X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/5bb11227e0d7d37cc6cf574b5d5f289afd1a43b1..63b03a39adfd78961c5bbb6a3a2d02ccd8c92e4d:/sdk/python/arvados/arvfile.py?ds=sidebyside diff --git a/sdk/python/arvados/arvfile.py b/sdk/python/arvados/arvfile.py index 29db2cb996..f9f91cf51a 100644 --- a/sdk/python/arvados/arvfile.py +++ b/sdk/python/arvados/arvfile.py @@ -2,20 +2,25 @@ import functools import os import zlib import bz2 -from .ranges import * +from ._ranges import locators_and_ranges, replace_range, Range from arvados.retry import retry_method import config import hashlib -import hashlib import threading import Queue import copy +import errno +from .errors import KeepWriteError, AssertionError +from .keep import KeepLocator +from _normalize_stream import normalize_stream 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 '.'. + Separate the stream name and file name in a /-separated stream path and + return a tuple (stream_name, file_name). If no stream name is available, + assume '.'. + """ try: stream_name, file_name = path.rsplit('/', 1) @@ -23,7 +28,7 @@ def split(path): stream_name, file_name = '.', path return stream_name, file_name -class ArvadosFileBase(object): +class _FileLikeObjectBase(object): def __init__(self, name, mode): self.name = name self.mode = mode @@ -32,11 +37,11 @@ class ArvadosFileBase(object): @staticmethod def _before_close(orig_func): @functools.wraps(orig_func) - def wrapper(self, *args, **kwargs): + def before_close_wrapper(self, *args, **kwargs): if self.closed: raise ValueError("I/O operation on closed stream file") return orig_func(self, *args, **kwargs) - return wrapper + return before_close_wrapper def __enter__(self): return self @@ -52,16 +57,9 @@ class ArvadosFileBase(object): self.closed = True -class ArvadosFileReaderBase(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 - +class ArvadosFileReaderBase(_FileLikeObjectBase): def __init__(self, name, mode, num_retries=None): - super(ArvadosFileReaderBase, self).__init__(self._NameAttribute(name), mode) + super(ArvadosFileReaderBase, self).__init__(name, mode) self._filepos = 0L self.num_retries = num_retries self._readline_cache = (None, None) @@ -76,7 +74,7 @@ class ArvadosFileReaderBase(ArvadosFileBase): def decompressed_name(self): return re.sub('\.(bz2|gz)$', '', self.name) - @ArvadosFileBase._before_close + @_FileLikeObjectBase._before_close def seek(self, pos, whence=os.SEEK_CUR): if whence == os.SEEK_CUR: pos += self._filepos @@ -87,7 +85,7 @@ class ArvadosFileReaderBase(ArvadosFileBase): def tell(self): return self._filepos - @ArvadosFileBase._before_close + @_FileLikeObjectBase._before_close @retry_method def readall(self, size=2**20, num_retries=None): while True: @@ -96,7 +94,7 @@ class ArvadosFileReaderBase(ArvadosFileBase): break yield data - @ArvadosFileBase._before_close + @_FileLikeObjectBase._before_close @retry_method def readline(self, size=float('inf'), num_retries=None): cache_pos, cache_data = self._readline_cache @@ -120,7 +118,7 @@ class ArvadosFileReaderBase(ArvadosFileBase): self._readline_cache = (self.tell(), data[nextline_index:]) return data[:nextline_index] - @ArvadosFileBase._before_close + @_FileLikeObjectBase._before_close @retry_method def decompress(self, decompress, size, num_retries=None): for segment in self.readall(size, num_retries): @@ -128,7 +126,7 @@ class ArvadosFileReaderBase(ArvadosFileBase): if data: yield data - @ArvadosFileBase._before_close + @_FileLikeObjectBase._before_close @retry_method def readall_decompressed(self, size=2**20, num_retries=None): self.seek(0) @@ -143,7 +141,7 @@ class ArvadosFileReaderBase(ArvadosFileBase): else: return self.readall(size, num_retries=num_retries) - @ArvadosFileBase._before_close + @_FileLikeObjectBase._before_close @retry_method def readlines(self, sizehint=float('inf'), num_retries=None): data = [] @@ -166,8 +164,15 @@ class ArvadosFileReaderBase(ArvadosFileBase): class StreamFileReader(ArvadosFileReaderBase): + 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__(name, 'rb', num_retries=stream.num_retries) + super(StreamFileReader, self).