import arvados.commands._util as arv_cmd
CAUGHT_SIGNALS = [signal.SIGINT, signal.SIGQUIT, signal.SIGTERM]
+api_client = None
upload_opts = argparse.ArgumentParser(add_help=False)
""")
upload_opts.add_argument('--project-uuid', metavar='UUID', help="""
-When a Collection is made, make a Link to save it under the specified project.
+Store the collection in the specified project, instead of your Home
+project.
""")
upload_opts.add_argument('--name', help="""
-When a Collection is linked to a project, use the specified name.
+Save the collection with the specified name, rather than the default
+generic name "Saved at {time} by {username}@{host}".
""")
_group = upload_opts.add_mutually_exclusive_group()
STATE_PROPS = (arvados.ResumableCollectionWriter.STATE_PROPS +
['bytes_written', '_seen_inputs'])
- def __init__(self, cache=None, reporter=None, bytes_expected=None):
+ def __init__(self, cache=None, reporter=None, bytes_expected=None,
+ api_client=None):
self.bytes_written = 0
self._seen_inputs = []
self.cache = cache
self.reporter = reporter
self.bytes_expected = bytes_expected
- super(ArvPutCollectionWriter, self).__init__()
+ super(ArvPutCollectionWriter, self).__init__(api_client)
@classmethod
def from_cache(cls, cache, reporter=None, bytes_expected=None):
def check_project_exists(project_uuid):
try:
- arvados.api('v1').groups().get(uuid=project_uuid).execute()
+ api_client.groups().get(uuid=project_uuid).execute()
except (apiclient.errors.Error, arvados.errors.NotFoundError) as error:
raise ValueError("Project {} not found ({})".format(project_uuid,
error))
# to create the desired project link for this Collection, or None.
# Raises ValueError if the arguments request something impossible.
making_collection = not (args.raw or args.stream)
- any_link_spec = args.project_uuid or args.name
if not making_collection:
- if any_link_spec:
+ if args.name or args.project_uuid:
raise ValueError("Requested a Link without creating a Collection")
return None
- elif not any_link_spec:
- stderr.write(
- "arv-put: No --project-uuid or --name specified. This data will be cached\n"
- "in Keep. You will need to find this upload by its locator(s) later.\n")
- return None
- elif not args.project_uuid:
- raise ValueError("--name requires --project-uuid")
- elif not project_exists(args.project_uuid):
+ link = {'tail_uuid': args.project_uuid,
+ 'link_class': 'name',
+ 'name': args.name}
+ if not link['tail_uuid']:
+ link['tail_uuid'] = api_client.users().current().execute()['uuid']
+ elif not project_exists(link['tail_uuid']):
raise ValueError("Project {} not found".format(args.project_uuid))
- link = {'tail_uuid': args.project_uuid, 'link_class': 'name'}
- if args.name:
- link['name'] = args.name
+ if not link['name']:
+ link['name'] = "Saved at {} by {}@{}".format(
+ datetime.datetime.utcnow().strftime("%Y-%m-%d %H:%M:%S UTC"),
+ pwd.getpwuid(os.getuid()).pw_name,
+ socket.gethostname())
+ stderr.write(
+ "arv-put: No --name specified. Saving as \"%s\"\n" % link['name'])
+ link['owner_uuid'] = link['tail_uuid']
return link
def create_project_link(locator, link):
link['head_uuid'] = locator
- link.setdefault('name', "Collection saved by {}@{} at {}".format(
- pwd.getpwuid(os.getuid()).pw_name,
- socket.gethostname(),
- datetime.datetime.utcnow().strftime("%Y-%m-%d %H:%M:%S UTC")))
- return arvados.api('v1').links().create(body=link).execute()
+ return api_client.links().create(body=link).execute()
def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr):
+ global api_client
+ if api_client is None:
+ api_client = arvados.api('v1')
status = 0
args = parse_arguments(arguments)
if resume_cache is None:
writer = ArvPutCollectionWriter(resume_cache, reporter, bytes_expected)
else:
- resume_cache.restart()
writer = ArvPutCollectionWriter.from_cache(
resume_cache, reporter, bytes_expected)
output = ','.join(writer.data_locators())
else:
# Register the resulting collection in Arvados.
- collection = arvados.api().collections().create(
+ collection = api_client.collections().create(
body={
- 'uuid': writer.finish(),
'manifest_text': writer.manifest_text(),
+ 'owner_uuid': project_link['tail_uuid']
},
).execute()
- # Print the locator (uuid) of the new collection.
output = collection['uuid']
if project_link is not None:
+ # Update collection name
try:
- create_project_link(output, project_link)
+ if 'name' in collection:
+ arvados.api().collections().update(uuid=output,
+ body={"name": project_link["name"]}).execute()
+ else:
+ create_project_link(output, project_link)
except apiclient.errors.Error as error:
print >>stderr, (
"arv-put: Error adding Collection to project: {}.".format(
error))
status = 1
+ # Print the locator (uuid) of the new collection.
stdout.write(output)
if not output.endswith('\n'):
stdout.write('\n')