import argparse
import arvados
import base64
+import datetime
import errno
import fcntl
import hashlib
import json
import os
+import pwd
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)
+
+upload_opts.add_argument('paths', metavar='path', type=str, nargs='*',
+ help="""
+Local file or directory. Default: read from standard input.
+""")
+
+_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
+as a single stream in the manifest. If N=0, the manifest will contain
+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="""
+Synonym for --stream.
+""")
+
+_group.add_argument('--stream', action='store_true',
+ 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="""
+Synonym for --manifest.
+""")
+
+_group.add_argument('--in-manifest', action='store_true', dest='manifest',
+ help="""
+Synonym for --manifest.
+""")
+
+_group.add_argument('--manifest', action='store_true',
+ 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="""
+Synonym for --raw.
+""")
+
+_group.add_argument('--raw', action='store_true',
+ 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="""
+Synonym for --filename.
+""")
+
+upload_opts.add_argument('--filename', type=str, default=None,
+ 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
+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.
+""")
+
+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)
+
+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="""
+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="""
+Do not display human-readable progress on stderr, even if stderr is a
+tty.
+""")
+
+_group.add_argument('--batch-progress', action='store_true',
+ 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="""
+Continue interrupted uploads from cached state (default).
+""")
+_group.add_argument('--no-resume', action='store_false', dest='resume',
+ help="""
+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, arv_cmd.retry_opt])
def parse_arguments(arguments):
- parser = argparse.ArgumentParser(
- description='Copy data from the local filesystem to Keep.')
-
- parser.add_argument('paths', metavar='path', type=str, nargs='*',
- help="""
- Local file or directory. Default: read from standard input.
- """)
-
- parser.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
- as a single stream in the manifest. If N=0, the manifest will contain
- a single stream. Default: -1 (unlimited), i.e., exactly one manifest
- stream per filesystem directory that contains files.
- """)
-
- group = parser.add_mutually_exclusive_group()
-
- group.add_argument('--as-stream', action='store_true', dest='stream',
- help="""
- Synonym for --stream.
- """)
-
- group.add_argument('--stream', action='store_true',
- 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="""
- Synonym for --manifest.
- """)
-
- group.add_argument('--in-manifest', action='store_true', dest='manifest',
- help="""
- Synonym for --manifest.
- """)
-
- group.add_argument('--manifest', action='store_true',
- 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="""
- Synonym for --raw.
- """)
-
- group.add_argument('--raw', action='store_true',
- 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.
- """)
-
- parser.add_argument('--use-filename', type=str, default=None,
- dest='filename', help="""
- Synonym for --filename.
- """)
-
- parser.add_argument('--filename', type=str, default=None,
- 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
- it is not a directory. Implies --manifest.
- """)
-
- group = parser.add_mutually_exclusive_group()
- group.add_argument('--progress', action='store_true',
- 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="""
- Do not display human-readable progress on stderr, even if stderr is a
- tty.
- """)
-
- group.add_argument('--batch-progress', action='store_true',
- help="""
- Display machine-readable progress on stderr (bytes and, if known,
- total data size).
- """)
-
- group = parser.add_mutually_exclusive_group()
- group.add_argument('--resume', action='store_true', default=True,
- help="""
- Continue interrupted uploads from cached state (default).
- """)
- group.add_argument('--no-resume', action='store_false', dest='resume',
- help="""
- Do not continue interrupted uploads from cached state.
- """)
-
- args = parser.parse_args(arguments)
+ args = arg_parser.parse_args(arguments)
if len(args.paths) == 0:
args.paths += ['/dev/stdin']
if len(args.paths) != 1 or os.path.isdir(args.paths[0]):
if args.filename:
- parser.error("""
+ arg_parser.error("""
--filename argument cannot be used when storing a directory or
multiple files.
