sdk/python/arvados/collection.py

   1 import functools
   2 import logging
   3 import os
   4 import re
   5
   6 from collections import deque
   7 from stat import *
   8
   9 from .arvfile import ArvadosFileBase, split, ArvadosFile, ArvadosFileWriter, ArvadosFileReader
  10 from keep import *
  11 from .stream import StreamReader, normalize_stream, locator_block_size
  12 from .ranges import Range, LocatorAndRange
  13 import config
  14 import errors
  15 import util
  16
  17 _logger = logging.getLogger('arvados.collection')
  18
  19 class CollectionBase(object):
  20     def __enter__(self):
  21         return self
  22
  23     def __exit__(self, exc_type, exc_value, traceback):
  24         pass
  25
  26     def _my_keep(self):
  27         if self._keep_client is None:
  28             self._keep_client = KeepClient(api_client=self._api_client,
  29                                            num_retries=self.num_retries)
  30         return self._keep_client
  31
  32     def stripped_manifest(self):
  33         """
  34         Return the manifest for the current collection with all
  35         non-portable hints (i.e., permission signatures and other
  36         hints other than size hints) removed from the locators.
  37         """
  38         raw = self.manifest_text()
  39         clean = []
  40         for line in raw.split("\n"):
  41             fields = line.split()
  42             if fields:
  43                 clean_fields = fields[:1] + [
  44                     (re.sub(r'\+[^\d][^\+]*', '', x)
  45                      if re.match(util.keep_locator_pattern, x)
  46                      else x)
  47                     for x in fields[1:]]
  48                 clean += [' '.join(clean_fields), "\n"]
  49         return ''.join(clean)
  50
  51
  52 class CollectionReader(CollectionBase):
  53     def __init__(self, manifest_locator_or_text, api_client=None,
  54                  keep_client=None, num_retries=0):
  55         """Instantiate a CollectionReader.
  56
  57         This class parses Collection manifests to provide a simple interface
  58         to read its underlying files.
  59
  60         Arguments:
  61         * manifest_locator_or_text: One of a Collection UUID, portable data
  62           hash, or full manifest text.
  63         * api_client: The API client to use to look up Collections.  If not
  64           provided, CollectionReader will build one from available Arvados
  65           configuration.
  66         * keep_client: The KeepClient to use to download Collection data.
  67           If not provided, CollectionReader will build one from available
  68           Arvados configuration.
  69         * num_retries: The default number of times to retry failed
  70           service requests.  Default 0.  You may change this value
  71           after instantiation, but note those changes may not
  72           propagate to related objects like the Keep client.
  73         """
  74         self._api_client = api_client
  75         self._keep_client = keep_client
  76         self.num_retries = num_retries
  77         if re.match(util.keep_locator_pattern, manifest_locator_or_text):
  78             self._manifest_locator = manifest_locator_or_text
  79             self._manifest_text = None
  80         elif re.match(util.collection_uuid_pattern, manifest_locator_or_text):
  81             self._manifest_locator = manifest_locator_or_text
  82             self._manifest_text = None
  83         elif re.match(util.manifest_pattern, manifest_locator_or_text):
  84             self._manifest_text = manifest_locator_or_text
  85             self._manifest_locator = None
  86         else:
  87             raise errors.ArgumentError(
  88                 "Argument to CollectionReader must be a manifest or a collection UUID")
  89         self._api_response = None
  90         self._streams = None
  91
  92     def _populate_from_api_server(self):
  93         # As in KeepClient itself, we must wait until the last
  94         # possible moment to instantiate an API client, in order to
  95         # avoid tripping up clients that don't have access to an API
  96         # server.  If we do build one, make sure our Keep client uses
  97         # it.  If instantiation fails, we'll fall back to the except
  98         # clause, just like any other Collection lookup
  99         # failure. Return an exception, or None if successful.
 100         try:
 101             if self._api_client is None:
 102                 self._api_client = arvados.api('v1')
 103                 self._keep_client = None  # Make a new one with the new api.
 104             self._api_response = self._api_client.collections().get(
 105                 uuid=self._manifest_locator).execute(
 106                 num_retries=self.num_retries)
 107             self._manifest_text = self._api_response['manifest_text']
 108             return None
 109         except Exception as e:
 110             return e
 111
 112     def _populate_from_keep(self):
 113         # Retrieve a manifest directly from Keep. This has a chance of
 114         # working if [a] the locator includes a permission signature
 115         # or [b] the Keep services are operating in world-readable
 116         # mode. Return an exception, or None if successful.
