def test_datatypes_groups(self):
"""
Tests if the dataType group is set correct on the dataTypes resulted from the same operation group.
"""
flow_service = FlowService()
all_operations = dao.get_filtered_operations(self.test_project.id, None)
self.assertEqual(len(all_operations), 0, "There should be no operation")
algogroup = dao.find_group('tvb_test.adapters.testadapter3', 'TestAdapter3')
group, _ = flow_service.prepare_adapter(self.test_project.id, algogroup)
adapter_instance = flow_service.build_adapter_instance(group)
data = {'first_range': 'param_5', 'param_5': [1, 2]}
## Create Group of operations
flow_service.fire_operation(adapter_instance, self.test_user, self.test_project.id, **data)
all_operations = dao.get_filtered_operations(self.test_project.id, None)
self.assertEqual(len(all_operations), 1, "Expected one operation group")
self.assertEqual(all_operations[0][2], 2, "Expected 2 operations in group")
operation_group_id = all_operations[0][3]
self.assertNotEquals(operation_group_id, None, "The operation should be part of a group.")
self.operation_service.stop_operation(all_operations[0][0])
self.operation_service.stop_operation(all_operations[0][1])
## Make sure operations are executed
self.operation_service.launch_operation(all_operations[0][0], False)
self.operation_service.launch_operation(all_operations[0][1], False)
resulted_datatypes = dao.get_datatype_in_group(operation_group_id)
self.assertTrue(len(resulted_datatypes) >= 2, "Expected at least 2, but: " + str(len(resulted_datatypes)))
dt = dao.get_datatype_by_id(resulted_datatypes[0].id)
datatype_group = dao.get_datatypegroup_by_op_group_id(operation_group_id)
self.assertEqual(dt.fk_datatype_group, datatype_group.id, "DataTypeGroup is incorrect")
class SpatioTemporalController(base.BaseController):
"""
Base class which contains methods related to spatio-temporal actions.
"""
def __init__(self):
base.BaseController.__init__(self)
self.flow_service = FlowService()
self.logger = get_logger(__name__)
editable_entities = [
dict(link='/spatial/stimulus/region/step_1_submit/1/1',
title='Region Stimulus',
subsection='regionstim',
description='Create a new Stimulus on Region level'),
dict(link='/spatial/stimulus/surface/step_1_submit/1/1',
title='Surface Stimulus',
subsection='surfacestim',
description='Create a new Stimulus on Surface level')
]
self.submenu_list = editable_entities
@cherrypy.expose
@using_template('base_template')
@logged()
@settings()
def index(self, **data):
"""
Displays the main page for the spatio temporal section.
"""
template_specification = dict(title="Spatio temporal", data=data)
template_specification['mainContent'] = 'header_menu'
return self.fill_default_attributes(template_specification)
@staticmethod
def get_connectivity_parameters(input_connectivity, surface_data=None):
"""
Returns a dictionary which contains all the needed data for drawing a connectivity.
"""
viewer = ConnectivityViewer()
global_params, global_pages = viewer.compute_connectivity_global_params(
input_connectivity, surface_data)
global_params.update(global_pages)
global_params['selectedConnectivityGid'] = input_connectivity.gid
return global_params
def get_data_from_burst_configuration(self):
"""
Returns the model, integrator, connectivity and surface instances from the burst configuration.
"""
### Read from session current burst-configuration
burst_configuration = base.get_from_session(base.KEY_BURST_CONFIG)
if burst_configuration is None:
return None, None, None
first_range = burst_configuration.get_simulation_parameter_value(
'first_range')
second_range = burst_configuration.get_simulation_parameter_value(
'second_range')
if ((first_range is not None
and str(first_range).startswith(MODEL_PARAMETERS))
or (second_range is not None
and str(second_range).startswith(MODEL_PARAMETERS))):
base.set_error_message(
"When configuring model parameters you are not allowed to specify range values."
)
raise cherrypy.HTTPRedirect("/burst/")
group = self.flow_service.get_algorithm_by_module_and_class(
SIMULATOR_MODULE, SIMULATOR_CLASS)[1]
simulator_adapter = self.flow_service.build_adapter_instance(group)
try:
params_dict = simulator_adapter.convert_ui_inputs(
burst_configuration.get_all_simulator_values()[0], False)
except Exception, excep:
self.logger.exception(excep)
base.set_error_message(
"Some of the provided parameters have an invalid value.")
raise cherrypy.HTTPRedirect("/burst/")
### Prepare Model instance
model = burst_configuration.get_simulation_parameter_value(PARAM_MODEL)
model_parameters = params_dict[MODEL_PARAMETERS]
noise_framework.build_noise(model_parameters)
try:
model = get_traited_instance_for_name(model, Model,
model_parameters)
except Exception, ex:
self.logger.exception(ex)
self.logger.info(
"Could not create the model instance with the given parameters. "
"A new model instance will be created with the default values."
