def initialize(introspected_modules, load_xml_events=True):
"""
Initialize when Application is starting.
Check for new algorithms or new DataTypes.
"""
SettingsService().check_db_url(TvbProfile.current.db.DB_URL)
## Initialize DB
is_db_empty = initialize_startup()
## Create Projects storage root in case it does not exist.
initialize_storage()
## Populate DB algorithms, by introspection
event_folders = []
start_introspection_time = datetime.datetime.now()
for module in introspected_modules:
introspector = Introspector(module)
# Introspection is always done, even if DB was not empty.
introspector.introspect(True)
event_path = introspector.get_events_path()
if event_path:
event_folders.append(event_path)
# Now remove or mark as removed any unverified Algo-Group, Algo-Category or Portlet
to_invalidate, to_remove = dao.get_non_validated_entities(
start_introspection_time)
for entity in to_invalidate:
entity.removed = True
dao.store_entities(to_invalidate)
for entity in to_remove:
dao.remove_entity(entity.__class__, entity.id)
## Populate events
if load_xml_events:
read_events(event_folders)
if not TvbProfile.is_first_run():
## Create default users.
if is_db_empty:
dao.store_entity(
model.User(TvbProfile.current.web.admin.SYSTEM_USER_NAME, None,
None, True, None))
UserService().create_user(
username=TvbProfile.current.web.admin.ADMINISTRATOR_NAME,
password=TvbProfile.current.web.admin.ADMINISTRATOR_PASSWORD,
email=TvbProfile.current.web.admin.ADMINISTRATOR_EMAIL,
role=model.ROLE_ADMINISTRATOR)
## In case actions related to latest code-changes are needed, make sure they are executed.
CodeUpdateManager().run_all_updates()
## In case the H5 version changed, run updates on all DataTypes
if TvbProfile.current.version.DATA_CHECKED_TO_VERSION < TvbProfile.current.version.DATA_VERSION:
thread = threading.Thread(
target=FilesUpdateManager().run_all_updates)
thread.start()
## Clean tvb-first-time-run temporary folder, as we are no longer at the first run:
shutil.rmtree(TvbProfile.current.FIRST_RUN_STORAGE, True)
def setUp(self):
"""
Introspect supplementary folder:
"""
core_path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
TvbProfile.current.web.CURRENT_DIR = os.path.dirname(core_path)
self.introspector = Introspector("tvb.tests.framework")
self.introspector.introspect(True)
def setUp(self):
"""
Reset the database before each test.
"""
self.reset_database()
#tvb_test path
core_path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
self.old_path = cfg.CURRENT_DIR
cfg.CURRENT_DIR = os.path.dirname(core_path)
self.introspector = Introspector("tvb_test")
def setUp(self):
"""
Introspect supplementary folder:
"""
core_path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
TvbProfile.current.web.CURRENT_DIR = os.path.dirname(core_path)
adapters_init.__xml_folders__ = [os.path.join("core", "adapters")]
self.introspector = Introspector("tvb.tests.framework")
self.introspector.introspect(True)
def initialize(introspected_modules, load_xml_events=True):
"""
Initialize when Application is starting.
Check for new algorithms or new DataTypes.
"""
SettingsService().check_db_url(TvbProfile.current.db.DB_URL)
## Initialize DB
is_db_empty = initialize_startup()
## Create Projects storage root in case it does not exist.
initialize_storage()
## Populate DB algorithms, by introspection
event_folders = []
start_introspection_time = datetime.datetime.now()
for module in introspected_modules:
introspector = Introspector(module)
# Introspection is always done, even if DB was not empty.
introspector.introspect(True)
event_path = introspector.get_events_path()
if event_path:
event_folders.append(event_path)
# Now remove or mark as removed any unverified Algo-Group, Algo-Category or Portlet
to_invalidate, to_remove = dao.get_non_validated_entities(start_introspection_time)
for entity in to_invalidate:
entity.removed = True
dao.store_entities(to_invalidate)
for entity in to_remove:
dao.remove_entity(entity.__class__, entity.id)
## Populate events
if load_xml_events:
read_events(event_folders)
if not TvbProfile.is_first_run():
## Create default users.
if is_db_empty:
dao.store_entity(model.User(TvbProfile.current.web.admin.SYSTEM_USER_NAME, None, None, True, None))
UserService().create_user(username=TvbProfile.current.web.admin.ADMINISTRATOR_NAME,
password=TvbProfile.current.web.admin.ADMINISTRATOR_PASSWORD,
email=TvbProfile.current.web.admin.ADMINISTRATOR_EMAIL,
role=model.ROLE_ADMINISTRATOR)
## In case actions related to latest code-changes are needed, make sure they are executed.
CodeUpdateManager().run_all_updates()
## In case the H5 version changed, run updates on all DataTypes
if TvbProfile.current.version.DATA_CHECKED_TO_VERSION < TvbProfile.current.version.DATA_VERSION:
thread = threading.Thread(target=FilesUpdateManager().run_all_updates)
thread.start()
## Clean tvb-first-time-run temporary folder, as we are no longer at the first run:
shutil.rmtree(TvbProfile.current.FIRST_RUN_STORAGE, True)
class IntrospectorTest(BaseTestCase):
"""
Test class for the introspection module.
"""
old_current_dir = TvbProfile.current.web.CURRENT_DIR
def setUp(self):
"""
Introspect supplementary folder:
"""
core_path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
TvbProfile.current.web.CURRENT_DIR = os.path.dirname(core_path)
self.introspector = Introspector("tvb.tests.framework")
self.introspector.introspect(True)
def tearDown(self):
"""
Revert changes settings and remove recently imported algorithms
"""
TvbProfile.current.web.CURRENT_DIR = self.old_current_dir
def test_introspect(self):
"""
Test that expected categories and groups are found in DB after introspection.
We also check algorithms introspected during base_testcase.init_test_env
"""
all_categories = dao.get_algorithm_categories()
category_ids = [
cat.id for cat in all_categories
if cat.displayname == "AdaptersTest"
]
adapters = dao.get_adapters_from_categories(category_ids)
self.assertEqual(8, len(adapters), "Introspection failed!")
nr_adapters_mod2 = 0
for algorithm in adapters:
self.assertTrue(
algorithm.module in [
'tvb.tests.framework.adapters.testadapter1',
'tvb.tests.framework.adapters.testadapter2',
'tvb.tests.framework.adapters.testadapter3',
'tvb.tests.framework.adapters.ndimensionarrayadapter',
'tvb.tests.framework.adapters.testgroupadapter'
], "Unknown Adapter module:" + str(algorithm.module))
self.assertTrue(
algorithm.classname in [
"TestAdapter1", "TestAdapterDatatypeInput", "TestAdapter2",
"TestAdapter22", "TestAdapterHugeMemoryRequired",
"TestAdapter3", "TestAdapterHDDRequired",
"NDimensionArrayAdapter"
], "Unknown Adapter Class:" + str(algorithm.classname))
if algorithm.module == 'tvb.tests.framework.adapters.testadapter2':
nr_adapters_mod2 += 1
self.assertEqual(nr_adapters_mod2, 2)
class IntrospectorTest(BaseTestCase):
"""
Test class for the introspection module.
