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JBrowse: enable callbacks in style options #2442

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JBrowse: enable callbacks in style options #2442

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6be2661
add failing test
loraine-gueguen Jun 4, 2019
cf86da0
adjust test output file
loraine-gueguen Jun 4, 2019
cafe125
replace mapped_chars for style.label and style.description
loraine-gueguen Jun 4, 2019
6b62d15
adjust test lines_diff value
loraine-gueguen Jun 5, 2019
0c8d9d8
bump version
loraine-gueguen Jun 5, 2019
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37 changes: 20 additions & 17 deletions tools/jbrowse/jbrowse.py
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Original file line number Diff line number Diff line change
Expand Up @@ -690,12 +690,16 @@ def traverse_to_option_parent(self, splitKey, outputTrackConfig):
assert isinstance(trackConfigSubDict, dict), 'Config element {} is not a dict'.format(trackConfigSubDict)
return trackConfigSubDict

def revert_mapped_chars_in_string(self, stringValue, mapped_chars):
for char, mapped_char in mapped_chars.items():
stringValue = stringValue.replace(mapped_char, char)
return stringValue

def get_formatted_option(self, valType2ValDict, mapped_chars):
assert isinstance(valType2ValDict, dict) and len(valType2ValDict.items()) == 1
for valType, value in valType2ValDict.items():
if valType == "text":
for char, mapped_char in mapped_chars.items():
value = value.replace(mapped_char, char)
self.revert_mapped_chars_in_string(value, mapped_chars)
elif valType == "integer":
value = int(value)
elif valType == "float":
Expand All @@ -713,17 +717,6 @@ def set_custom_track_options(self, customTrackConfig, outputTrackConfig, mapped_

def process_annotations(self, track):
category = track['category'].replace('__pd__date__pd__', TODAY)
outputTrackConfig = {
'style': {
'label': track['style'].get('label', 'description'),
'className': track['style'].get('className', 'feature'),
'description': track['style'].get('description', ''),
},
'overridePlugins': track['style'].get('overridePlugins', False) == 'True',
'overrideDraggable': track['style'].get('overrideDraggable', False) == 'True',
'maxHeight': track['style'].get('maxHeight', '600'),
'category': category,
}

mapped_chars = {
'>': '__gt__',
Expand All @@ -739,10 +732,21 @@ def process_annotations(self, track):
"": '__cn__'
}

outputTrackConfig = {
'style': {
'label': self.revert_mapped_chars_in_string(track['style'].get('label', 'description'), mapped_chars),
'className': track['style'].get('className', 'feature'),
'description': self.revert_mapped_chars_in_string(track['style'].get('description', ''), mapped_chars),
},
'overridePlugins': track['style'].get('overridePlugins', False) == 'True',
'overrideDraggable': track['style'].get('overrideDraggable', False) == 'True',
'maxHeight': track['style'].get('maxHeight', '600'),
'category': category,
}

for i, (dataset_path, dataset_ext, track_human_label, extra_metadata) in enumerate(track['trackfiles']):
# Unsanitize labels (element_identifiers are always sanitized by Galaxy)
for key, value in mapped_chars.items():
track_human_label = track_human_label.replace(value, key)
self.revert_mapped_chars_in_string(track_human_label, mapped_chars)

log.info('Processing %s / %s', category, track_human_label)
outputTrackConfig['key'] = track_human_label
Expand Down Expand Up @@ -814,8 +818,7 @@ def process_annotations(self, track):
self.add_rest(track['conf']['options']['rest']['url'], outputTrackConfig)
elif dataset_ext == 'sparql':
sparql_query = track['conf']['options']['sparql']['query']
for key, value in mapped_chars.items():
sparql_query = sparql_query.replace(value, key)
self.revert_mapped_chars_in_string(sparql_query, mapped_chars)
self.add_sparql(track['conf']['options']['sparql']['url'], sparql_query, outputTrackConfig)
else:
log.warn('Do not know how to handle %s', dataset_ext)
Expand Down
26 changes: 26 additions & 0 deletions tools/jbrowse/jbrowse.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -964,6 +964,32 @@ $trackxml &&
<param name="uglyTestingHack" value="enabled" />
<output name="output" file="track_config/test.xml" lines_diff="30"/>
</test>
<!-- test callbacks in style options -->
<test>
<param name="reference_genome|genome_type_select" value="history"/>
<param name="reference_genome|genome" value="merlin.fa"/>
<param name="gencode" value="11" />
<param name="standalone" value="Data Directory" />