)
model = get_traited_instance_for_name(model, Model, {})
class ProjectStructureTest(TransactionalTestCase):
"""
Test ProjectService methods.
"""
def setUp(self):
"""
Prepare before each test.
"""
self.project_service = ProjectService()
self.flow_service = FlowService()
self.structure_helper = FilesHelper()
self.test_user = TestFactory.create_user()
self.test_project = TestFactory.create_project(self.test_user,
"ProjectStructure")
self.relevant_filter = StaticFiltersFactory.build_datatype_filters(
single_filter=StaticFiltersFactory.RELEVANT_VIEW)
self.full_filter = StaticFiltersFactory.build_datatype_filters(
single_filter=StaticFiltersFactory.FULL_VIEW)
def tearDown(self):
self.delete_project_folders()
# def tearDown(self):
# """
# Remove project folders and clean up database.
# """
# self.clean_database(True)
def test_set_operation_visibility(self):
"""
Check if the visibility for an operation is set correct.
"""
self.__init_algorithmn()
op1 = model.Operation(self.test_user.id, self.test_project.id,
self.algo_inst.id, "")
op1 = dao.store_entity(op1)
self.assertTrue(op1.visible, "The operation should be visible.")
self.project_service.set_operation_and_group_visibility(op1.gid, False)
updated_op = dao.get_operation_by_id(op1.id)
self.assertFalse(updated_op.visible,
"The operation should not be visible.")
def test_set_op_and_group_visibility(self):
"""
When changing the visibility for an operation that belongs to an operation group, we
should also change the visibility for the entire group of operations.
"""
_, group_id = TestFactory.create_group(self.test_user,
subject="test-subject-1")
list_of_operations = dao.get_operations_in_group(group_id)
for operation in list_of_operations:
self.assertTrue(operation.visible,
"The operation should be visible.")
self.project_service.set_operation_and_group_visibility(
list_of_operations[0].gid, False)
operations = dao.get_operations_in_group(group_id)
for operation in operations:
self.assertFalse(operation.visible,
"The operation should not be visible.")
def test_set_op_group_visibility(self):
"""
Tests if the visibility for an operation group is set correct.
"""
_, group_id = TestFactory.create_group(self.test_user,
subject="test-subject-1")
list_of_operations = dao.get_operations_in_group(group_id)
for operation in list_of_operations:
self.assertTrue(operation.visible,
"The operation should be visible.")
op_group = dao.get_operationgroup_by_id(group_id)
self.project_service.set_operation_and_group_visibility(
op_group.gid, False, True)
operations = dao.get_operations_in_group(group_id)
for operation in operations:
self.assertFalse(operation.visible,
"The operation should not be visible.")
def test_is_upload_operation(self):
self.__init_algorithmn()
upload_algo = self._create_algo_for_upload()
op1 = model.Operation(self.test_user.id, self.test_project.id,
self.algo_inst.id, "")
op2 = model.Operation(self.test_user.id, self.test_project.id,
upload_algo.id, "")
operations = dao.store_entities([op1, op2])
is_upload_operation = self.project_service.is_upload_operation(
operations[0].gid)
self.assertFalse(is_upload_operation,
"The operation is not an upload operation.")
is_upload_operation = self.project_service.is_upload_operation(
operations[1].gid)
self.assertTrue(is_upload_operation,
"The operation is an upload operation.")
def test_get_upload_operations(self):
"""
Test get_all when filter is for Upload category.
"""
self.__init_algorithmn()
upload_algo = self._create_algo_for_upload()
project = model.Project("test_proj_2", self.test_user.id, "desc")
project = dao.store_entity(project)
op1 = model.Operation(self.test_user.id, self.test_project.id,
self.algo_inst.id, "")
op2 = model.Operation(self.test_user.id,
project.id,
upload_algo.id,
"",
status=model.STATUS_FINISHED)
op3 = model.Operation(self.test_user.id, self.test_project.id,
upload_algo.id, "")
op4 = model.Operation(self.test_user.id,
self.test_project.id,
upload_algo.id,
"",
status=model.STATUS_FINISHED)
op5 = model.Operation(self.test_user.id,
self.test_project.id,
upload_algo.id,
"",
status=model.STATUS_FINISHED)
operations = dao.store_entities([op1, op2, op3, op4, op5])
upload_operations = self.project_service.get_all_operations_for_uploaders(
self.test_project.id)
self.assertEqual(2, len(upload_operations),
"Wrong number of upload operations.")
upload_ids = [operation.id for operation in upload_operations]
for i in [3, 4]:
self.assertTrue(operations[i].id in upload_ids,
"The operation should be an upload operation.")
for i in [0, 1, 2]:
self.assertFalse(
operations[i].id in upload_ids,
"The operation should not be an upload operation.")
def test_is_datatype_group(self):
"""
Tests if a datatype is group.
