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14198: Refactor and add support for --submit-runner-cluster
[arvados.git]
/
sdk
/
cwl
/
arvados_cwl
/
arvdocker.py
diff --git
a/sdk/cwl/arvados_cwl/arvdocker.py
b/sdk/cwl/arvados_cwl/arvdocker.py
index f42e6d8c9c356cfcee7c165d554359cdec40623b..6bca07c883e4c0d8fd4c85a1c21b56b9bb361e58 100644
(file)
--- a/
sdk/cwl/arvados_cwl/arvdocker.py
+++ b/
sdk/cwl/arvados_cwl/arvdocker.py
@@
-31,12
+31,12
@@
def arv_docker_get_image(api_client, dockerRequirement, pull_image, project_uuid
global cached_lookups_lock
with cached_lookups_lock:
if dockerRequirement["dockerImageId"] in cached_lookups:
global cached_lookups_lock
with cached_lookups_lock:
if dockerRequirement["dockerImageId"] in cached_lookups:
- return
dockerRequirement["dockerImageId"
]
+ return
cached_lookups[dockerRequirement["dockerImageId"]
]
- with SourceLine(dockerRequirement, "dockerImageId", WorkflowException):
+ with SourceLine(dockerRequirement, "dockerImageId", WorkflowException
, logger.isEnabledFor(logging.DEBUG)
):
sp = dockerRequirement["dockerImageId"].split(":")
image_name = sp[0]
sp = dockerRequirement["dockerImageId"].split(":")
image_name = sp[0]
- image_tag = sp[1] if len(sp) > 1 else
None
+ 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,
images = arvados.commands.keepdocker.list_images_in_arv(api_client, 3,
image_name=image_name,
@@
-44,18
+44,21
@@
def arv_docker_get_image(api_client, dockerRequirement, pull_image, project_uuid
if not images:
# Fetch Docker image if necessary.
if not images:
# Fetch Docker image if necessary.
- cwltool.docker.get_image(dockerRequirement, pull_image)
+ try:
+ cwltool.docker.DockerCommandLineJob.get_image(dockerRequirement, pull_image)
+ 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)
# 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:]))
+ args.append(image_tag)
+ logger.info("Uploading Docker image %s:%s", image_name, image_tag)
try:
try:
- arvados.commands.keepdocker.main(args, stdout=sys.stderr)
+ 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:
raise WorkflowException("keepdocker exited with code %s" % e.code)
except SystemExit as e:
if e.code:
raise WorkflowException("keepdocker exited with code %s" % e.code)
@@
-67,10
+70,12
@@
def arv_docker_get_image(api_client, dockerRequirement, pull_image, project_uuid
if not images:
raise WorkflowException("Could not find Docker image %s:%s" % (image_name, 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:
with cached_lookups_lock:
- cached_lookups[dockerRequirement["dockerImageId"]] =
True
+ cached_lookups[dockerRequirement["dockerImageId"]] =
pdh
- return
dockerRequirement["dockerImageId"]
+ return
pdh
def arv_docker_clear_cache():
global cached_lookups
def arv_docker_clear_cache():
global cached_lookups