<repeat name="track_groups">
<param name="category" value="With callbacks in style options" />
<repeat name="data_tracks">
<conditional name="data_format">
<param name="data_format_select" value="gene_calls"/>
<param name="annotation" value="gff3/1.gff"/>
<conditional name="match_part">
<param name="match_part_select" value="false"/>
</conditional>
<section name="jbstyle">
<param name="style_label" value="function(featureObject,value) { return featureObject.parent().get('id')}"/>
<param name="style_description" value="function(featureObject,value) { return featureObject.parent().get('note')}"/>
</section>
</conditional>
</repeat>
</repeat>
<param name="uglyTestingHack" value="enabled" />
<output name="output" file="style_config/test.xml" lines_diff="16"/>
</test>
<test>
<param name="reference_genome|genome_type_select" value="history"/>
<param name="reference_genome|genome" value="merlin.fa"/>
Expand Down
2 changes: 1 addition & 1 deletion tools/jbrowse/macros.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
</requirements>
</xml>
<token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
<token name="@WRAPPER_VERSION@">galaxy3</token>
<token name="@WRAPPER_VERSION@">galaxy4</token>
<token name="@ATTRIBUTION@"><![CDATA[
**Attribution**

Expand Down
106 changes: 106 additions & 0 deletions tools/jbrowse/test-data/style_config/test.xml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,106 @@
<?xml version="1.0"?>
<root>
<metadata>
<gencode>11</gencode>
<genomes>
<genome path="/tmp/tmpWtvfKr/files/000/dataset_17.dat">
<metadata>
<dataset id="27ee89e2e3d631e0" hid="1"
size="171.6 KB"
edam_format="format_1929"
file_ext="fasta" />
<history id="7b55dbb89df8f4e5"
user_email="[email protected]"
user_id="2"
display_name="test_history"/>
<metadata
dbkey="?"
data_lines="2881"
sequences="1"
/>
<tool
tool_id="upload1"
tool_version="1.1.6"
/>
</metadata>
</genome>
</genomes>
<general>
<defaultLocation></defaultLocation>
<trackPadding>20</trackPadding>

<shareLink>true</shareLink>
<aboutDescription></aboutDescription>
<show_tracklist>true</show_tracklist>
<show_nav>true</show_nav>
<show_overview>true</show_overview>
<show_menu>true</show_menu>
<hideGenomeOptions>false</hideGenomeOptions>
</general>
<galaxyUrl>http://localhost</galaxyUrl>
</metadata>
<tracks>
<track cat="With callbacks in style options" format="gene_calls" visibility="default_off">
<files>
<trackFile path="/tmp/tmpWtvfKr/files/000/dataset_18.dat" ext="gff3" label="1.gff">
<metadata>
<dataset id="61f03d5eef6f1538" hid="2"
size="2.3 KB"
edam_format="format_1975"
file_ext="gff3" />
<history id="7b55dbb89df8f4e5"
user_email="[email protected]"
user_id="2"
display_name="test_history"/>
<metadata
dbkey="?"
data_lines="27"
comment_lines="19"
columns="9"
delimiter="__tc__"
attributes="6"
/>
<tool
tool_id="upload1"
tool_version="1.1.6"
/>
</metadata>
</trackFile>
</files>

<options>
<style>
<overridePlugins>False</overridePlugins>
<overrideDraggable>False</overrideDraggable>
<className>feature</className>
<description>function(featureObject,value) { return featureObject.parent().get('note')}</description>
<label>function(featureObject,value) { return featureObject.parent().get('id')}</label>
<height>10px</height>
<maxHeight>600</maxHeight>
</style>
<scaling>
<method>ignore</method>
<scheme>
<color>__auto__</color>
</scheme>
</scaling>
<menus>
</menus>
<custom_config>
</custom_config>

<gff>
<trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType>
<index>false</index>
</gff>
</options>
</track>
</tracks>
<plugins
ComboTrackSelector=""
Bookmarks=""
GCContent=""
BlastView="True"
theme=""
/>
</root>