-import gflags
-import httplib
-import httplib2
+import functools
import logging
import os
-import pprint
-import sys
-import types
-import subprocess
-import json
-import UserDict
import re
-import hashlib
-import string
-import bz2
-import zlib
-import fcntl
-import time
-import threading
+import errno
from collections import deque
from stat import *
+from .arvfile import ArvadosFileBase, split, ArvadosFile, ArvadosFileWriter, ArvadosFileReader, BlockManager
from keep import *
-from stream import *
+from .stream import StreamReader, normalize_stream, locator_block_size
+from .ranges import Range, LocatorAndRange
import config
import errors
import util
_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 == 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 != None:
- stream_tokens.append("{0}:{1}:{2}".format(current_span[0], current_span[1] - current_span[0], fout))
-
- if len(stream[f]) == 0:
- stream_tokens.append("0:0:{0}".format(fout))
-
- return stream_tokens
-
-def normalize(collection):
- streams = {}
- for s in collection.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]))
-
- normalized_streams = []
- sortedstreams = list(streams.keys())
- sortedstreams.sort()
- for s in sortedstreams:
- normalized_streams.append(normalize_stream(s, streams[s]))
- return normalized_streams
-
-
class CollectionBase(object):
def __enter__(self):
- pass
+ return self
- def __exit__(self):
+ def __exit__(self, exc_type, exc_value, traceback):
pass
def _my_keep(self):
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,
self._api_client = api_client
self._keep_client = keep_client
self.num_retries = num_retries
- if re.match(r'[a-f0-9]{32}(\+\d+)?(\+\S+)*$', manifest_locator_or_text):
+ if re.match(util.keep_locator_pattern, manifest_locator_or_text):
self._manifest_locator = manifest_locator_or_text
self._manifest_text = None
- elif re.match(r'[a-z0-9]{5}-[a-z0-9]{5}-[a-z0-9]{15}$', manifest_locator_or_text):
+ 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(r'((\S+)( +[a-f0-9]{32}(\+\d+)(\+\S+)*)+( +\d+:\d+:\S+)+$)+', manifest_locator_or_text, re.MULTILINE):
+ 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._api_response = None
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.
+ self._api_response = self._api_client.collections().get(
+ uuid=self._manifest_locator).execute(
+ num_retries=self.num_retries)
+ self._manifest_text = self._api_response['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 is not None:
- return
- if not self._manifest_text:
- try:
- # 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 = 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']
- except Exception as e:
- if not util.portable_data_hash_pattern.match(
- self._manifest_locator):
- raise
- _logger.warning(
- "API server did not return Collection '%s'. " +
- "Trying to fetch directly from Keep (deprecated).",
- self._manifest_locator)
- self._manifest_text = self._my_keep().get(
- self._manifest_locator, num_retries=self.num_retries)
+ error_via_api = None
+ error_via_keep = None
+ should_try_keep = ((self._manifest_text is None) and
+ util.keep_locator_pattern.match(
+ self._manifest_locator))
+ if ((self._manifest_text is None) and
+ util.signed_locator_pattern.match(self._manifest_locator)):
+ error_via_keep = self._populate_from_keep()
+ if self._manifest_text is None:
+ 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 ((self._manifest_text is None) 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 self._manifest_text is None:
+ # 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, keep=self._my_keep()).manifest_text() for stream in self._streams])
- #print "result", self._manifest_text
+ def _populate_first(orig_func):
+ # Decorator for methods that read actual Collection data.
+ @functools.wraps(orig_func)
+ def wrapper(self, *args, **kwargs):
+ if self._streams is None:
+ self._populate()
+ return orig_func(self, *args, **kwargs)
+ return wrapper
+
+ @_populate_first
+ def api_response(self):
+ """api_response() -> dict or None
+
+ Returns information about this Collection fetched from the API server.
+ If the Collection exists in Keep but not the API server, currently
+ returns None. Future versions may provide a synthetic response.
+ """
+ return self._api_response
+ @_populate_first
+ def normalize(self):
+ # Rearrange streams
+ streams = {}
+ for s in self.all_streams():
+ for f in s.all_files():
+ streamname, filename = split(s.name() + "/" + f.name())
+ 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.locator, r.range_size))
+
+ 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])
+
+ @_populate_first
+ def open(self, streampath, filename=None):
+ """open(streampath[, filename]) -> file-like object
+
+ Pass in the path of a file to read from the Collection, either as a
+ single string or as two separate stream name and file name arguments.
