def fixture_deepen_negation_service(events_service, processor_watcher, processor_timeout):
port = str(find_free_port())
address = '127.0.0.1:' + port
p = Popen(
['python', '-m', 'biomedicus.negation.deepen', '-p', port, '--events', events_service],
stdin=PIPE, stdout=PIPE, stderr=STDOUT)
yield from processor_watcher(address, p, processor_timeout)
def fixture_concepts_service(events_service, processor_watcher, processor_timeout):
port = str(find_free_port())
address = '127.0.0.1:' + port
biomedicus_jar = biomedicus.biomedicus_jar()
p = Popen(['java', '-cp', biomedicus_jar,
'edu.umn.biomedicus.concepts.DictionaryConceptDetector', '-p', port,
'--events', events_service], stdin=PIPE, stdout=PIPE, stderr=PIPE)
yield from processor_watcher(address, p, timeout=processor_timeout)
def fixture_java_hello_processor(python_events, processor_watcher):
mtap_jar = os.environ['MTAP_JAR']
port = str(find_free_port())
p = Popen(['java', '-cp', mtap_jar, 'edu.umn.nlpie.mtap.examples.HelloWorldExample',
'-p', port, '--events', python_events],
stdin=PIPE, stdout=PIPE, stderr=STDOUT)
address = "127.0.0.1:" + port
yield from processor_watcher(address=address, process=p)
def fixture_modification_detector_service(events_service, processor_watcher, processor_timeout):
port = str(find_free_port())
address = '127.0.0.1:' + port
biomedicus_jar = biomedicus.biomedicus_jar()
p = Popen(['java', '-cp', biomedicus_jar,
'edu.umn.biomedicus.modification.ModificationDetector', '-p', port,
'--events', events_service], stdin=PIPE, stdout=PIPE, stderr=STDOUT)
yield from processor_watcher(address, p, timeout=processor_timeout)
def fixture_java_references_processor(python_events, processor_watcher):
mtap_jar = os.environ['MTAP_JAR']
mtap_jar = mtap_jar + ':' + str(Path(__file__).parents[1] / 'slf4j-simple-1.7.30.jar')
env = dict(os.environ)
port = str(find_free_port())
p = Popen(['java', '-cp', mtap_jar,
'edu.umn.nlpie.mtap.examples.ReferenceLabelsExampleProcessor',
'-p', port, '-e', python_events], stdin=PIPE, stdout=PIPE, stderr=STDOUT, env=env)
yield from processor_watcher(address="127.0.0.1:" + port, process=p)
def fixture_normalization_processor(events_service, processor_watcher, processor_timeout):
port = str(find_free_port())
address = '127.0.0.1:' + port
biomedicus_jar = biomedicus.biomedicus_jar()
p = Popen(['java', '-cp', biomedicus_jar,
'edu.umn.biomedicus.normalization.NormalizationProcessor',
'-p', port, '--events', events_service],
start_new_session=True, stdin=PIPE, stdout=PIPE, stderr=PIPE)
yield from processor_watcher(address, p, timeout=processor_timeout)
def fixture_pos_tags_service(events_service, processor_watcher, processor_timeout):
port = str(find_free_port())
address = '127.0.0.1:' + port
biomedicus_jar = biomedicus.biomedicus_jar()
p = Popen(['java', '-cp', biomedicus_jar,
'edu.umn.biomedicus.tagging.tnt.TntPosTaggerProcessor', '-p', port,
'--events', events_service],
start_new_session=True, stdin=PIPE, stdout=PIPE, stderr=STDOUT)
yield from processor_watcher(address, p, timeout=processor_timeout)
def fixture_python_processor(python_events, processor_watcher):
port = str(find_free_port())
p = Popen([
'python', '-m', 'mtap.examples.example_processor', '-p', port,
'--events', python_events
],
stdin=PIPE,
stdout=PIPE,
stderr=STDOUT)
yield from processor_watcher(address="127.0.0.1:" + port, process=p)
def fixture_hello_processor(python_events, processor_watcher):
