updateTimeoutId ){\n clearTimeout( this.updateTimeoutId );\n this.updateTimeoutId = null;\n }\n },\n\n // ........................................................................ ajax\n /** override to use actual Dates objects for create/update times */\n parse : function( response, options ){\n var parsed = Backbone.Model.prototype.parse.call( this, response, options );\n if( parsed.create_time ){\n parsed.create_time = new Date( parsed.create_time );\n }\n if( parsed.update_time ){\n parsed.update_time = new Date( parsed.update_time );\n }\n return parsed;\n },\n\n /** fetch this histories data (using options) then it's contents (using contentsOptions) */\n fetchWithContents : function( options, contentsOptions ){\n options = options || {};\n var self = this;\n\n // console.log( this + '.fetchWithContents' );\n // TODO: push down to a base class\n options.view = 'dev-detailed';\n\n // fetch history then use history data to fetch (paginated) contents\n return this.fetch( options ).then( function getContents( history ){\n self.contents.history = self;\n self.contents.setHistoryId( history.id );\n return self.fetchContents( contentsOptions );\n });\n },\n\n /** fetch this histories contents, adjusting options based on the stored history preferences */\n fetchContents : function( options ){\n options = options || {};\n var self = this;\n\n // we're updating, reset the update time\n self.lastUpdateTime = new Date();\n return self.contents.fetchCurrentPage( options );\n },\n\n /** save this history, _Mark_ing it as deleted (just a flag) */\n _delete : function( options ){\n if( this.get( 'deleted' ) ){ return jQuery.when(); }\n return this.save( { deleted: true }, options );\n },\n /** purge this history, _Mark_ing it as purged and removing all dataset data from the server */\n purge : function( options ){\n if( this.get( 'purged' ) ){ return jQuery.when(); }\n return this.save( { deleted: true, purged: true }, options );\n },\n /** save this history, _Mark_ing it as undeleted */\n undelete : function( options ){\n if( !this.get( 'deleted' ) ){ return jQuery.when(); }\n return this.save( { deleted: false }, options );\n },\n\n /** Make a copy of this history on the server\n * @param {Boolean} current if true, set the copy as the new current history (default: true)\n * @param {String} name name of new history (default: none - server sets to: Copy of )\n * @fires copied passed this history and the response JSON from the copy\n * @returns {xhr}\n */\n copy : function( current, name, allDatasets ){\n current = ( current !== undefined )?( current ):( true );\n if( !this.id ){\n throw new Error( 'You must set the history ID before copying it.' );\n }\n\n var postData = { history_id : this.id };\n if( current ){\n postData.current = true;\n }\n if( name ){\n postData.name = name;\n }\n if( !allDatasets ){\n postData.all_datasets = false;\n }\n postData.view = 'dev-detailed';\n\n var history = this;\n var copy = jQuery.post( this.urlRoot, postData );\n // if current - queue to setAsCurrent before firing 'copied'\n if( current ){\n return copy.then( function( response ){\n var newHistory = new History( response );\n return newHistory.setAsCurrent()\n .done( function(){\n history.trigger( 'copied', history, response );\n });\n });\n }\n return copy.done( function( response ){\n history.trigger( 'copied', history, response );\n });\n },\n\n setAsCurrent : function(){\n var history = this,\n xhr = jQuery.getJSON( Galaxy.root + 'history/set_as_current?id=' + this.id );\n\n xhr.done( function(){\n history.trigger( 'set-as-current', history );\n });\n return xhr;\n },\n\n // ........................................................................ misc\n toString : function(){\n return 'History(' + this.get( 'id' ) + ',' + this.get( 'name' ) + ')';\n }\n}));\n\n\n//==============================================================================\nvar _collectionSuper = CONTROLLED_FETCH_COLLECTION.InfinitelyScrollingCollection;\n/** @class A collection of histories (per user)\n * that maintains the current history as the first in the collection.\n * New or copied histories become the current history.\n */\nvar HistoryCollection = _collectionSuper.extend( BASE_MVC.LoggableMixin ).extend({\n _logNamespace : 'history',\n\n model : History,\n /** @type {String} initial order used by collection */\n order : 'update_time',\n /** @type {Number} limit used for the first fetch (or a reset) */\n limitOnFirstFetch : 10,\n /** @type {Number} limit used for each subsequent fetch */\n limitPerFetch : 10,\n\n initialize : function( models, options ){\n options = options || {};\n this.log( 'HistoryCollection.initialize', models, options );\n _collectionSuper.prototype.initialize.call( this, models, options );\n\n /** @type {boolean} should deleted histories be included */\n this.includeDeleted = options.includeDeleted || false;\n\n /** @type {String} encoded id of the history that's current */\n this.currentHistoryId = options.currentHistoryId;\n\n this.setUpListeners();\n // note: models are sent to reset *after* this fn ends; up to this point\n // the collection *is empty*\n },\n\n urlRoot : Galaxy.root + 'api/histories',\n url : function(){ return this.urlRoot; },\n\n /** set up reflexive event handlers */\n setUpListeners : function setUpListeners(){\n return this.on({\n // when a history is deleted, remove it from the collection (if optionally set to do so)\n 'change:deleted' : function( history ){\n // TODO: this becomes complicated when more filters are used\n this.debug( 'change:deleted', this.includeDeleted, history.get( 'deleted' ) );\n if( !this.includeDeleted && history.get( 'deleted' ) ){\n this.remove( history );\n }\n },\n // listen for a history copy, setting it to current\n 'copied' : function( original, newData ){\n this.setCurrent( new History( newData, [] ) );\n },\n // when a history is made current, track the id in the collection\n 'set-as-current' : function( history ){\n var oldCurrentId = this.currentHistoryId;\n this.trigger( 'no-longer-current', oldCurrentId );\n this.currentHistoryId = history.id;\n }\n });\n },\n\n /** override to change view */\n _buildFetchData : function( options ){\n return _.extend( _collectionSuper.prototype._buildFetchData.call( this, options ), {\n view : 'dev-detailed'\n });\n },\n\n /** override to filter out deleted and purged */\n _buildFetchFilters : function( options ){\n var superFilters = _collectionSuper.prototype._buildFetchFilters.call( this, options ) || {};\n var filters = {};\n if( !this.includeDeleted ){\n filters.deleted = false;\n filters.purged = false;\n } else {\n // force API to return both deleted and non\n //TODO: when the API is updated, remove this\n filters.deleted = null;\n }\n return _.defaults( superFilters, filters );\n },\n\n /** override to fetch current as well (as it may be outside the first 10, etc.) */\n fetchFirst : function( options ){\n var self = this;\n // TODO: batch?\n var xhr = $.when();\n if( this.currentHistoryId ){\n xhr = _collectionSuper.prototype.fetchFirst.call( self, {\n silent: true,\n limit : 1,\n filters: {\n // without these a deleted current history will return [] here and block the other xhr\n 'purged' : '',\n 'deleted' : '',\n 'encoded_id-in' : this.currentHistoryId,\n }\n });\n }\n return xhr.then( function(){\n options = options || {};\n options.offset = 0;\n return self.fetchMore( options );\n });\n },\n\n /** @type {Object} map of collection available sorting orders containing comparator fns */\n comparators : _.extend( _.clone( _collectionSuper.prototype.comparators ), {\n 'name' : BASE_MVC.buildComparator( 'name', { ascending: true }),\n 'name-dsc' : BASE_MVC.buildComparator( 'name', { ascending: false }),\n 'size' : BASE_MVC.buildComparator( 'size', { ascending: false }),\n 'size-asc' : BASE_MVC.buildComparator( 'size', { ascending: true }),\n }),\n\n /** override to always have the current history first */\n sort : function( options ){\n options = options || {};\n var silent = options.silent;\n var currentHistory = this.remove( this.get( this.currentHistoryId ) );\n _collectionSuper.prototype.sort.call( this, _.defaults({ silent: true }, options ) );\n this.unshift( currentHistory, { silent: true });\n if( !silent ){\n this.trigger( 'sort', this, options );\n }\n return this;\n },\n\n /** create a new history and by default set it to be the current history */\n create : function create( data, hdas, historyOptions, xhrOptions ){\n //TODO: .create is actually a collection function that's overridden here\n var collection = this,\n xhr = jQuery.getJSON( Galaxy.root + 'history/create_new_current' );\n return xhr.done( function( newData ){\n collection.setCurrent( new History( newData, [], historyOptions || {} ) );\n });\n },\n\n /** set the current history to the given history, placing it first in the collection.\n * Pass standard bbone options for use in unshift.\n * @triggers new-current passed history and this collection\n */\n setCurrent : function( history, options ){\n options = options || {};\n // new histories go in the front\n this.unshift( history, options );\n this.currentHistoryId = history.get( 'id' );\n if( !options.silent ){\n this.trigger( 'new-current', history, this );\n }\n return this;\n },\n\n toString: function toString(){\n return 'HistoryCollection(' + this.length + ',current:' + this.currentHistoryId + ')';\n }\n});\n\n\n//==============================================================================\nreturn {\n History : History,\n HistoryCollection : HistoryCollection\n};});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/history/history-model.js","define([\n \"mvc/list/list-item\",\n \"ui/loading-indicator\",\n \"mvc/base-mvc\",\n \"utils/localization\",\n \"ui/search-input\"\n], function( LIST_ITEM, LoadingIndicator, BASE_MVC, _l ){\n\n'use strict';\n\nvar logNamespace = 'list';\n/* ============================================================================\nTODO:\n\n============================================================================ */\n/** @class View for a list/collection of models and the sub-views of those models.\n * Sub-views must (at least have the interface if not) inherit from ListItemView.\n * (For a list panel that also includes some 'container' model (History->HistoryContents)\n * use ModelWithListPanel)\n *\n * Allows for:\n * searching collection/sub-views\n * selecting/multi-selecting sub-views\n *\n * Currently used:\n * for dataset/dataset-choice\n * as superclass of ModelListPanel\n */\nvar ListPanel = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend(/** @lends ListPanel.prototype */{\n _logNamespace : logNamespace,\n\n /** class to use for constructing the sub-views */\n viewClass : LIST_ITEM.ListItemView,\n /** class to used for constructing collection of sub-view models */\n collectionClass : Backbone.Collection,\n\n tagName : 'div',\n className : 'list-panel',\n\n /** (in ms) that jquery effects will use */\n fxSpeed : 'fast',\n\n /** string to display when the collection has no contents */\n emptyMsg : _l( 'This list is empty' ),\n /** displayed when no items match the search terms */\n noneFoundMsg : _l( 'No matching items found' ),\n /** string used for search placeholder */\n searchPlaceholder : _l( 'search' ),\n\n // ......................................................................... SET UP\n /** Set up the view, set up storage, bind listeners to HistoryContents events\n * @param {Object} attributes optional settings for the list\n */\n initialize : function( attributes, options ){\n attributes = attributes || {};\n // set the logger if requested\n if( attributes.logger ){\n this.logger = attributes.logger;\n }\n this.log( this + '.initialize:', attributes );\n\n // ---- instance vars\n /** how quickly should jquery fx run? */\n this.fxSpeed = _.has( attributes, 'fxSpeed' )?( attributes.fxSpeed ):( this.fxSpeed );\n\n /** filters for displaying subviews */\n this.filters = [];\n /** current search terms */\n this.searchFor = attributes.searchFor || '';\n\n /** loading indicator */\n // this.indicator = new LoadingIndicator( this.$el );\n\n /** currently showing selectors on items? */\n this.selecting = ( attributes.selecting !== undefined )? attributes.selecting : true;\n //this.selecting = false;\n\n /** cached selected item.model.ids to persist btwn renders */\n this.selected = attributes.selected || [];\n /** the last selected item.model.id */\n this.lastSelected = null;\n\n /** are sub-views draggable */\n this.dragItems = attributes.dragItems || false;\n\n /** list item view class (when passed models) */\n this.viewClass = attributes.viewClass || this.viewClass;\n\n /** list item views */\n this.views = [];\n /** list item models */\n this.collection = attributes.collection || this._createDefaultCollection();\n\n /** filter fns run over collection items to see if they should show in the list */\n this.filters = attributes.filters || [];\n\n /** override $scrollContainer fn via attributes - fn should return jq for elem to call scrollTo on */\n this.$scrollContainer = attributes.$scrollContainer || this.