"""
old_current_dir = TvbProfile.current.web.CURRENT_DIR
def setUp(self):
"""
Introspect supplementary folder:
"""
core_path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
TvbProfile.current.web.CURRENT_DIR = os.path.dirname(core_path)
self.introspector = Introspector("tvb.tests.framework")
self.introspector.introspect(True)
def tearDown(self):
"""
Revert changes settings and remove recently imported algorithms
"""
TvbProfile.current.web.CURRENT_DIR = self.old_current_dir
def test_introspect(self):
"""
Test that expected categories and groups are found in DB after introspection.
We also check algorithms introspected during base_testcase.init_test_env
"""
all_categories = dao.get_algorithm_categories()
category_ids = [cat.id for cat in all_categories if cat.displayname == "AdaptersTest"]
adapters = dao.get_adapters_from_categories(category_ids)
self.assertEqual(8, len(adapters), "Introspection failed!")
nr_adapters_mod2 = 0
for algorithm in adapters:
self.assertTrue(algorithm.module in ['tvb.tests.framework.adapters.testadapter1',
'tvb.tests.framework.adapters.testadapter2',
'tvb.tests.framework.adapters.testadapter3',
'tvb.tests.framework.adapters.ndimensionarrayadapter',
'tvb.tests.framework.adapters.testgroupadapter'],
"Unknown Adapter module:" + str(algorithm.module))
self.assertTrue(algorithm.classname in ["TestAdapter1", "TestAdapterDatatypeInput",
"TestAdapter2", "TestAdapter22", "TestAdapterHugeMemoryRequired",
"TestAdapter3", "TestAdapterHDDRequired",
"NDimensionArrayAdapter"
],
"Unknown Adapter Class:" + str(algorithm.classname))
if algorithm.module == 'tvb.tests.framework.adapters.testadapter2':
nr_adapters_mod2 += 1
self.assertEqual(nr_adapters_mod2, 2)
def setUp(self):
"""
This method sets up the necessary paths for testing.
"""
self.folder_path = os.path.dirname(__file__)
#tvb_test path
core_path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
self.old_path = cfg.CURRENT_DIR
cfg.CURRENT_DIR = os.path.dirname(core_path)
adapters_init.__xml_folders__ = [os.path.join('core', 'adapters')]
self.introspector = Introspector("tvb_test")
self.introspector.introspect(True)
xml_group_path = os.path.join('core', 'adapters', "test_group.xml")
algo_group = dao.find_group('tvb_test.adapters.testgroupadapter', 'TestGroupAdapter', xml_group_path)
self.xml_group_adapter = ABCAdapter.build_adapter(algo_group)
self.xml_group_reader = self.xml_group_adapter.xml_reader
def initialize(introspected_modules, load_xml_events=True):
"""
Initialize when Application is starting.
Check for new algorithms or new DataTypes.
"""
SettingsService().check_db_url(cfg.DB_URL)
## Initialize DB
is_db_empty = initialize_startup()
## Create Projects storage root in case it does not exist.
initialize_storage()
## Populate DB algorithms, by introspection
event_folders = []
start_introspection_time = datetime.datetime.now()
for module in introspected_modules:
introspector = Introspector(module)
# Introspection is always done, even if DB was not empty.
introspector.introspect(True)
event_path = introspector.get_events_path()
if event_path:
event_folders.append(event_path)
# Now remove any unverified Algo-Groups, categories or Portlets
invalid_stored_entities = dao.get_non_validated_entities(
start_introspection_time)
for entity in invalid_stored_entities:
dao.remove_entity(entity.__class__, entity.id)
## Populate events
if load_xml_events:
eventhandler.read_events(event_folders)
## Make sure DB events are linked.
db_events.attach_db_events()
## Create default users.
if is_db_empty:
dao.store_entity(
model.User(cfg.SYSTEM_USER_NAME, None, None, True, None))
UserService().create_user(username=cfg.ADMINISTRATOR_NAME,
password=cfg.ADMINISTRATOR_PASSWORD,
email=cfg.ADMINISTRATOR_EMAIL,
role=ROLE_ADMINISTRATOR)
## In case actions related to latest code-changes are needed, make sure they are executed.
CodeUpdateManager().update_all()
def setUp(self):
"""
Introspect supplementary folder:
"""
core_path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
TvbProfile.current.web.CURRENT_DIR = os.path.dirname(core_path)
self.introspector = Introspector("tvb.tests.framework")
self.introspector.introspect(True)
def initialize(introspected_modules, load_xml_events=True):
"""
Initialize when Application is starting.
Check for new algorithms or new DataTypes.
"""
SettingsService().check_db_url(cfg.DB_URL)
## Initialize DB
is_db_empty = initialize_startup()
## Create Projects storage root in case it does not exist.
initialize_storage()
## Populate DB algorithms, by introspection
event_folders = []
start_introspection_time = datetime.datetime.now()
for module in introspected_modules:
introspector = Introspector(module)
# Introspection is always done, even if DB was not empty.
introspector.introspect(True)
event_path = introspector.get_events_path()
if event_path:
event_folders.append(event_path)
# Now remove any unverified Algo-Groups, categories or Portlets
invalid_stored_entities = dao.get_non_validated_entities(start_introspection_time)
for entity in invalid_stored_entities:
dao.remove_entity(entity.__class__, entity.id)
## Populate events
if load_xml_events:
read_events(event_folders)
## Make sure DB events are linked.
db_events.attach_db_events()
## Create default users.
if is_db_empty:
dao.store_entity(model.User(cfg.SYSTEM_USER_NAME, None, None, True, None))
UserService().create_user(username=cfg.ADMINISTRATOR_NAME, password=cfg.ADMINISTRATOR_PASSWORD,
email=cfg.ADMINISTRATOR_EMAIL, role=model.ROLE_ADMINISTRATOR)
## In case actions related to latest code-changes are needed, make sure they are executed.
CodeUpdateManager().update_all()
def setUp(self):
"""
Set up any additionally needed parameters.
