sdk/python/arvados/collection.py

   1 # Copyright (C) The Arvados Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: Apache-2.0
   4
   5 from __future__ import absolute_import
   6 from future.utils import listitems, listvalues, viewkeys
   7 from builtins import str
   8 from past.builtins import basestring
   9 from builtins import object
  10 import ciso8601
  11 import datetime
  12 import errno
  13 import functools
  14 import hashlib
  15 import io
  16 import logging
  17 import os
  18 import re
  19 import sys
  20 import threading
  21 import time
  22
  23 from collections import deque
  24 from stat import *
  25
  26 from .arvfile import split, _FileLikeObjectBase, ArvadosFile, ArvadosFileWriter, ArvadosFileReader, WrappableFile, _BlockManager, synchronized, must_be_writable, NoopLock
  27 from .keep import KeepLocator, KeepClient
  28 from .stream import StreamReader
  29 from ._normalize_stream import normalize_stream, escape
  30 from ._ranges import Range, LocatorAndRange
  31 from .safeapi import ThreadSafeApiCache
  32 import arvados.config as config
  33 import arvados.errors as errors
  34 import arvados.util
  35 import arvados.events as events
  36 from arvados.retry import retry_method
  37
  38 _logger = logging.getLogger('arvados.collection')
  39
  40
  41 if sys.version_info >= (3, 0):
  42     TextIOWrapper = io.TextIOWrapper
  43 else:
  44     class TextIOWrapper(io.TextIOWrapper):
  45         """To maintain backward compatibility, cast str to unicode in
  46         write('foo').
  47
  48         """
  49         def write(self, data):
  50             if isinstance(data, basestring):
  51                 data = unicode(data)
  52             return super(TextIOWrapper, self).write(data)
  53
  54
  55 class CollectionBase(object):
  56     """Abstract base class for Collection classes."""
  57
  58     def __enter__(self):
  59         return self
  60
  61     def __exit__(self, exc_type, exc_value, traceback):
  62         pass
  63
  64     def _my_keep(self):
  65         if self._keep_client is None:
  66             self._keep_client = KeepClient(api_client=self._api_client,
  67                                            num_retries=self.num_retries)
  68         return self._keep_client
  69
  70     def stripped_manifest(self):
  71         """Get the manifest with locator hints stripped.
  72
  73         Return the manifest for the current collection with all
  74         non-portable hints (i.e., permission signatures and other
  75         hints other than size hints) removed from the locators.
  76         """
  77         raw = self.manifest_text()
  78         clean = []
  79         for line in raw.split("\n"):
  80             fields = line.split()
  81             if fields:
  82                 clean_fields = fields[:1] + [
  83                     (re.sub(r'\+[^\d][^\+]*', '', x)
  84                      if re.match(arvados.util.keep_locator_pattern, x)
  85                      else x)
  86                     for x in fields[1:]]
  87                 clean += [' '.join(clean_fields), "\n"]
  88         return ''.join(clean)
  89
  90
  91 class _WriterFile(_FileLikeObjectBase):
  92     def __init__(self, coll_writer, name):
  93         super(_WriterFile, self).__init__(name, 'wb')
  94         self.dest = coll_writer
  95
  96     def close(self):
  97         super(_WriterFile, self).close()
  98         self.dest.finish_current_file()
  99
 100     @_FileLikeObjectBase._before_close
 101     def write(self, data):
 102         self.dest.write(data)
 103
 104     @_FileLikeObjectBase._before_close
 105     def writelines(self, seq):
 106         for data in seq:
 107             self.write(data)
 108
 109     @_FileLikeObjectBase._before_close
 110     def flush(self):
 111         self.dest.flush_data()
 112
 113
 114 class CollectionWriter(CollectionBase):
 115     """Deprecated, use Collection instead."""
 116
 117     def __init__(self, api_client=None, num_retries=0, replication=None):
 118         """Instantiate a CollectionWriter.
 119
 120         CollectionWriter lets you build a new Arvados Collection from scratch.
 121         Write files to it.  The CollectionWriter will upload data to Keep as
 122         appropriate, and provide you with the Collection manifest text when
 123         you're finished.
 124
 125         Arguments:
 126         * api_client: The API client to use to look up Collections.  If not
 127           provided, CollectionReader will build one from available Arvados
 128           configuration.
 129         * num_retries: The default number of times to retry failed
 130           service requests.  Default 0.  You may change this value
 131           after instantiation, but note those changes may not
 132           propagate to related objects like the Keep client.
 133         * replication: The number of copies of each block to store.
 134           If this argument is None or not supplied, replication is
 135           the server-provided default if available, otherwise 2.
 136         """
 137         self._api_client = api_client
 138         self.num_retries = num_retries
 139         self.replication = (2 if replication is None else replication)
 140         self._keep_client = None
 141         self._data_buffer = []
 142         self._data_buffer_len = 0
 143         self._current_stream_files = []
 144         self._current_stream_length = 0
 145         self._current_stream_locators = []
 146         self._current_stream_name = '.'
 147         self._current_file_name = None
 148         self._current_file_pos = 0
 149         self._finished_streams = []
 150         self._close_file = None
 151         self._queued_file = None
 152         self._queued_dirents = deque()
 153         self._queued_trees = deque()
 154         self._last_open = None
 155
 156     def __exit__(self, exc_type, exc_value, traceback):
 157         if exc_type is None:
 158             self.finish()
 159
 160     def do_queued_work(self):
 161         # The work queue consists of three pieces:
 162         # * _queued_file: The file object we're currently writing to the
 163         #   Collection.
 164         # * _queued_dirents: Entries under the current directory
 165         #   (_queued_trees[0]) that we want to write or recurse through.
 166         #   This may contain files from subdirectories if
 167         #   max_manifest_depth == 0 for this directory.
 168         # * _queued_trees: Directories that should be written as separate
 169         #   streams to the Collection.
 170         # This function handles the smallest piece of work currently queued
 171         # (current file, then current directory, then next directory) until
 172         # no work remains.  The _work_THING methods each do a unit of work on
 173         # THING.  _queue_THING methods add a THING to the work queue.
 174         while True:
 175             if self._queued_file:
 176                 self._work_file()
 177             elif self._queued_dirents:
 178                 self._work_dirents()
 179             elif self._queued_trees:
 180                 self._work_trees()
 181             else:
 182                 break
 183
 184     def _work_file(self):
 185         while True:
 186             buf = self._queued_file.read(config.KEEP_BLOCK_SIZE)
 187             if not buf:
 188                 break
 189             self.write(buf)
 190         self.finish_current_file()
 191         if self._close_file:
 192             self._queued_file.close()
 193         self._close_file = None
 194         self._queued_file = None
 195
 196     def _work_dirents(self):
 197         path, stream_name, max_manifest_depth = self._queued_trees[0]
 198         if stream_name != self.current_stream_name():
 199             self.start_new_stream(stream_name)
 200         while self._queued_dirents:
 201             dirent = self._queued_dirents.popleft()
 202             target = os.path.join(path, dirent)
 203             if os.path.isdir(target):
 204                 self._queue_tree(target,
 205                                  os.path.join(stream_name, dirent),
 206                                  max_manifest_depth - 1)
 207             else:
 208                 self._queue_file(target, dirent)
 209                 break
 210         if not self._queued_dirents:
 211             self._queued_trees.popleft()
 212
 213     def _work_trees(self):
 214         path, stream_name, max_manifest_depth = self._queued_trees[0]
 215         d = arvados.util.listdir_recursive(
 216             path, max_depth = (None if max_manifest_depth == 0 else 0))
 217         if d:
 218             self._queue_dirents(stream_name, d)
 219         else:
 220             self._queued_trees.popleft()
 221
 222     def _queue_file(self, source, filename=None):
 223         assert (self._queued_file is None), "tried to queue more than one file"
 224         if not hasattr(source, 'read'):
 225             source = open(source, 'rb')
 226             self._close_file = True
 227         else:
 228             self._close_file = False
 229         if filename is None:
 230             filename = os.path.basename(source.name)
 231         self.start_new_file(filename)
 232         self._queued_file = source
 233
 234     def _queue_dirents(self, stream_name, dirents):
 235         assert (not self._queued_dirents), "tried to queue more than one tree"
 236         self._queued_dirents = deque(sorted(dirents))
 237
 238     def _queue_tree(self, path, stream_name, max_manifest_depth):
 239         self._queued_trees.append((path, stream_name, max_manifest_depth))
 240
 241     def write_file(self, source, filename=None):
 242         self._queue_file(source, filename)
 243         self.do_queued_work()
 244
 245     def write_directory_tree(self,
 246                              path, stream_name='.', max_manifest_depth=-1):
 247         self._queue_tree(path, stream_name, max_manifest_depth)
 248         self.do_queued_work()
 249
 250     def write(self, newdata):
 251         if isinstance(newdata, bytes):
 252             pass
 253         elif isinstance(newdata, str):
 254             newdata = newdata.encode()
 255         elif hasattr(newdata, '__iter__'):
 256             for s in newdata:
 257                 self.write(s)
 258             return
 259         self._data_buffer.append(newdata)
 260         self._data_buffer_len += len(newdata)
 261         self._current_stream_length += len(newdata)
 262         while self._data_buffer_len >= config.KEEP_BLOCK_SIZE:
 263             self.flush_data()
 264
 265     def open(self, streampath, filename=None):
 266         """open(streampath[, filename]) -> file-like object
 267
 268         Pass in the path of a file to write to the Collection, either as a
 269         single string or as two separate stream name and file name arguments.
