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
20 from .retry import retry_method
25 _logger = logging.getLogger('arvados.arvfile')
28 """split(path) -> streamname, filename
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,
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
41 class _FileLikeObjectBase(object):
42 def __init__(self, name, mode):
48 def _before_close(orig_func):
49 @functools.wraps(orig_func)
50 def before_close_wrapper(self, *args, **kwargs):
52 raise ValueError("I/O operation on closed stream file")
53 return orig_func(self, *args, **kwargs)
54 return before_close_wrapper
59 def __exit__(self, exc_type, exc_value, traceback):
70 class ArvadosFileReaderBase(_FileLikeObjectBase):
71 def __init__(self, name, mode, num_retries=None):
72 super(ArvadosFileReaderBase, self).__init__(name, mode)
74 self.num_retries = num_retries
75 self._readline_cache = (None, None)
79 data = self.readline()
84 def decompressed_name(self):
85 return re.sub('\.(bz2|gz)$', '', self.name)
87 @_FileLikeObjectBase._before_close
88 def seek(self, pos, whence=os.SEEK_SET):
89 if whence == os.SEEK_CUR:
91 elif whence == os.SEEK_END:
93 self._filepos = min(max(pos, 0L), self.size())
98 @_FileLikeObjectBase._before_close
100 def readall(self, size=2**20, num_retries=None):
102 data = self.read(size, num_retries=num_retries)
107 @_FileLikeObjectBase._before_close
109 def readline(self, size=float('inf'), num_retries=None):
110 cache_pos, cache_data = self._readline_cache
111 if self.tell() == cache_pos:
113 self._filepos += len(cache_data)
116 data_size = len(data[-1])
117 while (data_size < size) and ('\n' not in data[-1]):
118 next_read = self.read(2 ** 20, num_retries=num_retries)
121 data.append(next_read)
122 data_size += len(next_read)
125 nextline_index = data.index('\n') + 1
127 nextline_index = len(data)
128 nextline_index = min(nextline_index, size)
129 self._filepos -= len(data) - nextline_index
130 self._readline_cache = (self.tell(), data[nextline_index:])
131 return data[:nextline_index]
133 @_FileLikeObjectBase._before_close
135 def decompress(self, decompress, size, num_retries=None):
136 for segment in self.readall(size, num_retries=num_retries):
137 data = decompress(segment)
141 @_FileLikeObjectBase._before_close
143 def readall_decompressed(self, size=2**20, num_retries=None):
145 if self.name.endswith('.bz2'):
146 dc = bz2.BZ2Decompressor()
147 return self.decompress(dc.decompress, size,
148 num_retries=num_retries)
149 elif self.name.endswith('.gz'):
150 dc = zlib.decompressobj(16+zlib.MAX_WBITS)
151 return self.decompress(lambda segment: dc.decompress(dc.unconsumed_tail + segment),
152 size, num_retries=num_retries)
154 return self.readall(size, num_retries=num_retries)
156 @_FileLikeObjectBase._before_close
158 def readlines(self, sizehint=float('inf'), num_retries=None):
161 for s in self.readall(num_retries=num_retries):
164 if data_size >= sizehint:
166 return ''.join(data).splitlines(True)
169 raise NotImplementedError()
171 def read(self, size, num_retries=None):
172 raise NotImplementedError()
174 def readfrom(self, start, size, num_retries=None):
175 raise NotImplementedError()
178 class StreamFileReader(ArvadosFileReaderBase):
179 class _NameAttribute(str):
180 # The Python file API provides a plain .name attribute.
181 # Older SDK provided a name() method.
182 # This class provides both, for maximum compatibility.
