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 import logging
  10 import os
  11 import json
  12 from arvados.api import OrderedJsonModel
  13
  14 api = arvados.api("v1")
  15
  16 try:
  17     job_order_object = arvados.current_job()['script_parameters']
  18
  19     print job_order_object
  20
  21     for k,v in job_order_object.items():
  22         if arvados.util.keep_locator_pattern.match(v):
  23             job_order_object[k] = "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], v)
  24
  25     runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))
  26
  27     t = cwltool.main.load_tool(job_order_object, False, True, runner.arvMakeTool, True)
  28
  29     outputObj = runner.arvExecutor(t, job_order_object, "", None)
  30
  31     c = arvados.collection.Collection()
  32     with c.open("cwl.output.json", "w") as f:
  33         json.dump(outputObj, f, indent=4)
  34
  35     api.job_tasks().update(uuid=arvados.current_task()['uuid'],
  36                                          body={
  37                                              'output': c.save_new(create_collection_record=False),
  38                                              'success': True,
  39                                              'progress':1.0
  40                                          }).execute()
  41 except Exception as e:
  42     logging.exception("Unhandled exception")
  43     api.job_tasks().update(uuid=arvados.current_task()['uuid'],
  44                                          body={
  45                                              'output': None,
  46                                              'success': False,
  47                                              'progress':1.0
  48                                          }).execute()