def __init__(self, filename="*&$#$%#", file_mode="r", cachesize=1048576): # If the filename isn't specified, use the default one (None has a # special meaning, so we can't use it - it means create a temp file) if filename == "*&$#$%#": filename = _DEFAULT_TREE_DATA logging.info("Initializing tree with data from %r", filename) self._tree = StringDBDict(persistent_file=filename, file_mode=file_mode, cachesize=cachesize) self._invlookup = None # Init the inverse name lookup database lazily self._origname = filename self.terms = self._tree.keys() self.terms.sort() # This one is for speedy retrieval and indexing self._term_list_as_dict = None self._search_dict = None self.num_terms = len(self.terms) return
def __init__(self, reader, graph_builder, ranker, eval_parameters, ranking_cutoff, mesh_tree_filename, distance_matrix_filename, distance_function, umls_converter_data_filename, umls_concept_data_filename, output_file): logging.debug("Setting up a Workflow instance.") logging.debug("My reader is: %r", reader) self._reader = reader logging.debug("My graph builder is: %r", graph_builder) self._graph_builder = graph_builder self._ranker = MappedRanker(ranker) logging.debug("My ranker is: %r", self._ranker) self._ranking_cutoff = ranking_cutoff logging.debug("My ranking cutoff is: %r", self._ranking_cutoff) logging.debug("Creating a Tree instance from %s", mesh_tree_filename) self._mesh_tree = Tree(mesh_tree_filename) logging.debug( "Creating SAVCC distance matrix with %r and distance " "function %r", distance_matrix_filename, distance_function) self._matrix = SavccNormalizedMatrix( open(distance_matrix_filename, "rb"), distance_function) logging.debug("Filling in the rest of the evaluation parameters.") self._eval_parameters = eval_parameters self._eval_parameters.mesh_tree = self._mesh_tree self._eval_parameters.savcc_matrix = self._matrix logging.debug("My evaluation parameters are: %r", self._eval_parameters) if umls_converter_data_filename is None: converter_data = None else: converter_data = pickle.load( open(umls_converter_data_filename, "rb")) self._umls_converter = RankedConverter( Converter(self._mesh_tree, converter_data)) logging.debug("My converter is: %r", self._umls_converter) logging.debug("Initializing Concept storage from %s", umls_concept_data_filename) if umls_concept_data_filename is None: Concept.init_storage() else: Concept.init_storage(StringDBDict(umls_concept_data_filename)) self._output_file = output_file logging.debug("My output file is: %r", self._output_file) return
def main(): mrsty_file=sys.argv[3] original_filename=sys.argv[2] data_store_name=sys.argv[1] original_file=Text(bz2.BZ2File(original_filename, 'r')) print "Loading semantic types from %s" % mrsty_file stypes=SemanticTypes() stypes.build_from_mrsty_file(MRSTYTable(bz2.BZ2File(mrsty_file))) print "Semantic types loaded." print "Turning the data from %s into %s. Please wait." % ( original_filename, data_store_name) data_store=StringDBDict(data_store_name, sync_every_transactions=0, write_out_every_transactions=200000, file_mode='c') data_store.sync_every=0 build_concept_dictionary(original_file, data_store, stypes) data_store.sync_every=100 print "Conversion done."
def __init__(self): try: self._cache_location = sys.argv[2] except IndexError: self._cache_location = DEFAULT_CACHE_NAME self._cache = StringDBDict(self._cache_location, file_mode="c")
def __init__(self): try: self._cache_location = sys.argv[2] except IndexError: self._cache_location = _DEFAULT_CONCEPT_STORAGE self._cache = StringDBDict(self._cache_location, file_mode="r")
chunk=chunk.strip() for k, v in tok_bact.iteritems(): chunk=chunk.replace(k, v) if reduce(operator.or_, [x in chunk.lower() for x in useless_lines]): continue if len(chunk) < 2: continue outfile.write('%010d|%s\n' % (chunkid, chunk)) chunkmap[fakename].append(chunkid) chunkid += 1 outfile.close() print "Saving chunkmap" pickle.dump(chunkmap, open(outmapname, "wb"), pickle.HIGHEST_PROTOCOL) print "These files couldn't be processed:" print '\n'.join(skipped) print "Opening (or creating) cache in", sys.argv[2] the_cache=StringDBDict(os.path.join(sys.argv[2], DEFAULT_CACHE_NAME), file_mode='c') PubMed.download_many([str(x) for x in known_articles if str(x) not in the_cache.keys()], download_callback, parser=Medline.RecordParser()) mti_filename=sys.argv[1]+'.mti' print "Finished processing the cache. Using the cache to build", \ mti_filename mti_file=open(mti_filename, "w") chunkmap={} hexfinder=re.compile(r'\\x[a-f0-9][a-f0-9]', re.IGNORECASE) for article in known_articles: try: article_record=the_cache[str(article)] except KeyError: print "Article doesn't exist in cache. Skipping." continue
trees[term] = TreeNode(term, role, synonyms, set(position)) return trees if __name__ == "__main__": # The pickling and unpickling make this horribly slow, so we'll trade some # memory for speed in the build process and later turn the dictionary into # a DB-backed one. tree_storage = {} for treefile in sys.argv[2:]: treesfile = bz2.BZ2File(treefile, 'rU') print "Reading %s..." % treefile tree_storage = build_tree_from_descriptor_file(treesfile, tree_storage) print "Tree built. It has %d unique terms." % len(tree_storage) print "For example... arm=", tree_storage['arm'], " and eye=", \ tree_storage['eye'] print "Done generating tree." print "Storing tree in", sys.argv[1] tree_on_disk = StringDBDict(persistent_file=sys.argv[1], sync_every_transactions=0, write_out_every_transactions=0, file_mode='c') write_counter = 0 for k, v in tree_storage.iteritems(): tree_on_disk[k] = v write_counter += 1 if write_counter % 1000 == 0: print "Stored", write_counter, "terms." tree_on_disk.sync_every = 1 print "Done storing."