"""
_, dt_group_id, first_dt, _ = self._create_datatype_group()
dt_group = dao.get_generic_entity(model.DataTypeGroup, dt_group_id)[0]
is_dt_group = self.project_service.is_datatype_group(dt_group.gid)
self.assertTrue(is_dt_group,
"The datatype should be a datatype group.")
is_dt_group = self.project_service.is_datatype_group(first_dt.gid)
self.assertFalse(is_dt_group,
"The datatype should not be a datatype group.")
def test_count_datatypes_in_group(self):
""" Test that counting dataTypes is correct. Happy flow."""
_, dt_group_id, first_dt, _ = self._create_datatype_group()
count = dao.count_datatypes_in_group(dt_group_id)
self.assertEqual(count, 2)
count = dao.count_datatypes_in_group(first_dt.id)
self.assertEqual(count, 0, "There should be no dataType.")
def test_set_datatype_visibility(self):
"""
Check if the visibility for a datatype is set correct.
"""
#it's a list of 3 elem.
mapped_arrays = self._create_mapped_arrays(self.test_project.id)
for mapped_array in mapped_arrays:
is_visible = dao.get_datatype_by_id(mapped_array[0]).visible
self.assertTrue(is_visible, "The data type should be visible.")
self.project_service.set_datatype_visibility(mapped_arrays[0][2],
False)
for i in xrange(len(mapped_arrays)):
is_visible = dao.get_datatype_by_id(mapped_arrays[i][0]).visible
if not i:
self.assertFalse(is_visible,
"The data type should not be visible.")
else:
self.assertTrue(is_visible, "The data type should be visible.")
def test_set_visibility_for_dt_in_group(self):
"""
Check if the visibility for a datatype from a datatype group is set correct.
"""
_, dt_group_id, first_dt, second_dt = self._create_datatype_group()
self.assertTrue(first_dt.visible, "The data type should be visible.")
self.assertTrue(second_dt.visible, "The data type should be visible.")
self.project_service.set_datatype_visibility(first_dt.gid, False)
db_dt_group = self.project_service.get_datatype_by_id(dt_group_id)
db_first_dt = self.project_service.get_datatype_by_id(first_dt.id)
db_second_dt = self.project_service.get_datatype_by_id(second_dt.id)
self.assertFalse(db_dt_group.visible,
"The data type should be visible.")
self.assertFalse(db_first_dt.visible,
"The data type should not be visible.")
self.assertFalse(db_second_dt.visible,
"The data type should be visible.")
def test_set_visibility_for_group(self):
"""
Check if the visibility for a datatype group is set correct.
"""
_, dt_group_id, first_dt, second_dt = self._create_datatype_group()
dt_group = dao.get_generic_entity(model.DataTypeGroup, dt_group_id)[0]
self.assertTrue(dt_group.visible,
"The data type group should be visible.")
self.assertTrue(first_dt.visible, "The data type should be visible.")
self.assertTrue(second_dt.visible, "The data type should be visible.")
self.project_service.set_datatype_visibility(dt_group.gid, False)
updated_dt_group = self.project_service.get_datatype_by_id(dt_group_id)
updated_first_dt = self.project_service.get_datatype_by_id(first_dt.id)
updated_second_dt = self.project_service.get_datatype_by_id(
second_dt.id)
self.assertFalse(updated_dt_group.visible,
"The data type group should be visible.")
self.assertFalse(updated_first_dt.visible,
"The data type should be visible.")
self.assertFalse(updated_second_dt.visible,
"The data type should be visible.")
def test_getdatatypes_from_dtgroup(self):
"""
Validate that we can retrieve all DTs from a DT_Group
"""
_, dt_group_id, first_dt, second_dt = self._create_datatype_group()
datatypes = self.project_service.get_datatypes_from_datatype_group(
dt_group_id)
self.assertEqual(
len(datatypes), 2,
"There should be 2 datatypes into the datatype group.")
expected_dict = {first_dt.id: first_dt, second_dt.id: second_dt}
actual_dict = {
datatypes[0].id: datatypes[0],
datatypes[1].id: datatypes[1]
}
for key in expected_dict.keys():
expected = expected_dict[key]
actual = actual_dict[key]
self.assertEqual(expected.id, actual.id, "Not the same id.")
self.assertEqual(expected.gid, actual.gid, "Not the same gid.")
self.assertEqual(expected.type, actual.type, "Not the same type.")
self.assertEqual(expected.subject, actual.subject,
"Not the same subject.")
self.assertEqual(expected.state, actual.state,
"Not the same state.")
self.assertEqual(expected.visible, actual.visible,
"The datatype visibility is not correct.")
