Merge pull request #6 from jmchilton/edam_api

Add EDAM Info to Tool's API.

lib/galaxy/datatypes/binary.py

@@ -142,6 +142,7 @@ class GenericAsn1Binary( Binary ):
 @dataproviders.decorators.has_dataproviders
 class Bam( Binary ):
     """Class describing a BAM binary file"""
+    edam_format = "format_2572"
     file_ext = "bam"
     track_type = "ReadTrack"
     data_sources = { "data": "bai", "index": "bigwig" }

lib/galaxy/tools/__init__.py

@@ -274,6 +274,14 @@ def __getitem__( self, index ):
     def __iter__( self ):
         return iter( ( self.format, self.metadata_source, self.parent ) )
 
+    def to_dict( self, view='collection', value_mapper=None, app=None ):
+        as_dict = super( ToolOutput, self ).to_dict( view=view, value_mapper=value_mapper )
+        format = self.format
+        if format and format != "input" and app:
+            edam_format = app.datatypes_registry.edam_formats.get(self.format)
+            as_dict["edam_format"] = edam_format
+        return as_dict
+
 
 class ToolOutputCollection( ToolOutputBase ):
     """
@@ -2212,7 +2220,7 @@ def to_dict( self, trans, link_details=False, io_details=False ):
         # Add input and output details.
         if io_details:
             tool_dict[ 'inputs' ] = [ input.to_dict( trans ) for input in self.inputs.values() ]
-            tool_dict[ 'outputs' ] = [ output.to_dict() for output in self.outputs.values() ]
+            tool_dict[ 'outputs' ] = [ output.to_dict( app=trans.app ) for output in self.outputs.values() ]
 
         tool_dict[ 'panel_section_id' ], tool_dict[ 'panel_section_name' ] = self.get_panel_section()
 

lib/galaxy/tools/parameters/basic.py

@@ -2165,7 +2165,12 @@ def _options_filter_attribute( self, value ):
     def to_dict( self, trans, view='collection', value_mapper=None, other_values=None ):
         # create dictionary and fill default parameters
         d = super( DataToolParameter, self ).to_dict( trans )
-        d['extensions'] = self.extensions
+        extensions = self.extensions
+        all_edam_formats = self._datatypes_registery( trans, self.tool ).edam_formats
+        edam_formats = map(lambda ext: all_edam_formats.get(ext, None),
+                           extensions)
+        d['extensions'] = extensions
+        d['edam_formats'] = edam_formats
         d['multiple'] = self.multiple
         d['options'] = {'hda': [], 'hdca': []}
 

lib/galaxy/webapps/galaxy/api/datatypes.py

@@ -114,6 +114,10 @@ def converters( self, trans, **kwd ):
 
         return converters
 
+    @expose_api_anonymous_and_sessionless
+    def edam_formats( self, trans, **kwds ):
+        return self._datatypes_registry.edam_formats
+
     @property
     def _datatypes_registry( self ):
         return self.app.datatypes_registry

lib/galaxy/webapps/galaxy/buildapp.py

@@ -244,7 +244,7 @@ def populate_api_routes( webapp, app ):
     webapp.mapper.resource( 'datatype',
                             'datatypes',
                             path_prefix='/api',
-                            collection={ 'sniffers': 'GET', 'mapping': 'GET', 'converters': 'GET' },
+                            collection={ 'sniffers': 'GET', 'mapping': 'GET', 'converters': 'GET', 'edam_formats': 'GET' },
                             parent_resources=dict( member_name='datatype', collection_name='datatypes' ) )
     webapp.mapper.resource( 'search', 'search', path_prefix='/api' )
     webapp.mapper.resource( 'page', 'pages', path_prefix="/api")