 270         This method returns a file-like object you can write to add it to the
 271         Collection.
 272
 273         You may only have one file object from the Collection open at a time,
 274         so be sure to close the object when you're done.  Using the object in
 275         a with statement makes that easy::
 276
 277           with cwriter.open('./doc/page1.txt') as outfile:
 278               outfile.write(page1_data)
 279           with cwriter.open('./doc/page2.txt') as outfile:
 280               outfile.write(page2_data)
 281         """
 282         if filename is None:
 283             streampath, filename = split(streampath)
 284         if self._last_open and not self._last_open.closed:
 285             raise errors.AssertionError(
 286                 u"can't open '{}' when '{}' is still open".format(
 287                     filename, self._last_open.name))
 288         if streampath != self.current_stream_name():
 289             self.start_new_stream(streampath)
 290         self.set_current_file_name(filename)
 291         self._last_open = _WriterFile(self, filename)
 292         return self._last_open
 293
 294     def flush_data(self):
 295         data_buffer = b''.join(self._data_buffer)
 296         if data_buffer:
 297             self._current_stream_locators.append(
 298                 self._my_keep().put(
 299                     data_buffer[0:config.KEEP_BLOCK_SIZE],
 300                     copies=self.replication))
 301             self._data_buffer = [data_buffer[config.KEEP_BLOCK_SIZE:]]
 302             self._data_buffer_len = len(self._data_buffer[0])
 303
 304     def start_new_file(self, newfilename=None):
 305         self.finish_current_file()
 306         self.set_current_file_name(newfilename)
 307
 308     def set_current_file_name(self, newfilename):
 309         if re.search(r'[\t\n]', newfilename):
 310             raise errors.AssertionError(
 311                 "Manifest filenames cannot contain whitespace: %s" %
 312                 newfilename)
 313         elif re.search(r'\x00', newfilename):
 314             raise errors.AssertionError(
 315                 "Manifest filenames cannot contain NUL characters: %s" %
 316                 newfilename)
 317         self._current_file_name = newfilename
 318
 319     def current_file_name(self):
 320         return self._current_file_name
 321
 322     def finish_current_file(self):
 323         if self._current_file_name is None:
 324             if self._current_file_pos == self._current_stream_length:
 325                 return
 326             raise errors.AssertionError(
 327                 "Cannot finish an unnamed file " +
 328                 "(%d bytes at offset %d in '%s' stream)" %
 329                 (self._current_stream_length - self._current_file_pos,
 330                  self._current_file_pos,
 331                  self._current_stream_name))
 332         self._current_stream_files.append([
 333                 self._current_file_pos,
 334                 self._current_stream_length - self._current_file_pos,
 335                 self._current_file_name])
 336         self._current_file_pos = self._current_stream_length
 337         self._current_file_name = None
 338
 339     def start_new_stream(self, newstreamname='.'):
 340         self.finish_current_stream()
 341         self.set_current_stream_name(newstreamname)
 342
 343     def set_current_stream_name(self, newstreamname):
 344         if re.search(r'[\t\n]', newstreamname):
 345             raise errors.AssertionError(
 346                 "Manifest stream names cannot contain whitespace: '%s'" %
 347                 (newstreamname))
 348         self._current_stream_name = '.' if newstreamname=='' else newstreamname
 349
 350     def current_stream_name(self):
 351         return self._current_stream_name
 352
 353     def finish_current_stream(self):
 354         self.finish_current_file()
 355         self.flush_data()
 356         if not self._current_stream_files:
 357             pass
 358         elif self._current_stream_name is None:
 359             raise errors.AssertionError(
 360                 "Cannot finish an unnamed stream (%d bytes in %d files)" %
 361                 (self._current_stream_length, len(self._current_stream_files)))
 362         else:
 363             if not self._current_stream_locators:
 364                 self._current_stream_locators.append(config.EMPTY_BLOCK_LOCATOR)
 365             self._finished_streams.append([self._current_stream_name,
 366                                            self._current_stream_locators,
 367                                            self._current_stream_files])
 368         self._current_stream_files = []
 369         self._current_stream_length = 0
 370         self._current_stream_locators = []
 371         self._current_stream_name = None
 372         self._current_file_pos = 0
 373         self._current_file_name = None
 374
 375     def finish(self):
 376         """Store the manifest in Keep and return its locator.
 377
 378         This is useful for storing manifest fragments (task outputs)
 379         temporarily in Keep during a Crunch job.
 380
 381         In other cases you should make a collection instead, by
 382         sending manifest_text() to the API server's "create
 383         collection" endpoint.
 384         """
 385         return self._my_keep().put(self.manifest_text().encode(),
 386                                    copies=self.replication)
 387
 388     def portable_data_hash(self):
 389         stripped = self.stripped_manifest().encode()
 390         return '{}+{}'.format(hashlib.md5(stripped).hexdigest(), len(stripped))
 391
 392     def manifest_text(self):
 393         self.finish_current_stream()
 394         manifest = ''
 395
 396         for stream in self._finished_streams:
 397             if not re.search(r'^\.(/.*)?$', stream[0]):
 398                 manifest += './'
 399             manifest += stream[0].replace(' ', '\\040')
 400             manifest += ' ' + ' '.join(stream[1])
 401             manifest += ' ' + ' '.join("%d:%d:%s" % (sfile[0], sfile[1], sfile[2].replace(' ', '\\040')) for sfile in stream[2])
 402             manifest += "\n"
 403
 404         return manifest
 405
 406     def data_locators(self):
 407         ret = []
 408         for name, locators, files in self._finished_streams:
 409             ret += locators
 410         return ret
 411
 412     def save_new(self, name=None):
 413         return self._api_client.collections().create(
 414             ensure_unique_name=True,
 415             body={
 416                 'name': name,
 417                 'manifest_text': self.manifest_text(),
 418             }).execute(num_retries=self.num_retries)
 419
 420
 421 class ResumableCollectionWriter(CollectionWriter):
 422     """Deprecated, use Collection instead."""
 423
 424     STATE_PROPS = ['_current_stream_files', '_current_stream_length',
 425                    '_current_stream_locators', '_current_stream_name',
 426                    '_current_file_name', '_current_file_pos', '_close_file',
 427                    '_data_buffer', '_dependencies', '_finished_streams',
 428                    '_queued_dirents', '_queued_trees']
 429
 430     def __init__(self, api_client=None, **kwargs):
 431         self._dependencies = {}
 432         super(ResumableCollectionWriter, self).__init__(api_client, **kwargs)
 433
 434     @classmethod
 435     def from_state(cls, state, *init_args, **init_kwargs):
 436         # Try to build a new writer from scratch with the given state.
 437         # If the state is not suitable to resume (because files have changed,
 438         # been deleted, aren't predictable, etc.), raise a
 439         # StaleWriterStateError.  Otherwise, return the initialized writer.
 440         # The caller is responsible for calling writer.do_queued_work()
 441         # appropriately after it's returned.
 442         writer = cls(*init_args, **init_kwargs)
 443         for attr_name in cls.STATE_PROPS:
 444             attr_value = state[attr_name]
 445             attr_class = getattr(writer, attr_name).__class__
 446             # Coerce the value into the same type as the initial value, if
 447             # needed.
 448             if attr_class not in (type(None), attr_value.__class__):
 449                 attr_value = attr_class(attr_value)
 450             setattr(writer, attr_name, attr_value)
 451         # Check dependencies before we try to resume anything.