186 def __init__(self, stream, segments, name):
187 super(StreamFileReader, self).__init__(self._NameAttribute(name), 'rb', num_retries=stream.num_retries)
188 self._stream = stream
189 self.segments = segments
191 def stream_name(self):
192 return self._stream.name()
195 n = self.segments[-1]
196 return n.range_start + n.range_size
198 @_FileLikeObjectBase._before_close
200 def read(self, size, num_retries=None):
201 """Read up to 'size' bytes from the stream, starting at the current file position"""
206 available_chunks = locators_and_ranges(self.segments, self._filepos, size)
208 lr = available_chunks[0]
209 data = self._stream.readfrom(lr.locator+lr.segment_offset,
211 num_retries=num_retries)
213 self._filepos += len(data)
216 @_FileLikeObjectBase._before_close
218 def readfrom(self, start, size, num_retries=None):
219 """Read up to 'size' bytes from the stream, starting at 'start'"""
224 for lr in locators_and_ranges(self.segments, start, size):
225 data.append(self._stream.readfrom(lr.locator+lr.segment_offset, lr.segment_size,
226 num_retries=num_retries))
229 def as_manifest(self):
231 for r in self.segments:
232 segs.extend(self._stream.locators_and_ranges(r.locator, r.range_size))
233 return " ".join(normalize_stream(".", {self.name: segs})) + "\n"
236 def synchronized(orig_func):
237 @functools.wraps(orig_func)
238 def synchronized_wrapper(self, *args, **kwargs):
240 return orig_func(self, *args, **kwargs)
241 return synchronized_wrapper
244 class StateChangeError(Exception):
245 def __init__(self, message, state, nextstate):
246 super(StateChangeError, self).__init__(message)
248 self.nextstate = nextstate
250 class _BufferBlock(object):
251 """A stand-in for a Keep block that is in the process of being written.
253 Writers can append to it, get the size, and compute the Keep locator.
254 There are three valid states:
260 Block is in the process of being uploaded to Keep, append is an error.
263 The block has been written to Keep, its internal buffer has been
264 released, fetching the block will fetch it via keep client (since we
265 discarded the internal copy), and identifiers referring to the BufferBlock
266 can be replaced with the block locator.
275 def __init__(self, blockid, starting_capacity, owner):
278 the identifier for this block
281 the initial buffer capacity
284 ArvadosFile that owns this block
287 self.blockid = blockid
288 self.buffer_block = bytearray(starting_capacity)
289 self.buffer_view = memoryview(self.buffer_block)
290 self.write_pointer = 0
291 self._state = _BufferBlock.WRITABLE
294 self.lock = threading.Lock()
295 self.wait_for_commit = threading.Event()
299 def append(self, data):
300 """Append some data to the buffer.
302 Only valid if the block is in WRITABLE state. Implements an expanding
303 buffer, doubling capacity as needed to accomdate all the data.
306 if self._state == _BufferBlock.WRITABLE:
307 while (self.write_pointer+len(data)) > len(self.buffer_block):
308 new_buffer_block = bytearray(len(self.buffer_block) * 2)
309 new_buffer_block[0:self.write_pointer] = self.buffer_block[0:self.write_pointer]
310 self.buffer_block = new_buffer_block
311 self.buffer_view = memoryview(self.buffer_block)
312 self.buffer_view[self.write_pointer:self.write_pointer+len(data)] = data
313 self.write_pointer += len(data)
316 raise AssertionError("Buffer block is not writable")
318 STATE_TRANSITIONS = frozenset([
320 (PENDING, COMMITTED),
325 def set_state(self, nextstate, val=None):
326 if (self._state, nextstate) not in self.STATE_TRANSITIONS:
327 raise StateChangeError("Invalid state change from %s to %s" % (self._state, nextstate), self._state, nextstate)
328 self._state = nextstate
330 if self._state == _BufferBlock.PENDING:
331 self.wait_for_commit.clear()
333 if self._state == _BufferBlock.COMMITTED:
335 self.buffer_view = None
336 self.buffer_block = None
337 self.wait_for_commit.set()
339 if self._state == _BufferBlock.ERROR:
341 self.wait_for_commit.set()
348 """The amount of data written to the buffer."""
349 return self.write_pointer
353 """The Keep locator for this buffer's contents."""