 117         try:
 118             self._manifest_text = self._my_keep().get(
 119                 self._manifest_locator, num_retries=self.num_retries)
 120         except Exception as e:
 121             return e
 122
 123     def _populate(self):
 124         error_via_api = None
 125         error_via_keep = None
 126         should_try_keep = ((self._manifest_text is None) and
 127                            util.keep_locator_pattern.match(
 128                 self._manifest_locator))
 129         if ((self._manifest_text is None) and
 130             util.signed_locator_pattern.match(self._manifest_locator)):
 131             error_via_keep = self._populate_from_keep()
 132         if self._manifest_text is None:
 133             error_via_api = self._populate_from_api_server()
 134             if error_via_api is not None and not should_try_keep:
 135                 raise error_via_api
 136         if ((self._manifest_text is None) and
 137             not error_via_keep and
 138             should_try_keep):
 139             # Looks like a keep locator, and we didn't already try keep above
 140             error_via_keep = self._populate_from_keep()
 141         if self._manifest_text is None:
 142             # Nothing worked!
 143             raise arvados.errors.NotFoundError(
 144                 ("Failed to retrieve collection '{}' " +
 145                  "from either API server ({}) or Keep ({})."
 146                  ).format(
 147                     self._manifest_locator,
 148                     error_via_api,
 149                     error_via_keep))
 150         self._streams = [sline.split()
 151                          for sline in self._manifest_text.split("\n")
 152                          if sline]
 153
 154     def _populate_first(orig_func):
 155         # Decorator for methods that read actual Collection data.
 156         @functools.wraps(orig_func)
 157         def wrapper(self, *args, **kwargs):
 158             if self._streams is None:
 159                 self._populate()
 160             return orig_func(self, *args, **kwargs)
 161         return wrapper
 162
 163     @_populate_first
 164     def api_response(self):
 165         """api_response() -> dict or None
 166
 167         Returns information about this Collection fetched from the API server.
 168         If the Collection exists in Keep but not the API server, currently
 169         returns None.  Future versions may provide a synthetic response.
 170         """
 171         return self._api_response
 172
 173     @_populate_first
 174     def normalize(self):
 175         # Rearrange streams
 176         streams = {}
 177         for s in self.all_streams():
 178             for f in s.all_files():
 179                 streamname, filename = split(s.name() + "/" + f.name())
 180                 if streamname not in streams:
 181                     streams[streamname] = {}
 182                 if filename not in streams[streamname]:
 183                     streams[streamname][filename] = []
 184                 for r in f.segments:
 185                     streams[streamname][filename].extend(s.locators_and_ranges(r.locator, r.range_size))
 186
 187         self._streams = [normalize_stream(s, streams[s])
 188                          for s in sorted(streams)]
 189
 190         # Regenerate the manifest text based on the normalized streams
 191         self._manifest_text = ''.join(
 192             [StreamReader(stream, keep=self._my_keep()).manifest_text()
 193              for stream in self._streams])
 194
 195     @_populate_first
 196     def open(self, streampath, filename=None):
 197         """open(streampath[, filename]) -> file-like object
 198
 199         Pass in the path of a file to read from the Collection, either as a
 200         single string or as two separate stream name and file name arguments.
 201         This method returns a file-like object to read that file.
 202         """
 203         if filename is None:
 204             streampath, filename = split(streampath)
 205         keep_client = self._my_keep()
 206         for stream_s in self._streams:
 207             stream = StreamReader(stream_s, keep_client,
 208                                   num_retries=self.num_retries)
 209             if stream.name() == streampath:
 210                 break
 211         else:
 212             raise ValueError("stream '{}' not found in Collection".
 213                              format(streampath))
 214         try:
 215             return stream.files()[filename]
 216         except KeyError:
 217             raise ValueError("file '{}' not found in Collection stream '{}'".
 218                              format(filename, streampath))
 219
 220     @_populate_first
 221     def all_streams(self):
 222         return [StreamReader(s, self._my_keep(), num_retries=self.num_retries)
 223                 for s in self._streams]
 224
 225     def all_files(self):
 226         for s in self.all_streams():
 227             for f in s.all_files():
 228                 yield f
 229
 230     @_populate_first
 231     def manifest_text(self, strip=False, normalize=False):
 232         if normalize:
 233             cr = CollectionReader(self.manifest_text())
 234             cr.normalize()
 235             return cr.manifest_text(strip=strip, normalize=False)
 236         elif strip:
 237             return self.stripped_manifest()
 238         else:
 239             return self._manifest_text
 240
 241
 242 class _WriterFile(ArvadosFileBase):
 243     def __init__(self, coll_writer, name):
 244         super(_WriterFile, self).__init__(name, 'wb')
 245         self.dest = coll_writer
 246
 247     def close(self):
 248         super(_WriterFile, self).close()
 249         self.dest.finish_current_file()
 250
 251     @ArvadosFileBase._before_close
 252     def write(self, data):
 253         self.dest.write(data)
 254
 255     @ArvadosFileBase._before_close
 256     def writelines(self, seq):
 257         for data in seq:
 258             self.write(data)
 259
 260     @ArvadosFileBase._before_close
 261     def flush(self):
 262         self.dest.flush_data()
 263
 264
 265 class CollectionWriter(CollectionBase):
 266     def __init__(self, api_client=None, num_retries=0):
 267         """Instantiate a CollectionWriter.
