def __init__(self, CUI):
self.__cui = CUI
if Concept.__storage is None:
logging.info("Initializing concept storage from default location."
" If this isn't what you want, call "
"Concept.init_storage() before allocating a Concept")
Concept.init_storage()
def __init__(self, tree, rule_data=None, skip_unknown_concepts=True,
accepted_types=set(['a', 'i'])):
logging.debug("Creating Converter with tree %r", tree)
self._tree=tree
if rule_data is None:
rule_data=pickle.load(open(_DEFAULT_CONVERTER_DATA, "rb"))
logging.info("Using converter data from %r",
_DEFAULT_CONVERTER_DATA)
self._data=rule_data
self._extra_checktags=set()
self._skip_unknown=skip_unknown_concepts
self._accepted_types=accepted_types
def __init__(self,
tree,
rule_data=None,
skip_unknown_concepts=True,
accepted_types=set(['a', 'i'])):
logging.debug("Creating Converter with tree %r", tree)
self._tree = tree
if rule_data is None:
rule_data = pickle.load(open(_DEFAULT_CONVERTER_DATA, "rb"))
logging.info("Using converter data from %r",
_DEFAULT_CONVERTER_DATA)
self._data = rule_data
self._extra_checktags = set()
self._skip_unknown = skip_unknown_concepts
self._accepted_types = accepted_types
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 graph_and_rank(self, article):
"""Turn the article into a graph, then a link matrix, and then rank
it. Returns the ranked list of nodes."""
article_graph=self.graph_article(article)
article_matrix=article_graph.as_mapped_link_matrix()
if len(article_matrix)==0:
logging.info("Skipping article %r. It has an empty matrix.",
article)
raise CouldNotRank("Article %r is not rankable." % article)
try:
ranked_article=self._ranker.evaluate(article_matrix)
except ValueError:
logging.info("%r returned an exception while ranking %r. "
"Skipping.", self._ranker, article)
raise CouldNotRank("There was an exception while ranking %r." %
article)
return ranked_article
def graph_and_rank(self, item):
"""Turn the item into a graph, then a link matrix, and then rank
it. Returns the ranked list of nodes."""
item_graph = self.graph_item(item)
logging.log(ULTRADEBUG, "The item graph is %r.", item_graph)
item_matrix = item_graph.as_mapped_link_matrix()
if len(item_matrix) == 0:
logging.info("Skipping item %r. It has an empty matrix.", item)
raise CouldNotRank("Item %r is not rankable." % item)
try:
ranked_item = self._ranker.evaluate(item_matrix)
except ValueError:
logging.info(
"%r returned an exception while ranking %r. "
"Skipping.", self._ranker, item)
raise CouldNotRank("There was an exception while ranking %r." %
item)
return ranked_item
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 graph_and_rank(self, article):
"""Turn the article into a graph, then a link matrix, and then rank
it. Returns the ranked list of nodes."""
article_graph = self.graph_article(article)
article_matrix = article_graph.as_mapped_link_matrix()
if len(article_matrix) == 0:
logging.info("Skipping article %r. It has an empty matrix.",
article)
raise CouldNotRank("Article %r is not rankable." % article)
try:
ranked_article = self._ranker.evaluate(article_matrix)
except ValueError:
logging.info(
"%r returned an exception while ranking %r. "
"Skipping.", self._ranker, article)
raise CouldNotRank("There was an exception while ranking %r." %
article)
return ranked_article
def graph_and_rank(self, item):
"""Turn the item into a graph, then a link matrix, and then rank
it. Returns the ranked list of nodes."""
