import logging
import arvados
+import arvados.commands._util as arv_cmd
logger = logging.getLogger('arvados.arv-get')
exit(code)
parser = argparse.ArgumentParser(
- description='Copy data from Keep to a local file or pipe.')
+ description='Copy data from Keep to a local file or pipe.',
+ parents=[arv_cmd.retry_opt])
parser.add_argument('locator', type=str,
help="""
Collection locator, optionally with a file path or prefix.
""")
-parser.add_argument('destination', type=str, nargs='?', default='/dev/stdout',
+parser.add_argument('destination', type=str, nargs='?', default='-',
help="""
-Local file or directory where the data is to be written. Default:
-/dev/stdout.
+Local file or directory where the data is to be written. Default: stdout.
""")
group = parser.add_mutually_exclusive_group()
group.add_argument('--progress', action='store_true',
help="""
Overwrite existing files while writing. The default behavior is to
refuse to write *anything* if any of the output files already
-exist. As a special case, -f is not needed to write to /dev/stdout.
+exist. As a special case, -f is not needed to write to stdout.
""")
group.add_argument('--skip-existing', action='store_true',
help="""
logger.debug("Appended source file name to destination directory: %s",
args.destination)
-if args.destination == '-':
- args.destination = '/dev/stdout'
if args.destination == '/dev/stdout':
+ args.destination = "-"
+
+if args.destination == '-':
# Normally you have to use -f to write to a file (or device) that
# already exists, but "-" and "/dev/stdout" are common enough to
# merit a special exception.
# that isn't a tty.
if (not (args.batch_progress or args.no_progress)
and sys.stderr.isatty()
- and (args.destination != '/dev/stdout'
+ and (args.destination != '-'
or not sys.stdout.isatty())):
args.progress = True
get_prefix = r.group(2)
if args.r and not get_prefix:
get_prefix = os.sep
-
-todo = []
-todo_bytes = 0
api_client = arvados.api('v1')
+reader = arvados.CollectionReader(collection, num_retries=args.retries)
+
if not get_prefix:
- try:
- if not args.n:
- if not args.f and os.path.exists(args.destination):
- abort('Local file %s already exists.' % (args.destination,))
- with open(args.destination, 'wb') as f:
- try:
- c = api_client.collections().get(uuid=collection).execute()
- manifest = c['manifest_text']
- except Exception as e:
- logger.warning(
- "Collection %s not found. " +
- "Trying to fetch directly from Keep (deprecated).",
- collection)
- manifest = arvados.KeepClient(
- api_client=api_client).get(collection)
- f.write(manifest)
- sys.exit(0)
- except arvados.errors.NotFoundError as e:
- abort(e)
-
-reader = arvados.CollectionReader(collection)
+ if not args.n:
+ open_flags = os.O_CREAT | os.O_WRONLY
+ if not args.f:
+ open_flags |= os.O_EXCL
+ try:
+ if args.destination == "-":
+ sys.stdout.write(reader.manifest_text())
+ else:
+ out_fd = os.open(args.destination, open_flags)
+ with os.fdopen(out_fd, 'wb') as out_file:
+ out_file.write(reader.manifest_text())
+ except (IOError, OSError) as error:
+ abort("can't write to '{}': {}".format(args.destination, error))
+ except (arvados.errors.ApiError, arvados.errors.KeepReadError) as error:
+ abort("failed to download '{}': {}".format(collection, error))
+ sys.exit(0)
+
+reader.normalize()
# 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 in reader.all_streams():
for f in s.all_files():
if 0 != string.find(os.path.join(s.name(), f.name()),
'.' + get_prefix):
continue
- dest_path = os.path.join(
- args.destination,
- os.path.join(s.name(), f.name())[len(get_prefix)+1:])
- if (not (args.n or args.f or args.skip_existing) and
- os.path.exists(dest_path)):
- abort('Local file %s already exists.' % (dest_path,))
+ if args.destination == "-":
+ dest_path = "-"
+ else:
+ dest_path = os.path.join(
+ args.destination,
+ os.path.join(s.name(), f.name())[len(get_prefix)+1:])
+ if (not (args.n or args.f or args.skip_existing) and
+ os.path.exists(dest_path)):
+ abort('Local file %s already exists.' % (dest_path,))
else:
if os.path.join(s.name(), f.name()) != '.' + get_prefix:
continue
outfile = None
digestor = None
if not args.n:
- if args.skip_existing and os.path.exists(outfilename):
- logger.debug('Local file %s exists. Skipping.', outfilename)
- continue
- elif not args.f and (os.path.isfile(outfilename) or
- os.path.isdir(outfilename)):
- # Good thing we looked again: apparently this file wasn't
- # here yet when we checked earlier.
- abort('Local file %s already exists.' % (outfilename,))
- if args.r:
- arvados.util.mkdir_dash_p(os.path.dirname(outfilename))
- try:
- outfile = open(outfilename, 'wb')
- except Exception as e:
- abort('Open(%s) failed: %s' % (outfilename, e))
+ if outfilename == "-":
+ outfile = sys.stdout
+ else:
+ if args.skip_existing and os.path.exists(outfilename):
+ logger.debug('Local file %s exists. Skipping.', outfilename)
+ continue
+ elif not args.f and (os.path.isfile(outfilename) or
+ os.path.isdir(outfilename)):
+ # Good thing we looked again: apparently this file wasn't
+ # here yet when we checked earlier.
+ abort('Local file %s already exists.' % (outfilename,))
+ if args.r:
+ arvados.util.mkdir_dash_p(os.path.dirname(outfilename))
+ try:
+ outfile = open(outfilename, 'wb')
+ except Exception as error:
+ abort('Open(%s) failed: %s' % (outfilename, error))
if args.hash:
digestor = hashlib.new(args.hash)
try:
sys.stderr.write("%s %s/%s\n"
% (digestor.hexdigest(), s.name(), f.name()))
except KeyboardInterrupt:
- if outfile and outfile != '/dev/stdout':
- os.unlink(outfilename)
+ if outfile and (outfile.fileno() > 2) and not outfile.closed:
+ os.unlink(outfile.name)
break
if args.progress:
projects / arvados.git / blobdiff