+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
from __future__ import absolute_import
from __future__ import division
from future import standard_library
class ArvadosFileReaderBase(_FileLikeObjectBase):
def __init__(self, name, mode, num_retries=None):
super(ArvadosFileReaderBase, self).__init__(name, mode)
- self._binary = 'b' in mode
- if sys.version_info >= (3, 0) and not self._binary:
- raise NotImplementedError("text mode {!r} is not implemented".format(mode))
self._filepos = 0
self.num_retries = num_retries
self._readline_cache = (None, None)
yield data
def decompressed_name(self):
- return re.sub('\.(bz2|gz)$', '', self.name)
+ return re.sub(r'\.(bz2|gz)$', '', self.name)
@_FileLikeObjectBase._before_close
def seek(self, pos, whence=os.SEEK_SET):
"""
DEFAULT_PUT_THREADS = 2
- DEFAULT_GET_THREADS = 2
- def __init__(self, keep, copies=None, put_threads=None):
+ def __init__(self, keep,
+ copies=None,
+ put_threads=None,
+ num_retries=None,
+ storage_classes_func=None):
"""keep: KeepClient object to use"""
self._keep = keep
self._bufferblocks = collections.OrderedDict()
self._put_queue = None
self._put_threads = None
- self._prefetch_queue = None
- self._prefetch_threads = None
self.lock = threading.Lock()
self.prefetch_enabled = True
- if put_threads:
- self.num_put_threads = put_threads
- else:
- self.num_put_threads = _BlockManager.DEFAULT_PUT_THREADS
- self.num_get_threads = _BlockManager.DEFAULT_GET_THREADS
+ self.num_put_threads = put_threads or _BlockManager.DEFAULT_PUT_THREADS
self.copies = copies
+ self.storage_classes = storage_classes_func or (lambda: [])
self._pending_write_size = 0
self.threads_lock = threading.Lock()
self.padding_block = None
- self._repacked_bb = {}
- self._repacked_bb_lock = threading.Lock()
+ self.num_retries = num_retries
@synchronized
def alloc_bufferblock(self, blockid=None, starting_capacity=2**14, owner=None):
return
if self.copies is None:
- loc = self._keep.put(bufferblock.buffer_view[0:bufferblock.write_pointer].tobytes())
+ loc = self._keep.put(bufferblock.buffer_view[0:bufferblock.write_pointer].tobytes(), num_retries=self.num_retries, classes=self.storage_classes())
else:
- loc = self._keep.put(bufferblock.buffer_view[0:bufferblock.write_pointer].tobytes(), copies=self.copies)
+ loc = self._keep.put(bufferblock.buffer_view[0:bufferblock.write_pointer].tobytes(), num_retries=self.num_retries, copies=self.copies, classes=self.storage_classes())
bufferblock.set_state(_BufferBlock.COMMITTED, loc)
-
- with self._repacked_bb_lock:
- # Check if this block was created by repacking smaller blocks
- if bufferblock.blockid in self._repacked_bb:
- # Update segment locators (with its tokens) of files within
- # this block
- old_loc = self._repacked_bb[bufferblock.blockid]['unsigned_loc']
- for f in self._repacked_bb[bufferblock.blockid]['files']:
- for s in [x for x in f._segments if x.locator == old_loc]:
- s.locator = loc
- del(self._repacked_bb[bufferblock.blockid])
except Exception as e:
bufferblock.set_state(_BufferBlock.ERROR, e)
finally:
# 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
+ # generating data more quickly than it can be sent to the Keep
# servers.
#
# With two upload threads and a queue size of 2, this means up to 4
thread.daemon = True
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:
- _logger.exception("Exception doing block prefetch")
-
- @synchronized
- def start_get_threads(self):
- if self._prefetch_threads is None:
- self._prefetch_queue = queue.Queue()
- self._prefetch_threads = []
- for i in range(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."""
