diff --git a/node_normalizer/server.py b/node_normalizer/server.py index 18ca7ca..42cc3a1 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_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() @@ -70,7 +72,8 @@ 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) + logger.info(f"Initialized Biolink Model Toolkit ({app.state.toolkit}) from {BIOLINK_MODEL_URL} (based on tag: {BIOLINK_MODEL_TAG}).") app.state.ancestor_map = {} @@ -120,6 +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",