def set_up(self):
Session.remove()
EntityTestCase.set_up(self)
local_settings = self.config.get_settings()
tractor_config_file = local_settings['tractor_config_file']
tractor_api = make_api_from_config(tractor_config_file)
self.config.registry.registerUtility(tractor_api, ITractor) # pylint: disable=E1103
def __setup_thelma(self, ini_file):
here_dir = os.getcwd()
config_uri = 'config:%s' % ini_file
self.logging_file_config(ini_file) # pylint: disable=E1101
settings = appconfig(config_uri, 'thelma', relative_to=here_dir)
reg = Registry('thelma')
# Some tools need to resolve URLs, so we need to set up a request
# and a service.
url = 'http://0.0.0.0:6543'
req = DummyRequest(application_url=url,
host_url=url,
path_url=url,
url=url,
registry=reg)
config = create_config(settings, registry=reg)
config.setup_registry(settings=settings)
config.begin(request=req)
config.load_zcml('configure.zcml')
srvc = config.get_registered_utility(IService)
req.root = srvc
# Set up repositories.
repo_mgr = config.get_registered_utility(IRepositoryManager)
repo_mgr.initialize_all()
# Start the everest service.
srvc.start()
# Configure the session maker.
session_maker.configure(extension=ZopeTransactionExtension())
# Set up machinery to enforce a session.flush() just before the
# report is run so we have proper IDs in the output.
# FIXME: This should be encapsulated better, perhaps depending on
# an option that selects the backend.
def on_session_begin(session, trx, conn): # pylint: disable=W0613
self._report_callback = lambda sess = session: sess.flush()
event.listen(Session, 'after_begin', on_session_begin)
return config
def set_up(self):
Session.remove()
EntityTestCase.set_up(self)
local_settings = self.config.get_settings()
tractor_config_file = local_settings['tractor_config_file']
tractor_api = make_api_from_config(tractor_config_file)
self.config.registry.registerUtility(tractor_api, ITractor) # pylint: disable=E1103
def run(self):
session = Session()
query = self.QUERY_TEMPLATE % self.CUSTOM_BITS[self.__molecule_type]
self.add_info('Running stock query for %s molecules.\n%s' %
(self.__molecule_type, query))
records = session.execute(query)
column_map = self.COLUMN_MAP.copy()
if self.__molecule_type == 'SIRNA':
column_map['library'] = 'Ambion Library'
column_map['modification'] = 'Modification'
column_map['silencerselect'] = 'Silencer Select'
elif self.__molecule_type in ('MIRNA_INHI', 'MIRNA_MIMI'):
column_map['library'] = 'Library Y/N'
csv_file = open(self.__output_file, 'w')
with csv_file:
csv_writer = DictWriter(csv_file, column_map.values(),
dialect='audit')
self.add_info('Exporting audit report to file "%s".'
% self.__output_file)
number_records = 0
csv_writer.writeheader()
for record in records:
# Translate keys to labels.
rec_map = {}
for key, label in column_map.iteritems():
rec_map[label] = record[key]
csv_writer.writerow(rec_map)
number_records += 1
self.add_info('Wrote %d records to file.' % number_records)
def teardown_class(cls):
base_cls = super(RdbTestCaseMixin, cls)
try:
base_cls.teardown_class()
except AttributeError:
pass
Session.remove()
assert not Session.registry.has()
reset_metadata()
def run(self):
sess = ScopedSessionMaker()
for bc in self.__barcodes:
rack = self.__get_rack(bc)
for src_cnt in itervalues_(rack.container_positions):
if not src_cnt is None:
if not src_cnt.sample is None:
sess.delete(src_cnt.sample)
rack.status = get_item_status_future()
def run(self):
sess = ScopedSessionMaker()
for bc in self.__barcodes:
rack = self.__get_rack(bc)
for src_cnt in itervalues_(rack.container_positions):
if not src_cnt is None:
if not src_cnt.sample is None:
sess.delete(src_cnt.sample)
rack.status = get_item_status_future()
def teardown_class(cls):
base_cls = super(RdbTestCaseMixin, cls)
try:
base_cls.teardown_class()
except AttributeError:
pass
Session.remove()
assert not Session.registry.has()
reset_metadata()
def __exit__(self, ext_type, value, tb):
# Roll back the outer transaction and close the connection.
self.__session.close()
self.__transaction.rollback()
self.__connection.close()
# Remove the session we created.
Session.remove()
# Restore flags.
Session.configure(autoflush=self.__old_autoflush_flag,
bind=get_engine(self.__engine_name))
self.__repo.join_transaction = self.__old_join_transaction_flag
def __exit__(self, ext_type, value, tb):
# Roll back the outer transaction and close the connection.
self.__session.close()
self.__transaction.rollback()
self.__connection.close()
# Remove the session we created.
Session.remove()