$scrollContainer;\n\n /** @type {String} generic title */\n this.title = attributes.title || '';\n /** @type {String} generic subtitle */\n this.subtitle = attributes.subtitle || '';\n\n this._setUpListeners();\n },\n\n // ------------------------------------------------------------------------ listeners\n /** create any event listeners for the list */\n _setUpListeners : function(){\n this.off();\n\n //TODO: move errorHandler down into list-view from history-view or\n // pass to global error handler (Galaxy)\n this.on({\n error: function( model, xhr, options, msg, details ){\n //this.errorHandler( model, xhr, options, msg, details );\n console.error( model, xhr, options, msg, details );\n },\n // show hide the loading indicator\n loading: function(){\n this._showLoadingIndicator( 'loading...', 40 );\n },\n 'loading-done': function(){\n this._hideLoadingIndicator( 40 );\n },\n });\n\n // throw the first render up as a diff namespace using once (for outside consumption)\n this.once( 'rendered', function(){\n this.trigger( 'rendered:initial', this );\n });\n\n this._setUpCollectionListeners();\n this._setUpViewListeners();\n return this;\n },\n\n /** create and return a collection for when none is initially passed */\n _createDefaultCollection : function(){\n // override\n return new this.collectionClass([]);\n },\n\n /** listening for collection events */\n _setUpCollectionListeners : function(){\n this.log( this + '._setUpCollectionListeners', this.collection );\n this.stopListening( this.collection );\n\n // bubble up error events\n this.listenTo( this.collection, {\n error : function( model, xhr, options, msg, details ){\n this.trigger( 'error', model, xhr, options, msg, details );\n },\n update : function( collection, options ){\n var changes = options.changes;\n // console.info( collection + ', update:', changes, '\\noptions:', options );\n // more than one: render everything\n if( options.renderAll || ( changes.added.length + changes.removed.length > 1 ) ){\n return this.renderItems();\n }\n // otherwise, let the single add/remove handlers do it\n if( changes.added.length === 1 ){\n return this.addItemView( _.first( changes.added ), collection, options );\n }\n if( changes.removed.length === 1 ){\n return this.removeItemView( _.first( changes.removed ), collection, options );\n }\n }\n });\n return this;\n },\n\n /** listening for sub-view events that bubble up with the 'view:' prefix */\n _setUpViewListeners : function(){\n this.log( this + '._setUpViewListeners' );\n\n // shift to select a range\n this.on({\n 'view:selected': function( view, ev ){\n if( ev && ev.shiftKey && this.lastSelected ){\n var lastSelectedView = this.viewFromModelId( this.lastSelected );\n if( lastSelectedView ){\n this.selectRange( view, lastSelectedView );\n }\n } else if( ev && ev.altKey && !this.selecting ){\n this.showSelectors();\n }\n this.selected.push( view.model.id );\n this.lastSelected = view.model.id;\n },\n\n 'view:de-selected': function( view, ev ){\n this.selected = _.without( this.selected, view.model.id );\n }\n });\n },\n\n // ------------------------------------------------------------------------ rendering\n /** Render this content, set up ui.\n * @param {Number or String} speed the speed of the render\n */\n render : function( speed ){\n this.log( this + '.render', speed );\n var $newRender = this._buildNewRender();\n this._setUpBehaviors( $newRender );\n this._queueNewRender( $newRender, speed );\n return this;\n },\n\n /** Build a temp div containing the new children for the view's $el. */\n _buildNewRender : function(){\n this.debug( this + '(ListPanel)._buildNewRender' );\n var $newRender = $( this.templates.el( {}, this ) );\n this._renderControls( $newRender );\n this._renderTitle( $newRender );\n this._renderSubtitle( $newRender );\n this._renderSearch( $newRender );\n this.renderItems( $newRender );\n return $newRender;\n },\n\n /** Build a temp div containing the new children for the view's $el. */\n _renderControls : function( $newRender ){\n this.debug( this + '(ListPanel)._renderControls' );\n var $controls = $( this.templates.controls( {}, this ) );\n $newRender.find( '.controls' ).replaceWith( $controls );\n return $controls;\n },\n\n /** return a jQuery object containing the title DOM */\n _renderTitle : function( $where ){\n //$where = $where || this.$el;\n //$where.find( '.title' ).replaceWith( ... )\n },\n\n /** return a jQuery object containing the subtitle DOM (if any) */\n _renderSubtitle : function( $where ){\n //$where = $where || this.$el;\n //$where.find( '.title' ).replaceWith( ... )\n },\n\n /** Fade out the old el, swap in the new contents, then fade in.\n * @param {Number or String} speed jq speed to use for rendering effects\n * @fires rendered when rendered\n */\n _queueNewRender : function( $newRender, speed ) {\n speed = ( speed === undefined )?( this.fxSpeed ):( speed );\n var panel = this;\n panel.log( '_queueNewRender:', $newRender, speed );\n\n $( panel ).queue( 'fx', [\n function( next ){\n panel.$el.fadeOut( speed, next );\n },\n function( next ){\n panel._swapNewRender( $newRender );\n next();\n },\n function( next ){\n panel.$el.fadeIn( speed, next );\n },\n function( next ){\n panel.trigger( 'rendered', panel );\n next();\n }\n ]);\n },\n\n /** empty out the current el, move the $newRender's children in */\n _swapNewRender : function( $newRender ){\n this.$el.empty().attr( 'class', this.className ).append( $newRender.children() );\n if( this.selecting ){ this.showSelectors( 0 ); }\n return this;\n },\n\n /** Set up any behaviors, handlers (ep. plugins) that need to be called when the entire view has been built but\n * not attached to the page yet.\n */\n _setUpBehaviors : function( $where ){\n $where = $where || this.$el;\n this.$controls( $where ).find('[title]').tooltip();\n // set up the pupup for actions available when multi selecting\n this._renderMultiselectActionMenu( $where );\n return this;\n },\n\n /** render a menu containing the actions available to sets of selected items */\n _renderMultiselectActionMenu : function( $where ){\n $where = $where || this.$el;\n var $menu = $where.find( '.list-action-menu' ),\n actions = this.multiselectActions();\n if( !actions.length ){\n return $menu.empty();\n }\n\n var $newMenu = $([\n '
',\n '',\n '
', '
',\n '
'\n ].join(''));\n var $actions = actions.map( function( action ){\n var html = [ '
'\n ].join('')),\n\n /** the middle: unpaired, divider, and paired */\n middle : _.template([\n // contains two flex rows (rows that fill available space) and a divider btwn\n '
'\n ].join('')),\n\n /** help content */\n helpContent : _.template([\n '
', _l([\n 'Collections of paired datasets are ordered lists of dataset pairs (often forward and reverse reads). ',\n 'These collections can be passed to tools and workflows in order to have analyses done on each member of ',\n 'the entire group. This interface allows you to create a collection, choose which datasets are paired, ',\n 'and re-order the final collection.'\n ].join( '' )), '
',\n '
', _l([\n 'Unpaired datasets are shown in the unpaired section ',\n '(hover over the underlined words to highlight below). ',\n 'Paired datasets are shown in the paired section.',\n '
To pair datasets, you can:',\n '
Click a dataset in the ',\n 'forward column ',\n 'to select it then click a dataset in the ',\n 'reverse column.',\n '
',\n '
Click one of the \"Pair these datasets\" buttons in the ',\n 'middle column ',\n 'to pair the datasets in a particular row.',\n '
',\n '
Click \"Auto-pair\" ',\n 'to have your datasets automatically paired based on name.',\n '
',\n '
'\n ].join( '' )), '',\n '
', _l([\n '
You can filter what is shown in the unpaired sections by:',\n '
Entering partial dataset names in either the ',\n 'forward filter or ',\n 'reverse filter.',\n '
',\n '
Choosing from a list of preset filters by clicking the ',\n '\"Choose filters\" link.',\n '
Clearing the filters by clicking the ',\n '\"Clear filters\" link.',\n '
',\n '
'\n ].join( '' )), '',\n '
', _l([\n 'To unpair individual dataset pairs, click the ',\n 'unpair buttons ( ). ',\n 'Click the \"Unpair all\" link to unpair all pairs.'\n ].join( '' )), '
',\n '
', _l([\n 'You can include or remove the file extensions (e.g. \".fastq\") from your pair names by toggling the ',\n '\"Remove file extensions from pair names?\" control.'\n ].join( '' )), '
',\n '
', _l([\n 'Once your collection is complete, enter a name and ',\n 'click \"Create list\". ',\n '(Note: you do not have to pair all unpaired datasets to finish.)'\n ].join( '' )), '
'\n ].join(''))\n })\n});\n\n//=============================================================================\n/** a modal version of the paired collection creator */\nvar pairedCollectionCreatorModal = function _pairedCollectionCreatorModal( datasets, options ){\n\n var deferred = jQuery.Deferred(),\n creator;\n\n options = _.defaults( options || {}, {\n datasets : datasets,\n oncancel : function(){\n Galaxy.modal.hide();\n deferred.reject( 'cancelled' );\n },\n oncreate : function( creator, response ){\n Galaxy.modal.hide();\n deferred.resolve( response );\n }\n });\n\n if( !window.Galaxy || !Galaxy.modal ){\n throw new Error( 'Galaxy or Galaxy.modal not found' );\n }\n\n creator = new PairedCollectionCreator( options );\n Galaxy.modal.show({\n title : 'Create a collection of paired datasets',\n body : creator.$el,\n width : '80%',\n height : '800px',\n closing_events: true\n });\n creator.render();\n window.creator = creator;\n\n //TODO: remove modal header\n return deferred;\n};\n\n\n//=============================================================================\nfunction createListOfPairsCollection( collection, defaultHideSourceItems ){\n var elements = collection.toJSON();\n//TODO: validate elements\n return pairedCollectionCreatorModal( elements, {\n historyId : collection.historyId,\n defaultHideSourceItems: defaultHideSourceItems\n });\n}\n\n\n//=============================================================================\n return {\n PairedCollectionCreator : PairedCollectionCreator,\n pairedCollectionCreatorModal : pairedCollectionCreatorModal,\n createListOfPairsCollection : createListOfPairsCollection\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js","define([\n \"mvc/collection/list-collection-creator\",\n \"mvc/history/hdca-model\",\n \"mvc/base-mvc\",\n \"utils/localization\"\n], function( LIST_CREATOR, HDCA, BASE_MVC, _l ){\n\n'use strict';\n\nvar logNamespace = 'collections';\n/*==============================================================================\nTODO:\n the paired creator doesn't really mesh with the list creator as parent\n it may be better to make an abstract super class for both\n composites may inherit from this (or vis-versa)\n PairedDatasetCollectionElementView doesn't make a lot of sense\n\n==============================================================================*/\n/** */\nvar PairedDatasetCollectionElementView = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend({\n _logNamespace : logNamespace,\n\n//TODO: use proper class (DatasetDCE or NestedDCDCE (or the union of both))\n tagName : 'li',\n className : 'collection-element',\n\n initialize : function( attributes ){\n this.element = attributes.element || {};\n this.identifier = attributes.identifier;\n },\n\n render : function(){\n this.$el\n .attr( 'data-element-id', this.element.id )\n .html( this.template({ identifier: this.identifier, element: this.element }) );\n return this;\n },\n\n //TODO: lots of unused space in the element - possibly load details and display them horiz.\n template : _.template([\n '<%- identifier %>',\n '<%- element.name %>',\n ].join('')),\n\n /** remove the DOM and any listeners */\n destroy : function(){\n this.off();\n this.$el.remove();\n },\n\n /** string rep */\n toString : function(){\n return 'DatasetCollectionElementView()';\n }\n});\n\n\n// ============================================================================\nvar _super = LIST_CREATOR.ListCollectionCreator;\n\n/** An interface for building collections.\n */\nvar PairCollectionCreator = _super.extend({\n\n /** the class used to display individual elements */\n elementViewClass : PairedDatasetCollectionElementView,\n /** the class this creator will create and save */\n collectionClass : HDCA.HistoryPairDatasetCollection,\n className : 'pair-collection-creator collection-creator flex-row-container',\n\n /** override to no-op */\n _mangleDuplicateNames : function(){},\n\n // TODO: this whole pattern sucks. There needs to be two classes of problem area:\n // bad inital choices and\n // when the user has painted his/her self into a corner during creation/use-of-the-creator\n /** render the entire interface */\n render : function( speed, callback ){\n if( this.workingElements.length === 2 ){\n return _super.prototype.render.call( this, speed, callback );\n }\n return this._renderInvalid( speed, callback );\n },\n\n // ------------------------------------------------------------------------ rendering elements\n /** render forward/reverse */\n _renderList : function( speed, callback ){\n //this.debug( '-- _renderList' );\n //precondition: there are two valid elements in workingElements\n var creator = this,\n $tmp = jQuery( '' ),\n $list = creator.$list();\n\n // lose the original views, create the new, append all at once, then call their renders\n _.each( this.elementViews, function( view ){\n view.destroy();\n creator.removeElementView( view );\n });\n $tmp.append( creator._createForwardElementView().$el );\n $tmp.append( creator._createReverseElementView().$el );\n $list.empty().append( $tmp.children() );\n _.invoke( creator.elementViews, 'render' );\n },\n\n /** create the forward element view */\n _createForwardElementView : function(){\n return this._createElementView( this.workingElements[0], { identifier: 'forward' } );\n },\n\n /** create the forward element view */\n _createReverseElementView : function(){\n return this._createElementView( this.workingElements[1], { identifier: 'reverse' } );\n },\n\n /** create an element view, cache in elementViews, and return */\n _createElementView : function( element, options ){\n var elementView = new this.elementViewClass( _.extend( options, {\n element : element,\n }));\n this.elementViews.push( elementView );\n return elementView;\n },\n\n /** swap the forward, reverse elements and re-render */\n swap : function(){\n this.workingElements = [\n this.workingElements[1],\n this.workingElements[0],\n ];\n this._renderList();\n },\n\n events : _.extend( _.clone( _super.prototype.events ), {\n 'click .swap' : 'swap',\n }),\n\n // ------------------------------------------------------------------------ templates\n //TODO: move to require text plugin and load these as text\n //TODO: underscore currently unnecc. bc no vars are used\n //TODO: better way of localizing text-nodes in long strings\n /** underscore template fns attached to class */\n templates : _.extend( _.clone( _super.prototype.templates ), {\n /** the middle: element list */\n middle : _.template([\n '
'\n ].join('')),\n\n /** help content */\n helpContent : _.template([\n '
', _l([\n 'Pair collections are permanent collections containing two datasets: one forward and one reverse. ',\n 'Often these are forward and reverse reads. The pair collections can be passed to tools and ',\n 'workflows in order to have analyses done on both datasets. This interface allows ',\n 'you to create a pair, name it, and swap which is forward and which reverse.'\n ].join( '' )), '
',\n '
',\n '
', _l([\n 'Click the \"Swap\" link to make your forward dataset the reverse ',\n 'and the reverse dataset forward.'\n ].join( '' )), '
',\n '
', _l([\n 'Click the \"Cancel\" button to exit the interface.'\n ].join( '' )), '
',\n '
',\n '
', _l([\n 'Once your collection is complete, enter a name and ',\n 'click \"Create list\".'\n ].join( '' )), '
