sdk/python/arvados/arvfile.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__ import division
   7 from future import standard_library
   8 from future.utils import listitems, listvalues
   9 standard_library.install_aliases()
  10 from builtins import range
  11 from builtins import object
  12 import bz2
  13 import collections
  14 import copy
  15 import errno
  16 import functools
  17 import hashlib
  18 import logging
  19 import os
  20 import queue
  21 import re
  22 import sys
  23 import threading
  24 import uuid
  25 import zlib
  26
  27 from . import config
  28 from .errors import KeepWriteError, AssertionError, ArgumentError
  29 from .keep import KeepLocator
  30 from ._normalize_stream import normalize_stream
  31 from ._ranges import locators_and_ranges, replace_range, Range, LocatorAndRange
  32 from .retry import retry_method
  33
  34 MOD = "mod"
  35 WRITE = "write"
  36
  37 _logger = logging.getLogger('arvados.arvfile')
  38
  39 def split(path):
  40     """split(path) -> streamname, filename
  41
  42     Separate the stream name and file name in a /-separated stream path and
  43     return a tuple (stream_name, file_name).  If no stream name is available,
  44     assume '.'.
  45
  46     """
  47     try:
  48         stream_name, file_name = path.rsplit('/', 1)
  49     except ValueError:  # No / in string
  50         stream_name, file_name = '.', path
  51     return stream_name, file_name
  52
  53
  54 class UnownedBlockError(Exception):
  55     """Raised when there's an writable block without an owner on the BlockManager."""
  56     pass
  57
  58
  59 class _FileLikeObjectBase(object):
  60     def __init__(self, name, mode):
  61         self.name = name
  62         self.mode = mode
  63         self.closed = False
  64
  65     @staticmethod
  66     def _before_close(orig_func):
  67         @functools.wraps(orig_func)
  68         def before_close_wrapper(self, *args, **kwargs):
  69             if self.closed:
  70                 raise ValueError("I/O operation on closed stream file")
  71             return orig_func(self, *args, **kwargs)
  72         return before_close_wrapper
  73
  74     def __enter__(self):
  75         return self
  76
  77     def __exit__(self, exc_type, exc_value, traceback):
  78         try:
  79             self.close()
  80         except Exception:
  81             if exc_type is None:
  82                 raise
  83
  84     def close(self):
  85         self.closed = True
  86
  87
  88 class ArvadosFileReaderBase(_FileLikeObjectBase):
  89     def __init__(self, name, mode, num_retries=None):
  90         super(ArvadosFileReaderBase, self).__init__(name, mode)
  91         self._filepos = 0
  92         self.num_retries = num_retries
  93         self._readline_cache = (None, None)
  94
  95     def __iter__(self):
  96         while True:
  97             data = self.readline()
  98             if not data:
  99                 break
 100             yield data
 101
 102     def decompressed_name(self):
 103         return re.sub('\.(bz2|gz)$', '', self.name)
 104
 105     @_FileLikeObjectBase._before_close
 106     def seek(self, pos, whence=os.SEEK_SET):
 107         if whence == os.SEEK_CUR:
 108             pos += self._filepos
 109         elif whence == os.SEEK_END:
 110             pos += self.size()
 111         if pos < 0:
 112             raise IOError(errno.EINVAL, "Tried to seek to negative file offset.")
 113         self._filepos = pos
 114         return self._filepos
 115
 116     def tell(self):
 117         return self._filepos
 118
 119     def readable(self):
 120         return True
 121
 122     def writable(self):
 123         return False
 124
 125     def seekable(self):
 126         return True
 127
 128     @_FileLikeObjectBase._before_close
 129     @retry_method
 130     def readall(self, size=2**20, num_retries=None):
 131         while True:
 132             data = self.read(size, num_retries=num_retries)
 133             if len(data) == 0:
 134                 break
 135             yield data
 136
 137     @_FileLikeObjectBase._before_close
 138     @retry_method
 139     def readline(self, size=float('inf'), num_retries=None):
 140         cache_pos, cache_data = self._readline_cache
 141         if self.tell() == cache_pos:
 142             data = [cache_data]
 143             self._filepos += len(cache_data)
 144         else:
 145             data = [b'']
 146         data_size = len(data[-1])
 147         while (data_size < size) and (b'\n' not in data[-1]):
 148             next_read = self.read(2 ** 20, num_retries=num_retries)
 149             if not next_read:
 150                 break
 151             data.append(next_read)
 152             data_size += len(next_read)
 153         data = b''.join(data)
 154         try:
 155             nextline_index = data.index(b'\n') + 1
 156         except ValueError:
 157             nextline_index = len(data)
 158         nextline_index = min(nextline_index, size)
 159         self._filepos -= len(data) - nextline_index
 160         self._readline_cache = (self.tell(), data[nextline_index:])
 161         return data[:nextline_index].decode()
 162
 163     @_FileLikeObjectBase._before_close
 164     @retry_method
 165     def decompress(self, decompress, size, num_retries=None):
 166         for segment in self.readall(size, num_retries=num_retries):
 167             data = decompress(segment)
 168             if data:
 169                 yield data
 170
 171     @_FileLikeObjectBase._before_close
 172     @retry_method
 173     def readall_decompressed(self, size=2**20, num_retries=None):
 174         self.seek(0)
 175         if self.name.endswith('.bz2'):
 176             dc = bz2.BZ2Decompressor()
 177             return self.decompress(dc.decompress, size,
 178                                    num_retries=num_retries)
 179         elif self.name.endswith('.gz'):
 180             dc = zlib.decompressobj(16+zlib.MAX_WBITS)
 181             return self.decompress(lambda segment: dc.decompress(dc.unconsumed_tail + segment),
 182                                    size, num_retries=num_retries)
 183         else:
 184             return self.readall(size, num_retries=num_retries)
 185
 186     @_FileLikeObjectBase._before_close
 187     @retry_method
 188     def readlines(self, sizehint=float('inf'), num_retries=None):
 189         data = []
 190         data_size = 0
 191         for s in self.readall(num_retries=num_retries):
 192             data.append(s)
 193             data_size += len(s)
 194             if data_size >= sizehint:
 195                 break
 196         return b''.join(data).decode().splitlines(True)
 197
 198     def size(self):
 199         raise IOError(errno.ENOSYS, "Not implemented")
 200
 201     def read(self, size, num_retries=None):
 202         raise IOError(errno.ENOSYS, "Not implemented")
 203
 204     def readfrom(self, start, size, num_retries=None):
 205         raise IOError(errno.ENOSYS, "Not implemented")
 206
 207
 208 class StreamFileReader(ArvadosFileReaderBase):
 209     class _NameAttribute(str):
 210         # The Python file API provides a plain .name attribute.
