import argparse
import arvados
+import arvados.collection
import base64
import datetime
import errno
args = arg_parser.parse_args(arguments)
if len(args.paths) == 0:
- args.paths += ['/dev/stdin']
+ args.paths = ['-']
+
+ args.paths = map(lambda x: "-" if x == "/dev/stdin" else x, args.paths)
if len(args.paths) != 1 or os.path.isdir(args.paths[0]):
if args.filename:
args.progress = True
if args.paths == ['-']:
- args.paths = ['/dev/stdin']
+ args.resume = False
if not args.filename:
- args.filename = '-'
+ args.filename = 'stdin'
return args
replication=replication)
except (TypeError, ValueError,
arvados.errors.StaleWriterStateError) as error:
- return cls(cache, reporter, bytes_expected, num_retries=num_retries)
+ return cls(cache, reporter, bytes_expected,
+ num_retries=num_retries,
+ replication=replication)
else:
return writer
def flush_data(self):
start_buffer_len = self._data_buffer_len
- start_block_count = self.bytes_written / self.KEEP_BLOCK_SIZE
+ start_block_count = self.bytes_written / arvados.config.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:
+ if (self.bytes_written / arvados.config.KEEP_BLOCK_SIZE) > start_block_count:
self.cache_state()
def _record_new_input(self, input_type, source_name, dest_name):
print >>stderr, error
sys.exit(1)
- # write_copies is how many copies of each data block we write to
- # Keep. args.replication is how many copies we instruct Arvados to
- # maintain (by passing it in collections().create() after all data
- # is written). If args.replication is given as None, it should
- # stay None, but we still need to write a suitable number of
- # copies to Keep.
+ # 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))
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):
+ if path == '-':
+ writer.start_new_stream()
+ writer.start_new_file(args.filename)
+ r = sys.stdin.read(64*1024)
+ while r:
+ # Need to bypass _queued_file check in ResumableCollectionWriter.write() to get
+ # CollectionWriter.write().
+ super(arvados.collection.ResumableCollectionWriter, writer).write(r)
+ r = sys.stdin.read(64*1024)
+ elif os.path.isdir(path):
writer.write_directory_tree(
path, max_manifest_depth=args.max_manifest_depth)
else:
if args.stream:
output = writer.manifest_text()
if args.normalize:
- output = CollectionReader(output).manifest_text(normalize=True)
+ output = arvados.collection.CollectionReader(output).manifest_text(normalize=True)
elif args.raw:
output = ','.join(writer.data_locators())
else:
try:
manifest_text = writer.manifest_text()
if args.normalize:
- manifest_text = CollectionReader(manifest_text).manifest_text(normalize=True)
+ manifest_text = arvados.collection.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 calls it 'redundancy' until #3410.
+ # API called it 'redundancy' before #3410.
replication_attr = 'redundancy'
# Register the resulting collection in Arvados.
collection = api_client.collections().create(