'\n ].join('')),\n\n /** a simplified page communicating what went wrong and why the user needs to reselect something else */\n invalidInitial : _.template([\n '
',\n '
',\n '',\n '<% if( _.size( problems ) ){ %>',\n _l( 'The following selections could not be included due to problems' ),\n '
<% _.each( problems, function( problem ){ %>',\n '
<%- problem.element.name %>: <%- problem.text %>
',\n '<% }); %>
',\n '<% } else if( _.size( elements ) === 0 ){ %>',\n _l( 'No datasets were selected' ), '.',\n '<% } else if( _.size( elements ) === 1 ){ %>',\n _l( 'Only one dataset was selected' ), ': <%- elements[0].name %>',\n '<% } else if( _.size( elements ) > 2 ){ %>',\n _l( 'Too many datasets were selected' ),\n ': <%- _.pluck( elements, \"name\" ).join( \", \") %>',\n '<% } %>',\n ' ',\n _l( 'Two (and only two) elements are needed for the pair' ), '. ',\n _l( 'You may need to ' ),\n '', _l( 'cancel' ), ' ',\n _l( 'and reselect new elements' ), '.',\n '',\n '
',\n '
',\n ''\n ].join('')),\n }),\n\n // ------------------------------------------------------------------------ misc\n /** string rep */\n toString : function(){ return 'PairCollectionCreator'; }\n});\n\n\n//==============================================================================\n/** List collection flavor of collectionCreatorModal. */\nvar pairCollectionCreatorModal = function _pairCollectionCreatorModal( elements, options ){\n options = options || {};\n options.title = _l( 'Create a collection from a pair of datasets' );\n return LIST_CREATOR.collectionCreatorModal( elements, options, PairCollectionCreator );\n};\n\n\n//==============================================================================\n/** Use a modal to create a pair collection, then add it to the given history contents.\n * @returns {Deferred} resolved when the collection is added to the history.\n */\nfunction createPairCollection( contents, defaultHideSourceItems ){\n var elements = contents.toJSON(),\n promise = pairCollectionCreatorModal( elements, {\n defaultHideSourceItems: defaultHideSourceItems,\n creationFn : function( elements, name, hideSourceItems ){\n elements = [\n { name: \"forward\", src: \"hda\", id: elements[0].id },\n { name: \"reverse\", src: \"hda\", id: elements[1].id }\n ];\n return contents.createHDCA( elements, 'paired', name, hideSourceItems );\n }\n });\n return promise;\n}\n\n//==============================================================================\n return {\n PairCollectionCreator : PairCollectionCreator,\n pairCollectionCreatorModal : pairCollectionCreatorModal,\n createPairCollection : createPairCollection,\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/collection/pair-collection-creator.js","// dependencies\ndefine([], function() {\n\n// grid model\nreturn Backbone.Model.extend({\n defaults: {\n url_base: '',\n async: false,\n async_ops: [],\n categorical_filters: [],\n filters: {},\n sort_key: null,\n show_item_checkboxes: false,\n advanced_search: false,\n cur_page: 1,\n num_pages: 1,\n operation: undefined,\n item_ids: undefined\n },\n\n /**\n * Return true if operation can be done asynchronously.\n */\n can_async_op: function(op) {\n return _.indexOf(this.attributes.async_ops, op) !== -1;\n },\n\n /**\n * Add filtering criterion.\n */\n add_filter: function(key, value, append) {\n // Update URL arg with new condition. \n if (append) {\n // Update or append value.\n var cur_val = this.attributes.filters[key],\n new_val;\n if (cur_val === null || cur_val === undefined) {\n new_val = value;\n } \n else if (typeof(cur_val) == 'string') {\n if (cur_val == 'All') {\n new_val = value;\n } else {\n // Replace string with array.\n var values = [];\n values[0] = cur_val;\n values[1] = value;\n new_val = values; \n }\n } \n else {\n // Current value is an array.\n new_val = cur_val;\n new_val.push(value);\n }\n this.attributes.filters[key] = new_val;\n } \n else {\n // Replace value.\n this.attributes.filters[key] = value;\n }\n },\n\n /**\n * Remove filtering criterion.\n */\n remove_filter: function(key, condition) {\n var cur_val = this.attributes.filters[key];\n if (cur_val === null || cur_val === undefined) {\n return false; \n }\n\n if (typeof(cur_val) === 'string') {\n // overwrite/remove condition.\n this.attributes.filters[key] = '';\n } else {\n // filter contains an array of conditions.\n var condition_index = _.indexOf(cur_val, condition);\n if (condition_index !== -1) {\n cur_val[condition_index] = '';\n }\n }\n },\n\n /**\n * Returns URL data for obtaining a new grid.\n */\n get_url_data: function() {\n var url_data = {\n async: this.attributes.async,\n sort: this.attributes.sort_key,\n page: this.attributes.cur_page,\n show_item_checkboxes: this.attributes.show_item_checkboxes,\n advanced_search: this.attributes.advanced_search\n };\n\n // Add operation, item_ids only if they have values.\n if (this.attributes.operation) {\n url_data.operation = this.attributes.operation;\n }\n if (this.attributes.item_ids) {\n url_data.id = this.attributes.item_ids;\n }\n\n // Add filter arguments to data, placing \"f-\" in front of all arguments.\n var self = this;\n _.each(_.pairs(self.attributes.filters), function(k) {\n url_data['f-' + k[0]] = k[1];\n });\n\n return url_data;\n },\n \n // Return URL for obtaining a new grid\n get_url: function (args) {\n return this.get('url_base') + \"?\" + $.param(this.get_url_data()) + '&' + $.param(args);\n }\n \n});\n\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/grid/grid-model.js","// dependencies\ndefine(['utils/utils'], function(Utils) {\n\n// grid view templates\nreturn {\n // template\n grid: function(options) {\n var tmpl = '';\n if (options.embedded) {\n tmpl = this.grid_header(options) + this.grid_table(options);\n } else {\n tmpl = '' +\n '
' +\n '
' +\n '
' +\n this.grid_header(options) +\n '
' +\n '
' +\n '
' +\n '
' +\n '
' +\n '
' +\n '
' +\n '
' +\n '
' +\n '
' +\n this.grid_table(options);\n }\n \n // add info text\n if (options.info_text) {\n tmpl += '
';\n \n // return template\n return tmpl;\n },\n \n // template\n body: function(options) {\n // initialize\n var tmpl = '';\n var num_rows_rendered = 0;\n var items_length = options.items.length;\n \n // empty grid?\n if (items_length == 0) {\n // No results.\n tmpl += '
No Items
';\n num_rows_rendered = 1;\n }\n \n // create rows\n for (var i in options.items) {\n \n // encode ids\n var item = options.items[i];\n var encoded_id = item.encode_id;\n var popupmenu_id = 'grid-' + i + '-popup';\n \n // Tag current\n tmpl += '
' +\n '
';\n }\n \n // Data columns\n for (j in options.columns) {\n var column = options.columns[j];\n if (column.visible) {\n // Nowrap\n var nowrap = '';\n if (column.nowrap) {\n nowrap = 'style=\"white-space:nowrap;\"';\n }\n \n // get column settings\n var column_settings = item.column_config[column.label];\n \n // load attributes\n var link = column_settings.link;\n var value = column_settings.value;\n var target = column_settings.target;\n \n // unescape value\n if (jQuery.type( value ) === 'string') {\n value = value.replace(/\\/\\//g, '/');\n }\n \n // Attach popup menu?\n var id = '';\n var cls = '';\n if (column.attach_popup) {\n id = 'grid-' + i + '-popup';\n cls = 'menubutton';\n if (link != '') {\n cls += ' split';\n }\n cls += ' popup';\n }\n \n // Check for row wrapping\n tmpl += '
';\n \n // Link\n if (link) {\n if (options.operations.length != 0) {\n tmpl += '
';\n }\n tmpl += '' + value + '';\n if (options.operations.length != 0) {\n tmpl += '
';\n }\n } else {\n tmpl += '';\n }\n tmpl += '
';\n }\n }\n tmpl += '
';\n num_rows_rendered++;\n }\n return tmpl;\n },\n\n // template\n footer: function(options) {\n \n // create template string\n var tmpl = '';\n \n // paging\n if (options.use_paging && options.num_pages > 1) {\n // get configuration\n var num_page_links = options.num_page_links;\n var cur_page_num = options.cur_page_num;\n var num_pages = options.num_pages;\n \n // First pass on min page.\n var page_link_range = num_page_links / 2;\n var min_page = cur_page_num - page_link_range\n var min_offset = 0;\n if (min_page <= 0) {\n // Min page is too low.\n min_page = 1;\n min_offset = page_link_range - ( cur_page_num - min_page );\n }\n \n // Set max page.\n var max_range = page_link_range + min_offset;\n var max_page = cur_page_num + max_range;\n if (max_page <= num_pages) {\n // Max page is fine.\n max_offset = 0;\n } else {\n // Max page is too high.\n max_page = num_pages;\n // +1 to account for the +1 in the loop below.\n max_offset = max_range - ( max_page + 1 - cur_page_num );\n }\n \n // Second and final pass on min page to add any unused\n // offset from max to min.\n if (max_offset != 0) {\n min_page -= max_offset\n if (min_page < 1) {\n min_page = 1\n }\n }\n \n // template header\n tmpl += '
';\n if (options.show_item_checkboxes) {\n tmpl += '
';\n }\n \n // Grid operations for multiple items.\n if (options.show_item_checkboxes) {\n // start template\n tmpl += '
' +\n '' +\n '
' +\n '
' +\n 'For selected items: ';\n \n // configure buttons for operations\n for (i in options.operations) {\n var operation = options.operations[i];\n if (operation.allow_multiple) {\n tmpl += ' ';\n }\n }\n \n // finalize template\n tmpl += '
' +\n '
';\n }\n \n // count global operations\n var found_global = false;\n for (i in options.operations) {\n if (options.operations[i].global_operation) {\n found_global = true;\n break;\n }\n }\n \n // add global operations\n if (found_global) {\n tmpl += '
' +\n '
';\n for (i in options.operations) {\n var operation = options.operations[i];\n if (operation.global_operation) {\n tmpl += '' + operation.label + '';\n }\n }\n tmpl += '
' +\n '' +\n '';\n },\n \n // template\n grid_filters: function (options) {\n \n // get filters\n var default_filter_dict = options.default_filter_dict;\n var filters = options.filters;\n\n // show advanced search if flag set or if there are filters for advanced search fields\n var advanced_search_display = 'none';\n if (options.advanced_search) {\n advanced_search_display = 'block';\n }\n \n // identify columns with advanced filtering\n var show_advanced_search_link = false;\n for (var i in options.columns) {\n var column = options.columns[i];\n if (column.filterable == 'advanced') {\n var column_key = column.key;\n var f_key = filters[column_key];\n var d_key = default_filter_dict[column_key];\n if (f_key && d_key && f_key != d_key) {\n advanced_search_display = 'block';\n }\n show_advanced_search_link = true;\n }\n }\n \n // hide standard search if advanced is shown\n var standard_search_display = 'block';\n if (advanced_search_display == 'block') {\n standard_search_display = 'none';\n }\n\n //\n // standard search\n //\n var tmpl = '
' +\n '
' +\n '
' +\n '
' +\n '
';\n \n // add standard filters\n for (var i in options.columns) {\n var column = options.columns[i];\n if (column.filterable == 'standard') {\n tmpl += this.grid_column_filter(options, column);\n }\n }\n \n // finalize standard search\n tmpl += '
' +\n '
' +\n '
' +\n '
' +\n '
';\n \n // show advanced search link in standard display\n if (show_advanced_search_link) {\n tmpl += 'Advanced Search';\n }\n \n // finalize standard search display\n tmpl += '
';\n \n // add advanced filters\n for (var i in options.columns) {\n var column = options.columns[i];\n if (column.filterable == 'advanced') {\n tmpl += this.grid_column_filter(options, column);\n }\n }\n \n // finalize advanced search template\n tmpl += '
' +\n '
';\n\n // return template\n return tmpl;\n },\n \n // template\n grid_column_filter: function(options, column) {\n \n // collect parameters\n var default_filter_dict = options.default_filter_dict;\n var filters = options.filters;\n var column_label = column.label;\n var column_key = column.key;\n if (column.filterable == 'advanced') {\n column_label = column_label.toLowerCase();\n }\n \n // start\n var tmpl = '
';\n \n if (column.filterable == 'advanced') {\n tmpl += '
' + column_label + ':
';\n }\n tmpl += '
';\n if (column.is_text) {\n tmpl += '';\n } else {\n // filter criteria\n tmpl += '';\n \n // add category filters\n var seperator = false;\n for (cf_label in options.categorical_filters[column_key]) {\n // get category filter\n var cf = options.categorical_filters[column_key][cf_label];\n \n // each filter will have only a single argument, so get that single argument\n var cf_key = '';\n var cf_arg = '';\n for (key in cf) {\n cf_key = key;\n cf_arg = cf[key];\n }\n \n // add seperator\n if (seperator) {\n tmpl += ' | ';\n }\n seperator = true;\n \n // add category\n var filter = filters[column_key];\n if (filter && cf[column_key] && filter == cf_arg) {\n tmpl += '' + cf_label + '';\n } else {\n tmpl += '' +\n '' + cf_label + '' +\n '';\n }\n }\n tmpl += '';\n }\n tmpl += '
' +\n '
';\n \n // return template\n return tmpl;\n },\n \n // template for filter items\n filter_element: function(filter_key, filter_value) {\n filter_value = Utils.sanitize(filter_value);\n return '' + filter_value +\n '' +\n '' +\n '' +\n '';\n\n }\n};\n\n});\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/grid/grid-template.js","define([\n \"mvc/ui/ui-modal\",\n \"mvc/ui/error-modal\",\n \"utils/localization\"\n], function( MODAL, ERROR_MODAL, _l ){\n\n'use strict';\n\n//==============================================================================\n/**\n * A dialog/modal that allows copying a user history or 'importing' from user\n * another. Generally called via historyCopyDialog below.\n * @type {Object}\n */\nvar CopyDialog = {\n\n // language related strings/fns\n defaultName : _.template( \"Copy of '<%- name %>'\" ),\n title : _.template( _l( 'Copying history' ) + ' \"<%- name %>\"' ),\n submitLabel : _l( 'Copy' ),\n errorMessage : _l( 'History could not be copied.' ),\n progressive : _l( 'Copying history' ),\n activeLabel : _l( 'Copy only the active, non-deleted datasets' ),\n allLabel : _l( 'Copy all datasets including deleted ones' ),\n anonWarning : _l( 'As an anonymous user, unless you login or register, you will lose your current history ' ) +\n _l( 'after copying this history. ' ),\n\n // template for modal body\n _template : _.template([\n //TODO: remove inline styles\n // show a warning message for losing current to anon users\n '<% if( isAnon ){ %>',\n '
',\n '<% } %>',\n ''\n ].join( '' )),\n\n // empty modal body and let the user know the copy is happening\n _showAjaxIndicator : function _showAjaxIndicator(){\n var indicator = '
' + this.progressive + '...
