Use base templates everywhere

NIPTool/API/external/api/api_v1/endpoints/download.py

@@ -2,14 +2,12 @@
 
 from fastapi import APIRouter, Depends, Request
 from fastapi.responses import FileResponse, RedirectResponse
-from fastapi.templating import Jinja2Templates
 from NIPTool.adapter.plugin import NiptAdapter
-from NIPTool.config import get_nipt_adapter
+from NIPTool.config import get_nipt_adapter, templates
 from NIPTool.crud import find
 from NIPTool.parse.batch import validate_file_path
 
 router = APIRouter()
-templates = Jinja2Templates(directory="templates")
 
 
 @router.get("/batch_download/{batch_id}/{file_id}")

NIPTool/API/external/api/api_v1/endpoints/index.py

@@ -1,8 +1,5 @@
 from fastapi import APIRouter, Request
-from fastapi.templating import Jinja2Templates
-
-
-templates = Jinja2Templates(directory="templates")
+from NIPTool.config import templates
 
 router = APIRouter()
 

NIPTool/API/external/api/api_v1/endpoints/login.py

@@ -1,17 +1,10 @@
-from fastapi import APIRouter, Response
-from fastapi.responses import RedirectResponse
+from datetime import timedelta
 
-from fastapi import Depends, HTTPException, status, Security
+from fastapi import APIRouter, Depends, HTTPException, status
+from fastapi.responses import RedirectResponse
 from fastapi.security import OAuth2PasswordRequestForm
-from NIPTool.models.server.login import Token, UserInDB, User
-
-from NIPTool.API.external.api.deps import (
-    get_current_active_user,
-    authenticate_user,
-    create_access_token,
-    temp_get_config,
-)
-from datetime import timedelta
+from NIPTool.API.external.api.deps import authenticate_user, create_access_token, temp_get_config
+from NIPTool.models.server.login import Token, UserInDB
 
 router = APIRouter()
 

NIPTool/API/external/api/api_v1/endpoints/sample.py

@@ -1,18 +1,16 @@
 from fastapi import APIRouter, Depends, Request
-from fastapi.templating import Jinja2Templates
 from NIPTool.adapter.plugin import NiptAdapter
 from NIPTool.API.external.utils import *
-from NIPTool.config import get_nipt_adapter
+from NIPTool.config import get_nipt_adapter, templates
 from NIPTool.crud import find
 from NIPTool.models.database import Batch, User
 
 router = APIRouter()
-templates = Jinja2Templates(directory="templates")
 
 
 @router.get("/samples/{sample_id}/")
 def sample(request: Request, sample_id: str, adapter: NiptAdapter = Depends(get_nipt_adapter)):
-    """Sample view with sample information."""
+    """Get sample with id"""
 
     sample: dict = find.sample(sample_id=sample_id, adapter=adapter).dict()
     batch: Batch = find.batch(batch_id=sample.get("batch_id"), adapter=adapter)
@@ -33,7 +31,7 @@ def sample(request: Request, sample_id: str, adapter: NiptAdapter = Depends(get_
 
 @router.post("/samples/{sample_id}/")
 def sample(request: Request, sample_id: str, adapter: NiptAdapter = Depends(get_nipt_adapter)):
-    """Sample view with sample information."""
+    """Post sample with id"""
 
     sample: dict = find.sample(sample_id=sample_id, adapter=adapter).dict()
     batch: Batch = find.batch(batch_id=sample.get("batch_id"), adapter=adapter)

NIPTool/API/external/api/api_v1/endpoints/statistics.py

@@ -1,17 +1,14 @@
 from fastapi import APIRouter, Depends, Request
 from NIPTool.adapter.plugin import NiptAdapter
-from NIPTool.models.database import User
 from NIPTool.API.external.utils import (
     get_last_batches,
     get_statistics_for_box_plot,
     get_statistics_for_scatter_plot,
 )
-from NIPTool.config import get_nipt_adapter
-
-from fastapi.templating import Jinja2Templates
+from NIPTool.config import get_nipt_adapter, templates
+from NIPTool.models.database import User
 
 router = APIRouter()
-templates = Jinja2Templates(directory="templates")
 
 
 @router.get("/statistics")

NIPTool/API/internal/api/api_v1/endpoints/insert.py

@@ -43,7 +43,7 @@ def user(
     """Function to load user into the database with rest"""
 
     if find.user(adapter=adapter, email=user.email):
-        return "user allready in database"
+        return "user already in database"
     insert_user(adapter=adapter, user=user)
 
     response.status_code = status.HTTP_200_OK

NIPTool/commands/base.py

@@ -6,15 +6,13 @@
 import click
 import pkg_resources
 import uvicorn
-from dotenv import dotenv_values
 
 # Get version and doc decorator
 from NIPTool import __version__
 from NIPTool.adapter import NiptAdapter
 from NIPTool.config import settings
 from NIPTool.crud import find
 from NIPTool.crud.insert import insert_batch, insert_samples
-from NIPTool.main import external_app, internal_app
 from NIPTool.models.database import Batch, Sample
 from NIPTool.models.server.load import BatchRequestBody
 from NIPTool.parse.batch import get_batch, get_samples