X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/2b6948ff7e11cd236ea26562ed76a534dcf3c0be..20abd5d545f9f1102bcd28ee4cab7a2453e28cb4:/sdk/python/arvados/commands/put.py diff --git a/sdk/python/arvados/commands/put.py b/sdk/python/arvados/commands/put.py index ac81ab8ddb..f556e7ecb5 100644 --- a/sdk/python/arvados/commands/put.py +++ b/sdk/python/arvados/commands/put.py @@ -27,11 +27,13 @@ api_client = None upload_opts = argparse.ArgumentParser(add_help=False) upload_opts.add_argument('paths', metavar='path', type=str, nargs='*', - help=""" + help=""" Local file or directory. Default: read from standard input. """) -upload_opts.add_argument('--max-manifest-depth', type=int, metavar='N', +_group = upload_opts.add_mutually_exclusive_group() + +_group.add_argument('--max-manifest-depth', type=int, metavar='N', default=-1, help=""" Maximum depth of directory tree to represent in the manifest structure. A directory structure deeper than this will be represented @@ -40,56 +42,62 @@ a single stream. Default: -1 (unlimited), i.e., exactly one manifest stream per filesystem directory that contains files. """) +_group.add_argument('--normalize', action='store_true', + help=""" +Normalize the manifest by re-ordering files and streams after writing +data. +""") + _group = upload_opts.add_mutually_exclusive_group() _group.add_argument('--as-stream', action='store_true', dest='stream', - help=""" + help=""" Synonym for --stream. """) _group.add_argument('--stream', action='store_true', - help=""" + help=""" Store the file content and display the resulting manifest on stdout. Do not write the manifest to Keep or save a Collection object in Arvados. """) _group.add_argument('--as-manifest', action='store_true', dest='manifest', - help=""" + help=""" Synonym for --manifest. """) _group.add_argument('--in-manifest', action='store_true', dest='manifest', - help=""" + help=""" Synonym for --manifest. """) _group.add_argument('--manifest', action='store_true', - help=""" + help=""" Store the file data and resulting manifest in Keep, save a Collection object in Arvados, and display the manifest locator (Collection uuid) on stdout. This is the default behavior. """) _group.add_argument('--as-raw', action='store_true', dest='raw', - help=""" + help=""" Synonym for --raw. """) _group.add_argument('--raw', action='store_true', - help=""" + help=""" Store the file content and display the data block locators on stdout, separated by commas, with a trailing newline. Do not store a manifest. """) upload_opts.add_argument('--use-filename', type=str, default=None, - dest='filename', help=""" + dest='filename', help=""" Synonym for --filename. """) upload_opts.add_argument('--filename', type=str, default=None, - help=""" + help=""" Use the given filename in the manifest, instead of the name of the local file. This is useful when "-" or "/dev/stdin" is given as an input file. It can be used only if there is exactly one path given and @@ -97,15 +105,16 @@ it is not a directory. Implies --manifest. """) upload_opts.add_argument('--portable-data-hash', action='store_true', - help=""" + help=""" Print the portable data hash instead of the Arvados UUID for the collection created by the upload. """) -upload_opts.add_argument('--normalize', action='store_true', - help=""" -Normalize the manifest by re-ordering files and streams after writing -data. This makes the --max-manifest-depth option ineffective. +upload_opts.add_argument('--replication', type=int, metavar='N', default=None, + help=""" +Set the replication level for the new collection: how many different +physical storage devices (e.g., disks) should have a copy of each data +block. Default is to use the server-provided default (if any) or 2. """) run_opts = argparse.ArgumentParser(add_help=False) @@ -121,31 +130,31 @@ Save the collection with the specified name. _group = run_opts.add_mutually_exclusive_group() _group.add_argument('--progress', action='store_true', - help=""" + help=""" Display human-readable progress on stderr (bytes and, if possible, percentage of total data size). This is the default behavior when stderr is a tty. """) _group.add_argument('--no-progress', action='store_true', - help=""" + help=""" Do not display