6 from arvados.retry import retry_method
14 """split(path) -> streamname, filename
16 Separate the stream name and file name in a /-separated stream path.
17 If no stream name is available, assume '.'.
20 stream_name, file_name = path.rsplit('/', 1)
21 except ValueError: # No / in string
22 stream_name, file_name = '.', path
23 return stream_name, file_name
25 class ArvadosFileBase(object):
26 def __init__(self, name, mode):
32 def _before_close(orig_func):
33 @functools.wraps(orig_func)
34 def wrapper(self, *args, **kwargs):
36 raise ValueError("I/O operation on closed stream file")
37 return orig_func(self, *args, **kwargs)
43 def __exit__(self, exc_type, exc_value, traceback):
54 class ArvadosFileReaderBase(ArvadosFileBase):
55 class _NameAttribute(str):
56 # The Python file API provides a plain .name attribute.
57 # Older SDK provided a name() method.
58 # This class provides both, for maximum compatibility.
62 def __init__(self, name, mode, num_retries=None):
63 super(ArvadosFileReaderBase, self).__init__(self._NameAttribute(name), mode)
65 self.num_retries = num_retries
66 self._readline_cache = (None, None)
70 data = self.readline()
75 def decompressed_name(self):
76 return re.sub('\.(bz2|gz)$', '', self.name)
78 @ArvadosFileBase._before_close
79 def seek(self, pos, whence=os.SEEK_CUR):
80 if whence == os.SEEK_CUR:
82 elif whence == os.SEEK_END:
84 self._filepos = min(max(pos, 0L), self.size())
89 @ArvadosFileBase._before_close
91 def readall(self, size=2**20, num_retries=None):
93 data = self.read(size, num_retries=num_retries)
98 @ArvadosFileBase._before_close
100 def readline(self, size=float('inf'), num_retries=None):
101 cache_pos, cache_data = self._readline_cache
102 if self.tell() == cache_pos:
106 data_size = len(data[-1])
107 while (data_size < size) and ('\n' not in data[-1]):
108 next_read = self.read(2 ** 20, num_retries=num_retries)
111 data.append(next_read)
112 data_size += len(next_read)
115 nextline_index = data.index('\n') + 1
117 nextline_index = len(data)
118 nextline_index = min(nextline_index, size)
119 self._readline_cache = (self.tell(), data[nextline_index:])
120 return data[:nextline_index]
122 @ArvadosFileBase._before_close
124 def decompress(self, decompress, size, num_retries=None):
125 for segment in self.readall(size, num_retries):
126 data = decompress(segment)
130 @ArvadosFileBase._before_close
132 def readall_decompressed(self, size=2**20, num_retries=None):
134 if self.name.endswith('.bz2'):
135 dc = bz2.BZ2Decompressor()
136 return self.decompress(dc.decompress, size,
137 num_retries=num_retries)
138 elif self.name.endswith('.gz'):
139 dc = zlib.decompressobj(16+zlib.MAX_WBITS)
140 return self.decompress(lambda segment: dc.decompress(dc.unconsumed_tail + segment),
141 size, num_retries=num_retries)
143 return self.readall(size, num_retries=num_retries)
145 @ArvadosFileBase._before_close
147 def readlines(self, sizehint=float('inf'), num_retries=None):
150 for s in self.readall(num_retries=num_retries):
153 if data_size >= sizehint:
155 return ''.join(data).splitlines(True)
158 class StreamFileReader(ArvadosFileReaderBase):
159 def __init__(self, stream, segments, name):
160 super(StreamFileReader, self).__init__(name, 'rb', num_retries=stream.num_retries)
161 self._stream = stream
162 self.segments = segments
164 def stream_name(self):
165 return self._stream.name()
168 n = self.segments[-1]
169 return n.range_start + n.range_size
171 @ArvadosFileBase._before_close
173 def read(self, size, num_retries=None):
174 """Read up to 'size' bytes from the stream, starting at the current file position"""
179 available_chunks = locators_and_ranges(self.segments, self._filepos, size)
181 lr = available_chunks[0]
182 data = self._stream._readfrom(lr.locator+lr.segment_offset,
184 num_retries=num_retries)
186 self._filepos += len(data)
189 @ArvadosFileBase._before_close
191 def readfrom(self, start, size, num_retries=None):
192 """Read up to 'size' bytes from the stream, starting at 'start'"""
197 for lr in locators_and_ranges(self.segments, start, size):
198 data.append(self._stream._readfrom(lr.locator+lr.segment_offset, lr.segment_size,
199 num_retries=num_retries))
202 def as_manifest(self):
203 from stream import normalize_stream
205 for r in self.segments:
206 segs.extend(self._stream.locators_and_ranges(r.locator, r.range_size))
207 return " ".join(normalize_stream(".", {self.name: segs})) + "\n"
210 class BufferBlock(object):
215 def __init__(self, blockid, starting_size):
216 self.blockid = blockid
217 self.buffer_block = bytearray(starting_size)
218 self.buffer_view = memoryview(self.buffer_block)
219 self.write_pointer = 0
220 self.state = BufferBlock.WRITABLE