""")
class ResumeCache(object):
- CACHE_DIR = os.path.expanduser('~/.cache/arvados/arv-put')
-
- @classmethod
- def setup_user_cache(cls):
- try:
- os.makedirs(cls.CACHE_DIR)
- except OSError as error:
- if error.errno != errno.EEXIST:
- raise
- else:
- os.chmod(cls.CACHE_DIR, 0o700)
+ CACHE_DIR = '.cache/arvados/arv-put'
def __init__(self, file_spec):
self.cache_file = open(file_spec, 'a+')
md5 = hashlib.md5()
md5.update(arvados.config.get('ARVADOS_API_HOST', '!nohost'))
realpaths = sorted(os.path.realpath(path) for path in args.paths)
- md5.update(''.join(realpaths))
+ md5.update('\0'.join(realpaths))
if any(os.path.isdir(path) for path in realpaths):
md5.update(str(max(args.max_manifest_depth, -1)))
elif args.filename:
md5.update(args.filename)
- return os.path.join(cls.CACHE_DIR, md5.hexdigest())
+ return os.path.join(
+ arv_cmd.make_home_conf_dir(cls.CACHE_DIR, 0o700, 'raise'),
+ md5.hexdigest())
def _lock_file(self, fileobj):
try:
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, **kwargs):
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__(**kwargs)
@classmethod
- def from_cache(cls, cache, reporter=None, bytes_expected=None):
+ def from_cache(cls, cache, reporter=None, bytes_expected=None,
+ 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)
+ writer = cls.from_state(state, cache, reporter, bytes_expected,
+ num_retries=num_retries,
+ replication=replication)
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
outfile.write(progress_func(bytes_written, bytes_expected))
return write_progress
-def main(arguments=None):
- ResumeCache.setup_user_cache()
+def exit_signal_handler(sigcode, frame):
+ sys.exit(-sigcode)
+
+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:
+ 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
+
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())
+
+ if args.project_uuid and (args.stream or args.raw):
+ print >>stderr, "Cannot use --project-uuid with --stream or --raw"
+ sys.exit(1)
+
+ # Determine the parent project
+ try:
+ 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)
+
+ # 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)
reporter = progress_writer(machine_progress)
else:
reporter = None
+ bytes_expected = expected_bytes_for(args.paths)
- try:
- resume_cache = ResumeCache(ResumeCache.make_path(args))
- if not args.resume:
- resume_cache.restart()
- except ResumeCacheConflict:
- print "arv-put: Another process is already uploading this data."
- sys.exit(1)
-
- writer = ArvPutCollectionWriter.from_cache(
- resume_cache, reporter, expected_bytes_for(args.paths))
+ resume_cache = None
+ if args.resume:
+ try:
+ resume_cache = ResumeCache(ResumeCache.make_path(args))
+ except (IOError, OSError, ValueError):
+ pass # Couldn't open cache directory/file. Continue without it.
+ except ResumeCacheConflict:
+ print >>stderr, "\n".join([
+ "arv-put: Another process is already uploading this data.",
+ " Use --no-resume if this is really what you want."])
+ sys.exit(1)
+
+ if resume_cache is None:
+ 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,
+ replication=write_copies)
- def signal_handler(sigcode, frame):
- writer.cache_state()
- sys.exit(-sigcode)
# Install our signal handler for each code in CAUGHT_SIGNALS, and save
# the originals.
- orig_signal_handlers = {sigcode: signal.signal(sigcode, signal_handler)
+ orig_signal_handlers = {sigcode: signal.signal(sigcode, exit_signal_handler)
for sigcode in CAUGHT_SIGNALS}
if writer.bytes_written > 0: # We're resuming a previous upload.
- print >>sys.stderr, "arv-put: Resuming previous upload. Bypass with the --no-resume option."
- writer.report_progress()
+ print >>stderr, "\n".join([
+ "arv-put: Resuming previous upload from last checkpoint.",
+ " Use the --no-resume option to start over."])
- try:
- writer.do_queued_work() # Do work resumed from cache.
- for path in args.paths: # Copy file data to Keep.
- if os.path.isdir(path):
- writer.write_directory_tree(
- path, max_manifest_depth=args.max_manifest_depth)
- else:
- writer.start_new_stream()
- writer.write_file(path, args.filename or os.path.basename(path))
- except Exception:
- writer.cache_state()
- raise
+ writer.report_progress()
+ writer.do_queued_work() # Do work resumed from cache.
+ for path in args.paths: # Copy file data to Keep.
+ if os.path.isdir(path):
+ writer.write_directory_tree(
+ path, max_manifest_depth=args.max_manifest_depth)
+ else:
+ writer.start_new_stream()
+ writer.write_file(path, args.filename or os.path.basename(path))
+ writer.finish_current_stream()
+
+ if args.progress: # Print newline to split stderr from stdout for humans.
+ print >>stderr
if args.stream:
- print writer.manifest_text(),
+ output = writer.manifest_text()
+ if args.normalize:
+ output = CollectionReader(output).manifest_text(normalize=True)
elif args.raw:
- writer.finish_current_stream()
- print ','.join(writer.data_locators())
+ output = ','.join(writer.data_locators())
else:
- # Register the resulting collection in Arvados.
- arvados.api().collections().create(
- body={
- 'uuid': writer.finish(),
- 'manifest_text': writer.manifest_text(),
- },
- ).execute()
+ try:
+ manifest_text = writer.manifest_text()
+ if args.normalize:
+ 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,
+ replication_attr: args.replication,
+ },
+ 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.
- print writer.finish()
+ # Print the locator (uuid) of the new collection.
+ stdout.write(output)
+ if not output.endswith('\n'):
+ stdout.write('\n')
for sigcode, orig_handler in orig_signal_handlers.items():
signal.signal(sigcode, orig_handler)
- resume_cache.destroy()
+ if status != 0:
+ sys.exit(status)
+
+ if resume_cache is not None:
+ resume_cache.destroy()
+
+ return output
if __name__ == '__main__':
main()
projects / arvados.git / blobdiff