def gene_to_variants():
variant_gene_dict = {}
for instance in list(PatientProcessor().build_list_of_aggregate_information(1)) + list(PatientAccessor().get_variant_for_gene_gene_fusions('', 'driverGene')) + list(PatientAccessor().get_variant_for_gene_gene_fusions('', 'partnerGene')):
if not AltIdentifierController.needs_an_alternative_identifier(instance['_id']["identifier"]):
if instance['_id']['identifier'] not in variant_gene_dict:
variant_gene_dict[instance['_id']['identifier']] = {}
if 'gene' in (instance['_id']).keys():
variant_gene_dict[instance['_id']['identifier']][instance['_id']['gene']] = instance['count'] + variant_gene_dict[instance['_id']['identifier']].get(str([instance['_id']['gene']]), 0)
else:
alternate_identifier = AltIdentifierController.create_new_identifier(instance)
if alternate_identifier not in variant_gene_dict:
variant_gene_dict[alternate_identifier] = {}
if 'gene' in (instance['_id']).keys():
variant_gene_dict[alternate_identifier][instance['_id']['gene']] = instance['count'] + variant_gene_dict[alternate_identifier].get(str([instance['_id']['gene']]), 0)
return jsonify({'gene for each variant': variant_gene_dict})
python类instance()的实例源码
def test_prepare_invalid_access(verify_token, options):
handler = mock_handler(base.AuthHandler)
handler.METHOD_ACCESS = {
"HEAD": "r",
"OPTIONS": "r",
"POST": "w",
"PATCH": "w",
"PUT": "w",
"DELETE": "w"
}
handler.request.method = 'GET'
with pytest.raises(base.HTTPError) as exc:
IOLoop.instance().run_sync(handler.prepare)
assert exc.value.status_code == 500
assert not verify_token.called
def listen(self, port, address="", **kwargs):
"""Starts an HTTP server for this application on the given port.
This is a convenience alias for creating an `.HTTPServer`
object and calling its listen method. Keyword arguments not
supported by `HTTPServer.listen <.TCPServer.listen>` are passed to the
`.HTTPServer` constructor. For advanced uses
(e.g. multi-process mode), do not use this method; create an
`.HTTPServer` and call its
`.TCPServer.bind`/`.TCPServer.start` methods directly.
Note that after calling this method you still need to call
``IOLoop.instance().start()`` to start the server.
"""
# import is here rather than top level because HTTPServer
# is not importable on appengine
from tornado.httpserver import HTTPServer
server = HTTPServer(self, **kwargs)
server.listen(port, address)
def tearDown(self):
# Clean up Subprocess, so it can be used again with a new ioloop.
Subprocess.uninitialize()
self.io_loop.clear_current()
if (not IOLoop.initialized() or
self.io_loop is not IOLoop.instance()):
# Try to clean up any file descriptors left open in the ioloop.
# This avoids leaks, especially when tests are run repeatedly
# in the same process with autoreload (because curl does not
# set FD_CLOEXEC on its file descriptors)
self.io_loop.close(all_fds=True)
super(AsyncTestCase, self).tearDown()
# In case an exception escaped or the StackContext caught an exception
# when there wasn't a wait() to re-raise it, do so here.
# This is our last chance to raise an exception in a way that the
# unittest machinery understands.
self.__rethrow()
def main(app: Flask, tornado: bool=False) -> None:
"""Run the Flask application."""
with app.app_context():
db.create_all()
print('[OK] Database creation complete.')