__init__(self._NameAttribute(name), 'rb', num_retries=stream.num_retries) self._stream = stream self.segments = segments @@ -178,7 +183,7 @@ class StreamFileReader(ArvadosFileReaderBase): n = self.segments[-1] return n.range_start + n.range_size - @ArvadosFileBase._before_close + @_FileLikeObjectBase._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""" @@ -189,14 +194,14 @@ class StreamFileReader(ArvadosFileReaderBase): available_chunks = locators_and_ranges(self.segments, self._filepos, size) if available_chunks: lr = available_chunks[0] - data = self._stream._readfrom(lr.locator+lr.segment_offset, + data = self._stream.readfrom(lr.locator+lr.segment_offset, lr.segment_size, num_retries=num_retries) self._filepos += len(data) return data - @ArvadosFileBase._before_close + @_FileLikeObjectBase._before_close @retry_method def readfrom(self, start, size, num_retries=None): """Read up to 'size' bytes from the stream, starting at 'start'""" @@ -205,37 +210,44 @@ class StreamFileReader(ArvadosFileReaderBase): data = [] for lr in locators_and_ranges(self.segments, start, size): - data.append(self._stream._readfrom(lr.locator+lr.segment_offset, lr.segment_size, + data.append(self._stream.readfrom(lr.locator+lr.segment_offset, lr.segment_size, num_retries=num_retries)) return ''.join(data) def as_manifest(self): - from stream import normalize_stream segs = [] for r in self.segments: segs.extend(self._stream.locators_and_ranges(r.locator, r.range_size)) return " ".join(normalize_stream(".", {self.name: segs})) + "\n" -class BufferBlock(object): -""" -A BufferBlock is a stand-in for a Keep block that is in the process of being -written. Writers can append to it, get the size, and compute the Keep locator. +def synchronized(orig_func): + @functools.wraps(orig_func) + def synchronized_wrapper(self, *args, **kwargs): + with self.lock: + return orig_func(self, *args, **kwargs) + return synchronized_wrapper + +class _BufferBlock(object): + """A stand-in for a Keep block that is in the process of being written. + + Writers can append to it, get the size, and compute the Keep locator. + There are three valid states: -There are three valid states: + WRITABLE + Can append to block. -WRITABLE - Can append to block. + PENDING + Block is in the process of being uploaded to Keep, append is an error. -PENDING - Block is in the process of being uploaded to Keep, append is an error. + COMMITTED + The block has been written to Keep, its internal buffer has been + released, fetching the block will fetch it via keep client (since we + discarded the internal copy), and identifiers referring to the BufferBlock + can be replaced with the block locator. + + """ -COMMITTED - The block has been written to Keep, its internal buffer has been - released, fetching the block will fetch it via keep client (since we - discarded the internal copy), and identifiers referring to the BufferBlock - can be replaced with the block locator. -""" WRITABLE = 0 PENDING = 1 COMMITTED = 2 @@ -250,22 +262,26 @@ COMMITTED :owner: ArvadosFile that owns this block + """ self.blockid = blockid self.buffer_block = bytearray(starting_capacity) self.buffer_view = memoryview(self.buffer_block) self.write_pointer = 0 - self.state = BufferBlock.WRITABLE + self._state = _BufferBlock.WRITABLE self._locator = None self.owner = owner + self.lock = threading.Lock() + @synchronized def append(self, data): + """Append some data to the buffer. + + Only valid if the block is in WRITABLE state. Implements an expanding + buffer, doubling capacity as needed to accomdate all the data. + """ - Append some data to the buffer. Only valid if the block is in WRITABLE - state. Implements an expanding buffer, doubling capacity as needed to - accomdate all the data. - """ - if self.state == BufferBlock.WRITABLE: + if self._state == _BufferBlock.WRITABLE: 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] @@ -277,39 +293,70 @@ COMMITTED else: raise AssertionError("Buffer block is not writable") + @synchronized + def set_state(self, nextstate, loc=None): + if ((self._state == _BufferBlock.WRITABLE and nextstate == _BufferBlock.PENDING) or + (self._state == _BufferBlock.PENDING and nextstate == _BufferBlock.COMMITTED)): + self._state = nextstate + if self._state == _BufferBlock.COMMITTED: + self._locator = loc + self.buffer_view = None + self.buffer_block = None + else: + raise AssertionError("Invalid state change from %s to %s" % (self.state, state)) + + @synchronized + def state(self): + return self._state + def size(self): - """Amount of data written to the buffer""" + """The amount of data written to the