Merge remote-tracking branch 'origin/main' into dependabot/pip/fastap…

…i-gte-0.103-and-lt-0.112

cada_prio/cli.py

@@ -9,6 +9,7 @@
 import cattr
 import click
 import logzero
+import yaml
 
 try:
  import optuna
@@ -140,6 +141,16 @@ def cli_dump_graph(
  inspection.dump_graph(path_graph, path_hgnc_info, hgnc_to_entrez)
 
 
+@cli_utils.command("dump-openapi-yaml")
+@click.argument("path_out", type=str)
+def cli_dump_openapi_yaml(path_out: str):
+ """Dump OpenAPI YAML file"""
+ from cada_prio import rest_server
+
+ with open(path_out, "wt") as f:
+ yaml.dump(rest_server.app.openapi(), f)
+
+
 @cli.group("tune")
 def cli_tune():
  """hyperparameter tuning"""

requirements.txt

@@ -0,0 +1 @@
+requirements/base.txt

requirements/base.txt

@@ -11,3 +11,4 @@ gensim >=4.3.2, <5.0
 uvicorn >=0.23.2
 fastapi >=0.103, <0.112
 python-dotenv >=1.0, <2.0
+pyyaml >=6.0, <7.0

requirements/test.txt

@@ -19,6 +19,7 @@ types-tabulate >=0.9.0.0
 types-jsonschema >=4.17.0
 types-tqdm >=4.66.0
 types-xmltodict >=0.13.0.3
+types-PyYAML >=6.0
 networkx-stubs
 
 sphinx

tests/test_rest_server.py

@@ -10,21 +10,21 @@
 @pytest.mark.asyncio
 async def test_version():
  with TestClient(rest_server.app) as client:
- response = client.get("/version")
+ response = client.get("/api/v1/version")
  assert response.status_code == 200
 
 
 @mock.patch("cada_prio.rest_server.PATH_DATA", "tests/data/model_smoke")
 @pytest.mark.asyncio
 async def test_predict_with_gene():
  with TestClient(rest_server.app) as client:
- response = client.get("/predict/?hpo_terms=HP:0008551&hpo=HP:0000007&gene=MKS1")
+ response = client.get("/api/v1/predict/?hpo_terms=HP:0008551&hpo=HP:0000007&gene=MKS1")
  assert response.status_code == 200
 
 
 @mock.patch("cada_prio.rest_server.PATH_DATA", "tests/data/model_smoke")
 @pytest.mark.asyncio
 async def test_predict_without_gene():
  with TestClient(rest_server.app) as client:
- response = client.get("/predict/?hpo_terms=HP:0008551&hpo=HP:0000007")
+ response = client.get("/api/v1/predict/?hpo_terms=HP:0008551&hpo=HP:0000007")
  assert response.status_code == 200