 211         # Older SDK provided a name() method.
 212         # This class provides both, for maximum compatibility.
 213         def __call__(self):
 214             return self
 215
 216     def __init__(self, stream, segments, name):
 217         super(StreamFileReader, self).__init__(self._NameAttribute(name), 'rb', num_retries=stream.num_retries)
 218         self._stream = stream
 219         self.segments = segments
 220
 221     def stream_name(self):
 222         return self._stream.name()
 223
 224     def size(self):
 225         n = self.segments[-1]
 226         return n.range_start + n.range_size
 227
 228     @_FileLikeObjectBase._before_close
 229     @retry_method
 230     def read(self, size, num_retries=None):
 231         """Read up to 'size' bytes from the stream, starting at the current file position"""
 232         if size == 0:
 233             return b''
 234
 235         data = b''
 236         available_chunks = locators_and_ranges(self.segments, self._filepos, size)
 237         if available_chunks:
 238             lr = available_chunks[0]
 239             data = self._stream.readfrom(lr.locator+lr.segment_offset,
 240                                          lr.segment_size,
 241                                          num_retries=num_retries)
 242
 243         self._filepos += len(data)
 244         return data
 245
 246     @_FileLikeObjectBase._before_close
 247     @retry_method
 248     def readfrom(self, start, size, num_retries=None):
 249         """Read up to 'size' bytes from the stream, starting at 'start'"""
 250         if size == 0:
 251             return b''
 252
 253         data = []
 254         for lr in locators_and_ranges(self.segments, start, size):
 255             data.append(self._stream.readfrom(lr.locator+lr.segment_offset, lr.segment_size,
 256                                               num_retries=num_retries))
 257         return b''.join(data)
 258
 259     def as_manifest(self):
 260         segs = []
 261         for r in self.segments:
 262             segs.extend(self._stream.locators_and_ranges(r.locator, r.range_size))
 263         return " ".join(normalize_stream(".", {self.name: segs})) + "\n"
 264
 265
 266 def synchronized(orig_func):
 267     @functools.wraps(orig_func)
 268     def synchronized_wrapper(self, *args, **kwargs):
 269         with self.lock:
 270             return orig_func(self, *args, **kwargs)
 271     return synchronized_wrapper
 272
 273
 274 class StateChangeError(Exception):
 275     def __init__(self, message, state, nextstate):
 276         super(StateChangeError, self).__init__(message)
 277         self.state = state
 278         self.nextstate = nextstate
 279
 280 class _BufferBlock(object):
 281     """A stand-in for a Keep block that is in the process of being written.
 282
 283     Writers can append to it, get the size, and compute the Keep locator.
 284     There are three valid states:
 285
 286     WRITABLE
 287       Can append to block.
 288
 289     PENDING
 290       Block is in the process of being uploaded to Keep, append is an error.
 291
 292     COMMITTED
 293       The block has been written to Keep, its internal buffer has been
 294       released, fetching the block will fetch it via keep client (since we
 295       discarded the internal copy), and identifiers referring to the BufferBlock
 296       can be replaced with the block locator.
 297
 298     """
 299
 300     WRITABLE = 0
 301     PENDING = 1
 302     COMMITTED = 2
 303     ERROR = 3
 304     DELETED = 4
 305
 306     def __init__(self, blockid, starting_capacity, owner):
 307         """
 308         :blockid:
 309           the identifier for this block
 310
 311         :starting_capacity:
 312           the initial buffer capacity
 313
 314         :owner:
 315           ArvadosFile that owns this block
 316
 317         """
 318         self.blockid = blockid
 319         self.buffer_block = bytearray(starting_capacity)
 320         self.buffer_view = memoryview(self.buffer_block)
 321         self.write_pointer = 0
 322         self._state = _BufferBlock.WRITABLE
 323         self._locator = None
 324         self.owner = owner
 325         self.lock = threading.Lock()
 326         self.wait_for_commit = threading.Event()
 327         self.error = None
 328
 329     @synchronized
 330     def append(self, data):
 331         """Append some data to the buffer.
 332
 333         Only valid if the block is in WRITABLE state.  Implements an expanding
 334         buffer, doubling capacity as needed to accomdate all the data.
 335
 336         """
 337         if self._state == _BufferBlock.WRITABLE:
 338             if not isinstance(data, bytes) and not isinstance(data, memoryview):
 339                 data = data.encode()
 340             while (self.write_pointer+len(data)) > len(self.buffer_block):
 341                 new_buffer_block = bytearray(len(self.buffer_block) * 2)
 342                 new_buffer_block[0:self.write_pointer] = self.buffer_block[0:self.write_pointer]
 343                 self.buffer_block = new_buffer_block
 344                 self.buffer_view = memoryview(self.buffer_block)
 345             self.buffer_view[self.write_pointer:self.write_pointer+len(data)] = data
 346             self.write_pointer += len(data)
 347             self._locator = None
 348         else:
 349             raise AssertionError("Buffer block is not writable")
 350
 351     STATE_TRANSITIONS = frozenset([
 352             (WRITABLE, PENDING),
 353             (PENDING, COMMITTED),
 354             (PENDING, ERROR),
 355             (ERROR, PENDING)])
 356
 357     @synchronized
 358     def set_state(self, nextstate, val=None):
 359         if (self._state, nextstate) not in self.STATE_TRANSITIONS:
 360             raise StateChangeError("Invalid state change from %s to %s" % (self._state, nextstate), self._state, nextstate)
 361         self._state = nextstate
 362
 363         if self._state == _BufferBlock.PENDING:
 364             self.wait_for_commit.clear()
 365
 366         if self._state == _BufferBlock.COMMITTED:
 367             self._locator = val
 368             self.buffer_view = None
 369             self.buffer_block = None
 370             self.wait_for_commit.set()
 371
 372         if self._state == _BufferBlock.ERROR:
 373             self.error = val
 374             self.wait_for_commit.set()
 375
 376     @synchronized
 377     def state(self):
 378         return self._state
 379
 380     def size(self):
 381         """The amount of data written to the buffer."""
