2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6b4139f8f40c/ Changeset: 6b4139f8f40c User: mike8115 Date: 2014-02-22 02:32:01 Summary: Trello Card #1437: Optional Input Datasets Not Compatible with Parallelism Tag multi.py edited to check for input.data is None. Affected #: 1 file diff -r 2403d6f67500ec35b16ce604142d98766286b65a -r 6b4139f8f40cda2bc21230fd4b32444474bfea8d lib/galaxy/jobs/splitters/multi.py --- a/lib/galaxy/jobs/splitters/multi.py +++ b/lib/galaxy/jobs/splitters/multi.py @@ -44,18 +44,26 @@ # For things like paired end alignment, we need two inputs to be split. Since all inputs to all # derived subtasks need to be correlated, allow only one input type to be split + # If shared_inputs are not specified, we assume all non-split inputs are shared inputs. + # For any input we must consider if each input is None. With optional arguments, a data input could be set to optional type_to_input_map = {} for input in parent_job.input_datasets: - if input.name in split_inputs: - type_to_input_map.setdefault(input.dataset.datatype, []).append(input.name) - elif input.name in shared_inputs: - pass # pass original file name - elif auto_shared_inputs: - shared_inputs.append(input.name) + if input.dataset is None: + if input.name in shared_inputs: + shared_inputs.remove(input.name) + else: + pass else: - log_error = "The input '%s' does not define a method for implementing parallelism" % str(input.name) - log.exception(log_error) - raise Exception(log_error) + if input.name in split_inputs: + type_to_input_map.setdefault(input.dataset.datatype, []).append(input.name) + elif input.name in shared_inputs: + pass # pass original file name + elif auto_shared_inputs: + shared_inputs.append(input.name) + else: + log_error = "The input '%s' does not define a method for implementing parallelism" % str(input.name) + log.exception(log_error) + raise Exception(log_error) if len(type_to_input_map) > 1: log_error = "The multi splitter does not support splitting inputs of more than one type" https://bitbucket.org/galaxy/galaxy-central/commits/dea106a05af8/ Changeset: dea106a05af8 User: dannon Date: 2014-03-18 13:57:36 Summary: Merged in mike8115/galaxy-central (pull request #334) Trello Card #1437: Optional Input Datasets Not Compatible with Parallelism Tag Affected #: 1 file diff -r c53fbb2655e2756c8977782df2381d883c5aa8af -r dea106a05af8597b66846bde6d28bfe97a8ea338 lib/galaxy/jobs/splitters/multi.py --- a/lib/galaxy/jobs/splitters/multi.py +++ b/lib/galaxy/jobs/splitters/multi.py @@ -44,18 +44,26 @@ # For things like paired end alignment, we need two inputs to be split. Since all inputs to all # derived subtasks need to be correlated, allow only one input type to be split + # If shared_inputs are not specified, we assume all non-split inputs are shared inputs. + # For any input we must consider if each input is None. With optional arguments, a data input could be set to optional type_to_input_map = {} for input in parent_job.input_datasets: - if input.name in split_inputs: - type_to_input_map.setdefault(input.dataset.datatype, []).append(input.name) - elif input.name in shared_inputs: - pass # pass original file name - elif auto_shared_inputs: - shared_inputs.append(input.name) + if input.dataset is None: + if input.name in shared_inputs: + shared_inputs.remove(input.name) + else: + pass else: - log_error = "The input '%s' does not define a method for implementing parallelism" % str(input.name) - log.exception(log_error) - raise Exception(log_error) + if input.name in split_inputs: + type_to_input_map.setdefault(input.dataset.datatype, []).append(input.name) + elif input.name in shared_inputs: + pass # pass original file name + elif auto_shared_inputs: + shared_inputs.append(input.name) + else: + log_error = "The input '%s' does not define a method for implementing parallelism" % str(input.name) + log.exception(log_error) + raise Exception(log_error) if len(type_to_input_map) > 1: log_error = "The multi splitter does not support splitting inputs of more than one type" 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.