class TestFlowService(TransactionalTestCase):
"""
This class contains tests for the tvb.core.services.flow_service module.
"""
def transactional_setup_method(self):
""" Prepare some entities to work with during tests:"""
self.flow_service = FlowService()
self.test_user = TestFactory.create_user()
self.test_project = TestFactory.create_project(admin=self.test_user)
category = dao.get_uploader_categories()[0]
self.algorithm = dao.store_entity(
model.Algorithm(TEST_ADAPTER_VALID_MODULE,
TEST_ADAPTER_VALID_CLASS, category.id))
def transactional_teardown_method(self):
dao.remove_entity(model.Algorithm, self.algorithm)
def test_get_uploaders(self):
result = self.flow_service.get_upload_algorithms()
assert 29 == len(result)
found = False
for algo in result:
if algo.classname == self.algorithm.classname and algo.module == self.algorithm.module:
found = True
break
assert found, "Uploader incorrectly returned"
def test_get_analyze_groups(self):
category, groups = self.flow_service.get_analyze_groups()
assert category.displayname == 'Analyze'
assert len(groups) > 1
assert isinstance(groups[0], model.AlgorithmTransientGroup)
def test_get_visualizers_for_group(self):
_, op_group_id = TestFactory.create_group(self.test_user,
self.test_project)
dt_group = dao.get_datatypegroup_by_op_group_id(op_group_id)
result = self.flow_service.get_visualizers_for_group(dt_group.gid)
# Only the discreet is expected
assert 1 == len(result)
assert DISCRETE_PSE_ADAPTER_CLASS == result[0].classname
def test_get_launchable_algorithms(self):
factory = DatatypesFactory()
conn = factory.create_connectivity(4)[1]
ts = factory.create_timeseries(conn)
result = self.flow_service.get_launchable_algorithms(ts.gid)
assert 'Analyze' in result
assert 'View' in result
def test_get_roup_by_identifier(self):
"""
Test for the get_algorithm_by_identifier.
"""
algo_ret = self.flow_service.get_algorithm_by_identifier(
self.algorithm.id)
assert algo_ret.id == self.algorithm.id, "ID-s are different!"
assert algo_ret.module == self.algorithm.module, "Modules are different!"
assert algo_ret.fk_category == self.algorithm.fk_category, "Categories are different!"
assert algo_ret.classname == self.algorithm.classname, "Class names are different!"
def test_build_adapter_instance(self):
"""
Test standard flow for building an adapter instance.
"""
adapter = TestFactory.create_adapter(TEST_ADAPTER_VALID_MODULE,
TEST_ADAPTER_VALID_CLASS)
assert isinstance(
adapter, ABCSynchronous), "Something went wrong with valid data!"
def test_build_adapter_invalid(self):
"""
Test flow for trying to build an adapter that does not inherit from ABCAdapter.
"""
group = dao.get_algorithm_by_module(TEST_ADAPTER_VALID_MODULE,
TEST_ADAPTER_INVALID_CLASS)
with pytest.raises(IntrospectionException):
ABCAdapter.build_adapter(group)
def test_prepare_adapter(self):
"""
Test preparation of an adapter.
"""
stored_adapter = dao.get_algorithm_by_module(TEST_ADAPTER_VALID_MODULE,
TEST_ADAPTER_VALID_CLASS)
interface = self.flow_service.prepare_adapter(self.test_project.id,
stored_adapter)
assert isinstance(
stored_adapter,
model.Algorithm), "Something went wrong with valid data!"
assert "name" in interface[0], "Bad interface created!"
assert interface[0]["name"] == "test", "Bad interface!"
assert "type" in interface[0], "Bad interface created!"
assert interface[0]["type"] == "int", "Bad interface!"
assert "default" in interface[0], "Bad interface created!"
assert interface[0]["default"] == "0", "Bad interface!"
def test_fire_operation(self):
"""
Test preparation of an adapter and launch mechanism.