buffer.""" return self.write_pointer + @synchronized def locator(self): """The Keep locator for this buffer's contents.""" if self._locator is None: self._locator = "%s+%i" % (hashlib.md5(self.buffer_view[0:self.write_pointer]).hexdigest(), self.size()) return self._locator + @synchronized + def clone(self, new_blockid, owner): + if self._state == _BufferBlock.COMMITTED: + raise AssertionError("Can only duplicate a writable or pending buffer block") + bufferblock = _BufferBlock(new_blockid, self.size(), owner) + bufferblock.append(self.buffer_view[0:self.size()]) + return bufferblock -class AsyncKeepWriteErrors(Exception): - """ - Roll up one or more Keep write exceptions (generated by background - threads) into a single one. - """ - def __init__(self, errors): - self.errors = errors - def __repr__(self): - return "\n".join(self.errors) +class NoopLock(object): + def __enter__(self): + return self + + def __exit__(self, exc_type, exc_value, traceback): + pass + + def acquire(self, blocking=False): + pass -def _synchronized(orig_func): + def release(self): + pass + +def must_be_writable(orig_func): @functools.wraps(orig_func) - def wrapper(self, *args, **kwargs): - with self.lock: - return orig_func(self, *args, **kwargs) - return wrapper + def must_be_writable_wrapper(self, *args, **kwargs): + if not self.writable(): + raise IOError((errno.EROFS, "Collection must be writable.")) + return orig_func(self, *args, **kwargs) + return must_be_writable_wrapper + + +class _BlockManager(object): + """BlockManager handles buffer blocks. + + Also handles background block uploads, and background block prefetch for a + Collection of ArvadosFiles. -class BlockManager(object): - """ - BlockManager handles buffer blocks, background block uploads, and - background block prefetch for a Collection of ArvadosFiles. """ def __init__(self, keep): """keep: KeepClient object to use""" @@ -321,11 +368,13 @@ class BlockManager(object): self._prefetch_queue = None self._prefetch_threads = None self.lock = threading.Lock() + self.prefetch_enabled = True + self.num_put_threads = 2 + self.num_get_threads = 2 - @_synchronized + @synchronized def alloc_bufferblock(self, blockid=None, starting_capacity=2**14, owner=None): - """ - Allocate a new, empty bufferblock in WRITABLE state and return it. + """Allocate a new, empty bufferblock in WRITABLE state and return it. :blockid: optional block identifier, otherwise one will be automatically assigned @@ -335,40 +384,38 @@ class BlockManager(object): :owner: ArvadosFile that owns this block + """ if blockid is None: blockid = "bufferblock%i" % len(self._bufferblocks) - bb = BufferBlock(blockid, starting_capacity=starting_capacity, owner=owner) - self._bufferblocks[bb.blockid] = bb - return bb + bufferblock = _BufferBlock(blockid, starting_capacity=starting_capacity, owner=owner) + self._bufferblocks[bufferblock.blockid] = bufferblock + return bufferblock - @_synchronized - def dup_block(self, blockid, owner): - """ - Create a new bufferblock in WRITABLE state, initialized with the content of an existing bufferblock. + @synchronized + def dup_block(self, block, owner): + """Create a new bufferblock initialized with the content of an existing bufferblock. - :blockid: - the block to copy. May be an existing buffer block id. + :block: + the buffer block to copy. :owner: ArvadosFile that owns the new block + """ new_blockid = "bufferblock%i" % len(self._bufferblocks) - block = self._bufferblocks[blockid] - bb = BufferBlock(new_blockid, len(block), owner) - bb.append(block) - self._bufferblocks[bb.blockid] = bb - return bb + bufferblock = block.clone(new_blockid, owner) + self._bufferblocks[bufferblock.blockid] = bufferblock + return bufferblock - @_synchronized - def is_bufferblock(self, id): - return id in self._bufferblocks + @synchronized + def is_bufferblock(self, locator): + return locator in self._bufferblocks - @_synchronized + @synchronized def stop_threads(self): - """ - Shut down and wait for background upload and download threads to finish. - """ + """Shut down and wait for background upload and download threads to finish.""" + if self._put_threads is not None: for t in self._put_threads: self._put_queue.put(None) @@ -387,27 +434,26 @@ class BlockManager(object): self._prefetch_queue = None def commit_bufferblock(self, block): + """Initiate a background upload of a