Merge pull request #47 from CUAHSI/main

main -> develop

.env.template

@@ -6,6 +6,8 @@ OAUTH2_CLIENT_SECRET="Get From Keycloak"
 
 VITE_APP_NAME=swotvis
 
+VITE_TEST_MODE=false
+
 # if using npm run dev, set VITE_APP_ORIGIN=http://localhost:5173
 VITE_APP_ORIGIN=https://localhost
 

.github/workflows/frontend-gh-pages.yml

@@ -40,6 +40,7 @@ jobs:
  - name: create env file
  run: |
  touch .env
+ echo VITE_TEST_MODE=${{ secrets.VITE_TEST_MODE }} >> .env
  echo VITE_APP_API_URL=${{ secrets.VITE_APP_API_URL }} >> .env
  echo VITE_APP_FULL_URL=${{ secrets.VITE_APP_FULL_URL }} >> .env
  echo VITE_OAUTH2_REDIRECT_URL=${{ secrets.VITE_OAUTH2_REDIRECT_URL }} >> .env

api/Dockerfile

@@ -11,10 +11,10 @@ RUN python -m wget https://dl.min.io/client/mc/release/linux-amd64/mc
 RUN chmod +x mc
 RUN mv mc /usr/local/bin/mc
 
-COPY ./subsetter /subsetter
+COPY ./swotvis /swotvis
 
-ENV PYTHONPATH "/subsetter/:${PYTHONPATH}"
+ENV PYTHONPATH "/swotvis/:${PYTHONPATH}"
 
 EXPOSE 8000
 
-CMD uvicorn --host 0.0.0.0 --port 8000 --proxy-headers subsetter.main:app
+CMD uvicorn --host 0.0.0.0 --port 8000 --proxy-headers swotvis.main:app

api/subsetter/app/db.py → api/swotvis/app/db.py

@@ -7,7 +7,7 @@
 from fastapi_users.db import BaseOAuthAccount, BeanieBaseUser, BeanieUserDatabase
 from pydantic import BaseModel, Field
 
-from subsetter.config import get_settings
+from swotvis.config import get_settings
 
 DATABASE_URL = get_settings().mongo_url
 client = motor.motor_asyncio.AsyncIOMotorClient(DATABASE_URL, uuidRepresentation="standard")

api/subsetter/app/models.py → api/swotvis/app/models.py

@@ -3,8 +3,8 @@
 from fastapi import Depends, HTTPException, Path, status
 from pydantic import BaseModel, Field
 
-from subsetter.app.db import Submission, User
-from subsetter.app.users import current_active_user
+from swotvis.app.db import Submission, User
+from swotvis.app.users import current_active_user
 
 
 class WorkflowParams(BaseModel):

api/swotvis/app/routers/access_control/__init__.py

@@ -0,0 +1 @@
+from swotvis.app.routers.access_control.router import router

api/subsetter/app/routers/access_control/policy_generation.py → api/swotvis/app/routers/access_control/policy_generation.py

@@ -49,7 +49,7 @@ def refresh_minio_policy(user):
 def bucket_name(resource_id: str):
  # raccess = ResourceAccess.objects.filter(resource__short_id=resource_id).first()
  # return raccess.owners.first().username
- return "subsetter-outputs"
+ return "swotvis-outputs"
 
 
 def create_view_statements(owner, submissions) -> list:

api/subsetter/app/routers/access_control/router.py → api/swotvis/app/routers/access_control/router.py

@@ -6,9 +6,9 @@
 from fastapi import APIRouter, Depends, HTTPException
 from pydantic import BaseModel
 
-from subsetter.app.db import Submission, User
-from subsetter.app.routers.access_control.policy_generation import minio_policy
-from subsetter.app.users import current_active_user
+from swotvis.app.db import Submission, User
+from swotvis.app.routers.access_control.policy_generation import minio_policy
+from swotvis.app.users import current_active_user
 
 router = APIRouter()
 

api/swotvis/app/routers/argo/__init__.py

@@ -0,0 +1 @@
+from swotvis.app.routers.argo.router import router

api/subsetter/app/routers/argo/router.py → api/swotvis/app/routers/argo/router.py

@@ -8,16 +8,16 @@
 from argo_workflows.api import workflow_service_api
 from fastapi import APIRouter, Depends, Query
 
