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Rename redis_connection[0-6] to their database names #271

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Jul 11, 2024
Merged

Rename redis_connection[0-6] to their database names #271

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20 changes: 10 additions & 10 deletions node_normalizer/normalizer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -495,7 +495,7 @@ async def get_info_content(
return {}

# call redis and get the value
info_contents = await app.state.redis_connection4.mget(*canonical_nonan, encoding='utf8')
info_contents = await app.state.info_content_db.mget(*canonical_nonan, encoding='utf8')

# get this into a list
info_contents = [round(float(ic_ids), 1) if ic_ids is not None else None for ic_ids in info_contents]
Expand All @@ -515,9 +515,9 @@ async def get_eqids_and_types(
batch_size = int(os.environ.get("EQ_BATCH_SIZE", 2500))
eqids = []
for i in range(0, len(canonical_nonan), batch_size):
eqids += await app.state.redis_connection1.mget(*canonical_nonan[i:i+batch_size], encoding='utf-8')
eqids += await app.state.id_to_eqids_db.mget(*canonical_nonan[i:i + batch_size], encoding='utf-8')
eqids = [json.loads(value) if value is not None else [None] for value in eqids]
types = await app.state.redis_connection2.mget(*canonical_nonan, encoding='utf-8')
types = await app.state.id_to_type_db.mget(*canonical_nonan, encoding='utf-8')
types_with_ancestors = []
for index, typ in enumerate(types):
if not typ:
Expand Down Expand Up @@ -552,7 +552,7 @@ async def get_normalized_nodes(

upper_curies = [c.upper() for c in curies]
try:
canonical_ids = await app.state.redis_connection0.mget(*upper_curies, encoding='utf-8')
canonical_ids = await app.state.eq_id_to_id_db.mget(*upper_curies, encoding='utf-8')
canonical_nonan = [canonical_id for canonical_id in canonical_ids if canonical_id is not None]
info_contents = {}

Expand All @@ -569,12 +569,12 @@ async def get_normalized_nodes(
other_ids = []

if conflate_gene_protein:
other_ids.extend(await app.state.redis_connection5.mget(*canonical_nonan, encoding='utf8'))
other_ids.extend(await app.state.gene_protein_db.mget(*canonical_nonan, encoding='utf8'))

# logger.error(f"After conflate_gene_protein: {other_ids}")

if conflate_chemical_drug:
other_ids.extend(await app.state.redis_connection6.mget(*canonical_nonan, encoding='utf8'))
other_ids.extend(await app.state.chemical_drug_db.mget(*canonical_nonan, encoding='utf8'))

# logger.error(f"After conflate_chemical_drug: {other_ids}")

Expand Down Expand Up @@ -657,7 +657,7 @@ async def get_info_content_attribute(app, canonical_nonan) -> dict:
:return:
"""
# get the information content value
ic_val = await app.state.redis_connection4.get(canonical_nonan, encoding='utf8')
ic_val = await app.state.info_content_db.get(canonical_nonan, encoding='utf8')

# did we get a good value
if ic_val is not None:
Expand Down Expand Up @@ -776,7 +776,7 @@ async def get_curie_prefixes(
if semantic_types:
for item in semantic_types:
# get the curies for this type
curies = await app.state.redis_connection3.get(item, encoding='utf-8')
curies = await app.state.curie_to_bl_type_db.get(item, encoding='utf-8')

# did we get any data
if not curies:
Expand All @@ -787,11 +787,11 @@ async def get_curie_prefixes(
# set the return data
ret_val[item] = {'curie_prefix': curies}
else:
types = await app.state.redis_connection3.lrange('semantic_types', 0, -1, encoding='utf-8')
types = await app.state.curie_to_bl_type_db.lrange('semantic_types', 0, -1, encoding='utf-8')

for item in types:
# get the curies for this type
curies = await app.state.redis_connection3.get(item, encoding='utf-8')
curies = await app.state.curie_to_bl_type_db.get(item, encoding='utf-8')

