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Merge branch 'master' into 7478-anm-spot-instances
[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 88c5dd2d4f428e946602c4eaeb5c59c1e4e4a2e6..7508febb08cc8bd704d251cc0490ea045a75053b 100644
(file)
--- a/
sdk/cwl/arvados_cwl/arvdocker.py
+++ b/
sdk/cwl/arvados_cwl/arvdocker.py
@@
-1,6
+1,11
@@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
import logging
import sys
import threading
import logging
import sys
import threading
+import copy
from schema_salad.sourceline import SourceLine
from schema_salad.sourceline import SourceLine
@@
-17,6
+22,7
@@
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:
"""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"]
dockerRequirement["dockerImageId"] = dockerRequirement["dockerPull"]
if hasattr(dockerRequirement, 'lc'):
dockerRequirement.lc.data["dockerImageId"] = dockerRequirement.lc.data["dockerPull"]
@@
-25,12
+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
cached_lookups[dockerRequirement["dockerImageId"]
]
+ return
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,
@@
-38,18
+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)
@@
-61,12
+70,10
@@
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"]] =
pdh
+ cached_lookups[dockerRequirement["dockerImageId"]] =
True
- return pdh
+ return dockerRequirement["dockerImageId"]
def arv_docker_clear_cache():
global cached_lookups
def arv_docker_clear_cache():
global cached_lookups