sdk/python/arvados/arvfile.py

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