import functools
+import os
+import zlib
+import bz2
+import config
+import hashlib
+import threading
+import Queue
+import copy
+import errno
+import re
+import logging
-class ArvadosFileBase(object):
+from .errors import KeepWriteError, AssertionError, ArgumentError
+from .keep import KeepLocator
+from ._normalize_stream import normalize_stream
+from ._ranges import locators_and_ranges, replace_range, Range
+from .retry import retry_method
+
+MOD = "mod"
+WRITE = "write"
+
+_logger = logging.getLogger('arvados.arvfile')
+
+def split(path):
+ """split(path) -> streamname, filename
+
+ Separate the stream name and file name in a /-separated stream path and
+ return a tuple (stream_name, file_name). If no stream name is available,
+ assume '.'.
+
+ """
+ try:
+ stream_name, file_name = path.rsplit('/', 1)
+ except ValueError: # No / in string
+ stream_name, file_name = '.', path
+ return stream_name, file_name
+
+class _FileLikeObjectBase(object):
def __init__(self, name, mode):
self.name = name
self.mode = mode
@staticmethod
def _before_close(orig_func):
@functools.wraps(orig_func)
- def wrapper(self, *args, **kwargs):
+ def before_close_wrapper(self, *args, **kwargs):
if self.closed:
raise ValueError("I/O operation on closed stream file")
return orig_func(self, *args, **kwargs)
- return wrapper
+ return before_close_wrapper
def __enter__(self):
return self
def close(self):
self.closed = True
+
+
+class ArvadosFileReaderBase(_FileLikeObjectBase):
+ def __init__(self, name, mode, num_retries=None):
+ super(ArvadosFileReaderBase, self).__init__(name, mode)
+ self._filepos = 0L
+ self.num_retries = num_retries
+ self._readline_cache = (None, None)
+
+ def __iter__(self):
+ while True:
+ data = self.readline()
+ if not data:
+ break
+ yield data
+
+ def decompressed_name(self):
+ return re.sub('\.(bz2|gz)$', '', self.name)
+
+ @_FileLikeObjectBase._before_close
+ def seek(self, pos, whence=os.SEEK_SET):
+ if whence == os.SEEK_CUR:
+ pos += self._filepos
+ elif whence == os.SEEK_END:
+ pos += self.size()
+ self._filepos = min(max(pos, 0L), self.size())
+
+ def tell(self):
+ return self._filepos
+
+ @_FileLikeObjectBase._before_close
+ @retry_method
+ def readall(self, size=2**20, num_retries=None):
+ while True:
+ data = self.read(size, num_retries=num_retries)
+ if data == '':
+ break
+ yield data
+
+ @_FileLikeObjectBase._before_close
+ @retry_method
+ def readline(self, size=float('inf'), num_retries=None):
+ cache_pos, cache_data = self._readline_cache
+ if self.tell() == cache_pos:
+ data = [cache_data]
+ else:
+ data = ['']
+ data_size = len(data[-1])
+ while (data_size < size) and ('\n' not in data[-1]):
+ next_read = self.read(2 ** 20, num_retries=num_retries)
+ if not next_read:
+ break
+ data.append(next_read)
+ data_size += len(next_read)
+ data = ''.join(data)
+ try:
+ nextline_index = data.index('\n') + 1
+ except ValueError:
+ nextline_index = len(data)
+ nextline_index = min(nextline_index, size)
+ self._readline_cache = (self.tell(), data[nextline_index:])
+ return data[:nextline_index]
+
+ @_FileLikeObjectBase._before_close
+ @retry_method
+ def decompress(self, decompress, size, num_retries=None):
+ for segment in self.readall(size, num_retries=num_retries):
+ data = decompress(segment)
+ if data:
+ yield data
+
+ @_FileLikeObjectBase._before_close
+ @retry_method
+ def readall_decompressed(self, size=2**20, num_retries=None):
+ self.seek(0)
+ if self.name.endswith('.bz2'):
+ dc = bz2.BZ2Decompressor()
+ return self.decompress(dc.decompress, size,
+ num_retries=num_retries)
+ elif self.name.endswith('.gz'):
+ dc = zlib.decompressobj(16+zlib.MAX_WBITS)
+ return self.decompress(lambda segment: dc.decompress(dc.unconsumed_tail + segment),
+ size, num_retries=num_retries)
+ else:
+ return self.readall(size, num_retries=num_retries)
+
+ @_FileLikeObjectBase._before_close
+ @retry_method
+ def readlines(self, sizehint=float('inf'), num_retries=None):
+ data = []
+ data_size = 0
+ for s in self.readall(num_retries=num_retries):
+ data.append(s)
+ data_size += len(s)
+ if data_size >= sizehint:
+ break
+ return ''.join(data).splitlines(True)
+
+ def size(self):
+ raise NotImplementedError()
+
+ def read(self, size, num_retries=None):
+ raise NotImplementedError()
+
+ def readfrom(self, start, size, num_retries=None):
+ raise NotImplementedError()
+
+
+class StreamFileReader(ArvadosFileReaderBase):
+ class _NameAttribute(str):
+ # The Python file API provides a plain .name attribute.
