2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/316db249f068/ Changeset: 316db249f068 Branch: next-stable User: jmchilton Date: 2014-05-21 22:09:52 Summary: Fix for running workflows with collection inptus. takadonet reported running such workflows were not behaving correctly when copying inputs to new history is enabled. Affected #: 1 file diff -r fc89661b92dcbd9684ac779171235525601d0f4a -r 316db249f068ded4e541415232b480250c7cdd56 lib/galaxy/workflow/run.py --- a/lib/galaxy/workflow/run.py +++ b/lib/galaxy/workflow/run.py @@ -203,9 +203,17 @@ # ds_map. if self.copy_inputs_to_history: for input_dataset_hda in out_data.values(): - new_hda = input_dataset_hda.copy( copy_children=True ) - self.target_history.add_dataset( new_hda ) - outputs[ step.id ][ 'input_ds_copy' ] = new_hda + content_type = input_dataset_hda.history_content_type + if content_type == "dataset": + new_hda = input_dataset_hda.copy( copy_children=True ) + self.target_history.add_dataset( new_hda ) + outputs[ step.id ][ 'input_ds_copy' ] = new_hda + elif content_type == "dataset_collection": + new_hdca = input_dataset_hda.copy() + self.target_history.add_dataset_collection( new_hdca ) + outputs[ step.id ][ 'input_ds_copy' ] = new_hdca + else: + raise Exception("Unknown history content encountered") if self.ds_map: outputs[ step.id ][ 'output' ] = self.ds_map[ str( step.id ) ][ 'hda' ] https://bitbucket.org/galaxy/galaxy-central/commits/6c3cc96d1fa7/ Changeset: 6c3cc96d1fa7 User: jmchilton Date: 2014-05-21 22:10:44 Summary: Merge next-stable. Affected #: 1 file diff -r e8f2c4f3e8c8ed63a99254a50ceb18fc33c52080 -r 6c3cc96d1fa7888b7af015dd73c7451df7338ad5 lib/galaxy/workflow/run.py --- a/lib/galaxy/workflow/run.py +++ b/lib/galaxy/workflow/run.py @@ -203,9 +203,17 @@ # ds_map. if self.copy_inputs_to_history: for input_dataset_hda in out_data.values(): - new_hda = input_dataset_hda.copy( copy_children=True ) - self.target_history.add_dataset( new_hda ) - outputs[ step.id ][ 'input_ds_copy' ] = new_hda + content_type = input_dataset_hda.history_content_type + if content_type == "dataset": + new_hda = input_dataset_hda.copy( copy_children=True ) + self.target_history.add_dataset( new_hda ) + outputs[ step.id ][ 'input_ds_copy' ] = new_hda + elif content_type == "dataset_collection": + new_hdca = input_dataset_hda.copy() + self.target_history.add_dataset_collection( new_hdca ) + outputs[ step.id ][ 'input_ds_copy' ] = new_hdca + else: + raise Exception("Unknown history content encountered") if self.ds_map: outputs[ step.id ][ 'output' ] = self.ds_map[ str( step.id ) ][ 'hda' ] 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.