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, normalizeFilesDirs
  23 from cwltool.load_tool import load_tool
  24 from cwltool.errors import WorkflowException
  25
  26 from .fsaccess import CollectionFetcher, CollectionFsAccess
  27
  28 logger = logging.getLogger('arvados.cwl-runner')
  29
  30 def run():
  31     # Timestamps are added by crunch-job, so don't print redundant timestamps.
  32     arvados.log_handler.setFormatter(logging.Formatter('%(name)s %(levelname)s: %(message)s'))
  33
  34     # Print package versions
  35     logger.info(arvados_cwl.versionstring())
  36
  37     api = arvados.api("v1")
  38
  39     arvados_cwl.add_arv_hints()
  40
  41     runner = None
  42     try:
  43         job_order_object = arvados.current_job()['script_parameters']
  44         toolpath = "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], job_order_object.pop("cwl:tool"))
  45
  46         pdh_path = re.compile(r'^[0-9a-f]{32}\+\d+(/.+)?$')
  47
  48         def keeppath(v):
  49             if pdh_path.match(v):
  50                 return "keep:%s" % v
  51             else:
  52                 return v
  53
  54         def keeppathObj(v):
  55             v["location"] = keeppath(v["location"])
  56
  57         for k,v in job_order_object.items():
  58             if isinstance(v, basestring) and arvados.util.keep_locator_pattern.match(v):
  59                 job_order_object[k] = {
  60                     "class": "File",
  61                     "location": "keep:%s" % v
  62                 }
  63
  64         adjustFileObjs(job_order_object, keeppathObj)
  65         adjustDirObjs(job_order_object, keeppathObj)
  66         normalizeFilesDirs(job_order_object)
  67
  68         output_name = None
  69         output_tags = None
  70         enable_reuse = True
  71         on_error = "continue"
  72         if "arv:output_name" in job_order_object:
  73             output_name = job_order_object["arv:output_name"]
  74             del job_order_object["arv:output_name"]
  75
  76         if "arv:output_tags" in job_order_object:
  77             output_tags = job_order_object["arv:output_tags"]
  78             del job_order_object["arv:output_tags"]
  79
  80         if "arv:enable_reuse" in job_order_object:
  81             enable_reuse = job_order_object["arv:enable_reuse"]
  82             del job_order_object["arv:enable_reuse"]
  83
  84         if "arv:on_error" in job_order_object:
  85             on_error = job_order_object["arv:on_error"]
  86             del job_order_object["arv:on_error"]
  87
  88         runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()),
  89                                           output_name=output_name, output_tags=output_tags)
  90
  91         make_fs_access = functools.partial(CollectionFsAccess,
  92                                  collection_cache=runner.collection_cache)
  93
  94         t = load_tool(toolpath, runner.arv_make_tool,
  95                       fetcher_constructor=functools.partial(CollectionFetcher,
  96                                                   api_client=runner.api,
  97                                                   fs_access=make_fs_access(""),
  98                                                   num_retries=runner.num_retries))
  99
 100         args = argparse.Namespace()
 101         args.project_uuid = arvados.current_job()["owner_uuid"]
 102         args.enable_reuse = enable_reuse
 103         args.on_error = on_error
 104         args.submit = False
 105         args.debug = False
 106         args.quiet = False
 107         args.ignore_docker_for_reuse = False
 108         args.basedir = os.getcwd()
 109         args.name = None
 110         args.cwl_runner_job={"uuid": arvados.current_job()["uuid"], "state": arvados.current_job()["state"]}
 111         args.make_fs_access = make_fs_access
 112
 113         runner.arv_executor(t, job_order_object, **vars(args))
 114     except Exception as e:
 115         if isinstance(e, WorkflowException):
 116             logging.info("Workflow error %s", e)
 117         else:
 118             logging.exception("Unhandled exception")
 119         if runner and runner.final_output_collection:
 120             outputCollection = runner.final_output_collection.portable_data_hash()
 121         else:
 122             outputCollection = None
 123         api.job_tasks().update(uuid=arvados.current_task()['uuid'],
 124                                              body={
 125                                                  'output': outputCollection,
 126                                                  'success': False,
 127                                                  'progress':1.0
 128                                              }).execute()