 382         return self.write_pointer
 383
 384     @synchronized
 385     def locator(self):
 386         """The Keep locator for this buffer's contents."""
 387         if self._locator is None:
 388             self._locator = "%s+%i" % (hashlib.md5(self.buffer_view[0:self.write_pointer]).hexdigest(), self.size())
 389         return self._locator
 390
 391     @synchronized
 392     def clone(self, new_blockid, owner):
 393         if self._state == _BufferBlock.COMMITTED:
 394             raise AssertionError("Cannot duplicate committed buffer block")
 395         bufferblock = _BufferBlock(new_blockid, self.size(), owner)
 396         bufferblock.append(self.buffer_view[0:self.size()])
 397         return bufferblock
 398
 399     @synchronized
 400     def clear(self):
 401         self._state = _BufferBlock.DELETED
 402         self.owner = None
 403         self.buffer_block = None
 404         self.buffer_view = None
 405
 406     @synchronized
 407     def repack_writes(self):
 408         """Optimize buffer block by repacking segments in file sequence.
 409
 410         When the client makes random writes, they appear in the buffer block in
 411         the sequence they were written rather than the sequence they appear in
 412         the file.  This makes for inefficient, fragmented manifests.  Attempt
 413         to optimize by repacking writes in file sequence.
 414
 415         """
 416         if self._state != _BufferBlock.WRITABLE:
 417             raise AssertionError("Cannot repack non-writable block")
 418
 419         segs = self.owner.segments()
 420
 421         # Collect the segments that reference the buffer block.
 422         bufferblock_segs = [s for s in segs if s.locator == self.blockid]
 423
 424         # Collect total data referenced by segments (could be smaller than
 425         # bufferblock size if a portion of the file was written and
 426         # then overwritten).
 427         write_total = sum([s.range_size for s in bufferblock_segs])
 428
 429         if write_total < self.size() or len(bufferblock_segs) > 1:
 430             # If there's more than one segment referencing this block, it is
 431             # due to out-of-order writes and will produce a fragmented
 432             # manifest, so try to optimize by re-packing into a new buffer.
 433             contents = self.buffer_view[0:self.write_pointer].tobytes()
 434             new_bb = _BufferBlock(None, write_total, None)
 435             for t in bufferblock_segs:
 436                 new_bb.append(contents[t.segment_offset:t.segment_offset+t.range_size])
 437                 t.segment_offset = new_bb.size() - t.range_size
 438
 439             self.buffer_block = new_bb.buffer_block
 440             self.buffer_view = new_bb.buffer_view
 441             self.write_pointer = new_bb.write_pointer
 442             self._locator = None
 443             new_bb.clear()
 444             self.owner.set_segments(segs)
 445
 446     def __repr__(self):
 447         return "<BufferBlock %s>" % (self.blockid)
 448
 449
 450 class NoopLock(object):
 451     def __enter__(self):
 452         return self
 453
 454     def __exit__(self, exc_type, exc_value, traceback):
 455         pass
 456
 457     def acquire(self, blocking=False):
 458         pass
 459
 460     def release(self):
 461         pass
 462
 463
 464 def must_be_writable(orig_func):
 465     @functools.wraps(orig_func)
 466     def must_be_writable_wrapper(self, *args, **kwargs):
 467         if not self.writable():
 468             raise IOError(errno.EROFS, "Collection is read-only.")
 469         return orig_func(self, *args, **kwargs)
 470     return must_be_writable_wrapper
 471
 472
 473 class _BlockManager(object):
 474     """BlockManager handles buffer blocks.
 475
 476     Also handles background block uploads, and background block prefetch for a
 477     Collection of ArvadosFiles.
 478
 479     """
 480
 481     DEFAULT_PUT_THREADS = 2
 482     DEFAULT_GET_THREADS = 4
 483
 484     def __init__(self, keep, copies=None, put_threads=None, num_retries=None, storage_classes_func=None):
 485         """keep: KeepClient object to use"""
 486         self._keep = keep
 487         self._bufferblocks = collections.OrderedDict()
 488         self._put_queue = None
 489         self._put_threads = None
 490         self._prefetch_queue = None
 491         self._prefetch_threads = None
 492         self.lock = threading.Lock()
 493         self.prefetch_enabled = True
 494         self.num_put_threads = put_threads or _BlockManager.DEFAULT_PUT_THREADS
 495         self.num_get_threads = _BlockManager.DEFAULT_GET_THREADS
 496         self.copies = copies
 497         self.storage_classes = storage_classes_func or (lambda: [])
 498         self._pending_write_size = 0
 499         self.threads_lock = threading.Lock()
 500         self.padding_block = None
 501         self.num_retries = num_retries
 502
 503     @synchronized
 504     def alloc_bufferblock(self, blockid=None, starting_capacity=2**14, owner=None):
 505         """Allocate a new, empty bufferblock in WRITABLE state and return it.
 506
 507         :blockid:
 508           optional block identifier, otherwise one will be automatically assigned
 509
 510         :starting_capacity:
 511           optional capacity, otherwise will use default capacity
 512
 513         :owner:
 514           ArvadosFile that owns this block
 515
 516         """
 517         return self._alloc_bufferblock(blockid, starting_capacity, owner)
 518
 519     def _alloc_bufferblock(self, blockid=None, starting_capacity=2**14, owner=None):
 520         if blockid is None:
 521             blockid = str(uuid.uuid4())
 522         bufferblock = _BufferBlock(blockid, starting_capacity=starting_capacity, owner=owner)
 523         self._bufferblocks[bufferblock.blockid] = bufferblock
 524         return bufferblock
 525
 526     @synchronized
 527     def dup_block(self, block, owner):
 528         """Create a new bufferblock initialized with the content of an existing bufferblock.
 529
 530         :block:
 531           the buffer block to copy.
 532
 533         :owner:
 534           ArvadosFile that owns the new block
 535
 536         """
 537         new_blockid = str(uuid.uuid4())
 538         bufferblock = block.clone(new_blockid, owner)
 539         self._bufferblocks[bufferblock.blockid] = bufferblock
 540         return bufferblock
 541
 542     @synchronized
 543     def is_bufferblock(self, locator):
 544         return locator in self._bufferblocks
 545
 546     def _commit_bufferblock_worker(self):
 547         """Background uploader thread."""