"""
super(GenshiTestGroup, self).setUp()
core_path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
self.old_path = cfg.CURRENT_DIR
cfg.CURRENT_DIR = os.path.dirname(core_path)
adapters_init.__xml_folders__ = [os.path.join('interfaces', 'web')]
self.introspector = Introspector("tvb_test")
self.introspector.introspect(True)
xml_group_path = os.path.join('interfaces', 'web', "test_group.xml")
algo_group = dao.find_group('tvb_test.adapters.testgroupadapter',
'TestGroupAdapter', xml_group_path)
self.xml_group_adapter = ABCAdapter.build_adapter(algo_group)
input_tree = self.xml_group_adapter.get_input_tree()
input_tree = ABCAdapter.prepare_param_names(input_tree)
self.template_specification['inputList'] = input_tree
self.template_specification[base.KEY_PARAMETERS_CONFIG] = False
resulted_html = _template2string(self.template_specification)
self.soup = BeautifulSoup(resulted_html)
def setUp(self):
"""
This method sets up the necessary paths for testing.
"""
self.folder_path = os.path.dirname(__file__)
core_path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
TvbProfile.current.web.CURRENT_DIR = os.path.dirname(core_path)
adapters_init.__xml_folders__ = [os.path.join('core', 'adapters')]
self.introspector = Introspector("tvb.tests.framework")
self.introspector.introspect(True)
xml_group_path = os.path.join('core', 'adapters', "test_group.xml")
algo_group = dao.find_group('tvb.tests.framework.adapters.testgroupadapter', 'TestGroupAdapter', xml_group_path)
self.xml_group_adapter = ABCAdapter.build_adapter(algo_group)
self.xml_group_reader = self.xml_group_adapter.xml_reader
class IntrospectorTest(BaseTestCase):
"""
Test class for the introspection module.
"""
old_current_dir = TvbProfile.current.web.CURRENT_DIR
old_xml_path = adapters_init.__xml_folders__
def setUp(self):
"""
Introspect supplementary folder:
"""
core_path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
TvbProfile.current.web.CURRENT_DIR = os.path.dirname(core_path)
adapters_init.__xml_folders__ = [os.path.join("core", "adapters")]
self.introspector = Introspector("tvb.tests.framework")
self.introspector.introspect(True)
def tearDown(self):
"""
Revert changes settings and remove recently imported algorithms
"""
TvbProfile.current.web.CURRENT_DIR = self.old_current_dir
adapters_init.__xml_folders__ = self.old_xml_path
for group in dao.get_generic_entity(model.AlgorithmGroup, "simple", "algorithm_param_name"):
dao.remove_entity(model.AlgorithmGroup, group.id)
def test_introspect(self):
"""
Test that expected categories and groups are found in DB after introspection.
We also check algorithms introspected during base_testcase.init_test_env
"""
all_categories = dao.get_algorithm_categories()
category_ids = [cat.id for cat in all_categories if cat.displayname == "AdaptersTest"]
groups = dao.get_groups_by_categories(category_ids)
self.assertEqual(12, len(groups), "Introspection failed!")
nr_adapters_mod2 = 0
nr_from_xml = 0
for algorithm in groups:
self.assertTrue(algorithm.module in ['tvb.tests.framework.adapters.testadapter1',
'tvb.tests.framework.adapters.testadapter2',
'tvb.tests.framework.adapters.testadapter3',
'tvb.tests.framework.adapters.ndimensionarrayadapter',
'tvb.tests.framework.adapters.testgroupadapter'],
"Unknown Adapter module:" + str(algorithm.module))
self.assertTrue(algorithm.classname in ["TestAdapter1", "TestAdapterDatatypeInput",
"TestAdapter2", "TestAdapter22", "TestAdapterHugeMemoryRequired",
"TestAdapter3", "TestAdapterHDDRequired",
"NDimensionArrayAdapter", "TestGroupAdapter"
],
"Unknown Adapter Class:" + str(algorithm.classname))
if algorithm.module == 'tvb.tests.framework.adapters.testadapter2':
nr_adapters_mod2 += 1
if algorithm.module == 'tvb.tests.framework.adapters.testgroupadapter':
nr_from_xml += 1
self.assertEqual(nr_adapters_mod2, 2)
self.assertEqual(nr_from_xml, 4)
def test_xml_introspection(self):
"""
Check that the new xml specified in setUp was correctly introspected.
"""
init_parameter = os.path.join("core", "adapters", "test_group.xml")
group = dao.find_group("tvb.tests.framework.adapters.testgroupadapter", "TestGroupAdapter", init_parameter)
self.assertTrue(group is not None, "The group was not found")
self.assertEqual(group.init_parameter, init_parameter, "Wrong init_parameter:" + str(group.init_parameter))
self.assertEqual(group.displayname, "Simple Python Analyzers", "The display-name of the group is not valid")
self.assertEqual(group.algorithm_param_name, "simple", "The algorithm_param_name of the group is not valid")
self.assertEqual(group.classname, "TestGroupAdapter", "The class-name of the group is not valid")
self.assertEqual(group.module, "tvb.tests.framework.adapters.testgroupadapter", "Group Module invalid")
class GenshiTestGroup(GenshiTest):
"""
For a group of algorithms interface test that
various fields are generated correctly.
"""
def setUp(self):
"""
Set up any additionally needed parameters.
"""
super(GenshiTestGroup, self).setUp()
core_path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
self.old_path = cfg.CURRENT_DIR
cfg.CURRENT_DIR = os.path.dirname(core_path)
adapters_init.__xml_folders__ = [os.path.join('interfaces', 'web')]
self.introspector = Introspector("tvb_test")
self.introspector.introspect(True)
xml_group_path = os.path.join('interfaces', 'web', "test_group.xml")
algo_group = dao.find_group('tvb_test.adapters.testgroupadapter',
'TestGroupAdapter', xml_group_path)
self.xml_group_adapter = ABCAdapter.build_adapter(algo_group)
input_tree = self.xml_group_adapter.get_input_tree()
input_tree = ABCAdapter.prepare_param_names(input_tree)
self.template_specification['inputList'] = input_tree
self.template_specification[base.KEY_PARAMETERS_CONFIG] = False
resulted_html = _template2string(self.template_specification)
self.soup = BeautifulSoup(resulted_html)
# file = open("output.html", 'w')
# file.write(self.soup.prettify())
# file.close()
def tearDown(self):
cfg.CURRENT_DIR = self.old_path
del adapters_init.__xml_folders__
self.reset_database()
def test_algorithm_select_is_first(self):
"""
Test that the first select input is always the algorithm selection
and that an updateDivContent is performed on it.
"""
first_select = self.soup.find('input', attrs=dict(type="radio"))
self.assertTrue(first_select['name'] == 'bct')
self.assertTrue("updateDivContent" in first_select['onchange'])
def test_sub_algorithms_correct(self):
"""
Test that the two subalgorithms are correctly generated and that
only one of them is not disabled.