item_graph=self.graph_item(item)
logging.log(ULTRADEBUG, "The item graph is %r.", item_graph)
item_matrix=item_graph.as_mapped_link_matrix()
if len(item_matrix)==0:
logging.info("Skipping item %r. It has an empty matrix.",
item)
raise CouldNotRank("Item %r is not rankable." % item)
try:
ranked_item=self._ranker.evaluate(item_matrix)
except ValueError:
logging.info("%r returned an exception while ranking %r. "
"Skipping.", self._ranker, item)
raise CouldNotRank("There was an exception while ranking %r." %
item)
return ranked_item
def run(self):
"""Perform the evaluation"""
logging.info("Starting workflow %r run", self)
all_results = {}
evaluator = self.create_evaluator()
count = 0
for each_article in self._reader:
count += 1
logging.info("Working on article %d: %r", count, each_article)
if not self.include_article(each_article):
logging.log(
ULTRADEBUG, "Skipping article %r due to exclusion "
" criteria.", each_article)
continue
try:
ranked_article = self.graph_and_rank(each_article)
except CouldNotRank:
continue
converted_terms = self.convert(ranked_article)
cut_terms = converted_terms.terms_higher_than_or_equal_to(
self._ranking_cutoff)
logging.debug(
"Lowest-ranking term is term #%d out of %d"
" (score=%1.5f, highest score=%1.5f)", len(cut_terms),
len(converted_terms), [x[1] for x in cut_terms][-1],
[x[1] for x in cut_terms][0])
medline_record_mesh_terms = ExpressionList().from_medline(
each_article.set_id.article_record().mesh_headings)
flat_medline = medline_record_mesh_terms.flatten()
flattened_terms = self.flatten_generated_terms(
flat_medline, cut_terms)
flattened_terms = self.limit_length(flat_medline, flattened_terms)
if len(flat_medline) == 0:
logging.warn(
"No gold standard available for article %r. "
"Omitting it from the result set.", each_article)
continue
eval_result = self.perform_evaluation(each_article, evaluator,
flat_medline,
flattened_terms)
flattened_major_headings=\
medline_record_mesh_terms.major_headings()
logging.debug("Original headings: %r Major headings: %r",
medline_record_mesh_terms, flattened_major_headings)
mh_result_temp = self.perform_evaluation(each_article, evaluator,
flattened_major_headings,
flattened_terms)
mh_result = NamedResultSet("mh_", mh_result_temp)
# Compute the total recall, too
total_recall = self.compute_total_recall(flat_medline,
converted_terms)
eval_result.add(total_recall)
# Unify the result sets
all_results[each_article.set_id] = eval_result | mh_result
logging.info("Writing out results.")
self.output(all_results)
self.output_metadata()
return
def run(self):
"""Perform the evaluation"""
logging.info("Starting workflow %r run", self)
all_results={}
evaluator=self.create_evaluator()
count=0
for each_article in self._reader:
count+=1
logging.info("Working on article %d: %r", count, each_article)
if not self.include_article(each_article):
logging.log(ULTRADEBUG, "Skipping article %r due to exclusion "
" criteria.", each_article)
continue
try:
ranked_article=self.graph_and_rank(each_article)
except CouldNotRank:
continue
converted_terms=self.convert(ranked_article)
cut_terms=converted_terms.terms_higher_than_or_equal_to(
self._ranking_cutoff)
logging.debug("Lowest-ranking term is term #%d out of %d"
" (score=%1.5f, highest score=%1.5f)",
len(cut_terms), len(converted_terms),
[x[1] for x in cut_terms][-1],
[x[1] for x in cut_terms][0])
medline_record_mesh_terms=ExpressionList().from_medline(
each_article.set_id.article_record().mesh_headings)
flat_medline=medline_record_mesh_terms.flatten()
flattened_terms=self.flatten_generated_terms(flat_medline,
cut_terms)
flattened_terms=self.limit_length(flat_medline, flattened_terms)
if len(flat_medline)==0:
logging.warn("No gold standard available for article %r. "
"Omitting it from the result set.", each_article)
continue
eval_result=self.perform_evaluation(each_article,
evaluator,
flat_medline,
flattened_terms)
flattened_major_headings=\
medline_record_mesh_terms.major_headings()
logging.debug("Original headings: %r Major headings: %r",
medline_record_mesh_terms,
flattened_major_headings)
mh_result_temp=self.perform_evaluation(each_article, evaluator,
flattened_major_headings,
flattened_terms)
mh_result=NamedResultSet("mh_", mh_result_temp)
# Compute the total recall, too
total_recall=self.compute_total_recall(flat_medline,
converted_terms)
eval_result.add(total_recall)
# Unify the result sets
all_results[each_article.set_id]=eval_result | mh_result
logging.info("Writing out results.")
