sdk/cwl/arvados_cwl/arvdocker.py

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