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')
return normalized_streams
-class CollectionReader(object):
- def __init__(self, manifest_locator_or_text):
- if re.search(r'^[a-f0-9]{32}(\+\d+)?(\+\S+)*$', manifest_locator_or_text):
+class CollectionBase(object):
+ def __enter__(self):
+ pass
+
+ def __exit__(self):
+ pass
+
+ def _my_keep(self):
+ if self._keep_client is None:
+ self._keep_client = KeepClient(api_client=self._api_client,
+ num_retries=self.num_retries)
+ return self._keep_client
+
+
+class CollectionReader(CollectionBase):
+ def __init__(self, manifest_locator_or_text, api_client=None,
+ keep_client=None, num_retries=0):
+ """Instantiate a CollectionReader.
+
+ This class parses Collection manifests to provide a simple interface
+ to read its underlying files.
+
+ Arguments:
+ * manifest_locator_or_text: One of a Collection UUID, portable data
+ hash, or full manifest text.
+ * api_client: The API client to use to look up Collections. If not
+ provided, CollectionReader will build one from available Arvados
+ configuration.
+ * keep_client: The KeepClient to use to download Collection data.
+ If not provided, CollectionReader will build one from available
+ Arvados configuration.
+ * num_retries: The default number of times to retry failed
+ service requests. Default 0. You may change this value
+ after instantiation, but note those changes may not
+ propagate to related objects like the Keep client.
+ """
+ self._api_client = api_client
+ self._keep_client = keep_client
+ self.num_retries = num_retries
+ if re.match(util.keep_locator_pattern, manifest_locator_or_text):
+ self._manifest_locator = manifest_locator_or_text
+ self._manifest_text = None
+ elif re.match(util.collection_uuid_pattern, 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(util.manifest_pattern, manifest_locator_or_text):
self._manifest_text = manifest_locator_or_text
self._manifest_locator = None
else:
"Argument to CollectionReader must be a manifest or a collection UUID")
self._streams = None
- def __enter__(self):
- pass
-
- def __exit__(self):
- pass
-
def _populate(self):
- if self._streams != None:
+ if self._streams is not None:
return
+ error_via_api = None
+ error_via_keep = None
+ should_try_keep = (not self._manifest_text and
+ util.keep_locator_pattern.match(
+ self._manifest_locator))
+ if (not self._manifest_text and
+ util.signed_locator_pattern.match(self._manifest_locator)):
+ try:
+ self._populate_from_keep()
+ except e:
+ error_via_keep = e
if not self._manifest_text:
try:
- c = arvados.api('v1').collections().get(
- uuid=self._manifest_locator).execute()
- self._manifest_text = c['manifest_text']
+ self._populate_from_api_server()
+ except Exception as e:
+ if not should_try_keep:
+ raise
+ error_via_api = e
+ if (not self._manifest_text and
+ not error_via_keep and
+ should_try_keep):
+ # Looks like a keep locator, and we didn't already try keep above
+ try:
+ self._populate_from_keep()
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)
- self._streams = []
- for stream_line in self._manifest_text.split("\n"):
- if stream_line != '':
- stream_tokens = stream_line.split()
- self._streams += [stream_tokens]
+ error_via_keep = e
+ if not self._manifest_text:
+ # Nothing worked!
+ raise arvados.errors.NotFoundError(
+ ("Failed to retrieve collection '{}' " +
+ "from either API server ({}) or Keep ({})."
+ ).format(
+ self._manifest_locator,
+ error_via_api,
+ error_via_keep))
+ self._streams = [sline.split()
+ for sline in self._manifest_text.split("\n")
+ if sline]
self._streams = normalize(self)
# 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._my_keep()).manifest_text() for stream in self._streams])
#print "result", self._manifest_text
def all_streams(self):
self._populate()
- resp = []
- for s in self._streams:
- resp.append(StreamReader(s))
- return resp
+ return [StreamReader(s, self._my_keep(), num_retries=self.num_retries)
+ for s in self._streams]
def all_files(self):
for s in self.all_streams():
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._my_keep()).manifest_text(strip=True) for stream in self._streams])
+ return m
+ else:
+ return self._manifest_text
+
-class CollectionWriter(object):
+class CollectionWriter(CollectionBase):
KEEP_BLOCK_SIZE = 2**26
- def __init__(self):
+ def __init__(self, api_client=None, num_retries=0):
+ """Instantiate a CollectionWriter.
+
+ CollectionWriter lets you build a new Arvados Collection from scratch.
+ Write files to it. The CollectionWriter will upload data to Keep as
+ appropriate, and provide you with the Collection manifest text when
+ you're finished.
+
+ Arguments:
+ * api_client: The API client to use to look up Collections. If not
+ provided, CollectionReader will build one from available Arvados
+ configuration.