+ # Older SDK provided a name() method.
+ # This class provides both, for maximum compatibility.
+ def __call__(self):
+ return self
+
+ def __init__(self, stream, segments, name):
+ super(StreamFileReader, self).__init__(self._NameAttribute(name), 'rb', num_retries=stream.num_retries)
+ self._stream = stream
+ self.segments = segments
+
+ def stream_name(self):
+ return self._stream.name()
+
+ def size(self):
+ n = self.segments[-1]
+ return n.range_start + n.range_size
+
+ @_FileLikeObjectBase._before_close
+ @retry_method
+ def read(self, size, num_retries=None):
+ """Read up to 'size' bytes from the stream, starting at the current file position"""
+ if size == 0:
+ return ''
+
+ data = ''
+ available_chunks = locators_and_ranges(self.segments, self._filepos, size)
+ if available_chunks:
+ lr = available_chunks[0]
+ data = self._stream.readfrom(lr.locator+lr.segment_offset,
+ lr.segment_size,
+ num_retries=num_retries)
+
+ self._filepos += len(data)
+ return data
+
+ @_FileLikeObjectBase._before_close
+ @retry_method
+ def readfrom(self, start, size, num_retries=None):
+ """Read up to 'size' bytes from the stream, starting at 'start'"""
+ if size == 0:
+ return ''
+
+ data = []
+ for lr in locators_and_ranges(self.segments, start, size):
+ data.append(self._stream.readfrom(lr.locator+lr.segment_offset, lr.segment_size,
+ num_retries=num_retries))
+ return ''.join(data)
+
+ def as_manifest(self):
+ segs = []
+ for r in self.segments:
+ segs.extend(self._stream.locators_and_ranges(r.locator, r.range_size))
+ return " ".join(normalize_stream(".", {self.name: segs})) + "\n"
+
+
+def synchronized(orig_func):
+ @functools.wraps(orig_func)
+ def synchronized_wrapper(self, *args, **kwargs):
+ with self.lock:
+ return orig_func(self, *args, **kwargs)
+ return synchronized_wrapper
+
+
+class StateChangeError(Exception):
+ def __init__(self, message, state, nextstate):
+ super(StateChangeError, self).__init__(message)
+ self.state = state
+ self.nextstate = nextstate
+
+class _BufferBlock(object):
+ """A stand-in for a Keep block that is in the process of being written.
+
+ Writers can append to it, get the size, and compute the Keep locator.
+ There are three valid states:
+
+ WRITABLE
+ Can append to block.
+
+ PENDING
+ Block is in the process of being uploaded to Keep, append is an error.
+
+ COMMITTED
+ The block has been written to Keep, its internal buffer has been
+ released, fetching the block will fetch it via keep client (since we
+ discarded the internal copy), and identifiers referring to the BufferBlock
+ can be replaced with the block locator.
+
+ """
+
+ WRITABLE = 0
+ PENDING = 1
+ COMMITTED = 2
+ ERROR = 3
+
+ def __init__(self, blockid, starting_capacity, owner):
+ """
+ :blockid:
+ the identifier for this block
+
+ :starting_capacity:
+ the initial buffer capacity
+
+ :owner:
+ ArvadosFile that owns this block
+
+ """
+ self.blockid = blockid
+ self.buffer_block = bytearray(starting_capacity)
+ self.buffer_view = memoryview(self.buffer_block)
+ self.write_pointer = 0
+ self._state = _BufferBlock.WRITABLE
+ self._locator = None
+ self.owner = owner
+ self.lock = threading.Lock()
+ self.wait_for_commit = threading.Event()
+ self.error = None
+
+ @synchronized
+ def append(self, data):
+ """Append some data to the buffer.
