def test_ontology_config_invalid_entity_name():
with pytest.raises(ValidationError) as excinfo:
ontology_config = read_configuration(
'./test_data/input_data/config/invalid_ontology_config/ontology_config_invalid_entity_name')
OntologyMapper('test').map(ontology_config.nodes)
assert 'Invalid concept code: InvalidEntity.taxonomy. ' \
'InvalidEntity is not a valid CSR entity.' in str(excinfo.value)
def test_ontology_config_invalid_concept_code():
with pytest.raises(ValidationError) as excinfo:
ontology_config = read_configuration(
'./test_data/input_data/config/invalid_ontology_config/ontology_config_invalid_concept_code')
OntologyMapper('test').map(ontology_config.nodes)
assert 'Invalid concept code format: gender. Concept code has to have format: ' \
'`<entity_name>.<entity_field>`' in str(excinfo.value)
def test_ontology_config_invalid_entity_field():
with pytest.raises(ValidationError) as excinfo:
ontology_config = read_configuration(
'./test_data/input_data/config/invalid_ontology_config/ontology_config_invalid_entity_field')
OntologyMapper('test').map(ontology_config.nodes)
assert 'Invalid concept code: Individual.not_existing_field. ' \
'Field: not_existing_field is not a valid field of Individual entity.' in str(excinfo.value)
def test_non_root_top_node():
ontology_config = read_configuration('./test_data/input_data/config')
tree_nodes = OntologyMapper('\\Root node\\Second level\\Top node\\').map(ontology_config.nodes)
assert len(tree_nodes) == 1
assert tree_nodes[0].name == 'Root node'
assert len(tree_nodes[0].children) == 1
assert tree_nodes[0].children[0].name == 'Second level'
assert len(tree_nodes[0].children[0].children) == 1
assert tree_nodes[0].children[0].children[0].name == 'Top node'
assert len(tree_nodes[0].children[0].children[0].children) == 5
def test_valid_ontology_config():
ontology_config = read_configuration('./test_data/input_data/config')
tree_nodes = OntologyMapper('test').map(ontology_config.nodes)
assert len(tree_nodes) == 1
assert len(tree_nodes[0].children) == 5
# Test if the birth date concept node is present and has Date value type.
patient_information = [node for node in tree_nodes[0].children if node.name == '01. Patient information'][0]
birth_date_node: ConceptNode = [node for node in patient_information.children
if node.name == '01. Date of birth'][0]
assert birth_date_node.concept.concept_code == 'Individual.birth_date'
assert birth_date_node.concept.value_type == ValueType.Date
def mapped_data_collection() -> DataCollection:
input_dir = './test_data/input_data/CSR2TRANSMART_TEST_DATA'
config_dir = './test_data/input_data/config'
study_id = 'CSR'
top_tree_node = '\\Central Subject Registry\\'
ontology_config: OntologyConfig = read_configuration(config_dir)
subject_registry_reader = SubjectRegistryReader(input_dir)
subject_registry: CentralSubjectRegistry = subject_registry_reader.read_subject_registry(
)
study_registry_reader = StudyRegistryReader(input_dir)
study_registry: StudyRegistry = study_registry_reader.read_study_registry()
mapper = CsrMapper(study_id, top_tree_node)
return mapper.map(subject_registry, study_registry, ontology_config.nodes)
def test_invalid_json():
with pytest.raises(DataException) as excinfo:
read_configuration('./test_data/input_data/config/invalid_ontology_config/invalid_json')
assert 'Error parsing ontology config file' in str(excinfo.value)
def test_duplicate_top_node_names_rejected():
with pytest.raises(ValidationError) as excinfo:
ontology_config = read_configuration(
'./test_data/input_data/config/invalid_ontology_config/duplicate_nodes')
OntologyMapper('test').map(ontology_config.nodes)
assert 'Duplicate node names: 01. Patient information' in str(excinfo.value)
def test_duplicate_child_names_rejected():
with pytest.raises(ValidationError) as excinfo:
ontology_config = read_configuration(
'./test_data/input_data/config/invalid_ontology_config/duplicate_children')
OntologyMapper('test').map(ontology_config.nodes)
assert 'Duplicate child names: 01. Date of birth' in str(excinfo.value)
def test_ontology_config_neither_children_nor_concept_code():
with pytest.raises(ValidationError) as excinfo:
ontology_config = read_configuration(
'./test_data/input_data/config/invalid_ontology_config/neither_children_nor_concept_code')
OntologyMapper('test').map(ontology_config.nodes)
assert 'Node must have either concept_code or children' in str(excinfo.value)
def test_ontology_config_mutually_exclusive_properties():
with pytest.raises(ValidationError) as excinfo:
ontology_config = read_configuration(
'./test_data/input_data/config/invalid_ontology_config/mutually_exclusive_properties')
OntologyMapper('test').map(ontology_config.nodes)
assert 'Node cannot have both concept_code and children' in str(excinfo.value)
def test_valid_ontology_config():
ontology_config = read_configuration('./test_data/input_data/config')
tree_nodes = OntologyMapper('test').map(ontology_config.nodes)
assert len(tree_nodes) == 1
assert len(tree_nodes[0].children) == 5
