import gflags import httplib import httplib2 import logging 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 from collections import deque from stat import * from keep import * from stream import * import config import errors import util def normalize_stream(s, stream): stream_tokens = [s] sortedfiles = list(stream.keys()) sortedfiles.sort() blocks = {} streamoffset = 0L for f in sortedfiles: for b in stream[f]: if b[arvados.LOCATOR] not in blocks: stream_tokens.append(b[arvados.LOCATOR]) blocks[b[arvados.LOCATOR]] = streamoffset streamoffset += b[arvados.BLOCKSIZE] for f in sortedfiles: current_span = None fout = f.replace(' ', '\\040') for segment in stream[f]: segmentoffset = blocks[segment[arvados.LOCATOR]] + segment[arvados.OFFSET] if current_span == None: current_span = [segmentoffset, segmentoffset + segment[arvados.SEGMENTSIZE]] else: if segmentoffset == current_span[1]: current_span[1] += segment[arvados.SEGMENTSIZE] else: stream_tokens.append("{0}:{1}:{2}".format(current_span[0], current_span[1] - current_span[0], fout)) current_span = [segmentoffset, segmentoffset + segment[arvados.SEGMENTSIZE]] if current_span != None: stream_tokens.append("{0}:{1}:{2}".format(current_span[0], current_span[1] - current_span[0], fout)) if len(stream[f]) == 0: stream_tokens.append("0:0:{0}".format(fout)) return stream_tokens def normalize(collection): streams = {} for s in collection.all_streams(): for f in s.all_files(): filestream = s.name() + "/" + f.name() r = filestream.rindex("/") streamname = filestream[:r] filename = filestream[r+1:] if streamname not in streams: streams[streamname] = {} if filename not in streams[streamname]: streams[streamname][filename] = [] for r in f.segments: streams[streamname][filename].extend(s.locators_and_ranges(r[0], r[1])) normalized_streams = [] sortedstreams = list(streams.keys()) sortedstreams.sort() for s in sortedstreams: normalized_streams.append(normalize_stream(s, streams[s])) return normalized_streams class CollectionReader(object): def __init__(self, manifest_locator_or_text): if re.search(r'^[a-f0-9]{32}(\+\d+)?(\+\S+)*$', manifest_locator_or_text): self._manifest_locator = manifest_locator_or_text self._manifest_text = None elif re.search(r'^\S+( [a-f0-9]{32,}(\+\S+)*)*( \d+:\d+:\S+)+\n', manifest_locator_or_text): self._manifest_text = manifest_locator_or_text self._manifest_locator = None else: raise errors.ArgumentError( "Argument to CollectionReader must be a manifest or a collection UUID") self._streams = None def __enter__(self): pass def __exit__(self): pass def _populate(self): if self._streams != None: return if not self._manifest_text: try: c = arvados.api('v1').collections().get( uuid=self._manifest_locator).execute() self._manifest_text = c['manifest_text'] except Exception as e: logging.warning("API lookup failed for collection %s (%s: %s)" % (self._manifest_locator, type(e), str(e))) self._manifest_text = Keep.get(self._manifest_locator) self._streams = [] for stream_line in self._manifest_text.split("\n"): if stream_line != '': stream_tokens = stream_line.split() self._streams += [stream_tokens] self._streams = normalize(self) # now regenerate the manifest text based on the normalized stream #print "normalizing", self._manifest_text self._manifest_text = ''.join([StreamReader(stream).manifest_text() for stream in self._streams]) #print "result", self._manifest_text def all_streams(self): self._populate() resp = [] for s in self._streams: resp.append(StreamReader(s)) return resp def all_files(self): for s in self.all_streams(): for f in s.all_files(): yield f def manifest_text(self): self._populate() return self._manifest_text class CollectionWriter(object): KEEP_BLOCK_SIZE = 2**26 def __init__(self): self._data_buffer = [] self._data_buffer_len = 0 self._current_stream_files = [] self._current_stream_length = 0 self._current_stream_locators = [] self._current_stream_name = '.' self._current_file_name = None self._current_file_pos = 0 self._finished_streams = [] self._close_file = None self._queued_file = None self._queued_dirents = deque() self._queued_trees = deque() def __enter__(self): pass def __exit__(self): self.finish() def do_queued_work(self): # The work queue consists of three pieces: # * _queued_file: The file object we're currently writing to the # Collection. # * _queued_dirents: Entries under the current directory # (_queued_trees[0]) that we want to write or recurse through. # This may contain files from subdirectories if # max_manifest_depth == 0 for this directory. # * _queued_trees: Directories that should be written as separate # streams to the Collection. # This function handles the smallest piece of work currently queued # (current file, then current directory, then next directory) until # no work