self.output(all_results)
self.output_metadata()
return
def processor(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,
my_input_queue, my_output_queue,
my_own_name=None):
logging.info("Setting up worker.")
if my_own_name is not None:
proctitle.setproctitle(my_own_name)
my_workflow=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
)
if extra_data_name is not None:
my_workflow.__setattr__(extra_data_name, extra_data_contents)
logging.info("Finished setting up worker process. Waiting for requests.")
try:
while True:
request=my_input_queue.get()
logging.log(ULTRADEBUG, "Processing request %r", request)
if request=='STOP':
logging.log(ULTRADEBUG, "Received stop request.")
break
try:
my_workflow.process_article(request)
# Recover the article, push it on the output queue
my_output_queue.put(my_workflow.all_results)
# Clear the output queue
my_workflow.all_results={}
except CouldNotRank:
#my_input_queue.put(request) # On error, push the task
# back into the queue
logging.info("Skipping unrankable article.")
except:
logging.warn("EXCEPTION RAISED: \n%s",
traceback.format_exc())
raise
finally:
logging.log(ULTRADEBUG, "Returning results to caller.")
logging.log(ULTRADEBUG, "Ending processor execution.")
return
def processor(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,
my_input_queue,
my_output_queue,
my_own_name=None):
logging.info("Setting up worker.")
if my_own_name is not None:
proctitle.setproctitle(my_own_name)
my_workflow = 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)
if extra_data_name is not None:
my_workflow.__setattr__(extra_data_name, extra_data_contents)
logging.info("Finished setting up worker process. Waiting for requests.")
try:
while True:
request = my_input_queue.get()
logging.log(ULTRADEBUG, "Processing request %r", request)
if request == 'STOP':
logging.log(ULTRADEBUG, "Received stop request.")
break
try:
my_workflow.process_article(request)
# Recover the article, push it on the output queue
my_output_queue.put(my_workflow.all_results)
# Clear the output queue
my_workflow.all_results = {}
except CouldNotRank:
#my_input_queue.put(request) # On error, push the task
# back into the queue
logging.info("Skipping unrankable article.")
except:
logging.warn("EXCEPTION RAISED: \n%s", traceback.format_exc())
raise
finally:
logging.log(ULTRADEBUG, "Returning results to caller.")
logging.log(ULTRADEBUG, "Ending processor execution.")
return
def build_idf_from_file(self, file_reader, default_score=None):
tempdict = {}
logging.info("Building the term frequency dictionary")
count = 1
logging.debug("Checking for a cache file, and loading from it.")
try:
self.populate_from_cache(
self.cache_file_name(file_reader.original_file.name))
logging.info("Loaded from cache. It's not necessary to build.")
return
except:
logging.debug("Nope. Proceeding with building the dictionary.")
for article in file_reader:
logging.debug(
"Processing article %r (number %d) for the term"
" frequency dictionary", article, count)
if article.set_id.pmid < 0:
logging.warn("Article with unknown PubMed ID - skipping")
continue
count += 1
tempcounts = {}
for line in article.lines:
try:
this_cui = line.CUI
except AttributeError:
continue
# Use the confidence as the score if no default is specified
#if default_score is None:
# try:
# this_score=line.confidence
# except AttributeError:
# continue
#else:
# this_score=default_score
#tempdict[this_cui]=tempdict.get(this_cui, 0.0)+this_score
tempcounts[this_cui] = 1
# Now have all the CUIs that appeared in the article. Update
# the total counts.
for k in tempcounts:
tempdict[k] = tempdict.get(k, 0) + 1
logging.debug("Built a dictionary with %d items. Computing IDFs.",
len(tempdict))
# max_value=max(tempdict.itervalues())
#logging.debug("Saving it to permanent storage.")
