import time
import threading
+from collections import deque
+from stat import *
+
from keep import *
from stream import *
import config
import errors
+import util
-class CollectionReader(object):
- def __init__(self, manifest_locator_or_text):
- if re.search(r'^\S+( [a-f0-9]{32,}(\+\S+)*)+( \d+:\d+:\S+)+\n', manifest_locator_or_text):
- self._manifest_text = manifest_locator_or_text
- self._manifest_locator = None
- else:
- self._manifest_locator = manifest_locator_or_text
- self._manifest_text = None
- self._streams = None
+_logger = logging.getLogger('arvados.collection')
+
+def normalize_stream(s, stream):
+ stream_tokens = [s]
+ sortedfiles = list(stream.keys())
+ sortedfiles.sort()
+
+ blocks = {}
+ streamoffset = 0L
+ for f in sortedfiles:
+ for b in stream[f]:
+ if b[arvados.LOCATOR] not in blocks:
+ stream_tokens.append(b[arvados.LOCATOR])
+ 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')
+ for segment in stream[f]:
+ segmentoffset = blocks[segment[arvados.LOCATOR]] + segment[arvados.OFFSET]
+ if current_span is None:
+ current_span = [segmentoffset, segmentoffset + segment[arvados.SEGMENTSIZE]]
+ else:
+ if segmentoffset == current_span[1]:
+ current_span[1] += segment[arvados.SEGMENTSIZE]
+ else:
+ stream_tokens.append("{0}:{1}:{2}".format(current_span[0], current_span[1] - current_span[0], fout))
+ current_span = [segmentoffset, segmentoffset + segment[arvados.SEGMENTSIZE]]
+
+ if current_span is not None:
+ stream_tokens.append("{0}:{1}:{2}".format(current_span[0], current_span[1] - current_span[0], fout))
+
+ if not stream[f]:
+ stream_tokens.append("0:0:{0}".format(fout))
+
+ return stream_tokens
+
+
+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
+
+ def stripped_manifest(self):
+ """
+ Return the manifest for the current collection with all
+ non-portable hints (i.e., permission signatures and other
+ hints other than size hints) removed from the locators.
+ """
+ raw = self.manifest_text()
+ clean = []
+ for line in raw.split("\n"):
+ fields = line.split()
+ if fields:
+ clean_fields = fields[:1] + [
+ (re.sub(r'\+[^\d][^\+]*', '', x)
+ if re.match(util.keep_locator_pattern, x)
+ else x)
+ for x in fields[1:]]
+ clean += [' '.join(clean_fields), "\n"]
+ return ''.join(clean)
+
+
+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.match(util.manifest_pattern, manifest_locator_or_text):
+ self._manifest_text = manifest_locator_or_text
+ self._manifest_locator = None
+ else:
+ raise errors.ArgumentError(
+ "Argument to CollectionReader must be a manifest or a collection UUID")
+ self._streams = None
+
+ def _populate_from_api_server(self):
+ # 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. Return an exception, or None if successful.
+ try:
+ if self._api_client is None:
+ self._api_client = arvados.api('v1')
+ self._keep_client = None # Make a new one with the new api.
+ c = self._api_client.collections().get(
+ uuid=self._manifest_locator).execute(
+ num_retries=self.num_retries)
+ self._manifest_text = c['manifest_text']
+ return None
+ except Exception as e:
+ return e
+
+ def _populate_from_keep(self):
+ # Retrieve a manifest directly from Keep. This has a chance of
+ # working if [a] the locator includes a permission signature
+ # or [b] the Keep services are operating in world-readable
+ # mode. Return an exception, or None if successful.