+ * num_retries: The default number of times to retry failed
+ service requests. Default 0. You may change this value
+ after instantiation, but note those changes may not
+ propagate to related objects like the Keep client.
+ """
+ self._api_client = api_client
+ self.num_retries = num_retries
+ self._keep_client = None
self._data_buffer = []
self._data_buffer_len = 0
self._current_stream_files = []
self._queued_dirents = deque()
self._queued_trees = deque()
- def __enter__(self):
- pass
-
def __exit__(self):
self.finish()
- def _do_queued_work(self):
+ def do_queued_work(self):
# The work queue consists of three pieces:
# * _queued_file: The file object we're currently writing to the
# Collection.
self._work_trees()
else:
break
- self.checkpoint_state()
-
- def checkpoint_state(self):
- # Subclasses can implement this method to, e.g., report or record state.
- pass
def _work_file(self):
while True:
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 write_file(self, source, filename=None):
self._queue_file(source, filename)
- self._do_queued_work()
+ self.do_queued_work()
def write_directory_tree(self,
path, stream_name='.', max_manifest_depth=-1):
self._queue_tree(path, stream_name, max_manifest_depth)
- self._do_queued_work()
+ self.do_queued_work()
def write(self, newdata):
if hasattr(newdata, '__iter__'):
for s in newdata:
self.write(s)
return
- self._data_buffer += [newdata]
+ self._data_buffer.append(newdata)
self._data_buffer_len += len(newdata)
self._current_stream_length += len(newdata)
while self._data_buffer_len >= self.KEEP_BLOCK_SIZE:
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])]
+ if data_buffer:
+ self._current_stream_locators.append(
+ self._my_keep().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.checkpoint_state()
def start_new_file(self, newfilename=None):
self.finish_current_file()
(self._current_stream_length - self._current_file_pos,
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_files.append([
+ self._current_file_pos,
+ self._current_stream_length - self._current_file_pos,
+ self._current_file_name])
self._current_file_pos = self._current_stream_length
+ self._current_file_name = None
def start_new_stream(self, newstreamname='.'):
self.finish_current_stream()
def finish_current_stream(self):
self.finish_current_file()
self.flush_data()
- if len(self._current_stream_files) == 0:
+ if not self._current_stream_files:
pass
- elif self._current_stream_name == None:
+ elif self._current_stream_name is None:
raise errors.AssertionError(
"Cannot finish an unnamed stream (%d bytes in %d files)" %
(self._current_stream_length, len(self._current_stream_files)))
else:
- 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]]
+ if not self._current_stream_locators:
+ self._current_stream_locators.append(config.EMPTY_BLOCK_LOCATOR)
+ self._finished_streams.append([self._current_stream_name,
+ 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.
+ return self._my_keep().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 manifest:
+ return CollectionReader(manifest, self._api_client).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, num_retries=0):
self._dependencies = {}
- super(ResumableCollectionWriter, self).__init__()
+ super(ResumableCollectionWriter, self).__init__(
+ api_client, num_retries=num_retries)
@classmethod
def from_state(cls, state, *init_args, **init_kwargs):
+ # Try to build a new writer from scratch with the given state.
+ # If the state is not suitable to resume (because files have changed,
+ # been deleted, aren't predictable, etc.), raise a
+ # StaleWriterStateError. Otherwise, return the initialized writer.
+ # The caller is responsible for calling writer.do_queued_work()
+ # appropriately after it's returned.
writer = cls(*init_args, **init_kwargs)
for attr_name in cls.STATE_PROPS:
attr_value = state[attr_name]
except IOError as error:
raise errors.StaleWriterStateError(
"failed to reopen active file {}: {}".format(path, error))
- writer._do_queued_work()
return writer
def check_dependencies(self):
raise errors.AssertionError("{} not a file path".format(source))
try:
path_stat = os.stat(src_path)
- except OSError as error:
- raise errors.AssertionError(
- "could not stat {}: {}".format(source, error))
+ except OSError as stat_error:
+ path_stat = None
super(ResumableCollectionWriter, self)._queue_file(source, filename)
fd_stat = os.fstat(self._queued_file.fileno())
- if path_stat.st_ino != fd_stat.st_ino:
+ if not S_ISREG(fd_stat.st_mode):
+ # We won't be able to resume from this cache anyway, so don't
+ # worry about further checks.
+ self._dependencies[source] = tuple(fd_stat)
+ elif path_stat is None:
+ raise errors.AssertionError(
+ "could not stat {}: {}".format(source, stat_error))
+ elif path_stat.st_ino != fd_stat.st_ino:
raise errors.AssertionError(
"{} changed between open and stat calls".format(source))
- self._dependencies[src_path] = tuple(fd_stat)
+ else:
+ self._dependencies[src_path] = tuple(fd_stat)
def write(self, data):
if self._queued_file is None:
projects / arvados.git / blobdiff