fix tests

Author: nolan1999

api/core/database.py

@@ -49,6 +49,11 @@ def backup(self) -> bool:
         """Backup the database. To be implemented by subclasses if supported."""
         return False
 
+    def empty(self) -> None:
+        """Empty the database by dropping and recreating all tables."""
+        Base.metadata.drop_all(bind=self.engine)
+        Base.metadata.create_all(bind=self.engine)
+
 
 class SqliteDatabase(Database):
     """SQLite database wrapper with optional S3 backup support."""

api/endpoints/auth_get.py

@@ -2,7 +2,8 @@
 
 from fastapi import APIRouter, Depends
 
-from api.dependencies import GroupClaims, current_user_dep
+from api.core.auth import GroupClaims
+from api.dependencies import current_user_dep
 from api.schemas.user import User
 from api.settings import cognito_client_id, cognito_region, cognito_user_pool_id
 

api/endpoints/jobs.py

@@ -32,7 +32,9 @@ def list_jobs(
     db: Session = Depends(session_dep),
 ) -> list[Job]:
     db_jobs = crud.get_jobs(db, request.state.current_user.username, offset, limit)
-    jobs = [Job.model_validate(db_job) for db_job in db_jobs]  # models -> schemas
+    jobs = [
+        Job.model_validate(db_job, from_attributes=True) for db_job in db_jobs
+    ]  # models -> schemas
     return sorted(jobs, key=lambda x: x.date_created, reverse=True)
 
 
@@ -45,7 +47,7 @@ def describe_job(
         raise HTTPException(
             status_code=status.HTTP_404_NOT_FOUND, detail="Job not found"
         )
-    return Job.model_validate(db_job)
+    return Job.model_validate(db_job, from_attributes=True)
 
 
 @router.post(
@@ -70,7 +72,7 @@ def start_job(
             user_id=request.state.current_user.username,
             user_email=request.state.current_user.email,
         )
-        return Job.model_validate(db_job)
+        return Job.model_validate(db_job, from_attributes=True)
     except FileNotFoundError as e:
         raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(e))
 

tests/integration/conftest.py

@@ -111,11 +111,12 @@ def filesystem_getter(
     base_user_dir: str,
     s3_testing_bucket: S3TestingBucket,
 ) -> Callable[[str], FileSystem]:
+    s3_fs = isinstance(base_filesystem, S3Filesystem)
     return user_filesystem_getter(
         user_data_root_path=base_user_dir,
-        filesystem="s3" if isinstance(base_filesystem, S3Filesystem) else "local",
-        s3_bucket=s3_testing_bucket.bucket_name,
-        s3_client=s3_testing_bucket.s3_client,
+        filesystem="s3" if s3_fs else "local",
+        s3_bucket=s3_testing_bucket.bucket_name if s3_fs else None,
+        s3_client=s3_testing_bucket.s3_client if s3_fs else None,
     )
 
 
@@ -127,12 +128,22 @@ def user_filesystem(
 
 
 @pytest.fixture(autouse=True)
-def override_db_dep(db: Database, monkeypatch: pytest.MonkeyPatch) -> None:
+def override_db_dep(
+    db: Database,
+    rds_testing_instance: RDSTestingInstance,
+    monkeypatch: pytest.MonkeyPatch,
+) -> Generator[None, None, None]:
     monkeypatch.setitem(
         app.dependency_overrides,  # type: ignore
         db_dep,
         lambda: db,
     )
+    yield
+    # Cleanup after every test
+    if isinstance(db, SqliteDatabase):
+        db.empty()
+    else:
+        rds_testing_instance.cleanup()
 
 
 @pytest.fixture(autouse=True)
@@ -269,6 +280,12 @@ def job_attrs() -> dict[str, Any]:
     }
 
 
+@pytest.fixture
+def db_session(db: Database) -> Generator[Session, None, None]:
+    with Session(db.engine) as session:
+        yield session
+
+
 @pytest.fixture
 def jobs(
     test_username: str,

tests/integration/endpoints/test_files.py

@@ -4,6 +4,8 @@
 import requests
 from fastapi.testclient import TestClient
 
+from api.core.filesystem import FileSystem, LocalFilesystem
+
 ENDPOINT = "/files"
 
 
@@ -167,21 +169,23 @@ def test_download_file_happy(client: TestClient, data_files: dict[str, str]) ->
 
 
 def test_get_url_file_happy(
-    env: str, client: TestClient, data_files: dict[str, str]
+    base_filesystem: FileSystem, client: TestClient, data_files: dict[str, str]
 ) -> None:
     data_file1_name, data_file1_contents = list(data_files.items())[0]
     response = client.get(f"{ENDPOINT}/{data_file1_name}/url")
     assert response.status_code == 200
     request_params = response.json()
     if "authorization" in request_params["headers"]:
         del request_params["headers"]["authorization"]
-    request_client = client if env == "local" else requests
+    request_client = (
+        client if isinstance(base_filesystem, LocalFilesystem) else requests
+    )
     response = request_client.request(**request_params)
     assert response.status_code == 200, response.text
     assert response.content.decode("utf-8") == data_file1_contents
 
 
-def test_post_url_file_happy(env: str, client: TestClient) -> None:
+def test_post_url_file_happy(base_filesystem: FileSystem, client: TestClient) -> None:
     data_file1_name = "data/test/data_file1.txt"
     data_file1_contents = "data file1 contents"
     response = client.post(f"{ENDPOINT}/{os.path.dirname(data_file1_name)}//url")
@@ -196,7 +200,9 @@ def test_post_url_file_happy(env: str, client: TestClient) -> None:
             "text/plain",
         )
     }
-    request_client = client if env == "local" else requests
+    request_client = (
+        client if isinstance(base_filesystem, LocalFilesystem) else requests
+    )
     request_client.request(**request_params, files=files)
     response = client.get(
         f"{ENDPOINT}//", params={"recursive": True, "show_dirs": False}

tests/integration/endpoints/test_job_update.py

@@ -38,6 +38,7 @@ def test_job_status_update(
         headers={"x-api-key": internal_api_key_secret},
     )
     assert response.status_code == 200
+    db_session.refresh(jobs[0])
     job = db_session.query(Job).filter(Job.id == jobs[0].id).first()
     assert job is not None
     assert job.status == "running"