Merge pull request #2570 from abretaud/identifier_bug

Fix element_identifier unavailable with data_collection input param

lib/galaxy/tools/parameters/basic.py

@@ -2152,6 +2152,7 @@ class DataCollectionToolParameter( BaseDataToolParameter ):
         return field
 
     def from_json( self, value, trans, other_values={} ):
+        rval = None
         if trans.workflow_building_mode is workflow_building_modes.ENABLED:
             return None
         if not value and not self.optional:

lib/galaxy/tools/wrappers.py

@@ -365,7 +365,7 @@ class DatasetCollectionWrapper( ToolParameterValueWrapper, HasDatasets ):
             if dataset_collection_element.is_collection:
                 element_wrapper = DatasetCollectionWrapper(job_working_directory, dataset_collection_element, dataset_paths, **kwargs )
             else:
-                element_wrapper = self._dataset_wrapper( element_object, dataset_paths, **kwargs)
+                element_wrapper = self._dataset_wrapper( element_object, dataset_paths, identifier=element_identifier, **kwargs)
 
             element_instances[element_identifier] = element_wrapper
             element_instance_list.append( element_wrapper )

test/api/test_tools.py

@@ -1,5 +1,6 @@
 # Test tools API.
 from base import api
+import json
 from operator import itemgetter
 from .helpers import DatasetPopulator
 from .helpers import DatasetCollectionPopulator
@@ -805,6 +806,38 @@ class ToolsTestCase( api.ApiTestCase ):
         output1_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output1 )
         self.assertEquals( output1_content.strip(), "Pasted Entry\nPasted Entry" )
 
+    @skip_without_tool( "identifier_collection" )
+    def test_identifier_with_data_collection( self ):
+        history_id = self.dataset_populator.new_history()
+
+        element_identifiers = self.dataset_collection_populator.list_identifiers( history_id )
+
+        payload = dict(
+            instance_type="history",
+            history_id=history_id,
+            element_identifiers=json.dumps(element_identifiers),
+            collection_type="list",
+        )
+
+        create_response = self._post( "dataset_collections", payload )
+        dataset_collection = create_response.json()
+
+        inputs = {
+            "input1": {'src': 'hdca', 'id': dataset_collection['id']},
+        }
+
+        self.dataset_populator.wait_for_history( history_id, assert_ok=True )
+        create_response = self._run( "identifier_collection", history_id, inputs )
+        self._assert_status_code_is( create_response, 200 )
+        create = create_response.json()
+        outputs = create[ 'outputs' ]
+        jobs = create[ 'jobs' ]
+        self.assertEquals( len( jobs ), 1 )
+        self.assertEquals( len( outputs ), 1 )
+        output1 = outputs[ 0 ]
+        output1_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output1 )
+        self.assertEquals( output1_content.strip(), '\n'.join([d['name'] for d in element_identifiers]) )
+
     @skip_without_tool( "cat1" )
     def test_map_over_nested_collections( self ):
         history_id = self.dataset_populator.new_history()

test/functional/tools/identifier_collection.xml

@@ -0,0 +1,15 @@
+<tool id="identifier_collection" name="identifier_collection">
+  <command>
+    #for $input in $input1:
+      echo '$input.element_identifier' >> 'output1';
+    #end for
+  </command>
+  <inputs>
+    <param type="data_collection" collection_type="list" name="input1" label="Input 1" />
+  </inputs>
+  <outputs>
+    <data name="output1" type="tabular" from_work_dir="output1" />
+  </outputs>
+  <tests>
+  </tests>
+</tool>

test/functional/tools/samples_tool_conf.xml

@@ -64,6 +64,7 @@
   <tool file="validation_empty_dataset.xml" />
   <tool file="identifier_single.xml" />
   <tool file="identifier_multiple.xml" />
+  <tool file="identifier_collection.xml" />
   <tool file="tool_directory.xml" />
   <tool file="output_action_change_format.xml" />
   <tool file="collection_paired_test.xml" />