upsert update works

gen3userdatalibrary/db.py

@@ -52,6 +52,60 @@
 async_sessionmaker = async_sessionmaker(engine, expire_on_commit=False)
 
 
+async def create_user_list_instance(user_list: dict, user_id):
+    now = datetime.datetime.now(datetime.timezone.utc)
+    name = user_list.get("name", f"Saved List {now}")
+    user_list_items = user_list.get("items", {})
+
+    for _, item_contents in user_list_items.items():
+        # TODO THIS NEEDS TO BE CFG
+        if item_contents.get("type") == "GA4GH_DRS":
+            try:
+                validate(instance=item_contents, schema=ITEMS_JSON_SCHEMA_DRS)
+            except ValidationError as e:
+                logging.debug(f"User-provided JSON is invalid: {e.message}")
+                raise
+        elif item_contents.get("type") == "Gen3GraphQL":
+            try:
+                validate(
+                    instance=item_contents,
+                    schema=ITEMS_JSON_SCHEMA_GEN3_GRAPHQL,
+                )
+            except ValidationError as e:
+                logging.debug(f"User-provided JSON is invalid: {e.message}")
+                raise
+        else:
+            try:
+                validate(
+                    instance=item_contents,
+                    schema=ITEMS_JSON_SCHEMA_GENERIC,
+                )
+            except ValidationError as e:
+                logging.debug(f"User-provided JSON is invalid: {e.message}")
+                raise
+
+            logging.warning(
+                "User-provided JSON is an unknown type. Creating anyway..."
+            )
+
+    if user_id is None:
+        # TODO make this a reasonable error type
+        raise Exception()
+    new_list = UserList(
+        version=0,
+        creator=str(user_id),
+        # temporarily set authz without the list ID since we haven't created the list in the db yet
+        authz={
+            "version": 0,
+            "authz": [f"/users/{user_id}/user-data-library/lists"],
+        },
+        name=name,
+        created_time=now,
+        updated_time=now,
+        items=user_list_items)
+    return new_list
+
+
 class DataAccessLayer():
     """
     Defines an abstract interface to manipulate the database. Instances are given a session to
@@ -62,58 +116,8 @@ def __init__(self, db_session: AsyncSession):
         self.db_session = db_session
 
     async def create_user_list(self, user_list) -> UserList:
-        now = datetime.datetime.now(datetime.timezone.utc)
-        name = user_list.get("name", f"Saved List {now}")
-        user_list_items = user_list.get("items", {})
-
-        for _, item_contents in user_list_items.items():
-            # TODO THIS NEEDS TO BE CFG
-            if item_contents.get("type") == "GA4GH_DRS":
-                try:
-                    validate(instance=item_contents, schema=ITEMS_JSON_SCHEMA_DRS)
-                except ValidationError as e:
-                    logging.debug(f"User-provided JSON is invalid: {e.message}")
-                    raise
-            elif item_contents.get("type") == "Gen3GraphQL":
-                try:
-                    validate(
-                        instance=item_contents,
-                        schema=ITEMS_JSON_SCHEMA_GEN3_GRAPHQL,
-                    )
-                except ValidationError as e:
-                    logging.debug(f"User-provided JSON is invalid: {e.message}")
-                    raise
-            else:
-                try:
-                    validate(
-                        instance=item_contents,
-                        schema=ITEMS_JSON_SCHEMA_GENERIC,
-                    )
-                except ValidationError as e:
-                    logging.debug(f"User-provided JSON is invalid: {e.message}")
-                    raise
-
-                logging.warning(
-                    "User-provided JSON is an unknown type. Creating anyway..."
-                )
-
         user_id = await get_user_id()
-
-        if user_id is None:
-            # TODO make this a reasonable error type
-            raise Exception()
-        new_list = UserList(
-            version=0,
-            creator=str(user_id),
-            # temporarily set authz without the list ID since we haven't created the list in the db yet
-            authz={
-                "version": 0,
-                "authz": [f"/users/{user_id}/user-data-library/lists"],
-            },
-            name=name,
-            created_time=now,
-            updated_time=now,
-            items=user_list_items)
+        new_list = await create_user_list_instance(user_list, user_id)
         self.db_session.add(new_list)
 
         # correct authz with id, but flush to get the autoincrement id
@@ -146,17 +150,18 @@ async def get_all_lists(self) -> List[UserList]:
     async def update_list(
             self,
             list_id: int,
-            user_list: UserList) -> str:
+            user_list: UserList) -> UserList:
         q = select(UserList).where(UserList.id == list_id)
-        existing_record = await self.db_session.execute(q)
+        result = await self.db_session.execute(q)
+        existing_record = result.scalar_one_or_none()
         if existing_record is None:
             raise ValueError(f"No UserList found with id {list_id}")
         for attr in dir(user_list):
             if not attr.startswith('_') and hasattr(existing_record, attr):
                 setattr(existing_record, attr, getattr(user_list, attr))
-        q.execution_options(synchronize_session="fetch")
+        existing_record.id = list_id
         await self.db_session.commit()
-        return existing_record.scalar_one()
+        return existing_record
 
     async def test_connection(self) -> None:
         await self.db_session.execute(text("SELECT 1;"))

gen3userdatalibrary/routes.py

@@ -13,7 +13,7 @@
 
 from gen3userdatalibrary import config, logging
 from gen3userdatalibrary.auth import authorize_request, get_user_id
-from gen3userdatalibrary.db import DataAccessLayer, get_data_access_layer
+from gen3userdatalibrary.db import DataAccessLayer, get_data_access_layer, create_user_list_instance
 from gen3userdatalibrary.models import UserList
 from gen3userdatalibrary.utils import add_user_list_metric
 from fastapi.responses import RedirectResponse
@@ -391,17 +391,18 @@ async def upsert_list_by_id(
         response = {"status": status_text, "timestamp": time.time(), "created_list": list_data[1].to_dict()}
         return JSONResponse(status_code=return_status, content=response)
     try:
-        list_as_orm = UserList(user_list)
-    except Exception:
+        user_id = await get_user_id()
+        list_as_orm = await create_user_list_instance(user_list, user_id)
+    except Exception as e:
         return_status = status.HTTP_400_BAD_REQUEST
         status_text = "UNHEALTHY"
         response = {"status": status_text, "timestamp": time.time(), "error": "malformed list, could not update"}
         return JSONResponse(status_code=return_status, content=response)
 
     try:
         outcome = await data_access_layer.update_list(ID, list_as_orm)
-        response = {"status": status_text, "timestamp": time.time(), "updated_name": outcome}
-    except Exception:
+        response = {"status": status_text, "timestamp": time.time(), "updated_list": outcome.to_dict()}
+    except Exception as e:
         return_status = status.HTTP_500_INTERNAL_SERVER_ERROR
         status_text = "UNHEALTHY"
         response = {"status": status_text, "timestamp": time.time()}