-import bz2
+from __future__ import print_function
+from __future__ import absolute_import
+from future.utils import listvalues
+from builtins import object
import collections
import hashlib
import os
import re
-import zlib
import threading
import functools
+import copy
-from .arvfile import ArvadosFileBase
+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 first_block(data_locators, range_start, range_size, debug=False):
- 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 None
- 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
-
- return i
-
-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
-
- i = first_block(data_locators, range_start, range_size, debug)
- if i is None:
- return []
-
- 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
-
-def replace_range(data_locators, range_start, range_size, new_locator, debug=False):
- '''
- Replace a range with a new block.
- 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
- new_locator: locator for new block to be inserted
- !!! data_locators will be updated in place !!!
- '''
- if range_size == 0:
- return
-
- range_start = long(range_start)
- range_size = long(range_size)
- range_end = range_start + range_size
-
- last = data_locators[-1]
- if (last[OFFSET]+last[BLOCKSIZE]) == range_start:
- # append new block
- data_locators.append([new_locator, range_size, range_start])
- return
-
- i = first_block(data_locators, range_start, range_size, debug)
- if i is None:
- return
-
- 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
- # split block into 3 pieces
- #resp.append([locator, block_size, range_start - block_start, range_size])
- pass
- elif range_start >= block_start and range_end > block_end:
- # range starts in this block
- # split block into 2 pieces
- #resp.append([locator, block_size, range_start - block_start, block_end - range_start])
- pass
- elif range_start < block_start and range_end > block_end:
- # range starts in a previous block and extends to further blocks
- # zero out this block
- #resp.append([locator, block_size, 0L, block_size])
- pass
- elif range_start < block_start and range_end <= block_end:
- # range starts in a previous block and ends in this block
- # split into 2 pieces
- #resp.append([locator, block_size, 0L, range_end - block_start])
- pass
- block_start = block_end
- i += 1
-
-
-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 StreamFileReader(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, stream, segments, name):
- super(StreamFileReader, self).__init__(self._NameAttribute(name), 'rb')
- self._stream = stream
- self.segments = segments
- self._filepos = 0L
- self.num_retries = stream.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)
-
- def stream_name(self):
- return self._stream.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
-
- def _size(self):
- n = self.segments[-1]
- return n[OFFSET] + n[BLOCKSIZE]
-
- def size(self):
- return self._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:
- locator, blocksize, segmentoffset, segmentsize = available_chunks[0]
- data = self._stream._readfrom(locator+segmentoffset, segmentsize,
- 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 locator, blocksize, segmentoffset, segmentsize in locators_and_ranges(self.segments, start, size):
- data.append(self._stream._readfrom(locator+segmentoffset, segmentsize,
- num_retries=num_retries))
- return ''.join(data)
-
- @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)
-
- 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(normalize=True)
-
+from arvados.keep import *
+from . import config
+from . import errors
+from ._normalize_stream import normalize_stream
class StreamReader(object):
def __init__(self, tokens, keep=None, debug=False, _empty=False,
self._keep = keep
self.num_retries = num_retries
- streamoffset = 0L
+ streamoffset = 0
# parse stream
for tok in tokens:
- if debug: print 'tok', tok
+ if debug: print('tok', tok)
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])
+ blocksize = int(s.group(1))
+ self._data_locators.append(Range(tok, streamoffset, blocksize, 0))
streamoffset += blocksize
continue
s = re.search(r'^(\d+):(\d+):(\S+)', tok)
if s:
- pos = long(s.group(1))
- size = long(s.group(2))
+ pos = int(s.group(1))
+ size = int(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, 0)], 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")
return self._files
def all_files(self):
- return self._files.values()
-
- def _size(self):
- n = self._data_locators[-1]
- return n[OFFSET] + n[BLOCKSIZE]
+ return listvalues(self._files)
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)
+ @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):
- self._readfrom(start, size, num_retries=num_retries)
-
- def _readfrom(self, start, size, num_retries=None):
"""Read up to 'size' bytes from the stream, starting at 'start'"""
if size == 0:
- return ''
+ return b''
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])
- return ''.join(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 b''.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()])
+ for f in listvalues(self._files)])
return ' '.join(manifest_text) + '\n'
-
-class BufferBlock(object):
- def __init__(self, locator, streamoffset):
- self.locator = locator
- self.buffer_block = bytearray(config.KEEP_BLOCK_SIZE)
- self.buffer_view = memoryview(self.buffer_block)
- self.write_pointer = 0
- self.locator_list_entry = [locator, 0, streamoffset]
-
- def append(self, data):
- 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 ['name', 'files', 'all_files', 'size', 'locators_and_ranges', 'readfrom', 'manifest_text']:
- locals()[_method_name] = _proxy_method(_method_name)
-
- 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 _append(self, data):
- if self.current_bblock is None:
- last = self._data_locators[-1]
- streamoffset = last[OFFSET] + last[BLOCKSIZE]
- 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)
- self.current_bblock.append(data)
-
- def append(self, data):
- with self.mutex:
- self._append(data)
-
-class StreamFileWriter(StreamFileReader):
- def __init__(self, stream, segments, name):
- super(StreamFileWriter, self).__init__(stream, segments, name)
- self.mode = 'wb'
-
- # wrap superclass methods in mutex
- def _proxy_method(name):
- method = getattr(StreamFileReader, name)
- @functools.wraps(method, ('__name__', '__doc__'))
- def wrapper(self, *args, **kwargs):
- with self._stream.mutex:
- return method(self, *args, **kwargs)
- return wrapper
-
- for _method_name in ['__iter__', 'seek', 'tell', 'size', 'read', 'readfrom', 'readall', 'readline', 'decompress', 'readall_decompressed', 'readlines', 'as_manifest']:
- locals()[_method_name] = _proxy_method(_method_name)
-
- def truncate(self, size=None):
- with self._stream.mutex:
- if size is None:
- size = self._filepos
-
- segs = locators_and_ranges(self.segments, 0, size)
-
- newstream = []
- self.segments = []
- streamoffset = 0L
- fileoffset = 0L
-
- for seg in segs:
- for locator, blocksize, segmentoffset, segmentsize in locators_and_ranges(self._stream._data_locators, seg[LOCATOR]+seg[OFFSET], seg[SEGMENTSIZE]):
- newstream.append([locator, blocksize, streamoffset])
- self.segments.append([streamoffset+segmentoffset, segmentsize, fileoffset])
- streamoffset += blocksize
- fileoffset += segmentsize
- if len(newstream) == 0:
- newstream.append(config.EMPTY_BLOCK_LOCATOR)
- self.segments.append([0, 0, 0])
- self._stream._data_locators = newstream
- if self._filepos > fileoffset:
- self._filepos = fileoffset
-
- def _writeto(self, offset, data):
- self._stream._append(data)
- replace_range(self.segments, self._filepos, len(data), self._stream._size()-len(data))
- self._filepos += len(data)
-
- def writeto(self, offset, data):
- with self._stream.mutex:
- self._writeto(offset, data)
-
- def write(self, data):
- with self._stream.mutex:
- self._writeto(self._filepos, data)
- self._filepos += len(data)
-
- def writelines(self, seq):
- with self._stream.mutex:
- for s in seq:
- self._writeto(self._filepos, s)
- self._filepos += len(s)
-
- def flush(self):
- pass