/lib/galaxy/jobs/splitters/basic.py

https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 24 lines · 17 code · 5 blank · 2 comment · 2 complexity · f15d1b7e4910a624e17bec76d4fc3a49 MD5 · raw file

  1. import logging
  2. import multi
  3. log = logging.getLogger( __name__ )
  4. def set_basic_defaults(job_wrapper):
  5. parent_job = job_wrapper.get_job()
  6. parallelism = job_wrapper.get_parallelism()
  7. parallelism.attributes['split_inputs'] = parent_job.input_datasets[0].name
  8. parallelism.attributes['merge_outputs'] = job_wrapper.get_output_hdas_and_fnames().keys()[0]
  9. def do_split (job_wrapper):
  10. if len(job_wrapper.get_input_fnames()) > 1 or len(job_wrapper.get_output_fnames()) > 1:
  11. log.error("The basic splitter is not capable of handling jobs with multiple inputs or outputs.")
  12. raise Exception, "Job Splitting Failed, the basic splitter only handles tools with one input and one output"
  13. # add in the missing information for splitting the one input and merging the one output
  14. set_basic_defaults(job_wrapper)
  15. return multi.do_split(job_wrapper)
  16. def do_merge( job_wrapper, task_wrappers):
  17. # add in the missing information for splitting the one input and merging the one output
  18. set_basic_defaults(job_wrapper)
  19. return multi.do_merge(job_wrapper, task_wrappers)