';\n this.modal.$( '.modal-body' ).empty().append( indicator ).css({ 'margin-top': '8px' });\n },\n\n // (sorta) public interface - display the modal, render the form, and potentially copy the history\n // returns a jQuery.Deferred done->history copied, fail->user cancelled\n dialog : function _dialog( modal, history, options ){\n options = options || {};\n\n var dialog = this,\n deferred = jQuery.Deferred(),\n // TODO: getting a little byzantine here\n defaultCopyNameFn = options.nameFn || this.defaultName,\n defaultCopyName = defaultCopyNameFn({ name: history.get( 'name' ) }),\n // TODO: these two might be simpler as one 3 state option (all,active,no-choice)\n defaultCopyWhat = options.allDatasets? 'copy-all' : 'copy-non-deleted',\n allowAll = !_.isUndefined( options.allowAll )? options.allowAll : true,\n autoClose = !_.isUndefined( options.autoClose )? options.autoClose : true;\n\n this.modal = modal;\n\n\n // validate the name and copy if good\n function checkNameAndCopy(){\n var name = modal.$( '#copy-modal-title' ).val();\n if( !name ){\n modal.$( '.invalid-title' ).show();\n return;\n }\n // get further settings, shut down and indicate the ajax call, then hide and resolve/reject\n var copyAllDatasets = modal.$( 'input[name=\"copy-what\"]:checked' ).val() === 'copy-all';\n modal.$( 'button' ).prop( 'disabled', true );\n dialog._showAjaxIndicator();\n history.copy( true, name, copyAllDatasets )\n .done( function( response ){\n deferred.resolve( response );\n })\n .fail( function( xhr, status, message ){\n var options = { name: name, copyAllDatasets: copyAllDatasets };\n ERROR_MODAL.ajaxErrorModal( history, xhr, options, dialog.errorMessage );\n deferred.rejectWith( deferred, arguments );\n })\n .done( function(){\n if( autoClose ){ modal.hide(); }\n });\n }\n\n var originalClosingCallback = options.closing_callback;\n modal.show( _.extend( options, {\n title : this.title({ name: history.get( 'name' ) }),\n body : $( dialog._template({\n name : defaultCopyName,\n isAnon : Galaxy.user.isAnonymous(),\n allowAll : allowAll,\n copyWhat : defaultCopyWhat,\n activeLabel : this.activeLabel,\n allLabel : this.allLabel,\n anonWarning : this.anonWarning,\n })),\n buttons : _.object([\n [ _l( 'Cancel' ), function(){ modal.hide(); } ],\n [ this.submitLabel, checkNameAndCopy ]\n ]),\n height : 'auto',\n closing_events : true,\n closing_callback: function _historyCopyClose( cancelled ){\n if( cancelled ){\n deferred.reject({ cancelled : true });\n }\n if( originalClosingCallback ){\n originalClosingCallback( cancelled );\n }\n }\n }));\n\n // set the default dataset copy, autofocus the title, and set up for a simple return\n modal.$( '#copy-modal-title' ).focus().select();\n modal.$( '#copy-modal-title' ).on( 'keydown', function( ev ){\n if( ev.keyCode === 13 ){\n ev.preventDefault();\n checkNameAndCopy();\n }\n });\n\n return deferred;\n },\n};\n\n//==============================================================================\n// maintain the (slight) distinction between copy and import\n/**\n * Subclass CopyDialog to use the import language.\n */\nvar ImportDialog = _.extend( {}, CopyDialog, {\n defaultName : _.template( \"imported: <%- name %>\" ),\n title : _.template( _l( 'Importing history' ) + ' \"<%- name %>\"' ),\n submitLabel : _l( 'Import' ),\n errorMessage : _l( 'History could not be imported.' ),\n progressive : _l( 'Importing history' ),\n activeLabel : _l( 'Import only the active, non-deleted datasets' ),\n allLabel : _l( 'Import all datasets including deleted ones' ),\n anonWarning : _l( 'As an anonymous user, unless you login or register, you will lose your current history ' ) +\n _l( 'after importing this history. ' ),\n\n});\n\n//==============================================================================\n/**\n * Main interface for both history import and history copy dialogs.\n * @param {Backbone.Model} history the history to copy\n * @param {Object} options a hash\n * @return {jQuery.Deferred} promise that fails on close and succeeds on copy\n *\n * options:\n * (this object is also passed to the modal used to display the dialog and accepts modal options)\n * {Function} nameFn if defined, use this to build the default name shown to the user\n * (the fn is passed: {name: })\n * {bool} useImport if true, use the 'import' language (instead of Copy)\n * {bool} allowAll if true, allow the user to choose between copying all datasets and\n * only non-deleted datasets\n * {String} allDatasets default initial checked radio button: 'copy-all' or 'copy-non-deleted',\n */\nvar historyCopyDialog = function( history, options ){\n options = options || {};\n // create our own modal if Galaxy doesn't have one (mako tab without use_panels)\n var modal = window.parent.Galaxy.modal || new MODAL.View({});\n return options.useImport?\n ImportDialog.dialog( modal, history, options ):\n CopyDialog.dialog( modal, history, options );\n};\n\n\n//==============================================================================\n return historyCopyDialog;\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/history/copy-dialog.js","define([\n \"mvc/dataset/dataset-li-edit\",\n \"mvc/history/hda-li\",\n \"mvc/base-mvc\",\n \"utils/localization\"\n], function( DATASET_LI_EDIT, HDA_LI, BASE_MVC, _l ){\n\n'use strict';\n\n//==============================================================================\nvar _super = DATASET_LI_EDIT.DatasetListItemEdit;\n/** @class Editing view for HistoryDatasetAssociation.\n */\nvar HDAListItemEdit = _super.extend(\n/** @lends HDAListItemEdit.prototype */{\n\n className : _super.prototype.className + \" history-content\",\n\n /** In this override, only get details if in the ready state, get rerunnable if in other states.\n * Note: fetch with no 'change' event triggering to prevent automatic rendering.\n */\n _fetchModelDetails : function(){\n var view = this;\n if( view.model.inReadyState() && !view.model.hasDetails() ){\n return view.model.fetch({ silent: true });\n\n // special case the need for the rerunnable and creating_job attributes\n // needed for rendering re-run button on queued, running datasets\n } else if( !view.model.has( 'rerunnable' ) ){\n return view.model.fetch({ silent: true, data: {\n // only fetch rerunnable and creating_job to keep overhead down\n keys: [ 'rerunnable', 'creating_job' ].join(',')\n }});\n }\n return jQuery.when();\n },\n\n /** event map */\n events : _.extend( _.clone( _super.prototype.events ), {\n 'click .unhide-link' : function( ev ){ this.model.unhide(); return false; }\n }),\n\n /** string rep */\n toString : function(){\n var modelString = ( this.model )?( this.model + '' ):( '(no model)' );\n return 'HDAListItemEdit(' + modelString + ')';\n }\n});\n\n\n// ............................................................................ TEMPLATES\n/** underscore templates */\nHDAListItemEdit.prototype.templates = (function(){\n\n var warnings = _.extend( {}, _super.prototype.templates.warnings, {\n hidden : BASE_MVC.wrapTemplate([\n '<% if( !dataset.visible ){ %>',\n // add a link to unhide a dataset\n '
',\n '<% } %>'\n ], 'dataset' )\n });\n\n return _.extend( {}, _super.prototype.templates, {\n //NOTE: *steal* the HDAListItemView titleBar\n titleBar : HDA_LI.HDAListItemView.prototype.templates.titleBar,\n warnings : warnings\n });\n}());\n\n\n//==============================================================================\n return {\n HDAListItemEdit : HDAListItemEdit\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/history/hda-li-edit.js","define([\n \"mvc/history/hdca-li\",\n \"mvc/collection/collection-view-edit\",\n \"ui/fa-icon-button\",\n \"utils/localization\"\n], function( HDCA_LI, DC_VIEW_EDIT, faIconButton, _l ){\n\n'use strict';\n\n//==============================================================================\nvar _super = HDCA_LI.HDCAListItemView;\n/** @class Editing view for HistoryDatasetCollectionAssociation.\n */\nvar HDCAListItemEdit = _super.extend(\n/** @lends HDCAListItemEdit.prototype */{\n\n /** logger used to record this.log messages, commonly set to console */\n //logger : console,\n\n /** Override to return editable versions of the collection panels */\n _getFoldoutPanelClass : function(){\n switch( this.model.get( 'collection_type' ) ){\n case 'list':\n return DC_VIEW_EDIT.ListCollectionViewEdit;\n case 'paired':\n return DC_VIEW_EDIT.PairCollectionViewEdit;\n case 'list:paired':\n return DC_VIEW_EDIT.ListOfPairsCollectionViewEdit;\n case 'list:list':\n return DC_VIEW_EDIT.ListOfListsCollectionViewEdit;\n }\n throw new TypeError( 'Uknown collection_type: ' + this.model.get( 'collection_type' ) );\n },\n\n // ......................................................................... delete\n /** In this override, add the delete button. */\n _renderPrimaryActions : function(){\n this.log( this + '._renderPrimaryActions' );\n // render the display, edit attr and delete icon-buttons\n return _super.prototype._renderPrimaryActions.call( this )\n .concat([\n this._renderDeleteButton()\n ]);\n },\n\n /** Render icon-button to delete this collection. */\n _renderDeleteButton : function(){\n var self = this,\n deleted = this.model.get( 'deleted' );\n return faIconButton({\n title : deleted? _l( 'Dataset collection is already deleted' ): _l( 'Delete' ),\n classes : 'delete-btn',\n faIcon : 'fa-times',\n disabled : deleted,\n onclick : function() {\n // ...bler... tooltips being left behind in DOM (hover out never called on deletion)\n self.$el.find( '.icon-btn.delete-btn' ).trigger( 'mouseout' );\n self.model[ 'delete' ]();\n }\n });\n },\n\n // ......................................................................... misc\n /** string rep */\n toString : function(){\n var modelString = ( this.model )?( this.model + '' ):( '(no model)' );\n return 'HDCAListItemEdit(' + modelString + ')';\n }\n});\n\n//==============================================================================\n return {\n HDCAListItemEdit : HDCAListItemEdit\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/history/hdca-li-edit.js","define([\n \"mvc/history/history-model\",\n \"mvc/history/history-view-edit\",\n \"mvc/base-mvc\",\n \"utils/localization\"\n], function( HISTORY_MODEL, HISTORY_VIEW_EDIT, BASE_MVC, _l ){\n\n'use strict';\n\n// ============================================================================\n/** session storage for history panel preferences (and to maintain state)\n */\nvar HistoryViewPrefs = BASE_MVC.SessionStorageModel.extend(\n/** @lends HistoryViewPrefs.prototype */{\n defaults : {\n /** should the tags editor be shown or hidden initially? */\n tagsEditorShown : false,\n /** should the annotation editor be shown or hidden initially? */\n annotationEditorShown : false,\n ///** what is the currently focused content (dataset or collection) in the current history?\n // * (the history panel will highlight and scroll to the focused content view)\n // */\n //focusedContentId : null\n /** Current scroll position */\n scrollPosition : 0\n },\n toString : function(){\n return 'HistoryViewPrefs(' + JSON.stringify( this.toJSON() ) + ')';\n }\n});\n\n/** key string to store panel prefs (made accessible on class so you can access sessionStorage directly) */\nHistoryViewPrefs.storageKey = function storageKey(){\n return ( 'history-panel' );\n};\n\n/* =============================================================================\nTODO:\n\n============================================================================= */\nvar _super = HISTORY_VIEW_EDIT.HistoryViewEdit;\n// used in root/index.mako\n/** @class View/Controller for the user's current history model as used in the history\n * panel (current right hand panel) of the analysis page.\n *\n * The only history panel that:\n * will poll for updates.\n * displays datasets in reverse hid order.\n */\nvar CurrentHistoryView = _super.extend(/** @lends CurrentHistoryView.prototype */{\n\n className : _super.prototype.className + ' current-history-panel',\n\n /** override to use drilldown (and not foldout) for how collections are displayed */\n HDCAViewClass : _super.prototype.HDCAViewClass.extend({\n foldoutStyle : 'drilldown'\n }),\n\n emptyMsg : [\n _l( 'This history is empty' ), '. ',\n _l( 'You can ' ),\n '',\n _l( 'load your own data' ),\n '',\n _l( ' or ' ),\n '',\n _l( 'get data from an external source' ),\n ''\n ].join(''),\n\n // ......................................................................... SET UP\n /** Set up the view, set up storage, bind listeners to HistoryContents events */\n initialize : function( attributes ){\n attributes = attributes || {};\n\n // ---- persistent preferences\n /** maintain state / preferences over page loads */\n this.preferences = new HistoryViewPrefs( _.extend({\n id : HistoryViewPrefs.storageKey()\n }, _.pick( attributes, _.keys( HistoryViewPrefs.prototype.defaults ) )));\n\n _super.prototype.initialize.call( this, attributes );\n\n /** sub-views that will overlay this panel (collections) */\n this.panelStack = [];\n\n /** id of currently focused content */\n this.currentContentId = attributes.currentContentId || null;\n //NOTE: purposely not sent to localstorage since panel recreation roughly lines up with a reset of this value\n },\n\n /** Override to cache the current scroll position with a listener */\n _setUpListeners : function(){\n _super.prototype._setUpListeners.call( this );\n\n var panel = this;\n // reset scroll position when there's a new history\n this.on( 'new-model', function(){\n panel.preferences.set( 'scrollPosition', 0 );\n });\n },\n\n // ------------------------------------------------------------------------ loading history/item models\n // TODO: next three more appropriate moved to the app level\n /** (re-)loads the user's current history & contents w/ details */\n loadCurrentHistory : function(){\n return this.loadHistory( null, { url : Galaxy.root + 'history/current_history_json' });\n },\n\n /** loads a history & contents w/ details and makes them the current history */\n switchToHistory : function( historyId, attributes ){\n if( Galaxy.user.isAnonymous() ){\n this.trigger( 'error', _l( 'You must be logged in to switch