 548
 549         while True:
 550             try:
 551                 bufferblock = self._put_queue.get()
 552                 if bufferblock is None:
 553                     return
 554
 555                 if self.copies is None:
 556                     loc = self._keep.put(bufferblock.buffer_view[0:bufferblock.write_pointer].tobytes(), num_retries=self.num_retries, classes=self.storage_classes())
 557                 else:
 558                     loc = self._keep.put(bufferblock.buffer_view[0:bufferblock.write_pointer].tobytes(), num_retries=self.num_retries, copies=self.copies, classes=self.storage_classes())
 559                 bufferblock.set_state(_BufferBlock.COMMITTED, loc)
 560             except Exception as e:
 561                 bufferblock.set_state(_BufferBlock.ERROR, e)
 562             finally:
 563                 if self._put_queue is not None:
 564                     self._put_queue.task_done()
 565
 566     def start_put_threads(self):
 567         with self.threads_lock:
 568             if self._put_threads is None:
 569                 # Start uploader threads.
 570
 571                 # If we don't limit the Queue size, the upload queue can quickly
 572                 # grow to take up gigabytes of RAM if the writing process is
 573                 # generating data more quickly than it can be sent to the Keep
 574                 # servers.
 575                 #
 576                 # With two upload threads and a queue size of 2, this means up to 4
 577                 # blocks pending.  If they are full 64 MiB blocks, that means up to
 578                 # 256 MiB of internal buffering, which is the same size as the
 579                 # default download block cache in KeepClient.
 580                 self._put_queue = queue.Queue(maxsize=2)
 581
 582                 self._put_threads = []
 583                 for i in range(0, self.num_put_threads):
 584                     thread = threading.Thread(target=self._commit_bufferblock_worker)
 585                     self._put_threads.append(thread)
 586                     thread.daemon = True
 587                     thread.start()
 588
 589     def _block_prefetch_worker(self):
 590         """The background downloader thread."""
 591         while True:
 592             try:
 593                 b = self._prefetch_queue.get()
 594                 if b is None:
 595                     return
 596                 if self._keep.has_cache_slot(b):
 597                     continue
 598                 _logger.debug("prefetching %s", b)
 599                 self._keep.get(b)
 600             except Exception:
 601                 _logger.exception("Exception doing block prefetch")
 602
 603     @synchronized
 604     def start_get_threads(self):
 605         if self._prefetch_threads is None:
 606             self._prefetch_queue = queue.Queue()
 607             self._prefetch_threads = []
 608             for i in range(0, self.num_get_threads):
 609                 thread = threading.Thread(target=self._block_prefetch_worker)
 610                 self._prefetch_threads.append(thread)
 611                 thread.daemon = True
 612                 thread.start()
 613
 614
 615     @synchronized
 616     def stop_threads(self):
 617         """Shut down and wait for background upload and download threads to finish."""
 618
 619         if self._put_threads is not None:
 620             for t in self._put_threads:
 621                 self._put_queue.put(None)
 622             for t in self._put_threads:
 623                 t.join()
 624         self._put_threads = None
 625         self._put_queue = None
 626
 627         if self._prefetch_threads is not None:
 628             for t in self._prefetch_threads:
 629                 self._prefetch_queue.put(None)
 630             for t in self._prefetch_threads:
 631                 t.join()
 632         self._prefetch_threads = None
 633         self._prefetch_queue = None
 634
 635     def __enter__(self):
 636         return self
 637
 638     def __exit__(self, exc_type, exc_value, traceback):
 639         self.stop_threads()
 640
 641     @synchronized
 642     def repack_small_blocks(self, force=False, sync=False, closed_file_size=0):
 643         """Packs small blocks together before uploading"""
 644
 645         self._pending_write_size += closed_file_size
 646
 647         # Check if there are enough small blocks for filling up one in full
 648         if not (force or (self._pending_write_size >= config.KEEP_BLOCK_SIZE)):
 649             return
 650
 651         # Search blocks ready for getting packed together before being
 652         # committed to Keep.
 653         # A WRITABLE block always has an owner.
 654         # A WRITABLE block with its owner.closed() implies that its
 655         # size is <= KEEP_BLOCK_SIZE/2.
 656         try:
 657             small_blocks = [b for b in listvalues(self._bufferblocks)
 658                             if b.state() == _BufferBlock.WRITABLE and b.owner.closed()]
 659         except AttributeError:
 660             # Writable blocks without owner shouldn't exist.
 661             raise UnownedBlockError()
 662
 663         if len(small_blocks) <= 1:
 664             # Not enough small blocks for repacking
 665             return
 666
 667         for bb in small_blocks:
 668             bb.repack_writes()
 669
 670         # Update the pending write size count with its true value, just in case
 671         # some small file was opened, written and closed several times.
 672         self._pending_write_size = sum([b.size() for b in small_blocks])
 673
 674         if self._pending_write_size < config.KEEP_BLOCK_SIZE and not force:
 675             return
 676
 677         new_bb = self._alloc_bufferblock()
 678         new_bb.owner = []
 679         files = []
 680         while len(small_blocks) > 0 and (new_bb.write_pointer + small_blocks[0].size()) <= config.KEEP_BLOCK_SIZE:
 681             bb = small_blocks.pop(0)
 682             new_bb.owner.append(bb.owner)
 683             self._pending_write_size -= bb.size()
 684             new_bb.append(bb.buffer_view[0:bb.write_pointer].tobytes())
 685             files.append((bb, new_bb.write_pointer - bb.size()))
 686
 687         self.commit_bufferblock(new_bb, sync=sync)
 688
 689         for bb, new_bb_segment_offset in files:
 690             newsegs = bb.owner.segments()
 691             for s in newsegs:
 692                 if s.locator == bb.blockid:
 693                     s.locator = new_bb.blockid
 694                     s.segment_offset = new_bb_segment_offset+s.segment_offset
 695             bb.owner.set_segments(newsegs)
 696             self._delete_bufferblock(bb.blockid)
 697
 698     def commit_bufferblock(self, block, sync):
 699         """Initiate a background upload of a bufferblock.
 700
 701         :block:
 702           The block object to upload
 703
 704         :sync:
 705           If `sync` is True, upload the block synchronously.
 706           If `sync` is False, upload the block asynchronously.  This will
 707           return immediately unless the upload queue is at capacity, in
 708           which case it will wait on an upload queue slot.
