Merge pull request #31 from Clinical-Genomics/refactor-load

Refactor server

NIPTool/parse/batch.py

@@ -29,7 +29,8 @@ def pars_segmental_calls(segmental_calls_path: Optional[str]) -> dict:
     return segmental_calls
 
 
-def validate_file_path(file_path: Optional[str]) -> bool:
+
+def validate_file_path(file_path: Optional[str])-> bool:
     """File path validation"""
 
     if not file_path:

NIPTool/schemas/server/login.py

@@ -0,0 +1,23 @@
+from pydantic import BaseModel
+from typing import Optional, List
+from datetime import datetime
+
+class User(BaseModel):
+    username: str
+    email: Optional[str] = None
+    disabled: Optional[bool] = None
+    added: Optional[datetime] = None
+    role: Optional[str]= None
+
+
+class UserInDB(User):
+    hashed_password: str
+
+class Token(BaseModel):
+    access_token: str
+    token_type: str
+
+
+class TokenData(BaseModel):
+    username: Optional[str] = None
+    scopes: List[str] = []

NIPTool/server/__init__.py

@@ -1,47 +0,0 @@
-import logging
-
-from flask import Flask
-from pymongo import MongoClient
-import yaml
-
-from NIPTool.adapter.plugin import NiptAdapter
-from NIPTool.server.login import login_bp, login_manager
-from NIPTool.server.views import server_bp
-
-logging.basicConfig(level=logging.INFO)
-LOG = logging.getLogger(__name__)
-
-
-def create_app(test=False):
-    app = Flask(__name__)
-    app.test = test
-    if test:
-        return app
-
-    try:
-        app.config.from_envvar('NIPT_CONFIG')
-        configure_app(app)
-    except:
-        pass
-
-    return app
-
-
-def configure_app(app, config=None):
-    if config:
-        app.config = {**app.config, **yaml.safe_load(config)}
-    app.config['SECRET_KEY'] = app.config['SECRET_KEY']
-    client = MongoClient(app.config['DB_URI'])
-    db_name = app.config['DB_NAME']
-    app.client = client
-    app.db = client[db_name]
-    app.adapter = NiptAdapter(client, db_name=db_name)
-    app.register_blueprint(login_bp)
-    app.register_blueprint(server_bp)
-    login_manager.init_app(app)
-
-    if app.config['DEBUG'] == 1:
-        from flask_debugtoolbar import DebugToolbarExtension
-        toolbar = DebugToolbarExtension(app)
-
-    return app