histories' ), _l( 'Anonymous user' ) );\n return $.when();\n }\n return this.loadHistory( historyId, { url : Galaxy.root + 'history/set_as_current?id=' + historyId });\n },\n\n /** creates a new history on the server and sets it as the user's current history */\n createNewHistory : function( attributes ){\n if( Galaxy.user.isAnonymous() ){\n this.trigger( 'error', _l( 'You must be logged in to create histories' ), _l( 'Anonymous user' ) );\n return $.when();\n }\n return this.loadHistory( null, { url : Galaxy.root + 'history/create_new_current' });\n },\n\n /** release/free/shutdown old models and set up panel for new models */\n setModel : function( model, attributes, render ){\n _super.prototype.setModel.call( this, model, attributes, render );\n if( this.model && this.model.id ){\n this.log( 'checking for updates' );\n this.model.checkForUpdates();\n }\n return this;\n },\n\n // ------------------------------------------------------------------------ history/content event listening\n /** listening for history events */\n _setUpModelListeners : function(){\n _super.prototype._setUpModelListeners.call( this );\n // re-broadcast any model change events so that listeners don't have to re-bind to each history\n return this.listenTo( this.model, {\n 'change:nice_size change:size' : function(){\n this.trigger( 'history-size-change', this, this.model, arguments );\n },\n 'change:id' : function(){\n this.once( 'loading-done', function(){ this.model.checkForUpdates(); });\n }\n });\n },\n\n /** listening for collection events */\n _setUpCollectionListeners : function(){\n _super.prototype._setUpCollectionListeners.call( this );\n // if a hidden item is created (gen. by a workflow), moves thru the updater to the ready state,\n // then: remove it from the collection if the panel is set to NOT show hidden datasets\n this.listenTo( this.collection, 'state:ready', function( model, newState, oldState ){\n if( ( !model.get( 'visible' ) )\n && ( !this.collection.storage.includeHidden() ) ){\n this.removeItemView( model );\n }\n });\n },\n\n // ------------------------------------------------------------------------ panel rendering\n /** override to add a handler to capture the scroll position when the parent scrolls */\n _setUpBehaviors : function( $where ){\n $where = $where || this.$el;\n // console.log( '_setUpBehaviors', this.$scrollContainer( $where ).get(0), this.$list( $where ) );\n // we need to call this in _setUpBehaviors which is called after render since the $el\n // may not be attached to $el.parent and $scrollContainer() may not work\n var panel = this;\n _super.prototype._setUpBehaviors.call( panel, $where );\n\n // cache the handler to remove and re-add so we don't pile up the handlers\n if( !this._debouncedScrollCaptureHandler ){\n this._debouncedScrollCaptureHandler = _.debounce( function scrollCapture(){\n // cache the scroll position (only if visible)\n if( panel.$el.is( ':visible' ) ){\n panel.preferences.set( 'scrollPosition', $( this ).scrollTop() );\n }\n }, 40 );\n }\n\n panel.$scrollContainer( $where )\n .off( 'scroll', this._debouncedScrollCaptureHandler )\n .on( 'scroll', this._debouncedScrollCaptureHandler );\n return panel;\n },\n\n /** In this override, handle null models and move the search input to the top */\n _buildNewRender : function(){\n if( !this.model ){ return $(); }\n var $newRender = _super.prototype._buildNewRender.call( this );\n $newRender.find( '.search' ).prependTo( $newRender.find( '> .controls' ) );\n this._renderQuotaMessage( $newRender );\n return $newRender;\n },\n\n /** render the message displayed when a user is over quota and can't run jobs */\n _renderQuotaMessage : function( $whereTo ){\n $whereTo = $whereTo || this.$el;\n return $( this.templates.quotaMsg( {}, this ) ).prependTo( $whereTo.find( '.messages' ) );\n },\n\n /** In this override, get and set current panel preferences when editor is used */\n _renderTags : function( $where ){\n var panel = this;\n // render tags and show/hide based on preferences\n _super.prototype._renderTags.call( panel, $where );\n if( panel.preferences.get( 'tagsEditorShown' ) ){\n panel.tagsEditor.toggle( true );\n }\n // store preference when shown or hidden\n panel.listenTo( panel.tagsEditor, 'hiddenUntilActivated:shown hiddenUntilActivated:hidden',\n function( tagsEditor ){\n panel.preferences.set( 'tagsEditorShown', tagsEditor.hidden );\n }\n );\n },\n\n /** In this override, get and set current panel preferences when editor is used */\n _renderAnnotation : function( $where ){\n var panel = this;\n // render annotation and show/hide based on preferences\n _super.prototype._renderAnnotation.call( panel, $where );\n if( panel.preferences.get( 'annotationEditorShown' ) ){\n panel.annotationEditor.toggle( true );\n }\n // store preference when shown or hidden\n panel.listenTo( panel.annotationEditor, 'hiddenUntilActivated:shown hiddenUntilActivated:hidden',\n function( annotationEditor ){\n panel.preferences.set( 'annotationEditorShown', annotationEditor.hidden );\n }\n );\n },\n\n /** Override to scroll to cached position (in prefs) after swapping */\n _swapNewRender : function( $newRender ){\n _super.prototype._swapNewRender.call( this, $newRender );\n var panel = this;\n _.delay( function(){\n var pos = panel.preferences.get( 'scrollPosition' );\n if( pos ){\n panel.scrollTo( pos, 0 );\n }\n }, 10 );\n //TODO: is this enough of a delay on larger histories?\n\n return this;\n },\n\n // ------------------------------------------------------------------------ sub-views\n /** Override to add the current-content highlight class to currentContentId's view */\n _attachItems : function( $whereTo ){\n _super.prototype._attachItems.call( this, $whereTo );\n var panel = this;\n if( panel.currentContentId ){\n panel._setCurrentContentById( panel.currentContentId );\n }\n return this;\n },\n\n /** Override to remove any drill down panels */\n addItemView : function( model, collection, options ){\n var view = _super.prototype.addItemView.call( this, model, collection, options );\n if( !view ){ return view; }\n if( this.panelStack.length ){ return this._collapseDrilldownPanel(); }\n return view;\n },\n\n // ------------------------------------------------------------------------ collection sub-views\n /** In this override, add/remove expanded/collapsed model ids to/from web storage */\n _setUpItemViewListeners : function( view ){\n var panel = this;\n _super.prototype._setUpItemViewListeners.call( panel, view );\n // use pub-sub to: handle drilldown expansion and collapse\n return panel.listenTo( view, {\n 'expanded:drilldown' : function( v, drilldown ){\n this._expandDrilldownPanel( drilldown );\n },\n 'collapsed:drilldown' : function( v, drilldown ){\n this._collapseDrilldownPanel( drilldown );\n },\n });\n },\n\n /** display 'current content': add a visible highlight and store the id of a content item */\n setCurrentContent : function( view ){\n this.$( '.history-content.current-content' ).removeClass( 'current-content' );\n if( view ){\n view.$el.addClass( 'current-content' );\n this.currentContentId = view.model.id;\n } else {\n this.currentContentId = null;\n }\n },\n\n /** find the view with the id and then call setCurrentContent on it */\n _setCurrentContentById : function( id ){\n var view = this.viewFromModelId( id ) || null;\n this.setCurrentContent( view );\n },\n\n /** Handle drill down by hiding this panels list and controls and showing the sub-panel */\n _expandDrilldownPanel : function( drilldown ){\n this.panelStack.push( drilldown );\n // hide this panel's controls and list, set the name for back navigation, and attach to the $el\n this.$controls().add( this.$list() ).hide();\n drilldown.parentName = this.model.get( 'name' );\n drilldown.delegateEvents().render().$el.appendTo( this.$el );\n },\n\n /** Handle drilldown close by freeing the panel and re-rendering this panel */\n _collapseDrilldownPanel : function( drilldown ){\n this.panelStack.pop();\n //TODO: MEM: free the panel\n this.$controls().add( this.$list() ).show();\n },\n\n // ........................................................................ panel events\n /** event map */\n events : _.extend( _.clone( _super.prototype.events ), {\n // the two links in the empty message\n 'click .uploader-link' : function( ev ){ Galaxy.upload.show( ev ); },\n 'click .get-data-link' : function( ev ){\n var $toolMenu = $( '.toolMenuContainer' );\n $toolMenu.parent().scrollTop( 0 );\n $toolMenu.find( 'span:contains(\"Get Data\")' ).click();\n }\n }),\n\n // ........................................................................ external objects/MVC\n listenToGalaxy : function( galaxy ){\n this.listenTo( galaxy, {\n // when the galaxy_main iframe is loaded with a new page,\n // compare the url to the following list and if there's a match\n // pull the id from url and indicate in the history view that\n // the dataset with that id is the 'current'ly active dataset\n 'galaxy_main:load': function( data ){\n var pathToMatch = data.fullpath;\n var hdaId = null;\n var useToURLRegexMap = {\n 'display' : /datasets\\/([a-f0-9]+)\\/display/,\n 'edit' : /datasets\\/([a-f0-9]+)\\/edit/,\n 'report_error' : /dataset\\/errors\\?id=([a-f0-9]+)/,\n 'rerun' : /tool_runner\\/rerun\\?id=([a-f0-9]+)/,\n 'show_params' : /datasets\\/([a-f0-9]+)\\/show_params/,\n // no great way to do this here? (leave it in the dataset event handlers above?)\n // 'visualization' : 'visualization',\n };\n _.find( useToURLRegexMap, function( regex, use ){\n // grab the more specific match result (1), save, and use it as the find flag\n hdaId = _.result( pathToMatch.match( regex ), 1 );\n return hdaId;\n });\n // need to type mangle to go from web route to history contents\n this._setCurrentContentById( hdaId? ( 'dataset-' + hdaId ) : null );\n },\n // when the center panel is given a new view, clear the current indicator\n 'center-panel:load': function( view ){\n this._setCurrentContentById();\n }\n });\n },\n\n //TODO: remove quota meter from panel and remove this\n /** add listeners to an external quota meter (mvc/user/user-quotameter.js) */\n connectToQuotaMeter : function( quotaMeter ){\n if( !quotaMeter ){\n return this;\n }\n // show/hide the 'over quota message' in the history when the meter tells it to\n this.listenTo( quotaMeter, 'quota:over', this.showQuotaMessage );\n this.listenTo( quotaMeter, 'quota:under', this.hideQuotaMessage );\n\n // having to add this to handle re-render of hview while overquota (the above do not fire)\n this.on( 'rendered rendered:initial', function(){\n if( quotaMeter && quotaMeter.isOverQuota() ){\n this.showQuotaMessage();\n }\n });\n return this;\n },\n\n /** Override to preserve the quota message */\n clearMessages : function( ev ){\n var $target = !_.isUndefined( ev )?\n $( ev.currentTarget )\n :this.$messages().children( '[class$=\"message\"]' );\n $target = $target.not( '.quota-message' );\n $target.fadeOut( this.fxSpeed, function(){\n $( this ).remove();\n });\n return this;\n },\n\n /** Show the over quota message (which happens to be in the history panel).\n */\n showQuotaMessage : function(){\n var $msg = this.$( '.quota-message' );\n if( $msg.is( ':hidden' ) ){ $msg.slideDown( this.fxSpeed ); }\n },\n\n /** Hide the over quota message (which happens to be in the history panel).\n */\n hideQuotaMessage : function(){\n var $msg = this.$( '.quota-message' );\n if( !$msg.is( ':hidden' ) ){ $msg.slideUp( this.fxSpeed ); }\n },\n\n // ........................................................................ options menu\n //TODO: remove to batch\n /** unhide any hidden datasets */\n unhideHidden : function() {\n var self = this;\n if( confirm( _l( 'Really unhide all hidden datasets?' ) ) ){\n // get all hidden, regardless of deleted/purged\n return self.model.contents._filterAndUpdate(\n { visible: false, deleted: '', purged: '' },\n { visible : true }\n ).done( function(){\n // TODO: would be better to render these as they're unhidden instead of all at once\n if( !self.model.contents.includeHidden ){\n self.renderItems();\n }\n });\n }\n return jQuery.when();\n },\n\n /** delete any hidden datasets */\n deleteHidden : function() {\n var self = this;\n if( confirm( _l( 'Really delete all hidden datasets?' ) ) ){\n return self.model.contents._filterAndUpdate(\n // get all hidden, regardless of deleted/purged\n { visible: false, deleted: '', purged: '' },\n // both delete *and* unhide them\n { deleted : true, visible: true }\n );\n }\n return jQuery.when();\n },\n\n /** Return a string rep of the history */\n toString : function(){\n return 'CurrentHistoryView(' + (( this.model )?( this.model.get( 'name' )):( '' )) + ')';\n }\n});\n\n\n//------------------------------------------------------------------------------ TEMPLATES\nCurrentHistoryView.prototype.templates = (function(){\n\n var quotaMsgTemplate = BASE_MVC.wrapTemplate([\n '
',\n _l( 'You are over your disk quota' ), '. ',\n _l( 'Tool execution is on hold until your disk usage drops below your allocated quota' ), '.',\n '