 268
 269         CollectionWriter lets you build a new Arvados Collection from scratch.
 270         Write files to it.  The CollectionWriter will upload data to Keep as
 271         appropriate, and provide you with the Collection manifest text when
 272         you're finished.
 273
 274         Arguments:
 275         * api_client: The API client to use to look up Collections.  If not
 276           provided, CollectionReader will build one from available Arvados
 277           configuration.
 278         * num_retries: The default number of times to retry failed
 279           service requests.  Default 0.  You may change this value
 280           after instantiation, but note those changes may not
 281           propagate to related objects like the Keep client.
 282         """
 283         self._api_client = api_client
 284         self.num_retries = num_retries
 285         self._keep_client = None
 286         self._data_buffer = []
 287         self._data_buffer_len = 0
 288         self._current_stream_files = []
 289         self._current_stream_length = 0
 290         self._current_stream_locators = []
 291         self._current_stream_name = '.'
 292         self._current_file_name = None
 293         self._current_file_pos = 0
 294         self._finished_streams = []
 295         self._close_file = None
 296         self._queued_file = None
 297         self._queued_dirents = deque()
 298         self._queued_trees = deque()
 299         self._last_open = None
 300
 301     def __exit__(self, exc_type, exc_value, traceback):
 302         if exc_type is None:
 303             self.finish()
 304
 305     def do_queued_work(self):
 306         # The work queue consists of three pieces:
 307         # * _queued_file: The file object we're currently writing to the
 308         #   Collection.
 309         # * _queued_dirents: Entries under the current directory
 310         #   (_queued_trees[0]) that we want to write or recurse through.
 311         #   This may contain files from subdirectories if
 312         #   max_manifest_depth == 0 for this directory.
 313         # * _queued_trees: Directories that should be written as separate
 314         #   streams to the Collection.
 315         # This function handles the smallest piece of work currently queued
 316         # (current file, then current directory, then next directory) until
 317         # no work remains.  The _work_THING methods each do a unit of work on
 318         # THING.  _queue_THING methods add a THING to the work queue.
 319         while True:
 320             if self._queued_file:
 321                 self._work_file()
 322             elif self._queued_dirents:
 323                 self._work_dirents()
 324             elif self._queued_trees:
 325                 self._work_trees()
 326             else:
 327                 break
 328
 329     def _work_file(self):
 330         while True:
 331             buf = self._queued_file.read(config.KEEP_BLOCK_SIZE)
 332             if not buf:
 333                 break
 334             self.write(buf)
 335         self.finish_current_file()
 336         if self._close_file:
 337             self._queued_file.close()
 338         self._close_file = None
 339         self._queued_file = None
 340
 341     def _work_dirents(self):
 342         path, stream_name, max_manifest_depth = self._queued_trees[0]
 343         if stream_name != self.current_stream_name():
 344             self.start_new_stream(stream_name)
 345         while self._queued_dirents:
 346             dirent = self._queued_dirents.popleft()
 347             target = os.path.join(path, dirent)
 348             if os.path.isdir(target):
 349                 self._queue_tree(target,
 350                                  os.path.join(stream_name, dirent),
 351                                  max_manifest_depth - 1)
 352             else:
 353                 self._queue_file(target, dirent)
 354                 break
 355         if not self._queued_dirents:
 356             self._queued_trees.popleft()
 357
 358     def _work_trees(self):
 359         path, stream_name, max_manifest_depth = self._queued_trees[0]
 360         d = util.listdir_recursive(
 361             path, max_depth = (None if max_manifest_depth == 0 else 0))
 362         if d:
 363             self._queue_dirents(stream_name, d)
 364         else:
 365             self._queued_trees.popleft()
 366
 367     def _queue_file(self, source, filename=None):
 368         assert (self._queued_file is None), "tried to queue more than one file"
 369         if not hasattr(source, 'read'):
 370             source = open(source, 'rb')
 371             self._close_file = True
 372         else:
 373             self._close_file = False
 374         if filename is None:
 375             filename = os.path.basename(source.name)
 376         self.start_new_file(filename)
 377         self._queued_file = source
 378
 379     def _queue_dirents(self, stream_name, dirents):
 380         assert (not self._queued_dirents), "tried to queue more than one tree"
 381         self._queued_dirents = deque(sorted(dirents))
 382
 383     def _queue_tree(self, path, stream_name, max_manifest_depth):
 384         self._queued_trees.append((path, stream_name, max_manifest_depth))
 385
 386     def write_file(self, source, filename=None):
 387         self._queue_file(source, filename)
 388         self.do_queued_work()
 389
 390     def write_directory_tree(self,
 391                              path, stream_name='.', max_manifest_depth=-1):
 392         self._queue_tree(path, stream_name, max_manifest_depth)
 393         self.do_queued_work()
 394
 395     def write(self, newdata):
 396         if hasattr(newdata, '__iter__'):
 397             for s in newdata:
 398                 self.write(s)
 399             return
 400         self._data_buffer.append(newdata)
 401         self._data_buffer_len += len(newdata)
 402         self._current_stream_length += len(newdata)
 403         while self._data_buffer_len >= config.KEEP_BLOCK_SIZE:
 404             self.flush_data()
 405
 406     def open(self, streampath, filename=None):
 407         """open(streampath[, filename]) -> file-like object
 408
 409         Pass in the path of a file to write to the Collection, either as a
 410         single string or as two separate stream name and file name arguments.
