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(r'\.(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
 483     def __init__(self, keep,
 484                  copies=None,
 485                  put_threads=None,
 486                  num_retries=None,
 487                  storage_classes_func=None):
 488         """keep: KeepClient object to use"""
 489         self._keep = keep
 490         self._bufferblocks = collections.OrderedDict()
 491         self._put_queue = None
 492         self._put_threads = None
 493         self.lock = threading.Lock()
 494         self.prefetch_enabled = True
 495         self.num_put_threads = put_threads or _BlockManager.DEFAULT_PUT_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     @synchronized
 590     def stop_threads(self):
 591         """Shut down and wait for background upload and download threads to finish."""
 592
 593         if self._put_threads is not None:
 594             for t in self._put_threads:
 595                 self._put_queue.put(None)
 596             for t in self._put_threads:
 597                 t.join()
 598         self._put_threads = None
 599         self._put_queue = None
 600
 601     def __enter__(self):
 602         return self
 603
 604     def __exit__(self, exc_type, exc_value, traceback):
 605         self.stop_threads()
 606
 607     @synchronized
 608     def repack_small_blocks(self, force=False, sync=False, closed_file_size=0):
 609         """Packs small blocks together before uploading"""
 610
 611         self._pending_write_size += closed_file_size
 612
 613         # Check if there are enough small blocks for filling up one in full
 614         if not (force or (self._pending_write_size >= config.KEEP_BLOCK_SIZE)):
 615             return
 616
 617         # Search blocks ready for getting packed together before being
 618         # committed to Keep.
 619         # A WRITABLE block always has an owner.
 620         # A WRITABLE block with its owner.closed() implies that its
 621         # size is <= KEEP_BLOCK_SIZE/2.
 622         try:
 623             small_blocks = [b for b in listvalues(self._bufferblocks)
 624                             if b.state() == _BufferBlock.WRITABLE and b.owner.closed()]
 625         except AttributeError:
 626             # Writable blocks without owner shouldn't exist.
 627             raise UnownedBlockError()
 628
 629         if len(small_blocks) <= 1:
 630             # Not enough small blocks for repacking
 631             return
 632
 633         for bb in small_blocks:
 634             bb.repack_writes()
 635
 636         # Update the pending write size count with its true value, just in case
 637         # some small file was opened, written and closed several times.
 638         self._pending_write_size = sum([b.size() for b in small_blocks])
 639
 640         if self._pending_write_size < config.KEEP_BLOCK_SIZE and not force:
 641             return
 642
 643         new_bb = self._alloc_bufferblock()
 644         new_bb.owner = []
 645         files = []
 646         while len(small_blocks) > 0 and (new_bb.write_pointer + small_blocks[0].size()) <= config.KEEP_BLOCK_SIZE:
 647             bb = small_blocks.pop(0)
 648             new_bb.owner.append(bb.owner)
 649             self._pending_write_size -= bb.size()
 650             new_bb.append(bb.buffer_view[0:bb.write_pointer].tobytes())
 651             files.append((bb, new_bb.write_pointer - bb.size()))
 652
 653         self.commit_bufferblock(new_bb, sync=sync)
 654
 655         for bb, new_bb_segment_offset in files:
 656             newsegs = bb.owner.segments()
 657             for s in newsegs:
 658                 if s.locator == bb.blockid:
 659                     s.locator = new_bb.blockid
 660                     s.segment_offset = new_bb_segment_offset+s.segment_offset
 661             bb.owner.set_segments(newsegs)
 662             self._delete_bufferblock(bb.blockid)
 663
 664     def commit_bufferblock(self, block, sync):
 665         """Initiate a background upload of a bufferblock.
 666
 667         :block:
 668           The block object to upload
 669
 670         :sync:
 671           If `sync` is True, upload the block synchronously.
 672           If `sync` is False, upload the block asynchronously.  This will
 673           return immediately unless the upload queue is at capacity, in
 674           which case it will wait on an upload queue slot.
 675
 676         """
 677         try:
 678             # Mark the block as PENDING so to disallow any more appends.