+ try:
+ self._manifest_text = self._my_keep().get(
+ self._manifest_locator, num_retries=self.num_retries)
+ except Exception as e:
+ return e
+
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)):
+ error_via_keep = self._populate_from_keep()
if not self._manifest_text:
- 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_api = self._populate_from_api_server()
+ if error_via_api is not None and not should_try_keep:
+ raise error_via_api
+ 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
+ error_via_keep = self._populate_from_keep()
+ 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]
+
+ def normalize(self):
+ self._populate()
+
+ # Rearrange streams
+ streams = {}
+ for s in self.all_streams():
+ for f in s.all_files():
+ filestream = s.name() + "/" + f.name()
+ r = filestream.rindex("/")
+ streamname = filestream[:r]
+ filename = filestream[r+1:]
+ if streamname not in streams:
+ streams[streamname] = {}
+ if filename not in streams[streamname]:
+ streams[streamname][filename] = []
+ for r in f.segments:
+ streams[streamname][filename].extend(s.locators_and_ranges(r[0], r[1]))
+
+ self._streams = [normalize_stream(s, streams[s])
+ for s in sorted(streams)]
+
+ # Regenerate the manifest text based on the normalized streams
+ self._manifest_text = ''.join(
+ [StreamReader(stream, keep=self._my_keep()).manifest_text()
+ for stream in self._streams])
def all_streams(self):
self._populate()
- resp = []
- for s in self._streams:
- resp += [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):
- self._populate()
- return self._manifest_text
+ def manifest_text(self, strip=False, normalize=False):
+ if normalize:
+ cr = CollectionReader(self.manifest_text())
+ cr.normalize()
+ return cr.manifest_text(strip=strip, normalize=False)
+ elif strip:
+ return self.stripped_manifest()
+ else:
+ self._populate()
+ 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._current_file_name = None
self._current_file_pos = 0
self._finished_streams = []
-
- def __enter__(self):
- pass
+ self._close_file = None
+ self._queued_file = None
+ self._queued_dirents = deque()
+ self._queued_trees = deque()
def __exit__(self):
self.finish()
- def write_directory_tree(self,
- path, stream_name='.', max_manifest_depth=-1):
- self.start_new_stream(stream_name)
- todo = []
- if max_manifest_depth == 0:
- dirents = sorted(util.listdir_recursive(path))
- else:
- dirents = sorted(os.listdir(path))
- for dirent in dirents:
+ def do_queued_work(self):
+ # The work queue consists of three pieces:
+ # * _queued_file: The file object we're currently writing to the
+ # Collection.
+ # * _queued_dirents: Entries under the current directory
+ # (_queued_trees[0]) that we want to write or recurse through.
+ # This may contain files from subdirectories if
+ # max_manifest_depth == 0 for this directory.
+ # * _queued_trees: Directories that should be written as separate
+ # streams to the Collection.
+ # This function handles the smallest piece of work currently queued
+ # (current file, then current directory, then next directory) until
+ # no work remains. The _work_THING methods each do a unit of work on
+ # THING. _queue_THING methods add a THING to the work queue.
+ while True:
+ if self._queued_file:
+ self._work_file()
+ elif self._queued_dirents:
+ self._work_dirents()
+ elif self._queued_trees:
+ self._work_trees()
+ else:
+ break
+
+ def _work_file(self):
+ while True:
+ buf = self._queued_file.read(self.KEEP_BLOCK_SIZE)
+ if not buf:
+ break
+ self.write(buf)
+ self.finish_current_file()
+ if self._close_file:
+ self._queued_file.close()
+ self._close_file = None
+ self._queued_file = None
+
+ def _work_dirents(self):
+ path, stream_name, max_manifest_depth = self._queued_trees[0]
+ if stream_name != self.current_stream_name():
+ self.start_new_stream(stream_name)
+ while self._queued_dirents:
+ dirent = self._queued_dirents.popleft()
target = os.path.join(path, dirent)
if os.path.isdir(target):
- todo += [[target,
- os.path.join(stream_name, dirent),
- max_manifest_depth-1]]
+ self._queue_tree(target,
+ os.path.join(stream_name, dirent),
+ max_manifest_depth - 1)
else:
- self.start_new_file(dirent)
- with open(target, 'rb') as f:
- while True:
- buf = f.read(2**26)
- if len(buf) == 0:
- break
- self.write(buf)
- self.finish_current_stream()
- map(lambda x: self.write_directory_tree(*x), todo)
+ self._queue_file(target, dirent)
+ break
+ if not self._queued_dirents:
+ self._queued_trees.popleft()
+
+ def _work_trees(self):
+ path, stream_name, max_manifest_depth = self._queued_trees[0]
+ d = util.listdir_recursive(
+ path, max_depth = (None if max_manifest_depth == 0 else 0))
+ if d:
+ 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"
+ if not hasattr(source, 'read'):
