Merge pull request #50 from Clinical-Genomics/update-demo

update demo

.gitignore

@@ -79,6 +79,7 @@ celerybeat-schedule
 
 # dotenv
 .env
+NIPTool/.env
 
 # virtualenv
 .venv

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

@@ -1,15 +1,12 @@
 from fastapi import APIRouter, Depends, Request
 from NIPTool.adapter.plugin import NiptAdapter
+from NIPTool.API.external.constants import TRISOMI_TRESHOLDS
+from NIPTool.API.external.utils import *
+from NIPTool.config import get_nipt_adapter, templates
 from NIPTool.crud import find
 from NIPTool.models.database import Batch, User
-from NIPTool.API.external.utils import *
-from NIPTool.API.external.constants import TRISOMI_TRESHOLDS
-from NIPTool.API.external.api.deps import get_nipt_adapter
-
-from fastapi.templating import Jinja2Templates
 
 router = APIRouter()
-templates = Jinja2Templates(directory="templates")
 CURRENT_USER = User(username="mayapapaya", email="mayabrandi@123.com", role="RW").dict()
 
 
@@ -18,7 +15,6 @@ def batches(
     request: Request, adapter: NiptAdapter = Depends(get_nipt_adapter)
 ):  # , user: User = Depends(get_current_active_user)):
     """List of all batches"""
-
     all_batches: List[Batch] = find.batches(adapter=adapter)
     return templates.TemplateResponse(
         "batches.html",
@@ -36,8 +32,8 @@ def batches(
     request: Request, adapter: NiptAdapter = Depends(get_nipt_adapter)
 ):  # , user: User = Depends(get_current_active_user)):
     """List of all batches"""
-
     all_batches: List[Batch] = find.batches(adapter=adapter)
+
     return templates.TemplateResponse(
         "batches.html",
         context={

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

@@ -1,13 +1,13 @@
+from pathlib import Path
+
 from fastapi import APIRouter, Depends, Request
+from fastapi.responses import FileResponse, RedirectResponse
 from NIPTool.adapter.plugin import NiptAdapter
-from NIPTool.API.external.api.deps import get_nipt_adapter, get_current_active_user
-from fastapi.templating import Jinja2Templates
+from NIPTool.config import get_nipt_adapter, templates
+from NIPTool.crud import find
 from NIPTool.parse.batch import validate_file_path
-from pathlib import Path
-from fastapi.responses import RedirectResponse, FileResponse
 
 router = APIRouter()
-templates = Jinja2Templates(directory="templates")
 
 
 @router.get("/batch_download/{batch_id}/{file_id}")
@@ -16,11 +16,11 @@ def batch_download(
 ):
     """View for batch downloads"""
 
-    batch = adapter.batch(batch_id)
+    batch: dict = find.batch(adapter=adapter, batch_id=batch_id).dict()
     file_path = batch.get(file_id)
 
     if not validate_file_path(file_path):
-        # handle the redirect responce!
+        # handle the redirect response!
         return RedirectResponse(request.url)
 
     path = Path(file_path)
@@ -36,10 +36,10 @@ def sample_download(
 ):
     """View for sample downloads"""
 
-    sample = adapter.sample(sample_id)
+    sample: dict = find.sample(adapter=adapter, sample_id=sample_id).dict()
     file_path = sample.get(file_id)
     if not validate_file_path(file_path):
-        # handle the redirect responce!
+        # handle the redirect response!
         return RedirectResponse(request.url)
 
     file = Path(file_path)

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

@@ -1,12 +1,9 @@
-
 from fastapi import APIRouter, Request
-from fastapi.templating import Jinja2Templates
-
-
-templates = Jinja2Templates(directory="templates")
+from NIPTool.config import templates
 
 router = APIRouter()
 
+
 @router.post("/")
 def index(request: Request):
     """Log in view."""

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

@@ -1,19 +1,16 @@
 from fastapi import APIRouter, Depends, Request
 from NIPTool.adapter.plugin import NiptAdapter
-from NIPTool.crud import find
-from NIPTool.models.database import User
 from NIPTool.API.external.utils import *
-from NIPTool.API.external.api.deps import get_nipt_adapter
-
-from fastapi.templating import Jinja2Templates
+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)
@@ -34,7 +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

@@ -1,19 +1,14 @@
-from typing import List
-
 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.API.external.api.deps 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/external/api/api_v1/endpoints/update.py

@@ -1,17 +1,15 @@
 import logging
+from datetime import datetime
 from typing import Iterable
 
 from fastapi import APIRouter, Depends, Request
 from fastapi.responses import RedirectResponse
-from starlette.datastructures import FormData
-
 from NIPTool.adapter.plugin import NiptAdapter
+from NIPTool.API.external.utils import *
+from NIPTool.config import get_nipt_adapter
 from NIPTool.crud import update
-
 from NIPTool.models.database import User
-from NIPTool.API.external.utils import *
-from NIPTool.API.external.api.deps import get_nipt_adapter, get_current_active_user
-from datetime import datetime
+from starlette.datastructures import FormData
 
 router = APIRouter()
 