if tornado:
from tornado.wsgi import WSGIContainer
from tornado.httpserver import HTTPServer
from tornado.ioloop import IOLoop
http_server = HTTPServer(WSGIContainer(app))
http_server.listen(int(app.config['INIT_PORT']))
IOLoop.instance().start()
else:
socketio.run(app, **app.config['INIT'])
def tearDown(self):
# Clean up Subprocess, so it can be used again with a new ioloop.
Subprocess.uninitialize()
self.io_loop.clear_current()
if (not IOLoop.initialized() or
self.io_loop is not IOLoop.instance()):
# Try to clean up any file descriptors left open in the ioloop.
# This avoids leaks, especially when tests are run repeatedly
# in the same process with autoreload (because curl does not
# set FD_CLOEXEC on its file descriptors)
self.io_loop.close(all_fds=True)
super(AsyncTestCase, self).tearDown()
# In case an exception escaped or the StackContext caught an exception
# when there wasn't a wait() to re-raise it, do so here.
# This is our last chance to raise an exception in a way that the
# unittest machinery understands.
self.__rethrow()
def run_tests():
url = options.url + '/getCaseCount'
control_ws = yield websocket_connect(url, None)
num_tests = int((yield control_ws.read_message()))
logging.info('running %d cases', num_tests)
msg = yield control_ws.read_message()
assert msg is None
for i in range(1, num_tests + 1):
logging.info('running test case %d', i)
url = options.url + '/runCase?case=%d&agent=%s' % (i, options.name)
test_ws = yield websocket_connect(url, None, compression_options={})
while True:
message = yield test_ws.read_message()
if message is None:
break
test_ws.write_message(message, binary=isinstance(message, bytes))
url = options.url + '/updateReports?agent=%s' % options.name
update_ws = yield websocket_connect(url, None)
msg = yield update_ws.read_message()
assert msg is None
IOLoop.instance().stop()
def tearDown(self):
# Clean up Subprocess, so it can be used again with a new ioloop.
Subprocess.uninitialize()
self.io_loop.clear_current()
if (not IOLoop.initialized() or
self.io_loop is not IOLoop.instance()):
# Try to clean up any file descriptors left open in the ioloop.
# This avoids leaks, especially when tests are run repeatedly
# in the same process with autoreload (because curl does not
# set FD_CLOEXEC on its file descriptors)
self.io_loop.close(all_fds=True)
super(AsyncTestCase, self).tearDown()
# In case an exception escaped or the StackContext caught an exception
# when there wasn't a wait() to re-raise it, do so here.
# This is our last chance to raise an exception in a way that the
# unittest machinery understands.
self.__rethrow()
def tearDown(self):
# Clean up Subprocess, so it can be used again with a new ioloop.
Subprocess.uninitialize()
self.io_loop.clear_current()
if (not IOLoop.initialized() or
self.io_loop is not IOLoop.instance()):
# Try to clean up any file descriptors left open in the ioloop.
# This avoids leaks, especially when tests are run repeatedly
# in the same process with autoreload (because curl does not
# set FD_CLOEXEC on its file descriptors)
self.io_loop.close(all_fds=True)
super(AsyncTestCase, self).tearDown()
# In case an exception escaped or the StackContext caught an exception
# when there wasn't a wait() to re-raise it, do so here.
# This is our last chance to raise an exception in a way that the
# unittest machinery understands.
self.__rethrow()
def start(self):
def go(app, port, data={}):
from httpretty import HTTPretty
HTTPretty.disable()
http = HTTPServer(app)
HTTPretty.disable()
http.listen(int(port))
IOLoop.instance().start()
app = self.get_handlers()
data = {}
args = (app, self.port, data)
HTTPretty.disable()
self.process = Process(target=go, args=args)
self.process.start()
time.sleep(1)
def run_tests():
url = options.url + '/getCaseCount'
control_ws = yield websocket_connect(url, None)
num_tests = int((yield control_ws.read_message()))
logging.info('running %d cases', num_tests)
msg = yield control_ws.read_message()
assert msg is None
for i in range(1, num_tests + 1):
logging.info('running test case %d', i)
url = options.url + '/runCase?case=%d&agent=%s' % (i, options.name)
test_ws = yield websocket_connect(url, None, compression_options={})
while True:
message = yield test_ws.read_message()
if message is None:
break
test_ws.write_message(message, binary=isinstance(message, bytes))
url = options.url + '/updateReports?agent=%s' % options.name
update_ws = yield websocket_connect(url, None)
msg = yield update_ws.read_message()
assert msg is None
IOLoop.instance().stop()
def tearDown(self):
