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+)*$', manifest_locator_or_text):
+ def __init__(self, manifest_locator_or_text, api_client=None, keep_client=None):
+ self._api_client = api_client
+ self._keep_client = keep_client
+ if re.match(r'[a-f0-9]{32}(\+\d+)?(\+\S+)*$', manifest_locator_or_text):
+ self._manifest_locator = manifest_locator_or_text
+ self._manifest_text = None
+ elif re.match(r'[a-z0-9]{5}-[a-z0-9]{5}-[a-z0-9]{15}$', manifest_locator_or_text):
self._manifest_locator = manifest_locator_or_text
self._manifest_text = None
- elif re.search(r'^\S+( [a-f0-9]{32,}(\+\S+)*)*( \d+:\d+:\S+)+\n', manifest_locator_or_text):
+ elif re.match(r'((\S+)( +[a-f0-9]{32}(\+\d+)(\+\S+)*)+( +\d+:\d+:\S+)+$)+', manifest_locator_or_text, re.MULTILINE):
self._manifest_text = manifest_locator_or_text
self._manifest_locator = None
else:
pass
def _populate(self):
- if self._streams != None:
+ if self._streams is not None:
return
if not self._manifest_text:
try:
- c = arvados.api('v1').collections().get(
+ # As in KeepClient itself, we must wait until the last possible
+ # moment to instantiate an API client, in order to avoid
+ # tripping up clients that don't have access to an API server.
+ # If we do build one, make sure our Keep client uses it.
+ # If instantiation fails, we'll fall back to the except clause,
+ # just like any other Collection lookup failure.
+ if self._api_client is None:
+ self._api_client = arvados.api('v1')
+ self._keep_client = KeepClient(api_client=self._api_client)
+ if self._keep_client is None:
+ self._keep_client = KeepClient(api_client=self._api_client)
+ c = self._api_client.collections().get(
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)))
- self._manifest_text = Keep.get(self._manifest_locator)
+ if not util.portable_data_hash_pattern.match(
+ self._manifest_locator):
+ raise
+ _logger.warning("API lookup failed for collection %s (%s: %s)",
+ self._manifest_locator, type(e), str(e))
+ if self._keep_client is None:
+ self._keep_client = KeepClient(api_client=self._api_client)
+ self._manifest_text = self._keep_client.get(self._manifest_locator)
self._streams = []
for stream_line in self._manifest_text.split("\n"):
if stream_line != '':
# now regenerate the manifest text based on the normalized stream
#print "normalizing", self._manifest_text
- self._manifest_text = ''.join([StreamReader(stream).manifest_text() for stream in self._streams])
+ self._manifest_text = ''.join([StreamReader(stream, keep=self._keep_client).manifest_text() for stream in self._streams])
#print "result", self._manifest_text
self._populate()
resp = []
for s in self._streams:
- resp.append(StreamReader(s))
+ resp.append(StreamReader(s, keep=self._keep_client))
return resp
def all_files(self):
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, keep=self._keep_client).manifest_text(strip=True) for stream in self._streams])
+ return m
+ else:
+ return self._manifest_text
class CollectionWriter(object):
KEEP_BLOCK_SIZE = 2**26
- def __init__(self):
+ def __init__(self, api_client=None):
+ self._api_client = api_client
+ self._keep_client = None
self._data_buffer = []
self._data_buffer_len = 0
self._current_stream_files = []
def __exit__(self):
self.finish()
+ def _prep_keep_client(self):
+ if self._keep_client is None:
+ self._keep_client = KeepClient(api_client=self._api_client)
+
def do_queued_work(self):
# The work queue consists of three pieces:
# * _queued_file: The file object we're currently writing to the
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"
def flush_data(self):
data_buffer = ''.join(self._data_buffer)
if data_buffer != '':
- self._current_stream_locators += [Keep.put(data_buffer[0:self.KEEP_BLOCK_SIZE])]
+ self._prep_keep_client()
+ self._current_stream_locators.append(
+ self._keep_client.put(data_buffer[0:self.KEEP_BLOCK_SIZE]))
self._data_buffer = [data_buffer[self.KEEP_BLOCK_SIZE:]]
self._data_buffer_len = len(self._data_buffer[0])
self._current_file_pos,
self._current_stream_name))
self._current_stream_files += [[self._current_file_pos,
- self._current_stream_length - self._current_file_pos,
- self._current_file_name]]
+ self._current_stream_length - self._current_file_pos,
+ self._current_file_name]]
self._current_file_pos = self._current_stream_length
def start_new_stream(self, newstreamname='.'):
if len(self._current_stream_locators) == 0:
self._current_stream_locators += [config.EMPTY_BLOCK_LOCATOR]
self._finished_streams += [[self._current_stream_name,
- self._current_stream_locators,
- self._current_stream_files]]
+ self._current_stream_locators,
+ self._current_stream_files]]
self._current_stream_files = []
self._current_stream_length = 0
self._current_stream_locators = []
self._current_file_name = None
def finish(self):
- return Keep.put(self.manifest_text())
+ # Store the manifest in Keep and return its locator.
+ self._prep_keep_client()
+ return self._keep_client.put(self.manifest_text())
+
+ def stripped_manifest(self):
+ """
+ Return the manifest for the current collection with all permission
+ hints removed from the locators in the manifest.
+ """
+ raw = self.manifest_text()
+ clean = ''
+ for line in raw.split("\n"):
+ fields = line.split()
+ if len(fields) > 0:
+ locators = [ re.sub(r'\+A[a-z0-9@_-]+', '', x)
+ 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 += ' ' + ' '.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 = []
'_data_buffer', '_dependencies', '_finished_streams',
'_queued_dirents', '_queued_trees']
- def __init__(self):
+ def __init__(self, api_client=None):
self._dependencies = {}
- super(ResumableCollectionWriter, self).__init__()
+ super(ResumableCollectionWriter, self).__init__(api_client)
@classmethod
def from_state(cls, state, *init_args, **init_kwargs):
projects / arvados.git / blobdiff