-#!/usr/bin/env python
+#!/usr/bin/env python3
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
import argparse
import hashlib
import arvados
import arvados.commands._util as arv_cmd
+import arvados.util as util
from arvados._version import __version__
-api_client = None
logger = logging.getLogger('arvados.arv-get')
parser = argparse.ArgumentParser(
refuse to write *anything* if any of the output files already
exist. As a special case, -f is not needed to write to stdout.
""")
+group.add_argument('-v', action='count', default=0,
+ help="""
+Once for verbose mode, twice for debug mode.
+""")
group.add_argument('--skip-existing', action='store_true',
help="""
Skip files that already exist. The default behavior is to refuse to
overwritten. This option causes even devices, sockets, and fifos to be
skipped.
""")
+group.add_argument('--strip-manifest', action='store_true', default=False,
+ help="""
+When getting a collection manifest, strip its access tokens before writing
+it.
+""")
+
+parser.add_argument('--threads', type=int, metavar='N', default=4,
+ help="""
+Set the number of download threads to be used. Take into account that
+using lots of threads will increase the RAM requirements. Default is
+to use 4 threads.
+On high latency installations, using a greater number will improve
+overall throughput.
+""")
def parse_arguments(arguments, stdout, stderr):
args = parser.parse_args(arguments)
return args
def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr):
- global api_client
-
+ if stdout is sys.stdout and hasattr(stdout, 'buffer'):
+ # in Python 3, write to stdout as binary
+ stdout = stdout.buffer
+
args = parse_arguments(arguments, stdout, stderr)
- if api_client is None:
- api_client = arvados.api('v1')
+ logger.setLevel(logging.WARNING - 10 * args.v)
+
+ request_id = arvados.util.new_request_id()
+ logger.info('X-Request-Id: '+request_id)
+
+ api_client = arvados.api('v1', request_id=request_id)
r = re.search(r'^(.*?)(/.*)?$', args.locator)
- collection = r.group(1)
+ col_loc = r.group(1)
get_prefix = r.group(2)
if args.r and not get_prefix:
get_prefix = os.sep
- reader = arvados.CollectionReader(collection, num_retries=args.retries)
+ # User asked to download the collection's manifest
if not get_prefix:
if not args.n:
open_flags = os.O_CREAT | os.O_WRONLY
open_flags |= os.O_EXCL
try:
if args.destination == "-":
- stdout.write(reader.manifest_text())
+ write_block_or_manifest(
+ dest=stdout, src=col_loc,
+ api_client=api_client, args=args)
else:
out_fd = os.open(args.destination, open_flags)
with os.fdopen(out_fd, 'wb') as out_file:
- out_file.write(reader.manifest_text())
+ write_block_or_manifest(
+ dest=out_file, src=col_loc,
+ api_client=api_client, args=args)
except (IOError, OSError) as error:
logger.error("can't write to '{}': {}".format(args.destination, error))
return 1
except (arvados.errors.ApiError, arvados.errors.KeepReadError) as error:
- logger.error("failed to download '{}': {}".format(collection, error))
+ logger.error("failed to download '{}': {}".format(col_loc, error))
return 1
+ except arvados.errors.ArgumentError as error:
+ if 'Argument to CollectionReader' in str(error):
+ logger.error("error reading collection: {}".format(error))
+ return 1
+ else:
+ raise
return 0
+ try:
+ reader = arvados.CollectionReader(
+ col_loc, api_client=api_client, num_retries=args.retries,
+ keep_client=arvados.keep.KeepClient(block_cache=arvados.keep.KeepBlockCache((args.threads+1)*64 * 1024 * 1024)),
+ get_threads=args.threads)
+ except Exception as error:
+ logger.error("failed to read collection: {}".format(error))