bufferblock. + + This will block if the upload queue is at capacity, otherwise it will + return immediately. + """ - Initiate a background upload of a bufferblock. This will block if the - upload queue is at capacity, otherwise it will return immediately. - """ - def worker(self): - """ - Background uploader thread. - """ + def commit_bufferblock_worker(self): + """Background uploader thread.""" + while True: try: - b = self._put_queue.get() - if b is None: + bufferblock = self._put_queue.get() + if bufferblock is None: return - b._locator = self._keep.put(b.buffer_view[0:b.write_pointer].tobytes()) - b.state = BufferBlock.COMMITTED - b.buffer_view = None - b.buffer_block = None + loc = self._keep.put(bufferblock.buffer_view[0:bufferblock.write_pointer].tobytes()) + bufferblock.set_state(_BufferBlock.COMMITTED, loc) + except Exception as e: - print e - self._put_errors.put(e) + self._put_errors.put((bufferblock.locator(), e)) finally: if self._put_queue is not None: self._put_queue.task_done() @@ -427,72 +473,91 @@ class BlockManager(object): # default download block cache in KeepClient. self._put_queue = Queue.Queue(maxsize=2) self._put_errors = Queue.Queue() - self._put_threads = [threading.Thread(target=worker, args=(self,)), - threading.Thread(target=worker, args=(self,))] - for t in self._put_threads: - t.daemon = True - t.start() + + self._put_threads = [] + for i in xrange(0, self.num_put_threads): + thread = threading.Thread(target=commit_bufferblock_worker, args=(self,)) + self._put_threads.append(thread) + thread.daemon = True + thread.start() # Mark the block as PENDING so to disallow any more appends. - block.state = BufferBlock.PENDING + block.set_state(_BufferBlock.PENDING) self._put_queue.put(block) - def get_block(self, locator, num_retries, cache_only=False): - """ - Fetch a block. First checks to see if the locator is a BufferBlock and - return that, if not, passes the request through to KeepClient.get(). + @synchronized + def get_bufferblock(self, locator): + return self._bufferblocks.get(locator) + + def get_block_contents(self, locator, num_retries, cache_only=False): + """Fetch a block. + + First checks to see if the locator is a BufferBlock and return that, if + not, passes the request through to KeepClient.get(). + """ with self.lock: if locator in self._bufferblocks: - bb = self._bufferblocks[locator] - if bb.state != BufferBlock.COMMITTED: - return bb.buffer_view[0:bb.write_pointer].tobytes() + bufferblock = self._bufferblocks[locator] + if bufferblock.state() != _BufferBlock.COMMITTED: + return bufferblock.buffer_view[0:bufferblock.write_pointer].tobytes() else: - locator = bb._locator - return self._keep.get(locator, num_retries=num_retries, cache_only=cache_only) + locator = bufferblock._locator + if cache_only: + return self._keep.get_from_cache(locator) + else: + return self._keep.get(locator, num_retries=num_retries) def commit_all(self): - """ - Commit all outstanding buffer blocks. Unlike commit_bufferblock(), this - is a synchronous call, and will not return until all buffer blocks are - uploaded. Raises AsyncKeepWriteErrors() if any blocks failed to - upload. + """Commit all outstanding buffer blocks. + + Unlike commit_bufferblock(), this is a synchronous call, and will not + return until all buffer blocks are uploaded. Raises + KeepWriteError() if any blocks failed to upload. + """ with self.lock: items = self._bufferblocks.items() for k,v in items: - if v.state == BufferBlock.WRITABLE: + if v.state() == _BufferBlock.WRITABLE: self.commit_bufferblock(v) with self.lock: if self._put_queue is not None: self._put_queue.join() + if not self._put_errors.empty(): - e = [] + err = [] try: while True: - e.append(self._put_errors.get(False)) + err.append(self._put_errors.get(False)) except Queue.Empty: pass - raise AsyncKeepWriteErrors(e) + raise KeepWriteError("Error writing some blocks", err, label="block") def block_prefetch(self, locator): + """Initiate a background download of a block. + + This assumes that the underlying KeepClient implements a block cache, + so repeated requests for the same block will not result in repeated + downloads (unless the block is evicted from the cache.) This method + does not block. + """ - Initiate a background download of a block. This assumes that the - underlying KeepClient implements a block cache, so repeated requests - for