crunch_scripts/cwl-runner

   1 #!/usr/bin/env python
   2
   3 import arvados
   4 import arvados_cwl
   5 import arvados.collection
   6 import arvados.util
   7 from cwltool.process import shortname
   8 import cwltool.main
   9
  10 api = arvados.api("v1")
  11
  12 try:
  13     job_order_object = arvados.current_job()['script_parameters']
  14
  15     for k,v in job_order_object.items():
  16         if arvados.util.keep_locator_pattern.match(v):
  17             job_order_object[k] = "%s/%s" % (os.environ['TASK_KEEPMOUNT'], v)
  18
  19     runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))
  20
  21     t = cwltool.main.load_tool(job_order_object, False, True, runner.arvMakeTool, True)
  22
  23     outputObj = runner.arvExecutor(t, job_order_object, "", None)
  24
  25     c = arvados.collection.Collection()
  26     with c.open("cwl.output.json") as f:
  27         json.dump(f, indent=4)
  28
  29     api.job_tasks().update(uuid=arvados.current_task()['uuid'],
  30                                          body={
  31                                              'output': c.save_new(create_collection_record=False),
  32                                              'success': True,
  33                                              'progress':1.0
  34                                          }).execute()
  35 except:
  36     api.job_tasks().update(uuid=arvados.current_task()['uuid'],
  37                                          body={
  38                                              'output': None,
  39                                              'success': False,
  40                                              'progress':1.0
  41                                          }).execute()