 411         This method returns a file-like object you can write to add it to the
 412         Collection.
 413
 414         You may only have one file object from the Collection open at a time,
 415         so be sure to close the object when you're done.  Using the object in
 416         a with statement makes that easy::
 417
 418           with cwriter.open('./doc/page1.txt') as outfile:
 419               outfile.write(page1_data)
 420           with cwriter.open('./doc/page2.txt') as outfile:
 421               outfile.write(page2_data)
 422         """
 423         if filename is None:
 424             streampath, filename = split(streampath)
 425         if self._last_open and not self._last_open.closed:
 426             raise errors.AssertionError(
 427                 "can't open '{}' when '{}' is still open".format(
 428                     filename, self._last_open.name))
 429         if streampath != self.current_stream_name():
 430             self.start_new_stream(streampath)
 431         self.set_current_file_name(filename)
 432         self._last_open = _WriterFile(self, filename)
 433         return self._last_open
 434
 435     def flush_data(self):
 436         data_buffer = ''.join(self._data_buffer)
 437         if data_buffer:
 438             self._current_stream_locators.append(
 439                 self._my_keep().put(data_buffer[0:config.KEEP_BLOCK_SIZE]))
 440             self._data_buffer = [data_buffer[config.KEEP_BLOCK_SIZE:]]
 441             self._data_buffer_len = len(self._data_buffer[0])
 442
 443     def start_new_file(self, newfilename=None):
 444         self.finish_current_file()
 445         self.set_current_file_name(newfilename)
 446
 447     def set_current_file_name(self, newfilename):
 448         if re.search(r'[\t\n]', newfilename):
 449             raise errors.AssertionError(
 450                 "Manifest filenames cannot contain whitespace: %s" %
 451                 newfilename)
 452         elif re.search(r'\x00', newfilename):
 453             raise errors.AssertionError(
 454                 "Manifest filenames cannot contain NUL characters: %s" %
 455                 newfilename)
 456         self._current_file_name = newfilename
 457
 458     def current_file_name(self):
 459         return self._current_file_name
 460
 461     def finish_current_file(self):
 462         if self._current_file_name is None:
 463             if self._current_file_pos == self._current_stream_length:
 464                 return
 465             raise errors.AssertionError(
 466                 "Cannot finish an unnamed file " +
 467                 "(%d bytes at offset %d in '%s' stream)" %
 468                 (self._current_stream_length - self._current_file_pos,
 469                  self._current_file_pos,
 470                  self._current_stream_name))
 471         self._current_stream_files.append([
 472                 self._current_file_pos,
 473                 self._current_stream_length - self._current_file_pos,
 474                 self._current_file_name])
 475         self._current_file_pos = self._current_stream_length
 476         self._current_file_name = None
 477
 478     def start_new_stream(self, newstreamname='.'):
 479         self.finish_current_stream()
 480         self.set_current_stream_name(newstreamname)
 481
 482     def set_current_stream_name(self, newstreamname):
 483         if re.search(r'[\t\n]', newstreamname):
 484             raise errors.AssertionError(
 485                 "Manifest stream names cannot contain whitespace")
 486         self._current_stream_name = '.' if newstreamname=='' else newstreamname
 487
 488     def current_stream_name(self):
 489         return self._current_stream_name
 490
 491     def finish_current_stream(self):
 492         self.finish_current_file()
 493         self.flush_data()
 494         if not self._current_stream_files:
 495             pass
 496         elif self._current_stream_name is None:
 497             raise errors.AssertionError(
 498                 "Cannot finish an unnamed stream (%d bytes in %d files)" %
 499                 (self._current_stream_length, len(self._current_stream_files)))
 500         else:
 501             if not self._current_stream_locators:
 502                 self._current_stream_locators.append(config.EMPTY_BLOCK_LOCATOR)
 503             self._finished_streams.append([self._current_stream_name,
 504                                            self._current_stream_locators,
 505                                            self._current_stream_files])
 506         self._current_stream_files = []
 507         self._current_stream_length = 0
 508         self._current_stream_locators = []
 509         self._current_stream_name = None
 510         self._current_file_pos = 0
 511         self._current_file_name = None
 512
 513     def finish(self):
 514         # Store the manifest in Keep and return its locator.