the same block will not result in repeated downloads (unless the - block is evicted from the cache.) This method does not block. - """ - def worker(self): - """Background downloader thread.""" + + if not self.prefetch_enabled: + return + + def block_prefetch_worker(self): + """The background downloader thread.""" while True: try: b = self._prefetch_queue.get() if b is None: return self._keep.get(b) - except: + except Exception: pass with self.lock: @@ -500,22 +565,30 @@ class BlockManager(object): return if self._prefetch_threads is None: self._prefetch_queue = Queue.Queue() - self._prefetch_threads = [threading.Thread(target=worker, args=(self,)), - threading.Thread(target=worker, args=(self,))] - for t in self._prefetch_threads: - t.daemon = True - t.start() + self._prefetch_threads = [] + for i in xrange(0, self.num_get_threads): + thread = threading.Thread(target=block_prefetch_worker, args=(self,)) + self._prefetch_threads.append(thread) + thread.daemon = True + thread.start() self._prefetch_queue.put(locator) class ArvadosFile(object): - """ - ArvadosFile manages the underlying representation of a file in Keep as a sequence of - segments spanning a set of blocks, and implements random read/write access. + """Represent a file in a Collection. + + ArvadosFile manages the underlying representation of a file in Keep as a + sequence of segments spanning a set of blocks, and implements random + read/write access. + + This object may be accessed from multiple threads. + """ def __init__(self, parent, stream=[], segments=[]): """ + ArvadosFile constructor. + :stream: a list of Range objects representing a block stream @@ -525,50 +598,99 @@ class ArvadosFile(object): self.parent = parent self._modified = True self._segments = [] + self.lock = parent.root_collection().lock for s in segments: self._add_segment(stream, s.locator, s.range_size) self._current_bblock = None - self.lock = threading.Lock() - @_synchronized + def writable(self): + return self.parent.writable() + + @synchronized def segments(self): return copy.copy(self._segments) - @_synchronized - def clone(self, num_retries): + @synchronized + def clone(self, new_parent): """Make a copy of this file.""" - cp = ArvadosFile() - cp.parent = self.parent - cp._modified = False + cp = ArvadosFile(new_parent) + cp.replace_contents(self) + return cp + + @must_be_writable + @synchronized + def replace_contents(self, other): + """Replace segments of this file with segments from another `ArvadosFile` object.""" map_loc = {} - for r in self._segments: - new_loc = r.locator - if self.parent._my_block_manager().is_bufferblock(r.locator): - if r.locator not in map_loc: - map_loc[r.locator] = self.parent._my_block_manager().dup_block(r.locator, cp).blockid - new_loc = map_loc[r.locator] + self._segments = [] + for other_segment in other.segments(): + new_loc = other_segment.locator + if other.parent._my_block_manager().is_bufferblock(other_segment.locator): + if other_segment.locator not in map_loc: + bufferblock = other.parent._my_block_manager().get_bufferblock(other_segment.locator) + if bufferblock.state() != _BufferBlock.WRITABLE: + map_loc[other_segment.locator] = bufferblock.locator() + else: + map_loc[other_segment.locator] = self.parent._my_block_manager().dup_block(bufferblock, self).blockid + new_loc = map_loc[other_segment.locator] + + self._segments.append(Range(new_loc, other_segment.range_start, other_segment.range_size, other_segment.segment_offset)) - cp.segments.append(Range(new_loc, r.range_start, r.range_size, r.segment_offset)) + self._modified = True - return cp + def __eq__(self, other): + if other is self: + return True + if not isinstance(other, ArvadosFile): + return False + + othersegs = other.segments() + with self.lock: + if len(self._segments) != len(othersegs): + return False + for i in xrange(0, len(othersegs)): + seg1 = self._segments[i] + seg2 = othersegs[i] + loc1 = seg1.locator + loc2 = seg2.locator + + if self.parent._my_block_manager().is_bufferblock(loc1): + loc1 = self.parent._my_block_manager().get_bufferblock(loc1).locator() + + if other.parent._my_block_manager().is_bufferblock(loc2): + loc2 = other.parent._my_block_manager().get_bufferblock(loc2).locator() + + if (KeepLocator(loc1).stripped() != KeepLocator(loc2).stripped() or + seg1.range_start != seg2.range_start or + seg1.range_size != seg2.range_size or + seg1.segment_offset != seg2.segment_offset): + return False + + return True + + def __ne__(self, other): + return not self.