sdk/cwl/arvados_cwl/arvdocker.py

   1 import logging
   2 import sys
   3 import threading
   4 import copy
   5
   6 from schema_salad.sourceline import SourceLine
   7
   8 import cwltool.docker
   9 from cwltool.errors import WorkflowException
  10 import arvados.commands.keepdocker
  11
  12 logger = logging.getLogger('arvados.cwl-runner')
  13
  14 cached_lookups = {}
  15 cached_lookups_lock = threading.Lock()
  16
  17 def arv_docker_get_image(api_client, dockerRequirement, pull_image, project_uuid):
  18     """Check if a Docker image is available in Keep, if not, upload it using arv-keepdocker."""
  19
  20     if "dockerImageId" not in dockerRequirement and "dockerPull" in dockerRequirement:
  21         dockerRequirement = copy.deepcopy(dockerRequirement)
  22         dockerRequirement["dockerImageId"] = dockerRequirement["dockerPull"]
  23         if hasattr(dockerRequirement, 'lc'):
  24             dockerRequirement.lc.data["dockerImageId"] = dockerRequirement.lc.data["dockerPull"]
  25
  26     global cached_lookups
  27     global cached_lookups_lock
  28     with cached_lookups_lock:
  29         if dockerRequirement["dockerImageId"] in cached_lookups:
  30             return cached_lookups[dockerRequirement["dockerImageId"]]
  31
  32     with SourceLine(dockerRequirement, "dockerImageId", WorkflowException):
  33         sp = dockerRequirement["dockerImageId"].split(":")
  34         image_name = sp[0]
  35         image_tag = sp[1] if len(sp) > 1 else None
  36
  37         images = arvados.commands.keepdocker.list_images_in_arv(api_client, 3,
  38                                                                 image_name=image_name,
  39                                                                 image_tag=image_tag)
  40
  41         if not images:
  42             # Fetch Docker image if necessary.
  43             cwltool.docker.get_image(dockerRequirement, pull_image)
  44
  45             # Upload image to Arvados
  46             args = []
  47             if project_uuid:
  48                 args.append("--project-uuid="+project_uuid)
  49             args.append(image_name)
  50             if image_tag:
  51                 args.append(image_tag)
  52             logger.info("Uploading Docker image %s", ":".join(args[1:]))
  53             try:
  54                 arvados.commands.keepdocker.main(args, stdout=sys.stderr)
  55             except SystemExit as e:
  56                 if e.code:
  57                     raise WorkflowException("keepdocker exited with code %s" % e.code)
  58
  59             images = arvados.commands.keepdocker.list_images_in_arv(api_client, 3,
  60                                                                     image_name=image_name,
  61                                                                     image_tag=image_tag)
  62
  63         if not images:
  64             raise WorkflowException("Could not find Docker image %s:%s" % (image_name, image_tag))
  65
  66         pdh = api_client.collections().get(uuid=images[0][0]).execute()["portable_data_hash"]
  67
  68         with cached_lookups_lock:
  69             cached_lookups[dockerRequirement["dockerImageId"]] = pdh
  70
  71         return pdh
  72
  73 def arv_docker_clear_cache():
  74     global cached_lookups
  75     global cached_lookups_lock
  76     with cached_lookups_lock:
  77         cached_lookups = {}