'\n ], 'history' );\n return _.extend( _.clone( _super.prototype.templates ), {\n quotaMsg : quotaMsgTemplate\n });\n\n}());\n\n\n//==============================================================================\n return {\n CurrentHistoryView : CurrentHistoryView\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/history/history-view-edit-current.js","define([\n \"mvc/history/history-view\",\n \"mvc/history/history-contents\",\n \"mvc/dataset/states\",\n \"mvc/history/hda-model\",\n \"mvc/history/hda-li-edit\",\n \"mvc/history/hdca-li-edit\",\n \"mvc/tag\",\n \"mvc/annotation\",\n \"mvc/collection/list-collection-creator\",\n \"mvc/collection/pair-collection-creator\",\n \"mvc/collection/list-of-pairs-collection-creator\",\n \"ui/fa-icon-button\",\n \"mvc/ui/popup-menu\",\n \"mvc/base-mvc\",\n \"utils/localization\",\n \"ui/editable-text\",\n], function(\n HISTORY_VIEW,\n HISTORY_CONTENTS,\n STATES,\n HDA_MODEL,\n HDA_LI_EDIT,\n HDCA_LI_EDIT,\n TAGS,\n ANNOTATIONS,\n LIST_COLLECTION_CREATOR,\n PAIR_COLLECTION_CREATOR,\n LIST_OF_PAIRS_COLLECTION_CREATOR,\n faIconButton,\n PopupMenu,\n BASE_MVC,\n _l\n){\n\n'use strict';\n\n/* =============================================================================\nTODO:\n\n============================================================================= */\nvar _super = HISTORY_VIEW.HistoryView;\n// base class for history-view-edit-current and used as-is in history/view.mako\n/** @class Editable View/Controller for the history model.\n *\n * Allows:\n * (everything HistoryView allows)\n * changing the name\n * displaying and editing tags and annotations\n * multi-selection and operations on mulitple content items\n */\nvar HistoryViewEdit = _super.extend(\n/** @lends HistoryViewEdit.prototype */{\n\n /** class to use for constructing the HistoryDatasetAssociation views */\n HDAViewClass : HDA_LI_EDIT.HDAListItemEdit,\n /** class to use for constructing the HistoryDatasetCollectionAssociation views */\n HDCAViewClass : HDCA_LI_EDIT.HDCAListItemEdit,\n\n // ......................................................................... SET UP\n /** Set up the view, set up storage, bind listeners to HistoryContents events\n * @param {Object} attributes\n */\n initialize : function( attributes ){\n attributes = attributes || {};\n _super.prototype.initialize.call( this, attributes );\n\n // ---- set up instance vars\n /** editor for tags - sub-view */\n this.tagsEditor = null;\n\n /** enable drag and drop - sub-view */\n this.dragItems = true;\n\n /** editor for annotations - sub-view */\n this.annotationEditor = null;\n\n /** allow user purge of dataset files? */\n this.purgeAllowed = attributes.purgeAllowed || false;\n\n // states/modes the panel can be in\n /** is the panel currently showing the dataset selection controls? */\n this.annotationEditorShown = attributes.annotationEditorShown || false;\n this.tagsEditorShown = attributes.tagsEditorShown || false;\n },\n\n /** Override to handle history as drag-drop target */\n _setUpListeners : function(){\n _super.prototype._setUpListeners.call( this );\n return this.on({\n 'droptarget:drop': function( ev, data ){\n // process whatever was dropped and re-hide the drop target\n this.dataDropped( data );\n this.dropTargetOff();\n },\n 'view:attached view:removed': function(){\n this._renderCounts();\n },\n 'search:loading-progress': this._renderSearchProgress,\n 'search:searching': this._renderSearchFindings,\n });\n },\n\n // ------------------------------------------------------------------------ listeners\n /** listening for history and HDA events */\n _setUpModelListeners : function(){\n _super.prototype._setUpModelListeners.call( this );\n this.listenTo( this.model, 'change:size', this.updateHistoryDiskSize );\n return this;\n },\n\n /** listening for collection events */\n _setUpCollectionListeners : function(){\n _super.prototype._setUpCollectionListeners.call( this );\n this.listenTo( this.collection, {\n 'change:deleted': this._handleItemDeletedChange,\n 'change:visible': this._handleItemVisibleChange,\n 'change:purged' : function( model ){\n // hafta get the new nice-size w/o the purged model\n this.model.fetch();\n },\n // loading indicators for deleted/hidden\n 'fetching-deleted' : function( collection ){\n this.$( '> .controls .deleted-count' )\n .html( '' + _l( 'loading...' ) + '' );\n },\n 'fetching-hidden' : function( collection ){\n this.$( '> .controls .hidden-count' )\n .html( '' + _l( 'loading...' ) + '' );\n },\n 'fetching-deleted-done fetching-hidden-done' : this._renderCounts,\n });\n return this;\n },\n\n // ------------------------------------------------------------------------ panel rendering\n /** In this override, add tag and annotation editors and a btn to toggle the selectors */\n _buildNewRender : function(){\n // create a new render using a skeleton template, render title buttons, render body, and set up events, etc.\n var $newRender = _super.prototype._buildNewRender.call( this );\n if( !this.model ){ return $newRender; }\n\n if( Galaxy && Galaxy.user && Galaxy.user.id && Galaxy.user.id === this.model.get( 'user_id' ) ){\n this._renderTags( $newRender );\n this._renderAnnotation( $newRender );\n }\n return $newRender;\n },\n\n /** Update the history size display (curr. upper right of panel). */\n updateHistoryDiskSize : function(){\n this.$( '.history-size' ).text( this.model.get( 'nice_size' ) );\n },\n\n /** override to render counts when the items are rendered */\n renderItems : function( $whereTo ){\n var views = _super.prototype.renderItems.call( this, $whereTo );\n if( !this.searchFor ){ this._renderCounts( $whereTo ); }\n return views;\n },\n\n /** override to show counts, what's deleted/hidden, and links to toggle those */\n _renderCounts : function( $whereTo ){\n $whereTo = $whereTo instanceof jQuery? $whereTo : this.$el;\n var html = this.templates.counts( this.model.toJSON(), this );\n return $whereTo.find( '> .controls .subtitle' ).html( html );\n },\n\n /** render the tags sub-view controller */\n _renderTags : function( $where ){\n var panel = this;\n this.tagsEditor = new TAGS.TagsEditor({\n model : this.model,\n el : $where.find( '.controls .tags-display' ),\n onshowFirstTime : function(){ this.render(); },\n // show hide sub-view tag editors when this is shown/hidden\n onshow : function(){\n panel.toggleHDATagEditors( true, panel.fxSpeed );\n },\n onhide : function(){\n panel.toggleHDATagEditors( false, panel.fxSpeed );\n },\n $activator : faIconButton({\n title : _l( 'Edit history tags' ),\n classes : 'history-tag-btn',\n faIcon : 'fa-tags'\n }).appendTo( $where.find( '.controls .actions' ) )\n });\n },\n /** render the annotation sub-view controller */\n _renderAnnotation : function( $where ){\n var panel = this;\n this.annotationEditor = new ANNOTATIONS.AnnotationEditor({\n model : this.model,\n el : $where.find( '.controls .annotation-display' ),\n onshowFirstTime : function(){ this.render(); },\n // show hide sub-view view annotation editors when this is shown/hidden\n onshow : function(){\n panel.toggleHDAAnnotationEditors( true, panel.fxSpeed );\n },\n onhide : function(){\n panel.toggleHDAAnnotationEditors( false, panel.fxSpeed );\n },\n $activator : faIconButton({\n title : _l( 'Edit history annotation' ),\n classes : 'history-annotate-btn',\n faIcon : 'fa-comment'\n }).appendTo( $where.find( '.controls .actions' ) )\n });\n },\n\n /** Set up HistoryViewEdit js/widget behaviours\n * In this override, make the name editable\n */\n _setUpBehaviors : function( $where ){\n $where = $where || this.$el;\n _super.prototype._setUpBehaviors.call( this, $where );\n if( !this.model ){ return; }\n\n // anon users shouldn't have access to any of the following\n if( ( !Galaxy.user || Galaxy.user.isAnonymous() )\n || ( Galaxy.user.id !== this.model.get( 'user_id' ) ) ){\n return;\n }\n\n var panel = this,\n nameSelector = '> .controls .name';\n $where.find( nameSelector )\n .attr( 'title', _l( 'Click to rename history' ) )\n .tooltip({ placement: 'bottom' })\n .make_text_editable({\n on_finish: function( newName ){\n var previousName = panel.model.get( 'name' );\n if( newName && newName !== previousName ){\n panel.$el.find( nameSelector ).text( newName );\n panel.model.save({ name: newName })\n .fail( function(){\n panel.$el.find( nameSelector ).text( panel.model.previous( 'name' ) );\n });\n } else {\n panel.$el.find( nameSelector ).text( previousName );\n }\n }\n });\n },\n\n /** return a new popup menu for choosing a multi selection action\n * ajax calls made for multiple datasets are queued\n */\n multiselectActions : function(){\n var panel = this,\n actions = [\n { html: _l( 'Hide datasets' ), func: function(){\n var action = HDA_MODEL.HistoryDatasetAssociation.prototype.hide;\n panel.getSelectedModels().ajaxQueue( action );\n }\n },\n { html: _l( 'Unhide datasets' ), func: function(){\n var action = HDA_MODEL.HistoryDatasetAssociation.prototype.unhide;\n panel.getSelectedModels().ajaxQueue( action );\n }\n },\n { html: _l( 'Delete datasets' ), func: function(){\n var action = HDA_MODEL.HistoryDatasetAssociation.prototype['delete'];\n panel.getSelectedModels().ajaxQueue( action );\n }\n },\n { html: _l( 'Undelete datasets' ), func: function(){\n var action = HDA_MODEL.HistoryDatasetAssociation.prototype.undelete;\n panel.getSelectedModels().ajaxQueue( action );\n }\n }\n ];\n if( panel.purgeAllowed ){\n actions.push({\n html: _l( 'Permanently delete datasets' ), func: function(){\n if( confirm( _l( 'This will permanently remove the data in your datasets. Are you sure?' ) ) ){\n var action = HDA_MODEL.HistoryDatasetAssociation.prototype.purge;\n panel.getSelectedModels().ajaxQueue( action );\n }\n }\n });\n }\n actions = actions.concat( panel._collectionActions() );\n return actions;\n },\n\n /** */\n _collectionActions : function(){\n var panel = this;\n return [\n { html: _l( 'Build Dataset List' ), func: function() { panel.buildCollection( \"list\") }\n },\n // TODO: Only show quick pair if two things selected.\n { html: _l( 'Build Dataset Pair' ), func: function() { panel.buildCollection( \"paired\") }\n },\n { html: _l( 'Build List of Dataset Pairs' ), func: function() { panel.buildCollection( \"list:paired\" ) }\n },\n ];\n },\n\n buildCollection : function( collectionType, selection, hideSourceItems ) {\n var panel = this;\n var selection = selection || panel.getSelectedModels();\n var hideSourceItems = hideSourceItems || false;\n var createFunc;\n if( collectionType == \"list\" ) {\n createFunc = LIST_COLLECTION_CREATOR.createListCollection;\n } else if( collectionType == \"paired\" ) {\n createFunc = PAIR_COLLECTION_CREATOR.createPairCollection;\n } else if( collectionType == \"list:paired\" ) {\n createFunc = LIST_OF_PAIRS_COLLECTION_CREATOR.createListOfPairsCollection;\n } else {\n console.warn( \"Unknown collectionType encountered \" + collectionType );\n }\n createFunc( selection, hideSourceItems ).done( function() { panel.model.refresh() } );\n },\n\n // ------------------------------------------------------------------------ sub-views\n /** In this override, add purgeAllowed and whether tags/annotation editors should be shown */\n _getItemViewOptions : function( model ){\n var options = _super.prototype._getItemViewOptions.call( this, model );\n _.extend( options, {\n purgeAllowed : this.purgeAllowed,\n tagsEditorShown : ( this.tagsEditor && !this.tagsEditor.hidden ),\n annotationEditorShown : ( this.annotationEditor && !this.annotationEditor.hidden )\n });\n return options;\n },\n\n /** If this item is deleted and we're not showing deleted items, remove the view\n * @param {Model} the item model to check\n */\n _handleItemDeletedChange : function( itemModel ){\n if( itemModel.get( 'deleted' ) ){\n this._handleItemDeletion( itemModel );\n } else {\n this._handleItemUndeletion( itemModel );\n }\n this._renderCounts();\n },\n\n _handleItemDeletion : function( itemModel ){\n var contentsShown = this.model.get( 'contents_active' );\n contentsShown.deleted += 1;\n contentsShown.active -= 1;\n if( !this.model.contents.includeDeleted ){\n this.removeItemView( itemModel );\n }\n this.model.set( 'contents_active', contentsShown );\n },\n\n _handleItemUndeletion : function( itemModel ){\n var contentsShown = this.model.get( 'contents_active' );\n contentsShown.deleted -= 1;\n if( !this.model.contents.includeDeleted ){\n contentsShown.active -= 1;\n }\n this.model.set( 'contents_active', contentsShown );\n },\n\n /** If this item is hidden and we're not showing hidden items, remove the view\n * @param {Model} the item model to check\n */\n _handleItemVisibleChange : function( itemModel ){\n if( itemModel.hidden() ){\n this._handleItemHidden( itemModel );\n } else {\n this._handleItemUnhidden( itemModel );\n }\n this._renderCounts();\n },\n\n _handleItemHidden : function( itemModel ){\n var contentsShown = this.model.get( 'contents_active' );\n contentsShown.hidden += 1;\n contentsShown.active -= 1;\n if( !this.model.contents.includeHidden ){\n this.removeItemView( itemModel );\n }\n this.model.set( 'contents_active', contentsShown );\n },\n\n _handleItemUnhidden : function( itemModel ){\n var contentsShown = this.model.get( 'contents_active' );\n contentsShown.hidden -= 1;\n if( !this.model.contents.includeHidden ){\n contentsShown.active -= 1;\n }\n this.model.set( 'contents_active', contentsShown );\n },\n\n /** toggle the visibility of each content's tagsEditor applying all the args sent to this function */\n toggleHDATagEditors : function( showOrHide, speed ){\n _.each( this.views, function( view ){\n if( view.tagsEditor ){\n view.tagsEditor.toggle( showOrHide, speed );\n }\n });\n },\n\n /** toggle the visibility of each content's annotationEditor applying all the args sent to this function */\n toggleHDAAnnotationEditors : function( showOrHide, speed ){\n _.each( this.views, function( view ){\n if( view.annotationEditor ){\n view.annotationEditor.toggle( showOrHide, speed );\n }\n });\n },\n\n // ------------------------------------------------------------------------ panel events\n /** event map */\n events : _.extend( _.clone( _super.prototype.events ), {\n 'click .show-selectors-btn' : 'toggleSelectors',\n 'click .toggle-deleted-link' : function( ev ){ this.toggleShowDeleted(); },\n 'click .toggle-hidden-link' : function( ev ){ this.toggleShowHidden(); }\n }),\n\n // ------------------------------------------------------------------------ search\n _renderSearchProgress : function( limit, offset ){\n var stop = limit + offset;\n return this.$( '> .controls .subtitle' ).html([\n '',\n _l( 'Searching ' ), stop, '/', this.model.contentsShown(),\n ''\n ].join(''));\n },\n\n /** override to display number found in subtitle */\n _renderSearchFindings : function(){\n this.$( '> .controls .subtitle' ).html([\n _l( 'Found' ), this.views.length\n ].join(' '));\n return this;\n },\n\n // ------------------------------------------------------------------------ as drop target\n /** turn all the drag and drop handlers on and add some help text above the drop area */\n dropTargetOn : function(){\n if( this.dropTarget ){ return this; }\n this.dropTarget = true;\n\n //TODO: to init\n var dropHandlers = {\n 'dragenter' : _.bind( this.dragenter, this ),\n 'dragover' : _.bind( this.dragover, this ),\n 'dragleave' : _.bind( this.dragleave, this ),\n 'drop' : _.bind( this.drop, this )\n };\n\n var $dropTarget = this._renderDropTarget();\n this.