Cleanup

.gitattributes

@@ -1,4 +1,3 @@
 entities/api/schema.json	linguist-generated=true
 entities/api/schema.graphql	linguist-generated=true
 entities/cli/gql_schema.py	linguist-generated=true
-workflows/entity_gql_schema.py	linguist-generated=true

entities/Makefile

@@ -57,7 +57,6 @@ codegen:  ## Update the GQL types used by the CLI
 	$(docker_compose_run) entities strawberry export-schema api.main:schema > api/schema.graphql
 	$(docker_compose) exec entities python3 -m sgqlc.introspection --exclude-deprecated --exclude-description http://localhost:8008/graphql api/schema.json
 	$(docker_compose) exec entities sgqlc-codegen schema api/schema.json cli/gql_schema.py
-	cp cli/gql_schema.py ../workflows/entity_gql_schema.py
 
 ### CERBOS #############################################
 cerbos-tests:

workflows/api/main.py

@@ -1,10 +1,7 @@
 import configparser
-import json
-import os
 import typing
 
 import database.models as db
-import entity_gql_schema as entity_schema
 import strawberry
 from cerbos.sdk.client import CerbosClient
 from cerbos.sdk.model import Principal
@@ -14,8 +11,6 @@
 from platformics.api.core.settings import APISettings
 from platformics.api.core.strawberry_extensions import DependencyExtension
 from platformics.database.connect import AsyncDB
-from sgqlc.endpoint.http import HTTPEndpoint
-from sgqlc.operation import Operation
 from sqlalchemy.ext.asyncio import AsyncSession
 from strawberry.fastapi import GraphQLRouter
 from strawberry_sqlalchemy_mapper import StrawberrySQLAlchemyMapper
@@ -94,30 +89,6 @@ async def get_workflow_runners(self) -> typing.List[WorkflowRunner]:
 
 @strawberry.type
 class Mutation:
-    @strawberry.mutation(extensions=[DependencyExtension()])
-    async def test_connection(self) -> str:
-        entity_service_url = os.getenv("ENTITY_SERVICE_URL")
-        entity_service_auth_token = os.getenv("ENTITY_SERVICE_AUTH_TOKEN")
-        headers = {"Authorization": f"Bearer {entity_service_auth_token}"}
-        endpoint = HTTPEndpoint(entity_service_url)
-
-        # Create query to list all samples
-        op = Operation(entity_schema.Query)
-        samples = op.samples()
-        samples.id()
-        samples.name()
-        samples.location()
-        data = endpoint(op, extra_headers=headers)
-        print(json.dumps(data["data"]["samples"], indent=4))
-
-        # Create a sample
-        op = Operation(entity_schema.Mutation)
-        op.create_sample(name="test", location="test", collection_id=444)
-        data = endpoint(op, extra_headers=headers)
-        print(json.dumps(data, indent=4))
-
-        return "Hello World"
-
     @strawberry.mutation(extensions=[DependencyExtension()])
     async def add_workflow(
         self,

workflows/docker-compose.yml

@@ -58,6 +58,7 @@ services:
       JWK_PUBLIC_KEY_FILE: "/workflows/test_infra/fixtures/public_key.pem"
       JWK_PRIVATE_KEY_FILE: "/workflows/test_infra/fixtures/private_key.pem"
       DEFAULT_UPLOAD_BUCKET: "local-bucket"
+      DEFAULT_UPLOAD_PROTOCOL: "S3"
       BOTO_ENDPOINT_URL: "http://motoserver.czidnet:4000"
       ENTITY_SERVICE_URL: "http://entity-service:8008"
       AWS_REGION: "us-west-2"