354 if self._locator is None:
355 self._locator = "%s+%i" % (hashlib.md5(self.buffer_view[0:self.write_pointer]).hexdigest(), self.size())
359 def clone(self, new_blockid, owner):
360 if self._state == _BufferBlock.COMMITTED:
361 raise AssertionError("Cannot duplicate committed buffer block")
362 bufferblock = _BufferBlock(new_blockid, self.size(), owner)
363 bufferblock.append(self.buffer_view[0:self.size()])
369 self.buffer_block = None
370 self.buffer_view = None
373 class NoopLock(object):
377 def __exit__(self, exc_type, exc_value, traceback):
380 def acquire(self, blocking=False):
387 def must_be_writable(orig_func):
388 @functools.wraps(orig_func)
389 def must_be_writable_wrapper(self, *args, **kwargs):
390 if not self.writable():
391 raise IOError(errno.EROFS, "Collection is read-only.")
392 return orig_func(self, *args, **kwargs)
393 return must_be_writable_wrapper
396 class _BlockManager(object):
397 """BlockManager handles buffer blocks.
399 Also handles background block uploads, and background block prefetch for a
400 Collection of ArvadosFiles.
404 DEFAULT_PUT_THREADS = 2
405 DEFAULT_GET_THREADS = 2
407 def __init__(self, keep, copies=None):
408 """keep: KeepClient object to use"""
410 self._bufferblocks = collections.OrderedDict()
411 self._put_queue = None
412 self._put_threads = None
413 self._prefetch_queue = None
414 self._prefetch_threads = None
415 self.lock = threading.Lock()
416 self.prefetch_enabled = True
417 self.num_put_threads = _BlockManager.DEFAULT_PUT_THREADS
418 self.num_get_threads = _BlockManager.DEFAULT_GET_THREADS
420 self._pending_write_size = 0
421 self.threads_lock = threading.Lock()
424 def alloc_bufferblock(self, blockid=None, starting_capacity=2**14, owner=None):
425 """Allocate a new, empty bufferblock in WRITABLE state and return it.
428 optional block identifier, otherwise one will be automatically assigned
431 optional capacity, otherwise will use default capacity
434 ArvadosFile that owns this block
437 return self._alloc_bufferblock(blockid, starting_capacity, owner)
439 def _alloc_bufferblock(self, blockid=None, starting_capacity=2**14, owner=None):
441 blockid = "%s" % uuid.uuid4()
442 bufferblock = _BufferBlock(blockid, starting_capacity=starting_capacity, owner=owner)
443 self._bufferblocks[bufferblock.blockid] = bufferblock
447 def dup_block(self, block, owner):
448 """Create a new bufferblock initialized with the content of an existing bufferblock.
451 the buffer block to copy.
454 ArvadosFile that owns the new block
457 new_blockid = "bufferblock%i" % len(self._bufferblocks)
458 bufferblock = block.clone(new_blockid, owner)
459 self._bufferblocks[bufferblock.blockid] = bufferblock
463 def is_bufferblock(self, locator):
464 return locator in self._bufferblocks
466 def _commit_bufferblock_worker(self):
467 """Background uploader thread."""
471 bufferblock = self._put_queue.get()
472 if bufferblock is None:
475 if self.copies is None:
476 loc = self._keep.put(bufferblock.buffer_view[0:bufferblock.write_pointer].tobytes())
478 loc = self._keep.put(bufferblock.buffer_view[0:bufferblock.write_pointer].tobytes(), copies=self.copies)
479 bufferblock.set_state(_BufferBlock.COMMITTED, loc)
481 except Exception as e:
482 bufferblock.set_state(_BufferBlock.ERROR, e)
484 if self._put_queue is not None:
485 self._put_queue.task_done()
487 def start_put_threads(self):
488 with self.threads_lock:
489 if self._put_threads is None:
490 # Start uploader threads.