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
return
new_bb = self._alloc_bufferblock()
+ new_bb.owner = []
files = []
while len(small_blocks) > 0 and (new_bb.write_pointer + small_blocks[0].size()) <= config.KEEP_BLOCK_SIZE:
bb = small_blocks.pop(0)
+ new_bb.owner.append(bb.owner)
self._pending_write_size -= bb.size()
new_bb.append(bb.buffer_view[0:bb.write_pointer].tobytes())
files.append((bb, new_bb.write_pointer - bb.size()))
- # If this repacked block will be committed asynchronously, take note
- # of its files so their segments' locators will be updated with
- # the correct permission token returned by the API server.
- if not sync:
- with self._repacked_bb_lock:
- self._repacked_bb[new_bb.blockid] = {
- 'unsigned_loc': new_bb.locator(),
- 'files': [bb.owner for bb, _ in files],
- }
-
self.commit_bufferblock(new_bb, sync=sync)
- with self._repacked_bb_lock:
- for bb, new_bb_segment_offset in files:
- newsegs = bb.owner.segments()
- for s in newsegs:
- if s.locator == bb.blockid:
- s.locator = new_bb.locator()
- s.segment_offset = new_bb_segment_offset+s.segment_offset
- bb.owner.set_segments(newsegs)
- self._delete_bufferblock(bb.blockid)
+ for bb, new_bb_segment_offset in files:
+ newsegs = bb.owner.segments()
+ for s in newsegs:
+ if s.locator == bb.blockid:
+ s.locator = new_bb.blockid
+ s.segment_offset = new_bb_segment_offset+s.segment_offset
+ bb.owner.set_segments(newsegs)
+ self._delete_bufferblock(bb.blockid)
def commit_bufferblock(self, block, sync):
"""Initiate a background upload of a bufferblock.
if sync:
try:
if self.copies is None:
- loc = self._keep.put(block.buffer_view[0:block.write_pointer].tobytes())
+ loc = self._keep.put(block.buffer_view[0:block.write_pointer].tobytes(), num_retries=self.num_retries, classes=self.storage_classes())
else:
- loc = self._keep.put(block.buffer_view[0:block.write_pointer].tobytes(), copies=self.copies)
+ loc = self._keep.put(block.buffer_view[0:block.write_pointer].tobytes(), num_retries=self.num_retries, copies=self.copies, classes=self.storage_classes())
block.set_state(_BufferBlock.COMMITTED, loc)
except Exception as e:
block.set_state(_BufferBlock.ERROR, e)
self._delete_bufferblock(locator)
def _delete_bufferblock(self, locator):
- bb = self._bufferblocks[locator]
- bb.clear()
- del self._bufferblocks[locator]
+ if locator in self._bufferblocks:
+ bb = self._bufferblocks[locator]
+ bb.clear()
+ del self._bufferblocks[locator]
def get_block_contents(self, locator, num_retries, cache_only=False):
"""Fetch a block.
for k,v in items:
if v.state() != _BufferBlock.COMMITTED and v.owner:
- v.owner.flush(sync=False)
+ # Ignore blocks with a list of owners, as if they're not in COMMITTED
+ # state, they're already being committed asynchronously.
+ if isinstance(v.owner, ArvadosFile):
+ v.owner.flush(sync=False)
with self.lock:
if self._put_queue is not None:
# flush again with sync=True to remove committed bufferblocks from
# the segments.
if v.owner:
- v.owner.flush(sync=True)
+ if isinstance(v.owner, ArvadosFile):
+ v.owner.flush(sync=True)
+ elif isinstance(v.owner, list) and len(v.owner) > 0:
+ # This bufferblock is referenced by many files as a result
+ # of repacking small blocks, so don't delete it when flushing
+ # its owners, just do it after flushing them all.
