Download edam ontology if not present

and beta edam tool panel enabled.

doc/source/admin/galaxy_options.rst

@@ -3198,8 +3198,18 @@
 :Description:
     Sets the path to EDAM ontology file.
     The value of this option will be resolved with respect to
-    <config_dir>.
-:Default: ``EDAM_1.23.tsv``
+    <data_dir>.
+:Default: ``EDAM.tsv``
+:Type: str
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+``beta_edam_ontology_url``
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Sets the url to the EDAM ontology file.
+:Default: ``http://edamontology.org/EDAM.tsv``
 :Type: str
 
 

lib/galaxy/config/sample/galaxy.yml.sample

@@ -1595,8 +1595,11 @@ galaxy:
 
   # Sets the path to EDAM ontology file.
   # The value of this option will be resolved with respect to
-  # <config_dir>.
-  #beta_edam_toolbox_ontology_path: EDAM_1.23.tsv
+  # <data_dir>.
+  #beta_edam_toolbox_ontology_path: EDAM.tsv
+
+  # Sets the url to the EDAM ontology file.
+  #beta_edam_ontology_url: http://edamontology.org/EDAM.tsv
 
   # Default format for the export of workflows. Possible values are 'ga'
   # or 'format2'.

lib/galaxy/tools/toolbox/base.py

@@ -23,6 +23,7 @@
 )
 from galaxy.tool_util.loader_directory import looks_like_a_tool
 from galaxy.util import (
+    download_to_file,
     etree,
     ExecutionTimer,
     listify,
@@ -32,6 +33,7 @@
 )
 from galaxy.util.bunch import Bunch
 from galaxy.util.dictifiable import Dictifiable
+from galaxy.util.renamed_temporary_file import RenamedTemporaryFile
 from .filters import FilterFactory
 from .integrated_panel import ManagesIntegratedToolPanelMixin
 from .lineages import LineageMap
@@ -110,16 +112,7 @@ def __init__(self, config_filenames, tool_root_dir, app, save_integrated_tool_pa
         self._filter_factory = FilterFactory(self)
         self._tool_tag_manager = tool_tag_manager(app)
         self._init_tools_from_configs(config_filenames)
-
-        if self.app.config.enable_beta_edam_toolbox:
-            with open(self.app.config.beta_edam_toolbox_ontology_path, 'r') as handle:
-                self.edam = {}
-                for idx, line in enumerate(handle.readlines()):
-                    fields = line.split('\t')
-                    if not fields[0].startswith('http://edamontology.org/'):
-                        continue
-                    term_id = fields[0][len('http://edamontology.org/'):]
-                    self.edam[term_id] = fields[1]  # preferred label
+        self.edam = self._load_edam_terms()
 
         if self.app.name == 'galaxy' and self._integrated_tool_panel_config_has_contents:
             # Load self._tool_panel based on the order in self._integrated_tool_panel.
@@ -139,6 +132,28 @@ def create_dynamic_tool(self, dynamic_tool):
     def can_load_config_file(self, config_filename):
         return True
 
+    def _load_edam_terms(self):
+        edam = {}
+        if self.app.config.enable_beta_edam_toolbox:
+            path_exists = os.path.exists(self.app.config.beta_edam_toolbox_ontology_path)
+            if not path_exists:
+                try:
+                    with RenamedTemporaryFile(self.app.config.beta_edam_toolbox_ontology_path) as out:
+                        download_to_file(self.app.config.beta_edam_ontology_url, out.name)
+                        path_exists = True
+                except Exception:
+                    log.exception()
+
+            if path_exists:
+                with open(self.app.config.beta_edam_toolbox_ontology_path, 'r') as handle:
+                    for line in handle.readlines():
+                        fields = line.split('\t')
+                        if not fields[0].startswith('http://edamontology.org/'):
+                            continue
+                        term_id = fields[0][len('http://edamontology.org/'):]
+                        edam[term_id] = fields[1]  # preferred label
+        return edam
+
     def _init_tools_from_configs(self, config_filenames):
         """ Read through all tool config files and initialize tools in each
         with init_tools_from_config below.

lib/galaxy/webapps/galaxy/config_schema.yml

@@ -2333,12 +2333,19 @@ mapping:
 
       beta_edam_toolbox_ontology_path:
         type: str
-        default: EDAM_1.23.tsv
-        path_resolves_to: config_dir
+        default: EDAM.tsv
+        path_resolves_to: data_dir
         required: false
         desc: |
           Sets the path to EDAM ontology file.
 
+      beta_edam_ontology_url:
+        type: str
+        default: http://edamontology.org/EDAM.tsv
+        required: false
+        desc: |
+          Sets the url to the EDAM ontology file.
+
       default_workflow_export_format:
         type: str
         default: ga

test/unit/config/test_config_values.py

@@ -111,6 +111,7 @@ def _load_paths(self):
             'datatypes_config_file': self._in_sample_dir('datatypes_conf.xml.sample'),
             'dependency_resolvers_config_file': self._in_config_dir('dependency_resolvers_conf.xml'),
             'dynamic_proxy_session_map': self._in_data_dir('session_map.sqlite'),
+            'beta_edam_toolbox_ontology_path' : self._in_data_dir('EDAM.tsv'),
             'error_report_file': self._in_config_dir('error_report.yml'),
             'file_path': self._in_data_dir('objects'),
             'file_sources_config_file': self._in_config_dir('file_sources_conf.yml'),