+ source = open(source, 'rb')
+ self._close_file = True
+ else:
+ self._close_file = False
+ if filename is None:
+ filename = os.path.basename(source.name)
+ self.start_new_file(filename)
+ self._queued_file = source
+
+ def _queue_dirents(self, stream_name, dirents):
+ assert (not self._queued_dirents), "tried to queue more than one tree"
+ self._queued_dirents = deque(sorted(dirents))
+
+ def _queue_tree(self, path, stream_name, max_manifest_depth):
+ self._queued_trees.append((path, stream_name, max_manifest_depth))
+
+ def write_file(self, source, filename=None):
+ self._queue_file(source, filename)
+ 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()
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])
return self._current_file_name
def finish_current_file(self):
- if self._current_file_name == None:
+ if self._current_file_name is None:
if self._current_file_pos == self._current_stream_length:
return
raise errors.AssertionError(
(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 portable_data_hash(self):
+ stripped = self.stripped_manifest()
+ return hashlib.md5(stripped).hexdigest() + '+' + str(len(stripped))
def manifest_text(self):
self.finish_current_stream()
manifest = ''
+
for stream in self._finished_streams:
if not re.search(r'^\.(/.*)?$', stream[0]):
manifest += './'
manifest += stream[0].replace(' ', '\\040')
- for locator in stream[1]:
- manifest += " %s" % locator
- for sfile in stream[2]:
- manifest += " %d:%d:%s" % (sfile[0], sfile[1], sfile[2].replace(' ', '\\040'))
+ manifest += ' ' + ' '.join(stream[1])
+ manifest += ' ' + ' '.join("%d:%d:%s" % (sfile[0], sfile[1], sfile[2].replace(' ', '\\040')) for sfile in stream[2])
manifest += "\n"
+
return manifest
def data_locators(self):
for name, locators, files in self._finished_streams:
ret += locators
return ret
+
+
+class ResumableCollectionWriter(CollectionWriter):
+ STATE_PROPS = ['_current_stream_files', '_current_stream_length',
+ '_current_stream_locators', '_current_stream_name',
+ '_current_file_name', '_current_file_pos', '_close_file',
+ '_data_buffer', '_dependencies', '_finished_streams',
+ '_queued_dirents', '_queued_trees']
+
+ def __init__(self, api_client=None, num_retries=0):
+ self._dependencies = {}
+ 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]
+ attr_class = getattr(writer, attr_name).__class__
+ # Coerce the value into the same type as the initial value, if
+ # needed.
+ if attr_class not in (type(None), attr_value.__class__):
+ attr_value = attr_class(attr_value)
+ setattr(writer, attr_name, attr_value)
+ # Check dependencies before we try to resume anything.
+ if any(KeepLocator(ls).permission_expired()
+ for ls in writer._current_stream_locators):
+ raise errors.StaleWriterStateError(
+ "locators include expired permission hint")
+ writer.check_dependencies()
+ if state['_current_file'] is not None:
+ path, pos = state['_current_file']
+ try:
+ writer._queued_file = open(path, 'rb')
+ writer._queued_file.seek(pos)
+ except IOError as error:
+ raise errors.StaleWriterStateError(
+ "failed to reopen active file {}: {}".format(path, error))
+ return writer
+
+ def check_dependencies(self):
+ for path, orig_stat in self._dependencies.items():
+ if not S_ISREG(orig_stat[ST_MODE]):
+ raise errors.StaleWriterStateError("{} not file".format(path))
+ try:
+ now_stat = tuple(os.stat(path))
+ except OSError as error:
+ raise errors.StaleWriterStateError(
+ "failed to stat {}: {}".format(path, error))
+ if ((not S_ISREG(now_stat[ST_MODE])) or
+ (orig_stat[ST_MTIME] != now_stat[ST_MTIME]) or
+ (orig_stat[ST_SIZE] != now_stat[ST_SIZE])):
+ raise errors.StaleWriterStateError("{} changed".format(path))
+
+ def dump_state(self, copy_func=lambda x: x):
+ state = {attr: copy_func(getattr(self, attr))
+ for attr in self.STATE_PROPS}
+ if self._queued_file is None:
+ state['_current_file'] = None
+ else:
+ state['_current_file'] = (os.path.realpath(self._queued_file.name),
+ self._queued_file.tell())
+ return state
+
+ def _queue_file(self, source, filename=None):
+ try:
+ src_path = os.path.realpath(source)
+ except Exception:
+ raise errors.AssertionError("{} not a file path".format(source))
+ try:
+ path_stat = os.stat(src_path)
+ except OSError as stat_error:
+ path_stat = None
+ super(ResumableCollectionWriter, self)._queue_file(source, filename)
+ fd_stat = os.fstat(self._queued_file.fileno())
+ 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))
+ else:
+ self._dependencies[src_path] = tuple(fd_stat)
+
+ def write(self, data):
+ if self._queued_file is None:
+ raise errors.AssertionError(
+ "resumable writer can't accept unsourced data")
+ return super(ResumableCollectionWriter, self).write(data)
projects / arvados.git / blobdiff