Unverified Commit bbe25047 authored by mvdbeek's avatar mvdbeek
Browse files

Fix skipping simple mapped over steps in conditional subworkflow steps

parent 06a43944

lib/galaxy/model/dataset_collections/structure.py

+9 −2
Original line number Diff line number Diff line
@@ -94,12 +94,19 @@ class Tree(BaseTree): 
            def get_element(collection):

                return collection[index]  # noqa: B023



            when_value = None

            if self.when_values:

                if len(self.when_values) == 1:

                    when_value = self.when_values[0]

                else:

                    when_value = self.when_values[index]



            if substructure.is_leaf:

                yield dict_map(get_element, collection_dict), self.when_values[index] if self.when_values else None

                yield dict_map(get_element, collection_dict), when_value

            else:

                sub_collections = dict_map(lambda collection: get_element(collection).child_collection, collection_dict)

                for element, _when_value in substructure._walk_collections(sub_collections):

                    yield element, self.when_values[index] if self.when_values else None

                    yield element, when_value



    @property

    def is_leaf(self):

lib/galaxy/workflow/modules.py

+9 −2
Original line number Diff line number Diff line
@@ -512,8 +512,15 @@ class WorkflowModule: 
        collections_to_match = self._find_collections_to_match(progress, step, all_inputs)

        # Have implicit collections...

        collection_info = self.trans.app.dataset_collection_manager.match_collections(collections_to_match)

        if collection_info and progress.subworkflow_collection_info:

        if collection_info:

            if progress.subworkflow_collection_info:

                # We've mapped over a subworkflow. Slices of the invocation might be conditional

                # and progress.subworkflow_collection_info.when_values holds the appropriate when_values

                collection_info.when_values = progress.subworkflow_collection_info.when_values

            else:

                # The invocation is not mapped over, but it might still be conditional.

                # Multiplication and linking should be handled by slice_collection()

                collection_info.when_values = progress.when_values

        return collection_info or progress.subworkflow_collection_info



    def _find_collections_to_match(self, progress, step, all_inputs):