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="""
+ 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
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
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="""
+ 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.
""")
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)
class ResumeCache(object):
CACHE_DIR = '.cache/arvados/arv-put'
- @classmethod
- def setup_user_cache(cls):
- return arv_cmd.make_home_conf_dir(cls.CACHE_DIR, 0o700)
-
def __init__(self, file_spec):
self.cache_file = open(file_spec, 'a+')
self._lock_file(self.cache_file)
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
def exit_signal_handler(sigcode, frame):
sys.exit(-sigcode)
-def main(arguments=None, output_to=sys.stdout):
+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)
bytes_expected = expected_bytes_for(args.paths)
resume_cache = None
- try:
- if ResumeCache.setup_user_cache() is not None:
+ if args.resume:
+ try:
resume_cache = ResumeCache(ResumeCache.make_path(args))
- except (IOError, OSError):
- pass # Couldn't open cache directory/file. Continue without it.
- except ResumeCacheConflict:
- output_to.write(
- "arv-put: Another process is already uploading this data.\n")
- sys.exit(1)
+ 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)
+ writer = ArvPutCollectionWriter(
+ resume_cache, reporter, bytes_expected,
+ num_retries=args.retries,
+ replication=write_copies)
else:
- if not args.resume:
- resume_cache.restart()
writer = ArvPutCollectionWriter.from_cache(
- resume_cache, reporter, bytes_expected)
+ 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.
for sigcode in CAUGHT_SIGNALS}
if writer.bytes_written > 0: # We're resuming a previous upload.
- print >>sys.stderr, "\n".join([
+ print >>stderr, "\n".join([
"arv-put: Resuming previous upload from last checkpoint.",
" Use the --no-resume option to start over."])
- writer.report_progress()
+ 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.finish_current_stream()
if args.progress: # Print newline to split stderr from stdout for humans.
- print >>sys.stderr
+ print >>stderr
if args.stream:
output = writer.manifest_text()
+ if args.normalize:
+ output = CollectionReader(output).manifest_text(normalize=True)
elif args.raw:
output = ','.join(writer.data_locators())
else:
- # Register the resulting collection in Arvados.
- collection = arvados.api().collections().create(
- body={
- 'uuid': writer.finish(),
- 'manifest_text': writer.manifest_text(),
- },
- ).execute()
-
- # Print the locator (uuid) of the new collection.
- output = collection['uuid']
-
- output_to.write(output)
+ 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'):
- output_to.write('\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()
projects / arvados.git / blobdiff