 679             block.set_state(_BufferBlock.PENDING)
 680         except StateChangeError as e:
 681             if e.state == _BufferBlock.PENDING:
 682                 if sync:
 683                     block.wait_for_commit.wait()
 684                 else:
 685                     return
 686             if block.state() == _BufferBlock.COMMITTED:
 687                 return
 688             elif block.state() == _BufferBlock.ERROR:
 689                 raise block.error
 690             else:
 691                 raise
 692
 693         if sync:
 694             try:
 695                 if self.copies is None:
 696                     loc = self._keep.put(block.buffer_view[0:block.write_pointer].tobytes(), num_retries=self.num_retries, classes=self.storage_classes())
 697                 else:
 698                     loc = self._keep.put(block.buffer_view[0:block.write_pointer].tobytes(), num_retries=self.num_retries, copies=self.copies, classes=self.storage_classes())
 699                 block.set_state(_BufferBlock.COMMITTED, loc)
 700             except Exception as e:
 701                 block.set_state(_BufferBlock.ERROR, e)
 702                 raise
 703         else:
 704             self.start_put_threads()
 705             self._put_queue.put(block)
 706
 707     @synchronized
 708     def get_bufferblock(self, locator):
 709         return self._bufferblocks.get(locator)
 710
 711     @synchronized
 712     def get_padding_block(self):
 713         """Get a bufferblock 64 MB in size consisting of all zeros, used as padding
 714         when using truncate() to extend the size of a file.
 715
 716         For reference (and possible future optimization), the md5sum of the
 717         padding block is: 7f614da9329cd3aebf59b91aadc30bf0+67108864
 718
 719         """
 720
 721         if self.padding_block is None:
 722             self.padding_block = self._alloc_bufferblock(starting_capacity=config.KEEP_BLOCK_SIZE)
 723             self.padding_block.write_pointer = config.KEEP_BLOCK_SIZE
 724             self.commit_bufferblock(self.padding_block, False)
 725         return self.padding_block
 726
 727     @synchronized
 728     def delete_bufferblock(self, locator):
 729         self._delete_bufferblock(locator)
 730
 731     def _delete_bufferblock(self, locator):
 732         if locator in self._bufferblocks:
 733             bb = self._bufferblocks[locator]
 734             bb.clear()
 735             del self._bufferblocks[locator]
 736
 737     def get_block_contents(self, locator, num_retries, cache_only=False):
 738         """Fetch a block.
 739
 740         First checks to see if the locator is a BufferBlock and return that, if
 741         not, passes the request through to KeepClient.get().
 742
 743         """
 744         with self.lock:
 745             if locator in self._bufferblocks:
 746                 bufferblock = self._bufferblocks[locator]
 747                 if bufferblock.state() != _BufferBlock.COMMITTED:
 748                     return bufferblock.buffer_view[0:bufferblock.write_pointer].tobytes()
 749                 else:
 750                     locator = bufferblock._locator
 751         if cache_only:
 752             return self._keep.get_from_cache(locator)
 753         else:
 754             return self._keep.get(locator, num_retries=num_retries)
 755
 756     def commit_all(self):
 757         """Commit all outstanding buffer blocks.
 758
 759         This is a synchronous call, and will not return until all buffer blocks
 760         are uploaded.  Raises KeepWriteError() if any blocks failed to upload.
 761
 762         """
 763         self.repack_small_blocks(force=True, sync=True)
 764
 765         with self.lock:
 766             items = listitems(self._bufferblocks)
 767
 768         for k,v in items:
 769             if v.state() != _BufferBlock.COMMITTED and v.owner:
 770                 # Ignore blocks with a list of owners, as if they're not in COMMITTED
 771                 # state, they're already being committed asynchronously.
 772                 if isinstance(v.owner, ArvadosFile):
 773                     v.owner.flush(sync=False)
 774
 775         with self.lock:
 776             if self._put_queue is not None:
 777                 self._put_queue.join()
 778
 779                 err = []
 780                 for k,v in items:
 781                     if v.state() == _BufferBlock.ERROR:
 782                         err.append((v.locator(), v.error))
 783                 if err:
 784                     raise KeepWriteError("Error writing some blocks", err, label="block")
 785
 786         for k,v in items:
 787             # flush again with sync=True to remove committed bufferblocks from
 788             # the segments.