# did we get any data
if not curies:
Expand Down
44 changes: 22 additions & 22 deletions node_normalizer/server.py
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Original file line number Diff line number Diff line change
Expand Up @@ -58,13 +58,13 @@ async def startup_event():
"""
redis_config_file = Path(__file__).parent.parent / "redis_config.yaml"
connection_factory = await RedisConnectionFactory.create_connection_pool(redis_config_file)
app.state.redis_connection0 = connection_factory.get_connection(connection_id="eq_id_to_id_db")
app.state.redis_connection1 = connection_factory.get_connection(connection_id="id_to_eqids_db")
app.state.redis_connection2 = connection_factory.get_connection(connection_id="id_to_type_db")
app.state.redis_connection3 = connection_factory.get_connection(connection_id="curie_to_bl_type_db")
app.state.redis_connection4 = connection_factory.get_connection(connection_id="info_content_db")
app.state.redis_connection5 = connection_factory.get_connection(connection_id="gene_protein_db")
app.state.redis_connection6 = connection_factory.get_connection(connection_id="chemical_drug_db")
app.state.eq_id_to_id_db = connection_factory.get_connection(connection_id="eq_id_to_id_db")
app.state.id_to_eqids_db = connection_factory.get_connection(connection_id="id_to_eqids_db")
app.state.id_to_type_db = connection_factory.get_connection(connection_id="id_to_type_db")
app.state.curie_to_bl_type_db = connection_factory.get_connection(connection_id="curie_to_bl_type_db")
app.state.info_content_db = connection_factory.get_connection(connection_id="info_content_db")
app.state.gene_protein_db = connection_factory.get_connection(connection_id="gene_protein_db")
app.state.chemical_drug_db = connection_factory.get_connection(connection_id="chemical_drug_db")
app.state.toolkit = Toolkit()
app.state.ancestor_map = {}

Expand All @@ -74,20 +74,20 @@ async def shutdown_event():
"""
Shut down Redis connection
"""
app.state.redis_connection0.close()
await app.state.redis_connection0.wait_closed()
app.state.redis_connection1.close()
await app.state.redis_connection1.wait_closed()
app.state.redis_connection2.close()
await app.state.redis_connection2.wait_closed()
app.state.redis_connection3.close()
await app.state.redis_connection3.wait_closed()
app.state.redis_connection4.close()
await app.state.redis_connection4.wait_closed()
app.state.redis_connection5.close()
await app.state.redis_connection5.wait_closed()
app.state.redis_connection6.close()
await app.state.redis_connection6.wait_closed()
app.state.eq_id_to_id_db.close()
await app.state.eq_id_to_id_db.wait_closed()
app.state.id_to_eqids_db.close()
await app.state.id_to_eqids_db.wait_closed()
app.state.id_to_type_db.close()
await app.state.id_to_type_db.wait_closed()
app.state.curie_to_bl_type_db.close()
await app.state.curie_to_bl_type_db.wait_closed()
app.state.info_content_db.close()
await app.state.info_content_db.wait_closed()
app.state.gene_protein_db.close()
await app.state.gene_protein_db.wait_closed()
app.state.chemical_drug_db.close()
await app.state.chemical_drug_db.wait_closed()


@app.post(
Expand Down Expand Up @@ -230,7 +230,7 @@ async def get_normalized_node_handler(curies: CurieList):
)
async def get_semantic_types_handler() -> SemanticTypes:
# look for all biolink semantic types
types = await app.state.redis_connection3.lrange("semantic_types", 0, -1, encoding="utf-8")
types = await app.state.curie_to_bl_type_db.lrange("semantic_types", 0, -1, encoding="utf-8")

# did we get any data
if not types:
Expand Down
12 changes: 6 additions & 6 deletions tests/test_norm.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,17 +18,17 @@ async def mget(self, *args, **kwargs):


# Id -> Canonical
app.state.redis_connection0 = MockRedis(
app.state.eq_id_to_id_db = MockRedis(
{"DOID:3812": "MONDO:0005002", "MONDO:0005002": "MONDO:0005002"}
)
# Canonical->Equiv
app.state.redis_connection1 = MockRedis(
app.state.id_to_eqids_db = MockRedis(
{"MONDO:0005002": json.dumps([{"i": "MONDO:0005002"}, {"i": "DOID:3812"}])}
)
app.state.redis_connection2 = MockRedis({"MONDO:0005002": "biolink:Disease"})
app.state.redis_connection3 = MockRedis({})
app.state.redis_connection4 = MockRedis({})
app.state.redis_connection5 = MockRedis({})
app.state.id_to_type_db = MockRedis({"MONDO:0005002": "biolink:Disease"})
app.state.curie_to_bl_type_db = MockRedis({})
app.state.info_content_db = MockRedis({})
app.state.gene_protein_db = MockRedis({})
#app.state.ancestor_map = {"biolink:Disease": ["biolink:Disease", "biolink:NamedThing"]}
app.state.toolkit = Toolkit()
app.state.ancestor_map = {}
Expand Down