 452         if any(KeepLocator(ls).permission_expired()
 453                for ls in writer._current_stream_locators):
 454             raise errors.StaleWriterStateError(
 455                 "locators include expired permission hint")
 456         writer.check_dependencies()
 457         if state['_current_file'] is not None:
 458             path, pos = state['_current_file']
 459             try:
 460                 writer._queued_file = open(path, 'rb')
 461                 writer._queued_file.seek(pos)
 462             except IOError as error:
 463                 raise errors.StaleWriterStateError(
 464                     u"failed to reopen active file {}: {}".format(path, error))
 465         return writer
 466
 467     def check_dependencies(self):
 468         for path, orig_stat in listitems(self._dependencies):
 469             if not S_ISREG(orig_stat[ST_MODE]):
 470                 raise errors.StaleWriterStateError(u"{} not file".format(path))
 471             try:
 472                 now_stat = tuple(os.stat(path))
 473             except OSError as error:
 474                 raise errors.StaleWriterStateError(
 475                     u"failed to stat {}: {}".format(path, error))
 476             if ((not S_ISREG(now_stat[ST_MODE])) or
 477                 (orig_stat[ST_MTIME] != now_stat[ST_MTIME]) or
 478                 (orig_stat[ST_SIZE] != now_stat[ST_SIZE])):
 479                 raise errors.StaleWriterStateError(u"{} changed".format(path))
 480
 481     def dump_state(self, copy_func=lambda x: x):
 482         state = {attr: copy_func(getattr(self, attr))
 483                  for attr in self.STATE_PROPS}
 484         if self._queued_file is None:
 485             state['_current_file'] = None
 486         else:
 487             state['_current_file'] = (os.path.realpath(self._queued_file.name),
 488                                       self._queued_file.tell())
 489         return state
 490
 491     def _queue_file(self, source, filename=None):
 492         try:
 493             src_path = os.path.realpath(source)
 494         except Exception:
 495             raise errors.AssertionError(u"{} not a file path".format(source))
 496         try:
 497             path_stat = os.stat(src_path)
 498         except OSError as stat_error:
 499             path_stat = None
 500         super(ResumableCollectionWriter, self)._queue_file(source, filename)
 501         fd_stat = os.fstat(self._queued_file.fileno())
 502         if not S_ISREG(fd_stat.st_mode):
 503             # We won't be able to resume from this cache anyway, so don't
 504             # worry about further checks.
 505             self._dependencies[source] = tuple(fd_stat)
 506         elif path_stat is None:
 507             raise errors.AssertionError(
 508                 u"could not stat {}: {}".format(source, stat_error))
 509         elif path_stat.st_ino != fd_stat.st_ino:
 510             raise errors.AssertionError(
 511                 u"{} changed between open and stat calls".format(source))
 512         else:
 513             self._dependencies[src_path] = tuple(fd_stat)
 514
 515     def write(self, data):
 516         if self._queued_file is None:
 517             raise errors.AssertionError(
 518                 "resumable writer can't accept unsourced data")
 519         return super(ResumableCollectionWriter, self).write(data)
 520
 521
 522 ADD = "add"
 523 DEL = "del"
 524 MOD = "mod"
 525 TOK = "tok"
 526 FILE = "file"
 527 COLLECTION = "collection"
 528
 529 class RichCollectionBase(CollectionBase):
 530     """Base class for Collections and Subcollections.
 531
 532     Implements the majority of functionality relating to accessing items in the
 533     Collection.
 534
 535     """
 536
 537     def __init__(self, parent=None):
 538         self.parent = parent
 539         self._committed = False
 540         self._has_remote_blocks = False
 541         self._callback = None
 542         self._items = {}
 543
 544     def _my_api(self):
 545         raise NotImplementedError()
 546
 547     def _my_keep(self):
 548         raise NotImplementedError()
 549
 550     def _my_block_manager(self):
 551         raise NotImplementedError()
 552
 553     def writable(self):
 554         raise NotImplementedError()
 555
 556     def root_collection(self):
 557         raise NotImplementedError()
 558
 559     def notify(self, event, collection, name, item):
 560         raise NotImplementedError()
 561
 562     def stream_name(self):
 563         raise NotImplementedError()
 564
 565
 566     @synchronized
 567     def has_remote_blocks(self):
 568         """Recursively check for a +R segment locator signature."""
 569
 570         if self._has_remote_blocks:
 571             return True
 572         for item in self:
 573             if self[item].has_remote_blocks():
 574                 return True
 575         return False
 576
 577     @synchronized
 578     def set_has_remote_blocks(self, val):
 579         self._has_remote_blocks = val
 580         if self.parent:
 581             self.parent.set_has_remote_blocks(val)
 582
 583     @must_be_writable
 584     @synchronized
 585     def find_or_create(self, path, create_type):
 586         """Recursively search the specified file path.
 587
 588         May return either a `Collection` or `ArvadosFile`.  If not found, will
 589         create a new item at the specified path based on `create_type`.  Will
 590         create intermediate subcollections needed to contain the final item in
 591         the path.
 592
 593         :create_type:
 594           One of `arvados.collection.FILE` or
 595           `arvados.collection.COLLECTION`.  If the path is not found, and value
 596           of create_type is FILE then create and return a new ArvadosFile for
 597           the last path component.  If COLLECTION, then create and return a new
 598           Collection for the last path component.
 599
 600         """
 601
 602         pathcomponents = path.split("/", 1)
 603         if pathcomponents[0]:
 604             item = self._items.get(pathcomponents[0])
 605             if len(pathcomponents) == 1:
 606                 if item is None:
 607                     # create new file
 608                     if create_type == COLLECTION:
 609                         item = Subcollection(self, pathcomponents[0])
 610                     else:
 611                         item = ArvadosFile(self, pathcomponents[0])
 612                     self._items[pathcomponents[0]] = item
 613                     self.set_committed(False)
 614                     self.notify(ADD, self, pathcomponents[0], item)
 615                 return item
 616             else:
 617                 if item is None:
 618                     # create new collection
 619                     item = Subcollection(self, pathcomponents[0])
 620                     self._items[pathcomponents[0]] = item
 621                     self.set_committed(False)
 622                     self.notify(ADD, self, pathcomponents[0], item)
 623                 if isinstance(item, RichCollectionBase):
 624                     return item.find_or_create(pathcomponents[1], create_type)
 625                 else:
 626                     raise IOError(errno.ENOTDIR, "Not a directory", pathcomponents[0])
 627         else:
 628             return self
 629
 630     @synchronized
 631     def find(self, path):
 632         """Recursively search the specified file path.
 633
 634         May return either a Collection or ArvadosFile. Return None if not
 635         found.
 636         If path is invalid (ex: starts with '/'), an IOError exception will be
 637         raised.
 638
 639         """
 640         if not path:
 641             raise errors.ArgumentError("Parameter 'path' is empty.")
 642
 643         pathcomponents = path.split("/", 1)
 644         if pathcomponents[0] == '':
 645             raise IOError(errno.ENOTDIR, "Not a directory", pathcomponents[0])
 646
 647         item = self._items.get(pathcomponents[0])
 648         if item is None:
 649             return None
 650         elif len(pathcomponents) == 1:
 651             return item
 652         else:
 653             if isinstance(item, RichCollectionBase):
 654                 if pathcomponents[1]:
 655                     return item.find(pathcomponents[1])
 656                 else:
 657                     return item
 658             else:
 659                 raise IOError(errno.ENOTDIR, "Not a directory", pathcomponents[0])
 660
 661     @synchronized
 662     def mkdirs(self, path):
 663         """Recursive subcollection create.
 664
 665         Like `os.makedirs()`.  Will create intermediate subcollections needed
 666         to contain the leaf subcollection path.
 667
 668         """
 669
 670         if self.find(path) != None:
 671             raise IOError(errno.EEXIST, "Directory or file exists", path)
 672
 673         return self.find_or_create(path, COLLECTION)
 674
 675     def open(self, path, mode="r", encoding=None):
 676         """Open a file-like object for access.
 677
 678         :path:
 679           path to a file in the collection
 680         :mode:
 681           a string consisting of "r", "w", or "a", optionally followed
 682           by "b" or "t", optionally followed by "+".
 683           :"b":
 684             binary mode: write() accepts bytes, read() returns bytes.
 685           :"t":
 686             text mode (default): write() accepts strings, read() returns strings.
 687           :"r":
 688             opens for reading
 689           :"r+":
 690             opens for reading and writing.  Reads/writes share a file pointer.
 691           :"w", "w+":
 692             truncates to 0 and opens for reading and writing.  Reads/writes share a file pointer.
 693           :"a", "a+":
 694             opens for reading and writing.  All writes are appended to
 695             the end of the file.  Writing does not affect the file pointer for
 696             reading.
 697
 698         """
 699
 700         if not re.search(r'^[rwa][bt]?\+?$', mode):
 701             raise errors.ArgumentError("Invalid mode {!r}".format(mode))
 702
 703         if mode[0] == 'r' and '+' not in mode:
 704             fclass = ArvadosFileReader
 705             arvfile = self.find(path)
 706         elif not self.writable():
 707             raise IOError(errno.EROFS, "Collection is read only")
 708         else:
 709             fclass = ArvadosFileWriter
 710             arvfile = self.find_or_create(path, FILE)
 711
 712         if arvfile is None:
 713             raise IOError(errno.ENOENT, "File not found", path)
 714         if not isinstance(arvfile, ArvadosFile):
 715             raise IOError(errno.EISDIR, "Is a directory", path)
 716
 717         if mode[0] == 'w':
 718             arvfile.truncate(0)
 719
 720         binmode = mode[0] + 'b' + re.sub('[bt]', '', mode[1:])
 721         f = fclass(arvfile, mode=binmode, num_retries=self.num_retries)
 722         if 'b' not in mode:
 723             bufferclass = io.BufferedRandom if f.writable() else io.BufferedReader
 724             f = TextIOWrapper(bufferclass(WrappableFile(f)), encoding=encoding)
 725         return f
 726
 727     def modified(self):
 728         """Determine if the collection has been modified since last commited."""