"""
fail_message = "The subalgorithms are not correctly generated"
exp = re.compile('data_bct*')
sub_algos = self.soup.findAll('div', attrs=dict(id=exp))
self.assertTrue(len(sub_algos) == 2, fail_message)
disabled = 0
for one_entry in sub_algos:
if one_entry.has_key('disabled'):
disabled += 1
self.assertTrue(disabled == 1, fail_message)
class GenshiTestSimple(GenshiTest):
"""
For a simple adapter interface (no group of algorithms) test that
various fields are generated correctly.
"""
def setUp(self):
"""
Set up any additionally needed parameters.
"""
super(GenshiTestSimple, self).setUp()
core_path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
self.old_path = cfg.CURRENT_DIR
cfg.CURRENT_DIR = os.path.dirname(core_path)
adapters_init.__xml_folders__ = [os.path.join('interfaces', 'web')]
self.introspector = Introspector("tvb_test")
self.introspector.introspect(True)
xml_group_path = os.path.join('interfaces', 'web', "test_simple.xml")
algo_group = dao.find_group('tvb_test.adapters.testgroupadapter',
'TestGroupAdapter', xml_group_path)
self.xml_group_adapter = ABCAdapter.build_adapter(algo_group)
input_tree = self.xml_group_adapter.get_input_tree()
input_tree = ABCAdapter.prepare_param_names(input_tree)
self.template_specification['inputList'] = input_tree
self.template_specification['draw_hidden_ranges'] = True
self.template_specification[base.KEY_PARAMETERS_CONFIG] = False
resulted_html = _template2string(self.template_specification)
self.soup = BeautifulSoup(resulted_html)
#file = open("output.html", 'w')
#file.write(self.soup.prettify())
#file.close()
def tearDown(self):
cfg.CURRENT_DIR = self.old_path
del adapters_init.__xml_folders__
self.reset_database()
def test_sub_algo_inputs(self):
"""
Check the name of inputs generated for each sub-algorithm is done
properly with only one option that is not disabled
"""
exp = re.compile(
'group_parameters_option_SIM_model_parameters_option_[^ \t\n\r\f\v]*_model_1$'
)
all_inputs = self.soup.findAll('input', attrs=dict(name=exp))
count_disabled = 0
for one_entry in all_inputs:
if one_entry.has_key('disabled'):
count_disabled += 1
self.assertEqual(
len(all_inputs), 5,
"Some inputs not generated or too many inputs generated")
self.assertEqual(count_disabled, 4,
"Disabling input fields was not done correctly")
def test_hidden_ranger_fields(self):
"""
Check that the default ranger hidden fields are generated correctly
"""
ranger1 = self.soup.findAll('input',
attrs=dict(type="hidden",
id="first_range"))
ranger2 = self.soup.findAll('input',
attrs=dict(type="hidden",
id="second_range"))
self.assertEqual(len(ranger1), 1, "First ranger generated wrong")
self.assertEqual(len(ranger2), 1, "Second ranger generated wrong")
def test_checkbox_range_component(self):
"""
Check that a range component is generated for the 'coupling method'
since the type is select and it does not have any sub-attributes,
nor are it's options dataTypes. Only two options are declared.
"""
range_id = self.soup.findAll(
'table',
attrs=dict(
id=
'data_groupSIMgroup_parameters_option_SIM_coupling_methodrange'
))
select_input = self.soup.findAll(
'input',
attrs=dict(name="group_parameters_option_SIM_coupling_method",
type="radio"))
self.assertEqual(2, len(select_input))
linear_checkbox = self.soup.findAll('input',
attrs=dict(type="checkbox",
value="Linear"))
nonlinear_checkbox = self.soup.findAll('input',
attrs=dict(type="checkbox",
value="NonLinear"))
hidden_value_field = self.soup.findAll(
'input',
attrs=dict(type="hidden",
name="group_parameters_option_SIM_coupling_method"))
fail_message = "Something went wrong with generating the range checkboxes component"
self.assertTrue(len(range_id) == 1, fail_message)
self.assertEqual(
linear_checkbox[0]['id'],
"data_groupSIMgroup_parameters_option_SIM_coupling_methodrangeLinearcheck",
fail_message)
self.assertEqual(
nonlinear_checkbox[0]['id'],
"data_groupSIMgroup_parameters_option_SIM_coupling_methodrangeNonLinearcheck",
fail_message)
self.assertEqual(
hidden_value_field[0]['id'],
"data_groupSIMgroup_parameters_option_SIM_coupling_methodrange_hidden",
fail_message)
def test_sub_algorithms(self):
"""
Check that the correct number of sub-algorithms is created
and that only one of them is not disable
"""
fail_message = "Something went wrong with generating the sub-algorithms."
exp = re.compile('data_group_parameters_option_SIM_model*')
enabled_algo = self.soup.findAll('div',
attrs=dict(id=exp,
style="display:block"))
all_algo_disabled = self.soup.findAll('div',
attrs=dict(id=exp,
disabled='disabled'))
self.assertTrue(
len(enabled_algo) == 1 and len(all_algo_disabled) == 6,
fail_message)
self.assertFalse(enabled_algo[0] in all_algo_disabled, fail_message)
def test_normal_ranger(self):
"""
Check the normal ranger generation. Only one ranger should be created
because the minValue/ maxValue is specified only for one field. It should
also be disabled because it is not as default.
"""
fail_message = "Something went wrong with generating the ranger."
exp = re.compile('data_group_parameters_option_SIM_model*')
ranger_parent = self.soup.findAll('table',
attrs={
'id': exp,
'class': "ranger-div-class"
})
self.assertTrue(len(ranger_parent) == 1, fail_message)
span_field = self.soup.findAll(
'span',
attrs=dict(
id="data_group_parameters_option_SIM_modelWilsonCowangroup_"
"parameters_option_SIM_model_parameters_option_WilsonCowan_"
"model_0_RANGER_interval_span"))
self.assertEqual(span_field[0].contents[0], '0.01 - 0.91',
fail_message)
spinner_field = self.soup.findAll(
'input',
attrs=dict(id="data_group_parameters_option_SIM_modelWilsonCowan"
"group_parameters_option_SIM_model_parameters_option_"
"WilsonCowan_model_0_RANGER_stepInput"))
self.assertEqual(str(spinner_field[0]['value']), '0.01', fail_message)
def test_multiple_select(self):
"""
Checks the correct creation of a multiple select component.