self.assertEqual(expected.module, actual.module,
"Not the same module.")
self.assertEqual(expected.user_tag_1, actual.user_tag_1,
"Not the same user_tag_1.")
self.assertEqual(expected.invalid, actual.invalid,
"The invalid field value is not correct.")
self.assertEqual(expected.is_nan, actual.is_nan,
"The is_nan field value is not correct.")
def test_get_operations_for_dt(self):
created_ops, datatype_gid = self._create_operations_with_inputs()
operations = self.project_service.get_operations_for_datatype(
datatype_gid, self.relevant_filter)
self.assertEqual(len(operations), 2)
self.assertTrue(
created_ops[0].id in [operations[0].id, operations[1].id],
"Retrieved wrong operations.")
self.assertTrue(
created_ops[2].id in [operations[0].id, operations[1].id],
"Retrieved wrong operations.")
operations = self.project_service.get_operations_for_datatype(
datatype_gid, self.full_filter)
self.assertEqual(len(operations), 4)
ids = [
operations[0].id, operations[1].id, operations[2].id,
operations[3].id
]
for i in range(4):
self.assertTrue(created_ops[i].id in ids,
"Retrieved wrong operations.")
operations = self.project_service.get_operations_for_datatype(
datatype_gid, self.relevant_filter, True)
self.assertEqual(len(operations), 1)
self.assertEqual(created_ops[4].id, operations[0].id,
"Incorrect number of operations.")
operations = self.project_service.get_operations_for_datatype(
datatype_gid, self.full_filter, True)
self.assertEqual(len(operations), 2)
self.assertTrue(
created_ops[4].id in [operations[0].id, operations[1].id],
"Retrieved wrong operations.")
self.assertTrue(
created_ops[5].id in [operations[0].id, operations[1].id],
"Retrieved wrong operations.")
def test_get_operations_for_dt_group(self):
created_ops, dt_group_id = self._create_operations_with_inputs(True)
ops = self.project_service.get_operations_for_datatype_group(
dt_group_id, self.relevant_filter)
self.assertEqual(len(ops), 2)
self.assertTrue(created_ops[0].id in [ops[0].id, ops[1].id],
"Retrieved wrong operations.")
self.assertTrue(created_ops[2].id in [ops[0].id, ops[1].id],
"Retrieved wrong operations.")
ops = self.project_service.get_operations_for_datatype_group(
dt_group_id, self.full_filter)
self.assertEqual(len(ops), 4, "Incorrect number of operations.")
ids = [ops[0].id, ops[1].id, ops[2].id, ops[3].id]
for i in range(4):
self.assertTrue(created_ops[i].id in ids,
"Retrieved wrong operations.")
ops = self.project_service.get_operations_for_datatype_group(
dt_group_id, self.relevant_filter, True)
self.assertEqual(len(ops), 1)
self.assertEqual(created_ops[4].id, ops[0].id,
"Incorrect number of operations.")
ops = self.project_service.get_operations_for_datatype_group(
dt_group_id, self.full_filter, True)
self.assertEqual(len(ops), 2)
self.assertTrue(created_ops[4].id in [ops[0].id, ops[1].id],
"Retrieved wrong operations.")
self.assertTrue(created_ops[5].id in [ops[0].id, ops[1].id],
"Retrieved wrong operations.")
def test_get_inputs_for_operation(self):
algo_group = dao.find_group('tvb_test.adapters.testadapter3',
'TestAdapter3')
algo = dao.get_algorithm_by_group(algo_group.id)
array_wrappers = self._create_mapped_arrays(self.test_project.id)
ids = []
for datatype in array_wrappers:
ids.append(datatype[0])
datatype = dao.get_datatype_by_id(ids[0])
datatype.visible = False
dao.store_entity(datatype)
parameters = json.dumps({
"param_5": "1",
"param_1": array_wrappers[0][2],
"param_2": array_wrappers[1][2],
"param_3": array_wrappers[2][2],
"param_6": "0"
})
operation = model.Operation(self.test_user.id, self.test_project.id,
algo.id, parameters)
operation = dao.store_entity(operation)
inputs = self.project_service.get_datatype_and_datatypegroup_inputs_for_operation(
operation.gid, self.relevant_filter)
self.assertEqual(len(inputs), 2)
self.assertTrue(ids[1] in [inputs[0].id, inputs[1].id],
"Retrieved wrong dataType.")
self.assertTrue(ids[2] in [inputs[0].id, inputs[1].id],
"Retrieved wrong dataType.")
self.assertFalse(ids[0] in [inputs[0].id, inputs[1].id],
"Retrieved wrong dataType.")
inputs = self.project_service.get_datatype_and_datatypegroup_inputs_for_operation(
operation.gid, self.full_filter)
self.assertEqual(len(inputs), 3, "Incorrect number of operations.")