"""
adapter = TestFactory.create_adapter(TEST_ADAPTER_VALID_MODULE,
TEST_ADAPTER_VALID_CLASS)
data = {"test": 5}
result = self.flow_service.fire_operation(adapter, self.test_user,
self.test_project.id, **data)
assert result.endswith("has finished."), "Operation fail"
def test_get_filtered_by_column(self):
"""
Test the filter function when retrieving dataTypes with a filter
after a column from a class specific table (e.g. DATA_arraywrapper).
"""
operation_1 = TestFactory.create_operation(
test_user=self.test_user, test_project=self.test_project)
operation_2 = TestFactory.create_operation(
test_user=self.test_user, test_project=self.test_project)
one_dim_array = numpy.arange(5)
two_dim_array = numpy.array([[1, 2], [2, 3], [1, 4]])
self._store_float_array(one_dim_array, "John Doe 1", operation_1.id)
self._store_float_array(one_dim_array, "John Doe 2", operation_1.id)
self._store_float_array(two_dim_array, "John Doe 3", operation_2.id)
count = self.flow_service.get_available_datatypes(
self.test_project.id, "tvb.datatypes.arrays.MappedArray")[1]
assert count, 3 == "Problems with inserting data"
first_filter = FilterChain(
fields=[FilterChain.datatype + '._nr_dimensions'],
operations=["=="],
values=[1])
count = self.flow_service.get_available_datatypes(
self.test_project.id, "tvb.datatypes.arrays.MappedArray",
first_filter)[1]
assert count, 2 == "Data was not filtered"
second_filter = FilterChain(
fields=[FilterChain.datatype + '._nr_dimensions'],
operations=["=="],
values=[2])
filtered_data = self.flow_service.get_available_datatypes(
self.test_project.id, "tvb.datatypes.arrays.MappedArray",
second_filter)[0]
assert len(filtered_data), 1 == "Data was not filtered"
assert filtered_data[0][3] == "John Doe 3"
third_filter = FilterChain(
fields=[FilterChain.datatype + '._length_1d'],
operations=["=="],
values=[3])
filtered_data = self.flow_service.get_available_datatypes(
self.test_project.id, "tvb.datatypes.arrays.MappedArray",
third_filter)[0]
assert len(filtered_data), 1 == "Data was not filtered correct"
assert filtered_data[0][3] == "John Doe 3"
try:
if os.path.exists('One_dim.txt'):
os.remove('One_dim.txt')
if os.path.exists('Two_dim.txt'):
os.remove('Two_dim.txt')
if os.path.exists('One_dim-1.txt'):
os.remove('One_dim-1.txt')
except Exception:
pass
@staticmethod
def _store_float_array(array_data, subject_name, operation_id):
"""Create Float Array and DB persist it"""
datatype_inst = MappedArray(user_tag_1=subject_name)
datatype_inst.set_operation_id(operation_id)
datatype_inst.array_data = array_data
datatype_inst.type = "MappedArray"
datatype_inst.module = "tvb.datatypes.arrays"
datatype_inst.subject = subject_name
datatype_inst.state = "RAW"
dao.store_entity(datatype_inst)
def test_get_filtered_datatypes(self):
"""
Test the filter function when retrieving dataTypes.
