Edit this page | Blame

CLI Utility Scripts

This documents the various utility scripts that are provided with the project whose purposes are to support the operation of the application in one way or another.

To get a list of the available scripts/flask commands that can be run, do:

FLASK_APP="main.py" flask --help

With that, you should get a list of commands, which as of 2023-05-26 are:

. . . output truncated to save space ...

Commands:
  apply-migrations     Apply the dabasase migrations.
  assign-system-admin  Assign user with ID `user_id` administrator role.
  init-dev-clients     Initialise a development client for OAuth2 sessions.
  init-dev-users       Initialise development users for OAuth2 sessions.
  routes               Show the routes for the app.
  run                  Run a development server.
  shell                Run a shell in the app context.

*NB*: You can simply do `export FLASK_APP="main.py"` at the beginning of your shell session and then just run the commands without prepending with the `FLASK_APP="main.py"` declaration.

Registering/Setting a User as System Administrator

You can register an new user and set them as the system administrator with:

FLASK_APP="main.py" flask register-admin

A typical session might go something like:

$ FLASK_APP="main.py" flask register-admin
Enter the user's name: CLI SysAdmin
Enter the administrator's email: someadmin@gmail.com
Enter password: 
Confirm password: 
$

You can also run the script directly (without flask) with:

$ python3 -m scripts.register_sys_admin /home/frederick/genenetwork/gn3_files/db/auth.db

changing "/home/frederick/genenetwork/gn3_files/db/auth.db" to the path to your database file.

Setting an Existing User to System Administrator

If a user already exists in your system, and you want to make that user system admin, you could do it with:

FLASK_APP="main.py" flask assign-system-admin 5b15ef01-a9d7-4ee4-9a38-fe9dd1d871b8

You can retrieve the user ID from the (SQLite) database, with something like:

$ sqlite3 /home/frederick/genenetwork/gn3_files/db/auth.db
SQLite version 3.40.0 2022-11-16 12:10:08
Enter ".help" for usage hints.
sqlite> SELECT * FROM users;
0ad1917c-57da-46dc-b79e-c81c91e5b928|test@development.user|Test Development User
9c5d4ddf-c361-4133-add3-9ab9845bb9f2|fredtest02@gmail.com|A New Group Member
b4a8ed7a-a878-4884-94e0-26d3fe0c56a3|fredleader@gmail.com|Frederick the Group Leader

Make Existing Data Publicly Visible

This will only act on any existing data that is not already linked with a user group in the new auth system.

This can be run using flask with

FLASK_APP="main.py" flask make-data-public

which will use the application's configuration settings for the auth(entic|oris)ation database and the MariaDB database.

You could also run the script directly with:

python3 -m scripts.migrate_existing_data AUTHDBPATH MYSQLDBURI

where `AUTHDBPATH` and `MYSQLDBURI` are replaced with the appropriate values, e.g.

python3 -m scripts.migrate_existing_data \
    /home/frederick/genenetwork/gn3_files/db/auth.db \
    mysql://webqtlout:webqtlout@127.0.0.1:3307/db_webqtl

List Available Routes

FLASK_APP="main.py" flask routes

Drop Into a Python Shell

FLASK_APP="main.py" flask shell

Development Scripts

The commands in this section are meant for easing development and are not to be run in a production environment.

Setting up a Sample User for Development

FLASK_APP="main.py" flask init-dev-users

That will initialise your development database with a development user with the following details:

- User ID: 0ad1917c-57da-46dc-b79e-c81c91e5b928 - Email: test@development.user - Password: testpasswd

Setting up Sample OAuth2 Client for Development

FLASK_APP="main.py" flask init-dev-clients