Add EDAM topics to tools and expose in API

lib/galaxy/tools/__init__.py

@@ -444,6 +444,7 @@ class Tool( object, Dictifiable ):
                 raise Exception( "Missing tool 'version' for tool with id '%s' at '%s'" % (self.id, tool_source) )
 
         self.edam_operations = tool_source.parse_edam_operations()
+        self.edam_topics = tool_source.parse_edam_topics()
 
         # Support multi-byte tools
         self.is_multi_byte = tool_source.parse_is_multi_byte()
@@ -1542,6 +1543,7 @@ class Tool( object, Dictifiable ):
         tool_dict = super( Tool, self ).to_dict()
 
         tool_dict["edam_operations"] = self.edam_operations
+        tool_dict["edam_topics"] = self.edam_topics
 
         # Fill in ToolShedRepository info
         if hasattr(self, 'tool_shed') and self.tool_shed:

lib/galaxy/tools/parser/xml.py

@@ -84,6 +84,12 @@ class XmlToolSource(ToolSource):
             return []
         return [ edam_op.text for edam_op in edam_ops.findall("edam_operation") ]
 
+    def parse_edam_topics(self):
+        edam_topics = self.root.find("edam_topics")
+        if edam_topics is None:
+            return []
+        return [ edam_topic.text for edam_topic in edam_topics.findall("edam_topic") ]
+
     def parse_description(self):
         return xml_text(self.root, "description")
 

lib/galaxy/tools/parser/yaml.py

@@ -36,6 +36,9 @@ class YamlToolSource(ToolSource):
     def parse_edam_operations(self):
         return self.root_dict.get("edam_operations", [])
 
+    def parse_edam_topics(self):
+        return self.root_dict.get("edam_topics", [])
+
     def parse_is_multi_byte(self):
         return self.root_dict.get("is_multi_byte", self.default_is_multi_byte)
 

test/functional/tools/simple_constructs.yml

@@ -6,6 +6,9 @@ description: Simple constructs
 edam_operations:
   - operation_0004
   - operation_0336
+edam_topics:
+  - topic_0003
+  - topic_3372
 command:
   >
     echo "$booltest"  >> $out_file1;

tools/stats/gsummary.xml

@@ -1,5 +1,8 @@
 <tool id="Summary_Statistics1" name="Summary Statistics" version="1.1.0">
   <description>for any numerical column</description>
+  <edam_topics>
+    <edam_topic>topic_2269</edam_topic>
+  </edam_topics>
   <command interpreter="python">gsummary.py $input $out_file1 "$cond"</command>
   <inputs>
     <param format="tabular" name="input" type="data" label="Summary statistics on" help="Dataset missing? See TIP below"/>