"""
#Create some test operations
start_dates = [
datetime.now(),
datetime.strptime("08-06-2010", "%m-%d-%Y"),
datetime.strptime("07-21-2010", "%m-%d-%Y"),
datetime.strptime("05-06-2010", "%m-%d-%Y"),
datetime.strptime("07-21-2011", "%m-%d-%Y")
]
end_dates = [
datetime.now(),
datetime.strptime("08-12-2010", "%m-%d-%Y"),
datetime.strptime("08-12-2010", "%m-%d-%Y"),
datetime.strptime("08-12-2011", "%m-%d-%Y"),
datetime.strptime("08-12-2011", "%m-%d-%Y")
]
for i in range(5):
operation = model.Operation(self.test_user.id,
self.test_project.id,
self.algorithm.id,
'test params',
status=model.STATUS_FINISHED,
start_date=start_dates[i],
completion_date=end_dates[i])
operation = dao.store_entity(operation)
storage_path = FilesHelper().get_project_folder(
self.test_project, str(operation.id))
if i < 4:
datatype_inst = Datatype1()
datatype_inst.type = "Datatype1"
datatype_inst.subject = "John Doe" + str(i)
datatype_inst.state = "RAW"
datatype_inst.set_operation_id(operation.id)
dao.store_entity(datatype_inst)
else:
for _ in range(2):
datatype_inst = Datatype2()
datatype_inst.storage_path = storage_path
datatype_inst.type = "Datatype2"
datatype_inst.subject = "John Doe" + str(i)
datatype_inst.state = "RAW"
datatype_inst.string_data = ["data"]
datatype_inst.set_operation_id(operation.id)
dao.store_entity(datatype_inst)
returned_data = self.flow_service.get_available_datatypes(
self.test_project.id, Datatype1)[0]
for row in returned_data:
if row[1] != 'Datatype1':
raise AssertionError("Some invalid data was returned!")
assert 4 == len(returned_data), "Invalid length of result"
filter_op = FilterChain(
fields=[
FilterChain.datatype + ".state",
FilterChain.operation + ".start_date"
],
values=["RAW", datetime.strptime("08-01-2010", "%m-%d-%Y")],
operations=["==", ">"])
returned_data = self.flow_service.get_available_datatypes(
self.test_project.id, Datatype1, filter_op)[0]
returned_subjects = [one_data[3] for one_data in returned_data]
if "John Doe0" not in returned_subjects or "John Doe1" not in returned_subjects or len(
returned_subjects) != 2:
raise AssertionError("DataTypes were not filtered properly!")
class TestFlowService(TransactionalTestCase):
"""
This class contains tests for the tvb.core.services.flow_service module.
"""
def transactional_setup_method(self):
""" Prepare some entities to work with during tests:"""
self.flow_service = FlowService()
category = dao.get_uploader_categories()[0]
self.algorithm = dao.store_entity(model_operation.Algorithm(TEST_ADAPTER_VALID_MODULE,
TEST_ADAPTER_VALID_CLASS, category.id))
def transactional_teardown_method(self):
dao.remove_entity(model_operation.Algorithm, self.algorithm)
def test_get_uploaders(self):
result = self.flow_service.get_upload_algorithms()
# Not sure if it is correct but I think there are not 29 algorithms anymore here
assert 19 == len(result)
found = False
for algo in result:
if algo.classname == self.algorithm.classname and algo.module == self.algorithm.module:
found = True
break
assert found, "Uploader incorrectly returned"
def test_get_analyze_groups(self):
category, groups = self.flow_service.get_analyze_groups()
assert category.displayname == 'Analyze'
assert len(groups) > 1
assert isinstance(groups[0], model_operation.AlgorithmTransientGroup)
def test_get_visualizers_for_group(self, datatype_group_factory):
group = datatype_group_factory()
dt_group = dao.get_datatypegroup_by_op_group_id(group.fk_from_operation)
result = self.flow_service.get_visualizers_for_group(dt_group.gid)
# Both discrete and isocline are expected due to the 2 ranges set in the factory
assert 2 == len(result)
result_classnames = [res.classname for res in result]
assert IntrospectionRegistry.ISOCLINE_PSE_ADAPTER_CLASS in result_classnames
assert IntrospectionRegistry.DISCRETE_PSE_ADAPTER_CLASS in result_classnames
def test_get_launchable_algorithms(self, time_series_region_index_factory, connectivity_factory,
region_mapping_factory):
conn = connectivity_factory()
rm = region_mapping_factory()
ts = time_series_region_index_factory(connectivity=conn, region_mapping=rm)
result, has_operations_warning = self.flow_service.get_launchable_algorithms(ts.gid)
assert 'Analyze' in result
assert 'View' in result
assert has_operations_warning is False
def test_get_group_by_identifier(self):
"""
Test for the get_algorithm_by_identifier.
