rebase into expressions... Fix for mapping expression collections ove…

…r non-data parameters.
common-workflow-lab · Jul 30, 2017 · 85a61ff · 85a61ff
1 parent a903abd
commit 85a61ff
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Showing 2 changed files with 34 additions and 20 deletions.
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
@@ -891,24 +891,27 @@ def execute( self, trans, progress, invocation, step ):
             # Connect up
             def callback( input, prefixed_name, **kwargs ):
                 replacement = NO_REPLACEMENT
-                if isinstance( input, DataToolParameter ) or isinstance( input, DataCollectionToolParameter ):
-                    if iteration_elements and prefixed_name in iteration_elements:
-                        if isinstance( input, DataToolParameter ):
-                            # Pull out dataset instance from element.
-                            replacement = iteration_elements[ prefixed_name ].dataset_instance
-                            if hasattr(iteration_elements[ prefixed_name ], u'element_identifier') and iteration_elements[ prefixed_name ].element_identifier:
-                                replacement.element_identifier = iteration_elements[ prefixed_name ].element_identifier
-                        else:
-                            # If collection - just use element model object.
-                            replacement = iteration_elements[ prefixed_name ]
+                if iteration_elements and prefixed_name in iteration_elements:
+                    if not isinstance( input, DataCollectionToolParameter ):
+                        # Pull out dataset instance from element.
+                        replacement = iteration_elements[ prefixed_name ].dataset_instance
+                        if hasattr(iteration_elements[ prefixed_name ], u'element_identifier') and iteration_elements[ prefixed_name ].element_identifier:
+                            replacement.element_identifier = iteration_elements[ prefixed_name ].element_identifier
                     else:
-                        replacement = progress.replacement_for_tool_input( step, input, prefixed_name )
+                        # If collection - just use element model object.
+                        replacement = iteration_elements[ prefixed_name ]
                 else:
-                    replacement = progress.replacement_for_tool_input( step, input, prefixed_name )
+                    # TODO: I guess never exapnd in progress - only exapnd up here!
+                    replacement = progress.replacement_for_tool_input( step, input, prefixed_name, expand_expressions=True )
 
                 if replacement is not NO_REPLACEMENT:
                     found_replacement_keys.add(prefixed_name)
 
+                is_data = isinstance( input, DataToolParameter ) or isinstance( input, DataCollectionToolParameter )
+                if not is_data and getattr( replacement, "history_content_type", None ) == "dataset":
+                    with open( replacement.file_name, "r" ) as f:
+                        replacement = loads(f.read())
+
                 return replacement
 
             try:
@@ -987,7 +990,7 @@ def callback( input, prefixed_name, **kwargs ):
                 data = progress.replacement_for_tool_input( step, input, prefixed_name )
                 if hasattr( data, "collection" ):
                     collections_to_match.add( prefixed_name, data )
-
+                return
             is_data_collection_param = isinstance( input, DataCollectionToolParameter )
             if is_data_collection_param and not input.multiple:
                 data = progress.replacement_for_tool_input( step, input, prefixed_name )
@@ -996,6 +999,12 @@ def callback( input, prefixed_name, **kwargs ):
                     subcollection_type_description = history_query.can_map_over( data )
                     if subcollection_type_description:
                         collections_to_match.add( prefixed_name, data, subcollection_type=subcollection_type_description.collection_type )
+                return
+
+            data = progress.replacement_for_tool_input( step, input, prefixed_name )
+            if data is not NO_REPLACEMENT:
+                if hasattr( data, "collection" ):
+                    collections_to_match.add( prefixed_name, data )
 
         visit_input_values( tool.inputs, step.state.inputs, callback )
         return collections_to_match

diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py
@@ -422,14 +422,19 @@ def replacement_for_connection( self, connection, is_data=True ):
                 raise modules.DelayedWorkflowEvaluation(why=delayed_why)
 
         is_hda = isinstance( replacement, model.HistoryDatasetAssociation )
-        if not is_data and is_hda:
-            if replacement.is_ok:
-                with open( replacement.file_name, 'r' ) as f:
-                    replacement = json.load( f )
-            elif replacement.is_pending:
-                raise modules.DelayedWorkflowEvaluation()
+        is_hdca = isinstance( replacement, model.HistoryDatasetCollectionAssociation )
+        if not is_data and (is_hda or is_hdca):
+            dataset_instances = []
+            if is_hda:
+                dataset_instances = [ replacement ]
             else:
-                raise modules.CancelWorkflowEvaluation()
+                dataset_instances = replacement.dataset_instances
+
+            for dataset_instance in dataset_instances:
+                if dataset_instance.is_pending:
+                    raise modules.DelayedWorkflowEvaluation()
+                elif not dataset_instance.is_ok:
+                    raise modules.CancelWorkflowEvaluation()
 
         return replacement