492 # If we don't limit the Queue size, the upload queue can quickly
493 # grow to take up gigabytes of RAM if the writing process is
494 # generating data more quickly than it can be send to the Keep
497 # With two upload threads and a queue size of 2, this means up to 4
498 # blocks pending. If they are full 64 MiB blocks, that means up to
499 # 256 MiB of internal buffering, which is the same size as the
500 # default download block cache in KeepClient.
501 self._put_queue = Queue.Queue(maxsize=2)
503 self._put_threads = []
504 for i in xrange(0, self.num_put_threads):
505 thread = threading.Thread(target=self._commit_bufferblock_worker)
506 self._put_threads.append(thread)
510 def _block_prefetch_worker(self):
511 """The background downloader thread."""
514 b = self._prefetch_queue.get()
522 def start_get_threads(self):
523 if self._prefetch_threads is None:
524 self._prefetch_queue = Queue.Queue()
525 self._prefetch_threads = []
526 for i in xrange(0, self.num_get_threads):
527 thread = threading.Thread(target=self._block_prefetch_worker)
528 self._prefetch_threads.append(thread)
534 def stop_threads(self):
535 """Shut down and wait for background upload and download threads to finish."""
537 if self._put_threads is not None:
538 for t in self._put_threads:
539 self._put_queue.put(None)
540 for t in self._put_threads:
542 self._put_threads = None
543 self._put_queue = None
545 if self._prefetch_threads is not None:
546 for t in self._prefetch_threads:
547 self._prefetch_queue.put(None)
548 for t in self._prefetch_threads:
550 self._prefetch_threads = None
551 self._prefetch_queue = None
556 def __exit__(self, exc_type, exc_value, traceback):
560 def repack_small_blocks(self, force=False, sync=False, closed_file_size=0):
561 """Packs small blocks together before uploading"""
562 self._pending_write_size += closed_file_size
564 # Check if there are enough small blocks for filling up one in full
565 if force or (self._pending_write_size >= config.KEEP_BLOCK_SIZE):
567 # Search blocks ready for getting packed together before being committed to Keep.
568 # A WRITABLE block always has an owner.
569 # A WRITABLE block with its owner.closed() implies that it's
570 # size is <= KEEP_BLOCK_SIZE/2.
571 small_blocks = [b for b in self._bufferblocks.values() if b.state() == _BufferBlock.WRITABLE and b.owner.closed()]
573 if len(small_blocks) <= 1:
574 # Not enough small blocks for repacking
577 # Update the pending write size count with its true value, just in case
578 # some small file was opened, written and closed several times.
580 self._pending_write_size = sum([b.size() for b in small_blocks])
581 if self._pending_write_size < config.KEEP_BLOCK_SIZE:
584 new_bb = self._alloc_bufferblock()
585 while len(small_blocks) > 0 and (new_bb.write_pointer + small_blocks[0].size()) <= config.KEEP_BLOCK_SIZE:
586 bb = small_blocks.pop(0)
588 self._pending_write_size -= bb.size()
589 new_bb.append(bb.buffer_view[0:bb.write_pointer].tobytes())
590 arvfile.set_segments([Range(new_bb.blockid,
593 new_bb.write_pointer - bb.size())])
594 self._delete_bufferblock(bb.blockid)
595 self.commit_bufferblock(new_bb, sync=sync)
597 def commit_bufferblock(self, block, sync):
598 """Initiate a background upload of a bufferblock.
601 The block object to upload
604 If `sync` is True, upload the block synchronously.
605 If `sync` is False, upload the block asynchronously. This will
606 return immediately unless the upload queue is at capacity, in
607 which case it will wait on an upload queue slot.
611 # Mark the block as PENDING so to disallow any more appends.