 729         return not self.committed()
 730
 731     @synchronized
 732     def committed(self):
 733         """Determine if the collection has been committed to the API server."""
 734         return self._committed
 735
 736     @synchronized
 737     def set_committed(self, value=True):
 738         """Recursively set committed flag.
 739
 740         If value is True, set committed to be True for this and all children.
 741
 742         If value is False, set committed to be False for this and all parents.
 743         """
 744         if value == self._committed:
 745             return
 746         if value:
 747             for k,v in listitems(self._items):
 748                 v.set_committed(True)
 749             self._committed = True
 750         else:
 751             self._committed = False
 752             if self.parent is not None:
 753                 self.parent.set_committed(False)
 754
 755     @synchronized
 756     def __iter__(self):
 757         """Iterate over names of files and collections contained in this collection."""
 758         return iter(viewkeys(self._items))
 759
 760     @synchronized
 761     def __getitem__(self, k):
 762         """Get a file or collection that is directly contained by this collection.
 763
 764         If you want to search a path, use `find()` instead.
 765
 766         """
 767         return self._items[k]
 768
 769     @synchronized
 770     def __contains__(self, k):
 771         """Test if there is a file or collection a directly contained by this collection."""
 772         return k in self._items
 773
 774     @synchronized
 775     def __len__(self):
 776         """Get the number of items directly contained in this collection."""
 777         return len(self._items)
 778
 779     @must_be_writable
 780     @synchronized
 781     def __delitem__(self, p):
 782         """Delete an item by name which is directly contained by this collection."""
 783         del self._items[p]
 784         self.set_committed(False)
 785         self.notify(DEL, self, p, None)
 786
 787     @synchronized
 788     def keys(self):
 789         """Get a list of names of files and collections directly contained in this collection."""
 790         return self._items.keys()
 791
 792     @synchronized
 793     def values(self):
 794         """Get a list of files and collection objects directly contained in this collection."""
 795         return listvalues(self._items)
 796
 797     @synchronized
 798     def items(self):
 799         """Get a list of (name, object) tuples directly contained in this collection."""
 800         return listitems(self._items)
 801
 802     def exists(self, path):
 803         """Test if there is a file or collection at `path`."""
 804         return self.find(path) is not None
 805
 806     @must_be_writable
 807     @synchronized
 808     def remove(self, path, recursive=False):
 809         """Remove the file or subcollection (directory) at `path`.
 810
 811         :recursive:
 812           Specify whether to remove non-empty subcollections (True), or raise an error (False).
 813         """
 814
 815         if not path:
 816             raise errors.ArgumentError("Parameter 'path' is empty.")
 817
 818         pathcomponents = path.split("/", 1)
 819         item = self._items.get(pathcomponents[0])
 820         if item is None:
 821             raise IOError(errno.ENOENT, "File not found", path)
 822         if len(pathcomponents) == 1:
 823             if isinstance(self._items[pathcomponents[0]], RichCollectionBase) and len(self._items[pathcomponents[0]]) > 0 and not recursive:
 824                 raise IOError(errno.ENOTEMPTY, "Directory not empty", path)
 825             deleteditem = self._items[pathcomponents[0]]
 826             del self._items[pathcomponents[0]]
 827             self.set_committed(False)
 828             self.notify(DEL, self, pathcomponents[0], deleteditem)
 829         else:
 830             item.remove(pathcomponents[1])
 831
 832     def _clonefrom(self, source):
 833         for k,v in listitems(source):
 834             self._items[k] = v.clone(self, k)
 835
 836     def clone(self):
 837         raise NotImplementedError()
 838
 839     @must_be_writable
 840     @synchronized
 841     def add(self, source_obj, target_name, overwrite=False, reparent=False):
 842         """Copy or move a file or subcollection to this collection.
 843
 844         :source_obj:
 845           An ArvadosFile, or Subcollection object
 846
 847         :target_name:
 848           Destination item name.  If the target name already exists and is a
 849           file, this will raise an error unless you specify `overwrite=True`.
 850
 851         :overwrite:
 852           Whether to overwrite target file if it already exists.
 853
 854         :reparent:
 855           If True, source_obj will be moved from its parent collection to this collection.
 856           If False, source_obj will be copied and the parent collection will be
 857           unmodified.
 858
 859         """
 860
 861         if target_name in self and not overwrite:
 862             raise IOError(errno.EEXIST, "File already exists", target_name)
 863
 864         modified_from = None
 865         if target_name in self:
 866             modified_from = self[target_name]
 867
 868         # Actually make the move or copy.
 869         if reparent:
 870             source_obj._reparent(self, target_name)
 871             item = source_obj
 872         else:
 873             item = source_obj.clone(self, target_name)
 874
 875         self._items[target_name] = item
 876         self.set_committed(False)
 877         if not self._has_remote_blocks and source_obj.has_remote_blocks():
 878             self.set_has_remote_blocks(True)
 879
 880         if modified_from:
 881             self.notify(MOD, self, target_name, (modified_from, item))
 882         else:
 883             self.notify(ADD, self, target_name, item)
 884
 885     def _get_src_target(self, source, target_path, source_collection, create_dest):
 886         if source_collection is None:
 887             source_collection = self
 888
 889         # Find the object
 890         if isinstance(source, basestring):
 891             source_obj = source_collection.find(source)
 892             if source_obj is None:
 893                 raise IOError(errno.ENOENT, "File not found", source)
 894             sourcecomponents = source.split("/")
 895         else:
 896             source_obj = source
 897             sourcecomponents = None
 898
 899         # Find parent collection the target path
 900         targetcomponents = target_path.split("/")
 901
 902         # Determine the name to use.
 903         target_name = targetcomponents[-1] if targetcomponents[-1] else sourcecomponents[-1]
 904
 905         if not target_name:
 906             raise errors.ArgumentError("Target path is empty and source is an object.  Cannot determine destination filename to use.")
 907
 908         if create_dest:
 909             target_dir = self.find_or_create("/".join(targetcomponents[0:-1]), COLLECTION)
 910         else:
 911             if len(targetcomponents) > 1:
 912                 target_dir = self.find("/".join(targetcomponents[0:-1]))
 913             else:
 914                 target_dir = self
 915
 916         if target_dir is None:
 917             raise IOError(errno.ENOENT, "Target directory not found", target_name)
 918
 919         if target_name in target_dir and isinstance(target_dir[target_name], RichCollectionBase) and sourcecomponents:
 920             target_dir = target_dir[target_name]
 921             target_name = sourcecomponents[-1]
 922
 923         return (source_obj, target_dir, target_name)
 924
 925     @must_be_writable
 926     @synchronized
 927     def copy(self, source, target_path, source_collection=None, overwrite=False):
 928         """Copy a file or subcollection to a new path in this collection.
 929
 930         :source:
 931           A string with a path to source file or subcollection, or an actual ArvadosFile or Subcollection object.
 932
 933         :target_path:
 934           Destination file or path.  If the target path already exists and is a
 935           subcollection, the item will be placed inside the subcollection.  If
 936           the target path already exists and is a file, this will raise an error
 937           unless you specify `overwrite=True`.
 938
 939         :source_collection:
 940           Collection to copy `source_path` from (default `self`)
 941
 942         :overwrite:
 943           Whether to overwrite target file if it already exists.
 944         """
 945
 946         source_obj, target_dir, target_name = self._get_src_target(source, target_path, source_collection, True)
 947         target_dir.add(source_obj, target_name, overwrite, False)
 948
 949     @must_be_writable
 950     @synchronized
 951     def rename(self, source, target_path, source_collection=None, overwrite=False):
 952         """Move a file or subcollection from `source_collection` to a new path in this collection.
 953
 954         :source:
 955           A string with a path to source file or subcollection.
 956
 957         :target_path:
 958           Destination file or path.  If the target path already exists and is a
 959           subcollection, the item will be placed inside the subcollection.  If
 960           the target path already exists and is a file, this will raise an error
 961           unless you specify `overwrite=True`.
 962
 963         :source_collection:
 964           Collection to copy `source_path` from (default `self`)
 965
 966         :overwrite:
 967           Whether to overwrite target file if it already exists.
 968         """
 969
 970         source_obj, target_dir, target_name = self._get_src_target(source, target_path, source_collection, False)
 971         if not source_obj.writable():
 972             raise IOError(errno.EROFS, "Source collection is read only", source)
 973         target_dir.add(source_obj, target_name, overwrite, True)
 974
 975     def portable_manifest_text(self, stream_name="."):
 976         """Get the manifest text for this collection, sub collections and files.