+
+ Only valid if the block is in WRITABLE state. Implements an expanding
+ buffer, doubling capacity as needed to accomdate all the data.
+
+ """
+ if self._state == _BufferBlock.WRITABLE:
+ while (self.write_pointer+len(data)) > len(self.buffer_block):
+ new_buffer_block = bytearray(len(self.buffer_block) * 2)
+ new_buffer_block[0:self.write_pointer] = self.buffer_block[0:self.write_pointer]
+ self.buffer_block = new_buffer_block
+ self.buffer_view = memoryview(self.buffer_block)
+ self.buffer_view[self.write_pointer:self.write_pointer+len(data)] = data
+ self.write_pointer += len(data)
+ self._locator = None
+ else:
+ raise AssertionError("Buffer block is not writable")
+
+ STATE_TRANSITIONS = frozenset([
+ (WRITABLE, PENDING),
+ (PENDING, COMMITTED),
+ (PENDING, ERROR),
+ (ERROR, PENDING)])
+
+ @synchronized
+ def set_state(self, nextstate, val=None):
+ if (self._state, nextstate) not in self.STATE_TRANSITIONS:
+ raise StateChangeError("Invalid state change from %s to %s" % (self.state, nextstate), self.state, nextstate)
+ self._state = nextstate
+
+ if self._state == _BufferBlock.PENDING:
+ self.wait_for_commit.clear()
+
+ if self._state == _BufferBlock.COMMITTED:
+ self._locator = val
+ self.buffer_view = None
+ self.buffer_block = None
+ self.wait_for_commit.set()
+
+ if self._state == _BufferBlock.ERROR:
+ self.error = val
+ self.wait_for_commit.set()
+
+ @synchronized
+ def state(self):
+ return self._state
+
+ def size(self):
+ """The amount of data written to the buffer."""
+ return self.write_pointer
+
+ @synchronized
+ def locator(self):
+ """The Keep locator for this buffer's contents."""
+ if self._locator is None:
+ self._locator = "%s+%i" % (hashlib.md5(self.buffer_view[0:self.write_pointer]).hexdigest(), self.size())
+ return self._locator
+
+ @synchronized
+ def clone(self, new_blockid, owner):
+ if self._state == _BufferBlock.COMMITTED:
+ raise AssertionError("Cannot duplicate committed buffer block")
+ bufferblock = _BufferBlock(new_blockid, self.size(), owner)
+ bufferblock.append(self.buffer_view[0:self.size()])
+ return bufferblock
+
+ @synchronized
+ def clear(self):
+ self.owner = None
+ self.buffer_block = None
+ self.buffer_view = None
+
+
+class NoopLock(object):
+ def __enter__(self):
+ return self
+
+ def __exit__(self, exc_type, exc_value, traceback):
+ pass
+
+ def acquire(self, blocking=False):
+ pass
+
+ def release(self):
+ pass
+
+
+def must_be_writable(orig_func):
+ @functools.wraps(orig_func)
+ def must_be_writable_wrapper(self, *args, **kwargs):
+ if not self.writable():
+ raise IOError(errno.EROFS, "Collection is read-only.")
+ return orig_func(self, *args, **kwargs)
+ return must_be_writable_wrapper
+
+
+class _BlockManager(object):
+ """BlockManager handles buffer blocks.
+
+ Also handles background block uploads, and background block prefetch for a
+ Collection of ArvadosFiles.
+
+ """
+
+ DEFAULT_PUT_THREADS = 2
+ DEFAULT_GET_THREADS = 2
+
+ def __init__(self, keep):
+ """keep: KeepClient object to use"""
+ self._keep = keep
+ self._bufferblocks = {}
+ self._put_queue = None
+ self._put_threads = None
+ self._prefetch_queue = None
+ self._prefetch_threads = None
+ self.lock = threading.Lock()
+ self.prefetch_enabled = True
+ self.num_put_threads = _BlockManager.DEFAULT_PUT_THREADS
+ self.num_get_threads = _BlockManager.DEFAULT_GET_THREADS
+
+ @synchronized
+ def alloc_bufferblock(self, blockid=None, starting_capacity=2**14, owner=None):
+ """Allocate a new, empty bufferblock in WRITABLE state and return it.
