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).
- """)
-
- 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')
+ CACHE_DIR = '.cache/arvados/arv-put'
def __init__(self, file_spec):
- try:
- self.cache_file = open(file_spec, 'a+')
- except TypeError:
- file_spec = self.make_path(file_spec)
- self.cache_file = open(file_spec, 'a+')
+ self.cache_file = open(file_spec, 'a+')
self._lock_file(self.cache_file)
self.filename = self.cache_file.name
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:
raise
self.close()
+ def restart(self):
+ self.destroy()
+ self.__init__(self.filename)
-class CollectionWriterWithProgress(arvados.CollectionWriter):
- def flush_data(self, *args, **kwargs):
- if not getattr(self, 'display_type', None):
- return
- if not hasattr(self, 'bytes_flushed'):
- self.bytes_flushed = 0
- self.bytes_flushed += self._data_buffer_len
- super(CollectionWriterWithProgress, self).flush_data(*args, **kwargs)
- self.bytes_flushed -= self._data_buffer_len
- if self.display_type == 'machine':
- sys.stderr.write('%s %d: %d written %d total\n' %
- (sys.argv[0],
- os.getpid(),
- self.bytes_flushed,
- getattr(self, 'bytes_expected', -1)))
- elif getattr(self, 'bytes_expected', 0) > 0:
- pct = 100.0 * self.bytes_flushed / self.bytes_expected
- sys.stderr.write('\r%dM / %dM %.1f%% ' %
- (self.bytes_flushed >> 20,
- self.bytes_expected >> 20, pct))
- else:
- sys.stderr.write('\r%d ' % self.bytes_flushed)
-
- def manifest_text(self, *args, **kwargs):
- manifest_text = (super(CollectionWriterWithProgress, self)
- .manifest_text(*args, **kwargs))
- if getattr(self, 'display_type', None):
- if self.display_type == 'human':
- sys.stderr.write('\n')
- self.display_type = None
- return manifest_text
+class ArvPutCollectionWriter(arvados.ResumableCollectionWriter):
+ STATE_PROPS = (arvados.ResumableCollectionWriter.STATE_PROPS +
+ ['bytes_written', '_seen_inputs'])
-def main(arguments=None):
- args = parse_arguments(arguments)
+ 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__(**kwargs)
- if args.progress:
- writer = CollectionWriterWithProgress()
- writer.display_type = 'human'
- elif args.batch_progress:
- writer = CollectionWriterWithProgress()
- writer.display_type = 'machine'
- else:
- writer = arvados.CollectionWriter()
+ @classmethod
+ 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,
+ num_retries=num_retries,
+ replication=replication)
+ except (TypeError, ValueError,
+ arvados.errors.StaleWriterStateError) as error:
+ return cls(cache, reporter, bytes_expected, num_retries=num_retries)
+ else:
+ return writer
+ def cache_state(self):
+ if self.cache is None:
+ return
+ state = self.dump_state()
+ # Transform attributes for serialization.
+ for attr, value in state.items():
+ if attr == '_data_buffer':
+ state[attr] = base64.encodestring(''.join(value))
+ elif hasattr(value, 'popleft'):
+ state[attr] = list(value)
+ self.cache.save(state)
+
+ def report_progress(self):
+ if self.reporter is not None:
+ self.reporter(self.bytes_written, self.bytes_expected)
+
+ def flush_data(self):
+ start_buffer_len = self._data_buffer_len
+ start_block_count = self.bytes_written / self.KEEP_BLOCK_SIZE
+ super(ArvPutCollectionWriter, self).flush_data()
+ if self._data_buffer_len < start_buffer_len: # We actually PUT data.
+ self.bytes_written += (start_buffer_len - self._data_buffer_len)
+ self.report_progress()
+ if (self.bytes_written / self.KEEP_BLOCK_SIZE) > start_block_count:
+ self.cache_state()
+
+ def _record_new_input(self, input_type, source_name, dest_name):
+ # The key needs to be a list because that's what we'll get back
+ # from JSON deserialization.
+ key = [input_type, source_name, dest_name]
+ if key in self._seen_inputs:
+ return False
+ self._seen_inputs.append(key)
+ return True
+
+ def write_file(self, source, filename=None):
+ if self._record_new_input('file', source, filename):
+ super(ArvPutCollectionWriter, self).write_file(source, filename)
+
+ def write_directory_tree(self,
+ path, stream_name='.', max_manifest_depth=-1):
+ if self._record_new_input('directory', path, stream_name):
+ super(ArvPutCollectionWriter, self).write_directory_tree(
+ path, stream_name, max_manifest_depth)
+
+
+def expected_bytes_for(pathlist):
# Walk the given directory trees and stat files, adding up file sizes,
# so we can display progress as percent
- writer.bytes_expected = 0
- for path in args.paths:
+ bytesum = 0
+ for path in pathlist:
if os.path.isdir(path):
for filename in arvados.util.listdir_recursive(path):
- writer.bytes_expected += os.path.getsize(
- os.path.join(path, filename))
+ bytesum += os.path.getsize(os.path.join(path, filename))
elif not os.path.isfile(path):
- del writer.bytes_expected
- break
+ return None
else:
- writer.bytes_expected += os.path.getsize(path)
+ bytesum += os.path.getsize(path)
+ return bytesum
+
+_machine_format = "{} {}: {{}} written {{}} total\n".format(sys.argv[0],
+ os.getpid())
+def machine_progress(bytes_written, bytes_expected):
+ return _machine_format.format(
+ bytes_written, -1 if (bytes_expected is None) else bytes_expected)
+
+def human_progress(bytes_written, bytes_expected):
+ if bytes_expected:
+ return "\r{}M / {}M {:.1%} ".format(
+ bytes_written >> 20, bytes_expected >> 20,
+ float(bytes_written) / bytes_expected)
+ else:
+ return "\r{} ".format(bytes_written)
+
+def progress_writer(progress_func, outfile=sys.stderr):
+ def write_progress(bytes_written, bytes_expected):
+ outfile.write(progress_func(bytes_written, bytes_expected))
+ return write_progress
+
+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)
+ elif args.batch_progress:
+ reporter = progress_writer(machine_progress)
+ else:
+ reporter = None
+ bytes_expected = expected_bytes_for(args.paths)
- # Copy file data to Keep.
- for path in 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)
+
+ # Install our signal handler for each code in CAUGHT_SIGNALS, and save
+ # the originals.
+ 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 >>stderr, "\n".join([
+ "arv-put: Resuming previous upload from last checkpoint.",
+ " Use the --no-resume option to start over."])
+
+ 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()
-
- # Print the locator (uuid) of the new collection.
- print writer.finish()
+ 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.
+ 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)
+
+ if status != 0:
+ sys.exit(status)
+
+ if resume_cache is not None:
+ resume_cache.destroy()
+
+ return output
if __name__ == '__main__':
main()