 977
 978         This method does not flush outstanding blocks to Keep.  It will return
 979         a normalized manifest with access tokens stripped.
 980
 981         :stream_name:
 982           Name to use for this stream (directory)
 983
 984         """
 985         return self._get_manifest_text(stream_name, True, True)
 986
 987     @synchronized
 988     def manifest_text(self, stream_name=".", strip=False, normalize=False,
 989                       only_committed=False):
 990         """Get the manifest text for this collection, sub collections and files.
 991
 992         This method will flush outstanding blocks to Keep.  By default, it will
 993         not normalize an unmodified manifest or strip access tokens.
 994
 995         :stream_name:
 996           Name to use for this stream (directory)
 997
 998         :strip:
 999           If True, remove signing tokens from block locators if present.
1000           If False (default), block locators are left unchanged.
1001
1002         :normalize:
1003           If True, always export the manifest text in normalized form
1004           even if the Collection is not modified.  If False (default) and the collection
1005           is not modified, return the original manifest text even if it is not
1006           in normalized form.
1007
1008         :only_committed:
1009           If True, don't commit pending blocks.
1010
1011         """
1012
1013         if not only_committed:
1014             self._my_block_manager().commit_all()
1015         return self._get_manifest_text(stream_name, strip, normalize,
1016                                        only_committed=only_committed)
1017
1018     @synchronized
1019     def _get_manifest_text(self, stream_name, strip, normalize, only_committed=False):
1020         """Get the manifest text for this collection, sub collections and files.
1021
1022         :stream_name:
1023           Name to use for this stream (directory)
1024
1025         :strip:
1026           If True, remove signing tokens from block locators if present.
1027           If False (default), block locators are left unchanged.
1028
1029         :normalize:
1030           If True, always export the manifest text in normalized form
1031           even if the Collection is not modified.  If False (default) and the collection
1032           is not modified, return the original manifest text even if it is not
1033           in normalized form.
1034
1035         :only_committed:
1036           If True, only include blocks that were already committed to Keep.
1037
1038         """
1039
1040         if not self.committed() or self._manifest_text is None or normalize:
1041             stream = {}
1042             buf = []
1043             sorted_keys = sorted(self.keys())
1044             for filename in [s for s in sorted_keys if isinstance(self[s], ArvadosFile)]:
1045                 # Create a stream per file `k`
1046                 arvfile = self[filename]
1047                 filestream = []
1048                 for segment in arvfile.segments():
1049                     loc = segment.locator
1050                     if arvfile.parent._my_block_manager().is_bufferblock(loc):
1051                         if only_committed:
1052                             continue
1053                         loc = arvfile.parent._my_block_manager().get_bufferblock(loc).locator()
1054                     if strip:
1055                         loc = KeepLocator(loc).stripped()
1056                     filestream.append(LocatorAndRange(loc, KeepLocator(loc).size,
1057                                          segment.segment_offset, segment.range_size))
1058                 stream[filename] = filestream
1059             if stream:
1060                 buf.append(" ".join(normalize_stream(stream_name, stream)) + "\n")
1061             for dirname in [s for s in sorted_keys if isinstance(self[s], RichCollectionBase)]:
1062                 buf.append(self[dirname].manifest_text(
1063                     stream_name=os.path.join(stream_name, dirname),
1064                     strip=strip, normalize=True, only_committed=only_committed))
1065             return "".join(buf)
1066         else:
1067             if strip:
1068                 return self.stripped_manifest()
1069             else:
1070                 return self._manifest_text
1071
1072     @synchronized
1073     def _copy_remote_blocks(self, remote_blocks={}):
1074         """Scan through the entire collection and ask Keep to copy remote blocks.
1075
1076         When accessing a remote collection, blocks will have a remote signature
1077         (+R instead of +A). Collect these signatures and request Keep to copy the
1078         blocks to the local cluster, returning local (+A) signatures.
1079
1080         :remote_blocks:
1081           Shared cache of remote to local block mappings. This is used to avoid
1082           doing extra work when blocks are shared by more than one file in
1083           different subdirectories.
1084
1085         """
1086         for item in self:
1087             remote_blocks = self[item]._copy_remote_blocks(remote_blocks)
1088         return remote_blocks
1089
1090     @synchronized
1091     def diff(self, end_collection, prefix=".", holding_collection=None):
1092         """Generate list of add/modify/delete actions.
1093
1094         When given to `apply`, will change `self` to match `end_collection`
1095
1096         """
1097         changes = []
1098         if holding_collection is None:
1099             holding_collection = Collection(api_client=self._my_api(), keep_client=self._my_keep())
1100         for k in self:
1101             if k not in end_collection:
1102                changes.append((DEL, os.path.join(prefix, k), self[k].clone(holding_collection, "")))
1103         for k in end_collection:
1104             if k in self:
1105                 if isinstance(end_collection[k], Subcollection) and isinstance(self[k], Subcollection):
1106                     changes.extend(self[k].diff(end_collection[k], os.path.join(prefix, k), holding_collection))
1107                 elif end_collection[k] != self[k]:
1108                     changes.append((MOD, os.path.join(prefix, k), self[k].clone(holding_collection, ""), end_collection[k].clone(holding_collection, "")))
1109                 else:
1110                     changes.append((TOK, os.path.join(prefix, k), self[k].clone(holding_collection, ""), end_collection[k].clone(holding_collection, "")))
1111             else:
1112                 changes.append((ADD, os.path.join(prefix, k), end_collection[k].clone(holding_collection, "")))
1113         return changes
1114
1115     @must_be_writable
1116     @synchronized
1117     def apply(self, changes):
1118         """Apply changes from `diff`.
1119
1120         If a change conflicts with a local change, it will be saved to an
1121         alternate path indicating the conflict.
1122
1123         """
1124         if changes:
1125             self.set_committed(False)
1126         for change in changes:
1127             event_type = change[0]
1128             path = change[1]
1129             initial = change[2]
1130             local = self.find(path)
1131             conflictpath = "%s~%s~conflict~" % (path, time.strftime("%Y%m%d-%H%M%S",
1132                                                                     time.gmtime()))
1133             if event_type == ADD:
1134                 if local is None:
1135                     # No local file at path, safe to copy over new file
1136                     self.copy(initial, path)
1137                 elif local is not None and local != initial:
1138                     # There is already local file and it is different:
1139                     # save change to conflict file.
1140                     self.copy(initial, conflictpath)
1141             elif event_type == MOD or event_type == TOK:
1142                 final = change[3]
1143                 if local == initial:
1144                     # Local matches the "initial" item so it has not
1145                     # changed locally and is safe to update.
1146                     if isinstance(local, ArvadosFile) and isinstance(final, ArvadosFile):
1147                         # Replace contents of local file with new contents
1148                         local.replace_contents(final)
1149                     else:
1150                         # Overwrite path with new item; this can happen if
1151                         # path was a file and is now a collection or vice versa
1152                         self.copy(final, path, overwrite=True)
1153                 else:
1154                     # Local is missing (presumably deleted) or local doesn't
1155                     # match the "start" value, so save change to conflict file
1156                     self.copy(final, conflictpath)
1157             elif event_type == DEL:
1158                 if local == initial:
1159                     # Local item matches "initial" value, so it is safe to remove.
1160                     self.remove(path, recursive=True)
1161                 # else, the file is modified or already removed, in either
1162                 # case we don't want to try to remove it.
1163
1164     def portable_data_hash(self):
1165         """Get the portable data hash for this collection's manifest."""
1166         if self._manifest_locator and self.committed():
1167             # If the collection is already saved on the API server, and it's committed
1168             # then return API server's PDH response.
1169             return self._portable_data_hash
1170         else:
1171             stripped = self.portable_manifest_text().encode()
1172             return '{}+{}'.format(hashlib.md5(stripped).hexdigest(), len(stripped))
1173
1174     @synchronized
1175     def subscribe(self, callback):
1176         if self._callback is None:
1177             self._callback = callback
1178         else:
1179             raise errors.ArgumentError("A callback is already set on this collection.")
1180
1181     @synchronized
1182     def unsubscribe(self):
1183         if self._callback is not None:
1184             self._callback = None
1185
1186     @synchronized
1187     def notify(self, event, collection, name, item):
1188         if self._callback:
1189             self._callback(event, collection, name, item)
1190         self.root_collection().notify(event, collection, name, item)
1191
1192     @synchronized
1193     def __eq__(self, other):
1194         if other is self:
1195             return True
1196         if not isinstance(other, RichCollectionBase):
1197             return False
1198         if len(self._items) != len(other):
1199             return False
1200         for k in self._items:
1201             if k not in other:
1202                 return False
1203             if self._items[k] != other[k]:
1204                 return False
1205         return True
1206
1207     def __ne__(self, other):
1208         return not self.__eq__(other)
1209
1210     @synchronized
1211     def flush(self):
1212         """Flush bufferblocks to Keep."""
