X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/d13a369065b4e72047c8c267d6ceaa5c84d50c3d..0c847cae0cb8ad2c55cf9330b84b49ce9d54b4e8:/sdk/cwl/arvados_cwl/arvdocker.py diff --git a/sdk/cwl/arvados_cwl/arvdocker.py b/sdk/cwl/arvados_cwl/arvdocker.py index 7f6ab587d3..04e2a4cffc 100644 --- a/sdk/cwl/arvados_cwl/arvdocker.py +++ b/sdk/cwl/arvados_cwl/arvdocker.py @@ -1,6 +1,15 @@ +# Copyright (C) The Arvados Authors. All rights reserved. +# +# SPDX-License-Identifier: Apache-2.0 + import logging import sys import threading +import copy +import re +import subprocess + +from schema_salad.sourceline import SourceLine import cwltool.docker from cwltool.errors import WorkflowException @@ -11,11 +20,54 @@ 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): +def determine_image_id(dockerImageId): + for line in ( + subprocess.check_output( # nosec + ["docker", "images", "--no-trunc", "--all"] + ) + .decode("utf-8") + .splitlines() + ): + try: + match = re.match(r"^([^ ]+)\s+([^ ]+)\s+([^ ]+)", line) + split = dockerImageId.split(":") + if len(split) == 1: + split.append("latest") + elif len(split) == 2: + # if split[1] doesn't match valid tag names, it is a part of repository + if not re.match(r"[\w][\w.-]{0,127}", split[1]): + split[0] = split[0] + ":" + split[1] + split[1] = "latest" + elif len(split) == 3: + if re.match(r"[\w][\w.-]{0,127}", split[2]): + split[0] = split[0] + ":" + split[1] + split[1] = split[2] + del split[2] + + # check for repository:tag match or image id match + if match and ( + (split[0] == match.group(1) and split[1] == match.group(2)) + or dockerImageId == match.group(3) + ): + return match.group(3) + except ValueError: + pass + + return None + + +def arv_docker_get_image(api_client, dockerRequirement, pull_image, project_uuid, + force_pull, tmp_outdir_prefix, match_local_docker): """Check if a Docker image is available in Keep, if not, upload it using arv-keepdocker.""" + if "http://arvados.org/cwl#dockerCollectionPDH" in dockerRequirement: + return dockerRequirement["http://arvados.org/cwl#dockerCollectionPDH"] + 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 @@ -23,43 +75,65 @@ def arv_docker_get_image(api_client, dockerRequirement, pull_image, project_uuid if dockerRequirement["dockerImageId"] in cached_lookups: return cached_lookups[dockerRequirement["dockerImageId"]] - 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) + with SourceLine(dockerRequirement, "dockerImageId", WorkflowException, logger.isEnabledFor(logging.DEBUG)): + sp = dockerRequirement["dockerImageId"].split(":") + image_name = sp[0] + image_tag = sp[1] if len(sp) > 1 else "latest" 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"] - - with cached_lookups_lock: - cached_lookups[dockerRequirement["dockerImageId"]] = pdh + if images and match_local_docker: + local_image_id = determine_image_id(dockerRequirement["dockerImageId"]) + if local_image_id: + # find it in the list + found = False + for i in images: + if i[1]["dockerhash"] == local_image_id: + found = True + images = [i] + break + if not found: + # force re-upload. + images = [] + + if not images: + # Fetch Docker image if necessary. + try: + result = cwltool.docker.DockerCommandLineJob.get_image(dockerRequirement, pull_image, + force_pull, tmp_outdir_prefix) + if not result: + raise WorkflowException("Docker image '%s' not available" % dockerRequirement["dockerImageId"]) + except OSError as e: + raise WorkflowException("While trying to get Docker image '%s', failed to execute 'docker': %s" % (dockerRequirement["dockerImageId"], e)) + + # Upload image to Arvados + args = [] + if project_uuid: + args.append("--project-uuid="+project_uuid) + args.append(image_name) + args.append(image_tag) + logger.info("Uploading Docker image %s:%s", image_name, image_tag) + try: + arvados.commands.put.api_client = api_client + arvados.commands.keepdocker.main(args, stdout=sys.stderr, install_sig_handlers=False, api=api_client) + except SystemExit as e: + # If e.code is None or zero, then keepdocker exited normally and we can continue + 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)) + + pdh = api_client.collections().get(uuid=images[0][0]).execute()["portable_data_hash"] + + with cached_lookups_lock: + cached_lookups[dockerRequirement["dockerImageId"]] = pdh return pdh