X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/cc946c07eade09974423955f8d4b080941f53c7b..acc7d4a40ae78e866c983624ec36b7bae3b918a9:/sdk/python/arvados/stream.py diff --git a/sdk/python/arvados/stream.py b/sdk/python/arvados/stream.py index bbbbb9513e..3a42aa0101 100644 --- a/sdk/python/arvados/stream.py +++ b/sdk/python/arvados/stream.py @@ -6,56 +6,13 @@ import threading import functools import copy -from .ranges import * -from .arvfile import ArvadosFileBase, StreamFileReader, StreamFileWriter +from ._ranges import locators_and_ranges, Range +from .arvfile import StreamFileReader from arvados.retry import retry_method from keep import * import config import errors - -def normalize_stream(s, stream): - ''' - s is the stream name - stream is a StreamReader object - ''' - stream_tokens = [s] - sortedfiles = list(stream.keys()) - sortedfiles.sort() - - blocks = {} - streamoffset = 0L - for f in sortedfiles: - for b in stream[f]: - if b[arvados.LOCATOR] not in blocks: - stream_tokens.append(b[arvados.LOCATOR]) - blocks[b[arvados.LOCATOR]] = streamoffset - streamoffset += b[arvados.BLOCKSIZE] - - if len(stream_tokens) == 1: - stream_tokens.append(config.EMPTY_BLOCK_LOCATOR) - - for f in sortedfiles: - current_span = None - fout = f.replace(' ', '\\040') - for segment in stream[f]: - segmentoffset = blocks[segment[arvados.LOCATOR]] + segment[arvados.OFFSET] - if current_span is None: - current_span = [segmentoffset, segmentoffset + segment[arvados.SEGMENTSIZE]] - else: - if segmentoffset == current_span[1]: - current_span[1] += segment[arvados.SEGMENTSIZE] - else: - stream_tokens.append("{0}:{1}:{2}".format(current_span[0], current_span[1] - current_span[0], fout)) - current_span = [segmentoffset, segmentoffset + segment[arvados.SEGMENTSIZE]] - - if current_span is not None: - stream_tokens.append("{0}:{1}:{2}".format(current_span[0], current_span[1] - current_span[0], fout)) - - if not stream[f]: - stream_tokens.append("0:0:{0}".format(fout)) - - return stream_tokens - +from _normalize_stream import normalize_stream class StreamReader(object): def __init__(self, tokens, keep=None, debug=False, _empty=False, @@ -78,7 +35,7 @@ class StreamReader(object): s = re.match(r'^[0-9a-f]{32}\+(\d+)(\+\S+)*$', tok) if s: blocksize = long(s.group(1)) - self._data_locators.append([tok, blocksize, streamoffset]) + self._data_locators.append(Range(tok, streamoffset, blocksize)) streamoffset += blocksize continue @@ -88,10 +45,10 @@ class StreamReader(object): size = long(s.group(2)) name = s.group(3).replace('\\040', ' ') if name not in self._files: - self._files[name] = StreamFileReader(self, [[pos, size, 0]], name) + self._files[name] = StreamFileReader(self, [Range(pos, 0, size)], name) else: filereader = self._files[name] - filereader.segments.append([pos, size, filereader.size()]) + filereader.segments.append(Range(pos, filereader.size(), size)) continue raise errors.SyntaxError("Invalid manifest format") @@ -105,12 +62,9 @@ class StreamReader(object): def all_files(self): return self._files.values() - def _size(self): - n = self._data_locators[-1] - return n[OFFSET] + n[BLOCKSIZE] - def size(self): - return self._size() + n = self._data_locators[-1] + return n.range_start + n.range_size def locators_and_ranges(self, range_start, range_size): return locators_and_ranges(self._data_locators, range_start, range_size) @@ -121,173 +75,25 @@ class StreamReader(object): @retry_method def readfrom(self, start, size, num_retries=None): - return self._readfrom(start, size, num_retries=num_retries) - - @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 '' if self._keep is None: self._keep = KeepClient(num_retries=self.num_retries) data = [] - for locator, blocksize, segmentoffset, segmentsize in locators_and_ranges(self._data_locators, start, size): - data.append(self._keepget(locator, num_retries=num_retries)[segmentoffset:segmentoffset+segmentsize]) + for lr in locators_and_ranges(self._data_locators, start, size): + data.append(self._keepget(lr.locator, num_retries=num_retries)[lr.segment_offset:lr.segment_offset+lr.segment_size]) return ''.join(data) def manifest_text(self, strip=False): manifest_text = [self.name().replace(' ', '\\040')] if strip: for d in self._data_locators: - m = re.match(r'^[0-9a-f]{32}\+\d+', d[LOCATOR]) + m = re.match(r'^[0-9a-f]{32}\+\d+', d.locator) manifest_text.append(m.group(0)) else: - manifest_text.extend([d[LOCATOR] for d in self._data_locators]) - manifest_text.extend([' '.join(["{}:{}:{}".format(seg[LOCATOR], seg[BLOCKSIZE], f.name.replace(' ', '\\040')) + manifest_text.extend([d.locator for d in self._data_locators]) + manifest_text.extend([' '.join(["{}:{}:{}".format(seg.locator, seg.range_size, f.name.replace(' ', '\\040')) for seg in f.segments]) for f in self._files.values()]) return ' '.join(manifest_text) + '\n' - - -class BufferBlock(object): - def __init__(self, locator, streamoffset, starting_size=2**16): - self.locator = locator - self.buffer_block = bytearray(starting_size) - self.buffer_view = memoryview(self.buffer_block) - self.write_pointer = 0 - self.locator_list_entry = [locator, 0, streamoffset] - - def append(self, data): - 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_list_entry[1] = self.write_pointer - - -class StreamWriter(StreamReader): - def __init__(self, tokens, keep=None, debug=False, _empty=False, - num_retries=0): - super(StreamWriter, self).