223 def append(self, data):
224 if self.state == BufferBlock.WRITABLE:
225 while (self.write_pointer+len(data)) > len(self.buffer_block):
226 new_buffer_block = bytearray(len(self.buffer_block) * 2)
227 new_buffer_block[0:self.write_pointer] = self.buffer_block[0:self.write_pointer]
228 self.buffer_block = new_buffer_block
229 self.buffer_view = memoryview(self.buffer_block)
230 self.buffer_view[self.write_pointer:self.write_pointer+len(data)] = data
231 self.write_pointer += len(data)
234 raise AssertionError("Buffer block is not writable")
237 return self.write_pointer
240 if self._locator is None:
241 self._locator = "%s+%i" % (hashlib.md5(self.buffer_view[0:self.write_pointer]).hexdigest(), self.size())
244 class AsyncKeepWriteErrors(Exception):
245 def __init__(self, errors):
249 return "\n".join(self.errors)
251 class BlockManager(object):
252 def __init__(self, keep):
254 self._bufferblocks = {}
255 self._put_queue = None
256 self._put_errors = None
257 self._put_threads = None
258 self._prefetch_queue = None
259 self._prefetch_threads = None
261 def alloc_bufferblock(self, blockid=None, starting_size=2**14):
263 blockid = "bufferblock%i" % len(self._bufferblocks)
264 bb = BufferBlock(blockid, starting_size=starting_size)
265 self._bufferblocks[bb.blockid] = bb
268 def stop_threads(self):
269 if self._put_threads is not None:
270 for t in self._put_threads:
271 self._put_queue.put(None)
272 for t in self._put_threads:
274 self._put_threads = None
275 self._put_queue = None
276 self._put_errors = None
278 if self._prefetch_threads is not None:
279 for t in self._prefetch_threads:
280 self._prefetch_queue.put(None)
281 for t in self._prefetch_threads:
283 self._prefetch_threads = None
284 self._prefetch_queue = None
286 def commit_bufferblock(self, block):
290 b = self._put_queue.get()
293 b._locator = self._keep.put(b.buffer_view[0:b.write_pointer].tobytes())
294 b.state = BufferBlock.COMMITTED
296 b.buffer_block = None
297 except Exception as e:
299 self._put_errors.put(e)
301 if self._put_queue is not None:
302 self._put_queue.task_done()
304 if self._put_threads is None:
305 self._put_queue = Queue.Queue(maxsize=2)
306 self._put_errors = Queue.Queue()
307 self._put_threads = [threading.Thread(target=worker, args=(self,)), threading.Thread(target=worker, args=(self,))]
308 for t in self._put_threads:
311 block.state = BufferBlock.PENDING
312 self._put_queue.put(block)
314 def get_block(self, locator, num_retries):
315 if locator in self._bufferblocks:
316 bb = self._bufferblocks[locator]
317 if bb.state != BufferBlock.COMMITTED:
318 return bb.buffer_view[0:bb.write_pointer].tobytes()
320 locator = bb._locator
321 return self._keep.get(locator, num_retries=num_retries)
323 def commit_all(self):
324 for k,v in self._bufferblocks.items():
325 if v.state == BufferBlock.WRITABLE:
326 self.commit_bufferblock(v)
327 if self._put_queue is not None:
328 self._put_queue.join()
329 if not self._put_errors.empty():
333 e.append(self._put_errors.get(False))
336 raise AsyncKeepWriteErrors(e)
338 def block_prefetch(self, locator):
342 b = self._prefetch_queue.get()
349 if locator in self._bufferblocks:
351 if self._prefetch_threads is None:
352 self._prefetch_queue = Queue.Queue()
353 self._prefetch_threads = [threading.Thread(target=worker, args=(self,)),
354 threading.Thread(target=worker, args=(self,))]
355 self._prefetch_threads[0].start()
356 self._prefetch_threads[1].start()
357 self._prefetch_queue.put(locator)
359 class ArvadosFile(object):
360 def __init__(self, parent, stream=[], segments=[]):
362 stream: a list of Range objects representing a block stream
363 segments: a list of Range objects representing segments
366 self._modified = True
369 self.add_segment(stream, s.range_start, s.range_size)
370 self._current_bblock = None
372 def set_unmodified(self):
373 self._modified = False
376 return self._modified
378 def truncate(self, size):
380 for r in self.segments:
381 range_end = r.range_start+r.range_size
382 if r.range_start >= size:
383 # segment is past the trucate size, all done
385 elif size < range_end:
386 nr = Range(r.locator, r.range_start, size - r.range_start)
387 nr.segment_offset = r.segment_offset
393 self.segments = new_segs
394 self._modified = True
396 def readfrom(self, offset, size, num_retries):
397 if size == 0 or offset >= self.size():
401 for lr in locators_and_ranges(self.segments, offset, size + config.KEEP_BLOCK_SIZE):
402 self.parent._my_block_manager().block_prefetch(lr.locator)
404 for lr in locators_and_ranges(self.segments, offset, size):
405 # TODO: if data is empty, wait on block get, otherwise only
406 # get more data if the block is already in the cache.
