def test_format_attribute():
trapi_kg_response = {
"knowledge_graph": {
"nodes": {
"CURIE:1": {
"attributes": [{
"original_attribute_name": "pub",
"attribute_type_id": "CURIE:x"
}]
}
}
}
}
expected_trapi = {
"knowledge_graph": {
"nodes": {
"CURIE:1": {
"attributes": [{
"attribute_type_id": "CURIE:x",
"value_type_id": "biolink:Attribute",
"original_attribute_name": "pub"
}]
}
}
}
}
q = Question(question_json={})
# test if attribute_id if provided from neo4j response is preserved
# test if value_type is added to default 'biolink:Attribute'
assert q.transform_attributes(trapi_kg_response) == expected_trapi
expected_trapi = {
"knowledge_graph": {
"nodes": {
"CURIE:1": {
"attributes": [{
"attribute_type_id": "EDAM:data_0006",
"value": "x",
"original_attribute_name": "pub",
"value_type_id": "oo"
}]
}
}
}
}
trapi_kg_response = {
"knowledge_graph": {
"nodes": {
"CURIE:1": {
"attributes": [{
"original_attribute_name": "pub",
"value": "x",
"value_type_id": "oo"
}]
}
}
}
}
# test default attribute to be EDAM:data_0006
# test if value_type is preserved if in response from neo4j
assert q.transform_attributes(trapi_kg_response) == expected_trapi
def test_format_attribute():
# note that this test does not run through the reasoner code that does the attribute mapping.
# so the values in the expected results must account for that
trapi_kg_response = {
"knowledge_graph": {
"nodes": {
"CURIE:1": {
"attributes": [{
"original_attribute_name": "pub",
"attribute_type_id": "CURIE:x"
}, {
"original_attribute_name":
"biolink:original_knowledge_source",
"value": "infores:kg_source"
}]
}
}
}
}
expected_trapi = {
"knowledge_graph": {
"nodes": {
"CURIE:1": {
"attributes": [{
"original_attribute_name": "pub",
"attribute_type_id": "CURIE:x",
"value_type_id": "EDAM:data_0006"
}, {
"original_attribute_name":
"biolink:original_knowledge_source",
"value":
"infores:kg_source",
"attribute_type_id":
"biolink:original_knowledge_source",
"value_type_id":
"biolink:InformationResource"
}, {
"attribute_type_id":
"biolink:aggregator_knowledge_source",
"value":
"infores:automat.notspecified",
"value_type_id":
"biolink:InformationResource",
"original_attribute_name":
"biolink:aggregator_knowledge_source"
}]
}
}
}
}
q = Question(question_json={})
graph_interface = MOCK_GRAPH_ADAPTER()
transformed = q.transform_attributes(trapi_kg_response,
graph_interface=MOCK_GRAPH_ADAPTER)
# test attribute_id if provided from neo4j response is preserved
# test if value_type is added to default 'biolink:Attribute'
assert transformed == expected_trapi
t2_trapi_kg_response = {
"knowledge_graph": {
"nodes": {
"CURIE:1": {
"attributes": [{
"original_attribute_name": "pub",
"value": "x",
"value_type_id": "oo",
"attribute_type_id": "preserved_attrib"
}, {
"original_attribute_name": "publications",
"value": "x"
}, {
"original_attribute_name": "endogenous",
"value": "false"
}, {
"original_attribute_name": "p-value",
"value": "1.234"
}, {
"original_attribute_name": "chi-squared-statistic",
"value": "2.345"
}, {
"original_attribute_name": "equivalent_identifiers",
"attribute_type_id": "biolink:same_as",
"value": ["some_identifier"]
}, {
"original_attribute_name":
"biolink:original_knowledge_source",
"value": "infores:kg_source"
}]
}
}
}
}
t2_expected_trapi = {
'knowledge_graph': {
'nodes': {
'CURIE:1': {
'attributes': [{
'original_attribute_name': 'pub',
'value': 'x',
'value_type_id': 'EDAM:data_0006',
'attribute_type_id': 'preserved_attrib'
}, {
'original_attribute_name': 'publications',
'value': 'x',
'value_type_id': 'EDAM:data_0006',
'attribute_type_id': 'biolink:publications'
}, {
'original_attribute_name': 'endogenous',
'value': 'false',
'value_type_id': 'xsd:boolean',
'attribute_type_id': 'aragorn:endogenous'
}, {
'original_attribute_name': 'p-value',
'value': '1.234',
'value_type_id': 'EDAM:data_0006',
'attribute_type_id': 'biolink:Attribute'
}, {
'original_attribute_name': 'chi-squared-statistic',
'value': '2.345',
'value_type_id': 'EDAM:data_0006',
'attribute_type_id': 'biolink:Attribute'
}, {
"original_attribute_name": "equivalent_identifiers",
"attribute_type_id": "biolink:same_as",
"value": ["some_identifier"],
'value_type_id': 'metatype:uriorcurie'
}, {
"original_attribute_name":
"biolink:original_knowledge_source",
"value":
"infores:kg_source",
"attribute_type_id":
"biolink:original_knowledge_source",
"value_type_id":
"biolink:InformationResource"
}, {
'attribute_type_id':
'biolink:aggregator_knowledge_source',
'value':
'infores:automat.notspecified',
'value_type_id':
'biolink:InformationResource',
'original_attribute_name':
'biolink:aggregator_knowledge_source'
}]
}
}
}
}
q = Question(question_json={})
transformed = q.transform_attributes(t2_trapi_kg_response,
graph_interface=MOCK_GRAPH_ADAPTER)
# test default attribute to be EDAM:data_0006
# test if value_type is preserved if in response from neo4j
assert transformed == t2_expected_trapi