# Restore flags.
Session.configure(autoflush=self.__old_autoflush_flag,
bind=get_engine(self.__engine_name))
self.__repo.join_transaction = self.__old_join_transaction_flag
def __setup_thelma(self, ini_file):
here_dir = os.getcwd()
config_uri = 'config:%s' % ini_file
self.logging_file_config(ini_file) # pylint: disable=E1101
settings = appconfig(config_uri, 'thelma', relative_to=here_dir)
reg = Registry('thelma')
# Some tools need to resolve URLs, so we need to set up a request
# and a service.
url = 'http://0.0.0.0:6543'
req = DummyRequest(application_url=url,
host_url=url,
path_url=url,
url=url,
registry=reg)
config = create_config(settings, registry=reg)
config.setup_registry(settings=settings)
config.begin(request=req)
config.load_zcml('configure.zcml')
srvc = config.get_registered_utility(IService)
req.root = srvc
# Set up repositories.
repo_mgr = config.get_registered_utility(IRepositoryManager)
repo_mgr.initialize_all()
# Start the everest service.
srvc.start()
# Configure the session maker.
session_maker.configure(extension=ZopeTransactionExtension())
# Set up machinery to enforce a session.flush() just before the
# report is run so we have proper IDs in the output.
# FIXME: This should be encapsulated better, perhaps depending on
# an option that selects the backend.
def on_session_begin(session, trx, conn): # pylint: disable=W0613
self._report_callback = lambda sess=session: sess.flush()
event.listen(Session, 'after_begin', on_session_begin)
return config
def __enter__(self):
# We set up an outer transaction that allows us to roll back all
# changes (including commits) the unittest may want to make.
engine = get_engine(self.__engine_name)
self.__connection = engine.connect()
self.__transaction = self.__connection.begin()
reg = get_current_registry()
repo_mgr = reg.getUtility(IRepositoryManager)
self.__repo = repo_mgr.get(self.__engine_name)
# Configure the autoflush behavior of the session.
if Session.registry.has():
self.__old_autoflush_flag = Session.autoflush # pylint:disable=E1101
else:
self.__old_autoflush_flag = self.__autoflush
Session.remove()
Session.configure(autoflush=self.__autoflush)
# Create a new session for the tests.
Session.configure(bind=self.__connection)
self.__old_join_transaction_flag = self.__repo.join_transaction
self.__repo.join_transaction = False
self.__session = self.__repo.session_factory()
return self.__session
def __enter__(self):
# We set up an outer transaction that allows us to roll back all
# changes (including commits) the unittest may want to make.
engine = get_engine(self.__engine_name)
self.__connection = engine.connect()
self.__transaction = self.__connection.begin()
reg = get_current_registry()
repo_mgr = reg.getUtility(IRepositoryManager)
self.__repo = repo_mgr.get(self.__engine_name)
# Configure the autoflush behavior of the session.
if Session.registry.has():
self.__old_autoflush_flag = Session.autoflush # pylint:disable=E1101
else:
self.__old_autoflush_flag = self.__autoflush
Session.remove()
Session.configure(autoflush=self.__autoflush)
# Create a new session for the tests.
Session.configure(bind=self.__connection)
self.__old_join_transaction_flag = self.__repo.join_transaction
self.__repo.join_transaction = False
self.__session = self.__repo.session_factory()
return self.__session
def set_up(self):
Session.remove()
ResourceTestCase.set_up(self)
#
self.config.testing_securitypolicy("it")
self._request.environ.update(create_extra_environ())
def tear_down():
Session.remove()
assert not Session.registry.has()
reset_metadata()
def tear_down(self):
Session.remove()
EntityTestCase.tear_down(self)
def tear_down():
Session.remove()
def tear_down(self):
transaction.abort()
Session.remove()
FunctionalTestCase.tear_down(self)
def tear_down(self):
Session.remove()
ResourceTestCase.tear_down(self)
def __enter__(self):
Session.remove()
def tear_down(self):
Session.remove()
ResourceTestCase.tear_down(self)
def tear_down(self):
super(RdbTestCaseMixin, self).tear_down()
Session.remove()
def tear_down():
Session.remove()
assert not Session.registry.has()
reset_metadata()
def tear_down(self):
super(RdbTestCaseMixin, self).tear_down()
Session.remove()
def tear_down():
Session.remove()
def __exit__(self, ext_type, value, tb):
Session.remove()
def __enter__(self):
Session.remove()
def __exit__(self, ext_type, value, tb):
Session.remove()
def tear_down(self):
transaction.abort()
Session.remove()
FunctionalTestCase.tear_down(self)
def __initialize_session(self):
# Initializes a session for ORM operations.
self.__session = ScopedSessionMaker()
def tear_down(self):
Session.remove()
EntityTestCase.tear_down(self)
def set_up(self):
Session.remove()
ResourceTestCase.set_up(self)
#
self.config.testing_securitypolicy("it")
self._request.environ.update(create_extra_environ())
