async def test_fetch():
"""
Test that the fetch method converts to and from
the specified prefixes when contacting a KP
"""
portal = KnowledgePortal()
portal.tservers["ctd"] = ThrottledServer(
"ctd",
url="http://ctd/query",
request_qty=1,
request_duration=1,
)
preferred_prefixes = {
"biolink:Disease": ["DOID"],
"biolink:ChemicalSubstance": ["MESH"],
}
query_graph = {
"nodes": {
"n0": {"ids": ["MESH:D008687"]},
"n1": {"categories": ["biolink:Disease"]},
},
"edges": {
"e01": {
"subject": "n0",
"object": "n1",
"predicates": ["biolink:treats"],
}
},
}
async with portal.tservers["ctd"]:
response = await portal.fetch(
kp_id="ctd",
request={"message": {"query_graph": query_graph}},
)
allowed_response_prefixes = [
prefix for prefix_list in preferred_prefixes.values() for prefix in prefix_list
]
# Check query graph node prefixes
for node in response["query_graph"]["nodes"].values():
if node.get("ids", None):
assert all(
any(curie.startswith(prefix) for prefix in allowed_response_prefixes)
for curie in node["ids"]
)
# Check node binding prefixes
for result in response["results"]:
for binding_list in result["node_bindings"].values():
for binding in binding_list:
assert any(
binding["id"].startswith(prefix)
for prefix in allowed_response_prefixes
)
async def test_prefix_not_specified():
"""
Test that if we get a category with no preferred_prefixes
we make no changes.
"""
portal = KnowledgePortal()
preferred_prefixes = {}
query_graph = {
"nodes": {
"n0": {"ids": ["DOID:9352"]},
},
"edges": {},
}
msg = Message.parse_obj({"query_graph": query_graph})
await portal.map_prefixes(
msg,
preferred_prefixes,
)
# n0 should be unchanged
assert msg.dict()["query_graph"]["nodes"]["n0"]["ids"] == ["DOID:9352"]
async def test_unknown_prefix():
"""
Test that if passed an unknown prefix we
assume it doesn't need to be changed.
"""
portal = KnowledgePortal()
preferred_prefixes = {"biolink:Disease": ["MONDO"]}
query_graph = {
"nodes": {
"n0": {"ids": ["UNKNOWN:000000"]},
},
"edges": {},
}
msg = Message.parse_obj({"query_graph": query_graph})
await portal.map_prefixes(
msg,
preferred_prefixes,
)
# n0 should be unchanged
assert msg.dict()["query_graph"]["nodes"]["n0"]["ids"] == ["UNKNOWN:000000"]
async def test_map_prefixes_small_example():
"""
Test that prefixes are mapped properly and that already
mapped prefixes are unchanged.
"""
portal = KnowledgePortal()
preferred_prefixes = {"biolink:Disease": ["MONDO"]}
query_graph = {
"nodes": {
"n0": {"ids": ["DOID:9352"]},
"n1": {"ids": ["MONDO:0005148"]},
},
"edges": {},
}
msg = Message.parse_obj({"query_graph": query_graph})
await portal.map_prefixes(
msg,
preferred_prefixes,
)
msg = msg.dict()
# n0 should be converted to the correct prefix
assert msg["query_graph"]["nodes"]["n0"]["ids"] == ["MONDO:0005148"]
# There should be no change to n1
assert msg["query_graph"]["nodes"]["n1"]["ids"] == ["MONDO:0005148"]
async def test_normalizer_not_reachable(caplog):
"""
Test that if the normalizer is completely unavailable we make
no changes to the query graph and continue on while adding a
a warning to the log
"""
portal = KnowledgePortal()
preferred_prefixes = {"biolink:Disease": ["MONDO"]}
query_graph = {
"nodes": {
"n0": {"ids": ["DOID:9352"]},
},
"edges": {},
}
msg = Message.parse_obj({"query_graph": query_graph})
await portal.map_prefixes(
msg,
preferred_prefixes,
)
# n0 should be unchanged
assert msg.dict()["query_graph"]["nodes"]["n0"]["ids"] == ["DOID:9352"]
assert "RequestError contacting normalizer" in caplog.text
async def test_normalizer_no_synonyms_available(caplog):
"""
Test that if we send a node with no synonyms
to the normalizer that we continue working and add
a warning to the log
"""
portal = KnowledgePortal()
preferred_prefixes = {"biolink:Disease": ["MONDO"]}
query_graph = {
"nodes": {
"n0": {"ids": ["DOID:9352"]},
},
"edges": {},
}
msg = Message.parse_obj({"query_graph": query_graph})
await portal.map_prefixes(
msg,
preferred_prefixes,
)
# n0 should be unchanged
assert msg.dict()["query_graph"]["nodes"]["n0"]["ids"] == ["DOID:9352"]
# The error we recieved from the normalizer should be in the logs
assert normalizer_error_no_matches in caplog.text
async def test_normalizer_500(caplog):
"""
Test that if the normalizer returns 500 we make
no changes to the query graph and continue on while adding a
a warning to the log
"""
portal = KnowledgePortal()
preferred_prefixes = {"biolink:Disease": ["MONDO"]}
query_graph = {
"nodes": {
"n0": {"ids": ["DOID:9352"]},
},
"edges": {},
}
fixed_msg = await portal.map_prefixes(
{"query_graph": query_graph},
preferred_prefixes,
)
# n0 should be unchanged
assert fixed_msg["query_graph"]["nodes"]["n0"]["ids"] == ["DOID:9352"]
assert "Error contacting normalizer" in caplog.text