[CZID-8454] Add tests for file queries (#40)

* Rearrange test layout.

* Add test coverage for file queries.

entities/api/conftest.py

@@ -0,0 +1,89 @@
+import json
+import typing
+from typing import Optional
+
+import pytest_asyncio
+from cerbos.sdk.model import Principal
+from database.connect import AsyncDB
+from fastapi import FastAPI
+from httpx import AsyncClient
+from sqlalchemy.ext.asyncio import AsyncSession
+from starlette.requests import Request
+
+from api.core.deps import get_auth_principal, get_db_session, get_engine, require_auth_principal
+from api.main import get_app
+
+
+class GQLTestClient:
+    def __init__(self, http_client: AsyncClient):
+        self.http_client = http_client
+
+    # Utility function for making GQL HTTP queries
+    async def query(
+        self,
+        query: str,
+        user_id: Optional[int] = None,
+        member_projects: Optional[list[int]] = None,
+        admin_projects: Optional[list[int]] = None,
+    ):
+        if not user_id:
+            user_id = 111
+        if not admin_projects:
+            admin_projects = []
+        if not member_projects:
+            member_projects = []
+        gql_headers = {
+            "content-type": "application/json",
+            "accept": "application/json",
+            "user_id": str(user_id),
+            "member_projects": json.dumps(member_projects),
+            "admin_projects": json.dumps(admin_projects),
+        }
+        result = await self.http_client.post("/graphql", json={"query": query}, headers=gql_headers)
+        return result.json()
+
+
+@pytest_asyncio.fixture()
+async def gql_client(http_client: AsyncClient) -> GQLTestClient:
+    client = GQLTestClient(http_client)
+    return client
+
+
+async def patched_authprincipal(request: Request) -> Principal:
+    user_id = request.headers.get("user_id")
+    if not user_id:
+        raise Exception("user_id not found in request headers")
+    principal = Principal(
+        user_id,
+        roles=["user"],
+        attr={
+            "user_id": int(user_id),
+            "member_projects": json.loads(request.headers.get("member_projects", "[]")),
+            "admin_projects": json.loads(request.headers.get("admin_projects", "[]")),
+        },
+    )
+    return principal
+
+
+@pytest_asyncio.fixture()
+async def api(
+    async_db: AsyncDB,
+) -> FastAPI:
+    async def patched_session() -> typing.AsyncGenerator[AsyncSession, None]:
+        session = async_db.session()
+        try:
+            yield session
+        finally:
+            await session.close()
+
+    api = get_app()
+    api.dependency_overrides[get_engine] = lambda: async_db
+    api.dependency_overrides[get_db_session] = patched_session
+    api.dependency_overrides[require_auth_principal] = patched_authprincipal
+    api.dependency_overrides[get_auth_principal] = patched_authprincipal
+    return api
+
+
+@pytest_asyncio.fixture()
+async def http_client(api: FastAPI) -> AsyncClient:
+    return AsyncClient(app=api, base_url="http://test")

entities/api/core/gql_loaders.py

@@ -257,7 +257,7 @@ def generate_strawberry_arguments(action, sql_model, gql_type):
             continue
 
         # Get GQL field
-        field = gql_type._type_definition.get_field(sql_column)
+        field = gql_type.__strawberry_definition__.get_field(sql_column)
         if field:
             # When updating an entity, only entity ID is required
             is_optional_field = action == CERBOS_ACTION_UPDATE and field.name != "entity_id"

entities/api/main.py

@@ -32,23 +32,18 @@ class EntityInterface:
     pass
 
 
-@strawberry_sqlalchemy_mapper.type(db.Entity)
-class Entity:
+@strawberry_sqlalchemy_mapper.type(db.File)
+class File:
     pass
 
 
 @strawberry_sqlalchemy_mapper.type(db.Sample)
-class Sample:
+class Sample(EntityInterface):
     pass
 
 
 @strawberry_sqlalchemy_mapper.type(db.SequencingRead)
-class SequencingRead:
-    pass
-
-
-@strawberry_sqlalchemy_mapper.type(db.File)
-class File:
+class SequencingRead(EntityInterface):
     pass
 
 
@@ -59,7 +54,6 @@ class File:
 
 @strawberry.type
 class Query:
-    entity: typing.List[Sample] = get_base_loader(db.Entity, EntityInterface)
     samples: typing.List[Sample] = get_base_loader(db.Sample, Sample)
     sequencing_reads: typing.List[SequencingRead] = get_base_loader(db.SequencingRead, SequencingRead)
     files: typing.List[File] = get_file_loader(db.File, File)

entities/api/schema.graphql

@@ -1,3 +1,11 @@
+type Entity implements EntityInterface {
+  id: UUID!
+  type: String!
+  producingRunId: Int
+  ownerUserId: Int!
+  collectionId: Int!
+}
+
 interface EntityInterface {
   id: UUID!
   type: String!
@@ -6,17 +14,33 @@ interface EntityInterface {
   collectionId: Int!
 }
 
+type File {
+  id: UUID!
+  entityId: UUID
+  entityFieldName: String
+  status: String!
+  protocol: String!
+  namespace: String!
+  path: String!
+  fileFormat: String!
+  compressionType: String!
+  size: Int!
+  entity: EntityInterface
+}
+
 type Mutation {
   createSample(name: String!, location: String!, collectionId: Int!): Sample!
-  createSequencingRead(nucleotide: String!, sequence: String!, protocol: String!, sampleId: UUID!, collectionId: Int!): SequencingRead!
+  createSequencingRead(nucleotide: String!, sequence: String!, protocol: String!, sequenceFileId: UUID, sampleId: UUID!, collectionId: Int!): SequencingRead!
+  updateSample(entityId: UUID!, name: String!, location: String!): Sample!
 }
 
 type Query {
   samples(id: UUID = null): [Sample!]!
   sequencingReads(id: UUID = null): [SequencingRead!]!
+  files(id: UUID = null): [File!]!
 }
 
-type Sample {
+type Sample implements EntityInterface {
   id: UUID!
   type: String!
   producingRunId: Int
@@ -28,7 +52,7 @@ type Sample {
   sequencingReads: SequencingReadConnection!
 }
 
-type SequencingRead {
+type SequencingRead implements EntityInterface {
   id: UUID!
   type: String!
   producingRunId: Int
@@ -38,7 +62,9 @@ type SequencingRead {
   nucleotide: String!
   sequence: String!
   protocol: String!
+  sequenceFileId: UUID
   sampleId: UUID!
+  sequenceFile: File
   sample: Sample!
 }