+ return 1
+
# Scan the collection. Make an array of (stream, file, local
# destination filename) tuples, and add up total size to extract.
todo = []
todo_bytes = 0
try:
- for s, f in files_in_collection(reader):
- if get_prefix and get_prefix[-1] == os.sep:
- if 0 != string.find(os.path.join(s.stream_name(), f.name),
- '.' + get_prefix):
- continue
- if args.destination == "-":
- dest_path = "-"
- else:
- dest_path = os.path.join(
- args.destination,
- os.path.join(s.stream_name(), f.name)[len(get_prefix)+1:])
- if (not (args.n or args.f or args.skip_existing) and
- os.path.exists(dest_path)):
- logger.error('Local file %s already exists.' % (dest_path,))
- return 1
- else:
- if os.path.join(s.stream_name(), f.name) != '.' + get_prefix:
- continue
- dest_path = args.destination
- todo += [(s, f, dest_path)]
- todo_bytes += f.size()
- except arvados.errors.NotFoundError as e:
+ if get_prefix == os.sep:
+ item = reader
+ else:
+ item = reader.find('.' + get_prefix)
+
+ if isinstance(item, arvados.collection.Subcollection) or isinstance(item, arvados.collection.CollectionReader):
+ # If the user asked for a file and we got a subcollection, error out.
+ if get_prefix[-1] != os.sep:
+ logger.error("requested file '{}' is in fact a subcollection. Append a trailing '/' to download it.".format('.' + get_prefix))
+ return 1
+ # If the user asked stdout as a destination, error out.
+ elif args.destination == '-':
+ logger.error("cannot use 'stdout' as destination when downloading multiple files.")
+ return 1
+ # User asked for a subcollection, and that's what was found. Add up total size
+ # to download.
+ for s, f in files_in_collection(item):
+ dest_path = os.path.join(
+ args.destination,
+ os.path.join(s.stream_name(), f.name)[len(get_prefix)+1:])
+ if (not (args.n or args.f or args.skip_existing) and
+ os.path.exists(dest_path)):
+ logger.error('Local file %s already exists.' % (dest_path,))
+ return 1
+ todo += [(s, f, dest_path)]
+ todo_bytes += f.size()
+ elif isinstance(item, arvados.arvfile.ArvadosFile):
+ todo += [(item.parent, item, args.destination)]
+ todo_bytes += item.size()
+ else:
+ logger.error("'{}' not found.".format('.' + get_prefix))
+ return 1
+ except (IOError, arvados.errors.NotFoundError) as e:
logger.error(e)
return 1
if args.hash:
digestor = hashlib.new(args.hash)
try:
- with s.open(f.name, 'r') as file_reader:
+ with s.open(f.name, 'rb') as file_reader:
for data in file_reader.readall():
if outfile:
outfile.write(data)
if todo_bytes==0
else 100.0*out_bytes/todo_bytes)))
elif args.batch_progress:
- stderr.write('%s %d read %d total\n' %
+ stderr.write('%s %d read %d total %d\n' %
(sys.argv[0], os.getpid(),
out_bytes, todo_bytes))
if digestor:
if outfile and (outfile.fileno() > 2) and not outfile.closed:
os.unlink(outfile.name)
break
+ finally:
+ if outfile != None and outfile != stdout:
+ outfile.close()
if args.progress:
stderr.write('\n')
+ return 0
def files_in_collection(c):
# Sort first by file type, then alphabetically by file path.
- for i in sorted(c.keys(),
+ for i in sorted(list(c.keys()),
key=lambda k: (
isinstance(c[k], arvados.collection.Subcollection),
k.upper())):
elif isinstance(c[i], arvados.collection.Subcollection):
for s, f in files_in_collection(c[i]):
yield (s, f)
+
+def write_block_or_manifest(dest, src, api_client, args):
+ if '+A' in src:
+ # block locator
+ kc = arvados.keep.KeepClient(api_client=api_client)
+ dest.write(kc.get(src, num_retries=args.retries))
+ else:
+ # collection UUID or portable data hash
+ reader = arvados.CollectionReader(
+ src, api_client=api_client, num_retries=args.retries)
+ dest.write(reader.manifest_text(strip=args.strip_manifest).encode())
projects / arvados.git / blobdiff