+
+ :blockid:
+ optional block identifier, otherwise one will be automatically assigned
+
+ :starting_capacity:
+ optional capacity, otherwise will use default capacity
+
+ :owner:
+ ArvadosFile that owns this block
+
+ """
+ if blockid is None:
+ blockid = "bufferblock%i" % len(self._bufferblocks)
+ bufferblock = _BufferBlock(blockid, starting_capacity=starting_capacity, owner=owner)
+ self._bufferblocks[bufferblock.blockid] = bufferblock
+ return bufferblock
+
+ @synchronized
+ def dup_block(self, block, owner):
+ """Create a new bufferblock initialized with the content of an existing bufferblock.
+
+ :block:
+ the buffer block to copy.
+
+ :owner:
+ ArvadosFile that owns the new block
+
+ """
+ new_blockid = "bufferblock%i" % len(self._bufferblocks)
+ bufferblock = block.clone(new_blockid, owner)
+ self._bufferblocks[bufferblock.blockid] = bufferblock
+ return bufferblock
+
+ @synchronized
+ def is_bufferblock(self, locator):
+ return locator in self._bufferblocks
+
+ def _commit_bufferblock_worker(self):
+ """Background uploader thread."""
+
+ while True:
+ try:
+ bufferblock = self._put_queue.get()
+ if bufferblock is None:
+ return
+
+ loc = self._keep.put(bufferblock.buffer_view[0:bufferblock.write_pointer].tobytes())
+ bufferblock.set_state(_BufferBlock.COMMITTED, loc)
+
+ except Exception as e:
+ bufferblock.set_state(_BufferBlock.ERROR, e)
+ finally:
+ if self._put_queue is not None:
+ self._put_queue.task_done()
+
+ @synchronized
+ def start_put_threads(self):
+ if self._put_threads is None:
+ # Start uploader threads.
+
+ # If we don't limit the Queue size, the upload queue can quickly
+ # grow to take up gigabytes of RAM if the writing process is
+ # generating data more quickly than it can be send to the Keep
+ # servers.
+ #
+ # With two upload threads and a queue size of 2, this means up to 4
+ # blocks pending. If they are full 64 MiB blocks, that means up to
+ # 256 MiB of internal buffering, which is the same size as the
+ # default download block cache in KeepClient.
+ self._put_queue = Queue.Queue(maxsize=2)
+
+ self._put_threads = []
+ for i in xrange(0, self.num_put_threads):
+ thread = threading.Thread(target=self._commit_bufferblock_worker)
+ self._put_threads.append(thread)
+ thread.daemon = False
+ thread.start()
+
+ def _block_prefetch_worker(self):
+ """The background downloader thread."""
+ while True:
+ try:
+ b = self._prefetch_queue.get()
+ if b is None:
+ return
+ self._keep.get(b)
+ except Exception:
+ pass
+
+ @synchronized
+ def start_get_threads(self):
+ if self._prefetch_threads is None:
+ self._prefetch_queue = Queue.Queue()
+ self._prefetch_threads = []
+ for i in xrange(0, self.num_get_threads):
+ thread = threading.Thread(target=self._block_prefetch_worker)
+ self._prefetch_threads.append(thread)
+ thread.daemon = True
+ thread.start()
+
+
+ @synchronized
+ def stop_threads(self):
+ """Shut down and wait for background upload and download threads to finish."""
+
+ if self._put_threads is not None:
+ for t in self._put_threads:
+ self._put_queue.put(None)
+ for t in self._put_threads:
+ t.join()
+ self._put_threads = None
+ self._put_queue = None
+
+ if self._prefetch_threads is not None:
+ for t in self._prefetch_threads:
+ self._prefetch_queue.put(None)
+ for t in self._prefetch_threads:
+ t.join()
+ self._prefetch_threads = None
+ self._prefetch_queue = None
+
+ def __enter__(self):
+ return self
+
+ def __exit__(self, exc_type, exc_value, traceback):
+ self.stop_threads()
+
+ def __del__(self):
+ self.stop_threads()
+
+ def commit_bufferblock(self, block, sync):
+ """Initiate a background upload of a bufferblock.
+
+ :block:
+ The block object to upload
+
+ :sync:
+ If `sync` is True, upload the block synchronously.
+ If `sync` is False, upload the block asynchronously. This will
+ return immediately unless the upload queue is at capacity, in
+ which case it will wait on an upload queue slot.
+
+ """
+
+ try:
+ # Mark the block as PENDING so to disallow any more appends.
