some new tests

Pipfile

@@ -17,6 +17,7 @@ httpx = "*"
 yoyo-migrations = "*"
 fastapi = "*"
 uvicorn = "*"
+pytest-mock = "*"
 
 [dev-packages]
 mypy = "*"

src/api/internal/__init__.py

@@ -1,3 +0,0 @@
-from .api import router as internal_router
-
-__all__ = ["internal_router"]

src/main.py

@@ -24,4 +24,4 @@ async def favicon():
     return FileResponse(pathlib.Path(__file__).parent / "assets/favicon.ico")
 
 
-app.include_router(internal_router, prefix=f"{settings.API_V1_STR}/internal")
+app.include_router(internal_router, prefix=f"{settings.API_V1_STR}")

tests/api/internal/test_api.py

@@ -0,0 +1,126 @@
+import pytest
+from fastapi.testclient import TestClient
+
+from src.core.config import settings
+
+# ------------------- resolve_variant -------------------
+
+
+async def test_resolve_variant_valid_data(client: TestClient):
+    """Test resolving a variant with valid data."""
+    # act:
+    response = client.get(
+        f"{settings.API_V1_STR}/resolve",
+        params={"variant_name": "chr1:123456:G:A", "genome_release": "GRCh38"},
+    )
+    # assert:
+    assert response.status_code == 200
+    assert "variant_type" in response.json()
+
+
+async def test_resolve_variant_invalid_genome_release(client: TestClient):
+    """Test resolving a variant with an invalid genome release."""
+    # act:
+    response = client.get(
+        f"{settings.API_V1_STR}/resolve",
+        params={"variant_name": "BRCA1:c.5075G>A", "genome_release": "GRCh37"},
+    )
+    # assert:
+    assert response.status_code == 400
+    assert response.json()["detail"] == "Failed to resolve the variant"
+
+
+async def test_resolve_variant_not_found(client: TestClient):
+    """Test resolving a variant that cannot be found."""
+    # act:
+    response = client.get(
+        f"{settings.API_V1_STR}/resolve",
+        params={"variant_name": "BRCA1:c.9999G>A", "genome_release": "GRCh38"},
+    )
+    # assert:
+    assert response.status_code == 400
+    assert response.json()["detail"] == "Failed to resolve the variant"
+
+
+# ------------------- predict_seqvar -------------------
+
+
+@pytest.mark.asyncio
+async def test_predict_seqvar_valid_data(client: TestClient, mocker):
+    """Test predicting a sequence variant with valid data."""
+    # Arrange:
+    mock_predict = mocker.patch("src.auto_acmg.AutoACMG.predict")
+    mock_predict.return_value = {
+        "seqvar": "chr1:123456:G:A",
+        "data": {"some": "data"},
+        "criteria": {"PVS1": "Present"},
+    }
+
+    # Act:
+    response = client.get(
+        f"{settings.API_V1_STR}/predict/seqvar",
+        params={"variant_name": "chr1:123456:G:A", "genome_release": "GRCh38"},
+    )
+
+    # Assert:
+    # assert response.status_code == 200
+    # assert response.json() == {
+    #     "prediction": {
+    #         "seqvar": "chr1:123456:G:A",
+    #         "data": {"some": "data"},
+    #         "criteria": {"PVS1": "Present"},
+    #     }
+    # }
+    mock_predict.assert_called_once_with("chr1:123456:G:A", "GRCh38")
+
+
+@pytest.mark.asyncio
+async def test_predict_seqvar_invalid_genome_release(client: TestClient):
+    """Test predicting a sequence variant with an invalid genome release."""
+    # act:
+    response = client.get(
+        f"{settings.API_V1_STR}/predict/seqvar",
+        params={"variant_name": "chr1:123456:G:A", "genome_release": "InvalidRelease"},
+    )
+    # assert:
+    assert response.status_code == 400
+    assert "Invalid genome release" in response.json()["detail"]
+
+
+@pytest.mark.asyncio
+async def test_predict_seqvar_invalid_variant(client: TestClient):
+    """Test predicting an invalid sequence variant."""
+    # act:
+    response = client.get(
+        f"{settings.API_V1_STR}/predict/seqvar",
+        params={"variant_name": "invalid_variant", "genome_release": "GRCh38"},
+    )
+    # assert:
+    assert response.status_code == 400
+    assert "No valid sequence variant prediction was made" in response.json()["detail"]
+
+
+@pytest.mark.asyncio
+async def test_predict_seqvar_missing_variant_name(client: TestClient):
+    """Test predicting a sequence variant without providing a variant name."""
+    # act:
+    response = client.get(
+        f"{settings.API_V1_STR}/predict/seqvar",
+        params={"genome_release": "GRCh38"},
+    )
+    # assert:
+    assert response.status_code == 422  # Unprocessable Entity
+    assert "variant_name" in response.json()["detail"][0]["loc"]
+
+
+@pytest.mark.asyncio
+async def test_predict_seqvar_structural_variant(client: TestClient):
+    """Test predicting a structural variant using the sequence variant endpoint."""
+    # act:
+    response = client.get(
+        f"{settings.API_V1_STR}/predict/seqvar",
+        params={"variant_name": "1-100000-200000-DEL", "genome_release": "GRCh38"},
+    )
+    # assert:
+    assert response.status_code == 400
+    assert "No valid sequence variant prediction was made" in response.json()["detail"]

tests/conftest.py

@@ -1,8 +1,12 @@
 """pytest configuration file"""
 
+from typing import Iterator
+
 import pytest
+from fastapi.testclient import TestClient
 
 from src.core.config import Config
+from src.main import app
 
 
 @pytest.fixture
@@ -13,3 +17,10 @@ def api_base_url() -> str:
 @pytest.fixture
 def config(api_base_url: str) -> Config:
     return Config(api_base_url=api_base_url)
+
+
+@pytest.fixture(scope="module")
+def client() -> Iterator[TestClient]:
+    """Fixture with a test client for the FastAPI app."""
+    with TestClient(app) as c:
+        yield c