$list().before([ this._renderDropTargetHelp(), $dropTarget ]);\n for( var evName in dropHandlers ){\n if( dropHandlers.hasOwnProperty( evName ) ){\n //console.debug( evName, dropHandlers[ evName ] );\n $dropTarget.on( evName, dropHandlers[ evName ] );\n }\n }\n return this;\n },\n\n /** render a box to serve as a 'drop here' area on the history */\n _renderDropTarget : function(){\n this.$( '.history-drop-target' ).remove();\n return $( '' ).addClass( 'history-drop-target' );\n },\n\n /** tell the user how it works */\n _renderDropTargetHelp : function(){\n this.$( '.history-drop-target-help' ).remove();\n return $( '' ).addClass( 'history-drop-target-help' )\n .text( _l( 'Drag datasets here to copy them to the current history' ) );\n },\n\n /** shut down drag and drop event handlers and remove drop target */\n dropTargetOff : function(){\n if( !this.dropTarget ){ return this; }\n //this.log( 'dropTargetOff' );\n this.dropTarget = false;\n var dropTarget = this.$( '.history-drop-target' ).get(0);\n for( var evName in this._dropHandlers ){\n if( this._dropHandlers.hasOwnProperty( evName ) ){\n dropTarget.off( evName, this._dropHandlers[ evName ] );\n }\n }\n this.$( '.history-drop-target' ).remove();\n this.$( '.history-drop-target-help' ).remove();\n return this;\n },\n /** toggle the target on/off */\n dropTargetToggle : function(){\n if( this.dropTarget ){\n this.dropTargetOff();\n } else {\n this.dropTargetOn();\n }\n return this;\n },\n\n dragenter : function( ev ){\n //console.debug( 'dragenter:', this, ev );\n ev.preventDefault();\n ev.stopPropagation();\n this.$( '.history-drop-target' ).css( 'border', '2px solid black' );\n },\n dragover : function( ev ){\n ev.preventDefault();\n ev.stopPropagation();\n },\n dragleave : function( ev ){\n //console.debug( 'dragleave:', this, ev );\n ev.preventDefault();\n ev.stopPropagation();\n this.$( '.history-drop-target' ).css( 'border', '1px dashed black' );\n },\n /** when (text) is dropped try to parse as json and trigger an event */\n drop : function( ev ){\n ev.preventDefault();\n //ev.stopPropagation();\n\n var self = this;\n var dataTransfer = ev.originalEvent.dataTransfer;\n var data = dataTransfer.getData( \"text\" );\n\n dataTransfer.dropEffect = 'move';\n try {\n data = JSON.parse( data );\n } catch( err ){\n self.warn( 'error parsing JSON from drop:', data );\n }\n\n self.trigger( 'droptarget:drop', ev, data, self );\n return false;\n },\n\n /** handler that copies data into the contents */\n dataDropped : function( data ){\n var self = this;\n // HDA: dropping will copy it to the history\n if( _.isObject( data ) && data.model_class === 'HistoryDatasetAssociation' && data.id ){\n if( self.contents.currentPage !== 0 ){\n return self.contents.fetchPage( 0 )\n .then( function(){\n return self.model.contents.copy( data.id );\n });\n }\n return self.model.contents.copy( data.id );\n }\n return jQuery.when();\n },\n\n // ........................................................................ misc\n /** Return a string rep of the history */\n toString : function(){\n return 'HistoryViewEdit(' + (( this.model )?( this.model.get( 'name' )):( '' )) + ')';\n }\n});\n\n//------------------------------------------------------------------------------ TEMPLATES\nHistoryViewEdit.prototype.templates = (function(){\n\n var countsTemplate = BASE_MVC.wrapTemplate([\n '<% var shown = Math.max( view.views.length, history.contents_active.active ) %>',\n '<% if( shown ){ %>',\n '',\n '<%- shown %> ', _l( 'shown' ),\n '',\n '<% } %>',\n\n '<% if( history.contents_active.deleted ){ %>',\n '',\n '<% if( view.model.contents.includeDeleted ){ %>',\n '',\n _l( 'hide deleted' ),\n '',\n '<% } else { %>',\n '<%- history.contents_active.deleted %> ',\n '',\n _l( 'deleted' ),\n '',\n '<% } %>',\n '',\n '<% } %>',\n\n '<% if( history.contents_active.hidden ){ %>',\n '',\n '<% if( view.model.contents.includeHidden ){ %>',\n '',\n _l( 'hide hidden' ),\n '',\n '<% } else { %>',\n '<%- history.contents_active.hidden %> ',\n '',\n _l( 'hidden' ),\n '',\n '<% } %>',\n '',\n '<% } %>',\n ], 'history' );\n\n return _.extend( _.clone( _super.prototype.templates ), {\n counts : countsTemplate\n });\n}());\n\n\n//==============================================================================\n return {\n HistoryViewEdit : HistoryViewEdit\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/history/history-view-edit.js","define([\n \"mvc/list/list-view\",\n \"mvc/history/history-model\",\n \"mvc/history/history-contents\",\n \"mvc/history/history-preferences\",\n \"mvc/history/hda-li\",\n \"mvc/history/hdca-li\",\n \"mvc/user/user-model\",\n \"mvc/ui/error-modal\",\n \"ui/fa-icon-button\",\n \"mvc/base-mvc\",\n \"utils/localization\",\n \"ui/search-input\"\n], function(\n LIST_VIEW,\n HISTORY_MODEL,\n HISTORY_CONTENTS,\n HISTORY_PREFS,\n HDA_LI,\n HDCA_LI,\n USER,\n ERROR_MODAL,\n faIconButton,\n BASE_MVC,\n _l\n){\n'use strict';\n\n/* =============================================================================\nTODO:\n\n============================================================================= */\n/** @class non-editable, read-only View/Controller for a history model.\n * Allows:\n * changing the loaded history\n * displaying data, info, and download\n * tracking history attrs: size, tags, annotations, name, etc.\n * Does not allow:\n * changing the name\n */\nvar _super = LIST_VIEW.ModelListPanel;\nvar HistoryView = _super.extend(\n/** @lends HistoryView.prototype */{\n _logNamespace : 'history',\n\n /** class to use for constructing the HDA views */\n HDAViewClass : HDA_LI.HDAListItemView,\n /** class to use for constructing the HDCA views */\n HDCAViewClass : HDCA_LI.HDCAListItemView,\n /** class to used for constructing collection of sub-view models */\n collectionClass : HISTORY_CONTENTS.HistoryContents,\n /** key of attribute in model to assign to this.collection */\n modelCollectionKey : 'contents',\n\n tagName : 'div',\n className : _super.prototype.className + ' history-panel',\n\n /** string to display when the collection is empty */\n emptyMsg : _l( 'This history is empty' ),\n /** displayed when no items match the search terms */\n noneFoundMsg : _l( 'No matching datasets found' ),\n /** string used for search placeholder */\n searchPlaceholder : _l( 'search datasets' ),\n\n /** @type {Number} ms to wait after history load to fetch/decorate hdcas with element_count */\n FETCH_COLLECTION_COUNTS_DELAY : 2000,\n\n // ......................................................................... SET UP\n /** Set up the view, bind listeners.\n * @param {Object} attributes optional settings for the panel\n */\n initialize : function( attributes ){\n _super.prototype.initialize.call( this, attributes );\n // ---- instance vars\n // control contents/behavior based on where (and in what context) the panel is being used\n /** where should pages from links be displayed? (default to new tab/window) */\n this.linkTarget = attributes.linkTarget || '_blank';\n },\n\n /** create and return a collection for when none is initially passed */\n _createDefaultCollection : function(){\n // override\n return new this.collectionClass([], { history: this.model });\n },\n\n /** In this override, clear the update timer on the model */\n freeModel : function(){\n _super.prototype.freeModel.call( this );\n if( this.model ){\n this.model.clearUpdateTimeout();\n }\n return this;\n },\n\n /** create any event listeners for the panel\n * @fires: rendered:initial on the first render\n * @fires: empty-history when switching to a history with no contents or creating a new history\n */\n _setUpListeners : function(){\n _super.prototype._setUpListeners.call( this );\n this.on({\n error : function( model, xhr, options, msg, details ){\n this.errorHandler( model, xhr, options, msg, details );\n },\n 'loading-done' : function(){\n var self = this;\n // after the initial load, decorate with more time consuming fields (like HDCA element_counts)\n _.delay( function(){\n self.model.contents.fetchCollectionCounts();\n }, self.FETCH_COLLECTION_COUNTS_DELAY );\n },\n 'views:ready view:attached view:removed' : function( view ){\n this._renderSelectButton();\n },\n 'view:attached' : function( view ){\n this.scrollTo(0);\n },\n });\n // this.on( 'all', function(){ console.debug( arguments ); });\n },\n\n // ------------------------------------------------------------------------ loading history/hda models\n /** load the history with the given id then it's contents, sending ajax options to both */\n loadHistory : function( historyId, options, contentsOptions ){\n contentsOptions = _.extend( contentsOptions || { silent: true });\n this.info( 'loadHistory:', historyId, options, contentsOptions );\n var self = this;\n self.setModel( new HISTORY_MODEL.History({ id : historyId }) );\n\n contentsOptions.silent = true;\n self.trigger( 'loading' );\n return self.model\n .fetchWithContents( options, contentsOptions )\n .always( function(){\n self.render();\n self.trigger( 'loading-done' );\n });\n },\n\n /** convenience alias to the model. Updates the item list only (not the history) */\n refreshContents : function( options ){\n if( this.model ){\n return this.model.refresh( options );\n }\n // may have callbacks - so return an empty promise\n return $.when();\n },\n\n /** Override to reset web storage when the id changes (since it needs the id) */\n _setUpCollectionListeners : function(){\n _super.prototype._setUpCollectionListeners.call( this );\n return this.listenTo( this.collection, {\n // 'all' : function(){ console.log( this.collection + ':', arguments ); },\n 'fetching-more' : function(){\n this._toggleContentsLoadingIndicator( true );\n this.$emptyMessage().hide();\n },\n 'fetching-more-done': function(){ this._toggleContentsLoadingIndicator( false ); },\n });\n },\n\n // ------------------------------------------------------------------------ panel rendering\n /** hide the $el and display a loading indicator (in the $el's parent) when loading new data */\n _showLoadingIndicator : function( msg, speed, callback ){\n var $indicator = $( '
' );\n this.$el.html( $indicator.text( msg ).slideDown( !_.isUndefined( speed )? speed : this.fxSpeed ) );\n },\n\n /** hide the loading indicator */\n _hideLoadingIndicator : function( speed ){\n // make speed a bit slower to compensate for slow rendering of up to 500 contents\n this.$( '.loading-indicator' ).slideUp( !_.isUndefined( speed )? speed : ( this.fxSpeed + 200 ), function(){\n $( this ).remove();\n });\n },\n\n /** In this override, add a btn to toggle the selectors */\n _buildNewRender : function(){\n var $newRender = _super.prototype._buildNewRender.call( this );\n this._renderSelectButton( $newRender );\n return $newRender;\n },\n\n /** button for starting select mode */\n _renderSelectButton : function( $where ){\n $where = $where || this.$el;\n // do not render selector option if no actions\n if( !this.multiselectActions().length ){\n return null;\n }\n // do not render (and remove even) if nothing to select\n if( !this.views.length ){\n this.hideSelectors();\n $where.find( '.controls .actions .show-selectors-btn' ).remove();\n return null;\n }\n // don't bother rendering if there's one already\n var $existing = $where.find( '.controls .actions .show-selectors-btn' );\n if( $existing.length ){\n return $existing;\n }\n\n return faIconButton({\n title : _l( 'Operations on multiple datasets' ),\n classes : 'show-selectors-btn',\n faIcon : 'fa-check-square-o'\n }).prependTo( $where.find( '.controls .actions' ) );\n },\n\n /** override to avoid showing intial empty message using contents_active */\n _renderEmptyMessage : function( $whereTo ){\n var self = this;\n var $emptyMsg = self.$emptyMessage( $whereTo );\n\n var empty = self.model.get( 'contents_active' ).active <= 0;\n if( empty ){\n return $emptyMsg.empty().append( self.emptyMsg ).show();\n\n } else if( self.searchFor && self.model.contents.haveSearchDetails() && !self.views.length ){\n return $emptyMsg.empty().append( self.noneFoundMsg ).show();\n }\n $emptyMsg.hide();\n return $();\n },\n\n /** the scroll container for this panel - can be $el, $el.parent(), or grandparent depending on context */\n $scrollContainer : function( $where ){\n // override or set via attributes.$scrollContainer\n return this.$list( $where );\n },\n\n // ------------------------------------------------------------------------ subviews\n _toggleContentsLoadingIndicator : function( show ){\n if( !show ){\n this.$list().find( '.contents-loading-indicator' ).remove();\n } else {\n this.$list().html( '
'\n + '
