Unverified Commit d36888ad authored by mvdbeek's avatar mvdbeek
Browse files

Fix contains_collection check for empty root collections 

Comparing hdca_id with parent_id is just wrong, as hdca_id is the id for
a `HistoryDatasetCollectionAssociation`, while `parent_id` is the id for
a `DatasetCollection`. This happened to work regardless of the first if
check if the root collection contains at least one DCE, but that won't
work for collections without elements.
parent cba4677b

lib/galaxy/model/__init__.py

+3 −0
Original line number Diff line number Diff line
@@ -5811,6 +5811,9 @@ class HistoryDatasetCollectionAssociation( 
        """Checks to see that the indicated collection is a member of the

        hdca by using a recursive CTE sql query to find the collection's parents

        and checking to see if any of the parents are associated with this hdca"""

        if collection_id == self.collection_id:

            # collection_id is root collection

            return True



        sa_session = object_session(self)

        DCE = DatasetCollectionElement

lib/galaxy/webapps/galaxy/services/dataset_collections.py

+1 −1
Original line number Diff line number Diff line
@@ -240,7 +240,7 @@ class DatasetCollectionsService(ServiceBase, UsesLibraryMixinItems): 


        # check to make sure the dsc is part of the validated hdca

        decoded_parent_id = self.decode_id(parent_id)

        if parent_id != hdca_id and not hdca.contains_collection(decoded_parent_id):

        if not hdca.contains_collection(decoded_parent_id):

            raise exceptions.ObjectNotFound('Requested dataset collection is not contained within indicated history content')



        # retrieve contents

lib/galaxy_test/api/test_dataset_collections.py

+8 −0
Original line number Diff line number Diff line
@@ -358,6 +358,14 @@ class DatasetCollectionApiTestCase(ApiTestCase): 
        assert len(offset_contents) == 1

        assert offset_contents[0]['element_index'] == 1



    def test_collection_contents_empty_root(self):

        hdca = self.dataset_collection_populator.create_list_in_history(self.history_id, contents=[]).json()

        assert hdca["elements"] == []

        root_contents_url = hdca["contents_url"]

        response = self._get(root_contents_url)

        response.raise_for_status()

        assert response.json() == []



    def test_get_suitable_converters_single_datatype(self):

        response = self.dataset_collection_populator.upload_collection(self.history_id, "list:paired", elements=[

            {