"""
fail_message = "Something went wrong with creating multiple select."
exp = re.compile('group_parameters_option_SIM_monitors*')
all_multiple_options = self.soup.findAll('div', attrs=dict(id=exp))
disabled_options = self.soup.findAll('div',
attrs=dict(id=exp,
disabled='disabled'))
self.assertEqual(len(all_multiple_options), 4, fail_message)
self.assertEqual(len(disabled_options), 2, fail_message)
exp = re.compile('monitors_parameters*')
all_multiple_params = self.soup.findAll('input', attrs=dict(name=exp))
disabled_params = self.soup.findAll('input',
attrs=dict(name=exp,
disabled='disabled'))
self.assertEqual(len(all_multiple_params), 4, fail_message)
self.assertEqual(len(disabled_params), 2, fail_message)
class XML_Reader_Test(TransactionalTestCase):
"""
This is a test class for the tvb.core.adapters.xml_reader module.
"""
old_current_dir = TvbProfile.current.web.CURRENT_DIR
old_xml_path = adapters_init.__xml_folders__
def setUp(self):
"""
This method sets up the necessary paths for testing.
"""
self.folder_path = os.path.dirname(__file__)
core_path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
TvbProfile.current.web.CURRENT_DIR = os.path.dirname(core_path)
adapters_init.__xml_folders__ = [os.path.join('core', 'adapters')]
self.introspector = Introspector("tvb.tests.framework")
self.introspector.introspect(True)
xml_group_path = os.path.join('core', 'adapters', "test_group.xml")
algo_group = dao.find_group('tvb.tests.framework.adapters.testgroupadapter', 'TestGroupAdapter', xml_group_path)
self.xml_group_adapter = ABCAdapter.build_adapter(algo_group)
self.xml_group_reader = self.xml_group_adapter.xml_reader
def tearDown(self):
"""
Revert changes settings and remove recently imported algorithms
"""
TvbProfile.current.web.CURRENT_DIR = self.old_current_dir
adapters_init.__xml_folders__ = self.old_xml_path
for group in dao.get_generic_entity(model.AlgorithmGroup, "simple", "algorithm_param_name"):
dao.remove_entity(model.AlgorithmGroup, group.id)
def test_algorithm_group_attributes(self):
"""
Tests the attributes of an algorithm group
"""
self.assertEqual(self.xml_group_adapter.xml_reader.root_name, "simple")
self.assertEqual(self.xml_group_adapter.xml_reader.get_type(),
"tvb.tests.framework.adapters.testgroupadapter.TestGroupAdapter")
self.assertEqual(self.xml_group_adapter.xml_reader.get_ui_name(), "Simple Python Analyzers")
self.assertTrue("externals/BCT" in self.xml_group_adapter.xml_reader.get_additional_path())
def test_code_for_algorithm(self):
"""
Tests the code that has to be executed for an algorithm
"""
self.assertEqual(self.xml_group_adapter.get_call_code("CC"),
"cross_correlation(data1, data2, chan1, chan2, mode)")
def test_import_for_algorithm(self):
"""
Tests the code that has to be imported for an algorithm
"""
self.assertEqual(self.xml_group_adapter.get_import_code("CC"), "tvb.analyzers.simple_analyzers")
def test_inputs_for_algorithm(self):
"""
Tests the inputs for an algorithm
"""
inputs = self.xml_group_adapter.xml_reader.get_inputs("CC")
self.check_inputs(inputs)
def test_outputs_for_algorithm(self):
"""
Tests the outputs for an algorithm
"""
outputs = self.xml_group_adapter.xml_reader.get_outputs("CC")
self.check_outputs(outputs)
def test_get_interface(self):
"""
Tests the interface for an algorithm group
"""
interface = self.xml_group_adapter.get_input_tree()
self.assertEqual(len(interface), 1, "Didnt parse correctly.")
tree_root = interface[0]
self.assertEqual(tree_root[xml_reader.ATT_NAME], "simple")
self.assertEqual(tree_root[xml_reader.ATT_LABEL], "Analysis Algorithm:")
self.assertTrue(tree_root[xml_reader.ATT_REQUIRED])
self.assertEqual(tree_root[xml_reader.ATT_TYPE], xml_reader.TYPE_SELECT)
options = tree_root[xml_reader.ELEM_OPTIONS]
self.assertEqual(len(options), 1)
self.assertEqual(options[0][xml_reader.ATT_VALUE], "CC")
self.assertEqual(options[0][xml_reader.ATT_NAME], "Cross Correlation")
attributes = options[0][xml_reader.ATT_ATTRIBUTES]
self.assertEqual(len(attributes), 3, "Didnt parse correctly.")
self.check_inputs(attributes)
outputs = options[0][xml_reader.ELEM_OUTPUTS]
self.assertEqual(len(outputs), 2, "Didnt parse correctly.")
self.check_outputs(outputs)
def test_get_algorithms_dictionary(self):
"""
Tests the list of algorithms for an algorithm group
"""
algorithms = self.xml_group_adapter.xml_reader.get_algorithms_dictionary()
self.assertEqual(len(algorithms), 1, "Didn't parse correctly.")
algorithm = algorithms["CC"]
self.assertEqual(algorithm[xml_reader.ATT_IDENTIFIER], "CC")
self.assertEqual(algorithm[xml_reader.ATT_CODE], "cross_correlation(data1, data2, chan1, chan2, mode)")
self.assertEqual(algorithm[xml_reader.ATT_IMPORT], "tvb.analyzers.simple_analyzers")
self.assertEqual(algorithm[xml_reader.ATT_NAME], "Cross Correlation")
#check inputs
inputs = algorithms["CC"][xml_reader.INPUTS_KEY]
new_inputs = []
for inp in inputs.keys():
new_inputs.append(inputs[inp])
self.check_inputs(new_inputs)
#check outputs
outputs = algorithms["CC"][xml_reader.OUTPUTS_KEY]
self.check_outputs(outputs)
def test_get_all_outputs(self):
"""
Tests the all outputs of the algorithms from an algorithm group
"""
outputs = self.xml_group_reader.get_all_outputs()
self.assertEqual(len(outputs), 2, "Didnt parse correctly.")
self.check_outputs(outputs)
def test_no_algorithm_node(self):
"""
This test trys to load an invalid xml. The xml doesn't contains any
algorithm node.
"""
try:
xml_group_path = os.path.join(self.folder_path, "no_algorithm_node.xml")
xml_reader.XMLGroupReader.get_instance(xml_group_path)
self.fail("Test should fail. The xml doesn't contain algorithms")
except XmlParserException:
#OK, do nothing
pass
def test_no_code_node(self):
"""
This test trys to load an invalid xml. The xml doesn't contains all
the required nodes. The missing node is code from one of the algorithms.
"""
xml_group_path = os.path.join(self.folder_path, "no_code_node.xml")
self.assertRaises(XmlParserException, xml_reader.XMLGroupReader, xml_group_path)
#The call should fail.