1213         for e in listvalues(self):
1214             e.flush()
1215
1216
1217 class Collection(RichCollectionBase):
1218     """Represents the root of an Arvados Collection.
1219
1220     This class is threadsafe.  The root collection object, all subcollections
1221     and files are protected by a single lock (i.e. each access locks the entire
1222     collection).
1223
1224     Brief summary of
1225     useful methods:
1226
1227     :To read an existing file:
1228       `c.open("myfile", "r")`
1229
1230     :To write a new file:
1231       `c.open("myfile", "w")`
1232
1233     :To determine if a file exists:
1234       `c.find("myfile") is not None`
1235
1236     :To copy a file:
1237       `c.copy("source", "dest")`
1238
1239     :To delete a file:
1240       `c.remove("myfile")`
1241
1242     :To save to an existing collection record:
1243       `c.save()`
1244
1245     :To save a new collection record:
1246     `c.save_new()`
1247
1248     :To merge remote changes into this object:
1249       `c.update()`
1250
1251     Must be associated with an API server Collection record (during
1252     initialization, or using `save_new`) to use `save` or `update`
1253
1254     """
1255
1256     def __init__(self, manifest_locator_or_text=None,
1257                  api_client=None,
1258                  keep_client=None,
1259                  num_retries=None,
1260                  parent=None,
1261                  apiconfig=None,
1262                  block_manager=None,
1263                  replication_desired=None,
1264                  storage_classes_desired=None,
1265                  put_threads=None):
1266         """Collection constructor.
1267
1268         :manifest_locator_or_text:
1269           An Arvados collection UUID, portable data hash, raw manifest
1270           text, or (if creating an empty collection) None.
1271
1272         :parent:
1273           the parent Collection, may be None.
1274
1275         :apiconfig:
1276           A dict containing keys for ARVADOS_API_HOST and ARVADOS_API_TOKEN.
1277           Prefer this over supplying your own api_client and keep_client (except in testing).
1278           Will use default config settings if not specified.
1279
1280         :api_client:
1281           The API client object to use for requests.  If not specified, create one using `apiconfig`.
1282
1283         :keep_client:
1284           the Keep client to use for requests.  If not specified, create one using `apiconfig`.
1285
1286         :num_retries:
1287           the number of retries for API and Keep requests.
1288
1289         :block_manager:
1290           the block manager to use.  If not specified, create one.
1291
1292         :replication_desired:
1293           How many copies should Arvados maintain. If None, API server default
1294           configuration applies. If not None, this value will also be used
1295           for determining the number of block copies being written.
1296
1297         :storage_classes_desired:
1298           A list of storage class names where to upload the data. If None,
1299           the keep client is expected to store the data into the cluster's
1300           default storage class(es).
1301
1302         """
1303
1304         if storage_classes_desired and type(storage_classes_desired) is not list:
1305             raise errors.ArgumentError("storage_classes_desired must be list type.")
1306
1307         super(Collection, self).__init__(parent)
1308         self._api_client = api_client
1309         self._keep_client = keep_client
1310         self._block_manager = block_manager
1311         self.replication_desired = replication_desired
1312         self._storage_classes_desired = storage_classes_desired
1313         self.put_threads = put_threads
1314
1315         if apiconfig:
1316             self._config = apiconfig
1317         else:
1318             self._config = config.settings()
1319
1320         self.num_retries = num_retries if num_retries is not None else 0
1321         self._manifest_locator = None
1322         self._manifest_text = None
1323         self._portable_data_hash = None
1324         self._api_response = None
1325         self._past_versions = set()
1326
1327         self.lock = threading.RLock()
1328         self.events = None
1329
1330         if manifest_locator_or_text:
1331             if re.match(arvados.util.keep_locator_pattern, manifest_locator_or_text):
1332                 self._manifest_locator = manifest_locator_or_text
1333             elif re.match(arvados.util.collection_uuid_pattern, manifest_locator_or_text):
1334                 self._manifest_locator = manifest_locator_or_text
1335                 if not self._has_local_collection_uuid():
1336                     self._has_remote_blocks = True
1337             elif re.match(arvados.util.manifest_pattern, manifest_locator_or_text):
1338                 self._manifest_text = manifest_locator_or_text
1339                 if '+R' in self._manifest_text:
1340                     self._has_remote_blocks = True
1341             else:
1342                 raise errors.ArgumentError(
1343                     "Argument to CollectionReader is not a manifest or a collection UUID")
1344
1345             try:
1346                 self._populate()
1347             except (IOError, errors.SyntaxError) as e:
1348                 raise errors.ArgumentError("Error processing manifest text: %s", e)
1349
1350     def storage_classes_desired(self):
1351         return self._storage_classes_desired or []
1352
1353     def root_collection(self):
1354         return self
1355
1356     def get_properties(self):
1357         if self._api_response and self._api_response["properties"]:
1358             return self._api_response["properties"]
1359         else:
1360             return {}
1361
1362     def get_trash_at(self):
1363         if self._api_response and self._api_response["trash_at"]:
1364             try:
1365                 return ciso8601.parse_datetime(self._api_response["trash_at"])
1366             except ValueError:
1367                 return None
1368         else:
1369             return None
1370
1371     def stream_name(self):
1372         return "."
1373
1374     def writable(self):
1375         return True
1376
1377     @synchronized
1378     def known_past_version(self, modified_at_and_portable_data_hash):
1379         return modified_at_and_portable_data_hash in self._past_versions
1380
1381     @synchronized
1382     @retry_method
1383     def update(self, other=None, num_retries=None):
1384         """Merge the latest collection on the API server with the current collection."""
1385
1386         if other is None:
1387             if self._manifest_locator is None:
1388                 raise errors.ArgumentError("`other` is None but collection does not have a manifest_locator uuid")
1389             response = self._my_api().collections().get(uuid=self._manifest_locator).execute(num_retries=num_retries)
1390             if (self.known_past_version((response.get("modified_at"), response.get("portable_data_hash"))) and
1391                 response.get("portable_data_hash") != self.portable_data_hash()):
1392                 # The record on the server is different from our current one, but we've seen it before,
1393                 # so ignore it because it's already been merged.
1394                 # However, if it's the same as our current record, proceed with the update, because we want to update
1395                 # our tokens.
1396                 return
1397             else:
1398                 self._past_versions.add((response.get("modified_at"), response.get("portable_data_hash")))
1399             other = CollectionReader(response["manifest_text"])
1400         baseline = CollectionReader(self._manifest_text)
1401         self.apply(baseline.diff(other))
1402         self._manifest_text = self.manifest_text()
1403
1404     @synchronized
1405     def _my_api(self):
1406         if self._api_client is None:
1407             self._api_client = ThreadSafeApiCache(self._config)
1408             if self._keep_client is None:
1409                 self._keep_client = self._api_client.keep
1410         return self._api_client
1411
1412     @synchronized
1413     def _my_keep(self):
1414         if self._keep_client is None:
1415             if self._api_client is None:
1416                 self._my_api()
1417             else:
1418                 self._keep_client = KeepClient(api_client=self._api_client)
1419         return self._keep_client
1420
1421     @synchronized
1422     def _my_block_manager(self):
1423         if self._block_manager is None:
1424             copies = (self.replication_desired or
1425                       self._my_api()._rootDesc.get('defaultCollectionReplication',
1426                                                    2))
1427             self._block_manager = _BlockManager(self._my_keep(), copies=copies, put_threads=self.put_threads, num_retries=self.num_retries, storage_classes_func=self.storage_classes_desired)
1428         return self._block_manager
1429
1430     def _remember_api_response(self, response):
1431         self._api_response = response
1432         self._past_versions.add((response.get("modified_at"), response.get("portable_data_hash")))
1433
1434     def _populate_from_api_server(self):
1435         # As in KeepClient itself, we must wait until the last
1436         # possible moment to instantiate an API client, in order to
1437         # avoid tripping up clients that don't have access to an API
1438         # server.  If we do build one, make sure our Keep client uses
1439         # it.  If instantiation fails, we'll fall back to the except
1440         # clause, just like any other Collection lookup
1441         # failure. Return an exception, or None if successful.