+ This method returns a file-like object to read that file.
+ """
+ if filename is None:
+ streampath, filename = split(streampath)
+ keep_client = self._my_keep()
+ for stream_s in self._streams:
+ stream = StreamReader(stream_s, keep_client,
+ num_retries=self.num_retries)
+ if stream.name() == streampath:
+ break
+ else:
+ raise ValueError("stream '{}' not found in Collection".
+ format(streampath))
+ try:
+ return stream.files()[filename]
+ except KeyError:
+ raise ValueError("file '{}' not found in Collection stream '{}'".
+ format(filename, streampath))
+ @_populate_first
def all_streams(self):
- self._populate()
return [StreamReader(s, self._my_keep(), num_retries=self.num_retries)
for s in self._streams]
for f in s.all_files():
yield f
- def manifest_text(self, strip=False):
- self._populate()
- if strip:
- m = ''.join([StreamReader(stream, keep=self._my_keep()).manifest_text(strip=True) for stream in self._streams])
- return m
+ @_populate_first
+ 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:
return self._manifest_text
-class CollectionWriter(CollectionBase):
- KEEP_BLOCK_SIZE = 2**26
+class _WriterFile(ArvadosFileBase):
+ def __init__(self, coll_writer, name):
+ super(_WriterFile, self).__init__(name, 'wb')
+ self.dest = coll_writer
+
+ def close(self):
+ super(_WriterFile, self).close()
+ self.dest.finish_current_file()
+
+ @ArvadosFileBase._before_close
+ def write(self, data):
+ self.dest.write(data)
+
+ @ArvadosFileBase._before_close
+ def writelines(self, seq):
+ for data in seq:
+ self.write(data)
+
+ @ArvadosFileBase._before_close
+ def flush(self):
+ self.dest.flush_data()
+
+class CollectionWriter(CollectionBase):
def __init__(self, api_client=None, num_retries=0):
"""Instantiate a CollectionWriter.
self._queued_file = None
self._queued_dirents = deque()
self._queued_trees = deque()
+ self._last_open = None
- def __exit__(self):
- self.finish()
+ def __exit__(self, exc_type, exc_value, traceback):
+ if exc_type is None:
+ self.finish()
def do_queued_work(self):
# The work queue consists of three pieces:
def _work_file(self):
while True:
- buf = self._queued_file.read(self.KEEP_BLOCK_SIZE)
+ buf = self._queued_file.read(config.KEEP_BLOCK_SIZE)
if not buf:
break
self.write(buf)
def _work_trees(self):
path, stream_name, max_manifest_depth = self._queued_trees[0]
- make_dirents = (util.listdir_recursive if (max_manifest_depth == 0)
- else os.listdir)
- d = make_dirents(path)
- if len(d) > 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()
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:
+ while self._data_buffer_len >= config.KEEP_BLOCK_SIZE:
self.flush_data()
+ def open(self, streampath, filename=None):
+ """open(streampath[, filename]) -> file-like object
+
+ Pass in the path of a file to write to the Collection, either as a
+ single string or as two separate stream name and file name arguments.
+ This method returns a file-like object you can write to add it to the
+ Collection.
