def sign_out(self):
# Use public credentials when user signs out
self.res = connect(url=DEFAULT_URL)
# Remove username and
cm = CredentialManager(CREDENTIAL_MANAGER_SERVICE)
del cm.username
del cm.password
def sign_in(self):
self.server_cb_label.setStyleSheet(None)
self.username_label.setStyleSheet(None)
self.password_label.setStyleSheet(None)
self.error_msg.hide()
server = self.server_cb.currentText()
username = self.cm.username if self.cm.username else self.username_line_edit.text()
password = self.cm.password if self.cm.password else self.password_line_edit.text()
if not server:
self.server_cb_label.setStyleSheet('color:red')
return
if not username:
self.username_label.setStyleSheet('color:red')
return
if not password:
self.password_label.setStyleSheet('color:red')
return
try:
self.resolwe_instance = connect(username, password, url=server)
except ResolweAuthException:
self.error_msg.show()
return
self.cm.username = username
self.cm.password = password
self.accept()
def test_objects(self):
from orangecontrib.bioinformatics import resolwe
from orangecontrib.bioinformatics.resolwe.utils import etc_to_table
email = '*****@*****.**'
password = '******'
url = 'https://dictyexpress.research.bcm.edu'
gen = resolwe.connect(email, password, url, 'genesis')
etc_objects = gen.fetch_etc_objects()
self.assertEqual(type(etc_objects), list) # test if return type is list
self.assertTrue(etc_objects) # test if list is not empty
self.assertEqual(etc_objects[0].type, 'data:etc:') # test if it contains correct objects
# Test experiment D. purpureu
for obj in etc_objects:
if obj.name == 'D. purpureum':
test_experiment = obj
self.assertTrue(test_experiment)
self.assertEqual(test_experiment.id, '564a509e6b13390ffb40d4c8')
json, table_name = gen.download_etc_data(test_experiment.id)
self.assertEqual(type(json), dict)
self.assertEqual(len(json["etc"].keys()), 2)
self.assertEqual(len(json["etc"]["genes"].keys()), 12410)
self.assertEqual(json["etc"]["genes"]["DPU_G0071544"], [0.0, 0.1787337345055, 4.20485453935, 20.002575156149998,
19.52080354305, 18.7919080288, 12.38709403699])
self.assertEqual(json["etc"]["timePoints"], [0, 4, 8, 12, 16, 20, 24])
self.assertEqual(type(etc_to_table(json)), Orange.data.table.Table)
def test_login(self):
from orangecontrib.bioinformatics import resolwe
email = '*****@*****.**'
password = '******'
url = 'https://dictyexpress.research.bcm.edu'
self.assertTrue(resolwe.connect(email, password, url, 'genesis'))
self.assertRaises(Exception, resolwe.connect, email, "123", url, 'genesis')
def sign_out(self):
# Remove username and password
cm = get_credential_manager(resolwe.GENESIS_PLATFORM)
del cm.username
del cm.password
# Use public credentials when user signs out
self.res = connect(**self.genapi_pub_auth,
server_type=resolwe.GENESIS_PLATFORM)
def sign_out(self):
# Use public credentials when user signs out
self.res = resolwe.connect(url=resolwe.resapi.DEFAULT_URL,
server_type=resolwe.RESOLWE_PLATFORM)
# Remove username and password
cm = get_credential_manager(resolwe.RESOLWE_PLATFORM)
if cm.username:
del cm.username
if cm.password:
del cm.password
def sign_in(self, silent=False):
dialog = SignInForm(self)
if silent:
dialog.sign_in()
if dialog.resolwe_instance is not None:
self.res = dialog.resolwe_instance
else:
self.res = connect(url=DEFAULT_URL)
if not silent and dialog.exec_():
self.res = dialog.resolwe_instance
def sign_in(self, silent=False):
dialog = SignIn(self, server_type='genesis')
if silent:
dialog.sign_in()
if dialog.resolwe_instance is not None:
self.res = dialog.resolwe_instance
else:
self.res = connect(**self.genapi_pub_auth,
server_type=resolwe.GENESIS_PLATFORM)
if not silent and dialog.exec_():
self.res = dialog.resolwe_instance
def sign_in(self, silent=False):
dialog = SignIn(self, server_type=resolwe.RESOLWE_PLATFORM)
if silent:
dialog.sign_in()
if dialog.resolwe_instance is not None:
self.res = dialog.resolwe_instance
else:
self.res = resolwe.connect(
url=resolwe.resapi.DEFAULT_URL,
server_type=resolwe.RESOLWE_PLATFORM)
if not silent and dialog.exec_():
self.res = dialog.resolwe_instance
def connect(self):
self.res = None
self.Error.clear()
self.reset()
self.handle_cache_button(False)
user, password = resolwe.DEFAULT_EMAIL, resolwe.DEFAULT_PASSWD
if self.username or self.password:
user, password = self.username, self.password
try:
self.res = resolwe.connect(user, password, self.server, 'genesis')
except resolwe.ResolweAuthException:
self.Error.invalid_credentials()
else:
self.load_experiments()
self.handle_cache_button(True)
