Synopsis

FAIRMDLipids Databank -- A portal for visualization of molecular simulations

System Dependencies

• PHP >= 8.3
• composer
• php-mysql MySQL-client/server >= 8
• php-pdo
• php-xml
• php-gd
• This version is compatible with Laravel 12 (will be installed by composer)

Installation

• clone this repository
• cd BilayerUI_laravel
• Install the PHP dependencies with composer install
• Install more dependencies with npm install && npm install node
• Create a .env configuration file from the example environment cp .env-example .env
• Create the pp key: php artisan key:generate
• Create the database (default database name and user is laravel) and set privileges
• Edit the configuration file .env and add the database credentials and key
• Optionally: configure server host and port (default: localhost9000)
• Create the database: php artisan migrate
• To create a link to display resources in storage/ : php artisan storage:link
• This will set up a system with a MySQL database with the NMRLipids schema (default db name laravel), and empty tables.
• npm run build to set up resources managed by Vite

Using the built-in dev server:

• composer run dev

Using Laravel's native Docker environment

• You can use Laravel Sail to set up Docker integration
• Clone the repository
• You need only composer, and Docker on the hosting computer
• Create a customized .env file
• start Docker
• Follow the instructions to install and run Sail here https://laravel.com/docs/12.x/sail
  • composer require laravel/sail --dev --dev is optional
  • php artisan sail:install --devcontainer (The dev-container can be used by your IDE)
• ./vendor/bin/sail up to start the container
• commands to the Docker instance can be issued using sail e.g.

./vendor/bin/sail bash
./vendor/bin/sail mysql

• Update the application key: ./vendor/bin/sail artisan key:generate
• Create a fresh empty database: ./vendor/bin/sail artisan migrate:fresh
• Create the link to the storage-directory: ./vendor/bin/sail artisan storage:link
• /vendor/bin/sail npm run dev set up the Vite server
• The web server will by default be accessible at http://localhost:80

Populating the database

• The database can be populated using the FAIRMD Python Modules

• Install and set up the Python module and the BilayerData

• Set up the environment pointing to a folder containing the BilayerData to display

• cd BilayerUI_laravel/Python

• Set up a config.json file with your DB connection details:

   {
      "host": "127.0.0.1",
      "port": 3306,
      "user": "laravel",
      "password": "your_db_password",
      "database": "laravel"  
   }
  

• Import Data:

  artisan migrate:fresh # prefix ../vendor/bin/sail if running via sail 
  ./UI_DB_Update.py -c config.json
  

• Check the output for any error messages.

• All data required for display are now stored in the DB and you can delete the BilayerData if you do not need them

Running function tests

Tests are run automatically as a CI workflow. You can run tests manually by:

artisan test

If running via sail:

./vendor/bin/sail artisan test

In order to be allowed to merge a PR into main, all tests must pass and at least one reviewer needs to accept these changes.