+
+ You may only have one file object from the Collection open at a time,
+ so be sure to close the object when you're done. Using the object in
+ a with statement makes that easy::
+
+ with cwriter.open('./doc/page1.txt') as outfile:
+ outfile.write(page1_data)
+ with cwriter.open('./doc/page2.txt') as outfile:
+ outfile.write(page2_data)
+ """
+ if filename is None:
+ streampath, filename = split(streampath)
+ if self._last_open and not self._last_open.closed:
+ raise errors.AssertionError(
+ "can't open '{}' when '{}' is still open".format(
+ filename, self._last_open.name))
+ if streampath != self.current_stream_name():
+ self.start_new_stream(streampath)
+ self.set_current_file_name(filename)
+ self._last_open = _WriterFile(self, filename)
+ return self._last_open
+
def flush_data(self):
data_buffer = ''.join(self._data_buffer)
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._my_keep().put(data_buffer[0:config.KEEP_BLOCK_SIZE]))
+ self._data_buffer = [data_buffer[config.KEEP_BLOCK_SIZE:]]
self._data_buffer_len = len(self._data_buffer[0])
def start_new_file(self, newfilename=None):
raise errors.AssertionError(
"Manifest filenames cannot contain whitespace: %s" %
newfilename)
+ elif re.search(r'\x00', newfilename):
+ raise errors.AssertionError(
+ "Manifest filenames cannot contain NUL characters: %s" %
+ newfilename)
self._current_file_name = newfilename
def current_file_name(self):
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_name])
self._current_file_pos = self._current_stream_length
+ self._current_file_name = None
def start_new_stream(self, newstreamname='.'):
self.finish_current_stream()
# 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 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 += ' ' + ' '.join("%d:%d:%s" % (sfile[0], sfile[1], sfile[2].replace(' ', '\\040')) for sfile in stream[2])
manifest += "\n"
- if manifest:
- return CollectionReader(manifest, self._api_client).manifest_text()
- else:
- return ""
+ return manifest
def data_locators(self):
ret = []
raise errors.AssertionError(
"resumable writer can't accept unsourced data")
return super(ResumableCollectionWriter, self).write(data)
+
+
+class Collection(CollectionBase):
+ def __init__(self, manifest_locator_or_text=None, parent=None, api_client=None,
+ keep_client=None, num_retries=0, block_manager=None):
+
+ self.parent = parent
+ self._items = None
+ self._api_client = api_client
+ self._keep_client = keep_client
+ self._block_manager = block_manager
+
+ self.num_retries = num_retries
+ self._manifest_locator = None
+ self._manifest_text = None
+ self._api_response = None
+
+ if manifest_locator_or_text:
+ if re.match(util.keep_locator_pattern, manifest_locator_or_text):
+ self._manifest_locator = manifest_locator_or_text
+ elif re.match(util.collection_uuid_pattern, manifest_locator_or_text):
+ self._manifest_locator = manifest_locator_or_text
+ elif re.match(util.manifest_pattern, manifest_locator_or_text):
+ self._manifest_text = manifest_locator_or_text
+ else:
+ raise errors.ArgumentError(
+ "Argument to CollectionReader must be a manifest or a collection UUID")
+
+ def _my_api(self):
+ if self._api_client is None:
+ if self.parent is not None:
+ return self.parent._my_api()
+ self._api_client = arvados.api('v1')
+ self._keep_client = None # Make a new one with the new api.
+ return self._api_client
+
+ def _my_keep(self):
+ if self._keep_client is None:
+ if self.parent is not None:
+ return self.parent._my_keep()
+ self._keep_client = KeepClient(api_client=self._my_api(),
+ num_retries=self.num_retries)
+ return self._keep_client
+
+ def _my_block_manager(self):
+ if self._block_manager is None:
+ if self.parent is not None:
+ return self.parent._my_block_manager()
+ self._block_manager = BlockManager(self._my_keep())
+ return self._block_manager
+
+ 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:
+ self._api_response = self._my_api().collections().get(
+ uuid=self._manifest_locator).execute(
+ num_retries=self.num_retries)
+ self._manifest_text = self._api_response['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):
+ self._items = {}
+ if self._manifest_locator is None and self._manifest_text is None:
+ return
+ error_via_api = None
+ error_via_keep = None
+ should_try_keep = ((self._manifest_text is None) and
+ util.keep_locator_pattern.match(
+ self._manifest_locator))
+ if ((self._manifest_text is None) and
+ util.signed_locator_pattern.match(self._manifest_locator)):
+ error_via_keep = self._populate_from_keep()
+ if self._manifest_text is None:
+ 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 ((self._manifest_text is None) 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 self._manifest_text is None:
+ # 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))
+ # populate
+ import_manifest(self._manifest_text, self)
+
+ def _populate_first(orig_func):
+ # Decorator for methods that read actual Collection data.
+ @functools.wraps(orig_func)
+ def wrapper(self, *args, **kwargs):
+ if self._items is None:
+ self._populate()
+ return orig_func(self, *args, **kwargs)
+ return wrapper
+
+ def __enter__(self):
+ return self
+
+ def __exit__(self, exc_type, exc_value, traceback):
+ self.save(no_locator=True)
+ if self._block_manager is not None:
+ self._block_manager.stop_threads()
+
+ @_populate_first
+ def find(self, path, create=False, create_collection=False):
+ p = path.split("/")
+ if p[0] == '.':
+ del p[0]
+
+ if len(p) > 0:
+ item = self._items.get(p[0])
+ if len(p) == 1:
+ # item must be a file
+ if item is None and create:
+ # create new file
+ if create_collection:
+ item = Collection(parent=self, num_retries=self.num_retries)
+ else:
+ item = ArvadosFile(self)
+ self._items[p[0]] = item
+ return item
+ else:
+ if item is None and create:
+ # create new collection
+ item = Collection(parent=self, num_retries=self.num_retries)
+ self._items[p[0]] = item
+ del p[0]
+ return item.find("/".join(p), create=create)
+ else:
+ return self
+
+ @_populate_first
+ def api_response(self):
+ """api_response() -> dict or None
+
+ Returns information about this Collection fetched from the API server.