 515         return self._my_keep().put(self.manifest_text())
 516
 517     def portable_data_hash(self):
 518         stripped = self.stripped_manifest()
 519         return hashlib.md5(stripped).hexdigest() + '+' + str(len(stripped))
 520
 521     def manifest_text(self):
 522         self.finish_current_stream()
 523         manifest = ''
 524
 525         for stream in self._finished_streams:
 526             if not re.search(r'^\.(/.*)?$', stream[0]):
 527                 manifest += './'
 528             manifest += stream[0].replace(' ', '\\040')
 529             manifest += ' ' + ' '.join(stream[1])
 530             manifest += ' ' + ' '.join("%d:%d:%s" % (sfile[0], sfile[1], sfile[2].replace(' ', '\\040')) for sfile in stream[2])
 531             manifest += "\n"
 532
 533         return manifest
 534
 535     def data_locators(self):
 536         ret = []
 537         for name, locators, files in self._finished_streams:
 538             ret += locators
 539         return ret
 540
 541
 542 class ResumableCollectionWriter(CollectionWriter):
 543     STATE_PROPS = ['_current_stream_files', '_current_stream_length',
 544                    '_current_stream_locators', '_current_stream_name',
 545                    '_current_file_name', '_current_file_pos', '_close_file',
 546                    '_data_buffer', '_dependencies', '_finished_streams',
 547                    '_queued_dirents', '_queued_trees']
 548
 549     def __init__(self, api_client=None, num_retries=0):
 550         self._dependencies = {}
 551         super(ResumableCollectionWriter, self).__init__(
 552             api_client, num_retries=num_retries)
 553
 554     @classmethod
 555     def from_state(cls, state, *init_args, **init_kwargs):
 556         # Try to build a new writer from scratch with the given state.
 557         # If the state is not suitable to resume (because files have changed,
 558         # been deleted, aren't predictable, etc.), raise a
 559         # StaleWriterStateError.  Otherwise, return the initialized writer.
 560         # The caller is responsible for calling writer.do_queued_work()
 561         # appropriately after it's returned.
 562         writer = cls(*init_args, **init_kwargs)
 563         for attr_name in cls.STATE_PROPS:
 564             attr_value = state[attr_name]
 565             attr_class = getattr(writer, attr_name).__class__
 566             # Coerce the value into the same type as the initial value, if
 567             # needed.
 568             if attr_class not in (type(None), attr_value.__class__):
 569                 attr_value = attr_class(attr_value)
 570             setattr(writer, attr_name, attr_value)
 571         # Check dependencies before we try to resume anything.
 572         if any(KeepLocator(ls).permission_expired()
 573                for ls in writer._current_stream_locators):
 574             raise errors.StaleWriterStateError(
 575                 "locators include expired permission hint")
 576         writer.check_dependencies()
 577         if state['_current_file'] is not None:
 578             path, pos = state['_current_file']
 579             try:
 580                 writer._queued_file = open(path, 'rb')
 581                 writer._queued_file.seek(pos)
 582             except IOError as error:
 583                 raise errors.StaleWriterStateError(
 584                     "failed to reopen active file {}: {}".format(path, error))
 585         return writer
 586
 587     def check_dependencies(self):
 588         for path, orig_stat in self._dependencies.items():
 589             if not S_ISREG(orig_stat[ST_MODE]):
 590                 raise errors.StaleWriterStateError("{} not file".format(path))
 591             try:
 592                 now_stat = tuple(os.stat(path))
 593             except OSError as error:
 594                 raise errors.StaleWriterStateError(
 595                     "failed to stat {}: {}".format(path, error))
 596             if ((not S_ISREG(now_stat[ST_MODE])) or
 597                 (orig_stat[ST_MTIME] != now_stat[ST_MTIME]) or
 598                 (orig_stat[ST_SIZE] != now_stat[ST_SIZE])):
 599                 raise errors.StaleWriterStateError("{} changed".format(path))
 600
 601     def dump_state(self, copy_func=lambda x: x):
 602         state = {attr: copy_func(getattr(self, attr))
 603                  for attr in self.STATE_PROPS}
 604         if self._queued_file is None:
 605             state['_current_file'] = None
 606         else:
 607             state['_current_file'] = (os.path.realpath(self._queued_file.name),
 608                                       self._queued_file.tell())
 609         return state
 610
 611     def _queue_file(self, source, filename=None):
 612         try:
 613             src_path = os.path.realpath(source)
 614         except Exception:
 615             raise errors.AssertionError("{} not a file path".format(source))
 616         try:
 617             path_stat = os.stat(src_path)
 618         except OSError as stat_error:
 619             path_stat = None
 620         super(ResumableCollectionWriter, self)._queue_file(source, filename)
 621         fd_stat = os.fstat(self._queued_file.fileno())
 622         if not S_ISREG(fd_stat.st_mode):
 623             # We won't be able to resume from this cache anyway, so don't
 624             # worry about further checks.
