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