1442         self._remember_api_response(self._my_api().collections().get(
1443             uuid=self._manifest_locator).execute(
1444                 num_retries=self.num_retries))
1445         self._manifest_text = self._api_response['manifest_text']
1446         self._portable_data_hash = self._api_response['portable_data_hash']
1447         # If not overriden via kwargs, we should try to load the
1448         # replication_desired and storage_classes_desired from the API server
1449         if self.replication_desired is None:
1450             self.replication_desired = self._api_response.get('replication_desired', None)
1451         if self._storage_classes_desired is None:
1452             self._storage_classes_desired = self._api_response.get('storage_classes_desired', None)
1453
1454     def _populate(self):
1455         if self._manifest_text is None:
1456             if self._manifest_locator is None:
1457                 return
1458             else:
1459                 self._populate_from_api_server()
1460         self._baseline_manifest = self._manifest_text
1461         self._import_manifest(self._manifest_text)
1462
1463     def _has_collection_uuid(self):
1464         return self._manifest_locator is not None and re.match(arvados.util.collection_uuid_pattern, self._manifest_locator)
1465
1466     def _has_local_collection_uuid(self):
1467         return self._has_collection_uuid and \
1468             self._my_api()._rootDesc['uuidPrefix'] == self._manifest_locator.split('-')[0]
1469
1470     def __enter__(self):
1471         return self
1472
1473     def __exit__(self, exc_type, exc_value, traceback):
1474         """Support scoped auto-commit in a with: block."""
1475         if exc_type is None:
1476             if self.writable() and self._has_collection_uuid():
1477                 self.save()
1478         self.stop_threads()
1479
1480     def stop_threads(self):
1481         if self._block_manager is not None:
1482             self._block_manager.stop_threads()
1483
1484     @synchronized
1485     def manifest_locator(self):
1486         """Get the manifest locator, if any.
1487
1488         The manifest locator will be set when the collection is loaded from an
1489         API server record or the portable data hash of a manifest.
1490
1491         The manifest locator will be None if the collection is newly created or
1492         was created directly from manifest text.  The method `save_new()` will
1493         assign a manifest locator.
1494
1495         """
1496         return self._manifest_locator
1497
1498     @synchronized
1499     def clone(self, new_parent=None, new_name=None, readonly=False, new_config=None):
1500         if new_config is None:
1501             new_config = self._config
1502         if readonly:
1503             newcollection = CollectionReader(parent=new_parent, apiconfig=new_config)
1504         else:
1505             newcollection = Collection(parent=new_parent, apiconfig=new_config)
1506
1507         newcollection._clonefrom(self)
1508         return newcollection
1509
1510     @synchronized
1511     def api_response(self):
1512         """Returns information about this Collection fetched from the API server.
1513
1514         If the Collection exists in Keep but not the API server, currently
1515         returns None.  Future versions may provide a synthetic response.
1516
1517         """
1518         return self._api_response
1519
1520     def find_or_create(self, path, create_type):
1521         """See `RichCollectionBase.find_or_create`"""
1522         if path == ".":
1523             return self
1524         else:
1525             return super(Collection, self).find_or_create(path[2:] if path.startswith("./") else path, create_type)
1526
1527     def find(self, path):
1528         """See `RichCollectionBase.find`"""
1529         if path == ".":
1530             return self
1531         else:
1532             return super(Collection, self).find(path[2:] if path.startswith("./") else path)
1533
1534     def remove(self, path, recursive=False):
1535         """See `RichCollectionBase.remove`"""
1536         if path == ".":
1537             raise errors.ArgumentError("Cannot remove '.'")
1538         else:
1539             return super(Collection, self).remove(path[2:] if path.startswith("./") else path, recursive)
1540
1541     @must_be_writable
1542     @synchronized
1543     @retry_method
1544     def save(self,
1545              properties=None,
1546              storage_classes=None,
1547              trash_at=None,
1548              merge=True,
1549              num_retries=None):
1550         """Save collection to an existing collection record.
1551
1552         Commit pending buffer blocks to Keep, merge with remote record (if
1553         merge=True, the default), and update the collection record. Returns
1554         the current manifest text.
1555
1556         Will raise AssertionError if not associated with a collection record on
1557         the API server.  If you want to save a manifest to Keep only, see
1558         `save_new()`.
1559
1560         :properties:
1561           Additional properties of collection. This value will replace any existing
1562           properties of collection.
1563
1564         :storage_classes:
1565           Specify desirable storage classes to be used when writing data to Keep.
1566
1567         :trash_at:
1568           A collection is *expiring* when it has a *trash_at* time in the future.
1569           An expiring collection can be accessed as normal,
1570           but is scheduled to be trashed automatically at the *trash_at* time.
1571
1572         :merge:
1573           Update and merge remote changes before saving.  Otherwise, any
1574           remote changes will be ignored and overwritten.
1575
1576         :num_retries:
1577           Retry count on API calls (if None,  use the collection default)
1578
1579         """
1580         if properties and type(properties) is not dict:
1581             raise errors.ArgumentError("properties must be dictionary type.")
1582
1583         if storage_classes and type(storage_classes) is not list:
1584             raise errors.ArgumentError("storage_classes must be list type.")
1585         if storage_classes:
1586             self._storage_classes_desired = storage_classes
1587
1588         if trash_at and type(trash_at) is not datetime.datetime:
1589             raise errors.ArgumentError("trash_at must be datetime type.")
1590
1591         body={}
1592         if properties:
1593             body["properties"] = properties
1594         if self.storage_classes_desired():
1595             body["storage_classes_desired"] = self.storage_classes_desired()
1596         if trash_at:
1597             t = trash_at.strftime("%Y-%m-%dT%H:%M:%S.%fZ")
1598             body["trash_at"] = t
1599
1600         if not self.committed():
1601             if self._has_remote_blocks:
1602                 # Copy any remote blocks to the local cluster.
1603                 self._copy_remote_blocks(remote_blocks={})
1604                 self._has_remote_blocks = False
1605             if not self._has_collection_uuid():
1606                 raise AssertionError("Collection manifest_locator is not a collection uuid.  Use save_new() for new collections.")
1607             elif not self._has_local_collection_uuid():
1608                 raise AssertionError("Collection manifest_locator is from a remote cluster. Use save_new() to save it on the local cluster.")
1609
1610             self._my_block_manager().commit_all()
1611
1612             if merge:
1613                 self.update()
1614
1615             text = self.manifest_text(strip=False)
1616             body['manifest_text'] = text
1617
1618             self._remember_api_response(self._my_api().collections().update(
1619                 uuid=self._manifest_locator,
1620                 body=body
1621                 ).execute(num_retries=num_retries))
1622             self._manifest_text = self._api_response["manifest_text"]
1623             self._portable_data_hash = self._api_response["portable_data_hash"]
1624             self.set_committed(True)
1625         elif body:
1626             self._remember_api_response(self._my_api().collections().update(
1627                 uuid=self._manifest_locator,
1628                 body=body
1629                 ).execute(num_retries=num_retries))
1630
1631         return self._manifest_text
1632
1633
1634     @must_be_writable
1635     @synchronized
1636     @retry_method
1637     def save_new(self, name=None,
1638                  create_collection_record=True,
1639                  owner_uuid=None,
1640                  properties=None,
1641                  storage_classes=None,
1642                  trash_at=None,
1643                  ensure_unique_name=False,
1644                  num_retries=None):
1645         """Save collection to a new collection record.
1646
1647         Commit pending buffer blocks to Keep and, when create_collection_record
1648         is True (default), create a new collection record.  After creating a
1649         new collection record, this Collection object will be associated with
1650         the new record used by `save()`. Returns the current manifest text.
1651
1652         :name:
1653           The collection name.
1654
1655         :create_collection_record:
1656            If True, create a collection record on the API server.
1657            If False, only commit blocks to Keep and return the manifest text.
1658
1659         :owner_uuid:
1660           the user, or project uuid that will own this collection.
1661           If None, defaults to the current user.
1662
1663         :properties:
1664           Additional properties of collection. This value will replace any existing
1665           properties of collection.
1666
1667         :storage_classes:
1668           Specify desirable storage classes to be used when writing data to Keep.
1669
1670         :trash_at:
1671           A collection is *expiring* when it has a *trash_at* time in the future.
1672           An expiring collection can be accessed as normal,
1673           but is scheduled to be trashed automatically at the *trash_at* time.
1674
1675         :ensure_unique_name:
1676           If True, ask the API server to rename the collection
1677           if it conflicts with a collection with the same name and owner.  If
1678           False, a name conflict will result in an error.
1679
1680         :num_retries:
1681           Retry count on API calls (if None,  use the collection default)
1682
1683         """
1684         if properties and type(properties) is not dict:
1685             raise errors.ArgumentError("properties must be dictionary type.")
1686
1687         if storage_classes and type(storage_classes) is not list:
1688             raise errors.ArgumentError("storage_classes must be list type.")
1689
1690         if trash_at and type(trash_at) is not datetime.datetime:
1691             raise errors.ArgumentError("trash_at must be datetime type.")
1692
1693         if self._has_remote_blocks:
1694             # Copy any remote blocks to the local cluster.
