import logging import sys import threading import copy from schema_salad.sourceline import SourceLine import cwltool.docker from cwltool.errors import WorkflowException import arvados.commands.keepdocker logger = logging.getLogger('arvados.cwl-runner') cached_lookups = {} cached_lookups_lock = threading.Lock() 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 = copy.deepcopy(dockerRequirement) dockerRequirement["dockerImageId"] = dockerRequirement["dockerPull"] if hasattr(dockerRequirement, 'lc'): dockerRequirement.lc.data["dockerImageId"] = dockerRequirement.lc.data["dockerPull"] global cached_lookups global cached_lookups_lock with cached_lookups_lock: if dockerRequirement["dockerImageId"] in cached_lookups: return dockerRequirement["dockerImageId"] with SourceLine(dockerRequirement, "dockerImageId", WorkflowException): 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 = [] if project_uuid: args.append("--project-uuid="+project_uuid) args.append(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 as e: if e.code: raise WorkflowException("keepdocker exited with code %s" % e.code) 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)) with cached_lookups_lock: cached_lookups[dockerRequirement["dockerImageId"]] = True return dockerRequirement["dockerImageId"] def arv_docker_clear_cache(): global cached_lookups global cached_lookups_lock with cached_lookups_lock: cached_lookups = {}