self.assertTrue(ids[0] in [inputs[0].id, inputs[1].id, inputs[2].id],
"Retrieved wrong dataType.")
self.assertTrue(ids[1] in [inputs[0].id, inputs[1].id, inputs[2].id],
"Retrieved wrong dataType.")
self.assertTrue(ids[2] in [inputs[0].id, inputs[1].id, inputs[2].id],
"Retrieved wrong dataType.")
project, dt_group_id, first_dt, _ = self._create_datatype_group()
first_dt.visible = False
dao.store_entity(first_dt)
parameters = json.dumps({"other_param": "_", "param_1": first_dt.gid})
operation = model.Operation(self.test_user.id, project.id, algo.id,
parameters)
operation = dao.store_entity(operation)
inputs = self.project_service.get_datatype_and_datatypegroup_inputs_for_operation(
operation.gid, self.relevant_filter)
self.assertEqual(len(inputs), 0, "Incorrect number of dataTypes.")
inputs = self.project_service.get_datatype_and_datatypegroup_inputs_for_operation(
operation.gid, self.full_filter)
self.assertEqual(len(inputs), 1, "Incorrect number of dataTypes.")
self.assertEqual(inputs[0].id, dt_group_id, "Wrong dataType.")
self.assertTrue(inputs[0].id != first_dt.id, "Wrong dataType.")
def test_get_inputs_for_op_group(self):
"""
Tests method get_datatypes_inputs_for_operation_group.
The DataType inputs will be from a DataType group.
"""
project, dt_group_id, first_dt, second_dt = self._create_datatype_group(
)
first_dt.visible = False
dao.store_entity(first_dt)
second_dt.visible = False
dao.store_entity(second_dt)
op_group = model.OperationGroup(project.id, "group", "range1[1..2]")
op_group = dao.store_entity(op_group)
params_1 = json.dumps({
"param_5": "1",
"param_1": first_dt.gid,
"param_6": "2"
})
params_2 = json.dumps({
"param_5": "1",
"param_4": second_dt.gid,
"param_6": "5"
})
algo_group = dao.find_group('tvb_test.adapters.testadapter3',
'TestAdapter3')
algo = dao.get_algorithm_by_group(algo_group.id)
op1 = model.Operation(self.test_user.id,
project.id,
algo.id,
params_1,
op_group_id=op_group.id)
op2 = model.Operation(self.test_user.id,
project.id,
algo.id,
params_2,
op_group_id=op_group.id)
dao.store_entities([op1, op2])
inputs = self.project_service.get_datatypes_inputs_for_operation_group(
op_group.id, self.relevant_filter)
self.assertEqual(len(inputs), 0)
inputs = self.project_service.get_datatypes_inputs_for_operation_group(
op_group.id, self.full_filter)
self.assertEqual(len(inputs), 1, "Incorrect number of dataTypes.")
self.assertFalse(first_dt.id == inputs[0].id,
"Retrieved wrong dataType.")
self.assertFalse(second_dt.id == inputs[0].id,
"Retrieved wrong dataType.")
self.assertTrue(dt_group_id == inputs[0].id,
"Retrieved wrong dataType.")
first_dt.visible = True
dao.store_entity(first_dt)
inputs = self.project_service.get_datatypes_inputs_for_operation_group(
op_group.id, self.relevant_filter)
self.assertEqual(len(inputs), 1, "Incorrect number of dataTypes.")
self.assertFalse(first_dt.id == inputs[0].id,
"Retrieved wrong dataType.")
self.assertFalse(second_dt.id == inputs[0].id,
"Retrieved wrong dataType.")
self.assertTrue(dt_group_id == inputs[0].id,
"Retrieved wrong dataType.")
inputs = self.project_service.get_datatypes_inputs_for_operation_group(
op_group.id, self.full_filter)
self.assertEqual(len(inputs), 1, "Incorrect number of dataTypes.")
self.assertFalse(first_dt.id == inputs[0].id,
"Retrieved wrong dataType.")
self.assertFalse(second_dt.id == inputs[0].id,
"Retrieved wrong dataType.")
self.assertTrue(dt_group_id == inputs[0].id,
"Retrieved wrong dataType.")
def test_get_inputs_for_op_group_simple_inputs(self):
"""
Tests method get_datatypes_inputs_for_operation_group.
The dataType inputs will not be part of a dataType group.