-from subsetter.app.db import Submission, User
-from subsetter.app.models import (
+from swotvis.app.db import Submission, User
+from swotvis.app.models import (
  LogsResponseModel,
  SubmissionResponseModel,
  UrlResponseModel,
  UserSubmissionsResponseModel,
  WorkflowDep,
 )
-from subsetter.app.users import current_active_user
-from subsetter.config import get_minio_client, get_settings
+from swotvis.app.users import current_active_user
+from swotvis.config import get_minio_client, get_settings
 from .transformer import transform_latlon
 
 if get_settings().cloud_run:
@@ -220,7 +220,7 @@ async def logs(workflow_params: WorkflowDep) -> LogsResponseModel:
 async def signed_url_minio(workflow_params: WorkflowDep) -> UrlResponseModel:
  submission = workflow_params.user.get_submission(workflow_params.workflow_id)
  url = get_minio_client().presigned_get_object(
- "subsetter-outputs",
+ "swotvis-outputs",
  f"{workflow_params.user.username}/{submission.workflow_name}/{submission.workflow_id}/all.gz",
  )
  return {'url': url}

api/swotvis/app/routers/storage/__init__.py

@@ -0,0 +1 @@
+from swotvis.app.routers.storage.router import router

api/subsetter/app/routers/storage/router.py → api/swotvis/app/routers/storage/router.py

@@ -1,7 +1,7 @@
 from fastapi import APIRouter
 
-from subsetter.app.models import WorkflowDep
-from subsetter.config import get_minio_client
+from swotvis.app.models import WorkflowDep
+from swotvis.config import get_minio_client
 
 router = APIRouter()
 
@@ -46,7 +46,7 @@ async def share_workflow_with_user(
 # @router.post('/extract/{workflow_id}')
 # async def extract_workflow_artifact(workflow_params: WorkflowDep) -> SubmissionResponseModel:
 # workflow_id = str(uuid.uuid4())
-# bucket = "subsetter-outputs"
+# bucket = "swotvis-outputs"
 # submission = workflow_params.user.get_submission(workflow_params.workflow_id)
 # path_key = f'{submission.workflow_name}/{submission.workflow_id}/subset.gz'
 # api_instance.submit_workflow(

api/swotvis/app/routers/test/__init__.py

@@ -0,0 +1 @@
+from swotvis.app.routers.test.router import router

api/swotvis/app/routers/test/router.py

@@ -0,0 +1,8 @@
+from fastapi import APIRouter
+
+router = APIRouter()
+
+
+@router.get('/', description="Test endpoint")
+async def test_endpoint():
+ return {"message": "Hello, world!"}

api/subsetter/app/users.py → api/swotvis/app/users.py

@@ -10,8 +10,8 @@
 from httpx_oauth.exceptions import GetIdEmailError
 from httpx_oauth.oauth2 import OAuth2
 
-from subsetter.app.db import User, get_user_db
-from subsetter.config import get_settings, get_minio_client
+from swotvis.app.db import User, get_user_db
+from swotvis.config import get_settings, get_minio_client
 
 SECRET = "SECRET"
 

api/subsetter/main.py → api/swotvis/main.py

@@ -1,18 +1,17 @@
 import subprocess
-import httpx
 
 from beanie import init_beanie
-from fastapi import FastAPI, Request
-from fastapi.responses import JSONResponse
+from fastapi import FastAPI
 from fastapi.middleware.cors import CORSMiddleware
 
-from subsetter.app.db import User, db
-from subsetter.app.routers.access_control import router as access_control_router
-from subsetter.app.routers.argo import router as argo_router
-from subsetter.app.routers.storage import router as storage_router
-from subsetter.app.schemas import UserRead, UserUpdate
-from subsetter.app.users import SECRET, auth_backend, cuahsi_oauth_client, fastapi_users
-from subsetter.config import get_settings
+from swotvis.app.db import User, db
+from swotvis.app.routers.access_control import router as access_control_router
+from swotvis.app.routers.argo import router as argo_router
+from swotvis.app.routers.storage import router as storage_router
+from swotvis.app.routers.test import router as test_router
+from swotvis.app.schemas import UserRead, UserUpdate
+from swotvis.app.users import SECRET, auth_backend, cuahsi_oauth_client, fastapi_users
+from swotvis.config import get_settings
 
 # TODO: get oauth working with swagger/redoc
 # Setting the base url for swagger docs
@@ -81,6 +80,12 @@
  tags=["users"],
 )
 
+app.include_router(
+ test_router,
+ prefix="/test",
+ tags=["test"],
+)
+
 
 @app.on_event("startup")
 async def on_startup():