Source code for galaxy.jobs.splitters.basic

import logging

from . import multi

log = logging.getLogger(__name__)


[docs]def set_basic_defaults(job_wrapper):
    parent_job = job_wrapper.get_job()
    parallelism = job_wrapper.get_parallelism()
    parallelism.attributes["split_inputs"] = parent_job.input_datasets[0].name
    parallelism.attributes["merge_outputs"] = next(iter(job_wrapper.job_io.get_output_hdas_and_fnames()))


[docs]def do_split(job_wrapper):
    if len(job_wrapper.job_io.get_input_datasets()) > 1 or len(job_wrapper.job_io.get_output_fnames()) > 1:
        log.error("The basic splitter is not capable of handling jobs with multiple inputs or outputs.")
        raise Exception("Job Splitting Failed, the basic splitter only handles tools with one input and one output")
    # 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)


[docs]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)