human-readable progress on stderr, even if stderr is a tty. """) _group.add_argument('--batch-progress', action='store_true', - help=""" + help=""" Display machine-readable progress on stderr (bytes and, if known, total data size). """) _group = run_opts.add_mutually_exclusive_group() _group.add_argument('--resume', action='store_true', default=True, - help=""" + help=""" Continue interrupted uploads from cached state (default). """) _group.add_argument('--no-resume', action='store_false', dest='resume', - help=""" + help=""" Do not continue interrupted uploads from cached state. """) @@ -251,24 +260,23 @@ class ArvPutCollectionWriter(arvados.ResumableCollectionWriter): STATE_PROPS = (arvados.ResumableCollectionWriter.STATE_PROPS + ['bytes_written', '_seen_inputs']) - def __init__(self, cache=None, reporter=None, bytes_expected=None, - api_client=None, num_retries=0): + def __init__(self, cache=None, reporter=None, bytes_expected=None, **kwargs): self.bytes_written = 0 self._seen_inputs = [] self.cache = cache self.reporter = reporter self.bytes_expected = bytes_expected - super(ArvPutCollectionWriter, self).__init__( - api_client, num_retries=num_retries) + super(ArvPutCollectionWriter, self).__init__(**kwargs) @classmethod def from_cache(cls, cache, reporter=None, bytes_expected=None, - num_retries=0): + num_retries=0, replication=0): try: state = cache.load() state['_data_buffer'] = [base64.decodestring(state['_data_buffer'])] writer = cls.from_state(state, cache, reporter, bytes_expected, - num_retries=num_retries) + num_retries=num_retries, + replication=replication) except (TypeError, ValueError, arvados.errors.StaleWriterStateError) as error: return cls(cache, reporter, bytes_expected, num_retries=num_retries) @@ -400,6 +408,19 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr): print >>stderr, error sys.exit(1) + # write_copies diverges from args.replication here. + # args.replication is how many copies we will instruct Arvados to + # maintain (by passing it in collections().create()) after all + # data is written -- and if None was given, we'll use None there. + # Meanwhile, write_copies is how many copies of each data block we + # write to Keep, which has to be a number. + # + # If we simply changed args.replication from None to a default + # here, we'd end up erroneously passing the default replication + # level (instead of None) to collections().create(). + write_copies = (args.replication or + api_client._rootDesc.get('defaultCollectionReplication', 2)) + if args.progress: reporter = progress_writer(human_progress) elif args.batch_progress: @@ -421,11 +442,15 @@ 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, - num_retries=args.retries) + writer = ArvPutCollectionWriter( + resume_cache, reporter, bytes_expected, + num_retries=args.retries, + replication=write_copies) else: writer = ArvPutCollectionWriter.from_cache( - resume_cache, reporter, bytes_expected, num_retries=args.retries) + resume_cache, reporter, bytes_expected, + num_retries=args.retries, + replication=write_copies) # Install our signal handler for each code in CAUGHT_SIGNALS, and save # the originals. @@ -454,20 +479,25 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr): if args.stream: output = writer.manifest_text() if args.normalize: - output = CollectionReader(output).normalize().manifest_text() + output = CollectionReader(output).manifest_text(normalize=True) elif args.raw: output = ','.join(writer.data_locators()) else: try: manifest_text = writer.manifest_text() if args.normalize: - manifest_text = CollectionReader(manifest_text).normalize().manifest_text() + manifest_text = CollectionReader(manifest_text).manifest_text(normalize=True) + replication_attr = 'replication_desired' + if api_client._schema.schemas['Collection']['properties'].get(replication_attr, None) is None: + # API called it 'redundancy' before #3410. + replication_attr = 'redundancy' # Register the resulting collection in Arvados. collection = api_client.collections().create( body={ 'owner_uuid': project_uuid, 'name': collection_name, - 'manifest_text': manifest_text + 'manifest_text': manifest_text, + replication_attr: args.replication, }, ensure_unique_name=True ).execute(num_retries=args.retries)