 625             self._dependencies[source] = tuple(fd_stat)
 626         elif path_stat is None:
 627             raise errors.AssertionError(
 628                 "could not stat {}: {}".format(source, stat_error))
 629         elif path_stat.st_ino != fd_stat.st_ino:
 630             raise errors.AssertionError(
 631                 "{} changed between open and stat calls".format(source))
 632         else:
 633             self._dependencies[src_path] = tuple(fd_stat)
 634
 635     def write(self, data):
 636         if self._queued_file is None:
 637             raise errors.AssertionError(
 638                 "resumable writer can't accept unsourced data")
 639         return super(ResumableCollectionWriter, self).write(data)
 640
 641
 642 class Collection(CollectionBase):
 643     def __init__(self, manifest_locator_or_text=None, api_client=None,
 644                  keep_client=None, num_retries=0):
 645
 646         self._items = None
 647         self._api_client = api_client
 648         self._keep_client = keep_client
 649         self.num_retries = num_retries
 650         self._manifest_locator = None
 651         self._manifest_text = None
 652         self._api_response = None
 653
 654         if manifest_locator_or_text:
 655             if re.match(util.keep_locator_pattern, manifest_locator_or_text):
 656                 self._manifest_locator = manifest_locator_or_text
 657             elif re.match(util.collection_uuid_pattern, manifest_locator_or_text):
 658                 self._manifest_locator = manifest_locator_or_text
 659             elif re.match(util.manifest_pattern, manifest_locator_or_text):
 660                 self._manifest_text = manifest_locator_or_text
 661             else:
 662                 raise errors.ArgumentError(
 663                     "Argument to CollectionReader must be a manifest or a collection UUID")
 664
 665     def _populate_from_api_server(self):
 666         # As in KeepClient itself, we must wait until the last
 667         # possible moment to instantiate an API client, in order to
 668         # avoid tripping up clients that don't have access to an API
 669         # server.  If we do build one, make sure our Keep client uses
 670         # it.  If instantiation fails, we'll fall back to the except
 671         # clause, just like any other Collection lookup
 672         # failure. Return an exception, or None if successful.
 673         try:
 674             if self._api_client is None:
 675                 self._api_client = arvados.api('v1')
 676                 self._keep_client = None  # Make a new one with the new api.
 677             self._api_response = self._api_client.collections().get(
 678                 uuid=self._manifest_locator).execute(
 679                     num_retries=self.num_retries)
 680             self._manifest_text = self._api_response['manifest_text']
 681             return None
 682         except Exception as e:
 683             return e
 684
 685     def _populate_from_keep(self):
 686         # Retrieve a manifest directly from Keep. This has a chance of
 687         # working if [a] the locator includes a permission signature
 688         # or [b] the Keep services are operating in world-readable
 689         # mode. Return an exception, or None if successful.
 690         try:
 691             self._manifest_text = self._my_keep().get(
 692                 self._manifest_locator, num_retries=self.num_retries)
 693         except Exception as e:
 694             return e
 695
 696     def _populate(self):
 697         self._items = {}
 698         if self._manifest_locator is None and self._manifest_text is None:
 699             return
 700         error_via_api = None
 701         error_via_keep = None
 702         should_try_keep = ((self._manifest_text is None) and
 703                            util.keep_locator_pattern.match(
 704                 self._manifest_locator))
 705         if ((self._manifest_text is None) and
 706             util.signed_locator_pattern.match(self._manifest_locator)):
 707             error_via_keep = self._populate_from_keep()
 708         if self._manifest_text is None:
 709             error_via_api = self._populate_from_api_server()
 710             if error_via_api is not None and not should_try_keep:
 711                 raise error_via_api
 712         if ((self._manifest_text is None) and
 713             not error_via_keep and
 714             should_try_keep):
 715             # Looks like a keep locator, and we didn't already try keep above
 716             error_via_keep = self._populate_from_keep()
 717         if self._manifest_text is None:
 718             # Nothing worked!