' );\n }\n },\n\n /** override to render pagination also */\n renderItems: function( $whereTo ){\n // console.log( this + '.renderItems-----------------', new Date() );\n $whereTo = $whereTo || this.$el;\n var self = this;\n var $list = self.$list( $whereTo );\n\n // TODO: bootstrap hack to remove orphaned tooltips\n $( '.tooltip' ).remove();\n\n $list.empty();\n self.views = [];\n\n var models = self._filterCollection();\n if( models.length ){\n self._renderPagination( $whereTo );\n self.views = self._renderSomeItems( models, $list );\n } else {\n // TODO: consolidate with _renderPagination above by (???) passing in models/length?\n $whereTo.find( '> .controls .list-pagination' ).empty();\n }\n self._renderEmptyMessage( $whereTo ).toggle( !models.length );\n\n self.trigger( 'views:ready', self.views );\n return self.views;\n },\n\n /** render pagination controls if not searching and contents says we're paginating */\n _renderPagination: function( $whereTo ){\n var $paginationControls = $whereTo.find( '> .controls .list-pagination' );\n if( this.searchFor || !this.model.contents.shouldPaginate() ) return $paginationControls.empty();\n\n $paginationControls.html( this.templates.pagination({\n // pagination is 1-based for the user\n current : this.model.contents.currentPage + 1,\n last : this.model.contents.getLastPage() + 1,\n }, this ));\n $paginationControls.find( 'select.pages' ).tooltip();\n return $paginationControls;\n },\n\n /** render a subset of the entire collection (client-side pagination) */\n _renderSomeItems: function( models, $list ){\n var self = this;\n var views = [];\n $list.append( models.map( function( m ){\n var view = self._createItemView( m );\n views.push( view );\n return self._renderItemView$el( view );\n }));\n return views;\n },\n\n // ------------------------------------------------------------------------ sub-views\n /** in this override, check if the contents would also display based on includeDeleted/hidden */\n _filterItem : function( model ){\n var self = this;\n var contents = self.model.contents;\n return ( contents.includeHidden || !model.hidden() )\n && ( contents.includeDeleted || !model.isDeletedOrPurged() )\n && ( _super.prototype._filterItem.call( self, model ) );\n },\n\n /** In this override, since history contents are mixed,\n * get the appropo view class based on history_content_type\n */\n _getItemViewClass : function( model ){\n var contentType = model.get( \"history_content_type\" );\n switch( contentType ){\n case 'dataset':\n return this.HDAViewClass;\n case 'dataset_collection':\n return this.HDCAViewClass;\n }\n throw new TypeError( 'Unknown history_content_type: ' + contentType );\n },\n\n /** in this override, add a linktarget, and expand if id is in web storage */\n _getItemViewOptions : function( model ){\n var options = _super.prototype._getItemViewOptions.call( this, model );\n return _.extend( options, {\n linkTarget : this.linkTarget,\n expanded : this.model.contents.storage.isExpanded( model.id ),\n hasUser : this.model.ownedByCurrUser()\n });\n },\n\n /** In this override, add/remove expanded/collapsed model ids to/from web storage */\n _setUpItemViewListeners : function( view ){\n var panel = this;\n _super.prototype._setUpItemViewListeners.call( panel, view );\n //TODO: send from content view: this.model.collection.storage.addExpanded\n // maintain a list of items whose bodies are expanded\n return panel.listenTo( view, {\n 'expanded': function( v ){\n panel.model.contents.storage.addExpanded( v.model );\n },\n 'collapsed': function( v ){\n panel.model.contents.storage.removeExpanded( v.model );\n }\n });\n },\n\n /** override to remove expandedIds from webstorage */\n collapseAll : function(){\n this.model.contents.storage.clearExpanded();\n _super.prototype.collapseAll.call( this );\n },\n\n // ------------------------------------------------------------------------ selection\n /** Override to correctly set the historyId of the new collection */\n getSelectedModels : function(){\n var collection = _super.prototype.getSelectedModels.call( this );\n collection.historyId = this.collection.historyId;\n return collection;\n },\n\n\n // ------------------------------------------------------------------------ panel events\n /** event map */\n events : _.extend( _.clone( _super.prototype.events ), {\n 'click .show-selectors-btn' : 'toggleSelectors',\n 'click > .controls .prev' : '_clickPrevPage',\n 'click > .controls .next' : '_clickNextPage',\n 'change > .controls .pages' : '_changePageSelect',\n // allow (error) messages to be clicked away\n 'click .messages [class$=message]' : 'clearMessages',\n }),\n\n _clickPrevPage : function( ev ){\n this.model.clearUpdateTimeout();\n this.model.contents.fetchPrevPage();\n },\n\n _clickNextPage : function( ev ){\n this.model.clearUpdateTimeout();\n this.model.contents.fetchNextPage();\n },\n\n _changePageSelect : function( ev ){\n this.model.clearUpdateTimeout();\n var page = $( ev.currentTarget ).val();\n this.model.contents.fetchPage( page );\n },\n\n /** Toggle and store the deleted visibility and re-render items\n * @returns {Boolean} new setting\n */\n toggleShowDeleted : function( show, options ){\n show = ( show !== undefined )?( show ):( !this.model.contents.includeDeleted );\n var self = this;\n var contents = self.model.contents;\n contents.setIncludeDeleted( show, options );\n self.trigger( 'show-deleted', show );\n\n contents.fetchCurrentPage({ renderAll: true });\n return show;\n },\n\n /** Toggle and store whether to render explicity hidden contents\n * @returns {Boolean} new setting\n */\n toggleShowHidden : function( show, store, options ){\n // console.log( 'toggleShowHidden', show, store );\n show = ( show !== undefined )?( show ):( !this.model.contents.includeHidden );\n var self = this;\n var contents = self.model.contents;\n contents.setIncludeHidden( show, options );\n self.trigger( 'show-hidden', show );\n\n contents.fetchCurrentPage({ renderAll: true });\n return show;\n },\n\n /** On the first search, if there are no details - load them, then search */\n _firstSearch : function( searchFor ){\n var self = this;\n var inputSelector = '> .controls .search-input';\n this.log( 'onFirstSearch', searchFor );\n\n // if the contents already have enough details to search, search and return now\n if( self.model.contents.haveSearchDetails() ){\n self.searchItems( searchFor );\n return;\n }\n\n // otherwise, load the details progressively here\n self.$( inputSelector ).searchInput( 'toggle-loading' );\n // set this now so that only results will show during progress\n self.searchFor = searchFor;\n var xhr = self.model.contents.progressivelyFetchDetails({ silent: true })\n .progress( function( response, limit, offset ){\n self.renderItems();\n self.trigger( 'search:loading-progress', limit, offset );\n })\n .always( function(){\n self.$el.find( inputSelector ).searchInput( 'toggle-loading' );\n })\n .done( function(){\n self.searchItems( searchFor, 'force' );\n });\n },\n\n /** clear the search filters and show all views that are normally shown */\n clearSearch : function( searchFor ){\n var self = this;\n if( !self.searchFor ) return self;\n //self.log( 'onSearchClear', self );\n self.searchFor = '';\n self.trigger( 'search:clear', self );\n self.$( '> .controls .search-query' ).val( '' );\n // NOTE: silent + render prevents collection update event with merge only\n // - which causes an empty page due to event handler above\n self.model.contents.fetchCurrentPage({ silent: true })\n .done( function(){\n self.renderItems();\n });\n return self;\n },\n\n // ........................................................................ error handling\n /** Event handler for errors (from the panel, the history, or the history's contents)\n * Alternately use two strings for model and xhr to use custom message and title (respectively)\n * @param {Model or View} model the (Backbone) source of the error\n * @param {XMLHTTPRequest} xhr any ajax obj. assoc. with the error\n * @param {Object} options the options map commonly used with bbone ajax\n */\n errorHandler : function( model, xhr, options ){\n //TODO: to mixin or base model\n // interrupted ajax or no connection\n if( xhr && xhr.status === 0 && xhr.readyState === 0 ){\n // return ERROR_MODAL.offlineErrorModal();\n // fail silently\n return;\n }\n // otherwise, leave something to report in the console\n this.error( model, xhr, options );\n // and feedback to a modal\n // if sent two strings (and possibly details as 'options'), use those as message and title\n if( _.isString( model ) && _.isString( xhr ) ){\n var message = model;\n var title = xhr;\n return ERROR_MODAL.errorModal( message, title, options );\n }\n // bad gateway\n // TODO: possibly to global handler\n if( xhr && xhr.status === 502 ){\n return ERROR_MODAL.badGatewayErrorModal();\n }\n return ERROR_MODAL.ajaxErrorModal( model, xhr, options );\n },\n\n /** Remove all messages from the panel. */\n clearMessages : function( ev ){\n var $target = !_.isUndefined( ev )?\n $( ev.currentTarget )\n :this.$messages().children( '[class$=\"message\"]' );\n $target.fadeOut( this.fxSpeed, function(){\n $( this ).remove();\n });\n return this;\n },\n\n // ........................................................................ scrolling\n /** Scrolls the panel to show the content sub-view with the given hid.\n * @param {Integer} hid the hid of item to scroll into view\n * @returns {HistoryView} the panel\n */\n scrollToHid : function( hid ){\n return this.scrollToItem( _.first( this.viewsWhereModel({ hid: hid }) ) );\n },\n\n // ........................................................................ misc\n /** utility for adding -st, -nd, -rd, -th to numbers */\n ordinalIndicator : function( number ){\n var numStr = number + '';\n switch( numStr.charAt( numStr.length - 1 )){\n case '1': return numStr + 'st';\n case '2': return numStr + 'nd';\n case '3': return numStr + 'rd';\n default : return numStr + 'th';\n }\n },\n\n /** Return a string rep of the history */\n toString : function(){\n return 'HistoryView(' + (( this.model )?( this.model.get( 'name' )):( '' )) + ')';\n }\n});\n\n\n//------------------------------------------------------------------------------ TEMPLATES\nHistoryView.prototype.templates = (function(){\n\n var mainTemplate = BASE_MVC.wrapTemplate([\n // temp container\n '
',\n '',\n '
',\n '',\n '
'\n ]);\n\n var controlsTemplate = BASE_MVC.wrapTemplate([\n '
Trackster uses this information to populate the select box for chrom/contig, and' +\n 'to set the maximum basepair of the track browser. You may either upload a .len file' +\n 'of this format (Len File option), or directly enter the information into the box ' +\n '(Len Entry option).
' +\n 'You are using ' + options.nice_total_disk_usage + ' of disk space in this Galaxy instance. ' +\n ( Galaxy.config.enable_quotas ? 'Your disk quota is: ' + options.quota + '. ' : '' ) +\n 'Is your usage more than expected? See the documentation for tips on how to find all of the data in your account.' +\n '
';\n }\n });\n\n /** View of individual user forms */\n var Forms = Backbone.View.extend({\n\n initialize: function( options ) {\n this.model = new Model( options );\n this.page = this.model.get( options.form_id );\n this.setElement( '' );\n this.render();\n },\n\n render: function() {\n var self = this;\n $.ajax({\n url : Galaxy.root + this.page.url,\n type : 'GET'\n }).done( function( response ) {\n var options = $.extend( {}, self.page, response );\n var form = new Form({\n title : options.title,\n icon : options.icon,\n inputs : options.inputs,\n operations: {\n 'submit': new Ui.ButtonIcon({\n tooltip : options.submit_tooltip,\n title : options.submit_title || 'Save settings',\n icon : options.submit_icon || 'fa-save',\n onclick : function() { self._submit( form, options ) }\n })\n }\n });\n self.$el.empty().append( form.$el );\n }).fail( function( response ) {\n self.$el.empty().append( new Ui.Message({\n message : 'Failed to load resource ' + self.page.url + '.',\n status : 'danger',\n persistent : true\n }).$el );\n });\n },\n\n _submit: function( form, options ) {\n var self = this;\n $.ajax( {\n url : Galaxy.root + options.url,\n data : JSON.stringify( form.data.create() ),\n type : 'PUT',\n contentType : 'application/json'\n }).done( function( response ) {\n form.data.matchModel( response, function ( input, input_id ) {\n form.field_list[ input_id ].value( input.value );\n });\n form.message.update( { message: response.message, status: 'success' } );\n }).fail( function( response ) {\n form.message.update( { message: response.responseJSON.err_msg, status: 'danger' } );\n });\n }\n });\n\n return {\n View : View,\n Forms : Forms\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/user/user-preferences.js","/** Configure Workflow Menu View */\ndefine( [], function() {\n var View = Backbone.View.extend({\n\n initialize: function( options ) {\n this.setElement( '' );\n this.render();\n },\n\n render: function() {\n var self = this;\n $.getJSON( Galaxy.root + 'api/workflows/menu/', function( response ) {\n var workflows = response.workflows,\n ids_in_menu = response.ids_in_menu,\n $el_config_worflow = null;\n\n // Add configure workflow header\n self.$el.empty().append( self._templateConfigWorkflowHeader() );\n $el_config_worflow = self.$el.find( '.configure-workflows' );\n $el_config_worflow.append( self._templateActionButtons() );\n if( workflows.length > 0 ) {\n $el_config_worflow.append( self._templateConfigureWorkflow( self, workflows, ids_in_menu ) );\n self.save_workflow_menu( self );\n self.make_checked( self, ids_in_menu );\n self.register_check_uncheck_all( self );\n }\n else {\n $el_config_worflow.append( self._templateNoWorkflow() );\n }\n });\n },\n\n /** Register check and uncheck all callbacks*/\n register_check_uncheck_all: function( self ) {\n var $el_check_all = self.$el.find( '.check-all-wf' ),\n $el_uncheck_all = self.$el.find( '.uncheck-all-wf' );\n \n $el_check_all.click(function( e ) {\n self.check_uncheck_all( self, true );\n });\n $el_uncheck_all.click(function( e ) {\n self.check_uncheck_all( self, false );\n });\n },\n\n /** Check or uncheck all workflows */\n check_uncheck_all: function( self, checked ) {\n $.each(self.$el.find( '.wf-config-item' ), function() {\n var wf_checkbox = $( this )[0];\n wf_checkbox.checked = checked;\n });\n },\n\n /** Make the worflows as checked if present in the menu */\n make_checked: function( self, ids_in_menu ) {\n $.each(self.$el.find( '.wf-config-item' ), function() {\n var wf_checkbox = $( this )[0];\n _.each( ids_in_menu, function( id ) {\n if ( parseInt( wf_checkbox.value ) === id ) {\n wf_checkbox.checked = true;\n }\n });\n });\n },\n\n /** Save the changes for workflow menu */\n save_workflow_menu: function( self ) {\n var $el_save_workflow_menu = self.$el.find( '.wf-save-menu' );\n $el_save_workflow_menu.click( function( e ) {\n var ids = [];\n $.each(self.$el.find( '.wf-config-item' ), function() {\n var wf_checkbox = $( this )[0];\n if( wf_checkbox.checked || wf_checkbox.checked === 'true' ) {\n ids.push( parseInt( wf_checkbox.value ) );\n }\n });\n $.ajax({\n type: 'PUT',\n url: Galaxy.root + 'api/workflows/menu/',\n data: JSON.stringify( { 'workflow_ids': ids } ),\n contentType : 'application/json'\n }).done( function( response ) {\n window.location = Galaxy.root + 'workflow?status='+ response.status +'&message=' + response.message;\n });\n });\n },\n\n /** Template for actions buttons */\n _templateActionButtons: function() {\n return '