import functools
+import os
+import zlib
+import bz2
+from .ranges import *
+from arvados.retry import retry_method
+import config
+import hashlib
+import hashlib
+import threading
+import Queue
+
+def split(path):
+ """split(path) -> streamname, filename
+
+ Separate the stream name and file name in a /-separated stream path.
+ 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 ArvadosFileBase(object):
def __init__(self, name, mode):
def close(self):
self.closed = True
+
+
+class ArvadosFileReaderBase(ArvadosFileBase):
+ 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, name, mode, num_retries=None):
+ super(ArvadosFileReaderBase, self).__init__(self._NameAttribute(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)
+
+ @ArvadosFileBase._before_close
+ def seek(self, pos, whence=os.SEEK_CUR):
+ 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
+
+ @ArvadosFileBase._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
+
+ @ArvadosFileBase._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]
+
+ @ArvadosFileBase._before_close
+ @retry_method
+ def decompress(self, decompress, size, num_retries=None):
+ for segment in self.readall(size, num_retries):
+ data = decompress(segment)
+ if data:
+ yield data
+
+ @ArvadosFileBase._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)
+
+ @ArvadosFileBase._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)
+
+
+class StreamFileReader(ArvadosFileReaderBase):
+ def __init__(self, stream, segments, name):
+ super(StreamFileReader, self).__init__(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
+
+ @ArvadosFileBase._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
+
+ @ArvadosFileBase._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):
+ from stream import normalize_stream
+ 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"
+
+
+class BufferBlock(object):
+'''
+A BufferBlock is 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
+
+PENDING - 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, and the BufferBlock should be discarded in favor of fetching the
+block through normal Keep means.
+'''
+ WRITABLE = 0
+ PENDING = 1
+ COMMITTED = 2
+
+ def __init__(self, blockid, starting_capacity):
+ '''
+ blockid: the identifier for this block
+ starting_capacity: the initial buffer capacity
+ '''
+ 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
+
+ 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")
+
+ def size(self):
+ '''Amount of data written to the buffer'''
+ return self.write_pointer
+
+ 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
+
+class AsyncKeepWriteErrors(Exception):
+ '''
+ Roll up one or more Keep write exceptions (generated by background
+ threads) into a single one.
+ '''
+ def __init__(self, errors):
+ self.errors = errors
+
+ def __repr__(self):
+ return "\n".join(self.errors)
+
+class BlockManager(object):
+ '''
+ BlockManager handles buffer blocks, background block uploads, and
+ background block prefetch for a Collection of ArvadosFiles.
+ '''
+ def __init__(self, keep):
+ '''keep: KeepClient object to use'''
+ self._keep = keep
+ self._bufferblocks = {}
+ self._put_queue = None
+ self._put_errors = None
+ self._put_threads = None
+ self._prefetch_queue = None
+ self._prefetch_threads = None
+
+ def alloc_bufferblock(self, blockid=None, starting_capacity=2**14):
+ '''
+ 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
+ '''
+ if blockid is None:
+ blockid = "bufferblock%i" % len(self._bufferblocks)
+ bb = BufferBlock(blockid, starting_capacity=starting_capacity)
+ self._bufferblocks[bb.blockid] = bb
+ return bb
+
+ 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
+ self._put_errors = 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 commit_bufferblock(self, block):
+ '''
+ Initiate a background upload of a bufferblock. This will block if the
+ upload queue is at capacity, otherwise it will return immediately.
+ '''
+
+ def worker(self):
+ '''
+ Background uploader thread.
+ '''
+ while True:
+ try:
+ b = self._put_queue.get()
+ if b is None:
+ return
+ b._locator = self._keep.put(b.buffer_view[0:b.write_pointer].tobytes())
+ b.state = BufferBlock.COMMITTED
+ b.buffer_view = None
+ b.buffer_block = None
+ except Exception as e:
+ print e
+ self._put_errors.put(e)
+ finally:
+ if self._put_queue is not None:
+ self._put_queue.task_done()
+
+ 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_errors = Queue.Queue()
+ self._put_threads = [threading.Thread(target=worker, args=(self,)),
+ threading.Thread(target=worker, args=(self,))]
+ for t in self._put_threads:
+ t.daemon = True
+ t.start()
+
+ # Mark the block as PENDING so to disallow any more appends.