__eq__(other) - @_synchronized + @synchronized def set_unmodified(self): """Clear the modified flag""" self._modified = False - @_synchronized + @synchronized def modified(self): """Test the modified flag""" return self._modified - @_synchronized + @must_be_writable + @synchronized def truncate(self, size): - """ - Adjust the size of the file. If `size` is less than the size of the file, - the file contents after `size` will be discarded. If `size` is greater - than the current size of the file, an IOError will be raised. + """Shrink the size of the file. + + If `size` is less than the size of the file, the file contents after + `size` will be discarded. If `size` is greater than the current size + of the file, an IOError will be raised. + """ if size < self.size(): new_segs = [] @@ -590,32 +712,34 @@ class ArvadosFile(object): elif size > self.size(): raise IOError("truncate() does not support extending the file size") - @_synchronized def readfrom(self, offset, size, num_retries): - """ - read upto `size` bytes from the file starting at `offset`. - """ - if size == 0 or offset >= self.size(): - return '' - data = [] + """Read upto `size` bytes from the file starting at `offset`.""" + + with self.lock: + if size == 0 or offset >= self.size(): + return '' + prefetch = locators_and_ranges(self._segments, offset, size + config.KEEP_BLOCK_SIZE) + readsegs = locators_and_ranges(self._segments, offset, size) - for lr in locators_and_ranges(self._segments, offset, size + config.KEEP_BLOCK_SIZE): + for lr in prefetch: self.parent._my_block_manager().block_prefetch(lr.locator) - for lr in locators_and_ranges(self._segments, offset, size): - d = self.parent._my_block_manager().get_block(lr.locator, num_retries=num_retries, cache_only=bool(data)) - if d: - data.append(d[lr.segment_offset:lr.segment_offset+lr.segment_size]) + data = [] + for lr in readsegs: + block = self.parent._my_block_manager().get_block_contents(lr.locator, num_retries=num_retries, cache_only=bool(data)) + if block: + data.append(block[lr.segment_offset:lr.segment_offset+lr.segment_size]) else: break return ''.join(data) 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 + """Test if the buffer block has more data than 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._segments @@ -627,18 +751,21 @@ class ArvadosFile(object): if write_total < self._current_bblock.size(): # 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 = self.parent._my_block_manager().alloc_bufferblock(self._current_bblock.blockid, starting_size=write_total, owner=self) + new_bb = self.parent._my_block_manager().alloc_bufferblock(self._current_bblock.blockid, starting_capacity=write_total, owner=self) for t in bufferblock_segs: new_bb.append(self._current_bblock.buffer_view[t.segment_offset:t.segment_offset+t.range_size].tobytes()) t.segment_offset = new_bb.size() - t.range_size self._current_bblock = new_bb - @_synchronized + @must_be_writable + @synchronized def writeto(self, offset, data, num_retries): - """ - Write `data` to the file starting at `offset`. This will update - existing bytes and/or extend the size of the file as necessary. + """Write `data` to the file starting at `offset`. + + This will update existing bytes and/or extend the size of the file as + necessary. + """ if len(data) == 0: return @@ -651,7 +778,7 @@ class ArvadosFile(object): self._modified = True - if self._current_bblock is None or self._current_bblock.state != BufferBlock.WRITABLE: + if self._current_bblock is None or self._current_bblock.state() != _BufferBlock.WRITABLE: self._current_bblock = self.parent._my_block_manager().alloc_bufferblock(owner=self) if (self._current_bblock.size() + len(data)) > config.KEEP_BLOCK_SIZE: @@ -661,28 +788,38 @@ class ArvadosFile(object): self._current_bblock = self.parent._my_block_manager().alloc_bufferblock(owner=self) self._current_bblock.append(data) + replace_range(self._segments, offset, len(data), self._current_bblock.blockid, self._current_bblock.write_pointer - len(data)) - @_synchronized + @synchronized + def flush(self): + if self._current_bblock: + self._repack_writes() + self.parent._my_block_manager().commit_bufferblock(self._current_bblock) + + + @must_be_writable + @synchronized