612 block.set_state(_BufferBlock.PENDING)
613 except StateChangeError as e:
614 if e.state == _BufferBlock.PENDING:
616 block.wait_for_commit.wait()
619 if block.state() == _BufferBlock.COMMITTED:
621 elif block.state() == _BufferBlock.ERROR:
628 if self.copies is None:
629 loc = self._keep.put(block.buffer_view[0:block.write_pointer].tobytes())
631 loc = self._keep.put(block.buffer_view[0:block.write_pointer].tobytes(), copies=self.copies)
632 block.set_state(_BufferBlock.COMMITTED, loc)
633 except Exception as e:
634 block.set_state(_BufferBlock.ERROR, e)
637 self.start_put_threads()
638 self._put_queue.put(block)
641 def get_bufferblock(self, locator):
642 return self._bufferblocks.get(locator)
645 def delete_bufferblock(self, locator):
646 self._delete_bufferblock(locator)
648 def _delete_bufferblock(self, locator):
649 bb = self._bufferblocks[locator]
651 del self._bufferblocks[locator]
653 def get_block_contents(self, locator, num_retries, cache_only=False):
656 First checks to see if the locator is a BufferBlock and return that, if
657 not, passes the request through to KeepClient.get().
661 if locator in self._bufferblocks:
662 bufferblock = self._bufferblocks[locator]
663 if bufferblock.state() != _BufferBlock.COMMITTED:
664 return bufferblock.buffer_view[0:bufferblock.write_pointer].tobytes()
666 locator = bufferblock._locator
668 return self._keep.get_from_cache(locator)
670 return self._keep.get(locator, num_retries=num_retries)
672 def commit_all(self):
673 """Commit all outstanding buffer blocks.
675 This is a synchronous call, and will not return until all buffer blocks
676 are uploaded. Raises KeepWriteError() if any blocks failed to upload.
679 self.repack_small_blocks(force=True, sync=True)
682 items = self._bufferblocks.items()
685 if v.state() != _BufferBlock.COMMITTED and v.owner:
686 v.owner.flush(sync=False)
689 if self._put_queue is not None:
690 self._put_queue.join()
694 if v.state() == _BufferBlock.ERROR:
695 err.append((v.locator(), v.error))
697 raise KeepWriteError("Error writing some blocks", err, label="block")
700 # flush again with sync=True to remove committed bufferblocks from
703 v.owner.flush(sync=True)
705 def block_prefetch(self, locator):
706 """Initiate a background download of a block.
708 This assumes that the underlying KeepClient implements a block cache,
709 so repeated requests for the same block will not result in repeated
710 downloads (unless the block is evicted from the cache.) This method
715 if not self.prefetch_enabled:
718 if self._keep.get_from_cache(locator) is not None:
722 if locator in self._bufferblocks:
725 self.start_get_threads()
726 self._prefetch_queue.put(locator)
729 class ArvadosFile(object):
730 """Represent a file in a Collection.
732 ArvadosFile manages the underlying representation of a file in Keep as a
733 sequence of segments spanning a set of blocks, and implements random
736 This object may be accessed from multiple threads.
740 def __init__(self, parent, name, stream=[], segments=[]):
742 ArvadosFile constructor.
745 a list of Range objects representing a block stream
748 a list of Range objects representing segments
752 self._writers = set()
753 self._committed = False
755 self.lock = parent.root_collection().lock
757 self._add_segment(stream, s.locator, s.range_size)
758 self._current_bblock = None
761 return self.parent.writable()
765 return copy.copy(self._segments)
768 def clone(self, new_parent, new_name):
769 """Make a copy of this file."""
770 cp = ArvadosFile(new_parent, new_name)
771 cp.replace_contents(self)
776 def replace_contents(self, other):
777 """Replace segments of this file with segments from another `ArvadosFile` object."""