+ block.state = BufferBlock.PENDING
+ self._put_queue.put(block)
+
+ def get_block(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().
+ '''
+ if locator in self._bufferblocks:
+ bb = self._bufferblocks[locator]
+ if bb.state != BufferBlock.COMMITTED:
+ return bb.buffer_view[0:bb.write_pointer].tobytes()
+ else:
+ locator = bb._locator
+ return self._keep.get(locator, num_retries=num_retries, cache_only=cache_only)
+
+ def commit_all(self):
+ '''
+ Commit all outstanding buffer blocks. Unlike commit_bufferblock(), this
+ is a synchronous call, and will not return until all buffer blocks are
+ uploaded. Raises AsyncKeepWriteErrors() if any blocks failed to
+ upload.
+ '''
+ for k,v in self._bufferblocks.items():
+ if v.state == BufferBlock.WRITABLE:
+ self.commit_bufferblock(v)
+ if self._put_queue is not None:
+ self._put_queue.join()
+ if not self._put_errors.empty():
+ e = []
+ try:
+ while True:
+ e.append(self._put_errors.get(False))
+ except Queue.Empty:
+ pass
+ raise AsyncKeepWriteErrors(e)
+
+ 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.
+ '''
+ def worker(self):
+ '''Background downloader thread.'''
+ while True:
+ try:
+ b = self._prefetch_queue.get()
+ if b is None:
+ return
+ self._keep.get(b)
+ except:
+ pass
+
+ if locator in self._bufferblocks:
+ return
+ if self._prefetch_threads is None:
+ self._prefetch_queue = Queue.Queue()
+ self._prefetch_threads = [threading.Thread(target=worker, args=(self,)),
+ threading.Thread(target=worker, args=(self,))]
+ for t in self._prefetch_threads:
+ t.daemon = True
+ t.start()
+ self._prefetch_queue.put(locator)
+
+class ArvadosFile(object):
+ '''
+ Manages the underyling representation of a file in Keep as a sequence of
+ segments over a set of blocks, supporting random read/write access.
+ '''
+
+ def __init__(self, parent, stream=[], segments=[]):
+ '''
+ stream: a list of Range objects representing a block stream
+ segments: a list of Range objects representing segments
+ '''
+ self.parent = parent
+ self._modified = True
+ self.segments = []
+ for s in segments:
+ self.add_segment(stream, s.locator, s.range_size)
+ self._current_bblock = None
+ self.lock = threading.Lock()
+
+ def clone(self):
+ '''
+ Make a copy of this file.
+ '''
+ # TODO: copy bufferblocks.
+ with self.lock:
+ cp = ArvadosFile()
+ cp.parent = self.parent
+ cp._modified = False
+ cp.segments = [Range(r.locator, r.range_start, r.range_size, r.segment_offset) for r in self.segments]
+ return cp
+
+ def set_unmodified(self):
+ self._modified = False
+
+ def modified(self):
+ return self._modified
+
+ def truncate(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)
+ nr.segment_offset = r.segment_offset
+ new_segs.append(nr)
+ break
+ else:
+ new_segs.append(r)
+
+ self.segments = new_segs
+ self._modified = True
+
+ def readfrom(self, offset, size, num_retries):
+ if size == 0 or offset >= self.size():
+ return ''
+ data = []
+
+ for lr in locators_and_ranges(self.segments, offset, size + config.KEEP_BLOCK_SIZE):
+ self.parent._my_block_manager().block_prefetch(lr.locator)
+
+ for lr in locators_and_ranges(self.segments, offset, size):
+ d = self.parent._my_block_manager().get_block(lr.locator, num_retries=num_retries, cache_only=bool(data))
+ if d:
+ data.append(d[lr.segment_offset:lr.segment_offset+lr.segment_size])
+ else:
+ break
+ return ''.join(data)
+
+ def _repack_writes(self):
+ '''Test if the buffer block has more data than is referenced by 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.