+ block.set_state(_BufferBlock.PENDING)
+ except StateChangeError as e:
+ if e.state == _BufferBlock.PENDING and sync:
+ block.wait_for_commit.wait()
+ if block.state() == _BufferBlock.ERROR:
+ raise block.error
+ return
+
+ if sync:
+ try:
+ loc = self._keep.put(block.buffer_view[0:block.write_pointer].tobytes())
+ block.set_state(_BufferBlock.COMMITTED, loc)
+ except Exception as e:
+ block.set_state(_BufferBlock.ERROR, e)
+ raise
+ else:
+ self.start_put_threads()
+ self._put_queue.put(block)
+
+ @synchronized
+ def get_bufferblock(self, locator):
+ return self._bufferblocks.get(locator)
+
+ @synchronized
+ def delete_bufferblock(self, locator):
+ bb = self._bufferblocks[locator]
+ bb.clear()
+ del self._bufferblocks[locator]
+
+ def get_block_contents(self, locator, num_retries, cache_only=False):
+ """Fetch a block.
+
+ First checks to see if the locator is a BufferBlock and return that, if
+ not, passes the request through to KeepClient.get().
+
+ """
+ with self.lock:
+ if locator in self._bufferblocks:
+ bufferblock = self._bufferblocks[locator]
+ if bufferblock.state() != _BufferBlock.COMMITTED:
+ return bufferblock.buffer_view[0:bufferblock.write_pointer].tobytes()
+ else:
+ locator = bufferblock._locator
+ if cache_only:
+ return self._keep.get_from_cache(locator)
+ else:
+ return self._keep.get(locator, num_retries=num_retries)
+
+ def commit_all(self):
+ """Commit all outstanding buffer blocks.
+
+ This is a synchronous call, and will not return until all buffer blocks
+ are uploaded. Raises KeepWriteError() if any blocks failed to upload.
+
+ """
+ with self.lock:
+ items = self._bufferblocks.items()
+
+ for k,v in items:
+ if v.state() != _BufferBlock.COMMITTED:
+ v.owner.flush(sync=False)
+
+ with self.lock:
+ if self._put_queue is not None:
+ self._put_queue.join()
+
+ err = []
+ for k,v in items:
+ if v.state() == _BufferBlock.ERROR:
+ err.append((v.locator(), v.error))
+ if err:
+ raise KeepWriteError("Error writing some blocks", err, label="block")
+
+ for k,v in items:
+ # flush again with sync=True to remove committed bufferblocks from
+ # the segments.
+ if v.owner:
+ v.owner.flush(sync=True)
+
+ def block_prefetch(self, locator):
+ """Initiate a background download of a block.
+
+ This assumes that the underlying KeepClient implements a block cache,
+ so repeated requests for the same block will not result in repeated
+ downloads (unless the block is evicted from the cache.) This method
+ does not block.
+
+ """
+
+ if not self.prefetch_enabled:
+ return
+
+ if self._keep.get_from_cache(locator) is not None:
+ return
+
+ with self.lock:
+ if locator in self._bufferblocks:
+ return
+
+ self.start_get_threads()
+ self._prefetch_queue.put(locator)
+
+
+class ArvadosFile(object):
+ """Represent a file in a Collection.
+
+ ArvadosFile manages the underlying representation of a file in Keep as a
+ sequence of segments spanning a set of blocks, and implements random
+ read/write access.
+
+ This object may be accessed from multiple threads.
+
+ """
+
+ def __init__(self, parent, name, stream=[], segments=[]):
+ """
+ ArvadosFile constructor.
+
+ :stream:
+ a list of Range objects representing a block stream
+
+ :segments:
+ a list of Range objects representing segments
+ """
+ self.parent = parent
+ self.name = name
+ self._committed = False
+ self._segments = []
+ self.lock = parent.root_collection().lock
+ for s in segments:
+ self._add_segment(stream, s.locator, s.range_size)
+ self._current_bblock = None
+
+ def writable(self):
+ return self.parent.writable()
+
+ @synchronized
+ def segments(self):
+ return copy.copy(self._segments)
+
+ @synchronized
+ def clone(self, new_parent, new_name):
+ """Make a copy of this file."""
+ cp = ArvadosFile(new_parent, new_name)
+ cp.replace_contents(self)
+ return cp
+
+ @must_be_writable
+ @synchronized
+ def replace_contents(self, other):
+ """Replace segments of this file with segments from another `ArvadosFile` object."""
