async def test_ops(connection: aiosqlite.Connection):
"""Test KP operations."""
await add_data_from_string(
connection,
data="""
MONDO:0005148(( category biolink:Disease ))
MONDO:0005148<-- predicate biolink:treats --CHEBI:6801
CHEBI:6801(( category biolink:ChemicalSubstance ))
""",
)
kp = KnowledgeProvider(connection)
ops = await kp.get_operations()
assert len(ops) == 1
await add_data_from_string(
connection,
data="""
CHEBI:6801(( category biolink:ChemicalSubstance ))
CHEBI:6801-- predicate biolink:treats -->MONDO:0005148
MONDO:0005148(( category biolink:Disease ))
""",
)
kp = KnowledgeProvider(connection)
ops = await kp.get_operations()
assert len(ops) == 1
async def test_database_file():
"""Test database file."""
f = tempfile.NamedTemporaryFile()
filename = f.name
async with aiosqlite.connect(filename) as connection:
# add data to sqlite
await add_data_from_string(
connection,
data="""
MONDO:0005148(( category biolink:Disease ))
MONDO:0005148<-- predicate biolink:treats --CHEBI:6801
CHEBI:6801(( category biolink:ChemicalSubstance ))
""",
)
async with KnowledgeProvider(filename) as kp:
qgraph = {
"nodes": {
"n0": {
"categories": ["biolink:ChemicalSubstance"],
},
"n1": {
"categories": ["biolink:Disease"],
"ids": ["MONDO:0005148"],
},
},
"edges": {
"e01": {
"subject": "n0",
"object": "n1",
"predicates": ["biolink:treats"],
},
},
}
kgraph, results = await kp.get_results(qgraph)
assert results
async def test_reverse(connection: aiosqlite.Connection):
"""Test simple KP."""
await add_data_from_string(
connection,
data="""
MONDO:0005148(( category biolink:Disease ))
MONDO:0005148<-- predicate biolink:treats --CHEBI:6801
CHEBI:6801(( category biolink:ChemicalSubstance ))
""",
)
kp = KnowledgeProvider(connection)
message = {
"query_graph": {
"nodes": {
"n0": {
"categories": ["biolink:Disease"],
"ids": ["MONDO:0005148"],
},
"n1": {
"categories": ["biolink:ChemicalSubstance"],
},
},
"edges": {
"e01": {
"subject": "n1",
"object": "n0",
"predicates": ["biolink:treats"],
},
},
}
}
kgraph, results = await kp.get_results(message["query_graph"])
assert results
async def test_list_properties(connection: aiosqlite.Connection):
"""Test that we correctly handle query graph where categories, ids, and predicates are lists."""
await add_data_from_string(
connection,
data="""
CHEBI:136043(( category biolink:ChemicalSubstance ))
CHEBI:136043-- predicate biolink:treats -->MONDO:0005148
MONDO:0005148(( category biolink:Disease ))
""",
)
kp = KnowledgeProvider(connection)
message = {
"query_graph": {
"nodes": {
"n0": {
"categories": ["biolink:ChemicalSubstance"],
"ids": ["CHEBI:136043"],
},
"n1": {
"categories": ["biolink:Disease"],
},
},
"edges": {
"e01": {
"subject": "n0",
"object": "n1",
"predicates": ["biolink:treats"],
},
},
}
}
kgraph, results = await kp.get_results(message["query_graph"])
assert results
async def test_symmetric(connection: aiosqlite.Connection):
"""Test symmetric predicate."""
await add_data_from_string(
connection,
data="""
MONDO:0005148(( category biolink:Disease ))
MONDO:0005148<-- predicate biolink:treats --CHEBI:6801
CHEBI:6801(( category biolink:ChemicalSubstance ))
""",
)
kp = KnowledgeProvider(connection)
message = {
"query_graph": {
"nodes": {
"n0": {
"categories": ["biolink:Disease"],
"ids": ["MONDO:0005148"],
},
"n1": {
"categories": ["biolink:ChemicalSubstance"],
},
},
"edges": {
"e01": {
"subject": "n0",
"object": "n1",
"predicates": ["biolink:related_to"],
},
},
}
}
kgraph, results = await kp.get_results(message["query_graph"])
assert len(results) == 1
assert results[0]["node_bindings"]["n0"][0]["id"] == "MONDO:0005148"
assert results[0]["node_bindings"]["n1"][0]["id"] == "CHEBI:6801"
async def test_subclass(connection: aiosqlite.Connection):
"""Test unrecognized key."""
