# Identify the kind of object we have been given, and begin copying.
t = uuid_type(src_arv, args.object_uuid)
- if t == 'Collection':
- set_src_owner_uuid(src_arv.collections(), args.object_uuid, args)
- result = copy_collection(args.object_uuid,
- src_arv, dst_arv,
- args)
- elif t == 'Workflow':
- set_src_owner_uuid(src_arv.workflows(), args.object_uuid, args)
- result = copy_workflow(args.object_uuid, src_arv, dst_arv, args)
- elif t == 'Group':
- set_src_owner_uuid(src_arv.groups(), args.object_uuid, args)
- result = copy_project(args.object_uuid, src_arv, dst_arv, args.project_uuid, args)
- elif t == 'httpURL':
- result = copy_from_http(args.object_uuid, src_arv, dst_arv, args)
- else:
- abort("cannot copy object {} of type {}".format(args.object_uuid, t))
+
+ try:
+ if t == 'Collection':
+ set_src_owner_uuid(src_arv.collections(), args.object_uuid, args)
+ result = copy_collection(args.object_uuid,
+ src_arv, dst_arv,
+ args)
+ elif t == 'Workflow':
+ set_src_owner_uuid(src_arv.workflows(), args.object_uuid, args)
+ result = copy_workflow(args.object_uuid, src_arv, dst_arv, args)
+ elif t == 'Group':
+ set_src_owner_uuid(src_arv.groups(), args.object_uuid, args)
+ result = copy_project(args.object_uuid, src_arv, dst_arv, args.project_uuid, args)
+ elif t == 'httpURL':
+ result = copy_from_http(args.object_uuid, src_arv, dst_arv, args)
+ else:
+ abort("cannot copy object {} of type {}".format(args.object_uuid, t))
+ except Exception as e:
+ logger.error("%s", e, exc_info=args.verbose)
+ exit(1)
# Clean up any outstanding temp git repositories.
for d in listvalues(local_repo_dir):
shutil.rmtree(d, ignore_errors=True)
+ if not result:
+ exit(1)
+
# If no exception was thrown and the response does not have an
# error_token field, presume success
if result is None or 'error_token' in result or 'uuid' not in result:
# copy collections and docker images
if args.recursive and wf["definition"]:
- wf_def = yaml.safe_load(wf["definition"])
- if wf_def is not None:
- locations = []
- docker_images = {}
- graph = wf_def.get('$graph', None)
- if graph is not None:
- workflow_collections(graph, locations, docker_images)
- else:
- workflow_collections(wf_def, locations, docker_images)
+ env = {"ARVADOS_API_HOST": urllib.parse.urlparse(src._rootDesc["rootUrl"]).netloc,
+ "ARVADOS_API_TOKEN": src.api_token,
+ "PATH": os.environ["PATH"]}
+ try:
+ result = subprocess.run(["arvados-cwl-runner", "--quiet", "--print-keep-deps", "arvwf:"+wf_uuid],
+ capture_output=True, env=env)
+ except FileNotFoundError:
+ no_arv_copy = True
+ else:
+ no_arv_copy = result.returncode == 2
+
+ if no_arv_copy:
+ raise Exception('Copying workflows requires arvados-cwl-runner 2.7.1 or later to be installed in PATH.')
+ elif result.returncode != 0:
+ raise Exception('There was an error getting Keep dependencies from workflow using arvados-cwl-runner --print-keep-deps')
- if locations:
- copy_collections(locations, src, dst, args)
+ locations = json.loads(result.stdout)
- for image in docker_images:
- copy_docker_image(image, docker_images[image], src, dst, args)
+ if locations:
+ copy_collections(locations, src, dst, args)
# copy the workflow itself
del wf['uuid']
dst_keep = arvados.keep.KeepClient(api_client=dst, num_retries=args.retries)
dst_manifest = io.StringIO()
dst_locators = {}
- bytes_written = [0]
+ bytes_written = 0
bytes_expected = total_collection_size(manifest)
if args.progress:
progress_writer = ProgressWriter(human_progress)
# Drain the 'get' queue so we end early
while True:
get_queue.get(False)
+ get_queue.task_done()
except queue.Empty:
pass
finally:
get_queue.task_done()
def put_thread():
+ nonlocal bytes_written
while True:
item = put_queue.get()
if item is None:
dst_locator = dst_keep.put(data, classes=(args.storage_classes or []))
with lock:
dst_locators[blockhash] = dst_locator
- bytes_written[0] += loc.size
+ bytes_written += loc.size
if progress_writer:
- progress_writer.report(obj_uuid, bytes_written[0], bytes_expected)
+ progress_writer.report(obj_uuid, bytes_written, bytes_expected)
except e:
logger.error("Error putting block %s (%s bytes): %s", blockhash, loc.size, e)
try:
# Drain the 'get' queue so we end early
while True:
get_queue.get(False)
+ get_queue.task_done()
except queue.Empty:
pass
transfer_error.append(e)
dst_manifest.write("\n")
if progress_writer:
- progress_writer.report(obj_uuid, bytes_written[0], bytes_expected)
+ progress_writer.report(obj_uuid, bytes_written, bytes_expected)
progress_writer.finish()
# Copy the manifest and save the collection.
projects / arvados.git / blobdiff