X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/d84737275793fcab0ac253c4abe734ad5e84ea12..90fc79852a995fd8e665cf48ae20c49a9bbc78eb:/sdk/python/arvados/stream.py diff --git a/sdk/python/arvados/stream.py b/sdk/python/arvados/stream.py index 8570b97c7c..e13e1a6eff 100644 --- a/sdk/python/arvados/stream.py +++ b/sdk/python/arvados/stream.py @@ -1,7 +1,6 @@ import gflags import httplib import httplib2 -import logging import os import pprint import sys @@ -17,16 +16,98 @@ import zlib import fcntl import time import threading +import collections from keep import * +import config +import errors + +LOCATOR = 0 +BLOCKSIZE = 1 +OFFSET = 2 +SEGMENTSIZE = 3 + +def locators_and_ranges(data_locators, range_start, range_size, debug=False): + ''' + Get blocks that are covered by the range + data_locators: list of [locator, block_size, block_start], assumes that blocks are in order and contigous + range_start: start of range + range_size: size of range + returns list of [block locator, blocksize, segment offset, segment size] that satisfies the range + ''' + if range_size == 0: + return [] + resp = [] + range_start = long(range_start) + range_size = long(range_size) + range_end = range_start + range_size + block_start = 0L + + # range_start/block_start is the inclusive lower bound + # range_end/block_end is the exclusive upper bound + + hi = len(data_locators) + lo = 0 + i = int((hi + lo) / 2) + block_size = data_locators[i][BLOCKSIZE] + block_start = data_locators[i][OFFSET] + block_end = block_start + block_size + if debug: print '---' + + # perform a binary search for the first block + # assumes that all of the blocks are contigious, so range_start is guaranteed + # to either fall into the range of a block or be outside the block range entirely + while not (range_start >= block_start and range_start < block_end): + if lo == i: + # must be out of range, fail + return [] + if range_start > block_start: + lo = i + else: + hi = i + i = int((hi + lo) / 2) + if debug: print lo, i, hi + block_size = data_locators[i][BLOCKSIZE] + block_start = data_locators[i][OFFSET] + block_end = block_start + block_size + + while i < len(data_locators): + locator, block_size, block_start = data_locators[i] + block_end = block_start + block_size + if debug: + print locator, "range_start", range_start, "block_start", block_start, "range_end", range_end, "block_end", block_end + if range_end <= block_start: + # range ends before this block starts, so don't look at any more locators + break + + #if range_start >= block_end: + # range starts after this block ends, so go to next block + # we should always start at the first block due to the binary above, so this test is redundant + #next + + if range_start >= block_start and range_end <= block_end: + # range starts and ends in this block + resp.append([locator, block_size, range_start - block_start, range_size]) + elif range_start >= block_start and range_end > block_end: + # range starts in this block + resp.append([locator, block_size, range_start - block_start, block_end - range_start]) + elif range_start < block_start and range_end > block_end: + # range starts in a previous block and extends to further blocks + resp.append([locator, block_size, 0L, block_size]) + elif range_start < block_start and range_end <= block_end: + # range starts in a previous block and ends in this block + resp.append([locator, block_size, 0L, range_end - block_start]) + block_start = block_end + i += 1 + return resp + class StreamFileReader(object): - def __init__(self, stream, pos, size, name): + def __init__(self, stream, segments, name): self._stream = stream - self._pos = pos - self._size = size + self.segments = segments self._name = name - self._filepos = 0 + self._filepos = 0L def name(self): return self._name @@ -34,45 +115,64 @@ class StreamFileReader(object): def decompressed_name(self): return re.sub('\.