tests: experiment results api

authz_plugins/api_key/authz.module.py

@@ -1,6 +1,6 @@
 from logging import Logger
 from typing import Annotated, Any, Awaitable, Callable, Coroutine, Sequence
-from fastapi import Depends, FastAPI, HTTPException, Header, Request, Response
+from fastapi import Depends, HTTPException, Header, Request, Response
 from fastapi.responses import JSONResponse
 
 from transcriptomics_data_service.authz.middleware_base import BaseAuthzMiddleware
@@ -40,9 +40,6 @@ def __init__(self, config: Config, logger: Logger) -> None:
 
     # Middleware lifecycle
 
-    def attach(self, app: FastAPI):
-        app.middleware("http")(self.dispatch)
-
     async def dispatch(
         self, request: Request, call_next: Callable[[Request], Awaitable[Response]]
     ) -> Coroutine[Any, Any, Response]:

tests/conftest.py

@@ -6,6 +6,7 @@
 import pytest_asyncio
 from httpx._types import HeaderTypes
 
+from tests.test_db import TEST_EXPERIMENT_RESULT
 from transcriptomics_data_service.db import Database, get_db
 from transcriptomics_data_service.logger import get_logger
 
@@ -51,6 +52,11 @@ async def db_cleanup(db: Database):
     await db.close()
 
 
+@pytest_asyncio.fixture
+async def db_with_experiment(db: Database):
+    await db.create_experiment_result(TEST_EXPERIMENT_RESULT)
+
+
 @pytest.fixture
 def test_client(db: Database):
     with TestClient(app) as client:
@@ -61,6 +67,9 @@ def test_client(db: Database):
 @pytest.fixture
 def authz_headers(config) -> HeaderTypes:
     api_key = config.model_extra.get("api_key")
-    return {
-        "x-api-key": api_key
-    }
+    return {"x-api-key": api_key}
+
+
+@pytest.fixture
+def authz_headers_bad() -> HeaderTypes:
+    return {"x-api-key": "bad key"}

tests/test_authz_plugin.py

@@ -1,8 +1,10 @@
 from transcriptomics_data_service.authz.plugin import import_module_from_path
 
 
+class AuthzDisabled:
+    bento_authz_enabled = False
+
+
 def test_import_authz_plugin_disabled():
-    config = lambda: None
-    config.bento_authz_enabled = False
-    authz_plugin = import_module_from_path("", config)
-    assert authz_plugin == None
+    authz_plugin = import_module_from_path("", AuthzDisabled())
+    assert authz_plugin is None

tests/test_experiments.py

@@ -0,0 +1,52 @@
+from fastapi import status
+
+from tests.test_db import TEST_EXPERIMENT_RESULT
+from transcriptomics_data_service.config import get_config
+from transcriptomics_data_service.logger import get_logger
+from transcriptomics_data_service.models import ExperimentResult
+
+config = get_config()
+logger = get_logger(config)
+
+
+def test_get_experiment(test_client, authz_headers, db_with_experiment, db_cleanup):
+    # TEST_EXPERIMENT_RESULT_ID
+    response = test_client.get(
+        f"/experiment/{TEST_EXPERIMENT_RESULT.experiment_result_id}",
+        headers=authz_headers,
+    )
+    assert response.status_code == status.HTTP_200_OK
+    data = response.json()
+    assert TEST_EXPERIMENT_RESULT == ExperimentResult(**data)
+
+
+# EMPTY DB
+def test_get_experiment_400(test_client):
+    # Missing api-key
+    response = test_client.get("/experiment/non-existant")
+    assert response.status_code == status.HTTP_400_BAD_REQUEST
+
+
+def test_get_experiment_200_empty(test_client, authz_headers):
+    # Missing api-key
+    response = test_client.get("/experiment/non-existant", headers=authz_headers)
+    assert response.status_code == status.HTTP_200_OK
+    assert response.json() is None
+
+
+def test_delete_experiment_400(test_client):
+    # Missing api-key
+    response = test_client.delete("/experiment/non-existant")
+    assert response.status_code == status.HTTP_400_BAD_REQUEST
+
+
+def test_delete_experiment_403(test_client, authz_headers_bad):
+    # Missing api-key
+    response = test_client.delete("/experiment/non-existant", headers=authz_headers_bad)
+    assert response.status_code == status.HTTP_403_FORBIDDEN
+
+
+def test_delete_experiment_200(test_client, authz_headers):
+    # Missing api-key
+    response = test_client.delete("/experiment/non-existant", headers=authz_headers)
+    assert response.status_code == status.HTTP_200_OK

tests/test_expressions.py

@@ -9,10 +9,12 @@
 
 api_key = config.model_extra.get("api_key")
 