+
+ map_loc = {}
+ self._segments = []
+ for other_segment in other.segments():
+ new_loc = other_segment.locator
+ if other.parent._my_block_manager().is_bufferblock(other_segment.locator):
+ if other_segment.locator not in map_loc:
+ bufferblock = other.parent._my_block_manager().get_bufferblock(other_segment.locator)
+ if bufferblock.state() != _BufferBlock.WRITABLE:
+ map_loc[other_segment.locator] = bufferblock.locator()
+ else:
+ map_loc[other_segment.locator] = self.parent._my_block_manager().dup_block(bufferblock, self).blockid
+ new_loc = map_loc[other_segment.locator]
+
+ self._segments.append(Range(new_loc, other_segment.range_start, other_segment.range_size, other_segment.segment_offset))
+
+ self._committed = False
+
+ def __eq__(self, other):
+ if other is self:
+ return True
+ if not isinstance(other, ArvadosFile):
+ return False
+
+ othersegs = other.segments()
+ with self.lock:
+ if len(self._segments) != len(othersegs):
+ return False
+ for i in xrange(0, len(othersegs)):
+ seg1 = self._segments[i]
+ seg2 = othersegs[i]
+ loc1 = seg1.locator
+ loc2 = seg2.locator
+
+ if self.parent._my_block_manager().is_bufferblock(loc1):
+ loc1 = self.parent._my_block_manager().get_bufferblock(loc1).locator()
+
+ if other.parent._my_block_manager().is_bufferblock(loc2):
+ loc2 = other.parent._my_block_manager().get_bufferblock(loc2).locator()
+
+ if (KeepLocator(loc1).stripped() != KeepLocator(loc2).stripped() or
+ seg1.range_start != seg2.range_start or
+ seg1.range_size != seg2.range_size or
+ seg1.segment_offset != seg2.segment_offset):
+ return False
+
+ return True
+
+ def __ne__(self, other):
+ return not self.__eq__(other)
+
+ @synchronized
+ def set_committed(self):
+ """Set committed flag to False"""
+ self._committed = True
+
+ @synchronized
+ def committed(self):
+ """Get whether this is committed or not."""
+ return self._committed
+
+ @must_be_writable
+ @synchronized
+ def truncate(self, size):
+ """Shrink the size of the file.
+
+ If `size` is less than the size of the file, the file contents after
+ `size` will be discarded. If `size` is greater than the current size
+ of the file, an IOError will be raised.
+
+ """
+ if size < self.size():
+ new_segs = []
+ for r in self._segments:
+ range_end = r.range_start+r.range_size
+ if r.range_start >= size:
+ # segment is past the trucate size, all done
+ break
+ elif size < range_end:
+ nr = Range(r.locator, r.range_start, size - r.range_start, 0)
+ nr.segment_offset = r.segment_offset
+ new_segs.append(nr)
+ break
+ else:
+ new_segs.append(r)
+
+ self._segments = new_segs
+ self._committed = False
+ elif size > self.size():
+ raise IOError(errno.EINVAL, "truncate() does not support extending the file size")
+
+ def readfrom(self, offset, size, num_retries, exact=False):
+ """Read up to `size` bytes from the file starting at `offset`.
+
+ :exact:
+ If False (default), return less data than requested if the read
+ crosses a block boundary and the next block isn't cached. If True,
+ only return less data than requested when hitting EOF.
+ """
+
+ with self.lock:
+ if size == 0 or offset >= self.size():
+ return ''
+ readsegs = locators_and_ranges(self._segments, offset, size)
+ prefetch = locators_and_ranges(self._segments, offset + size, config.KEEP_BLOCK_SIZE, limit=32)
+
+ locs = set()
+ data = []
+ for lr in readsegs:
+ block = self.parent._my_block_manager().get_block_contents(lr.locator, num_retries=num_retries, cache_only=(bool(data) and not exact))
+ if block:
+ blockview = memoryview(block)
+ data.append(blockview[lr.segment_offset:lr.segment_offset+lr.segment_size].tobytes())
+ locs.add(lr.locator)
+ else:
+ break
+
+ for lr in prefetch:
+ if lr.locator not in locs:
+ self.parent._my_block_manager().block_prefetch(lr.locator)
+ locs.add(lr.locator)
+
+ return ''.join(data)
+
+ def _repack_writes(self, num_retries):
+ """Test if the buffer block has more data than actual segments.
+
+ This happens when a buffered write over-writes a file range written in
+ a previous buffered write. Re-pack the buffer block for efficiency
+ and to avoid leaking information.
+
+ """
+ segs = self._segments
+
+ # Sum up the segments to get the total bytes of the file referencing
+ # into the buffer block.
