X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/a3222e35cda68c8e48a17921c33ac37ecb5c3bac..66c13b6055a363cb08197b8c5d040ed9a511c8ca:/sdk/python/arvados/commands/put.py diff --git a/sdk/python/arvados/commands/put.py b/sdk/python/arvados/commands/put.py index 335ef174de..4a926c701c 100644 --- a/sdk/python/arvados/commands/put.py +++ b/sdk/python/arvados/commands/put.py @@ -3,7 +3,6 @@ # TODO: # --md5sum - display md5 of each file as read from disk -import apiclient.errors import argparse import arvados import base64 @@ -18,10 +17,12 @@ import signal import socket import sys import tempfile +from apiclient import errors as apiclient_errors 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) @@ -39,16 +40,6 @@ a single stream. Default: -1 (unlimited), i.e., exactly one manifest stream per filesystem directory that contains files. """) -upload_opts.add_argument('--project-uuid', metavar='UUID', help=""" -Store the collection in the specified project, instead of your Home -project. -""") - -upload_opts.add_argument('--name', help=""" -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() _group.add_argument('--as-stream', action='store_true', dest='stream', @@ -105,7 +96,23 @@ input file. It can be used only if there is exactly one path given and it is not a directory. Implies --manifest. """) +upload_opts.add_argument('--portable-data-hash', action='store_true', + help=""" +Print the portable data hash instead of the Arvados UUID for the collection +created by the upload. +""") + run_opts = argparse.ArgumentParser(add_help=False) + +run_opts.add_argument('--project-uuid', metavar='UUID', help=""" +Store the collection in the specified project, instead of your Home +project. +""") + +run_opts.add_argument('--name', help=""" +Save the collection with the specified name. +""") + _group = run_opts.add_mutually_exclusive_group() _group.add_argument('--progress', action='store_true', help=""" @@ -138,7 +145,7 @@ Do not continue interrupted uploads from cached state. arg_parser = argparse.ArgumentParser( description='Copy data from the local filesystem to Keep.', - parents=[upload_opts, run_opts]) + parents=[upload_opts, run_opts, arv_cmd.retry_opt]) def parse_arguments(arguments): args = arg_parser.parse_args(arguments) @@ -238,23 +245,27 @@ class ArvPutCollectionWriter(arvados.ResumableCollectionWriter): 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, num_retries=0): 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, num_retries=num_retries) @classmethod - def from_cache(cls, cache, reporter=None, bytes_expected=None): + def from_cache(cls, cache, reporter=None, bytes_expected=None, + num_retries=0): try: state = cache.load() state['_data_buffer'] = [base64.decodestring(state['_data_buffer'])] - writer = cls.from_state(state, cache, reporter, bytes_expected) + writer = cls.from_state(state, cache, reporter, bytes_expected, + num_retries=num_retries) except (TypeError, ValueError, arvados.errors.StaleWriterStateError) as error: - return cls(cache, reporter, bytes_expected) + return cls(cache, reporter, bytes_expected, num_retries=num_retries) else: return writer @@ -340,54 +351,48 @@ def progress_writer(progress_func, outfile=sys.stderr): def exit_signal_handler(sigcode, frame): sys.exit(-sigcode) -def check_project_exists(project_uuid): - try: - arvados.api('v1').groups().get(uuid=project_uuid).execute() - except (apiclient.errors.Error, arvados.errors.NotFoundError) as error: - raise ValueError("Project {} not found ({})".format(project_uuid, - error)) +def desired_project_uuid(api_client, project_uuid, num_retries): + if not project_uuid: + query = api_client.users().current() + elif arvados.util.user_uuid_pattern.match(project_uuid): + query = api_client.users().get(uuid=project_uuid) + elif arvados.util.group_uuid_pattern.match(project_uuid): + query = api_client.groups().get(uuid=project_uuid) else: - return True + raise ValueError("Not a valid project UUID: {}".format(project_uuid)) + return query.execute(num_retries=num_retries)['uuid'] + +def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr): + global api_client -def prep_project_link(args, stderr, project_exists=check_project_exists): - # Given the user's command line arguments, return a dictionary with data - # 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) - if not making_collection: - if args.name or args.project_uuid: - raise ValueError("Requested a Link without creating a Collection") - return None - link = {'tail_uuid': args.project_uuid, - 'link_class': 'name', - 'name': args.name} - if not link['tail_uuid']: - link['tail_uuid'] = arvados.api('v1').users().current().execute()['uuid'] - elif not project_exists(link['tail_uuid']): - raise ValueError("Project {} not found".format(args.project_uuid)) - if not link['name']: - link['name'] = "Saved at {} by {}@{}".format( + args = parse_arguments(arguments) + status = 0 + if api_client is None: + api_client = arvados.api('v1') + + # Determine the name to use + if args.name: + if args.stream or args.raw: + print >>stderr, "Cannot use --name with --stream or --raw" + sys.exit(1) + collection_name = args.name + else: + collection_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 - return arvados.api('v1').links().create(body=link).execute() -def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr): - status = 0 + if args.project_uuid and (args.stream or args.raw): + print >>stderr, "Cannot use --project-uuid with --stream or --raw" + sys.exit(1) - args = parse_arguments(arguments) + # Determine the parent project try: - project_link = prep_project_link(args, stderr) - except ValueError as error: - print >>stderr, "arv-put: {}.".format(error) - sys.exit(2) + project_uuid = desired_project_uuid(api_client, args.project_uuid, + args.retries) + except (apiclient_errors.Error, ValueError) as error: + print >>stderr, error + sys.exit(1) if args.progress: reporter = progress_writer(human_progress) @@ -410,10 +415,11 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr): sys.exit(1) if resume_cache is None: - writer = ArvPutCollectionWriter(resume_cache, reporter, bytes_expected) + writer = ArvPutCollectionWriter(resume_cache, reporter, bytes_expected, + num_retries=args.retries) else: writer = ArvPutCollectionWriter.from_cache( - resume_cache, reporter, bytes_expected) + resume_cache, reporter, bytes_expected, num_retries=args.retries) # Install our signal handler for each code in CAUGHT_SIGNALS, and save # the originals. @@ -444,24 +450,31 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr): elif args.raw: output = ','.join(writer.data_locators()) else: - # Register the resulting collection in Arvados. - collection = arvados.api().collections().create( - body={ - 'manifest_text': writer.manifest_text(), - }, - ).execute() - - # Print the locator (uuid) of the new collection. - output = collection['uuid'] - if project_link is not None: - try: - 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 - + try: + # Register the resulting collection in Arvados. + collection = api_client.collections().create( + body={ + 'owner_uuid': project_uuid, + 'name': collection_name, + 'manifest_text': writer.manifest_text() + }, + ensure_unique_name=True + ).execute(num_retries=args.retries) + + print >>stderr, "Collection saved as '%s'" % collection['name'] + + if args.portable_data_hash and 'portable_data_hash' in collection and collection['portable_data_hash']: + output = collection['portable_data_hash'] + else: + output = collection['uuid'] + + except apiclient_errors.Error as error: + print >>stderr, ( + "arv-put: Error creating Collection on project: {}.".format( + error)) + status = 1 + + # Print the locator (uuid) of the new collection. stdout.write(output) if not output.endswith('\n'): stdout.write('\n')