"""
algo_ret = self.flow_service.get_algorithm_by_identifier(self.algorithm.id)
assert algo_ret.id == self.algorithm.id, "ID-s are different!"
assert algo_ret.module == self.algorithm.module, "Modules are different!"
assert algo_ret.fk_category == self.algorithm.fk_category, "Categories are different!"
assert algo_ret.classname == self.algorithm.classname, "Class names are different!"
def test_build_adapter_invalid(self):
"""
Test flow for trying to build an adapter that does not inherit from ABCAdapter.
"""
group = dao.get_algorithm_by_module(TEST_ADAPTER_VALID_MODULE, TEST_ADAPTER_INVALID_CLASS)
with pytest.raises(IntrospectionException):
ABCAdapter.build_adapter(group)
def test_prepare_adapter(self):
"""
Test preparation of an adapter.
"""
stored_adapter = dao.get_algorithm_by_module(TEST_ADAPTER_VALID_MODULE, TEST_ADAPTER_VALID_CLASS)
assert isinstance(stored_adapter, model_operation.Algorithm), "Something went wrong with valid data!"
adapter = self.flow_service.prepare_adapter(stored_adapter)
assert isinstance(adapter, TestAdapter1), "Adapter incorrectly built"
assert adapter.get_form_class() == TestAdapter1Form
assert adapter.get_view_model() == TestModel
def test_fire_operation(self):
"""
Test preparation of an adapter and launch mechanism.
"""
adapter = TestFactory.create_adapter(TEST_ADAPTER_VALID_MODULE, TEST_ADAPTER_VALID_CLASS)
test_user = TestFactory.create_user()
test_project = TestFactory.create_project(admin=test_user)
result = self.flow_service.fire_operation(adapter, test_user, test_project.id,
view_model=adapter.get_view_model()())
assert result.endswith("has finished."), "Operation fail"
class FlowServiceTest(TransactionalTestCase):
"""
This class contains tests for the tvb.core.services.flow_service module.
"""
def setUp(self):
""" Prepare some entities to work with during tests:"""
self.flow_service = FlowService()
self.test_user = TestFactory.create_user()
self.test_project = TestFactory.create_project(admin=self.test_user)
category = dao.get_uploader_categories()[0]
self.algorithm = dao.store_entity(model.Algorithm(TEST_ADAPTER_VALID_MODULE,
TEST_ADAPTER_VALID_CLASS, category.id))
def tearDown(self):
dao.remove_entity(model.Algorithm, self.algorithm)
def test_get_uploaders(self):
result = self.flow_service.get_upload_algorithms()
self.assertEqual(29, len(result))
found = False
for algo in result:
if algo.classname == self.algorithm.classname and algo.module == self.algorithm.module:
found = True
break
self.assertTrue(found, "Uploader incorrectly returned")
def test_get_analyze_groups(self):
category, groups = self.flow_service.get_analyze_groups()
self.assertEqual(category.displayname, 'Analyze')
self.assertTrue(len(groups) > 1)
self.assertTrue(isinstance(groups[0], model.AlgorithmTransientGroup))
def test_get_visualizers_for_group(self):
_, op_group_id = TestFactory.create_group(self.test_user, self.test_project)
dt_group = dao.get_datatypegroup_by_op_group_id(op_group_id)
result = self.flow_service.get_visualizers_for_group(dt_group.gid)
# Only the discreet is expected
self.assertEqual(1, len(result))
self.assertEqual(DISCRETE_PSE_ADAPTER_CLASS, result[0].classname)
def test_get_launchable_algorithms(self):
factory = DatatypesFactory()
conn = factory.create_connectivity(4)[1]
ts = factory.create_timeseries(conn)
result = self.flow_service.get_launchable_algorithms(ts.gid)
self.assertTrue('Analyze' in result)
self.assertTrue('View' in result)
def test_get_roup_by_identifier(self):
"""
Test for the get_algorithm_by_identifier.