 789             if v.owner:
 790                 if isinstance(v.owner, ArvadosFile):
 791                     v.owner.flush(sync=True)
 792                 elif isinstance(v.owner, list) and len(v.owner) > 0:
 793                     # This bufferblock is referenced by many files as a result
 794                     # of repacking small blocks, so don't delete it when flushing
 795                     # its owners, just do it after flushing them all.
 796                     for owner in v.owner:
 797                         owner.flush(sync=True)
 798                     self.delete_bufferblock(k)
 799
 800         self.stop_threads()
 801
 802     def block_prefetch(self, locator):
 803         """Initiate a background download of a block.
 804         """
 805
 806         if not self.prefetch_enabled:
 807             return
 808
 809         with self.lock:
 810             if locator in self._bufferblocks:
 811                 return
 812
 813         self._keep.block_prefetch(locator)
 814
 815
 816 class ArvadosFile(object):
 817     """Represent a file in a Collection.
 818
 819     ArvadosFile manages the underlying representation of a file in Keep as a
 820     sequence of segments spanning a set of blocks, and implements random
 821     read/write access.
 822
 823     This object may be accessed from multiple threads.
 824
 825     """
 826
 827     __slots__ = ('parent', 'name', '_writers', '_committed',
 828                  '_segments', 'lock', '_current_bblock', 'fuse_entry')
 829
 830     def __init__(self, parent, name, stream=[], segments=[]):
 831         """
 832         ArvadosFile constructor.
 833
 834         :stream:
 835           a list of Range objects representing a block stream
 836
 837         :segments:
 838           a list of Range objects representing segments
 839         """
 840         self.parent = parent
 841         self.name = name
 842         self._writers = set()
 843         self._committed = False
 844         self._segments = []
 845         self.lock = parent.root_collection().lock
 846         for s in segments:
 847             self._add_segment(stream, s.locator, s.range_size)
 848         self._current_bblock = None
 849
 850     def writable(self):
 851         return self.parent.writable()
 852
 853     @synchronized
 854     def permission_expired(self, as_of_dt=None):
 855         """Returns True if any of the segment's locators is expired"""
 856         for r in self._segments:
 857             if KeepLocator(r.locator).permission_expired(as_of_dt):
 858                 return True
 859         return False
 860
 861     @synchronized
 862     def has_remote_blocks(self):
 863         """Returns True if any of the segment's locators has a +R signature"""
 864
 865         for s in self._segments:
 866             if '+R' in s.locator:
 867                 return True
 868         return False
 869
 870     @synchronized
 871     def _copy_remote_blocks(self, remote_blocks={}):
 872         """Ask Keep to copy remote blocks and point to their local copies.
 873
 874         This is called from the parent Collection.
 875
 876         :remote_blocks:
 877             Shared cache of remote to local block mappings. This is used to avoid
 878             doing extra work when blocks are shared by more than one file in
 879             different subdirectories.
 880         """
 881
 882         for s in self._segments:
 883             if '+R' in s.locator:
 884                 try:
 885                     loc = remote_blocks[s.locator]
 886                 except KeyError:
 887                     loc = self.parent._my_keep().refresh_signature(s.locator)
 888                     remote_blocks[s.locator] = loc
 889                 s.locator = loc
 890                 self.parent.set_committed(False)
 891         return remote_blocks
 892
 893     @synchronized
 894     def segments(self):
 895         return copy.copy(self._segments)
 896
 897     @synchronized
 898     def clone(self, new_parent, new_name):
 899         """Make a copy of this file."""
 900         cp = ArvadosFile(new_parent, new_name)
 901         cp.replace_contents(self)
 902         return cp
 903
 904     @must_be_writable
 905     @synchronized
 906     def replace_contents(self, other):
 907         """Replace segments of this file with segments from another `ArvadosFile` object."""
