Parse EDAM ontology to decode names

doc/source/admin/galaxy_options.rst

@@ -3191,6 +3191,18 @@
 :Type: bool
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``beta_edam_toolbox_ontology_path``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+: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``
+:Type: str
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``default_workflow_export_format``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

@@ -1593,6 +1593,11 @@ galaxy:
   # sections in lieu of EDAM topics only.
   #enable_beta_edam_toolbox: false
 
+  # 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
+
   # Default format for the export of workflows. Possible values are 'ga'
   # or 'format2'.
   #default_workflow_export_format: ga

lib/galaxy/tools/toolbox/base.py

@@ -110,6 +110,17 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         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
+
         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.
             if self.app.config.enable_beta_edam_toolbox:
@@ -404,7 +415,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
         edam = tool.edam_operations + tool.edam_topics
         if len(edam) > 0:
             # TODO nicer edam names.
-            sec_id, sec_nm = edam[0], edam[0]
+            sec_id, sec_nm = edam[0], self.edam.get(edam[0], 'New term')
         else:
             sec_id, sec_nm = 'uncategorized', 'Uncategorized'
         return sec_id, sec_nm

lib/galaxy/webapps/galaxy/config_schema.yml

@@ -486,7 +486,7 @@ mapping:
 
       file_sources_config_file:
         type: str
-        default: file_sources_conf.yml        
+        default: file_sources_conf.yml
         path_resolves_to: config_dir
         required: false
         desc: |
@@ -2331,6 +2331,14 @@ mapping:
           Enable beta EDAM organised toolbox which ignores admin managed
           sections in lieu of EDAM topics only.
 
+      beta_edam_toolbox_ontology_path:
+        type: str
+        default: EDAM_1.23.tsv
+        path_resolves_to: config_dir
+        required: false
+        desc: |
+          Sets the path to EDAM ontology file.
+
       default_workflow_export_format:
         type: str
         default: ga