From c83b1419920c872cc650bb2324a3161a17d11b68 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Thu, 18 Dec 2025 17:47:10 -0500 Subject: [PATCH 1/4] Load a particular version of Biolink Model as per BIOLINK_MODEL_VERSION. --- node_normalizer/server.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/node_normalizer/server.py b/node_normalizer/server.py index 18ca7ca..87ea812 100644 --- a/node_normalizer/server.py +++ b/node_normalizer/server.py @@ -52,6 +52,8 @@ redis_host = os.environ.get("REDIS_HOST", loader.get_config()["redis_host"]) redis_port = os.environ.get("REDIS_PORT", loader.get_config()["redis_port"]) +BIOLINK_MODEL_VERSION = os.environ.get("BIOLINK_MODEL_VERSION", "master") # Note that this should be the complete Biolink Model tag, i.e. including the "v" prefix. +BIOLINK_MODEL_URL = f"https://raw.githubusercontent.com/biolink/biolink-model/{BIOLINK_MODEL_VERSION}/biolink-model.yaml" async_query_tasks = set() @@ -70,7 +72,7 @@ async def startup_event(): 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.toolkit = Toolkit(BIOLINK_MODEL_URL) app.state.ancestor_map = {} From 1f021198cf8efbcc8248cb5dd36a1c3020e383c0 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Thu, 18 Dec 2025 17:50:23 -0500 Subject: [PATCH 2/4] Improved env var name. --- node_normalizer/server.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/node_normalizer/server.py b/node_normalizer/server.py index 87ea812..007ce22 100644 --- a/node_normalizer/server.py +++ b/node_normalizer/server.py @@ -52,8 +52,8 @@ redis_host = os.environ.get("REDIS_HOST", loader.get_config()["redis_host"]) redis_port = os.environ.get("REDIS_PORT", loader.get_config()["redis_port"]) -BIOLINK_MODEL_VERSION = os.environ.get("BIOLINK_MODEL_VERSION", "master") # Note that this should be the complete Biolink Model tag, i.e. including the "v" prefix. -BIOLINK_MODEL_URL = f"https://raw.githubusercontent.com/biolink/biolink-model/{BIOLINK_MODEL_VERSION}/biolink-model.yaml" +BIOLINK_MODEL_TAG = os.environ.get("BIOLINK_MODEL_TAG", "master") # Note that this should be a tag from the Biolink Model repo, e.g. "master" or "v4.3.6". +BIOLINK_MODEL_URL = f"https://raw.githubusercontent.com/biolink/biolink-model/{BIOLINK_MODEL_TAG}/biolink-model.yaml" async_query_tasks = set() From acc444fede8eea4bab7c40a8ffe2722e315d28d1 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Thu, 18 Dec 2025 17:51:28 -0500 Subject: [PATCH 3/4] Added a log message for starting the Biolink Model Toolkit. --- node_normalizer/server.py | 1 + 1 file changed, 1 insertion(+) diff --git a/node_normalizer/server.py b/node_normalizer/server.py index 007ce22..00fcab4 100644 --- a/node_normalizer/server.py +++ b/node_normalizer/server.py @@ -73,6 +73,7 @@ async def startup_event(): 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(BIOLINK_MODEL_URL) + logger.info(f"Initialized Biolink Model Toolkit ({app.state.toolkit}) from {BIOLINK_MODEL_URL} (based on tag: {BIOLINK_MODEL_TAG}).") app.state.ancestor_map = {} From 75e841974ce2aaa48ea1f87454a730b059fb6edd Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Thu, 18 Dec 2025 17:55:08 -0500 Subject: [PATCH 4/4] Added Biolink Model information to /status. --- node_normalizer/server.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/node_normalizer/server.py b/node_normalizer/server.py index 00fcab4..42cc3a1 100644 --- a/node_normalizer/server.py +++ b/node_normalizer/server.py @@ -123,6 +123,11 @@ async def status() -> Dict: "status": "running", "babel_version": babel_version, "babel_version_url": babel_version_url, + "biolink_model": { + "tag": BIOLINK_MODEL_TAG, + "url": f"https://github.com/biolink/biolink-model/tree/{BIOLINK_MODEL_TAG}", + "download_url": BIOLINK_MODEL_URL, + }, "databases": { "eq_id_to_id_db": { "dbname": "id-id",