(bz2|gz)$', '', self._name) - def size(self): - return self._size - def stream_name(self): return self._stream.name() - def read(self, size, **kwargs): - self._stream.seek(self._pos + self._filepos) - data = self._stream.read(min(size, self._size - self._filepos)) + def seek(self, pos): + self._filepos = min(max(pos, 0L), self.size()) + + def tell(self): + return self._filepos + + def size(self): + n = self.segments[-1] + return n[OFFSET] + n[BLOCKSIZE] + + def read(self, size): + """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: + locator, blocksize, segmentoffset, segmentsize = available_chunks[0] + data = self._stream.readfrom(locator+segmentoffset, segmentsize) + self._filepos += len(data) return data - def readall(self, size=2**20, **kwargs): + def readfrom(self, start, size): + """Read up to 'size' bytes from the stream, starting at 'start'""" + if size == 0: + return '' + + data = '' + for locator, blocksize, segmentoffset, segmentsize in locators_and_ranges(self.segments, start, size): + data += self._stream.readfrom(locator+segmentoffset, segmentsize) + return data + + def readall(self, size=2**20): while True: - data = self.read(size, **kwargs) + data = self.read(size) if data == '': break yield data - def bunzip2(self, size): - decompressor = bz2.BZ2Decompressor() - for chunk in self.readall(size): - data = decompressor.decompress(chunk) - if data and data != '': - yield data - - def gunzip(self, size): - decompressor = zlib.decompressobj(16+zlib.MAX_WBITS) - for chunk in self.readall(size): - data = decompressor.decompress(decompressor.unconsumed_tail + chunk) + def decompress(self, decompress, size): + for segment in self.readall(size): + data = decompress(segment) if data and data != '': yield data def readall_decompressed(self, size=2**20): - self._stream.seek(self._pos + self._filepos) + self.seek(0) if re.search('\.bz2$', self._name): - return self.bunzip2(size) + dc = bz2.BZ2Decompressor() + return self.decompress(lambda segment: dc.decompress(segment), size) elif re.search('\.gz$', self._name): - return self.gunzip(size) + dc = zlib.decompressobj(16+zlib.MAX_WBITS) + return self.decompress(lambda segment: dc.decompress(dc.unconsumed_tail + segment), size) else: return self.readall(size) @@ -80,7 +180,6 @@ class StreamFileReader(object): if decompress: datasource = self.readall_decompressed() else: - self._stream.seek(self._pos + self._filepos) datasource = self.readall() data = '' for newdata in datasource: @@ -97,129 +196,85 @@ class StreamFileReader(object): yield data def as_manifest(self): - if self.size() == 0: - return ("%s %s 0:0:%s\n" - % (self._stream.name(), EMPTY_BLOCK_LOCATOR, self.name())) - return string.join(self._stream.tokens_for_range(self._pos, self._size), - " ") + "\n" + manifest_text = ['.'] + manifest_text.extend([d[LOCATOR] for d in self._stream._data_locators]) + manifest_text.extend(["{}:{}:{}".format(seg[LOCATOR], seg[BLOCKSIZE], self.name().replace(' ', '\\040')) for seg in self.segments]) + return arvados.CollectionReader(' '.join(manifest_text) + '\n').manifest_text() class StreamReader(object): - def __init__(self, tokens): - self._tokens = tokens - self._current_datablock_data = None - self._current_datablock_pos = 0 - self._current_datablock_index = -1 - self._pos = 0 - + def __init__(self, tokens, keep=None, debug=False, _empty=False): self._stream_name = None - self.data_locators = [] - self.files = [] + self._data_locators = [] + self._files = collections.OrderedDict() - for tok in self._tokens: + if keep is None: + keep = KeepClient() + self._keep = keep + + streamoffset = 0L + + # parse stream + for tok in tokens: + if debug: print 'tok', tok if self._stream_name == None: self._stream_name = tok.replace('\\040', ' ') - elif re.search(r'^[0-9a-f]{32}(\+\S+)*$', tok): - self.data_locators += [tok] - elif re.search(r'^\d+:\d+:\S+', tok): - pos, size, name = tok.split(':',2) - self.files += [[int(pos), int(size), name.replace('\\040', ' ')]] - else: - raise errors.SyntaxError("Invalid manifest format") - - def tokens(self): - return self._tokens - - def tokens_for_range(self, range_start, range_size): - resp = [self._stream_name] - return_all_tokens = False - block_start = 0 - token_bytes_skipped = 0 - for locator in self.data_locators: - sizehint = re.search(r'\+(\d+)', locator) - if not sizehint: - return_all_tokens = True - if return_all_tokens: - resp += [locator] - next - blocksize = int(sizehint.group(0)) - if range_start + range_size <= block_start: - break - if range_start < block_start + blocksize: - resp += [locator] - else: - token_bytes_skipped += blocksize - block_start += blocksize - for f in self.files: - if ((f[0] < range_start + range_size) - and - (f[0] + f[1] > range_start) - and - f[1] > 0): - resp += ["%d:%d:%s" % (f[0] - token_bytes_skipped, f[1], f[2])] - return resp + continue + + 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]) + streamoffset += blocksize + continue + + s = re.search(r'^(\d+):(\d+):(\S+)', tok) + if s: + pos = long(s.group(1)) + 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) + else: + n = self._files[name] + n.segments.append([pos, size, n.size()]) + continue + + raise errors.SyntaxError("Invalid manifest format") def name(self): return self._stream_name + def files(self): + return self._files + def all_files(self): - for f in self.files: - pos, size, name = f - yield StreamFileReader(self, pos, size, name) - - def nextdatablock(self): - if self._current_datablock_index < 0: - self._current_datablock_pos = 0 - self._current_datablock_index = 0 - else: - self._current_datablock_pos += self.current_datablock_size() - self._current_datablock_index += 1 - self._current_datablock_data = None - - def current_datablock_data(self): - if self._current_datablock_data == None: - self._current_datablock_data = Keep.get(self.data_locators[self._current_datablock_index]) - return self._current_datablock_data - - def current_datablock_size(self): - if self._current_datablock_index < 0: - self.nextdatablock() - sizehint = re.search('\+(\d+)', self.data_locators[self._current_datablock_index]) - if sizehint: - return int(sizehint.group(0)) - return len(self.current_datablock_data()) + return self._files.values() - def seek(self, pos): - """Set the position of the next read operation.""" - self._pos = pos - - def really_seek(self): - """Find and load the appropriate data block, so the byte at - _pos is in memory. - """ - if self._pos == self._current_datablock_pos: - return True - if (self._current_datablock_pos != None and - self._pos >= self._current_datablock_pos and - self._pos <= self._current_datablock_pos + self.current_datablock_size()): - return True - if self._pos < self._current_datablock_pos: - self._current_datablock_index = -1 - self.nextdatablock() - while (self._pos > self._current_datablock_pos and - self._pos > self._current_datablock_pos + self.current_datablock_size()): - self.nextdatablock() + def size(self): + n = self._data_locators[-1] + return n[OFFSET] + n[BLOCKSIZE] - def read(self, size): - """Read no more than size bytes -- but at least one byte, - unless _pos is already at the end of the stream. - """ + def locators_and_ranges(self, range_start, range_size): + return locators_and_ranges(self._data_locators, range_start, range_size) + + def readfrom(self, start, size): + """Read up to 'size' bytes from the stream, starting at 'start'""" if size == 0: return '' - self.really_seek() - while self._pos >= self._current_datablock_pos + self.current_datablock_size(): - self.nextdatablock() - if self._current_datablock_index >= len(self.data_locators): - return None - data = self.current_datablock_data()[self._pos - self._current_datablock_pos : self._pos - self._current_datablock_pos + size] - self._pos += len(data) + data = '' + for locator, blocksize, segmentoffset, segmentsize in locators_and_ranges(self._data_locators, start, size): + data += self._keep.get(locator)[segmentoffset:segmentoffset+segmentsize] return 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]) + 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')) + for seg in f.segments]) + for f in self._files.values()]) + return ' '.join(manifest_text) + '\n'