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 import argparse
  13 from arvados.api import OrderedJsonModel
  14 from cwltool.process import adjustFiles
  15
  16 api = arvados.api("v1")
  17
  18 try:
  19     job_order_object = arvados.current_job()['script_parameters']
  20
  21     print job_order_object
  22
  23     for k,v in job_order_object.items():
  24         if arvados.util.keep_locator_pattern.match(v):
  25             job_order_object[k] = "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], v)
  26
  27     runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))
  28
  29     t = cwltool.main.load_tool(job_order_object, False, True, runner.arvMakeTool, True)
  30
  31     np = argparse.Namespace()
  32     np.project_uuid = arvados.current_job()["owner_uuid"]
  33     np.enable_reuse = True
  34     outputObj = runner.arvExecutor(t, job_order_object, "", np)
  35
  36     files = {}
  37     def capture(path):
  38         sp = path.split("/")
  39         col = sp[0][5:]
  40         if col not in files:
  41             files[col] = set()
  42         files[col].add("/".join(sp[1:]))
  43         return path
  44
  45     adjustFiles(outputObj, capture)
  46
  47     final = arvados.collection.Collection()
  48
  49     for k,v in files.iteritems():
  50         with arvados.collection.Collection(k) as c:
  51             for f in c:
  52                 final.copy(f, f, c, True)
  53
  54     def makeRelative(path):
  55         return "/".join(path.split("/")[1:])
  56
  57     adjustFiles(outputObj, makeRelative)
  58
  59     with final.open("cwl.output.json", "w") as f:
  60         json.dump(outputObj, f, indent=4)
  61
  62     api.job_tasks().update(uuid=arvados.current_task()['uuid'],
  63                                          body={
  64                                              'output': final.save_new(create_collection_record=False),
  65                                              'success': True,
  66                                              'progress':1.0
  67                                          }).execute()
  68 except Exception as e:
  69     logging.exception("Unhandled exception")
  70     api.job_tasks().update(uuid=arvados.current_task()['uuid'],
  71                                          body={
  72                                              'output': None,
  73                                              'success': False,
  74                                              'progress':1.0
  75                                          }).execute()