+ for owner in v.owner:
+ owner.flush(sync=True)
+ self.delete_bufferblock(k)
+
+ self.stop_threads()
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)
+ self._keep.block_prefetch(locator)
class ArvadosFile(object):
"""
+ __slots__ = ('parent', 'name', '_writers', '_committed',
+ '_segments', 'lock', '_current_bblock', 'fuse_entry')
+
def __init__(self, parent, name, stream=[], segments=[]):
"""
ArvadosFile constructor.
return True
return False
+ @synchronized
+ def has_remote_blocks(self):
+ """Returns True if any of the segment's locators has a +R signature"""
+
+ for s in self._segments:
+ if '+R' in s.locator:
+ return True
+ return False
+
+ @synchronized
+ def _copy_remote_blocks(self, remote_blocks={}):
+ """Ask Keep to copy remote blocks and point to their local copies.
+
+ This is called from the parent Collection.
+
+ :remote_blocks:
+ Shared cache of remote to local block mappings. This is used to avoid
+ doing extra work when blocks are shared by more than one file in
+ different subdirectories.
+ """
+
+ for s in self._segments:
+ if '+R' in s.locator:
+ try:
+ loc = remote_blocks[s.locator]
+ except KeyError:
+ loc = self.parent._my_keep().refresh_signature(s.locator)
+ remote_blocks[s.locator] = loc
+ s.locator = loc
+ self.parent.set_committed(False)
+ return remote_blocks
+
@synchronized
def segments(self):
return copy.copy(self._segments)
if size == 0 or offset >= self.size():
return b''
readsegs = locators_and_ranges(self._segments, offset, size)
- prefetch = locators_and_ranges(self._segments, offset + size, config.KEEP_BLOCK_SIZE, limit=32)
+ if self.parent._my_block_manager()._keep.num_prefetch_threads > 0:
+ prefetch = locators_and_ranges(self._segments, offset + size, config.KEEP_BLOCK_SIZE * self.parent._my_block_manager()._keep.num_prefetch_threads, limit=32)
locs = set()
data = []
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())
+ data.append(blockview[lr.segment_offset:lr.segment_offset+lr.segment_size])
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)
+ if self.parent._my_block_manager()._keep.num_prefetch_threads > 0:
+ for lr in prefetch:
+ if lr.locator not in locs:
+ self.parent._my_block_manager().block_prefetch(lr.locator)
+ locs.add(lr.locator)
- return b''.join(data)
+ if len(data) == 1:
+ return data[0]
+ else:
+ return b''.join(data)
@must_be_writable
@synchronized
to_delete.add(s.locator)
s.locator = bb.locator()
for s in to_delete:
- self.parent._my_block_manager().delete_bufferblock(s)
+ # Don't delete the bufferblock if it's owned by many files. It'll be
+ # deleted after all of its owners are flush()ed.
+ if self.parent._my_block_manager().get_bufferblock(s).owner is self:
+ self.parent._my_block_manager().delete_bufferblock(s)
self.parent.notify(MOD, self.parent, self.name, (self, self))
def stream_name(self):
return self.arvadosfile.parent.stream_name()
+ def readinto(self, b):
+ data = self.read(len(b))
+ b[:len(data)] = data
+ return len(data)
+
@_FileLikeObjectBase._before_close
@retry_method
def read(self, size=None, num_retries=None):
if not self.closed:
self.arvadosfile.remove_writer(self, flush)
super(ArvadosFileWriter, self).close()
+
+
+class WrappableFile(object):
+ """An interface to an Arvados file that's compatible with io wrappers.
+
+ """
+ def __init__(self, f):
+ self.f = f
+ self.closed = False
+ def close(self):
+ self.closed = True
+ return self.f.close()
+ def flush(self):
+ return self.f.flush()
+ def read(self, *args, **kwargs):
+ return self.f.read(*args, **kwargs)
+ def readable(self):
+ return self.f.readable()
+ def readinto(self, *args, **kwargs):
+ return self.f.readinto(*args, **kwargs)
+ def seek(self, *args, **kwargs):
+ return self.f.seek(*args, **kwargs)
+ def seekable(self):
+ return self.f.seekable()
+ def tell(self):
+ return self.f.tell()
+ def writable(self):
+ return self.f.writable()
+ def write(self, *args, **kwargs):
+ return self.f.write(*args, **kwargs)
projects / arvados.git / blobdiff