"""
#it's a list of 3 elem.
array_wrappers = self._create_mapped_arrays(self.test_project.id)
array_wrapper_ids = []
for datatype in array_wrappers:
array_wrapper_ids.append(datatype[0])
datatype = dao.get_datatype_by_id(array_wrapper_ids[0])
datatype.visible = False
dao.store_entity(datatype)
op_group = model.OperationGroup(self.test_project.id, "group",
"range1[1..2]")
op_group = dao.store_entity(op_group)
params_1 = json.dumps({
"param_5": "2",
"param_1": array_wrappers[0][2],
"param_2": array_wrappers[1][2],
"param_6": "7"
})
params_2 = json.dumps({
"param_5": "5",
"param_3": array_wrappers[2][2],
"param_2": array_wrappers[1][2],
"param_6": "6"
})
algo_group = dao.find_group('tvb_test.adapters.testadapter3',
'TestAdapter3')
algo = dao.get_algorithm_by_group(algo_group.id)
op1 = model.Operation(self.test_user.id,
self.test_project.id,
algo.id,
params_1,
op_group_id=op_group.id)
op2 = model.Operation(self.test_user.id,
self.test_project.id,
algo.id,
params_2,
op_group_id=op_group.id)
dao.store_entities([op1, op2])
inputs = self.project_service.get_datatypes_inputs_for_operation_group(
op_group.id, self.relevant_filter)
self.assertEqual(len(inputs), 2)
self.assertFalse(array_wrapper_ids[0] in [inputs[0].id, inputs[1].id],
"Retrieved wrong dataType.")
self.assertTrue(array_wrapper_ids[1] in [inputs[0].id, inputs[1].id],
"Retrieved wrong dataType.")
self.assertTrue(array_wrapper_ids[2] in [inputs[0].id, inputs[1].id],
"Retrieved wrong dataType.")
inputs = self.project_service.get_datatypes_inputs_for_operation_group(
op_group.id, self.full_filter)
self.assertEqual(len(inputs), 3, "Incorrect number of dataTypes.")
self.assertTrue(
array_wrapper_ids[0] in [inputs[0].id, inputs[1].id, inputs[2].id])
self.assertTrue(
array_wrapper_ids[1] in [inputs[0].id, inputs[1].id, inputs[2].id])
self.assertTrue(
array_wrapper_ids[2] in [inputs[0].id, inputs[1].id, inputs[2].id])
def test_remove_datatype(self):
"""
Tests the deletion of a datatype.
"""
#it's a list of 3 elem.
array_wrappers = self._create_mapped_arrays(self.test_project.id)
dt_list = []
for array_wrapper in array_wrappers:
dt_list.append(dao.get_datatype_by_id(array_wrapper[0]))
self.project_service.remove_datatype(self.test_project.id,
dt_list[0].gid)
self._check_if_datatype_was_removed(dt_list[0])
def test_remove_datatype_from_group(self):
"""
Tests the deletion of a datatype group.
"""
project, dt_group_id, first_dt, second_dt = self._create_datatype_group(
)
datatype_group = dao.get_generic_entity(model.DataTypeGroup,
dt_group_id)[0]
self.project_service.remove_datatype(project.id, first_dt.gid)
self._check_if_datatype_was_removed(first_dt)
self._check_if_datatype_was_removed(second_dt)
self._check_if_datatype_was_removed(datatype_group)
self._check_datatype_group_removed(dt_group_id,
datatype_group.fk_operation_group)
def test_remove_datatype_group(self):
"""
Tests the deletion of a datatype group.
"""
project, dt_group_id, first_dt, second_dt = self._create_datatype_group(
)
datatype_group = dao.get_generic_entity(model.DataTypeGroup,
dt_group_id)[0]
self.project_service.remove_datatype(project.id, datatype_group.gid)
self._check_if_datatype_was_removed(first_dt)
self._check_if_datatype_was_removed(second_dt)
self._check_if_datatype_was_removed(datatype_group)
self._check_datatype_group_removed(dt_group_id,
datatype_group.fk_operation_group)
def _create_mapped_arrays(self, project_id):
array_wrappers = self.flow_service.get_available_datatypes(
project_id, "tvb.datatypes.arrays.MappedArray")
self.assertEqual(len(array_wrappers), 0)
algo_group = dao.find_group('tvb_test.adapters.ndimensionarrayadapter',
'NDimensionArrayAdapter')
group, _ = self.flow_service.prepare_adapter(project_id, algo_group)
adapter_instance = self.flow_service.build_adapter_instance(group)
data = {'param_1': 'some value'}
#create 3 data types
self.flow_service.fire_operation(adapter_instance, self.test_user,
project_id, **data)
array_wrappers = self.flow_service.get_available_datatypes(
project_id, "tvb.datatypes.arrays.MappedArray")
self.assertEqual(len(array_wrappers), 1)
self.flow_service.fire_operation(adapter_instance, self.test_user,
project_id, **data)
array_wrappers = self.flow_service.get_available_datatypes(
project_id, "tvb.datatypes.arrays.MappedArray")
self.assertEqual(len(array_wrappers), 2)
self.flow_service.fire_operation(adapter_instance, self.test_user,
project_id, **data)
array_wrappers = self.flow_service.get_available_datatypes(
project_id, "tvb.datatypes.arrays.MappedArray")
self.assertEqual(len(array_wrappers), 3)
return array_wrappers
def _create_operation(self, project_id, algorithm_id):
algorithm = dao.get_algorithm_by_id(algorithm_id)
meta = {
DataTypeMetaData.KEY_SUBJECT: "John Doe",
DataTypeMetaData.KEY_STATE: "RAW"
}
operation = model.Operation(self.test_user.id,
project_id,
algorithm.id,
'test params',
meta=json.dumps(meta),
status="FINISHED",
method_name=ABCAdapter.LAUNCH_METHOD)
return dao.store_entity(operation)
def _create_datatype_group(self):
"""
Creates a project, one DataTypeGroup with 2 DataTypes into the new group.