# Clean up Subprocess, so it can be used again with a new ioloop.
Subprocess.uninitialize()
self.io_loop.clear_current()
if (not IOLoop.initialized() or
self.io_loop is not IOLoop.instance()):
# Try to clean up any file descriptors left open in the ioloop.
# This avoids leaks, especially when tests are run repeatedly
# in the same process with autoreload (because curl does not
# set FD_CLOEXEC on its file descriptors)
self.io_loop.close(all_fds=True)
super(AsyncTestCase, self).tearDown()
# In case an exception escaped or the StackContext caught an exception
# when there wasn't a wait() to re-raise it, do so here.
# This is our last chance to raise an exception in a way that the
# unittest machinery understands.
self.__rethrow()
def tearDown(self):
# Clean up Subprocess, so it can be used again with a new ioloop.
Subprocess.uninitialize()
self.io_loop.clear_current()
if (not IOLoop.initialized() or
self.io_loop is not IOLoop.instance()):
# Try to clean up any file descriptors left open in the ioloop.
# This avoids leaks, especially when tests are run repeatedly
# in the same process with autoreload (because curl does not
# set FD_CLOEXEC on its file descriptors)
self.io_loop.close(all_fds=True)
super(AsyncTestCase, self).tearDown()
# In case an exception escaped or the StackContext caught an exception
# when there wasn't a wait() to re-raise it, do so here.
# This is our last chance to raise an exception in a way that the
# unittest machinery understands.
self.__rethrow()
def tearDown(self):
# Clean up Subprocess, so it can be used again with a new ioloop.
Subprocess.uninitialize()
self.io_loop.clear_current()
if (not IOLoop.initialized() or
self.io_loop is not IOLoop.instance()):
# Try to clean up any file descriptors left open in the ioloop.
# This avoids leaks, especially when tests are run repeatedly
# in the same process with autoreload (because curl does not
# set FD_CLOEXEC on its file descriptors)
self.io_loop.close(all_fds=True)
super(AsyncTestCase, self).tearDown()
# In case an exception escaped or the StackContext caught an exception
# when there wasn't a wait() to re-raise it, do so here.
# This is our last chance to raise an exception in a way that the
# unittest machinery understands.
self.__rethrow()
def tearDown(self):
# Clean up Subprocess, so it can be used again with a new ioloop.
Subprocess.uninitialize()
self.io_loop.clear_current()
if (not IOLoop.initialized() or
self.io_loop is not IOLoop.instance()):
# Try to clean up any file descriptors left open in the ioloop.
# This avoids leaks, especially when tests are run repeatedly
# in the same process with autoreload (because curl does not
# set FD_CLOEXEC on its file descriptors)
self.io_loop.close(all_fds=True)
super(AsyncTestCase, self).tearDown()
# In case an exception escaped or the StackContext caught an exception
# when there wasn't a wait() to re-raise it, do so here.
# This is our last chance to raise an exception in a way that the
# unittest machinery understands.
self.__rethrow()
def run_tests():
url = options.url + '/getCaseCount'
control_ws = yield websocket_connect(url, None)
num_tests = int((yield control_ws.read_message()))
logging.info('running %d cases', num_tests)
msg = yield control_ws.read_message()
assert msg is None
for i in range(1, num_tests + 1):
logging.info('running test case %d', i)
url = options.url + '/runCase?case=%d&agent=%s' % (i, options.name)
test_ws = yield websocket_connect(url, None, compression_options={})
while True:
message = yield test_ws.read_message()
if message is None:
break
test_ws.write_message(message, binary=isinstance(message, bytes))
url = options.url + '/updateReports?agent=%s' % options.name
update_ws = yield websocket_connect(url, None)
msg = yield update_ws.read_message()
assert msg is None
IOLoop.instance().stop()