+ If the Collection exists in Keep but not the API server, currently
+ returns None. Future versions may provide a synthetic response.
+ """
+ return self._api_response
+
+ def open(self, path, mode):
+ mode = mode.replace("b", "")
+ if len(mode) == 0 or mode[0] not in ("r", "w", "a"):
+ raise ArgumentError("Bad mode '%s'" % mode)
+ create = (mode != "r")
+
+ f = self.find(path, create=create)
+ if f is None:
+ raise IOError((errno.ENOENT, "File not found"))
+ if not isinstance(f, ArvadosFile):
+ raise IOError((errno.EISDIR, "Path must refer to a file."))
+
+ if mode[0] == "w":
+ f.truncate(0)
+
+ if mode == "r":
+ return ArvadosFileReader(f, path, mode)
+ else:
+ return ArvadosFileWriter(f, path, mode)
+
+ @_populate_first
+ def modified(self):
+ for k,v in self._items.items():
+ if v.modified():
+ return True
+ return False
+
+ @_populate_first
+ def set_unmodified(self):
+ for k,v in self._items.items():
+ v.set_unmodified()
+
+ @_populate_first
+ def __iter__(self):
+ return self._items.iterkeys()
+
+ @_populate_first
+ def iterkeys(self):
+ return self._items.iterkeys()
+
+ @_populate_first
+ def __getitem__(self, k):
+ return self._items[k]
+
+ @_populate_first
+ def __contains__(self, k):
+ return k in self._items
+
+ @_populate_first
+ def __len__(self):
+ return len(self._items)
+
+ @_populate_first
+ def __delitem__(self, p):
+ del self._items[p]
+
+ @_populate_first
+ def keys(self):
+ return self._items.keys()
+
+ @_populate_first
+ def values(self):
+ return self._items.values()
+
+ @_populate_first
+ def items(self):
+ return self._items.items()
+
+ @_populate_first
+ def exists(self, path):
+ return self.find(path) != None
+
+ @_populate_first
+ def remove(self, path):
+ p = path.split("/")
+ if p[0] == '.':
+ del p[0]
+
+ if len(p) > 0:
+ item = self._items.get(p[0])
+ if item is None:
+ raise IOError((errno.ENOENT, "File not found"))
+ if len(p) == 1:
+ del self._items[p[0]]
+ else:
+ del p[0]
+ item.remove("/".join(p))
+ else:
+ raise IOError((errno.ENOENT, "File not found"))
+
+ @_populate_first
+ def manifest_text(self, strip=False, normalize=False):
+ if self.modified() or self._manifest_text is None or normalize:
+ return export_manifest(self, stream_name=".", portable_locators=strip)
+ else:
+ if strip:
+ return self.stripped_manifest()
+ else:
+ return self._manifest_text
+
+ def portable_data_hash(self):
+ stripped = self.manifest_text(strip=True)
+ return hashlib.md5(stripped).hexdigest() + '+' + str(len(stripped))
+
+ @_populate_first
+ def save(self, no_locator=False):
+ if self.modified():
+ self._my_block_manager().commit_all()
+ self._my_keep().put(self.manifest_text(strip=True))
+ if self._manifest_locator is not None and re.match(util.collection_uuid_pattern, self._manifest_locator):
+ self._api_response = self._my_api().collections().update(
+ uuid=self._manifest_locator,
+ body={'manifest_text': self.manifest_text(strip=False)}
+ ).execute(
+ num_retries=self.num_retries)
+ elif not no_locator:
+ raise AssertionError("Collection manifest_locator must be a collection uuid. Use save_as() for new collections.")
