2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/954789571b9d/ Changeset: 954789571b9d User: jmchilton Date: 2014-05-15 01:25:50 Summary: Bugfix: Small fix for running workflows with subcollection mapping steps. Affected #: 1 file diff -r 9a1415f8108f6283181c7a5b564118920359decc -r 954789571b9d7c2c2ea2d1651d50f13aefaced7e lib/galaxy/dataset_collections/structure.py --- a/lib/galaxy/dataset_collections/structure.py +++ b/lib/galaxy/dataset_collections/structure.py @@ -42,7 +42,7 @@ if substructure.is_leaf: yield dict_map( element, collection_dict ) else: - sub_collections = dict_map( lambda collection: element( collection ).child_collection ) + sub_collections = dict_map( lambda collection: element( collection ).child_collection, collection_dict ) for element in substructure._walk_collections( sub_collections ): yield element https://bitbucket.org/galaxy/galaxy-central/commits/31e5817ba7d3/ Changeset: 31e5817ba7d3 User: jmchilton Date: 2014-05-15 01:25:50 Summary: Bugfix: Yet another bug fix for workflow extraction with collection operations. Fail, fail, fail. Affected #: 2 files diff -r 954789571b9d7c2c2ea2d1651d50f13aefaced7e -r 31e5817ba7d36a039c432205b32958e190cbabbc lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2864,6 +2864,13 @@ def dataset( self ): return self.dataset_instance.dataset + def first_dataset_instance( self ): + element_object = self.element_object + if isinstance( element_object, DatasetCollection ): + return element_object.dataset_instances[ 0 ] + else: + return element_object + def copy_to_collection( self, collection ): new_element = DatasetCollectionElement( element=self.element_object, diff -r 954789571b9d7c2c2ea2d1651d50f13aefaced7e -r 31e5817ba7d36a039c432205b32958e190cbabbc lib/galaxy/workflow/extract.py --- a/lib/galaxy/workflow/extract.py +++ b/lib/galaxy/workflow/extract.py @@ -293,6 +293,8 @@ # HACK: Nested associations are not yet working, but we # still need to clean them up so we can serialize # if not( prefix ): + if isinstance( tmp, model.DatasetCollectionElement ): + tmp = tmp.first_dataset_instance() if tmp: # this is false for a non-set optional dataset if not isinstance(tmp, list): associations.append( ( tmp.hid, prefix + key ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.