"""
algo_ret = self.flow_service.get_algorithm_by_identifier(self.algorithm.id)
self.assertEqual(algo_ret.id, self.algorithm.id, "ID-s are different!")
self.assertEqual(algo_ret.module, self.algorithm.module, "Modules are different!")
self.assertEqual(algo_ret.fk_category, self.algorithm.fk_category, "Categories are different!")
self.assertEqual(algo_ret.classname, self.algorithm.classname, "Class names are different!")
def test_build_adapter_instance(self):
"""
Test standard flow for building an adapter instance.
"""
adapter = TestFactory.create_adapter(TEST_ADAPTER_VALID_MODULE, TEST_ADAPTER_VALID_CLASS)
self.assertTrue(isinstance(adapter, ABCSynchronous), "Something went wrong with valid data!")
def test_build_adapter_invalid(self):
"""
Test flow for trying to build an adapter that does not inherit from ABCAdapter.
"""
group = dao.get_algorithm_by_module(TEST_ADAPTER_VALID_MODULE, TEST_ADAPTER_INVALID_CLASS)
self.assertRaises(IntrospectionException, ABCAdapter.build_adapter, group)
def test_prepare_adapter(self):
"""
Test preparation of an adapter.
"""
stored_adapter = dao.get_algorithm_by_module(TEST_ADAPTER_VALID_MODULE, TEST_ADAPTER_VALID_CLASS)
interface = self.flow_service.prepare_adapter(self.test_project.id, stored_adapter)
self.assertTrue(isinstance(stored_adapter, model.Algorithm), "Something went wrong with valid data!")
self.assertTrue("name" in interface[0], "Bad interface created!")
self.assertEquals(interface[0]["name"], "test", "Bad interface!")
self.assertTrue("type" in interface[0], "Bad interface created!")
self.assertEquals(interface[0]["type"], "int", "Bad interface!")
self.assertTrue("default" in interface[0], "Bad interface created!")
self.assertEquals(interface[0]["default"], "0", "Bad interface!")
def test_fire_operation(self):
"""
Test preparation of an adapter and launch mechanism.
"""
adapter = TestFactory.create_adapter(TEST_ADAPTER_VALID_MODULE, TEST_ADAPTER_VALID_CLASS)
data = {"test": 5}
result = self.flow_service.fire_operation(adapter, self.test_user, self.test_project.id, **data)
self.assertTrue(result.endswith("has finished."), "Operation fail")
def test_get_filtered_by_column(self):
"""
Test the filter function when retrieving dataTypes with a filter
after a column from a class specific table (e.g. DATA_arraywrapper).
"""
operation_1 = TestFactory.create_operation(test_user=self.test_user, test_project=self.test_project)
operation_2 = TestFactory.create_operation(test_user=self.test_user, test_project=self.test_project)
one_dim_array = numpy.arange(5)
two_dim_array = numpy.array([[1, 2], [2, 3], [1, 4]])
self._store_float_array(one_dim_array, "John Doe 1", operation_1.id)
self._store_float_array(one_dim_array, "John Doe 2", operation_1.id)
self._store_float_array(two_dim_array, "John Doe 3", operation_2.id)
count = self.flow_service.get_available_datatypes(self.test_project.id, "tvb.datatypes.arrays.MappedArray")[1]
self.assertEqual(count, 3, "Problems with inserting data")
first_filter = FilterChain(fields=[FilterChain.datatype + '._nr_dimensions'], operations=["=="], values=[1])
count = self.flow_service.get_available_datatypes(self.test_project.id,
"tvb.datatypes.arrays.MappedArray", first_filter)[1]
self.assertEqual(count, 2, "Data was not filtered")
second_filter = FilterChain(fields=[FilterChain.datatype + '._nr_dimensions'], operations=["=="], values=[2])
filtered_data = self.flow_service.get_available_datatypes(self.test_project.id,