"""
test_project = TestFactory.create_project(self.test_user, "NewProject")
all_operations = dao.get_filtered_operations(test_project.id, None)
self.assertEqual(len(all_operations), 0,
"There should be no operation.")
datatypes, op_group_id = TestFactory.create_group(
self.test_user, test_project)
dt_group = dao.get_datatypegroup_by_op_group_id(op_group_id)
return test_project, dt_group.id, datatypes[0], datatypes[1]
def _create_operations_with_inputs(self, is_group_parent=False):
"""
Method used for creating a complex tree of operations.
If 'if_group_parent' is True then a new group will be created and one of its entries it will be used as
input for the returned operations.
"""
group_dts, root_op_group_id = TestFactory.create_group(
self.test_user, self.test_project)
if is_group_parent:
datatype_gid = group_dts[0].gid
else:
datatype_gid = ProjectServiceTest._create_value_wrapper(
self.test_user, self.test_project)[1]
parameters = json.dumps({"param_name": datatype_gid})
ops = []
for i in range(4):
ops.append(
TestFactory.create_operation(test_user=self.test_user,
test_project=self.test_project))
if i in [1, 3]:
ops[i].visible = False
ops[i].parameters = parameters
ops[i] = dao.store_entity(ops[i])
#groups
_, ops_group = TestFactory.create_group(self.test_user,
self.test_project)
ops_group = dao.get_operations_in_group(ops_group)
self.assertEqual(2, len(ops_group))
ops_group[0].parameters = parameters
ops_group[0] = dao.store_entity(ops_group[0])
ops_group[1].visible = False
ops_group[1].parameters = parameters
ops_group[1] = dao.store_entity(ops_group[1])
ops.extend(ops_group)
if is_group_parent:
dt_group = dao.get_datatypegroup_by_op_group_id(root_op_group_id)
return ops, dt_group.id
return ops, datatype_gid
def _check_if_datatype_was_removed(self, datatype):
"""
Check if a certain datatype was removed.
"""
try:
dao.get_datatype_by_id(datatype.id)
self.fail("The datatype was not deleted.")
except Exception:
pass
try:
dao.get_operation_by_id(datatype.fk_from_operation)
self.fail("The operation was not deleted.")
except Exception:
pass
def _check_datatype_group_removed(self, datatype_group_id,
operation_groupp_id):
"""
Checks if the DataTypeGroup and OperationGroup was removed.
"""
try:
dao.get_generic_entity(model.DataTypeGroup, datatype_group_id)
self.fail("The DataTypeGroup entity was not removed.")
except Exception:
pass
try:
dao.get_operationgroup_by_id(operation_groupp_id)
self.fail("The OperationGroup entity was not removed.")
except Exception:
pass
def __init_algorithmn(self):
"""
Insert some starting data in the database.
"""
categ1 = model.AlgorithmCategory('one', True)
self.categ1 = dao.store_entity(categ1)
algo = model.AlgorithmGroup("tvb_test.core.services.flowservice_test",
"ValidTestAdapter", categ1.id)
adapter = dao.store_entity(algo)
algo = model.Algorithm(adapter.id,
'ident',
name='',
req_data='',
param_name='',
output='')
self.algo_inst = dao.store_entity(algo)
@staticmethod
def _create_algo_for_upload():
""" Creates a fake algorithm for an upload category. """
category = dao.store_entity(
model.AlgorithmCategory("upload_category", rawinput=True))
algo_group = dao.store_entity(
model.AlgorithmGroup("module", "classname", category.id))
return dao.store_entity(model.Algorithm(algo_group.id, "algo"))
class FlowServiceTest(TransactionalTestCase):
"""
This class contains tests for the tvb.core.services.flowservice module.
"""
def setUp(self):
"""
Reset the database before each test.