1695             self._copy_remote_blocks(remote_blocks={})
1696             self._has_remote_blocks = False
1697
1698         if storage_classes:
1699             self._storage_classes_desired = storage_classes
1700
1701         self._my_block_manager().commit_all()
1702         text = self.manifest_text(strip=False)
1703
1704         if create_collection_record:
1705             if name is None:
1706                 name = "New collection"
1707                 ensure_unique_name = True
1708
1709             body = {"manifest_text": text,
1710                     "name": name,
1711                     "replication_desired": self.replication_desired}
1712             if owner_uuid:
1713                 body["owner_uuid"] = owner_uuid
1714             if properties:
1715                 body["properties"] = properties
1716             if self.storage_classes_desired():
1717                 body["storage_classes_desired"] = self.storage_classes_desired()
1718             if trash_at:
1719                 t = trash_at.strftime("%Y-%m-%dT%H:%M:%S.%fZ")
1720                 body["trash_at"] = t
1721
1722             self._remember_api_response(self._my_api().collections().create(ensure_unique_name=ensure_unique_name, body=body).execute(num_retries=num_retries))
1723             text = self._api_response["manifest_text"]
1724
1725             self._manifest_locator = self._api_response["uuid"]
1726             self._portable_data_hash = self._api_response["portable_data_hash"]
1727
1728             self._manifest_text = text
1729             self.set_committed(True)
1730
1731         return text
1732
1733     _token_re = re.compile(r'(\S+)(\s+|$)')
1734     _block_re = re.compile(r'[0-9a-f]{32}\+(\d+)(\+\S+)*')
1735     _segment_re = re.compile(r'(\d+):(\d+):(\S+)')
1736
1737     def _unescape_manifest_path(self, path):
1738         return re.sub('\\\\([0-3][0-7][0-7])', lambda m: chr(int(m.group(1), 8)), path)
1739
1740     @synchronized
1741     def _import_manifest(self, manifest_text):
1742         """Import a manifest into a `Collection`.
1743
1744         :manifest_text:
1745           The manifest text to import from.
1746
1747         """
1748         if len(self) > 0:
1749             raise ArgumentError("Can only import manifest into an empty collection")
1750
1751         STREAM_NAME = 0
1752         BLOCKS = 1
1753         SEGMENTS = 2
1754
1755         stream_name = None
1756         state = STREAM_NAME
1757
1758         for token_and_separator in self._token_re.finditer(manifest_text):
1759             tok = token_and_separator.group(1)
1760             sep = token_and_separator.group(2)
1761
1762             if state == STREAM_NAME:
1763                 # starting a new stream
1764                 stream_name = self._unescape_manifest_path(tok)
1765                 blocks = []
1766                 segments = []
1767                 streamoffset = 0
1768                 state = BLOCKS
1769                 self.find_or_create(stream_name, COLLECTION)
1770                 continue
1771
1772             if state == BLOCKS:
1773                 block_locator = self._block_re.match(tok)
1774                 if block_locator:
1775                     blocksize = int(block_locator.group(1))
1776                     blocks.append(Range(tok, streamoffset, blocksize, 0))
1777                     streamoffset += blocksize
1778                 else:
1779                     state = SEGMENTS
1780
1781             if state == SEGMENTS:
1782                 file_segment = self._segment_re.match(tok)
1783                 if file_segment:
1784                     pos = int(file_segment.group(1))
1785                     size = int(file_segment.group(2))
1786                     name = self._unescape_manifest_path(file_segment.group(3))
1787                     if name.split('/')[-1] == '.':
1788                         # placeholder for persisting an empty directory, not a real file
1789                         if len(name) > 2:
1790                             self.find_or_create(os.path.join(stream_name, name[:-2]), COLLECTION)
1791                     else:
1792                         filepath = os.path.join(stream_name, name)
1793                         afile = self.find_or_create(filepath, FILE)
1794                         if isinstance(afile, ArvadosFile):
1795                             afile.add_segment(blocks, pos, size)
1796                         else:
1797                             raise errors.SyntaxError("File %s conflicts with stream of the same name.", filepath)
1798                 else:
1799                     # error!
1800                     raise errors.SyntaxError("Invalid manifest format, expected file segment but did not match format: '%s'" % tok)
1801
1802             if sep == "\n":
1803                 stream_name = None
1804                 state = STREAM_NAME
1805
1806         self.set_committed(True)
1807
1808     @synchronized
1809     def notify(self, event, collection, name, item):
1810         if self._callback:
1811             self._callback(event, collection, name, item)
1812
1813
1814 class Subcollection(RichCollectionBase):
1815     """This is a subdirectory within a collection that doesn't have its own API
1816     server record.
1817
1818     Subcollection locking falls under the umbrella lock of its root collection.
1819
1820     """
1821
1822     def __init__(self, parent, name):
1823         super(Subcollection, self).__init__(parent)
1824         self.lock = self.root_collection().lock
1825         self._manifest_text = None
1826         self.name = name
1827         self.num_retries = parent.num_retries
1828
1829     def root_collection(self):
1830         return self.parent.root_collection()
1831
1832     def writable(self):
1833         return self.root_collection().writable()
1834
1835     def _my_api(self):
1836         return self.root_collection()._my_api()
1837
1838     def _my_keep(self):
1839         return self.root_collection()._my_keep()
1840
1841     def _my_block_manager(self):
1842         return self.root_collection()._my_block_manager()
1843
1844     def stream_name(self):
1845         return os.path.join(self.parent.stream_name(), self.name)
1846
1847     @synchronized
1848     def clone(self, new_parent, new_name):
1849         c = Subcollection(new_parent, new_name)
1850         c._clonefrom(self)
1851         return c
1852
1853     @must_be_writable
1854     @synchronized
1855     def _reparent(self, newparent, newname):
1856         self.set_committed(False)
1857         self.flush()
1858         self.parent.remove(self.name, recursive=True)
1859         self.parent = newparent
1860         self.name = newname
1861         self.lock = self.parent.root_collection().lock
1862
1863     @synchronized
1864     def _get_manifest_text(self, stream_name, strip, normalize, only_committed=False):
1865         """Encode empty directories by using an \056-named (".") empty file"""
1866         if len(self._items) == 0:
1867             return "%s %s 0:0:\\056\n" % (
1868                 escape(stream_name), config.EMPTY_BLOCK_LOCATOR)
1869         return super(Subcollection, self)._get_manifest_text(stream_name,
1870                                                              strip, normalize,
1871                                                              only_committed)
1872
1873
1874 class CollectionReader(Collection):
1875     """A read-only collection object.
1876
1877     Initialize from a collection UUID or portable data hash, or raw
1878     manifest text.  See `Collection` constructor for detailed options.
1879
1880     """
1881     def __init__(self, manifest_locator_or_text, *args, **kwargs):
1882         self._in_init = True
1883         super(CollectionReader, self).__init__(manifest_locator_or_text, *args, **kwargs)
1884         self._in_init = False
1885
1886         # Forego any locking since it should never change once initialized.
1887         self.lock = NoopLock()
1888
1889         # Backwards compatability with old CollectionReader
1890         # all_streams() and all_files()
1891         self._streams = None
1892
1893     def writable(self):
1894         return self._in_init
1895
1896     def _populate_streams(orig_func):
1897         @functools.wraps(orig_func)
1898         def populate_streams_wrapper(self, *args, **kwargs):
1899             # Defer populating self._streams until needed since it creates a copy of the manifest.
1900             if self._streams is None:
1901                 if self._manifest_text:
1902                     self._streams = [sline.split()
1903                                      for sline in self._manifest_text.split("\n")
1904                                      if sline]
1905                 else:
1906                     self._streams = []
1907             return orig_func(self, *args, **kwargs)
1908         return populate_streams_wrapper
1909
1910     @_populate_streams
1911     def normalize(self):
1912         """Normalize the streams returned by `all_streams`.
1913
1914         This method is kept for backwards compatability and only affects the
1915         behavior of `all_streams()` and `all_files()`
1916
1917         """
1918
1919         # Rearrange streams
1920         streams = {}
1921         for s in self.all_streams():
1922             for f in s.all_files():
1923                 streamname, filename = split(s.name() + "/" + f.name())
1924                 if streamname not in streams:
1925                     streams[streamname] = {}
1926                 if filename not in streams[streamname]:
1927                     streams[streamname][filename] = []
1928                 for r in f.segments:
1929                     streams[streamname][filename].extend(s.locators_and_ranges(r.locator, r.range_size))
1930
1931         self._streams = [normalize_stream(s, streams[s])
1932                          for s in sorted(streams)]
1933     @_populate_streams
1934     def all_streams(self):
1935         return [StreamReader(s, self._my_keep(), num_retries=self.num_retries)
1936                 for s in self._streams]
1937
1938     @_populate_streams
1939     def all_files(self):
1940         for s in self.all_streams():
1941             for f in s.all_files():
1942                 yield f