 719             raise arvados.errors.NotFoundError(
 720                 ("Failed to retrieve collection '{}' " +
 721                  "from either API server ({}) or Keep ({})."
 722                  ).format(
 723                     self._manifest_locator,
 724                     error_via_api,
 725                     error_via_keep))
 726         # populate
 727         import_manifest(self._manifest_text, self)
 728
 729     def _populate_first(orig_func):
 730         # Decorator for methods that read actual Collection data.
 731         @functools.wraps(orig_func)
 732         def wrapper(self, *args, **kwargs):
 733             if self._items is None:
 734                 self._populate()
 735             return orig_func(self, *args, **kwargs)
 736         return wrapper
 737
 738     def __enter__(self):
 739         return self
 740
 741     def __exit__(self, exc_type, exc_value, traceback):
 742         self.save()
 743
 744     @_populate_first
 745     def find(self, path, create=False):
 746         p = path.split("/")
 747         if p[0] == '.':
 748             del p[0]
 749
 750         if len(p) > 0:
 751             item = self._items.get(p[0])
 752             if len(p) == 1:
 753                 # item must be a file
 754                 if item is None and create:
 755                     # create new file
 756                     item = ArvadosFile(keep=self._keep_client)
 757                     self._items[p[0]] = item
 758                 return item
 759             else:
 760                 if item is None and create:
 761                     # create new collection
 762                     item = Collection(api_client=self._api_client, keep=self._keep_client, num_retries=self.num_retries)
 763                     self._items[p[0]] = item
 764                 del p[0]
 765                 return item.find("/".join(p), create=create)
 766         else:
 767             return self
 768
 769     @_populate_first
 770     def api_response(self):
 771         """api_response() -> dict or None
 772
 773         Returns information about this Collection fetched from the API server.
 774         If the Collection exists in Keep but not the API server, currently
 775         returns None.  Future versions may provide a synthetic response.
 776         """
 777         return self._api_response
 778
 779     def open(self, path, mode):
 780         mode = mode.replace("b", "")
 781         if len(mode) == 0 or mode[0] not in ("r", "w", "a"):
 782             raise ArgumentError("Bad mode '%s'" % mode)
 783         create = (mode != "r")
 784
 785         f = self.find(path, create=create)
 786         if f is None:
 787             raise ArgumentError("File not found")
 788         if not isinstance(f, ArvadosFile):
 789             raise ArgumentError("Path must refer to a file.")
 790
 791         if mode[0] == "w":
 792             f.truncate(0)
 793
 794         if mode == "r":
 795             return ArvadosFileReader(f, path, mode)
 796         else:
 797             return ArvadosFileWriter(f, path, mode)
 798
 799     @_populate_first
 800     def modified(self):
 801         for k,v in self._items.items():
 802             if v.modified():
 803                 return True
 804         return False
 805
 806     @_populate_first
 807     def set_unmodified(self):
 808         for k,v in self._items.items():
 809             v.set_unmodified()
 810
 811     @_populate_first
 812     def __iter__(self):
 813         self._items.iterkeys()
 814
 815     @_populate_first
 816     def iterkeys(self):
 817         self._items.iterkeys()
 818
 819     @_populate_first
 820     def __getitem__(self, k):
 821         r = self.find(k)
 822         if r:
 823             return r
 824         else:
 825             raise KeyError(k)
 826
 827     @_populate_first
 828     def __contains__(self, k):
 829         return self.find(k) is not None
 830
 831     @_populate_first
 832     def __len__(self):
 833        return len(self._items)
 834
 835     @_populate_first
 836     def __delitem__(self, p):
 837         p = path.split("/")
 838         if p[0] == '.':
 839             del p[0]
 840
 841         if len(p) > 0:
 842             item = self._items.get(p[0])
 843             if item is None:
 844                 raise NotFoundError()
 845             if len(p) == 1:
 846                 del self._items[p[0]]
 847             else:
 848                 del p[0]
 849                 del item["/".join(p)]
 850         else:
 851             raise NotFoundError()
 852
 853     @_populate_first
 854     def keys(self):
 855         return self._items.keys()
 856
 857     @_populate_first
 858     def values(self):
 859         return self._items.values()
 860
 861     @_populate_first
 862     def items(self):
 863         return self._items.items()
 864
 865     @_populate_first
 866     def manifest_text(self, strip=False, normalize=False):
 867         if self.modified() or self._manifest_text is None or normalize:
 868             return export_manifest(self, stream_name=".", portable_locators=strip)
 869         else:
 870             if strip:
 871                 return self.stripped_manifest()
 872             else:
 873                 return self._manifest_text
 874
 875     def portable_data_hash(self):
 876         stripped = self.manifest_text(strip=True)
 877         return hashlib.md5(stripped).hexdigest() + '+' + str(len(stripped))
 878
 879     @_populate_first
 880     def commit_bufferblocks(self):
 881         pass
 882
 883     @_populate_first
 884     def save(self):
 885         if self.modified():
 886             self._my_keep().put(self.manifest_text(strip=True))
 887             if re.match(util.collection_uuid_pattern, self._manifest_locator):
 888                 self._api_response = self._api_client.collections().update(
 889                     uuid=self._manifest_locator,
 890                     body={'manifest_text': self.manifest_text(strip=False)}
 891                     ).execute(
 892                         num_retries=self.num_retries)
 893             else:
 894                 raise AssertionError("Collection manifest_locator must be a collection uuid.  Use save_as() for new collections.")