def multi_processor(reader, workflow_class, graph_builder_constructor, graph_builder_params, ranker_constructor, ranker_params, eval_parameters, ranking_cutoff, mesh_tree_filename, distance_matrix_filename, distance_function, umls_converter_data_filename, umls_concept_data_filename, extra_data_name, extra_data_contents, output_file, num_threads=None, queue_size=None, output_callback=output, output_headers_callback=output_headers, output_item_callback=output_one_item, performance_tuning=True): """ Perform the evaluation. Multithreading notes: It's the responsibility of the caller to make sure that extra_data_contents, if any, are thread-safe. """ if num_threads is None: num_threads=1 logging.debug("Initializing Concept storage from %s", umls_concept_data_filename) # Since there's no direct way of setting the concept cache's title, # we set it here, wait for it to be inherited, and then get the 'real' # process title for this one. if umls_concept_data_filename is None: Concept.init_storage() else: Concept.init_storage(StringDBDict(umls_concept_data_filename)) Pmid.init_storage() threads=[] logging.info("Creating %d worker threads.", num_threads) #task_queue=[JoinableQueue(queue_size) for x in xrange(num_processes)] task_queues=[Queue(queue_size) for x in xrange(num_threads)] this_output_queue=Queue(2*queue_size) # Create an output processor output_processor=Thread(target=output_callback, args=(output_file, this_output_queue, output_headers_callback, output_item_callback)) output_processor.start() for i in xrange(num_threads): this_thread=Thread(target=processor, args=(workflow_class, graph_builder_constructor, graph_builder_params, ranker_constructor, ranker_params, eval_parameters, ranking_cutoff, mesh_tree_filename, distance_matrix_filename, distance_function, umls_converter_data_filename, extra_data_name, extra_data_contents, task_queues[i], this_output_queue), name="MEDRank-Worker-%d" % i) logging.log(ULTRADEBUG, "Created thread: %r", this_thread) this_thread.start() threads.append((this_thread, this_output_queue, task_queues[i])) all_results={} count=0 # Use a single dispatch queue for automagical load balancing # CHANGED - Now uses multiple queues to avoid starving due to waiting on semlocks for each_article in reader: count+=1 # logging.info("Dispatching article %d: %r", count, each_article) target_thread=(count-1) % num_threads logging.info("Dispatching article %d: %s to %s", count, each_article.set_id, threads[target_thread][0].name) task_queues[target_thread].put(each_article) #task_queue[target_process].put(each_article) #task_queue.put(each_article) #logging.info("The task queue is approximately %d items long.", # task_queue.qsize()) logging.log(ULTRADEBUG, "Waiting for processing to end.") all_results={} alive_threads=[x for x in threads if x[0].is_alive()] remaining_threads=len(alive_threads) logging.info("There are %d threads (out of %d) still alive.", remaining_threads, num_threads) for i in xrange(remaining_threads): alive_threads[i][2].put('STOP') #alive_threads[i][2].close() logging.debug("Sent STOP requests. Notifying queue that no further " "requests will come.") logging.info("All information sent to the threads.") # Note end of output while len(threads)>0: a_thread=threads.pop() # We join the process to wait for the end of the reading a_thread[0].join() # logging.log(ULTRADEBUG, "Fetching results from finished process.") # all_results.update(a_process[1].get()) # Add results to result pool # logging.log(ULTRADEBUG, "Received results.") logging.info("Finishing writing out results.") this_output_queue.put("STOP") output_processor.join() logging.info("Results written. Finishing multithreading.") Pmid.close_storage() return
