1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/0ed4a546bee8/ changeset: 0ed4a546bee8 user: dannon date: 2012-07-12 01:53:59 summary: Fix issue caused in 1827729ed37e that failed to correctly order task directories prior to merging, and, whitespace cleanup. affected #: 2 files
diff -r 8c28c1898af85d8be0fb3b524518ce9916d14cac -r 0ed4a546bee81e94e1fb19b6b210a4ed4cee08a9 lib/galaxy/jobs/splitters/basic.py --- a/lib/galaxy/jobs/splitters/basic.py +++ b/lib/galaxy/jobs/splitters/basic.py @@ -15,9 +15,9 @@ # add in the missing information for splitting the one input and merging the one output set_basic_defaults(job_wrapper) return multi.do_split(job_wrapper) - + def do_merge( job_wrapper, task_wrappers): # add in the missing information for splitting the one input and merging the one output set_basic_defaults(job_wrapper) return multi.do_merge(job_wrapper, task_wrappers) - +
diff -r 8c28c1898af85d8be0fb3b524518ce9916d14cac -r 0ed4a546bee81e94e1fb19b6b210a4ed4cee08a9 lib/galaxy/jobs/splitters/multi.py --- a/lib/galaxy/jobs/splitters/multi.py +++ b/lib/galaxy/jobs/splitters/multi.py @@ -3,13 +3,13 @@
log = logging.getLogger( __name__ ) - + def do_split (job_wrapper): parent_job = job_wrapper.get_job() working_directory = os.path.abspath(job_wrapper.working_directory)
parallel_settings = job_wrapper.tool.parallelism.attributes - # Syntax: split_inputs="input1,input2" shared_inputs="genome" + # Syntax: split_inputs="input1,input2" shared_inputs="genome" # Designates inputs to be split or shared split_inputs=parallel_settings.get("split_inputs") if split_inputs is None: @@ -25,7 +25,7 @@ illegal_inputs = [x for x in shared_inputs if x in split_inputs] if len(illegal_inputs) > 0: raise Exception("Inputs have conflicting parallelism attributes: %s" % str( illegal_inputs )) - + subdir_index = [0] # use a list to get around Python 2.x lame closure support task_dirs = [] def get_new_working_directory_name(): @@ -35,7 +35,7 @@ os.makedirs(dir) task_dirs.append(dir) return dir - + # 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 type_to_input_map = {} @@ -53,7 +53,7 @@ log_error = "The multi splitter does not support splitting inputs of more than one type" log.error(log_error) raise Exception(log_error) - + # split the first one to build up the task directories input_datasets = [] for input in parent_job.input_datasets: @@ -64,7 +64,7 @@ log.error(log_error) raise Exception(log_error) input_datasets.append(input.dataset) - + input_type = type_to_input_map.keys()[0] # DBTODO execute an external task to do the splitting, this should happen at refactor. # If the number of tasks is sufficiently high, we can use it to calculate job completion % and give a running status. @@ -88,10 +88,9 @@ task = model.Task(parent_job, dir, prepare_files % dir) tasks.append(task) return tasks - +
def do_merge( job_wrapper, task_wrappers): - parent_job = job_wrapper.get_job() parallel_settings = job_wrapper.tool.parallelism.attributes # Syntax: merge_outputs="export" pickone_outputs="genomesize" # Designates outputs to be merged, or selected from as a representative @@ -105,14 +104,14 @@ pickone_outputs = [] else: pickone_outputs = [x.strip() for x in pickone_outputs.split(",")] - + illegal_outputs = [x for x in merge_outputs if x in pickone_outputs] if len(illegal_outputs) > 0: return ('Tool file error', 'Outputs have conflicting parallelism attributes: %s' % str( illegal_outputs )) - + stdout = '' stderr = '' - + try: working_directory = job_wrapper.working_directory task_dirs = [os.path.join(working_directory, x) for x in os.listdir(working_directory) if x.startswith('task_')] @@ -120,6 +119,7 @@ outputs = job_wrapper.get_output_hdas_and_fnames() pickone_done = [] task_dirs = [os.path.join(working_directory, x) for x in os.listdir(working_directory) if x.startswith('task_')] + task_dirs.sort(key = lambda x: int(x.split('task_')[-1])) for output in outputs: output_file_name = str(outputs[output][1]) base_output_name = os.path.basename(output_file_name) @@ -144,7 +144,6 @@ stdout = 'Error merging files'; log.exception( stdout ) stderr = str(e) -
for tw in task_wrappers: # Prevent repetitive output, e.g. "Sequence File Aligned"x20
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.