#One of the algorithms doesn't contain required attribute 'code'
def test_missing_required_attribute(self):
"""
This test trys to load an invalid xml. The xml doesn't contains all
the required attributes. The missing attribute is 'name' from one of the algorithms.
"""
try:
xml_group_path = os.path.join(self.folder_path, "missing_required_attribute.xml")
xml_reader.XMLGroupReader.get_instance(xml_group_path)
self.fail("Test should fail. One of the algorithms doesn't have required 'name' att")
except XmlParserException:
#OK, do nothing
pass
def test_invalid_schema_url(self):
"""
Test that when XML schema can not be found (e.g. due to no internet connection,
or server down) the XML is still read.
"""
xml_group_path = os.path.join(self.folder_path, "test_invalid_schema_url.xml")
self.xml_group_reader = xml_reader.XMLGroupReader.get_instance(xml_group_path)
self.test_inputs_for_algorithm()
self.test_outputs_for_algorithm()
def check_inputs(self, inputs_list):
"""
The given list of inputs is expected to be for the "CC" algorithm.
"""
inputs_dict = {}
for input_ in inputs_list:
inputs_dict[input_[xml_reader.ATT_NAME]] = input_
expected_conditions = {'fields': ['datatype_class._nr_dimensions'],
'values': ['2'], 'operations': ['==']}
self._check_input(inputs_dict, "data1", True, "tvb.datatypes.arrays.MappedArray", "First dataset:",
"First set of signals", "data", "default_data", None, expected_conditions)
self._check_input(inputs_dict, "chan1", False, "int", "First channel index:", None, None, None, None, None)
expected_options = {'valid': 'Valid', 'same': 'Same', 'full': 'Full'}
self._check_input(inputs_dict, "mode", True, "select", "Mode:", "Flag that indicates the size of the output",
None, "full", expected_options, None)
def _check_input(self, all_inputs, input_name, is_required, expected_type, expected_label, expected_description,
expected_field, expected_default, expected_options, expected_conditions):
"""Validate one input"""
input_ = all_inputs[input_name]
self.assertEqual(input_[xml_reader.ATT_NAME], input_name)
self.assertEqual(input_[xml_reader.ATT_LABEL], expected_label)
self.assertEqual(input_[xml_reader.ATT_TYPE], expected_type)
if is_required:
self.assertTrue(input_[xml_reader.ATT_REQUIRED])
else:
self.assertFalse(input_[xml_reader.ATT_REQUIRED])
if expected_description is None:
self.assertFalse(xml_reader.ATT_DESCRIPTION in input_.keys())
else:
self.assertEqual(input_[xml_reader.ATT_DESCRIPTION], expected_description)
if expected_field is None:
self.assertFalse(xml_reader.ATT_FIELD in input_.keys())
else:
self.assertEqual(input_[xml_reader.ATT_FIELD], expected_field)
if expected_default is None:
self.assertFalse(xml_reader.ATT_DEFAULT in input_.keys())
else:
self.assertEqual(input_[xml_reader.ATT_DEFAULT], expected_default)
if expected_options is None:
self.assertFalse(xml_reader.ELEM_OPTIONS in input_.keys())
else:
options = input_[xml_reader.ELEM_OPTIONS]
for opt in options:
self.assertTrue(opt[xml_reader.ATT_VALUE] in expected_options)
self.assertEquals(opt[xml_reader.ATT_NAME], expected_options[opt[xml_reader.ATT_VALUE]])
if expected_conditions is None:
self.assertFalse(xml_reader.ELEM_CONDITIONS in input_.keys())
else:
ops_filter = input_[xml_reader.ELEM_CONDITIONS]
for key_attr in expected_conditions.keys():
actual_values = getattr(ops_filter, key_attr)
self.assertEqual(len(actual_values), len(expected_conditions[key_attr]))
for att in actual_values:
self.assertTrue(att in expected_conditions[key_attr])
def check_outputs(self, outputs):
"""
The given list of outputs is expected to be for the "CC" algorithm.
"""
self.assertEqual(len(outputs), 2, "Didnt parse correctly.")
#first output
self.assertEqual(outputs[0][xml_reader.ATT_TYPE], "tvb.datatypes.arrays.MappedArray")
fields = outputs[0][xml_reader.ELEM_FIELD]
self.assertEqual(len(fields), 3, "Expected 3 fields.")
fields_dict = {}
for field_ in fields:
fields_dict[field_[xml_reader.ATT_NAME]] = field_
self.assertEqual(fields_dict["data"][xml_reader.ATT_REFERENCE], "$0#")
self.assertEqual(fields_dict["data_name"][xml_reader.ATT_VALUE], "Covariance matrix")
self.assertEqual(fields_dict["label_x"][xml_reader.ATT_VALUE], "Nodes")
#second output
self.assertEqual(outputs[1][xml_reader.ATT_TYPE], "tvb.datatypes.arrays.MappedArray")
fields = outputs[1][xml_reader.ELEM_FIELD]
self.assertEqual(len(fields), 2)
fields_dict = {}
for field_ in fields:
fields_dict[field_[xml_reader.ATT_NAME]] = field_
self.assertEqual(fields_dict["data"][xml_reader.ATT_REFERENCE], "$0#")
self.assertEqual(fields_dict["data_name"][xml_reader.ATT_VALUE], "Cross correlation")
class XML_Reader_Test(TransactionalTestCase):
"""
This is a test class for the tvb.core.adapters.xml_reader module.
"""
old_current_dir = TvbProfile.current.web.CURRENT_DIR
old_xml_path = adapters_init.__xml_folders__
def setUp(self):
"""
This method sets up the necessary paths for testing.
"""
self.folder_path = os.path.dirname(__file__)
core_path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
TvbProfile.current.web.CURRENT_DIR = os.path.dirname(core_path)
adapters_init.__xml_folders__ = [os.path.join('core', 'adapters')]
self.introspector = Introspector("tvb.tests.framework")
self.introspector.introspect(True)
xml_group_path = os.path.join('core', 'adapters', "test_group.xml")
algo_group = dao.find_group(
'tvb.tests.framework.adapters.testgroupadapter',
'TestGroupAdapter', xml_group_path)
self.xml_group_adapter = ABCAdapter.build_adapter(algo_group)
self.xml_group_reader = self.xml_group_adapter.xml_reader
def tearDown(self):
"""
Revert changes settings and remove recently imported algorithms
"""
TvbProfile.current.web.CURRENT_DIR = self.old_current_dir
adapters_init.__xml_folders__ = self.old_xml_path
for group in dao.get_generic_entity(model.AlgorithmGroup, "simple",
"algorithm_param_name"):
dao.remove_entity(model.AlgorithmGroup, group.id)
def test_algorithm_group_attributes(self):
"""
Tests the attributes of an algorithm group
"""
self.assertEqual(self.xml_group_adapter.xml_reader.root_name, "simple")
self.assertEqual(
self.xml_group_adapter.xml_reader.get_type(),
"tvb.tests.framework.adapters.testgroupadapter.TestGroupAdapter")
self.assertEqual(self.xml_group_adapter.xml_reader.get_ui_name(),
"Simple Python Analyzers")
self.assertTrue("externals/BCT" in self.xml_group_adapter.xml_reader.