def add_segment(self, blocks, pos, size): - # Synchronized public api, see _add_segment + """Add a segment to the end of the file. + + `pos` and `offset` reference a section of the stream described by + `blocks` (a list of Range objects) + + """ self._add_segment(blocks, pos, size) def _add_segment(self, blocks, pos, size): - """ - Add a segment to the end of the file, with `pos` and `offset` referencing a - section of the stream described by `blocks` (a list of Range objects) - """ + """Internal implementation of add_segment.""" self._modified = True for lr in locators_and_ranges(blocks, pos, size): last = self._segments[-1] if self._segments else Range(0, 0, 0) r = Range(lr.locator, last.range_start+last.range_size, lr.segment_size, lr.segment_offset) self._segments.append(r) - - @_synchronized + @synchronized def size(self): - """Get the file size""" + """Get the file size.""" if self._segments: n = self._segments[-1] return n.range_start + n.range_size @@ -690,7 +827,32 @@ class ArvadosFile(object): return 0 + @synchronized + def manifest_text(self, stream_name=".", portable_locators=False, normalize=False): + buf = "" + item = self + filestream = [] + for segment in item.segments: + loc = segment.locator + if loc.startswith("bufferblock"): + loc = item._bufferblocks[loc].calculate_locator() + if portable_locators: + loc = KeepLocator(loc).stripped() + filestream.append(LocatorAndRange(loc, locator_block_size(loc), + segment.segment_offset, segment.range_size)) + buf += ' '.join(normalize_stream(stream_name, {stream_name: filestream})) + buf += "\n" + return buf + + class ArvadosFileReader(ArvadosFileReaderBase): + """Wraps ArvadosFile in a file-like object supporting reading only. + + Be aware that this class is NOT thread safe as there is no locking around + updating file pointer. + + """ + def __init__(self, arvadosfile, name, mode="r", num_retries=None): super(ArvadosFileReader, self).__init__(name, mode, num_retries=num_retries) self.arvadosfile = arvadosfile @@ -698,18 +860,21 @@ class ArvadosFileReader(ArvadosFileReaderBase): def size(self): return self.arvadosfile.size() - @ArvadosFileBase._before_close + def stream_name(self): + return self.arvadosfile.parent.stream_name() + + @_FileLikeObjectBase._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""" - data = self.arvadosfile.readfrom(self._filepos, size, num_retries=num_retries) + """Read up to `size` bytes from the stream, starting at the current file position.""" + data = self.arvadosfile.readfrom(self._filepos, size, num_retries) self._filepos += len(data) return data - @ArvadosFileBase._before_close + @_FileLikeObjectBase._before_close @retry_method def readfrom(self, offset, size, num_retries=None): - """Read up to `size` bytes from the stream, starting at the current file position""" + """Read up to `size` bytes from the stream, starting at the current file position.""" return self.arvadosfile.readfrom(offset, size, num_retries) def flush(self): @@ -717,27 +882,44 @@ class ArvadosFileReader(ArvadosFileReaderBase): class ArvadosFileWriter(ArvadosFileReader): + """Wraps ArvadosFile in a file-like object supporting both reading and writing. + + Be aware that this class is NOT thread safe as there is no locking around + updating file pointer. + + """ + def __init__(self, arvadosfile, name, mode, num_retries=None): super(ArvadosFileWriter, self).__init__(arvadosfile, name, mode, num_retries=num_retries) - @ArvadosFileBase._before_close + @_FileLikeObjectBase._before_close @retry_method def write(self, data, num_retries=None): if self.mode[0] == "a": - self.arvadosfile.writeto(self.size(), data) + self.arvadosfile.writeto(self.size(), data, num_retries) else: self.arvadosfile.writeto(self._filepos, data, num_retries) self._filepos += len(data) - @ArvadosFileBase._before_close + @_FileLikeObjectBase._before_close @retry_method def writelines(self, seq, num_retries=None): for s in seq: - self.write(s) + self.write(s, num_retries) + @_FileLikeObjectBase._before_close def truncate(self, size=None): if size is None: size = self._filepos self.arvadosfile.truncate(size) if self._filepos > self.size(): self._filepos = self.size() + + @_FileLikeObjectBase._before_close + def flush(self): + self.arvadosfile.flush() + + @_FileLikeObjectBase._before_close + def close(self): + self.flush() + super(ArvadosFileWriter, self).close()