+ new_bb = self.parent._my_block_manager().alloc_bufferblock(self._current_bblock.blockid, starting_size=write_total)
+ for t in bufferblock_segs:
+ new_bb.append(self._current_bblock.buffer_view[t.segment_offset:t.segment_offset+t.range_size].tobytes())
+ t.segment_offset = new_bb.size() - t.range_size
+
+ self._current_bblock = new_bb
+
+ def writeto(self, offset, data, num_retries):
+ 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:
+ raise ArgumentError("Please append data in chunks smaller than %i bytes (config.KEEP_BLOCK_SIZE)" % (config.KEEP_BLOCK_SIZE))
+
+ self._modified = True
+
+ if self._current_bblock is None or self._current_bblock.state != BufferBlock.WRITABLE:
+ self._current_bblock = self.parent._my_block_manager().alloc_bufferblock()
+
+ if (self._current_bblock.size() + len(data)) > config.KEEP_BLOCK_SIZE:
+ self._repack_writes()
+ if (self._current_bblock.size() + len(data)) > config.KEEP_BLOCK_SIZE:
+ self.parent._my_block_manager().commit_bufferblock(self._current_bblock)
+ self._current_bblock = self.parent._my_block_manager().alloc_bufferblock()
+
+ self._current_bblock.append(data)
+ replace_range(self.segments, offset, len(data), self._current_bblock.blockid, self._current_bblock.write_pointer - len(data))
+
+ def add_segment(self, blocks, pos, size):
+ self._modified = True
+ for lr in locators_and_ranges(blocks, pos, size):
+ last = self.segments[-1] if self.segments else Range(0, 0, 0)
+ r = Range(lr.locator, last.range_start+last.range_size, lr.segment_size, lr.segment_offset)
+ self.segments.append(r)
+
+ def size(self):
+ if self.segments:
+ n = self.segments[-1]
+ return n.range_start + n.range_size
+ else:
+ return 0
+
+
+class ArvadosFileReader(ArvadosFileReaderBase):
+ def __init__(self, arvadosfile, name, mode="r", num_retries=None):
+ super(ArvadosFileReader, self).__init__(name, mode, num_retries=num_retries)
+ self.arvadosfile = arvadosfile.clone()
+
+ def size(self):
+ return self.arvadosfile.size()
+
+ @ArvadosFileBase._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"""
+ data = self.arvadosfile.readfrom(self._filepos, size, num_retries=num_retries)
+ self._filepos += len(data)
+ return data
+
+ @ArvadosFileBase._before_close
+ @retry_method
+ def readfrom(self, offset, size, num_retries=None):
+ """Read up to 'size' bytes from the stream, starting at the current file position"""
+ return self.arvadosfile.readfrom(offset, size, num_retries)
+
+ def flush(self):
+ pass
+
+
+class SynchronizedArvadosFile(object):
+ def __init__(self, arvadosfile):
+ self.arvadosfile = arvadosfile
+
+ def clone(self):
+ return self
+
+ def __getattr__(self, name):
+ with self.arvadosfile.lock:
+ return getattr(self.arvadosfile, name)
+
+
+class ArvadosFileWriter(ArvadosFileReader):
+ def __init__(self, arvadosfile, name, mode, num_retries=None):
+ self.arvadosfile = SynchronizedArvadosFile(arvadosfile)
+ super(ArvadosFileWriter, self).__init__(self.arvadosfile, name, mode, num_retries=num_retries)
+
+ @ArvadosFileBase._before_close
+ @retry_method
+ def write(self, data, num_retries=None):
+ if self.mode[0] == "a":
+ self.arvadosfile.writeto(self.size(), data)
+ else:
+ self.arvadosfile.writeto(self._filepos, data, num_retries)
+ self._filepos += len(data)
+
+ @ArvadosFileBase._before_close
+ @retry_method
+ def writelines(self, seq, num_retries=None):
+ for s in seq:
+ self.write(s)
+
+ 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()
projects / arvados.git / blobdiff