port = find_free_port()
p = Popen([
'python', '-m', 'mtap.examples.tutorial.hello', '-p',
str(port), '--events', python_events
],
stdin=PIPE,
stdout=PIPE,
stderr=STDOUT)
address = "127.0.0.1:" + str(port)
yield from processor_watcher(address=address, process=p)
def fixture_sentences_service(events_service, processor_watcher,
processor_timeout):
port = str(find_free_port())
address = '127.0.0.1:' + port
p = subprocess.Popen([
'python', '-m', 'biomedicus.sentences.bi_lstm', 'processor', '-p',
port, '--events', events_service
],
start_new_session=True,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
yield from processor_watcher(address, p, timeout=processor_timeout)
def fixture_dependencies_service(events_service, processor_watcher, processor_timeout):
try:
existing_address = os.environ['DEPENDENCIES_ADDRESS']
yield existing_address
return
except KeyError:
pass
port = str(find_free_port())
address = '127.0.0.1:' + port
p = Popen(['python', '-m', 'biomedicus.dependencies.stanza_selective_parser',
'-p', port,
'--events', events_service],
start_new_session=True, stdin=PIPE,
stdout=PIPE, stderr=STDOUT)
yield from processor_watcher(address, p, timeout=processor_timeout)
def fixture_python_references_processor(python_events, processor_watcher):
env = dict(os.environ)
port = str(find_free_port())
p = Popen(['python', '-m', 'mtap.examples.example_references_processor', '-p', port,
'--events', python_events, '--log-level', 'DEBUG'], stdin=PIPE, stdout=PIPE, stderr=STDOUT, env=env)
yield from processor_watcher(address="127.0.0.1:" + port, process=p)
def fixture_python_events():
port = find_free_port()
with subprocess_events_server(port=port) as address:
yield address
def fixture_api_gateway(python_events, python_processor, java_processor):
port = find_free_port()
config = {
'discovery': 'consul',
'grpc': {
'enable_proxy': False
},
'max_send_message_length': 104857600,
'max_receive_message_length': 104857600,
'consul': {
'host': 'localhost',
'port': 8500,
'scheme': 'http',
# Python uses {python_naming_scheme}:address[:port][,address[:port],...] as grpc targets
'python_naming_scheme': 'ipv4'
},
'gateway': {
'port':
port,
'refresh_interval':
10,
'events':
python_events,
'processors': [{
'Identifier': 'mtap-example-processor-python',
'Endpoint': python_processor
}, {
'Identifier': 'mtap-example-processor-java',
'Endpoint': java_processor
}]
}
}
with tempfile.NamedTemporaryFile('w', suffix='.yml') as conf_file:
yaml.dump(config, conf_file, Dumper=Dumper)
conf_file.flush()
p = Popen([
'mtap-gateway', '-logtostderr', '-v=3',
'-mtap-config=' + conf_file.name
],
stdin=PIPE,
stdout=PIPE,
stderr=STDOUT)
session = requests.Session()
session.trust_env = False
gateway = '127.0.0.1:{}'.format(port)
try:
if p.returncode is not None:
raise ValueError("Failed to launch go gateway")
for i in range(6):
if i == 5:
raise ValueError("Failed to connect to go gateway")
try:
time.sleep(3)
resp = session.get(
"http://{}/v1/processors".format(gateway), timeout=1)
if resp.status_code == 200 and len(
resp.json()['Processors']) == 2:
break
except RequestException:
pass
yield gateway
finally:
session.close()
p.send_signal(signal.SIGINT)
try:
stdout, _ = p.communicate(timeout=1)
print("api gateway exited with code: ", p.returncode)
print(stdout.decode('utf-8'))
except TimeoutExpired:
print("timed out waiting for api gateway to terminate")