 709
 710         """
 711         try:
 712             # Mark the block as PENDING so to disallow any more appends.
 713             block.set_state(_BufferBlock.PENDING)
 714         except StateChangeError as e:
 715             if e.state == _BufferBlock.PENDING:
 716                 if sync:
 717                     block.wait_for_commit.wait()
 718                 else:
 719                     return
 720             if block.state() == _BufferBlock.COMMITTED:
 721                 return
 722             elif block.state() == _BufferBlock.ERROR:
 723                 raise block.error
 724             else:
 725                 raise
 726
 727         if sync:
 728             try:
 729                 if self.copies is None:
 730                     loc = self._keep.put(block.buffer_view[0:block.write_pointer].tobytes(), num_retries=self.num_retries, classes=self.storage_classes())
 731                 else:
 732                     loc = self._keep.put(block.buffer_view[0:block.write_pointer].tobytes(), num_retries=self.num_retries, copies=self.copies, classes=self.storage_classes())
 733                 block.set_state(_BufferBlock.COMMITTED, loc)
 734             except Exception as e:
 735                 block.set_state(_BufferBlock.ERROR, e)
 736                 raise
 737         else:
 738             self.start_put_threads()
 739             self._put_queue.put(block)
 740
 741     @synchronized
 742     def get_bufferblock(self, locator):
 743         return self._bufferblocks.get(locator)
 744
 745     @synchronized
 746     def get_padding_block(self):
 747         """Get a bufferblock 64 MB in size consisting of all zeros, used as padding
 748         when using truncate() to extend the size of a file.
 749
 750         For reference (and possible future optimization), the md5sum of the
 751         padding block is: 7f614da9329cd3aebf59b91aadc30bf0+67108864
 752
 753         """
 754
 755         if self.padding_block is None:
 756             self.padding_block = self._alloc_bufferblock(starting_capacity=config.KEEP_BLOCK_SIZE)
 757             self.padding_block.write_pointer = config.KEEP_BLOCK_SIZE
 758             self.commit_bufferblock(self.padding_block, False)
 759         return self.padding_block
 760
 761     @synchronized
 762     def delete_bufferblock(self, locator):
 763         self._delete_bufferblock(locator)
 764
 765     def _delete_bufferblock(self, locator):
 766         if locator in self._bufferblocks:
 767             bb = self._bufferblocks[locator]
 768             bb.clear()
 769             del self._bufferblocks[locator]
 770
 771     def get_block_contents(self, locator, num_retries, cache_only=False):
 772         """Fetch a block.
 773
 774         First checks to see if the locator is a BufferBlock and return that, if
 775         not, passes the request through to KeepClient.get().
 776
 777         """
 778         with self.lock:
 779             if locator in self._bufferblocks:
 780                 bufferblock = self._bufferblocks[locator]
 781                 if bufferblock.state() != _BufferBlock.COMMITTED:
 782                     return bufferblock.buffer_view[0:bufferblock.write_pointer].tobytes()
 783                 else:
 784                     locator = bufferblock._locator
 785         if cache_only:
 786             return self._keep.get_from_cache(locator)
 787         else:
 788             return self._keep.get(locator, num_retries=num_retries)
 789
 790     def commit_all(self):
 791         """Commit all outstanding buffer blocks.
 792
 793         This is a synchronous call, and will not return until all buffer blocks
 794         are uploaded.  Raises KeepWriteError() if any blocks failed to upload.
 795
 796         """
 797         self.repack_small_blocks(force=True, sync=True)
 798
 799         with self.lock:
 800             items = listitems(self._bufferblocks)
 801
 802         for k,v in items:
 803             if v.state() != _BufferBlock.COMMITTED and v.owner:
 804                 # Ignore blocks with a list of owners, as if they're not in COMMITTED
 805                 # state, they're already being committed asynchronously.
 806                 if isinstance(v.owner, ArvadosFile):
 807                     v.owner.flush(sync=False)
 808
 809         with self.lock:
 810             if self._put_queue is not None:
 811                 self._put_queue.join()
 812
 813                 err = []
 814                 for k,v in items:
 815                     if v.state() == _BufferBlock.ERROR:
 816                         err.append((v.locator(), v.error))
 817                 if err:
 818                     raise KeepWriteError("Error writing some blocks", err, label="block")
 819
 820         for k,v in items:
 821             # flush again with sync=True to remove committed bufferblocks from
 822             # the segments.
 823             if v.owner:
 824                 if isinstance(v.owner, ArvadosFile):
 825                     v.owner.flush(sync=True)
 826                 elif isinstance(v.owner, list) and len(v.owner) > 0:
 827                     # This bufferblock is referenced by many files as a result
 828                     # of repacking small blocks, so don't delete it when flushing
 829                     # its owners, just do it after flushing them all.
 830                     for owner in v.owner:
 831                         owner.flush(sync=True)
 832                     self.delete_bufferblock(k)
 833
 834     def block_prefetch(self, locator):
 835         """Initiate a background download of a block.
 836
 837         This assumes that the underlying KeepClient implements a block cache,
 838         so repeated requests for the same block will not result in repeated
 839         downloads (unless the block is evicted from the cache.)  This method
 840         does not block.
 841
 842         """
 843
 844         if not self.prefetch_enabled:
 845             return
 846
 847         if self._keep.has_cache_slot(locator):
 848             return
 849
 850         with self.lock:
 851             if locator in self._bufferblocks:
 852                 return
 853
 854         self.start_get_threads()
 855         # _logger.debug("pushing %s to prefetch", locator)
 856         self._prefetch_queue.put(locator)
 857
 858
 859 class ArvadosFile(object):
 860     """Represent a file in a Collection.
 861
 862     ArvadosFile manages the underlying representation of a file in Keep as a
 863     sequence of segments spanning a set of blocks, and implements random
 864     read/write access.