await add_data_from_string(
connection,
data="""
CHEBI:6801(( category biolink:ChemicalSubstance ))
MONDO:0005148(( category biolink:Disease ))
HP:0004324(( category biolink:PhenotypicFeature ))
CHEBI:6801-- predicate biolink:treats -->MONDO:0005148
MONDO:0005148-- predicate biolink:has_phenotype -->HP:0004324
""",
)
kp = KnowledgeProvider(connection)
message = {
"query_graph": {
"nodes": {
"n0": {
"categories": ["biolink:NamedThing"],
"ids": ["CHEBI:6801"],
},
"n1": {
"categories": ["biolink:Disease"],
},
},
"edges": {
"e01": {
"subject": "n0",
"object": "n1",
"predicates": ["biolink:treats"],
},
},
}
}
kgraph, results = await kp.get_results(message["query_graph"])
assert results
async def test_self_edge(connection: aiosqlite.Connection):
"""Test self-edge."""
await add_data_from_string(
connection,
data="""
MONDO:0005148(( category biolink:Disease ))
MONDO:0005148<-- predicate biolink:related_to --MONDO:0005148
""",
)
kp = KnowledgeProvider(connection)
message = {
"query_graph": {
"nodes": {
"n0": {
"ids": ["MONDO:0005148"],
},
},
"edges": {
"e01": {
"subject": "n0",
"object": "n0",
},
},
}
}
kgraph, results = await kp.get_results(message["query_graph"])
assert len(results) == 1
async def test_branch(connection: aiosqlite.Connection):
"""Test a simple branch."""
await add_data_from_string(
connection,
data="""
MONDO:0005148(( category biolink:Disease ))
NCBIGene:123(( category biolink:Gene ))
CHEBI:6801(( category biolink:ChemicalSubstance ))
CELL:123(( category biolink:Cell ))
NCBIGene:123<-- predicate biolink:affected_by --MONDO:0005148
NCBIGene:123<-- predicate biolink:affects --CHEBI:6801
CELL:123<-- predicate biolink:affected_by --NCBIGene:123
""",
)
kp = KnowledgeProvider(connection)
message = {
"query_graph": {
"nodes": {
"disease": {
"categories": ["biolink:Disease"],
"ids": ["MONDO:0005148"],
},
"gene": {
"categories": ["biolink:Gene"],
},
"drug": {
"categories": ["biolink:ChemicalSubstance"],
},
"cell": {
"categories": ["biolink:Cell"],
},
},
"edges": {
"e10": {
"subject": "drug",
"object": "gene",
"predicates": ["biolink:affects"],
},
"e21": {
"subject": "disease",
"object": "gene",
"predicates": ["biolink:affected_by"],
},
"e02": {
"subject": "gene",
"object": "cell",
"predicates": ["biolink:affected_by"],
},
},
}
}
kgraph, results = await kp.get_results(message["query_graph"])
assert len(results) == 1
async def test_prefixes(connection: aiosqlite.Connection):
"""Test CURIE prefixes."""
await add_data_from_string(
connection,
data="""
MONDO:0005148(( category biolink:Disease ))
CHEBI:6801(( category biolink:ChemicalSubstance ))
CHEBI:xxx(( category biolink:ChemicalSubstance ))
""",
)
kp = KnowledgeProvider(connection)
prefixes = await kp.get_curie_prefixes()
assert prefixes == {
"biolink:Disease": ["MONDO"],
"biolink:ChemicalSubstance": ["CHEBI"],
}
async def test_extra_ids(connection: aiosqlite.Connection):
"""Test extra qnode ids."""
await add_data_from_string(
connection,
data="""
CHEBI:6801(( category biolink:ChemicalSubstance ))
MONDO:0005148(( category biolink:Disease ))
CHEBI:6801-- predicate biolink:treats -->MONDO:0005148
""",
)
kp = KnowledgeProvider(connection, name="test")
message = {
"query_graph": {
"nodes": {
"n0": {
"ids": ["CHEBI:6801", "CHEBI:6802", "CHEBI:6803"],
},
"n1": {
"categories": ["biolink:Disease"],
},
},
"edges": {
"e01": {
"subject": "n0",
"object": "n1",
"predicates": ["biolink:treats"],
},
},
}
}
kgraph, results = await kp.get_results(message["query_graph"])
assert len(results) == 1
for kedge in kgraph["edges"].values():
attrs = kedge["attributes"]
assert len(attrs) == 1
assert attrs[0]["attribute_type_id"] == "biolink:knowledge_source"
assert attrs[0]["value"] == "infores:test"