"""
# self.reset_database()
self.flow_service = FlowService()
self.test_user = TestFactory.create_user()
self.test_project = TestFactory.create_project(admin=self.test_user)
### Insert some starting data in the database.
categ1 = model.AlgorithmCategory('one', True)
self.categ1 = dao.store_entity(categ1)
categ2 = model.AlgorithmCategory('two', rawinput=True)
self.categ2 = dao.store_entity(categ2)
algo = model.AlgorithmGroup("test_module1", "classname1", categ1.id)
self.algo1 = dao.store_entity(algo)
algo = model.AlgorithmGroup("test_module2", "classname2", categ2.id)
dao.store_entity(algo)
algo = model.AlgorithmGroup("tvb_test.core.services.flowservice_test", "ValidTestAdapter", categ2.id)
adapter = dao.store_entity(algo)
algo = model.Algorithm(adapter.id, 'ident', name='', req_data='', param_name='', output='')
self.algo_inst = dao.store_entity(algo)
algo = model.AlgorithmGroup("test_module3", "classname3", categ1.id)
dao.store_entity(algo)
algo = model.Algorithm(self.algo1.id, 'id', name='', req_data='', param_name='', output='')
self.algo_inst = dao.store_entity(algo)
def test_read_algorithm_categories(self):
"""
Read algorithm categories when they exist in the database.
"""
categories = self.flow_service.read_algorithm_categories()
self.assertEqual(len(categories), 8)
self.assertTrue(self.categ1 in categories, "Missing category")
self.assertTrue(self.categ2 in categories, "Missing category")
def test_groups_for_categories(self):
"""
Test getting algorithms for specific categories.
"""
category1 = self.flow_service.get_groups_for_categories([self.categ1])
category2 = self.flow_service.get_groups_for_categories([self.categ2])
dummy = model.AlgorithmCategory('dummy', rawinput=True)
dummy.id = 999
unexisting_cat = self.flow_service.get_groups_for_categories([dummy])
self.assertEqual(len(category1), 2)
for algorithm in category1:
if algorithm.module not in ["test_module1", "test_module3"]:
self.fail("Some invalid data retrieved")
for algorithm in category2:
if algorithm.module not in ["test_module2", "tvb_test.core.services.flowservice_test"]:
self.fail("Some invalid data retrieved")
self.assertEqual(len(category2), 2)
self.assertEqual(len(unexisting_cat), 0)
def test_get_broup_by_identifier(self):
"""
Test for the get_algorithm_by_identifier.
"""
algo_ret = self.flow_service.get_algo_group_by_identifier(self.algo1.id)
self.assertEqual(algo_ret.id, self.algo1.id, "ID-s are different!")
self.assertEqual(algo_ret.module, self.algo1.module, "Modules are different!")
self.assertEqual(algo_ret.fk_category, self.algo1.fk_category, "Categories are different!")
self.assertEqual(algo_ret.classname, self.algo1.classname, "Class names are different!")
def test_build_adapter_instance(self):
"""
Test standard flow for building an adapter instance.
"""
module = "tvb_test.core.services.flowservice_test"
class_name = "ValidTestAdapter"
algo_group = dao.find_group(module, class_name)
adapter = ABCAdapter.build_adapter(algo_group)
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.
"""
module = "tvb_test.core.services.flowservice_test"
class_name = "InvalidTestAdapter"
group = dao.find_group(module, class_name)
self.assertRaises(OperationException, self.flow_service.build_adapter_instance, group)
def test_prepare_adapter(self):
"""
Test preparation of an adapter.
"""
module = "tvb_test.core.services.flowservice_test"
class_name = "ValidTestAdapter"
algo_group = dao.find_group(module, class_name)
group, interface = self.flow_service.prepare_adapter(self.test_project.id, algo_group)
self.assertTrue(isinstance(group, model.AlgorithmGroup), "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.
"""
module = "tvb_test.core.services.flowservice_test"
class_name = "ValidTestAdapter"
algo_group = dao.find_group(module, class_name)
adapter = self.flow_service.build_adapter_instance(algo_group)
data = {"test": 5}
result = self.flow_service.fire_operation(adapter, self.test_user, self.test_project.id,
ABCAdapter.LAUNCH_METHOD, **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)
inserted_data = self.flow_service.get_available_datatypes(self.test_project.id,
"tvb.datatypes.arrays.MappedArray")
self.assertEqual(len(inserted_data), 3, "Problems with inserting data")
first_filter = FilterChain(fields=[FilterChain.datatype + '._nr_dimensions'], operations=["=="], values=[1])
filtered_data = self.flow_service.get_available_datatypes(self.test_project.id,
"tvb.datatypes.arrays.MappedArray", first_filter)
self.assertEqual(len(filtered_data), 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)
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)
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.algo_inst.id, 'test params',
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,
"tvb_test.datatypes.datatype1.Datatype1")
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,
"tvb_test.datatypes.datatype1.Datatype1", filter_op)
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!")