+ self.set_unmodified()
+
+ @_populate_first
+ def save_as(self, name, owner_uuid=None, ensure_unique_name=False):
+ self._my_block_manager().commit_all()
+ self._my_keep().put(self.manifest_text(strip=True))
+ body = {"manifest_text": self.manifest_text(strip=False),
+ "name": name}
+ if owner_uuid:
+ body["owner_uuid"] = owner_uuid
+ self._api_response = self._my_api().collections().create(ensure_unique_name=ensure_unique_name, body=body).execute(num_retries=self.num_retries)
+ self._manifest_locator = self._api_response["uuid"]
+ self.set_unmodified()
+
+ @_populate_first
+ def rename(self, old, new):
+ old_path, old_fn = os.path.split(old)
+ old_col = self.find(path)
+ if old_col is None:
+ raise IOError((errno.ENOENT, "File not found"))
+ if not isinstance(old_p, Collection):
+ raise IOError((errno.ENOTDIR, "Parent in path is a file, not a directory"))
+ if old_fn in old_col:
+ new_path, new_fn = os.path.split(new)
+ new_col = self.find(new_path, create=True, create_collection=True)
+ if not isinstance(new_col, Collection):
+ raise IOError((errno.ENOTDIR, "Destination is a file, not a directory"))
+ ent = old_col[old_fn]
+ del old_col[old_fn]
+ ent.parent = new_col
+ new_col[new_fn] = ent
+ else:
+ raise IOError((errno.ENOENT, "File not found"))
+
+def import_manifest(manifest_text, into_collection=None, api_client=None, keep=None, num_retries=None):
+ if into_collection is not None:
+ if len(into_collection) > 0:
+ raise ArgumentError("Can only import manifest into an empty collection")
+ c = into_collection
+ else:
+ c = Collection(api_client=api_client, keep_client=keep, num_retries=num_retries)
+
+ STREAM_NAME = 0
+ BLOCKS = 1
+ SEGMENTS = 2
+
+ stream_name = None
+ state = STREAM_NAME
+
+ for n in re.finditer(r'(\S+)(\s+|$)', manifest_text):
+ tok = n.group(1)
+ sep = n.group(2)
+
+ if state == STREAM_NAME:
+ # starting a new stream
+ stream_name = tok.replace('\\040', ' ')
+ blocks = []
+ segments = []
+ streamoffset = 0L
+ state = BLOCKS
+ continue
+
+ if state == BLOCKS:
+ s = re.match(r'[0-9a-f]{32}\+(\d+)(\+\S+)*', tok)
+ if s:
+ blocksize = long(s.group(1))
+ blocks.append(Range(tok, streamoffset, blocksize))
+ streamoffset += blocksize
+ else:
+ state = SEGMENTS
+
+ if state == SEGMENTS:
+ s = re.search(r'^(\d+):(\d+):(\S+)', tok)
+ if s:
+ pos = long(s.group(1))
+ size = long(s.group(2))
+ name = s.group(3).replace('\\040', ' ')
+ f = c.find("%s/%s" % (stream_name, name), create=True)
+ f.add_segment(blocks, pos, size)
+ else:
+ # error!
+ raise errors.SyntaxError("Invalid manifest format")
+
+ if sep == "\n":
+ stream_name = None
+ state = STREAM_NAME
+
+ c.set_unmodified()
+ return c
+
+def export_manifest(item, stream_name=".", portable_locators=False):
+ buf = ""
+ if isinstance(item, Collection):
+ stream = {}
+ sorted_keys = sorted(item.keys())
+ for k in [s for s in sorted_keys if isinstance(item[s], ArvadosFile)]:
+ v = item[k]
+ st = []
+ for s in v.segments:
+ loc = s.locator
+ if loc.startswith("bufferblock"):
+ loc = v.parent._my_block_manager()._bufferblocks[loc].locator()
+ if portable_locators:
+ loc = KeepLocator(loc).stripped()
+ st.append(LocatorAndRange(loc, locator_block_size(loc),
+ s.segment_offset, s.range_size))
+ stream[k] = st
+ if stream:
+ buf += ' '.join(normalize_stream(stream_name, stream))
+ buf += "\n"
+ for k in [s for s in sorted_keys if isinstance(item[s], Collection)]:
+ buf += export_manifest(item[k], stream_name=os.path.join(stream_name, k), portable_locators=portable_locators)
+ elif isinstance(item, ArvadosFile):
+ st = []
+ for s in item.segments:
+ loc = s.locator
+ if loc.startswith("bufferblock"):
+ loc = item._bufferblocks[loc].calculate_locator()
+ if portable_locators:
+ loc = KeepLocator(loc).stripped()
+ st.append(LocatorAndRange(loc, locator_block_size(loc),
+ s.segment_offset, s.range_size))
+ stream[stream_name] = st
+ buf += ' '.join(normalize_stream(stream_name, stream))
+ buf += "\n"
+ return buf