X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/e158f485053be1e840073b321033d60d686a55a8..276ca380e9ee106b3880708d0ac48e2ab3cca335:/sdk/python/arvados/arvfile.py diff --git a/sdk/python/arvados/arvfile.py b/sdk/python/arvados/arvfile.py index e8dac463e5..2ec1079af1 100644 --- a/sdk/python/arvados/arvfile.py +++ b/sdk/python/arvados/arvfile.py @@ -1,4 +1,26 @@ 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): @@ -27,3 +49,589 @@ class ArvadosFileBase(object): 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()