remains. The _work_THING methods each do a unit of work on # THING. _queue_THING methods add a THING to the work queue. while True: if self._queued_file: self._work_file() elif self._queued_dirents: self._work_dirents() elif self._queued_trees: self._work_trees() else: break def _work_file(self): while True: buf = self._queued_file.read(self.KEEP_BLOCK_SIZE) if not buf: break self.write(buf) self.finish_current_file() if self._close_file: self._queued_file.close() self._close_file = None self._queued_file = None def _work_dirents(self): path, stream_name, max_manifest_depth = self._queued_trees[0] if stream_name != self.current_stream_name(): self.start_new_stream(stream_name) while self._queued_dirents: dirent = self._queued_dirents.popleft() target = os.path.join(path, dirent) if os.path.isdir(target): self._queue_tree(target, os.path.join(stream_name, dirent), max_manifest_depth - 1) else: self._queue_file(target, dirent) break if not self._queued_dirents: self._queued_trees.popleft() def _work_trees(self): path, stream_name, max_manifest_depth = self._queued_trees[0] make_dirents = (util.listdir_recursive if (max_manifest_depth == 0) else os.listdir) self._queue_dirents(stream_name, make_dirents(path)) def _queue_file(self, source, filename=None): assert (self._queued_file is None), "tried to queue more than one file" if not hasattr(source, 'read'): source = open(source, 'rb') self._close_file = True else: self._close_file = False if filename is None: filename = os.path.basename(source.name) self.start_new_file(filename) self._queued_file = source def _queue_dirents(self, stream_name, dirents): assert (not self._queued_dirents), "tried to queue more than one tree" self._queued_dirents = deque(sorted(dirents)) def _queue_tree(self, path, stream_name, max_manifest_depth): self._queued_trees.append((path, stream_name, max_manifest_depth)) def write_file(self, source, filename=None): self._queue_file(source, filename) self.do_queued_work() def write_directory_tree(self, path, stream_name='.', max_manifest_depth=-1): self._queue_tree(path, stream_name, max_manifest_depth) self.do_queued_work() def write(self, newdata): if hasattr(newdata, '__iter__'): for s in newdata: self.write(s) return self._data_buffer += [newdata] self._data_buffer_len += len(newdata) self._current_stream_length += len(newdata) while self._data_buffer_len >= self.KEEP_BLOCK_SIZE: self.flush_data() def flush_data(self): data_buffer = ''.join(self._data_buffer) if data_buffer != '': self._current_stream_locators += [Keep.put(data_buffer[0:self.KEEP_BLOCK_SIZE])] self._data_buffer = [data_buffer[self.KEEP_BLOCK_SIZE:]] self._data_buffer_len = len(self._data_buffer[0]) def start_new_file(self, newfilename=None): self.finish_current_file() self.set_current_file_name(newfilename) def set_current_file_name(self, newfilename): if re.search(r'[\t\n]', newfilename): raise errors.AssertionError( "Manifest filenames cannot contain whitespace: %s" % newfilename) self._current_file_name = newfilename def current_file_name(self): return self._current_file_name def finish_current_file(self): if self._current_file_name == None: if self._current_file_pos == self._current_stream_length: return raise errors.AssertionError( "Cannot finish an unnamed file " + "(%d bytes at offset %d in '%s' stream)" % (self._current_stream_length - self._current_file_pos, self._current_file_pos, self._current_stream_name)) self._current_stream_files += [[self._current_file_pos, self._current_stream_length - self._current_file_pos, self._current_file_name]] self._current_file_pos = self._current_stream_length def start_new_stream(self, newstreamname='.'): self.finish_current_stream() self.set_current_stream_name(newstreamname) def set_current_stream_name(self, newstreamname): if re.search(r'[\t\n]', newstreamname): raise errors.AssertionError( "Manifest stream names cannot contain whitespace") self._current_stream_name = '.' if newstreamname=='' else newstreamname def current_stream_name(self): return self._current_stream_name def finish_current_stream(self): self.finish_current_file() self.flush_data() if len(self._current_stream_files) == 0: pass elif self._current_stream_name == None: raise errors.AssertionError( "Cannot finish an unnamed stream (%d bytes in %d files)" % (self._current_stream_length, len(self._current_stream_files))) else: if len(self._current_stream_locators) == 0: self._current_stream_locators += [config.EMPTY_BLOCK_LOCATOR] self._finished_streams += [[self._current_stream_name, self._current_stream_locators, self._current_stream_files]] self._current_stream_files = [] self._current_stream_length = 0 self._current_stream_locators = [] self._current_stream_name = None self._current_file_pos = 0 self._current_file_name = None def