 895             self.set_unmodified()
 896
 897     @_populate_first
 898     def save_as(self, name, owner_uuid=None):
 899         self._my_keep().put(self.manifest_text(strip=True))
 900         body = {"manifest_text": self.manifest_text(strip=False),
 901                 "name": name}
 902         if owner_uuid:
 903             body["owner_uuid"] = owner_uuid
 904         self._api_response = self._api_client.collections().create(body=body).execute(num_retries=self.num_retries)
 905         self._manifest_locator = self._api_response["uuid"]
 906         self.set_unmodified()
 907
 908
 909 def import_manifest(manifest_text, into_collection=None, api_client=None, keep=None, num_retries=None):
 910     if into_collection is not None:
 911         if len(into_collection) > 0:
 912             raise ArgumentError("Can only import manifest into an empty collection")
 913         c = into_collection
 914     else:
 915         c = Collection(api_client=api_client, keep_client=keep, num_retries=num_retries)
 916
 917     STREAM_NAME = 0
 918     BLOCKS = 1
 919     SEGMENTS = 2
 920
 921     stream_name = None
 922     state = STREAM_NAME
 923
 924     for n in re.finditer(r'(\S+)(\s+|$)', manifest_text):
 925         tok = n.group(1)
 926         sep = n.group(2)
 927
 928         if state == STREAM_NAME:
 929             # starting a new stream
 930             stream_name = tok.replace('\\040', ' ')
 931             blocks = []
 932             segments = []
 933             streamoffset = 0L
 934             state = BLOCKS
 935             continue
 936
 937         if state == BLOCKS:
 938             s = re.match(r'[0-9a-f]{32}\+(\d+)(\+\S+)*', tok)
 939             if s:
 940                 blocksize = long(s.group(1))
 941                 blocks.append(Range(tok, streamoffset, blocksize))
 942                 streamoffset += blocksize
 943             else:
 944                 state = SEGMENTS
 945
 946         if state == SEGMENTS:
 947             s = re.search(r'^(\d+):(\d+):(\S+)', tok)
 948             if s:
 949                 pos = long(s.group(1))
 950                 size = long(s.group(2))
 951                 name = s.group(3).replace('\\040', ' ')
 952                 f = c.find("%s/%s" % (stream_name, name), create=True)
 953                 f.add_segment(blocks, pos, size)
 954             else:
 955                 # error!
 956                 raise errors.SyntaxError("Invalid manifest format")
 957
 958         if sep == "\n":
 959             stream_name = None
 960             state = STREAM_NAME
 961
 962     c.set_unmodified()
 963     return c
 964
 965 def export_manifest(item, stream_name=".", portable_locators=False):
 966     buf = ""
 967     if isinstance(item, Collection):
 968         stream = {}
 969         sorted_keys = sorted(item.keys())
 970         for k in [s for s in sorted_keys if isinstance(item[s], ArvadosFile)]:
 971             v = item[k]
 972             st = []
 973             for s in v._segments:
 974                 loc = s.locator
 975                 if loc.startswith("bufferblock"):
 976                     loc = v._bufferblocks[loc].calculate_locator()
 977                 st.append(LocatorAndRange(loc, locator_block_size(loc),
 978                                      s.segment_offset, s.range_size))
 979             stream[k] = st
 980         buf += ' '.join(normalize_stream(stream_name, stream))
 981         buf += "\n"
 982         for k in [s for s in sorted_keys if isinstance(item[s], Collection)]:
 983             buf += export_manifest(item[k], stream_name=os.path.join(stream_name, k))
 984     elif isinstance(item, ArvadosFile):
 985         st = []
 986         for s in item._segments:
 987             loc = s.locator
 988             if loc.startswith("bufferblock"):
 989                 loc = item._bufferblocks[loc].calculate_locator()
 990             st.append(LocatorAndRange(loc, locator_block_size(loc),
 991                                  s.segment_offset, s.range_size))
 992         stream[stream_name] = st
 993         buf += ' '.join(normalize_stream(stream_name, stream))
 994         buf += "\n"
 995     return buf