+ bufferblock_segs = [s for s in segs if s.locator == self._current_bblock.blockid]
+ write_total = sum([s.range_size for s in bufferblock_segs])
+
+ if write_total < self._current_bblock.size():
+ # There is more data in the buffer block than is actually accounted for by segments, so
+ # re-pack into a new buffer by copying over to a new buffer block.
+ contents = self.parent._my_block_manager().get_block_contents(self._current_bblock.blockid, num_retries)
+ new_bb = self.parent._my_block_manager().alloc_bufferblock(self._current_bblock.blockid, starting_capacity=write_total, owner=self)
+ for t in bufferblock_segs:
+ new_bb.append(contents[t.segment_offset:t.segment_offset+t.range_size])
+ t.segment_offset = new_bb.size() - t.range_size
+
+ self._current_bblock = new_bb
+
+ @must_be_writable
+ @synchronized
+ def writeto(self, offset, data, num_retries):
+ """Write `data` to the file starting at `offset`.
+
+ This will update existing bytes and/or extend the size of the file as
+ necessary.
+
+ """
+ if len(data) == 0:
+ return
+
+ if offset > self.size():
+ raise ArgumentError("Offset is past the end of the file")
+
+ if len(data) > config.KEEP_BLOCK_SIZE:
+ # Chunk it up into smaller writes
+ n = 0
+ dataview = memoryview(data)
+ while n < len(data):
+ self.writeto(offset+n, dataview[n:n + config.KEEP_BLOCK_SIZE].tobytes(), num_retries)
+ n += config.KEEP_BLOCK_SIZE
+ return
+
+ self._committed = False
+
+ if self._current_bblock is None or self._current_bblock.state() != _BufferBlock.WRITABLE:
+ self._current_bblock = self.parent._my_block_manager().alloc_bufferblock(owner=self)
+
+ if (self._current_bblock.size() + len(data)) > config.KEEP_BLOCK_SIZE:
+ self._repack_writes(num_retries)
+ if (self._current_bblock.size() + len(data)) > config.KEEP_BLOCK_SIZE:
+ self.parent._my_block_manager().commit_bufferblock(self._current_bblock, sync=False)
+ self._current_bblock = self.parent._my_block_manager().alloc_bufferblock(owner=self)
+
+ self._current_bblock.append(data)
+
+ replace_range(self._segments, offset, len(data), self._current_bblock.blockid, self._current_bblock.write_pointer - len(data))
+
+ self.parent.notify(WRITE, self.parent, self.name, (self, self))
+
+ return len(data)
+
+ @synchronized
+ def flush(self, sync=True, num_retries=0):
+ """Flush the current bufferblock to Keep.
+
+ :sync:
+ If True, commit block synchronously, wait until buffer block has been written.
+ If False, commit block asynchronously, return immediately after putting block into
+ the keep put queue.
+ """
+ if self.committed():
+ return
+
+ if self._current_bblock and self._current_bblock.state() != _BufferBlock.COMMITTED:
+ if self._current_bblock.state() == _BufferBlock.WRITABLE:
+ self._repack_writes(num_retries)
+ self.parent._my_block_manager().commit_bufferblock(self._current_bblock, sync=sync)
+
+ if sync:
+ to_delete = set()
+ for s in self._segments:
+ bb = self.parent._my_block_manager().get_bufferblock(s.locator)
+ if bb:
+ if bb.state() != _BufferBlock.COMMITTED:
+ self.parent._my_block_manager().commit_bufferblock(self._current_bblock, sync=True)
+ to_delete.add(s.locator)
+ s.locator = bb.locator()
+ for s in to_delete:
+ self.parent._my_block_manager().delete_bufferblock(s)
+
+ self.parent.notify(MOD, self.parent, self.name, (self, self))
+
+ @must_be_writable
+ @synchronized
+ def add_segment(self, blocks, pos, size):
+ """Add a segment to the end of the file.
+
+ `pos` and `offset` reference a section of the stream described by
+ `blocks` (a list of Range objects)
+
+ """
+ self._add_segment(blocks, pos, size)
+
+ def _add_segment(self, blocks, pos, size):
+ """Internal implementation of add_segment."""
+ self._committed = False
+ for lr in locators_and_ranges(blocks, pos, size):
+ last = self._segments[-1] if self._segments else Range(0, 0, 0, 0)
+ r = Range(lr.locator, last.range_start+last.range_size, lr.segment_size, lr.segment_offset)
+ self._segments.append(r)
+
+ @synchronized
+ def size(self):
+ """Get the file size."""
