X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/a3222e35cda68c8e48a17921c33ac37ecb5c3bac..acc7d4a40ae78e866c983624ec36b7bae3b918a9:/sdk/python/arvados/stream.py diff --git a/sdk/python/arvados/stream.py b/sdk/python/arvados/stream.py index 7a29100a39..3a42aa0101 100644 --- a/sdk/python/arvados/stream.py +++ b/sdk/python/arvados/stream.py @@ -1,227 +1,41 @@ -import gflags -import httplib -import httplib2 +import collections +import hashlib import os -import pprint -import sys -import types -import subprocess -import json -import UserDict import re -import hashlib -import string -import bz2 -import zlib -import fcntl -import time import threading -import collections +import functools +import copy +from ._ranges import locators_and_ranges, Range +from .arvfile import StreamFileReader +from arvados.retry import retry_method 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, segments, name): - self._stream = stream - self.segments = segments - self._name = name - self._filepos = 0L - - def name(self): - return self._name - - def decompressed_name(self): - return re.sub('\.(bz2|gz)$', '', self._name) - - def stream_name(self): - return self._stream.name() - - def seek(self, pos): - self._filepos = min(max(pos, 0L), self.size()) - - def tell(self): - return self._filepos - - def size(self): - n = self.segments[-1] - return n[OFFSET] + n[BLOCKSIZE] - - def read(self, size): - """Read up to 'size' bytes from the stream, starting at the current file position""" - if size == 0: - return '' - - data = '' - for locator, blocksize, segmentoffset, segmentsize in locators_and_ranges(self.segments, self._filepos, size): - data += self._stream.readfrom(locator+segmentoffset, segmentsize) - self._filepos += len(data) - return data - - def readfrom(self, start, size): - """Read up to 'size' bytes from the stream, starting at 'start'""" - if size == 0: - return '' - - data = '' - for locator, blocksize, segmentoffset, segmentsize in locators_and_ranges(self.segments, start, size): - data += self._stream.readfrom(locator+segmentoffset, segmentsize) - return data - - def readall(self, size=2**20): - while True: - data = self.read(size) - if data == '': - break - yield data - - def decompress(self, decompress, size): - for segment in self.readall(size): - data = decompress(segment) - if data and data != '': - yield data - - def readall_decompressed(self, size=2**20): - self.seek(0) - if re.search('\.bz2$', self._name): - dc = bz2.BZ2Decompressor() - return self.decompress(lambda segment: dc.decompress(segment), size) - elif re.search('\.gz$', self._name): - dc = zlib.decompressobj(16+zlib.MAX_WBITS) - return self.decompress(lambda segment: dc.decompress(dc.unconsumed_tail + segment), size) - else: - return self.readall(size) - - def readlines(self, decompress=True): - if decompress: - datasource = self.readall_decompressed() - else: - datasource = self.readall() - data = '' - for newdata in datasource: - data += newdata - sol = 0 - while True: - eol = string.find(data, "\n", sol) - if eol < 0: - break - yield data[sol:eol+1] - sol = eol+1 - data = data[sol:] - if data != '': - yield data - - def as_manifest(self): - manifest_text = ['.'] - manifest_text.extend([d[LOCATOR] for d in self._stream._data_locators]) - manifest_text.extend(["{}:{}:{}".format(seg[LOCATOR], seg[BLOCKSIZE], self.name().replace(' ', '\\040')) for seg in self.segments]) - return arvados.CollectionReader(' '.join(manifest_text) + '\n').manifest_text() +from _normalize_stream import normalize_stream class StreamReader(object): - def __init__(self, tokens, keep=None, debug=False, _empty=False): + def __init__(self, tokens, keep=None, debug=False, _empty=False, + num_retries=0): self._stream_name = None self._data_locators = [] self._files = collections.OrderedDict() - - if keep != None: - self._keep = keep - else: - self._keep = Keep.global_client_object() + self._keep = keep + self.num_retries = num_retries streamoffset = 0L # parse stream for tok in tokens: if debug: print 'tok', tok - if self._stream_name == None: + if self._stream_name is None: self._stream_name = tok.replace('\\040', ' ') continue s = re.match(r'^[0-9a-f]{32}\+(\d+)(\+\S+)*$', tok) if s: blocksize = long(s.group(1)) - self._data_locators.append([tok, blocksize, streamoffset]) + self._data_locators.append(Range(tok, streamoffset, blocksize)) streamoffset += blocksize continue @@ -231,10 +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: - n = self._files[name] - n.segments.append([pos, size, n.size()]) + filereader = self._files[name] + filereader.segments.append(Range(pos, filereader.size(), size)) continue raise errors.SyntaxError("Invalid manifest format") @@ -250,29 +64,36 @@ class StreamReader(object): def size(self): n = self._data_locators[-1] - return n[OFFSET] + n[BLOCKSIZE] + 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) - def readfrom(self, start, size): + @retry_method + def _keepget(self, locator, num_retries=None): + return self._keep.get(locator, 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 '' - 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 + if self._keep is None: + self._keep = KeepClient(num_retries=self.num_retries) + data = [] + 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'