import errors
import util
+_logger = logging.getLogger('arvados.collection')
+
def normalize_stream(s, stream):
stream_tokens = [s]
sortedfiles = list(stream.keys())
blocks[b[arvados.LOCATOR]] = streamoffset
streamoffset += b[arvados.BLOCKSIZE]
+ if len(stream_tokens) == 1:
+ stream_tokens.append(config.EMPTY_BLOCK_LOCATOR)
+
for f in sortedfiles:
current_span = None
fout = f.replace(' ', '\\040')
class CollectionReader(object):
def __init__(self, manifest_locator_or_text):
- if re.search(r'^[a-f0-9]{32}(\+\d+)?(\+\S+)*$', manifest_locator_or_text):
+ if re.match(r'[a-f0-9]{32}(\+\d+)?(\+\S+)*$', manifest_locator_or_text):
self._manifest_locator = manifest_locator_or_text
self._manifest_text = None
- elif re.search(r'^\S+( [a-f0-9]{32,}(\+\S+)*)*( \d+:\d+:\S+)+\n', manifest_locator_or_text):
+ elif re.match(r'(\S+)( [a-f0-9]{32}(\+\d+)(\+\S+)*)+( \d+:\d+:\S+)+\n', manifest_locator_or_text):
self._manifest_text = manifest_locator_or_text
self._manifest_locator = None
else:
uuid=self._manifest_locator).execute()
self._manifest_text = c['manifest_text']
except Exception as e:
- logging.warning("API lookup failed for collection %s (%s: %s)" %
- (self._manifest_locator, type(e), str(e)))
+ _logger.warning("API lookup failed for collection %s (%s: %s)",
+ self._manifest_locator, type(e), str(e))
self._manifest_text = Keep.get(self._manifest_locator)
self._streams = []
for stream_line in self._manifest_text.split("\n"):
for f in s.all_files():
yield f
- def manifest_text(self):
+ def manifest_text(self, strip=False):
self._populate()
- return self._manifest_text
+ if strip:
+ m = ''.join([StreamReader(stream).manifest_text(strip=True) for stream in self._streams])
+ return m
+ else:
+ return self._manifest_text
class CollectionWriter(object):
KEEP_BLOCK_SIZE = 2**26
path, stream_name, max_manifest_depth = self._queued_trees[0]
make_dirents = (util.listdir_recursive if (max_manifest_depth == 0)
else os.listdir)
- self._queue_dirents(stream_name, make_dirents(path))
+ d = make_dirents(path)
+ if len(d) > 0:
+ self._queue_dirents(stream_name, d)
+ else:
+ self._queued_trees.popleft()
def _queue_file(self, source, filename=None):
assert (self._queued_file is None), "tried to queue more than one file"
for x in fields[1:-1] ]
clean += fields[0] + ' ' + ' '.join(locators) + ' ' + fields[-1] + "\n"
return clean
-
+
def manifest_text(self):
self.finish_current_stream()
manifest = ''
manifest += ' ' + ' '.join("%d:%d:%s" % (sfile[0], sfile[1], sfile[2].replace(' ', '\\040')) for sfile in stream[2])
manifest += "\n"
- #print 'writer',manifest
- #print 'after reader',CollectionReader(manifest).manifest_text()
-
- return CollectionReader(manifest).manifest_text()
+ if len(manifest) > 0:
+ return CollectionReader(manifest).manifest_text()
+ else:
+ return ""
def data_locators(self):
ret = []