 865
 866     This object may be accessed from multiple threads.
 867
 868     """
 869
 870     __slots__ = ('parent', 'name', '_writers', '_committed',
 871                  '_segments', 'lock', '_current_bblock', 'fuse_entry')
 872
 873     def __init__(self, parent, name, stream=[], segments=[]):
 874         """
 875         ArvadosFile constructor.
 876
 877         :stream:
 878           a list of Range objects representing a block stream
 879
 880         :segments:
 881           a list of Range objects representing segments
 882         """
 883         self.parent = parent
 884         self.name = name
 885         self._writers = set()
 886         self._committed = False
 887         self._segments = []
 888         self.lock = parent.root_collection().lock
 889         for s in segments:
 890             self._add_segment(stream, s.locator, s.range_size)
 891         self._current_bblock = None
 892
 893     def writable(self):
 894         return self.parent.writable()
 895
 896     @synchronized
 897     def permission_expired(self, as_of_dt=None):
 898         """Returns True if any of the segment's locators is expired"""
 899         for r in self._segments:
 900             if KeepLocator(r.locator).permission_expired(as_of_dt):
 901                 return True
 902         return False
 903
 904     @synchronized
 905     def has_remote_blocks(self):
 906         """Returns True if any of the segment's locators has a +R signature"""
 907
 908         for s in self._segments:
 909             if '+R' in s.locator:
 910                 return True
 911         return False
 912
 913     @synchronized
 914     def _copy_remote_blocks(self, remote_blocks={}):
 915         """Ask Keep to copy remote blocks and point to their local copies.
 916
 917         This is called from the parent Collection.
 918
 919         :remote_blocks:
 920             Shared cache of remote to local block mappings. This is used to avoid
 921             doing extra work when blocks are shared by more than one file in
 922             different subdirectories.
 923         """
 924
 925         for s in self._segments:
 926             if '+R' in s.locator:
 927                 try:
 928                     loc = remote_blocks[s.locator]
 929                 except KeyError:
 930                     loc = self.parent._my_keep().refresh_signature(s.locator)
 931                     remote_blocks[s.locator] = loc
 932                 s.locator = loc
 933                 self.parent.set_committed(False)
 934         return remote_blocks
 935
 936     @synchronized
 937     def segments(self):
 938         return copy.copy(self._segments)
 939
 940     @synchronized
 941     def clone(self, new_parent, new_name):
 942         """Make a copy of this file."""
 943         cp = ArvadosFile(new_parent, new_name)
 944         cp.replace_contents(self)
 945         return cp
 946
 947     @must_be_writable
 948     @synchronized
 949     def replace_contents(self, other):
 950         """Replace segments of this file with segments from another `ArvadosFile` object."""
 951
 952         map_loc = {}
 953         self._segments = []
 954         for other_segment in other.segments():
 955             new_loc = other_segment.locator
 956             if other.parent._my_block_manager().is_bufferblock(other_segment.locator):
 957                 if other_segment.locator not in map_loc:
 958                     bufferblock = other.parent._my_block_manager().get_bufferblock(other_segment.locator)
 959                     if bufferblock.state() != _BufferBlock.WRITABLE:
 960                         map_loc[other_segment.locator] = bufferblock.locator()
 961                     else:
 962                         map_loc[other_segment.locator] = self.parent._my_block_manager().dup_block(bufferblock, self).blockid
 963                 new_loc = map_loc[other_segment.locator]
 964
 965             self._segments.append(Range(new_loc, other_segment.range_start, other_segment.range_size, other_segment.segment_offset))
 966
 967         self.set_committed(False)
 968
 969     def __eq__(self, other):
 970         if other is self:
 971             return True
 972         if not isinstance(other, ArvadosFile):
 973             return False
 974
 975         othersegs = other.segments()
 976         with self.lock:
 977             if len(self._segments) != len(othersegs):
 978                 return False
 979             for i in range(0, len(othersegs)):
 980                 seg1 = self._segments[i]
 981                 seg2 = othersegs[i]
 982                 loc1 = seg1.locator
 983                 loc2 = seg2.locator
 984
 985                 if self.parent._my_block_manager().is_bufferblock(loc1):
 986                     loc1 = self.parent._my_block_manager().get_bufferblock(loc1).locator()
 987
 988                 if other.parent._my_block_manager().is_bufferblock(loc2):
 989                     loc2 = other.parent._my_block_manager().get_bufferblock(loc2).locator()
 990
 991                 if (KeepLocator(loc1).stripped() != KeepLocator(loc2).stripped() or
 992                     seg1.range_start != seg2.range_start or
 993                     seg1.range_size != seg2.range_size or
 994                     seg1.segment_offset != seg2.segment_offset):
 995                     return False
 996
 997         return True
 998
 999     def __ne__(self, other):
1000         return not self.__eq__(other)
1001
1002     @synchronized
1003     def set_segments(self, segs):
1004         self._segments = segs
1005
1006     @synchronized
1007     def set_committed(self, value=True):
1008         """Set committed flag.
1009
1010         If value is True, set committed to be True.
1011
1012         If value is False, set committed to be False for this and all parents.
1013         """
1014         if value == self._committed:
1015             return
1016         self._committed = value
1017         if self._committed is False and self.parent is not None:
1018             self.parent.set_committed(False)
1019
1020     @synchronized
1021     def committed(self):
1022         """Get whether this is committed or not."""
1023         return self._committed
1024
1025     @synchronized
1026     def add_writer(self, writer):
1027         """Add an ArvadosFileWriter reference to the list of writers"""
1028         if isinstance(writer, ArvadosFileWriter):
1029             self._writers.add(writer)
1030
1031     @synchronized
1032     def remove_writer(self, writer, flush):
1033         """
1034         Called from ArvadosFileWriter.close(). Remove a writer reference from the list
1035         and do some block maintenance tasks.
1036         """
1037         self._writers.remove(writer)
1038
1039         if flush or self.size() > config.KEEP_BLOCK_SIZE // 2:
1040             # File writer closed, not small enough for repacking
1041             self.flush()
1042         elif self.closed():
1043             # All writers closed and size is adequate for repacking
1044             self.parent._my_block_manager().repack_small_blocks(closed_file_size=self.size())
1045
1046     def closed(self):
1047         """
1048         Get whether this is closed or not. When the writers list is empty, the file
1049         is supposed to be closed.
1050         """
1051         return len(self._writers) == 0
1052
1053     @must_be_writable
1054     @synchronized
1055     def truncate(self, size):
1056         """Shrink or expand the size of the file.
1057
1058         If `size` is less than the size of the file, the file contents after
1059         `size` will be discarded.  If `size` is greater than the current size
1060         of the file, it will be filled with zero bytes.