"tvb.datatypes.arrays.MappedArray", second_filter)[0]
self.assertEqual(len(filtered_data), 1, "Data was not filtered")
self.assertEqual(filtered_data[0][3], "John Doe 3")
third_filter = FilterChain(fields=[FilterChain.datatype + '._length_1d'], operations=["=="], values=[3])
filtered_data = self.flow_service.get_available_datatypes(self.test_project.id,
"tvb.datatypes.arrays.MappedArray", third_filter)[0]
self.assertEqual(len(filtered_data), 1, "Data was not filtered correct")
self.assertEqual(filtered_data[0][3], "John Doe 3")
try:
if os.path.exists('One_dim.txt'):
os.remove('One_dim.txt')
if os.path.exists('Two_dim.txt'):
os.remove('Two_dim.txt')
if os.path.exists('One_dim-1.txt'):
os.remove('One_dim-1.txt')
except Exception:
pass
@staticmethod
def _store_float_array(array_data, subject_name, operation_id):
"""Create Float Array and DB persist it"""
datatype_inst = MappedArray(user_tag_1=subject_name)
datatype_inst.set_operation_id(operation_id)
datatype_inst.array_data = array_data
datatype_inst.type = "MappedArray"
datatype_inst.module = "tvb.datatypes.arrays"
datatype_inst.subject = subject_name
datatype_inst.state = "RAW"
dao.store_entity(datatype_inst)
def test_get_filtered_datatypes(self):
"""
Test the filter function when retrieving dataTypes.
"""
#Create some test operations
start_dates = [datetime.now(),
datetime.strptime("08-06-2010", "%m-%d-%Y"),
datetime.strptime("07-21-2010", "%m-%d-%Y"),
datetime.strptime("05-06-2010", "%m-%d-%Y"),
datetime.strptime("07-21-2011", "%m-%d-%Y")]
end_dates = [datetime.now(),
datetime.strptime("08-12-2010", "%m-%d-%Y"),
datetime.strptime("08-12-2010", "%m-%d-%Y"),
datetime.strptime("08-12-2011", "%m-%d-%Y"),
datetime.strptime("08-12-2011", "%m-%d-%Y")]
for i in range(5):
operation = model.Operation(self.test_user.id, self.test_project.id, self.algorithm.id, 'test params',
status=model.STATUS_FINISHED, start_date=start_dates[i],
completion_date=end_dates[i])
operation = dao.store_entity(operation)
storage_path = FilesHelper().get_project_folder(self.test_project, str(operation.id))
if i < 4:
datatype_inst = Datatype1()
datatype_inst.type = "Datatype1"
datatype_inst.subject = "John Doe" + str(i)
datatype_inst.state = "RAW"
datatype_inst.set_operation_id(operation.id)
dao.store_entity(datatype_inst)
else:
for _ in range(2):
datatype_inst = Datatype2()
datatype_inst.storage_path = storage_path
datatype_inst.type = "Datatype2"
datatype_inst.subject = "John Doe" + str(i)
datatype_inst.state = "RAW"
datatype_inst.string_data = ["data"]
datatype_inst.set_operation_id(operation.id)
dao.store_entity(datatype_inst)
returned_data = self.flow_service.get_available_datatypes(self.test_project.id, Datatype1)[0]
for row in returned_data:
if row[1] != 'Datatype1':
self.fail("Some invalid data was returned!")
self.assertEqual(4, len(returned_data), "Invalid length of result")
filter_op = FilterChain(fields=[FilterChain.datatype + ".state", FilterChain.operation + ".start_date"],
values=["RAW", datetime.strptime("08-01-2010", "%m-%d-%Y")], operations=["==", ">"])
returned_data = self.flow_service.get_available_datatypes(self.test_project.id, Datatype1, filter_op)[0]
returned_subjects = [one_data[3] for one_data in returned_data]
if "John Doe0" not in returned_subjects or "John Doe1" not in returned_subjects or len(returned_subjects) != 2:
self.fail("DataTypes were not filtered properly!")