__init__(tokens, keep, debug, _empty, num_retries) - - if len(self._files) != 1: - raise AssertionError("StreamWriter can only have one file at a time") - sr = self._files.popitem()[1] - self._files[sr.name] = StreamFileWriter(self, sr.segments, sr.name) - - self.mutex = threading.Lock() - self.current_bblock = None - self.bufferblocks = {} - - # wrap superclass methods in mutex - def _proxy_method(name): - method = getattr(StreamReader, name) - @functools.wraps(method, ('__name__', '__doc__')) - def wrapper(self, *args, **kwargs): - with self.mutex: - return method(self, *args, **kwargs) - return wrapper - - for _method_name in ['files', 'all_files', 'size', 'locators_and_ranges', 'readfrom', 'manifest_text']: - locals()[_method_name] = _proxy_method(_method_name) - - @retry_method - def _keepget(self, locator, num_retries=None): - if locator in self.bufferblocks: - bb = self.bufferblocks[locator] - return str(bb.buffer_block[0:bb.write_pointer]) - else: - return self._keep.get(locator, num_retries=num_retries) - - def _init_bufferblock(self): - last = self._data_locators[-1] - streamoffset = last[OFFSET] + last[BLOCKSIZE] - if last[BLOCKSIZE] == 0: - del self._data_locators[-1] - self.current_bblock = BufferBlock("bufferblock%i" % len(self.bufferblocks), streamoffset) - self.bufferblocks[self.current_bblock.locator] = self.current_bblock - self._data_locators.append(self.current_bblock.locator_list_entry) - - 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._files.values()[0].segments - - bufferblock_segs = [] - i = 0 - tmp_segs = copy.copy(segs) - while i < len(tmp_segs): - # Go through each segment and identify segments that include the buffer block - s = tmp_segs[i] - if s[LOCATOR] < self.current_bblock.locator_list_entry[OFFSET] and (s[LOCATOR] + s[BLOCKSIZE]) > self.current_bblock.locator_list_entry[OFFSET]: - # The segment straddles the previous block and the current buffer block. Split the segment. - b1 = self.current_bblock.locator_list_entry[OFFSET] - s[LOCATOR] - b2 = (s[LOCATOR] + s[BLOCKSIZE]) - self.current_bblock.locator_list_entry[OFFSET] - bb_seg = [self.current_bblock.locator_list_entry[OFFSET], b2, s[OFFSET]+b1] - tmp_segs[i] = [s[LOCATOR], b1, s[OFFSET]] - tmp_segs.insert(i+1, bb_seg) - bufferblock_segs.append(bb_seg) - i += 1 - elif s[LOCATOR] >= self.current_bblock.locator_list_entry[OFFSET]: - # The segment's data is in the buffer block. - bufferblock_segs.append(s) - i += 1 - - # Now sum up the segments to get the total bytes - # of the file referencing into the buffer block. - write_total = sum([s[BLOCKSIZE] for s in bufferblock_segs]) - - if write_total < self.current_bblock.locator_list_entry[BLOCKSIZE]: - # 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 = BufferBlock(self.current_bblock.locator, - self.current_bblock.locator_list_entry[OFFSET], - starting_size=write_total) - for t in bufferblock_segs: - t_start = t[LOCATOR] - self.current_bblock.locator_list_entry[OFFSET] - t_end = t_start + t[BLOCKSIZE] - t[0] = self.current_bblock.locator_list_entry[OFFSET] + new_bb.write_pointer - new_bb.append(self.current_bblock.buffer_block[t_start:t_end]) - - self.current_bblock = new_bb - self.bufferblocks[self.current_bblock.locator] = self.current_bblock - self._data_locators[-1] = self.current_bblock.locator_list_entry - self._files.values()[0].segments = tmp_segs - - def _commit(self): - # commit buffer block - - # TODO: do 'put' in the background? - pdh = self._keep.put(self.current_bblock.buffer_block[0:self.current_bblock.write_pointer]) - self._data_locators[-1][0] = pdh - self.current_bblock = None - - def commit(self): - with self.mutex: - self._repack_writes() - self._commit() - - def _append(self, data): - if len(data) > config.KEEP_BLOCK_SIZE: - raise ArgumentError("Please append data chunks smaller than config.KEEP_BLOCK_SIZE") - - if self.current_bblock is None: - self._init_bufferblock() - - if (self.current_bblock.write_pointer + len(data)) > config.KEEP_BLOCK_SIZE: - self._repack_writes() - if (self.current_bblock.write_pointer + len(data)) > config.KEEP_BLOCK_SIZE: - self._commit() - self._init_bufferblock() - - self.current_bblock.append(data) - - def append(self, data): - with self.mutex: - self._append(data)