1061
1062         """
1063         if size < self.size():
1064             new_segs = []
1065             for r in self._segments:
1066                 range_end = r.range_start+r.range_size
1067                 if r.range_start >= size:
1068                     # segment is past the trucate size, all done
1069                     break
1070                 elif size < range_end:
1071                     nr = Range(r.locator, r.range_start, size - r.range_start, 0)
1072                     nr.segment_offset = r.segment_offset
1073                     new_segs.append(nr)
1074                     break
1075                 else:
1076                     new_segs.append(r)
1077
1078             self._segments = new_segs
1079             self.set_committed(False)
1080         elif size > self.size():
1081             padding = self.parent._my_block_manager().get_padding_block()
1082             diff = size - self.size()
1083             while diff > config.KEEP_BLOCK_SIZE:
1084                 self._segments.append(Range(padding.blockid, self.size(), config.KEEP_BLOCK_SIZE, 0))
1085                 diff -= config.KEEP_BLOCK_SIZE
1086             if diff > 0:
1087                 self._segments.append(Range(padding.blockid, self.size(), diff, 0))
1088             self.set_committed(False)
1089         else:
1090             # size == self.size()
1091             pass
1092
1093     def readfrom(self, offset, size, num_retries, exact=False):
1094         """Read up to `size` bytes from the file starting at `offset`.
1095
1096         :exact:
1097          If False (default), return less data than requested if the read
1098          crosses a block boundary and the next block isn't cached.  If True,
1099          only return less data than requested when hitting EOF.
1100         """
1101
1102         with self.lock:
1103             if size == 0 or offset >= self.size():
1104                 return b''
1105             readsegs = locators_and_ranges(self._segments, offset, size)
1106             prefetch = locators_and_ranges(self._segments, offset + size, config.KEEP_BLOCK_SIZE*4, limit=32)
1107
1108         locs = set()
1109         data = []
1110         for lr in readsegs:
1111             block = self.parent._my_block_manager().get_block_contents(lr.locator, num_retries=num_retries, cache_only=(bool(data) and not exact))
1112             if block:
1113                 blockview = memoryview(block)
1114                 data.append(blockview[lr.segment_offset:lr.segment_offset+lr.segment_size].tobytes())
1115                 locs.add(lr.locator)
1116             else:
1117                 break
1118
1119         for lr in prefetch:
1120             if lr.locator not in locs:
1121                 self.parent._my_block_manager().block_prefetch(lr.locator)
1122                 locs.add(lr.locator)
1123
1124         if len(data) == 1:
1125             return data[0]
1126         else:
1127             return b''.join(data)
1128
1129     @must_be_writable
1130     @synchronized
1131     def writeto(self, offset, data, num_retries):
1132         """Write `data` to the file starting at `offset`.
1133
1134         This will update existing bytes and/or extend the size of the file as
1135         necessary.
1136
1137         """
1138         if not isinstance(data, bytes) and not isinstance(data, memoryview):
1139             data = data.encode()
1140         if len(data) == 0:
1141             return
1142
1143         if offset > self.size():
1144             self.truncate(offset)
1145
1146         if len(data) > config.KEEP_BLOCK_SIZE:
1147             # Chunk it up into smaller writes
1148             n = 0
1149             dataview = memoryview(data)
1150             while n < len(data):
1151                 self.writeto(offset+n, dataview[n:n + config.KEEP_BLOCK_SIZE].tobytes(), num_retries)
1152                 n += config.KEEP_BLOCK_SIZE
1153             return
1154
1155         self.set_committed(False)
1156
1157         if self._current_bblock is None or self._current_bblock.state() != _BufferBlock.WRITABLE:
1158             self._current_bblock = self.parent._my_block_manager().alloc_bufferblock(owner=self)
1159
1160         if (self._current_bblock.size() + len(data)) > config.KEEP_BLOCK_SIZE:
1161             self._current_bblock.repack_writes()
1162             if (self._current_bblock.size() + len(data)) > config.KEEP_BLOCK_SIZE:
1163                 self.parent._my_block_manager().commit_bufferblock(self._current_bblock, sync=False)
1164                 self._current_bblock = self.parent._my_block_manager().alloc_bufferblock(owner=self)
1165
1166         self._current_bblock.append(data)
1167
1168         replace_range(self._segments, offset, len(data), self._current_bblock.blockid, self._current_bblock.write_pointer - len(data))
1169
1170         self.parent.notify(WRITE, self.parent, self.name, (self, self))
1171
1172         return len(data)
1173
1174     @synchronized
1175     def flush(self, sync=True, num_retries=0):
1176         """Flush the current bufferblock to Keep.
1177
1178         :sync:
1179           If True, commit block synchronously, wait until buffer block has been written.
1180           If False, commit block asynchronously, return immediately after putting block into
1181           the keep put queue.
1182         """
1183         if self.committed():
1184             return
1185
1186         if self._current_bblock and self._current_bblock.state() != _BufferBlock.COMMITTED:
1187             if self._current_bblock.state() == _BufferBlock.WRITABLE:
1188                 self._current_bblock.repack_writes()
1189             if self._current_bblock.state() != _BufferBlock.DELETED:
1190                 self.parent._my_block_manager().commit_bufferblock(self._current_bblock, sync=sync)
1191
1192         if sync:
1193             to_delete = set()
1194             for s in self._segments:
1195                 bb = self.parent._my_block_manager().get_bufferblock(s.locator)
1196                 if bb:
1197                     if bb.state() != _BufferBlock.COMMITTED:
1198                         self.parent._my_block_manager().commit_bufferblock(bb, sync=True)
1199                     to_delete.add(s.locator)
1200                     s.locator = bb.locator()
1201             for s in to_delete:
1202                 # Don't delete the bufferblock if it's owned by many files. It'll be
1203                 # deleted after all of its owners are flush()ed.
1204                 if self.parent._my_block_manager().get_bufferblock(s).owner is self:
1205                     self.parent._my_block_manager().delete_bufferblock(s)
1206
1207         self.parent.notify(MOD, self.parent, self.name, (self, self))
1208
1209     @must_be_writable
1210     @synchronized
1211     def add_segment(self, blocks, pos, size):
1212         """Add a segment to the end of the file.
1213
1214         `pos` and `offset` reference a section of the stream described by
1215         `blocks` (a list of Range objects)
1216
1217         """
1218         self._add_segment(blocks, pos, size)
1219
1220     def _add_segment(self, blocks, pos, size):
1221         """Internal implementation of add_segment."""