781 for other_segment in other.segments():
782 new_loc = other_segment.locator
783 if other.parent._my_block_manager().is_bufferblock(other_segment.locator):
784 if other_segment.locator not in map_loc:
785 bufferblock = other.parent._my_block_manager().get_bufferblock(other_segment.locator)
786 if bufferblock.state() != _BufferBlock.WRITABLE:
787 map_loc[other_segment.locator] = bufferblock.locator()
789 map_loc[other_segment.locator] = self.parent._my_block_manager().dup_block(bufferblock, self).blockid
790 new_loc = map_loc[other_segment.locator]
792 self._segments.append(Range(new_loc, other_segment.range_start, other_segment.range_size, other_segment.segment_offset))
794 self._committed = False
796 def __eq__(self, other):
799 if not isinstance(other, ArvadosFile):
802 othersegs = other.segments()
804 if len(self._segments) != len(othersegs):
806 for i in xrange(0, len(othersegs)):
807 seg1 = self._segments[i]
812 if self.parent._my_block_manager().is_bufferblock(loc1):
813 loc1 = self.parent._my_block_manager().get_bufferblock(loc1).locator()
815 if other.parent._my_block_manager().is_bufferblock(loc2):
816 loc2 = other.parent._my_block_manager().get_bufferblock(loc2).locator()
818 if (KeepLocator(loc1).stripped() != KeepLocator(loc2).stripped() or
819 seg1.range_start != seg2.range_start or
820 seg1.range_size != seg2.range_size or
821 seg1.segment_offset != seg2.segment_offset):
826 def __ne__(self, other):
827 return not self.__eq__(other)
830 def set_segments(self, segs):
831 self._segments = segs
834 def set_committed(self):
835 """Set committed flag to True"""
836 self._committed = True
840 """Get whether this is committed or not."""
841 return self._committed
844 def add_writer(self, writer):
845 """Add an ArvadosFileWriter reference to the list of writers"""
846 if isinstance(writer, ArvadosFileWriter):
847 self._writers.add(writer)
850 def remove_writer(self, writer, flush):
852 Called from ArvadosFileWriter.close(). Remove a writer reference from the list
853 and do some block maintenance tasks.
855 self._writers.remove(writer)
857 if flush or self.size() > config.KEEP_BLOCK_SIZE / 2:
858 # File writer closed, not small enough for repacking
861 # All writers closed and size is adequate for repacking
862 self.parent._my_block_manager().repack_small_blocks(closed_file_size=self.size())
866 Get whether this is closed or not. When the writers list is empty, the file
867 is supposed to be closed.
869 return len(self._writers) == 0
873 def truncate(self, size):
874 """Shrink the size of the file.
876 If `size` is less than the size of the file, the file contents after
877 `size` will be discarded. If `size` is greater than the current size
878 of the file, an IOError will be raised.
881 if size < self.size():
883 for r in self._segments:
884 range_end = r.range_start+r.range_size
885 if r.range_start >= size:
886 # segment is past the trucate size, all done
888 elif size < range_end:
889 nr = Range(r.locator, r.range_start, size - r.range_start, 0)
890 nr.segment_offset = r.segment_offset
896 self._segments = new_segs
897 self._committed = False
898 elif size > self.size():
899 raise IOError(errno.EINVAL, "truncate() does not support extending the file size")
901 def readfrom(self, offset, size, num_retries, exact=False):
902 """Read up to `size` bytes from the file starting at `offset`.
905 If False (default), return less data than requested if the read
906 crosses a block boundary and the next block isn't cached. If True,
907 only return less data than requested when hitting EOF.
911 if size == 0 or offset >= self.size():
913 readsegs = locators_and_ranges(self._segments, offset, size)
914 prefetch = locators_and_ranges(self._segments, offset + size, config.KEEP_BLOCK_SIZE, limit=32)
919 block = self.parent._my_block_manager().get_block_contents(lr.locator, num_retries=num_retries, cache_only=(bool(data) and not exact))
921 blockview = memoryview(block)
922 data.append(blockview[lr.segment_offset:lr.segment_offset+lr.segment_size].tobytes())
928 if lr.locator not in locs:
929 self.parent._my_block_manager().block_prefetch(lr.locator)
934 def _repack_writes(self, num_retries):
935 """Test if the buffer block has more data than actual segments.
937 This happens when a buffered write over-writes a file range written in
938 a previous buffered write. Re-pack the buffer block for efficiency
939 and to avoid leaking information.
942 segs = self._segments
944 # Sum up the segments to get the total bytes of the file referencing
945 # into the buffer block.