get_additional_path())
def test_code_for_algorithm(self):
"""
Tests the code that has to be executed for an algorithm
"""
self.assertEqual(
self.xml_group_adapter.get_call_code("CC"),
"cross_correlation(data1, data2, chan1, chan2, mode)")
def test_import_for_algorithm(self):
"""
Tests the code that has to be imported for an algorithm
"""
self.assertEqual(self.xml_group_adapter.get_import_code("CC"),
"tvb.analyzers.simple_analyzers")
def test_inputs_for_algorithm(self):
"""
Tests the inputs for an algorithm
"""
inputs = self.xml_group_adapter.xml_reader.get_inputs("CC")
self.check_inputs(inputs)
def test_outputs_for_algorithm(self):
"""
Tests the outputs for an algorithm
"""
outputs = self.xml_group_adapter.xml_reader.get_outputs("CC")
self.check_outputs(outputs)
def test_get_interface(self):
"""
Tests the interface for an algorithm group
"""
interface = self.xml_group_adapter.get_input_tree()
self.assertEqual(len(interface), 1, "Didnt parse correctly.")
tree_root = interface[0]
self.assertEqual(tree_root[xml_reader.ATT_NAME], "simple")
self.assertEqual(tree_root[xml_reader.ATT_LABEL],
"Analysis Algorithm:")
self.assertTrue(tree_root[xml_reader.ATT_REQUIRED])
self.assertEqual(tree_root[xml_reader.ATT_TYPE],
xml_reader.TYPE_SELECT)
options = tree_root[xml_reader.ELEM_OPTIONS]
self.assertEqual(len(options), 1)
self.assertEqual(options[0][xml_reader.ATT_VALUE], "CC")
self.assertEqual(options[0][xml_reader.ATT_NAME], "Cross Correlation")
attributes = options[0][xml_reader.ATT_ATTRIBUTES]
self.assertEqual(len(attributes), 3, "Didnt parse correctly.")
self.check_inputs(attributes)
outputs = options[0][xml_reader.ELEM_OUTPUTS]
self.assertEqual(len(outputs), 2, "Didnt parse correctly.")
self.check_outputs(outputs)
def test_get_algorithms_dictionary(self):
"""
Tests the list of algorithms for an algorithm group
"""
algorithms = self.xml_group_adapter.xml_reader.get_algorithms_dictionary(
)
self.assertEqual(len(algorithms), 1, "Didn't parse correctly.")
algorithm = algorithms["CC"]
self.assertEqual(algorithm[xml_reader.ATT_IDENTIFIER], "CC")
self.assertEqual(
algorithm[xml_reader.ATT_CODE],
"cross_correlation(data1, data2, chan1, chan2, mode)")
self.assertEqual(algorithm[xml_reader.ATT_IMPORT],
"tvb.analyzers.simple_analyzers")
self.assertEqual(algorithm[xml_reader.ATT_NAME], "Cross Correlation")
#check inputs
inputs = algorithms["CC"][xml_reader.INPUTS_KEY]
new_inputs = []
for inp in inputs.keys():
new_inputs.append(inputs[inp])
self.check_inputs(new_inputs)
#check outputs
outputs = algorithms["CC"][xml_reader.OUTPUTS_KEY]
self.check_outputs(outputs)
def test_get_all_outputs(self):
"""
Tests the all outputs of the algorithms from an algorithm group
"""
outputs = self.xml_group_reader.get_all_outputs()
self.assertEqual(len(outputs), 2, "Didnt parse correctly.")
self.check_outputs(outputs)
def test_no_algorithm_node(self):
"""
This test trys to load an invalid xml. The xml doesn't contains any
algorithm node.
"""
try:
xml_group_path = os.path.join(self.folder_path,
"no_algorithm_node.xml")
xml_reader.XMLGroupReader.get_instance(xml_group_path)
self.fail("Test should fail. The xml doesn't contain algorithms")
except XmlParserException:
#OK, do nothing
pass
def test_no_code_node(self):
"""
This test trys to load an invalid xml. The xml doesn't contains all
the required nodes. The missing node is code from one of the algorithms.
"""
xml_group_path = os.path.join(self.folder_path, "no_code_node.xml")
self.assertRaises(XmlParserException, xml_reader.XMLGroupReader,
xml_group_path)
#The call should fail.
#One of the algorithms doesn't contain required attribute 'code'
def test_missing_required_attribute(self):
"""
This test trys to load an invalid xml. The xml doesn't contains all
the required attributes. The missing attribute is 'name' from one of the algorithms.
"""
try:
xml_group_path = os.path.join(self.folder_path,
"missing_required_attribute.xml")
xml_reader.XMLGroupReader.get_instance(xml_group_path)
self.fail(
"Test should fail. One of the algorithms doesn't have required 'name' att"
)
except XmlParserException:
#OK, do nothing
pass
def test_invalid_schema_url(self):
"""
Test that when XML schema can not be found (e.g. due to no internet connection,
or server down) the XML is still read.
"""
xml_group_path = os.path.join(self.folder_path,
"test_invalid_schema_url.xml")
self.xml_group_reader = xml_reader.XMLGroupReader.get_instance(
xml_group_path)
self.test_inputs_for_algorithm()
self.test_outputs_for_algorithm()
def check_inputs(self, inputs_list):
"""
The given list of inputs is expected to be for the "CC" algorithm.