407 data.append(self.parent._my_block_manager().get_block(lr.locator, num_retries=num_retries)[lr.segment_offset:lr.segment_offset+lr.segment_size])
410 def _repack_writes(self):
411 '''Test if the buffer block has more data than is referenced by actual segments
412 (this happens when a buffered write over-writes a file range written in
413 a previous buffered write). Re-pack the buffer block for efficiency
414 and to avoid leaking information.
418 # Sum up the segments to get the total bytes of the file referencing
419 # into the buffer block.
420 bufferblock_segs = [s for s in segs if s.locator == self._current_bblock.blockid]
421 write_total = sum([s.range_size for s in bufferblock_segs])
423 if write_total < self._current_bblock.size():
424 # There is more data in the buffer block than is actually accounted for by segments, so
425 # re-pack into a new buffer by copying over to a new buffer block.
426 new_bb = self.parent._my_block_manager().alloc_bufferblock(self._current_bblock.blockid, starting_size=write_total)
427 for t in bufferblock_segs:
428 new_bb.append(self._current_bblock.buffer_view[t.segment_offset:t.segment_offset+t.range_size].tobytes())
429 t.segment_offset = new_bb.size() - t.range_size
431 self._current_bblock = new_bb
433 def writeto(self, offset, data, num_retries):
437 if offset > self.size():
438 raise ArgumentError("Offset is past the end of the file")
440 if len(data) > config.KEEP_BLOCK_SIZE:
441 raise ArgumentError("Please append data in chunks smaller than %i bytes (config.KEEP_BLOCK_SIZE)" % (config.KEEP_BLOCK_SIZE))
443 self._modified = True
445 if self._current_bblock is None or self._current_bblock.state != BufferBlock.WRITABLE:
446 self._current_bblock = self.parent._my_block_manager().alloc_bufferblock()
448 if (self._current_bblock.size() + len(data)) > config.KEEP_BLOCK_SIZE:
449 self._repack_writes()
450 if (self._current_bblock.size() + len(data)) > config.KEEP_BLOCK_SIZE:
451 self.parent._my_block_manager().commit_bufferblock(self._current_bblock)
452 self._current_bblock = self.parent._my_block_manager().alloc_bufferblock()
454 self._current_bblock.append(data)
455 replace_range(self.segments, offset, len(data), self._current_bblock.blockid, self._current_bblock.write_pointer - len(data))
457 def add_segment(self, blocks, pos, size):
458 self._modified = True
459 for lr in locators_and_ranges(blocks, pos, size):
460 last = self.segments[-1] if self.segments else Range(0, 0, 0)
461 r = Range(lr.locator, last.range_start+last.range_size, lr.segment_size, lr.segment_offset)
462 self.segments.append(r)
466 n = self.segments[-1]
467 return n.range_start + n.range_size
472 class ArvadosFileReader(ArvadosFileReaderBase):
473 def __init__(self, arvadosfile, name, mode="r", num_retries=None):
474 super(ArvadosFileReader, self).__init__(name, mode, num_retries=num_retries)
475 self.arvadosfile = arvadosfile
478 return self.arvadosfile.size()
480 @ArvadosFileBase._before_close
482 def read(self, size, num_retries=None):
483 """Read up to 'size' bytes from the stream, starting at the current file position"""
484 data = self.arvadosfile.readfrom(self._filepos, size, num_retries=num_retries)
485 self._filepos += len(data)
488 @ArvadosFileBase._before_close
490 def readfrom(self, offset, size, num_retries=None):
491 """Read up to 'size' bytes from the stream, starting at the current file position"""
492 return self.arvadosfile.readfrom(offset, size, num_retries)
497 class ArvadosFileWriter(ArvadosFileReader):
498 def __init__(self, arvadosfile, name, mode, num_retries=None):
499 super(ArvadosFileWriter, self).__init__(arvadosfile, name, mode, num_retries=num_retries)
501 @ArvadosFileBase._before_close
503 def write(self, data, num_retries=None):
504 if self.mode[0] == "a":
505 self.arvadosfile.writeto(self.size(), data)
507 self.arvadosfile.writeto(self._filepos, data, num_retries)
508 self._filepos += len(data)
510 @ArvadosFileBase._before_close
512 def writelines(self, seq, num_retries=None):
516 def truncate(self, size=None):
519 self.arvadosfile.truncate(size)
520 if self._filepos > self.size():
521 self._filepos = self.size()