 908
 909         map_loc = {}
 910         self._segments = []
 911         for other_segment in other.segments():
 912             new_loc = other_segment.locator
 913             if other.parent._my_block_manager().is_bufferblock(other_segment.locator):
 914                 if other_segment.locator not in map_loc:
 915                     bufferblock = other.parent._my_block_manager().get_bufferblock(other_segment.locator)
 916                     if bufferblock.state() != _BufferBlock.WRITABLE:
 917                         map_loc[other_segment.locator] = bufferblock.locator()
 918                     else:
 919                         map_loc[other_segment.locator] = self.parent._my_block_manager().dup_block(bufferblock, self).blockid
 920                 new_loc = map_loc[other_segment.locator]
 921
 922             self._segments.append(Range(new_loc, other_segment.range_start, other_segment.range_size, other_segment.segment_offset))
 923
 924         self.set_committed(False)
 925
 926     def __eq__(self, other):
 927         if other is self:
 928             return True
 929         if not isinstance(other, ArvadosFile):
 930             return False
 931
 932         othersegs = other.segments()
 933         with self.lock:
 934             if len(self._segments) != len(othersegs):
 935                 return False
 936             for i in range(0, len(othersegs)):
 937                 seg1 = self._segments[i]
 938                 seg2 = othersegs[i]
 939                 loc1 = seg1.locator
 940                 loc2 = seg2.locator
 941
 942                 if self.parent._my_block_manager().is_bufferblock(loc1):
 943                     loc1 = self.parent._my_block_manager().get_bufferblock(loc1).locator()
 944
 945                 if other.parent._my_block_manager().is_bufferblock(loc2):
 946                     loc2 = other.parent._my_block_manager().get_bufferblock(loc2).locator()
 947
 948                 if (KeepLocator(loc1).stripped() != KeepLocator(loc2).stripped() or
 949                     seg1.range_start != seg2.range_start or
 950                     seg1.range_size != seg2.range_size or
 951                     seg1.segment_offset != seg2.segment_offset):
 952                     return False
 953
 954         return True
 955
 956     def __ne__(self, other):
 957         return not self.__eq__(other)
 958
 959     @synchronized
 960     def set_segments(self, segs):
 961         self._segments = segs
 962
 963     @synchronized
 964     def set_committed(self, value=True):
 965         """Set committed flag.
 966
 967         If value is True, set committed to be True.
 968
 969         If value is False, set committed to be False for this and all parents.
 970         """
 971         if value == self._committed:
 972             return
 973         self._committed = value
 974         if self._committed is False and self.parent is not None:
 975             self.parent.set_committed(False)
 976
 977     @synchronized
 978     def committed(self):
 979         """Get whether this is committed or not."""
 980         return self._committed
 981
 982     @synchronized
 983     def add_writer(self, writer):
 984         """Add an ArvadosFileWriter reference to the list of writers"""
 985         if isinstance(writer, ArvadosFileWriter):
 986             self._writers.add(writer)
 987
 988     @synchronized
 989     def remove_writer(self, writer, flush):
 990         """
 991         Called from ArvadosFileWriter.close(). Remove a writer reference from the list
 992         and do some block maintenance tasks.
 993         """
 994         self._writers.remove(writer)
 995
 996         if flush or self.size() > config.KEEP_BLOCK_SIZE // 2:
 997             # File writer closed, not small enough for repacking
 998             self.flush()
 999         elif self.closed():
1000             # All writers closed and size is adequate for repacking
1001             self.parent._my_block_manager().repack_small_blocks(closed_file_size=self.size())
1002
1003     def closed(self):
1004         """
1005         Get whether this is closed or not. When the writers list is empty, the file
1006         is supposed to be closed.
1007         """
1008         return len(self._writers) == 0
1009
1010     @must_be_writable
1011     @synchronized
1012     def truncate(self, size):
1013         """Shrink or expand the size of the file.
1014
1015         If `size` is less than the size of the file, the file contents after
1016         `size` will be discarded.  If `size` is greater than the current size
1017         of the file, it will be filled with zero bytes.
