sdk/cwl/arvados_cwl/arvdocker.py

   1 import logging
   2 import sys
   3
   4 import cwltool.docker
   5 from cwltool.errors import WorkflowException
   6 import arvados.commands.keepdocker
   7
   8
   9 logger = logging.getLogger('arvados.cwl-runner')
  10
  11 def arv_docker_get_image(api_client, dockerRequirement, pull_image, project_uuid):
  12     """Check if a Docker image is available in Keep, if not, upload it using arv-keepdocker."""
  13
  14     if "dockerImageId" not in dockerRequirement and "dockerPull" in dockerRequirement:
  15         dockerRequirement["dockerImageId"] = dockerRequirement["dockerPull"]
  16
  17     sp = dockerRequirement["dockerImageId"].split(":")
  18     image_name = sp[0]
  19     image_tag = sp[1] if len(sp) > 1 else None
  20
  21     images = arvados.commands.keepdocker.list_images_in_arv(api_client, 3,
  22                                                             image_name=image_name,
  23                                                             image_tag=image_tag)
  24
  25     if not images:
  26         # Fetch Docker image if necessary.
  27         cwltool.docker.get_image(dockerRequirement, pull_image)
  28
  29         # Upload image to Arvados
  30         args = ["--project-uuid="+project_uuid, image_name]
  31         if image_tag:
  32             args.append(image_tag)
  33         logger.info("Uploading Docker image %s", ":".join(args[1:]))
  34         try:
  35             arvados.commands.keepdocker.main(args, stdout=sys.stderr)
  36         except SystemExit:
  37             raise WorkflowException()
  38
  39         images = arvados.commands.keepdocker.list_images_in_arv(api_client, 3,
  40                                                                 image_name=image_name,
  41                                                                 image_tag=image_tag)
  42
  43     if not images:
  44         raise WorkflowException("Could not find Docker image %s:%s" % (image_name, image_tag))
  45
  46     pdh = api_client.collections().get(uuid=images[0][0]).execute()["portable_data_hash"]
  47     return pdh