"""
inputs_dict = {}
for input_ in inputs_list:
inputs_dict[input_[xml_reader.ATT_NAME]] = input_
expected_conditions = {
'fields': ['datatype_class._nr_dimensions'],
'values': ['2'],
'operations': ['==']
}
self._check_input(inputs_dict, "data1", True,
"tvb.datatypes.arrays.MappedArray", "First dataset:",
"First set of signals", "data", "default_data", None,
expected_conditions)
self._check_input(inputs_dict, "chan1", False, "int",
"First channel index:", None, None, None, None, None)
expected_options = {'valid': 'Valid', 'same': 'Same', 'full': 'Full'}
self._check_input(inputs_dict, "mode", True, "select", "Mode:",
"Flag that indicates the size of the output", None,
"full", expected_options, None)
def _check_input(self, all_inputs, input_name, is_required, expected_type,
expected_label, expected_description, expected_field,
expected_default, expected_options, expected_conditions):
"""Validate one input"""
input_ = all_inputs[input_name]
self.assertEqual(input_[xml_reader.ATT_NAME], input_name)
self.assertEqual(input_[xml_reader.ATT_LABEL], expected_label)
self.assertEqual(input_[xml_reader.ATT_TYPE], expected_type)
if is_required:
self.assertTrue(input_[xml_reader.ATT_REQUIRED])
else:
self.assertFalse(input_[xml_reader.ATT_REQUIRED])
if expected_description is None:
self.assertFalse(xml_reader.ATT_DESCRIPTION in input_.keys())
else:
self.assertEqual(input_[xml_reader.ATT_DESCRIPTION],
expected_description)
if expected_field is None:
self.assertFalse(xml_reader.ATT_FIELD in input_.keys())
else:
self.assertEqual(input_[xml_reader.ATT_FIELD], expected_field)
if expected_default is None:
self.assertFalse(xml_reader.ATT_DEFAULT in input_.keys())
else:
self.assertEqual(input_[xml_reader.ATT_DEFAULT], expected_default)
if expected_options is None:
self.assertFalse(xml_reader.ELEM_OPTIONS in input_.keys())
else:
options = input_[xml_reader.ELEM_OPTIONS]
for opt in options:
self.assertTrue(opt[xml_reader.ATT_VALUE] in expected_options)
self.assertEquals(opt[xml_reader.ATT_NAME],
expected_options[opt[xml_reader.ATT_VALUE]])
if expected_conditions is None:
self.assertFalse(xml_reader.ELEM_CONDITIONS in input_.keys())
else:
ops_filter = input_[xml_reader.ELEM_CONDITIONS]
for key_attr in expected_conditions.keys():
actual_values = getattr(ops_filter, key_attr)
self.assertEqual(len(actual_values),
len(expected_conditions[key_attr]))
for att in actual_values:
self.assertTrue(att in expected_conditions[key_attr])
def check_outputs(self, outputs):
"""
The given list of outputs is expected to be for the "CC" algorithm.
"""
self.assertEqual(len(outputs), 2, "Didnt parse correctly.")
#first output
self.assertEqual(outputs[0][xml_reader.ATT_TYPE],
"tvb.datatypes.arrays.MappedArray")
fields = outputs[0][xml_reader.ELEM_FIELD]
self.assertEqual(len(fields), 3, "Expected 3 fields.")
fields_dict = {}
for field_ in fields:
fields_dict[field_[xml_reader.ATT_NAME]] = field_
self.assertEqual(fields_dict["data"][xml_reader.ATT_REFERENCE], "$0#")
self.assertEqual(fields_dict["data_name"][xml_reader.ATT_VALUE],
"Covariance matrix")
self.assertEqual(fields_dict["label_x"][xml_reader.ATT_VALUE], "Nodes")
#second output
self.assertEqual(outputs[1][xml_reader.ATT_TYPE],
"tvb.datatypes.arrays.MappedArray")
fields = outputs[1][xml_reader.ELEM_FIELD]
self.assertEqual(len(fields), 2)
fields_dict = {}
for field_ in fields:
fields_dict[field_[xml_reader.ATT_NAME]] = field_
self.assertEqual(fields_dict["data"][xml_reader.ATT_REFERENCE], "$0#")
self.assertEqual(fields_dict["data_name"][xml_reader.ATT_VALUE],
"Cross correlation")
class IntrospectorTest(BaseTestCase):
"""
Test class for the introspector module.
"""
def setUp(self):
"""
Reset the database before each test.
"""
self.reset_database()
#tvb_test path
core_path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
self.old_path = cfg.CURRENT_DIR
cfg.CURRENT_DIR = os.path.dirname(core_path)
self.introspector = Introspector("tvb_test")
def tearDown(self):
"""
Reset the database when test is done.
"""
cfg.CURRENT_DIR = self.old_path
self.reset_database()
def test_introspect(self):
"""
Test the actual introspect module on a test structure created in:
tvb_test.dummy_adapters and tvb_test.dummy_datatypes
"""
self.introspector.introspect(True)
initialize_storage()
all_categories = dao.get_algorithm_categories()
category_ids = [
cat.id for cat in all_categories
if cat.displayname == "AdaptersTest"
]
groups = dao.get_groups_by_categories(category_ids)
self.assertEqual(len(groups), 11, "Introspection failed!")
nr_adapters_mod2 = 0
for algorithm in groups:
self.assertTrue(
algorithm.module in [
'tvb_test.adapters.testadapter1',
'tvb_test.adapters.testadapter2',
'tvb_test.adapters.testadapter3',
'tvb_test.adapters.ndimensionarrayadapter',
"tvb.adapters.analyzers.group_python_adapter",
"tvb_test.adapters.testgroupadapter"
], "Unknown Adapter:" + str(algorithm.module))
self.assertTrue(
algorithm.classname in [
"TestAdapter1", "TestAdapterDatatypeInput", "TestAdapter2",
"TestAdapter22", "TestAdapter3", "NDimensionArrayAdapter",
"PythonAdapter", "TestAdapterHDDRequired",
"TestAdapterHugeMemoryRequired",
"TestAdapterNoMemoryImplemented", "TestGroupAdapter"
], "Unknown Adapter Class:" + str(algorithm.classname))
if algorithm.module == 'tvb_test.adapters.testadapter2':
nr_adapters_mod2 = nr_adapters_mod2 + 1
self.assertEqual(
nr_adapters_mod2, 2,
"Two adapters should have been loaded from module tvb_test.adapters2!"
)
def test_xml_introspection(self):
"""
Check the XML introspection. The folders which are introspected
are defined in the variable __xml_folders__ from tvb_test/adapters/_init.py
"""
self.introspector.introspect(True)
initialize_storage()
init_parameter = os.path.join("core", "adapters", "test_group.xml")
group = dao.find_group("tvb_test.adapters.testgroupadapter",
"TestGroupAdapter", init_parameter)
self.assertTrue(group is not None, "The group was not found")
self.assertEqual(group.init_parameter, init_parameter,
"Wrong init_parameter:" + str(group.init_parameter))
self.assertEqual(group.displayname, "Simple Python Analyzers",
"The display-name of the group is not valid")
self.assertEqual(group.algorithm_param_name, "simple",
"The algorithm_param_name of the group is not valid")
self.assertEqual(group.classname, "TestGroupAdapter",
"The class-name of the group is not valid")
self.assertEqual(group.module, "tvb_test.adapters.testgroupadapter",
"Group Module invalid")