for k, v in tempdict.iteritems():
self[k] = math.log(count / float(v)) + 1.0
logging.info("Done building the dictionary. Dumping it to a cache "
"file.")
self.dump_to_cache(self.cache_file_name(
file_reader.original_file.name))
return
def build_idf_from_file(self, file_reader, default_score=None):
tempdict={}
logging.info("Building the term frequency dictionary")
count=1
logging.debug("Checking for a cache file, and loading from it.")
try:
self.populate_from_cache(
self.cache_file_name(file_reader.original_file.name))
logging.info("Loaded from cache. It's not necessary to build.")
return
except:
logging.debug("Nope. Proceeding with building the dictionary.")
for article in file_reader:
logging.debug("Processing article %r (number %d) for the term"
" frequency dictionary", article, count)
if article.set_id.pmid < 0:
logging.warn("Article with unknown PubMed ID - skipping")
continue
count+=1
tempcounts={}
for line in article.lines:
try:
this_cui=line.CUI
except AttributeError:
continue
# Use the confidence as the score if no default is specified
#if default_score is None:
# try:
# this_score=line.confidence
# except AttributeError:
# continue
#else:
# this_score=default_score
#tempdict[this_cui]=tempdict.get(this_cui, 0.0)+this_score
tempcounts[this_cui]=1
# Now have all the CUIs that appeared in the article. Update
# the total counts.
for k in tempcounts:
tempdict[k]=tempdict.get(k, 0)+1
logging.debug("Built a dictionary with %d items. Computing IDFs.",
len(tempdict))
# max_value=max(tempdict.itervalues())
#logging.debug("Saving it to permanent storage.")
for k, v in tempdict.iteritems():
self[k]=math.log(count/float(v))+1.0
logging.info("Done building the dictionary. Dumping it to a cache "
"file.")
self.dump_to_cache(
self.cache_file_name(file_reader.original_file.name))
return
def _generate_normalization_factors(self):
"""Computes the array of normalization factors for the current
matrix."""
import operator
logging.info("Generating array of normalization factors. This is a "
"slow operation. Please wait.")
for i in xrange(self._height):
logging.debug("Generating normalization factor for row %d", i)
# Add all of the elements of the row together
matrix_row=self._get_row(i)
logging.log(ULTRADEBUG, "Row %d contains: %s", i, matrix_row)
this_row=reduce(operator.add, matrix_row)
if this_row==0.0:
logging.info("Row %d in the matrix adds up to 0. This may "
"be a problem, depending on your evaluation function. Since "
"this is a normalization calculation, it will be replaced by "
"1.", i)
this_row=1.0
self.normfactors[i]=this_row
logging.log(ULTRADEBUG, "Normalization factor for row %d=%1.5f", i,
this_row)
logging.info("Normalization factor generation done.")
def _generate_normalization_factors(self):
"""Computes the array of normalization factors for the current
matrix."""
import operator
logging.info("Generating array of normalization factors. This is a "
"slow operation. Please wait.")
for i in xrange(self._height):
logging.debug("Generating normalization factor for row %d", i)
# Add all of the elements of the row together
matrix_row = self._get_row(i)
logging.log(ULTRADEBUG, "Row %d contains: %s", i, matrix_row)
this_row = reduce(operator.add, matrix_row)
if this_row == 0.0:
logging.info(
"Row %d in the matrix adds up to 0. This may "
"be a problem, depending on your evaluation function. Since "
"this is a normalization calculation, it will be replaced by "
"1.", i)
this_row = 1.0
self.normfactors[i] = this_row
logging.log(ULTRADEBUG, "Normalization factor for row %d=%1.5f", i,
this_row)
logging.info("Normalization factor generation done.")
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
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
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