finish(self): # Send the stripped manifest to Keep, to ensure that we use the # same UUID regardless of what hints are used on the collection. return Keep.put(self.stripped_manifest()) def stripped_manifest(self): """ Return the manifest for the current collection with all permission hints removed from the locators in the manifest. """ raw = self.manifest_text() clean = '' for line in raw.split("\n"): fields = line.split() if len(fields) > 0: locators = [ re.sub(r'\+A[a-z0-9@_-]+', '', x) for x in fields[1:-1] ] clean += fields[0] + ' ' + ' '.join(locators) + ' ' + fields[-1] + "\n" return clean def manifest_text(self): self.finish_current_stream() manifest = '' for stream in self._finished_streams: if not re.search(r'^\.(/.*)?$', stream[0]): manifest += './' manifest += stream[0].replace(' ', '\\040') manifest += ' ' + ' '.join(stream[1]) manifest += ' ' + ' '.join("%d:%d:%s" % (sfile[0], sfile[1], sfile[2].replace(' ', '\\040')) for sfile in stream[2]) manifest += "\n" #print 'writer',manifest #print 'after reader',CollectionReader(manifest).manifest_text() return CollectionReader(manifest).manifest_text() def data_locators(self): ret = [] for name, locators, files in self._finished_streams: ret += locators return ret class ResumableCollectionWriter(CollectionWriter): STATE_PROPS = ['_current_stream_files', '_current_stream_length', '_current_stream_locators', '_current_stream_name', '_current_file_name', '_current_file_pos', '_close_file', '_data_buffer', '_dependencies', '_finished_streams', '_queued_dirents', '_queued_trees'] def __init__(self): self._dependencies = {} super(ResumableCollectionWriter, self).__init__() @classmethod def from_state(cls, state, *init_args, **init_kwargs): # Try to build a new writer from scratch with the given state. # If the state is not suitable to resume (because files have changed, # been deleted, aren't predictable, etc.), raise a # StaleWriterStateError. Otherwise, return the initialized writer. # The caller is responsible for calling writer.do_queued_work() # appropriately after it's returned. writer = cls(*init_args, **init_kwargs) for attr_name in cls.STATE_PROPS: attr_value = state[attr_name] attr_class = getattr(writer, attr_name).__class__ # Coerce the value into the same type as the initial value, if # needed. if attr_class not in (type(None), attr_value.__class__): attr_value = attr_class(attr_value) setattr(writer, attr_name, attr_value) # Check dependencies before we try to resume anything. if any(KeepLocator(ls).permission_expired() for ls in writer._current_stream_locators): raise errors.StaleWriterStateError( "locators include expired permission hint") writer.check_dependencies() if state['_current_file'] is not None: path, pos = state['_current_file'] try: writer._queued_file = open(path, 'rb') writer._queued_file.seek(pos) except IOError as error: raise errors.StaleWriterStateError( "failed to reopen active file {}: {}".format(path, error)) return writer def check_dependencies(self): for path, orig_stat in self._dependencies.items(): if not S_ISREG(orig_stat[ST_MODE]): raise errors.StaleWriterStateError("{} not file".format(path)) try: now_stat = tuple(os.stat(path)) except OSError as error: raise errors.StaleWriterStateError( "failed to stat {}: {}".format(path, error)) if ((not S_ISREG(now_stat[ST_MODE])) or (orig_stat[ST_MTIME] != now_stat[ST_MTIME]) or (orig_stat[ST_SIZE] != now_stat[ST_SIZE])): raise errors.StaleWriterStateError("{} changed".format(path)) def dump_state(self, copy_func=lambda x: x): state = {attr: copy_func(getattr(self, attr)) for attr in self.STATE_PROPS} if self._queued_file is None: state['_current_file'] = None else: state['_current_file'] = (os.path.realpath(self._queued_file.name), self._queued_file.tell()) return state def _queue_file(self, source, filename=None): try: src_path = os.path.realpath(source) except Exception: raise errors.AssertionError("{} not a file path".format(source)) try: path_stat = os.stat(src_path) except OSError as stat_error: path_stat = None super(ResumableCollectionWriter, self)._queue_file(source, filename) fd_stat = os.fstat(self._queued_file.fileno()) if not S_ISREG(fd_stat.st_mode): # We won't be able to resume from this cache anyway, so don't # worry about further checks. self._dependencies[source] = tuple(fd_stat) elif path_stat is None: raise errors.AssertionError( "could not stat {}: {}".format(source, stat_error)) elif path_stat.st_ino != fd_stat.st_ino: raise errors.AssertionError( "{} changed between open and stat calls".format(source)) else: self._dependencies[src_path] = tuple(fd_stat) def write(self, data): if self._queued_file is None: raise errors.AssertionError( "resumable writer can't accept unsourced data") return super(ResumableCollectionWriter, self).write(data)