1018
1019         """
1020         if size < self.size():
1021             new_segs = []
1022             for r in self._segments:
1023                 range_end = r.range_start+r.range_size
1024                 if r.range_start >= size:
1025                     # segment is past the trucate size, all done
1026                     break
1027                 elif size < range_end:
1028                     nr = Range(r.locator, r.range_start, size - r.range_start, 0)
1029                     nr.segment_offset = r.segment_offset
1030                     new_segs.append(nr)
1031                     break
1032                 else:
1033                     new_segs.append(r)
1034
1035             self._segments = new_segs
1036             self.set_committed(False)
1037         elif size > self.size():
1038             padding = self.parent._my_block_manager().get_padding_block()
1039             diff = size - self.size()
1040             while diff > config.KEEP_BLOCK_SIZE:
1041                 self._segments.append(Range(padding.blockid, self.size(), config.KEEP_BLOCK_SIZE, 0))
1042                 diff -= config.KEEP_BLOCK_SIZE
1043             if diff > 0:
1044                 self._segments.append(Range(padding.blockid, self.size(), diff, 0))
1045             self.set_committed(False)
1046         else:
1047             # size == self.size()
1048             pass
1049
1050     def readfrom(self, offset, size, num_retries, exact=False):
1051         """Read up to `size` bytes from the file starting at `offset`.
1052
1053         :exact:
1054          If False (default), return less data than requested if the read
1055          crosses a block boundary and the next block isn't cached.  If True,
1056          only return less data than requested when hitting EOF.
1057         """
1058
1059         with self.lock:
1060             if size == 0 or offset >= self.size():
1061                 return b''
1062             readsegs = locators_and_ranges(self._segments, offset, size)
1063             if self.parent._my_block_manager()._keep.num_prefetch_threads > 0:
1064                 prefetch = locators_and_ranges(self._segments, offset + size, config.KEEP_BLOCK_SIZE * self.parent._my_block_manager()._keep.num_prefetch_threads, limit=32)
1065
1066         locs = set()
1067         data = []
1068         for lr in readsegs:
1069             block = self.parent._my_block_manager().get_block_contents(lr.locator, num_retries=num_retries, cache_only=(bool(data) and not exact))
1070             if block:
1071                 blockview = memoryview(block)
1072                 data.append(blockview[lr.segment_offset:lr.segment_offset+lr.segment_size])
1073                 locs.add(lr.locator)
1074             else:
1075                 break
1076
1077         if self.parent._my_block_manager()._keep.num_prefetch_threads > 0:
1078             for lr in prefetch:
1079                 if lr.locator not in locs:
1080                     self.parent._my_block_manager().block_prefetch(lr.locator)
1081                     locs.add(lr.locator)
1082
1083         if len(data) == 1:
1084             return data[0]
1085         else:
1086             return b''.join(data)
1087
1088     @must_be_writable
1089     @synchronized
1090     def writeto(self, offset, data, num_retries):
1091         """Write `data` to the file starting at `offset`.
1092
1093         This will update existing bytes and/or extend the size of the file as
1094         necessary.
1095
1096         """
1097         if not isinstance(data, bytes) and not isinstance(data, memoryview):
1098             data = data.encode()
1099         if len(data) == 0:
1100             return
1101
1102         if offset > self.size():
1103             self.truncate(offset)
1104
1105         if len(data) > config.KEEP_BLOCK_SIZE:
1106             # Chunk it up into smaller writes
1107             n = 0
1108             dataview = memoryview(data)
1109             while n < len(data):
1110                 self.writeto(offset+n, dataview[n:n + config.KEEP_BLOCK_SIZE].tobytes(), num_retries)
1111                 n += config.KEEP_BLOCK_SIZE
1112             return
1113
1114         self.set_committed(False)
1115
1116         if self._current_bblock is None or self._current_bblock.state() != _BufferBlock.WRITABLE:
1117             self._current_bblock = self.parent._my_block_manager().alloc_bufferblock(owner=self)
1118
1119         if (self._current_bblock.size() + len(data)) > config.KEEP_BLOCK_SIZE:
1120             self._current_bblock.repack_writes()
1121             if (self._current_bblock.size() + len(data)) > config.KEEP_BLOCK_SIZE:
1122                 self.parent._my_block_manager().commit_bufferblock(self._current_bblock, sync=False)
1123                 self._current_bblock = self.parent._my_block_manager().alloc_bufferblock(owner=self)
1124
1125         self._current_bblock.append(data)
1126
1127         replace_range(self._segments, offset, len(data), self._current_bblock.blockid, self._current_bblock.write_pointer - len(data))
1128
1129         self.parent.notify(WRITE, self.parent, self.name, (self, self))
1130
1131         return len(data)
1132
1133     @synchronized
1134     def flush(self, sync=True, num_retries=0):
1135         """Flush the current bufferblock to Keep.