+ if self._segments:
+ n = self._segments[-1]
+ return n.range_start + n.range_size
+ else:
+ return 0
+
+ @synchronized
+ def manifest_text(self, stream_name=".", portable_locators=False, normalize=False):
+ buf = ""
+ filestream = []
+ for segment in self.segments:
+ loc = segment.locator
+ if loc.startswith("bufferblock"):
+ loc = self._bufferblocks[loc].calculate_locator()
+ if portable_locators:
+ loc = KeepLocator(loc).stripped()
+ filestream.append(LocatorAndRange(loc, locator_block_size(loc),
+ segment.segment_offset, segment.range_size))
+ buf += ' '.join(normalize_stream(stream_name, {stream_name: filestream}))
+ buf += "\n"
+ return buf
+
+ @must_be_writable
+ @synchronized
+ def _reparent(self, newparent, newname):
+ self._committed = False
+ self.flush(sync=True)
+ self.parent.remove(self.name)
+ self.parent = newparent
+ self.name = newname
+ self.lock = self.parent.root_collection().lock
+
+
+class ArvadosFileReader(ArvadosFileReaderBase):
+ """Wraps ArvadosFile in a file-like object supporting reading only.
+
+ Be aware that this class is NOT thread safe as there is no locking around
+ updating file pointer.
+
+ """
+
+ def __init__(self, arvadosfile, num_retries=None):
+ super(ArvadosFileReader, self).__init__(arvadosfile.name, "r", num_retries=num_retries)
+ self.arvadosfile = arvadosfile
+
+ def size(self):
+ return self.arvadosfile.size()
+
+ def stream_name(self):
+ return self.arvadosfile.parent.stream_name()
+
+ @_FileLikeObjectBase._before_close
+ @retry_method
+ def read(self, size=None, num_retries=None):
+ """Read up to `size` bytes from the file and return the result.
+
+ Starts at the current file position. If `size` is None, read the
+ entire remainder of the file.
+ """
+ if size is None:
+ data = []
+ rd = self.arvadosfile.readfrom(self._filepos, config.KEEP_BLOCK_SIZE, num_retries)
+ while rd:
+ data.append(rd)
+ self._filepos += len(rd)
+ rd = self.arvadosfile.readfrom(self._filepos, config.KEEP_BLOCK_SIZE, num_retries)
+ return ''.join(data)
+ else:
+ data = self.arvadosfile.readfrom(self._filepos, size, num_retries, exact=True)
+ self._filepos += len(data)
+ return data
+
+ @_FileLikeObjectBase._before_close
+ @retry_method
+ def readfrom(self, offset, size, num_retries=None):
+ """Read up to `size` bytes from the stream, starting at the specified file offset.
+
+ This method does not change the file position.
+ """
+ return self.arvadosfile.readfrom(offset, size, num_retries)
+
+ def flush(self):
+ pass
+
+
+class ArvadosFileWriter(ArvadosFileReader):
+ """Wraps ArvadosFile in a file-like object supporting both reading and writing.
+
+ Be aware that this class is NOT thread safe as there is no locking around
+ updating file pointer.
+
+ """
+
+ def __init__(self, arvadosfile, mode, num_retries=None):
+ super(ArvadosFileWriter, self).__init__(arvadosfile, num_retries=num_retries)
+ self.mode = mode
+
+ @_FileLikeObjectBase._before_close
+ @retry_method
+ def write(self, data, num_retries=None):
+ if self.mode[0] == "a":
+ self.arvadosfile.writeto(self.size(), data, num_retries)
+ else:
+ self.arvadosfile.writeto(self._filepos, data, num_retries)
+ self._filepos += len(data)
+ return len(data)
+
+ @_FileLikeObjectBase._before_close
+ @retry_method
+ def writelines(self, seq, num_retries=None):
+ for s in seq:
+ self.write(s, num_retries=num_retries)
+
+ @_FileLikeObjectBase._before_close
+ def truncate(self, size=None):
+ if size is None:
+ size = self._filepos
+ self.arvadosfile.truncate(size)
+ if self._filepos > self.size():
+ self._filepos = self.size()
+
+ @_FileLikeObjectBase._before_close
+ def flush(self):
+ self.arvadosfile.flush()
+
+ def close(self):
+ if not self.closed:
+ self.flush()
+ super(ArvadosFileWriter, self).close()
projects / arvados.git / blobdiff