NIPTool/API/external/api/deps.py

@@ -1,23 +1,14 @@
-from pydantic import BaseSettings
-
-from NIPTool.adapter.plugin import NiptAdapter
-from pymongo import MongoClient
-from fastapi.security import OAuth2PasswordBearer
-from fastapi import HTTPException, status
-from NIPTool.models.server.login import User, UserInDB, TokenData
-from fastapi import Depends
-from passlib.context import CryptContext
 from datetime import datetime, timedelta
 from typing import Optional
-from jose import JWTError, jwt
-
-
-class Settings(BaseSettings):
-    db_uri: str = "test_uri"
-    db_name: str = "test_db"
-
 
-settings = Settings()
+from fastapi import Depends, HTTPException, status
+from fastapi.security import OAuth2PasswordBearer
+from jose import JWTError, jwt
+from NIPTool.adapter.plugin import NiptAdapter
+from NIPTool.config import get_nipt_adapter
+from NIPTool.crud import find
+from NIPTool.models.server.login import TokenData, User, UserInDB
+from passlib.context import CryptContext
 
 
 def temp_get_config():
@@ -30,11 +21,6 @@ def temp_get_config():
     }
 
 
-def get_nipt_adapter():
-    client = MongoClient(settings.db_uri)
-    return NiptAdapter(client, db_name=settings.db_name)
-
-
 oauth2_scheme = OAuth2PasswordBearer(
     tokenUrl="/api/v1/login/token",
     scopes={"me": "Read information about the current user.", "items": "Read items."},
@@ -61,10 +47,10 @@ def get_current_user(
         token_data = TokenData(username=username)
     except JWTError:
         raise credentials_exception
-    user = adapter.user(token_data.username)
+    user: User = find.user(adapter=adapter, user_name=token_data.username)
     if not user:
         raise credentials_exception
-    return User(**user)
+    return user
 
 
 def get_current_active_user(current_user: User = Depends(get_current_user)) -> User:
@@ -81,26 +67,25 @@ def get_password_hash(password):
     return pwd_context.hash(password)
 
 
-def authenticate_user(username: str, password: str) -> UserInDB:
+def authenticate_user(username: str, password: str) -> Optional[UserInDB]:
     adapter = get_nipt_adapter()
-    user_dict = adapter.user(username)
-    if not user_dict:
-        return False
-    user = UserInDB(**user_dict)
+    user: User = find.user(adapter=adapter, user_name=username)
     if not user:
-        return False
-    if not verify_password(password, user.hashed_password):
-        return False
-    return user
+        return None
+    db_user = UserInDB(**user.dict())
+    if not db_user:
+        return None
+    if not verify_password(password, db_user.hashed_password):
+        return None
+    return db_user
 
 
 def create_access_token(data: dict, expires_delta: Optional[timedelta] = None):
-    config: dict = temp_get_config()
+    configs: dict = temp_get_config()
     to_encode = data.copy()
     if expires_delta:
         expire = datetime.utcnow() + expires_delta
     else:
         expire = datetime.utcnow() + timedelta(minutes=15)
     to_encode.update({"exp": expire})
-    encoded_jwt = jwt.encode(to_encode, config.get("SECRET_KEY"), algorithm=config.get("ALGORITHM"))
-    return encoded_jwt
+    return jwt.encode(to_encode, configs.get("SECRET_KEY"), algorithm=configs.get("ALGORITHM"))

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

@@ -3,12 +3,12 @@
 
 from fastapi import APIRouter, Depends, Response, status
 from NIPTool.adapter.plugin import NiptAdapter
-from NIPTool.crud.insert import insert_batch, insert_samples, insert_user
+from NIPTool.config import get_nipt_adapter
 from NIPTool.crud import find
+from NIPTool.crud.insert import insert_batch, insert_samples, insert_user
 from NIPTool.models.database import Batch, Sample
 from NIPTool.models.server.load import BatchRequestBody, UserRequestBody
 from NIPTool.parse.batch import get_batch, get_samples
-from NIPTool.API.internal.api.deps import get_nipt_adapter
 
 router = APIRouter()
 
@@ -20,15 +20,14 @@ def batch(
     adapter: NiptAdapter = Depends(get_nipt_adapter),
 ):
     """Function to load batch data into the database with rest"""
-
     nipt_results = Path(batch_files.result_file)
     if not nipt_results.exists():
         response.status_code = status.HTTP_422_UNPROCESSABLE_ENTITY
         return {"message": "Results file missing."}
     samples: List[Sample] = get_samples(nipt_results)
     batch: Batch = get_batch(nipt_results)
     if find.batch(adapter=adapter, batch_id=batch.batch_id):
-        return "batch allready in database"
+        return "batch already in database"
 
     insert_batch(adapter=adapter, batch=batch, batch_files=batch_files)
     insert_samples(adapter=adapter, samples=samples, segmental_calls=batch_files.segmental_calls)
@@ -44,7 +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