1222         self.set_committed(False)
1223         for lr in locators_and_ranges(blocks, pos, size):
1224             last = self._segments[-1] if self._segments else Range(0, 0, 0, 0)
1225             r = Range(lr.locator, last.range_start+last.range_size, lr.segment_size, lr.segment_offset)
1226             self._segments.append(r)
1227
1228     @synchronized
1229     def size(self):
1230         """Get the file size."""
1231         if self._segments:
1232             n = self._segments[-1]
1233             return n.range_start + n.range_size
1234         else:
1235             return 0
1236
1237     @synchronized
1238     def manifest_text(self, stream_name=".", portable_locators=False,
1239                       normalize=False, only_committed=False):
1240         buf = ""
1241         filestream = []
1242         for segment in self._segments:
1243             loc = segment.locator
1244             if self.parent._my_block_manager().is_bufferblock(loc):
1245                 if only_committed:
1246                     continue
1247                 loc = self.parent._my_block_manager().get_bufferblock(loc).locator()
1248             if portable_locators:
1249                 loc = KeepLocator(loc).stripped()
1250             filestream.append(LocatorAndRange(loc, KeepLocator(loc).size,
1251                                  segment.segment_offset, segment.range_size))
1252         buf += ' '.join(normalize_stream(stream_name, {self.name: filestream}))
1253         buf += "\n"
1254         return buf
1255
1256     @must_be_writable
1257     @synchronized
1258     def _reparent(self, newparent, newname):
1259         self.set_committed(False)
1260         self.flush(sync=True)
1261         self.parent.remove(self.name)
1262         self.parent = newparent
1263         self.name = newname
1264         self.lock = self.parent.root_collection().lock
1265
1266
1267 class ArvadosFileReader(ArvadosFileReaderBase):
1268     """Wraps ArvadosFile in a file-like object supporting reading only.
1269
1270     Be aware that this class is NOT thread safe as there is no locking around
1271     updating file pointer.
1272
1273     """
1274
1275     def __init__(self, arvadosfile, mode="r", num_retries=None):
1276         super(ArvadosFileReader, self).__init__(arvadosfile.name, mode=mode, num_retries=num_retries)
1277         self.arvadosfile = arvadosfile
1278
1279     def size(self):
1280         return self.arvadosfile.size()
1281
1282     def stream_name(self):
1283         return self.arvadosfile.parent.stream_name()
1284
1285     def readinto(self, b):
1286         data = self.read(len(b))
1287         b[:len(data)] = data
1288         return len(data)
1289
1290     @_FileLikeObjectBase._before_close
1291     @retry_method
1292     def read(self, size=None, num_retries=None):
1293         """Read up to `size` bytes from the file and return the result.
1294
1295         Starts at the current file position.  If `size` is None, read the
1296         entire remainder of the file.
1297         """
1298         if size is None:
1299             data = []
1300             rd = self.arvadosfile.readfrom(self._filepos, config.KEEP_BLOCK_SIZE, num_retries)
1301             while rd:
1302                 data.append(rd)
1303                 self._filepos += len(rd)
1304                 rd = self.arvadosfile.readfrom(self._filepos, config.KEEP_BLOCK_SIZE, num_retries)
1305             return b''.join(data)
1306         else:
1307             data = self.arvadosfile.readfrom(self._filepos, size, num_retries, exact=True)
1308             self._filepos += len(data)
1309             return data
1310
1311     @_FileLikeObjectBase._before_close
1312     @retry_method
1313     def readfrom(self, offset, size, num_retries=None):
1314         """Read up to `size` bytes from the stream, starting at the specified file offset.
1315
1316         This method does not change the file position.
1317         """
1318         return self.arvadosfile.readfrom(offset, size, num_retries)
1319
1320     def flush(self):
1321         pass
1322
1323
1324 class ArvadosFileWriter(ArvadosFileReader):
1325     """Wraps ArvadosFile in a file-like object supporting both reading and writing.
1326
1327     Be aware that this class is NOT thread safe as there is no locking around
1328     updating file pointer.
1329
1330     """
1331
1332     def __init__(self, arvadosfile, mode, num_retries=None):
1333         super(ArvadosFileWriter, self).__init__(arvadosfile, mode=mode, num_retries=num_retries)
1334         self.arvadosfile.add_writer(self)
1335
1336     def writable(self):
1337         return True
1338
1339     @_FileLikeObjectBase._before_close
1340     @retry_method
1341     def write(self, data, num_retries=None):
1342         if self.mode[0] == "a":
1343             self._filepos = self.size()
1344         self.arvadosfile.writeto(self._filepos, data, num_retries)
1345         self._filepos += len(data)
1346         return len(data)
1347
1348     @_FileLikeObjectBase._before_close
1349     @retry_method
1350     def writelines(self, seq, num_retries=None):
1351         for s in seq:
1352             self.write(s, num_retries=num_retries)
1353
1354     @_FileLikeObjectBase._before_close
1355     def truncate(self, size=None):
1356         if size is None:
1357             size = self._filepos
1358         self.arvadosfile.truncate(size)
1359
1360     @_FileLikeObjectBase._before_close
1361     def flush(self):
1362         self.arvadosfile.flush()
1363
1364     def close(self, flush=True):
1365         if not self.closed:
1366             self.arvadosfile.remove_writer(self, flush)
1367             super(ArvadosFileWriter, self).close()
1368
1369
1370 class WrappableFile(object):
1371     """An interface to an Arvados file that's compatible with io wrappers.
1372
1373     """
1374     def __init__(self, f):
1375         self.f = f
1376         self.closed = False
1377     def close(self):
1378         self.closed = True
1379         return self.f.close()
1380     def flush(self):
1381         return self.f.flush()
1382     def read(self, *args, **kwargs):
1383         return self.f.read(*args, **kwargs)
1384     def readable(self):
1385         return self.f.readable()
1386     def readinto(self, *args, **kwargs):
1387         return self.f.readinto(*args, **kwargs)
1388     def seek(self, *args, **kwargs):
1389         return self.f.seek(*args, **kwargs)
1390     def seekable(self):
1391         return self.f.seekable()
1392     def tell(self):
1393         return self.f.tell()
1394     def writable(self):
1395         return self.f.writable()
1396     def write(self, *args, **kwargs):
1397         return self.f.write(*args, **kwargs)