add global config & refactor main folder

app/pmcff/config.py

+import os
+
+
+class Config:
+
+    # Auth
+    CLIENT_ID = os.environ.get("CLIENT_ID", None)
+    CLIENT_SECRET = os.environ.get("CLIENT_SECRET", None)
+    DISCOVERY_URL = "https://login.elixir-czech.org/oidc/.well-known/openid-configuration"
+    REDIRECT_URI = "https://pmcvff-correction.cerit-sc.cz/login/callback"
+
+    # General
+    DATABASE= "/var/lib/sqlite/sqlite_db"
+    PIPELINE_IMAGE = "spectraes/pipeline:2021-05-07"
+    GENERAL_NAME = "pmcvff-correction"
+    TEMPLATES_PATH = f"/app/pmcff/pipeline/templates"
+    YAMLS_PATH = "/srv"
+    RUN_AS = 0
+
+    # Pvc
+    PVC_NAME = f"{GENERAL_NAME}-claim"
+    PVC_STORAGE = "10Gi"
+
+    # Service
+    SERVICE_NAME = f"{GENERAL_NAME}-svc"
+    SERVICE_JUPYTERPORT = "jupyterport"
+
+    # Ingress
+    INGRESS_NAME = f"{GENERAL_NAME}-ingress"
+

app/pmcff/db.py

-# http://flask.pocoo.org/docs/1.0/tutorial/database/
+import click
 import sqlite3
 
-import click
-from flask import current_app, g
+from flask import current_app, g, current_app
 from flask.cli import with_appcontext
 
-DATABASE_PATH = "/var/lib/sqlite"
 
 def get_db():
     if "db" not in g:
         g.db = sqlite3.connect(
-            f"{DATABASE_PATH}/sqlite_db", detect_types=sqlite3.PARSE_DECLTYPES
+            current_app.config['DATABASE'], detect_types=sqlite3.PARSE_DECLTYPES
         )
         g.db.row_factory = sqlite3.Row
 
     return g.db
 
+
 def get_connection(db_file):
     conn = None
     try:
@@ -25,18 +24,21 @@ def get_connection(db_file):
 
     return conn
 
+
 def close_db(e=None):
     db = g.pop("db", None)
 
     if db is not None:
         db.close()
 
+
 def init_db():
     db = get_db()
 
     with current_app.open_resource("schema.sql") as f:
         db.executescript(f.read().decode("utf8"))
 
+
 @click.command("init-db")
 @with_appcontext
 def init_db_command():
@@ -44,6 +46,8 @@ def init_db_command():
     init_db()
     click.echo("Initialized the database.")
 
+
 def init_app(app):
     app.teardown_appcontext(close_db)
     app.cli.add_command(init_db_command)
+

app/pmcff/requirements.txt

-requests==2.21.0
-Flask==1.0.2
-oauthlib==3.0.1
-pyOpenSSL==19.0.0
-Flask-Login==0.4.1
-waitress==1.4.4
-ruamel.yaml==0.16.12

app/pmcff/schema.sql

@@ -5,3 +5,4 @@ CREATE TABLE user (
   dns_name TEXT UNIQUE,
   token TEXT UNIQUE
 );
+

app/pmcff/user.py

 from flask_login import UserMixin
+from pmcff.db import get_db
 
-from db import get_db
 
 class User(UserMixin):
     def __init__(self, id_, name, email, dns_name, token):
@@ -10,6 +10,7 @@ class User(UserMixin):
         self.dns_name = dns_name
         self.token = token
 
+
     @staticmethod
     def get(conn, user_id):
         db = conn.cursor()
@@ -25,6 +26,7 @@ class User(UserMixin):
         )
         return user
 
+
     @staticmethod
     def get_user_by_dns_name(conn, dns_name):
         db = conn.cursor()
@@ -40,6 +42,7 @@ class User(UserMixin):
         )
         return user
 
+
     @staticmethod
     def remove_container(conn, dns_name):
         user = User.get_user_by_dns_name(conn, dns_name)
@@ -51,6 +54,7 @@ class User(UserMixin):
 
         User.update(conn, new_user)
 
+
     @staticmethod
     def assign_dns_name(conn, user_id, dns_name):
         db = conn.cursor()
@@ -62,6 +66,7 @@ class User(UserMixin):
 
         conn.commit()
 
+
     @staticmethod
     def assign_token(conn, user_id, token):
         db = conn.cursor()
@@ -73,6 +78,7 @@ class User(UserMixin):
 
         conn.commit()
 
+
     @staticmethod
     def update(conn, user):
         db = conn.cursor()
@@ -84,6 +90,7 @@ class User(UserMixin):
 
         conn.commit()
 
+
     @staticmethod
     def create(conn, id_, name, email, dns_name, token):
         db = conn.cursor()