1136
1137         :sync:
1138           If True, commit block synchronously, wait until buffer block has been written.
1139           If False, commit block asynchronously, return immediately after putting block into
1140           the keep put queue.
1141         """
1142         if self.committed():
1143             return
1144
1145         if self._current_bblock and self._current_bblock.state() != _BufferBlock.COMMITTED:
1146             if self._current_bblock.state() == _BufferBlock.WRITABLE:
1147                 self._current_bblock.repack_writes()
1148             if self._current_bblock.state() != _BufferBlock.DELETED:
1149                 self.parent._my_block_manager().commit_bufferblock(self._current_bblock, sync=sync)
1150
1151         if sync:
1152             to_delete = set()
1153             for s in self._segments:
1154                 bb = self.parent._my_block_manager().get_bufferblock(s.locator)
1155                 if bb:
1156                     if bb.state() != _BufferBlock.COMMITTED:
1157                         self.parent._my_block_manager().commit_bufferblock(bb, sync=True)
1158                     to_delete.add(s.locator)
1159                     s.locator = bb.locator()
1160             for s in to_delete:
1161                 # Don't delete the bufferblock if it's owned by many files. It'll be
1162                 # deleted after all of its owners are flush()ed.
1163                 if self.parent._my_block_manager().get_bufferblock(s).owner is self:
1164                     self.parent._my_block_manager().delete_bufferblock(s)
1165
1166         self.parent.notify(MOD, self.parent, self.name, (self, self))
1167
1168     @must_be_writable
1169     @synchronized
1170     def add_segment(self, blocks, pos, size):
1171         """Add a segment to the end of the file.
1172
1173         `pos` and `offset` reference a section of the stream described by
1174         `blocks` (a list of Range objects)
1175
1176         """
1177         self._add_segment(blocks, pos, size)
1178
1179     def _add_segment(self, blocks, pos, size):
1180         """Internal implementation of add_segment."""
1181         self.set_committed(False)
1182         for lr in locators_and_ranges(blocks, pos, size):
1183             last = self._segments[-1] if self._segments else Range(0, 0, 0, 0)
1184             r = Range(lr.locator, last.range_start+last.range_size, lr.segment_size, lr.segment_offset)
1185             self._segments.append(r)
1186
1187     @synchronized
1188     def size(self):
1189         """Get the file size."""
1190         if self._segments:
1191             n = self._segments[-1]
1192             return n.range_start + n.range_size
1193         else:
1194             return 0
1195
1196     @synchronized
1197     def manifest_text(self, stream_name=".", portable_locators=False,
1198                       normalize=False, only_committed=False):
1199         buf = ""
1200         filestream = []
1201         for segment in self._segments:
1202             loc = segment.locator
1203             if self.parent._my_block_manager().is_bufferblock(loc):
1204                 if only_committed:
1205                     continue
1206                 loc = self.parent._my_block_manager().get_bufferblock(loc).locator()
1207             if portable_locators:
1208                 loc = KeepLocator(loc).stripped()
1209             filestream.append(LocatorAndRange(loc, KeepLocator(loc).size,
1210                                  segment.segment_offset, segment.range_size))
1211         buf += ' '.join(normalize_stream(stream_name, {self.name: filestream}))
1212         buf += "\n"
1213         return buf
1214
1215     @must_be_writable
1216     @synchronized
1217     def _reparent(self, newparent, newname):
1218         self.set_committed(False)
1219         self.flush(sync=True)
1220         self.parent.remove(self.name)
1221         self.parent = newparent
1222         self.name = newname
1223         self.lock = self.parent.root_collection().lock
1224
1225
1226 class ArvadosFileReader(ArvadosFileReaderBase):
1227     """Wraps ArvadosFile in a file-like object supporting reading only.
1228
1229     Be aware that this class is NOT thread safe as there is no locking around
1230     updating file pointer.
