import logging import sys import cwltool.docker from cwltool.errors import WorkflowException import arvados.commands.keepdocker logger = logging.getLogger('arvados.cwl-runner') def arv_docker_get_image(api_client, dockerRequirement, pull_image, project_uuid): """Check if a Docker image is available in Keep, if not, upload it using arv-keepdocker.""" if "dockerImageId" not in dockerRequirement and "dockerPull" in dockerRequirement: dockerRequirement["dockerImageId"] = dockerRequirement["dockerPull"] sp = dockerRequirement["dockerImageId"].split(":") image_name = sp[0] image_tag = sp[1] if len(sp) > 1 else None images = arvados.commands.keepdocker.list_images_in_arv(api_client, 3, image_name=image_name, image_tag=image_tag) if not images: # Fetch Docker image if necessary. cwltool.docker.get_image(dockerRequirement, pull_image) # Upload image to Arvados args = ["--project-uuid="+project_uuid, image_name] if image_tag: args.append(image_tag) logger.info("Uploading Docker image %s", ":".join(args[1:])) try: arvados.commands.keepdocker.main(args, stdout=sys.stderr) except SystemExit: raise WorkflowException() images = arvados.commands.keepdocker.list_images_in_arv(api_client, 3, image_name=image_name, image_tag=image_tag) if not images: raise WorkflowException("Could not find Docker image %s:%s" % (image_name, image_tag)) pdh = api_client.collections().get(uuid=images[0][0]).execute()["portable_data_hash"] return pdh