946 bufferblock_segs = [s for s in segs if s.locator == self._current_bblock.blockid]
947 write_total = sum([s.range_size for s in bufferblock_segs])
949 if write_total < self._current_bblock.size():
950 # There is more data in the buffer block than is actually accounted for by segments, so
951 # re-pack into a new buffer by copying over to a new buffer block.
952 contents = self.parent._my_block_manager().get_block_contents(self._current_bblock.blockid, num_retries)
953 new_bb = self.parent._my_block_manager().alloc_bufferblock(self._current_bblock.blockid, starting_capacity=write_total, owner=self)
954 for t in bufferblock_segs:
955 new_bb.append(contents[t.segment_offset:t.segment_offset+t.range_size])
956 t.segment_offset = new_bb.size() - t.range_size
958 self._current_bblock = new_bb
962 def writeto(self, offset, data, num_retries):
963 """Write `data` to the file starting at `offset`.
965 This will update existing bytes and/or extend the size of the file as
972 if offset > self.size():
973 raise ArgumentError("Offset is past the end of the file")
975 if len(data) > config.KEEP_BLOCK_SIZE:
976 # Chunk it up into smaller writes
978 dataview = memoryview(data)
980 self.writeto(offset+n, dataview[n:n + config.KEEP_BLOCK_SIZE].tobytes(), num_retries)
981 n += config.KEEP_BLOCK_SIZE
984 self._committed = False
986 if self._current_bblock is None or self._current_bblock.state() != _BufferBlock.WRITABLE:
987 self._current_bblock = self.parent._my_block_manager().alloc_bufferblock(owner=self)
989 if (self._current_bblock.size() + len(data)) > config.KEEP_BLOCK_SIZE:
990 self._repack_writes(num_retries)
991 if (self._current_bblock.size() + len(data)) > config.KEEP_BLOCK_SIZE:
992 self.parent._my_block_manager().commit_bufferblock(self._current_bblock, sync=False)
993 self._current_bblock = self.parent._my_block_manager().alloc_bufferblock(owner=self)
995 self._current_bblock.append(data)
997 replace_range(self._segments, offset, len(data), self._current_bblock.blockid, self._current_bblock.write_pointer - len(data))
999 self.parent.notify(WRITE, self.parent, self.name, (self, self))
1004 def flush(self, sync=True, num_retries=0):
1005 """Flush the current bufferblock to Keep.
1008 If True, commit block synchronously, wait until buffer block has been written.
1009 If False, commit block asynchronously, return immediately after putting block into
1012 if self.committed():
1015 if self._current_bblock and self._current_bblock.state() != _BufferBlock.COMMITTED:
1016 if self._current_bblock.state() == _BufferBlock.WRITABLE:
1017 self._repack_writes(num_retries)
1018 self.parent._my_block_manager().commit_bufferblock(self._current_bblock, sync=sync)
1022 for s in self._segments:
1023 bb = self.parent._my_block_manager().get_bufferblock(s.locator)
1025 if bb.state() != _BufferBlock.COMMITTED:
1026 self.parent._my_block_manager().commit_bufferblock(bb, sync=True)
1027 to_delete.add(s.locator)
1028 s.locator = bb.locator()
1030 self.parent._my_block_manager().delete_bufferblock(s)
1032 self.parent.notify(MOD, self.parent, self.name, (self, self))
1036 def add_segment(self, blocks, pos, size):
1037 """Add a segment to the end of the file.
1039 `pos` and `offset` reference a section of the stream described by
1040 `blocks` (a list of Range objects)
1043 self._add_segment(blocks, pos, size)
1045 def _add_segment(self, blocks, pos, size):
1046 """Internal implementation of add_segment."""
1047 self._committed = False
1048 for lr in locators_and_ranges(blocks, pos, size):
1049 last = self._segments[-1] if self._segments else Range(0, 0, 0, 0)
1050 r = Range(lr.locator, last.range_start+last.range_size, lr.segment_size, lr.segment_offset)
1051 self._segments.append(r)
1055 """Get the file size."""