1231
1232     """
1233
1234     def __init__(self, arvadosfile, mode="r", num_retries=None):
1235         super(ArvadosFileReader, self).__init__(arvadosfile.name, mode=mode, num_retries=num_retries)
1236         self.arvadosfile = arvadosfile
1237
1238     def size(self):
1239         return self.arvadosfile.size()
1240
1241     def stream_name(self):
1242         return self.arvadosfile.parent.stream_name()
1243
1244     def readinto(self, b):
1245         data = self.read(len(b))
1246         b[:len(data)] = data
1247         return len(data)
1248
1249     @_FileLikeObjectBase._before_close
1250     @retry_method
1251     def read(self, size=None, num_retries=None):
1252         """Read up to `size` bytes from the file and return the result.
1253
1254         Starts at the current file position.  If `size` is None, read the
1255         entire remainder of the file.
1256         """
1257         if size is None:
1258             data = []
1259             rd = self.arvadosfile.readfrom(self._filepos, config.KEEP_BLOCK_SIZE, num_retries)
1260             while rd:
1261                 data.append(rd)
1262                 self._filepos += len(rd)
1263                 rd = self.arvadosfile.readfrom(self._filepos, config.KEEP_BLOCK_SIZE, num_retries)
1264             return b''.join(data)
1265         else:
1266             data = self.arvadosfile.readfrom(self._filepos, size, num_retries, exact=True)
1267             self._filepos += len(data)
1268             return data
1269
1270     @_FileLikeObjectBase._before_close
1271     @retry_method
1272     def readfrom(self, offset, size, num_retries=None):
1273         """Read up to `size` bytes from the stream, starting at the specified file offset.
1274
1275         This method does not change the file position.
1276         """
1277         return self.arvadosfile.readfrom(offset, size, num_retries)
1278
1279     def flush(self):
1280         pass
1281
1282
1283 class ArvadosFileWriter(ArvadosFileReader):
1284     """Wraps ArvadosFile in a file-like object supporting both reading and writing.
1285
1286     Be aware that this class is NOT thread safe as there is no locking around
1287     updating file pointer.
1288
1289     """
1290
1291     def __init__(self, arvadosfile, mode, num_retries=None):
1292         super(ArvadosFileWriter, self).__init__(arvadosfile, mode=mode, num_retries=num_retries)
1293         self.arvadosfile.add_writer(self)
1294
1295     def writable(self):
1296         return True
1297
1298     @_FileLikeObjectBase._before_close
1299     @retry_method
1300     def write(self, data, num_retries=None):
1301         if self.mode[0] == "a":
1302             self._filepos = self.size()
1303         self.arvadosfile.writeto(self._filepos, data, num_retries)
1304         self._filepos += len(data)
1305         return len(data)
1306
1307     @_FileLikeObjectBase._before_close
1308     @retry_method
1309     def writelines(self, seq, num_retries=None):
1310         for s in seq:
1311             self.write(s, num_retries=num_retries)
1312
1313     @_FileLikeObjectBase._before_close
1314     def truncate(self, size=None):
1315         if size is None:
1316             size = self._filepos
1317         self.arvadosfile.truncate(size)
1318
1319     @_FileLikeObjectBase._before_close
1320     def flush(self):
1321         self.arvadosfile.flush()
1322
1323     def close(self, flush=True):
1324         if not self.closed:
1325             self.arvadosfile.remove_writer(self, flush)
1326             super(ArvadosFileWriter, self).close()
1327
1328
1329 class WrappableFile(object):
1330     """An interface to an Arvados file that's compatible with io wrappers.
1331
1332     """
1333     def __init__(self, f):
1334         self.f = f
1335         self.closed = False
1336     def close(self):
1337         self.closed = True
1338         return self.f.close()
1339     def flush(self):
1340         return self.f.flush()
1341     def read(self, *args, **kwargs):
1342         return self.f.read(*args, **kwargs)
1343     def readable(self):
1344         return self.f.readable()
1345     def readinto(self, *args, **kwargs):
1346         return self.f.readinto(*args, **kwargs)
1347     def seek(self, *args, **kwargs):
1348         return self.f.seek(*args, **kwargs)
1349     def seekable(self):
1350         return self.f.seekable()
1351     def tell(self):
1352         return self.f.tell()
1353     def writable(self):
1354         return self.f.writable()
1355     def write(self, *args, **kwargs):
1356         return self.f.write(*args, **kwargs)