Extend tool functional test framework to allow testing output dataset metadata.

Adding file test/functional/tools/metadata.xml demonstrating how to check output metadata - this file also demonstrates setting metadata on uploaded datasets and verifies both of these functionalities. Checking output metadata is only available for new API driven tool testing.

lib/galaxy/tools/test.py

@@ -265,10 +265,14 @@ class ToolTestBuilder( object ):
                     attributes['ftype'] = attrib['ftype']
                 for extra in output_elem.findall( 'extra_files' ):
                     extra_files.append( self.__parse_extra_files_elem( extra ) )
-                if not (assert_list or file or extra_files):
+                metadata = {}
+                for metadata_elem in output_elem.findall( 'metadata' ):
+                    metadata[ metadata_elem.get('name') ] = metadata_elem.get( 'value' )
+                if not (assert_list or file or extra_files or metadata):
                     raise Exception( "Test output defines not checks (e.g. must have a 'file' check against, assertions to check, etc...)")
                 attributes['assert_list'] = assert_list
                 attributes['extra_files'] = extra_files
+                attributes['metadata'] = metadata
                 self.__add_output( name, file, attributes )
         except Exception, e:
             self.error = True

test/functional/test_toolbox.py

@@ -88,6 +88,21 @@ class GalaxyInteractorApi( object ):
         fetcher = self.__dataset_fetcher( history_id )
         ## TODO: Twill version verifys dataset is 'ok' in here.
         self.twill_test_case.verify_hid( outfile, hda_id=hid, attributes=attributes, dataset_fetcher=fetcher, shed_tool_id=shed_tool_id )
+        metadata = attributes.get( 'metadata', {} )
+        if metadata:
+            dataset = self.__get( "histories/%s/contents/%s" % ( history_id, hid ) ).json()
+            for key, value in metadata.iteritems():
+                dataset_key = "metadata_%s" % key
+                try:
+                    dataset_value = dataset.get( dataset_key, None )
+                    if dataset_value != value:
+                        msg = "Dataset metadata verification for [%s] failed, expected [%s] but found [%s]."
+                        msg_params = ( key, value, dataset_value )
+                        msg = msg % msg_params
+                        raise Exception( msg )
+                except KeyError:
+                    msg = "Failed to verify dataset metadata, metadata key [%s] was not found." % key
+                    raise Exception( msg )
 
     def get_job_stream( self, history_id, output_data, stream ):
         hid = output_data.get( 'id' )

test/functional/tools/metadata.xml

@@ -0,0 +1,29 @@
+<tool id="metadata" name="metadata" version="1.0.0">
+  <command>mkdir $output_copy_of_input.extra_files_path; cp $input.extra_files_path/* $output_copy_of_input.extra_files_path; echo "$input.metadata.base_name" > $output_of_input_metadata</command>
+  <inputs>
+    <param name="input" type="data" format="velvet" label="Velvet Dataset" help="Prepared by velveth."/>
+  </inputs>
+  <outputs>
+    <data format="txt" name="output_of_input_metadata" />
+    <data format="velvet" name="output_copy_of_input" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="velveth_test1/output.html" ftype="velvet" >
+        <composite_data value='velveth_test1/Sequences' ftype="Sequences"/>
+        <composite_data value='velveth_test1/Roadmaps' ftype="Roadmaps"/>
+        <composite_data value='velveth_test1/Log'/>
+        <metadata name="base_name" value="Example Metadata" />
+      </param>
+      <!-- This ouptut tests setting input metadata above -->
+      <output name="output_of_input_metadata">
+        <assert_contents>
+          <has_line line="Example Metadata" />
+        </assert_contents>
+      </output>
+      <!-- This output tests an assertion about output metadata -->
+      <output name="output_copy_of_input" file="velveth_test1/output.html">
+        <metadata name="base_name" value="velvet" />
+      </output>
+    </test>
+  </tests></tool>

test/functional/tools/samples_tool_conf.xml

@@ -9,4 +9,5 @@
   <tool file="multi_select.xml" />
   <tool file="multi_output.xml" />
   <tool file="composite_output.xml" />
+  <tool file="metadata.xml" />
 </toolbox>