+
 def test_expressions_unauthorized(test_client: TestClient):
     response = test_client.get("/expressions")
     assert response.status_code == status.HTTP_400_BAD_REQUEST
 
+
 def test_expressions_authorized(test_client: TestClient, authz_headers):
     response = test_client.get("/expressions", headers=authz_headers)
     assert response.status_code == status.HTTP_200_OK

tests/test_ingest.py

@@ -45,55 +45,72 @@ def test_ingest_missing_api_key(test_client: TestClient, db_cleanup):
     assert response.status_code == status.HTTP_400_BAD_REQUEST
 
 
-def test_ingest_unauthorized(test_client: TestClient, db_cleanup):
+def test_ingest_unauthorized(test_client, authz_headers_bad, db_cleanup):
     response = _ingest_rcm_file(
         test_client,
         file_path=RCM_FILE_PATH,
-        headers={"x-api-key": "THIS KEY IS INVALID"},
+        headers=authz_headers_bad,
         **INGEST_ARGS,
     )
     assert response.status_code == status.HTTP_403_FORBIDDEN
 
 
-def test_ingest_authorized(test_client: TestClient, db_cleanup):
-    api_key = config.model_extra.get("api_key")
+def test_ingest_authorized(test_client, authz_headers, db_cleanup):
     response = _ingest_rcm_file(
         test_client,
         file_path=RCM_FILE_PATH,
-        headers={"x-api-key": api_key},
+        headers=authz_headers,
         **INGEST_ARGS,
     )
     assert response.status_code == status.HTTP_200_OK
 
 
-def test_ingest_authorized_duplicate(test_client: TestClient, db_cleanup):
-    api_key = config.model_extra.get("api_key")
+def test_ingest_authorized_duplicate(test_client, authz_headers, db_cleanup):
     response = _ingest_rcm_file(
         test_client,
         file_path=f"{TEST_FILES_DIR}/rcm_file_duplicates.csv",
-        headers={"x-api-key": api_key},
+        headers=authz_headers,
         **INGEST_ARGS,
     )
     assert response.status_code == status.HTTP_400_BAD_REQUEST
 
 
-def test_ingest_parser_error(test_client: TestClient, db_cleanup):
-    api_key = config.model_extra.get("api_key")
+def test_ingest_parser_error(test_client, authz_headers, db_cleanup):
     response = _ingest_rcm_file(
         test_client,
         file_path=f"{TEST_FILES_DIR}/rcm_file_bad_values.csv",
-        headers={"x-api-key": api_key},
+        headers=authz_headers,
         **INGEST_ARGS,
     )
     assert response.status_code == status.HTTP_400_BAD_REQUEST
 
 
-def test_ingest_invalid_csv(test_client: TestClient, db_cleanup):
-    api_key = config.model_extra.get("api_key")
+def test_ingest_invalid_csv(test_client, authz_headers, db_cleanup):
     response = _ingest_rcm_file(
         test_client,
         file_path=f"{TEST_FILES_DIR}/rcm_file_bad_column.csv",
-        headers={"x-api-key": api_key},
+        headers=authz_headers,
         **INGEST_ARGS,
     )
     assert response.status_code == status.HTTP_400_BAD_REQUEST
+
+
+def test_normalize_400(test_client: TestClient, db_cleanup):
+    response = test_client.post("/normalize/some-id")
+    assert response.status_code == status.HTTP_400_BAD_REQUEST
+
+
+def test_normalize_403(test_client: TestClient, authz_headers_bad, db_cleanup):
+    response = test_client.post("/normalize/some-id", headers=authz_headers_bad)
+    assert response.status_code == status.HTTP_403_FORBIDDEN
+
+
+def test_normalize_200(test_client: TestClient, authz_headers, db_cleanup):
+    # TODO real tests in normalization PR
+    with open(f"{TEST_FILES_DIR}/gene_lengths.csv", "rb") as file:
+        response = test_client.post(
+            url="/normalize/some-id",
+            files=[("features_lengths_file", file)],
+            headers=authz_headers,
+        )
+    assert response.status_code == status.HTTP_200_OK

transcriptomics_data_service/authz/plugin.py

@@ -6,6 +6,7 @@
 
 __all__ = ["authz_plugin"]
 
+
 def import_module_from_path(path, config) -> None | ModuleType:
     if config.bento_authz_enabled:
         spec = importlib.util.spec_from_file_location("authz_plugin", path)
@@ -17,6 +18,4 @@ def import_module_from_path(path, config) -> None | ModuleType:
 
 
 # Get the concrete authz middleware from the provided plugin module
-authz_plugin: BaseAuthzMiddleware = import_module_from_path(
-    "./lib/authz.module.py", get_config()
-)
+authz_plugin: BaseAuthzMiddleware = import_module_from_path("./lib/authz.module.py", get_config())