sdk/cwl/arvados_cwl/crunch_script.py

   1 # Crunch script integration for running arvados-cwl-runner (importing
   2 # arvados_cwl module) inside a crunch job.
   3 #
   4 # This gets the job record, transforms the script parameters into a valid CWL
   5 # input object, then executes the CWL runner to run the underlying workflow or
   6 # tool.  When the workflow completes, record the output object in an output
   7 # collection for this runner job.
   8
   9 import arvados
  10 import arvados_cwl
  11 import arvados.collection
  12 import arvados.util
  13 import cwltool.main
  14 import logging
  15 import os
  16 import json
  17 import argparse
  18 import re
  19 import functools
  20
  21 from arvados.api import OrderedJsonModel
  22 from cwltool.process import shortname, adjustFileObjs, adjustDirObjs, getListing, normalizeFilesDirs
  23 from cwltool.load_tool import load_tool
  24 from cwltool.errors import WorkflowException
  25
  26 logger = logging.getLogger('arvados.cwl-runner')
  27
  28 def run():
  29     # Timestamps are added by crunch-job, so don't print redundant timestamps.
  30     arvados.log_handler.setFormatter(logging.Formatter('%(name)s %(levelname)s: %(message)s'))
  31
  32     # Print package versions
  33     logger.info(arvados_cwl.versionstring())
  34
  35     api = arvados.api("v1")
  36
  37     arvados_cwl.add_arv_hints()
  38
  39     runner = None
  40     try:
  41         job_order_object = arvados.current_job()['script_parameters']
  42         toolpath = "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], job_order_object.pop("cwl:tool"))
  43
  44         pdh_path = re.compile(r'^[0-9a-f]{32}\+\d+(/.+)?$')
  45
  46         def keeppath(v):
  47             if pdh_path.match(v):
  48                 return "keep:%s" % v
  49             else:
  50                 return v
  51
  52         def keeppathObj(v):
  53             v["location"] = keeppath(v["location"])
  54
  55         for k,v in job_order_object.items():
  56             if isinstance(v, basestring) and arvados.util.keep_locator_pattern.match(v):
  57                 job_order_object[k] = {
  58                     "class": "File",
  59                     "location": "keep:%s" % v
  60                 }
  61
  62         adjustFileObjs(job_order_object, keeppathObj)
  63         adjustDirObjs(job_order_object, keeppathObj)
  64         normalizeFilesDirs(job_order_object)
  65         adjustDirObjs(job_order_object, functools.partial(getListing, arvados_cwl.fsaccess.CollectionFsAccess("", api_client=api)))
  66
  67         output_name = None
  68         output_tags = None
  69         enable_reuse = True
  70         on_error = "continue"
  71         if "arv:output_name" in job_order_object:
  72             output_name = job_order_object["arv:output_name"]
  73             del job_order_object["arv:output_name"]
  74
  75         if "arv:output_tags" in job_order_object:
  76             output_tags = job_order_object["arv:output_tags"]
  77             del job_order_object["arv:output_tags"]
  78
  79         if "arv:enable_reuse" in job_order_object:
  80             enable_reuse = job_order_object["arv:enable_reuse"]
  81             del job_order_object["arv:enable_reuse"]
  82
  83         if "arv:on_error" in job_order_object:
  84             on_error = job_order_object["arv:on_error"]
  85             del job_order_object["arv:on_error"]
  86
  87         runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()),
  88                                           output_name=output_name, output_tags=output_tags)
  89
  90         t = load_tool(toolpath, runner.arv_make_tool)
  91
  92         args = argparse.Namespace()
  93         args.project_uuid = arvados.current_job()["owner_uuid"]
  94         args.enable_reuse = enable_reuse
  95         args.on_error = on_error
  96         args.submit = False
  97         args.debug = False
  98         args.quiet = False
  99         args.ignore_docker_for_reuse = False
 100         args.basedir = os.getcwd()
 101         args.name = None
 102         args.cwl_runner_job={"uuid": arvados.current_job()["uuid"], "state": arvados.current_job()["state"]}
 103         runner.arv_executor(t, job_order_object, **vars(args))
 104     except Exception as e:
 105         if isinstance(e, WorkflowException):
 106             logging.info("Workflow error %s", e)
 107         else:
 108             logging.exception("Unhandled exception")
 109         if runner and runner.final_output_collection:
 110             outputCollection = runner.final_output_collection.portable_data_hash()
 111         else:
 112             outputCollection = None
 113         api.job_tasks().update(uuid=arvados.current_task()['uuid'],
 114                                              body={
 115                                                  'output': outputCollection,
 116                                                  'success': False,
 117                                                  'progress':1.0
 118                                              }).execute()