1057 n = self._segments[-1]
1058 return n.range_start + n.range_size
1063 def manifest_text(self, stream_name=".", portable_locators=False, normalize=False):
1066 for segment in self.segments:
1067 loc = segment.locator
1068 if loc.startswith("bufferblock"):
1069 loc = self._bufferblocks[loc].calculate_locator()
1070 if portable_locators:
1071 loc = KeepLocator(loc).stripped()
1072 filestream.append(LocatorAndRange(loc, locator_block_size(loc),
1073 segment.segment_offset, segment.range_size))
1074 buf += ' '.join(normalize_stream(stream_name, {stream_name: filestream}))
1080 def _reparent(self, newparent, newname):
1081 self._committed = False
1082 self.flush(sync=True)
1083 self.parent.remove(self.name)
1084 self.parent = newparent
1086 self.lock = self.parent.root_collection().lock
1089 class ArvadosFileReader(ArvadosFileReaderBase):
1090 """Wraps ArvadosFile in a file-like object supporting reading only.
1092 Be aware that this class is NOT thread safe as there is no locking around
1093 updating file pointer.
1097 def __init__(self, arvadosfile, num_retries=None):
1098 super(ArvadosFileReader, self).__init__(arvadosfile.name, "r", num_retries=num_retries)
1099 self.arvadosfile = arvadosfile
1102 return self.arvadosfile.size()
1104 def stream_name(self):
1105 return self.arvadosfile.parent.stream_name()
1107 @_FileLikeObjectBase._before_close
1109 def read(self, size=None, num_retries=None):
1110 """Read up to `size` bytes from the file and return the result.
1112 Starts at the current file position. If `size` is None, read the
1113 entire remainder of the file.
1117 rd = self.arvadosfile.readfrom(self._filepos, config.KEEP_BLOCK_SIZE, num_retries)
1120 self._filepos += len(rd)
1121 rd = self.arvadosfile.readfrom(self._filepos, config.KEEP_BLOCK_SIZE, num_retries)
1122 return ''.join(data)
1124 data = self.arvadosfile.readfrom(self._filepos, size, num_retries, exact=True)
1125 self._filepos += len(data)
1128 @_FileLikeObjectBase._before_close
1130 def readfrom(self, offset, size, num_retries=None):
1131 """Read up to `size` bytes from the stream, starting at the specified file offset.
1133 This method does not change the file position.
1135 return self.arvadosfile.readfrom(offset, size, num_retries)
1141 class ArvadosFileWriter(ArvadosFileReader):
1142 """Wraps ArvadosFile in a file-like object supporting both reading and writing.
1144 Be aware that this class is NOT thread safe as there is no locking around
1145 updating file pointer.
1149 def __init__(self, arvadosfile, mode, num_retries=None):
1150 super(ArvadosFileWriter, self).__init__(arvadosfile, num_retries=num_retries)
1152 self.arvadosfile.add_writer(self)
1154 @_FileLikeObjectBase._before_close
1156 def write(self, data, num_retries=None):
1157 if self.mode[0] == "a":
1158 self.arvadosfile.writeto(self.size(), data, num_retries)
1160 self.arvadosfile.writeto(self._filepos, data, num_retries)
1161 self._filepos += len(data)
1164 @_FileLikeObjectBase._before_close
1166 def writelines(self, seq, num_retries=None):
1168 self.write(s, num_retries=num_retries)
1170 @_FileLikeObjectBase._before_close
1171 def truncate(self, size=None):
1173 size = self._filepos
1174 self.arvadosfile.truncate(size)
1175 if self._filepos > self.size():
1176 self._filepos = self.size()
1178 @_FileLikeObjectBase._before_close
1180 self.arvadosfile.flush()
1182 def close(self, flush=True):
1184 self.arvadosfile.remove_writer(self, flush)
1185 super(ArvadosFileWriter, self).close()