def multi_processor(reader, workflow_class, graph_builder_constructor, graph_builder_params, ranker_constructor, ranker_params, eval_parameters, ranking_cutoff, mesh_tree_filename, distance_matrix_filename, distance_function, umls_converter_data_filename, umls_concept_data_filename, extra_data_name, extra_data_contents, output_file, num_processes=None, queue_size=None, output_callback=output, output_headers_callback=output_headers, output_item_callback=output_one_item, performance_tuning=True): """ Perform the evaluation. Multiprocessing notes: It's the responsibility of the caller to make sure that extra_data_contents, if any, are multiprocessing-safe. For example, by using a SyncManager and Namespace and passing the proxy. See umls/concept for an example. """ if num_processes is None: num_processes = cpu_count() if performance_tuning: # Since reading the file involves an awful lot of object creation # and destruction we'll tweak the gc adjustments to sweep less frequently # IOW - we have a LOT of short-lived objects. No sense garbage-collecting # the latter generations very often. # (this is about 10x, 5x, and 5x the usual) original_threshold = gc.get_threshold() gc.set_threshold(10 * original_threshold[0], 5 * original_threshold[1], 5 * original_threshold[1]) original_check_interval = sys.getcheckinterval() # Similarly, we'll try to minimize overhead from thread switches # 5x usual value sys.setcheckinterval(5 * original_check_interval) logging.debug("Initializing Concept storage from %s", umls_concept_data_filename) if umls_concept_data_filename is None: Concept.init_storage() else: Concept.init_storage(StringDBDict(umls_concept_data_filename)) Pmid.init_storage() proctitle.setproctitle("MEDRank-main") processes = [] logging.info("Creating %d worker processes.", num_processes) #task_queue=[JoinableQueue(queue_size) for x in xrange(num_processes)] task_queues = [Queue(queue_size) for x in xrange(num_processes)] this_output_queue = Queue(2 * queue_size) # Create an output processor output_processor = Process(target=output_callback, args=(output_file, this_output_queue, output_headers_callback, output_item_callback)) output_processor.start() for i in xrange(num_processes): this_process = Process( target=processor, args=(workflow_class, graph_builder_constructor, graph_builder_params, ranker_constructor, ranker_params, eval_parameters, ranking_cutoff, mesh_tree_filename, distance_matrix_filename, distance_function, umls_converter_data_filename, extra_data_name, extra_data_contents, task_queues[i], this_output_queue, "MEDRank-Worker-%d" % i), name="MEDRank-Worker-%d" % i) logging.log(ULTRADEBUG, "Created process: %r", this_process) this_process.start() processes.append((this_process, this_output_queue, task_queues[i])) all_results = {} count = 0 # Use a single dispatch queue for automagical load balancing # CHANGED - Now uses multiple queues to avoid starving due to waiting on semlocks for each_article in reader: count += 1 #queues_and_sizes=[(task_queues[x].qsize(), x) # for x in xrange(num_processes)] #queues_and_sizes.sort() #target_process=queues_and_sizes[0][1] # logging.info("Dispatching article %d: %r", count, each_article) target_process = (count - 1) % num_processes #Lowest-loaded process first. logging.info("Dispatching article %d: %s to %s", count, each_article.set_id, processes[target_process][0].name) task_queues[target_process].put(each_article) #task_queue[target_process].put(each_article) #task_queue.put(each_article) #logging.info("The task queue is approximately %d items long.", # task_queue.qsize()) logging.log(ULTRADEBUG, "Waiting for processing to end.") all_results = {} alive_processes = [x for x in processes if x[0].is_alive()] remaining_processes = len(alive_processes) logging.info("There are %d processes (out of %d) still alive.", remaining_processes, num_processes) for i in xrange(remaining_processes): alive_processes[i][2].put('STOP') alive_processes[i][2].close() logging.debug("Sent STOP requests. Notifying queue that no further " "requests will come.") logging.info("All information sent to the processors.") # Back to normal if performance_tuning: gc.set_threshold(original_threshold[0], original_threshold[1], original_threshold[2]) sys.setcheckinterval(original_check_interval) # Note end of output while len(processes) > 0: a_process = processes.pop() # We join the process to wait for the end of the reading a_process[0].join() # logging.log(ULTRADEBUG, "Fetching results from finished process.") # all_results.update(a_process[1].get()) # Add results to result pool # logging.log(ULTRADEBUG, "Received results.") logging.info("Finishing writing out results.") this_output_queue.put("STOP") output_processor.join() logging.info("Results written. Finishing multiprocessing.") return