Thoth Legacy Revived

Thoth is a web platform that supports the workflow of a Systematic Literature Review (SLR), including project organization, extraction activities, and progress tracking.

This repository is a revived and refactored version of the original Thoth legacy codebase, carried out as a learning experience. It modernizes the front-end stack and improves the internal architecture while preserving the original feature set.

For production usage and the latest features, visit Thoth 2.0.

What changed from the original legacy

The original codebase used plain PHP views, monolithic controllers, and static Bootstrap dist files copied directly into the project. This revived version introduces the following changes:

Twig template engine

All views were migrated from inline PHP to Twig. This enforces a clean separation between presentation and logic, makes templates more readable, and enables template inheritance through layouts and partials.

Controller refactoring

Several large, multi-responsibility controllers were broken down into smaller, focused controllers. This makes the routing and business logic easier to follow, test, and extend.

npm-managed front-end dependencies

Static vendor JS and CSS files were removed from the repository. All front-end dependencies are now declared in package.json and installed via npm. This includes:

• Bootstrap 5 (via npm, compiled from source)
• DataTables with Bootstrap 5 integration
• Highcharts
• Quill rich text editor
• Select2
• SweetAlert2
• JSZip and pdfmake

Bootstrap with SCSS

Instead of loading pre-compiled Bootstrap CSS from a dist/ folder, the project now imports Bootstrap via SCSS. Custom styles live in assets/scss/ and are compiled into a single assets/css/theme.css file using the sass CLI.

To rebuild styles:

npm run build-css

To watch for changes during development:

npm run watch-scss

Docker and PHP upgrade

The project was fully Dockerized using Docker Compose, making local setup reproducible without any manual PHP/Apache configuration. The PHP runtime was upgraded from the original PHP 5.x to PHP 8.1 (php:8.1-apache), bringing modern language features, improved performance, and continued security support.

Screenshot

Example of the Thoth dashboard and progress tracking interface.

Tech stack

Layer	Technology
Framework	CodeIgniter 3 (PHP 8.1)
Templating	Twig 3
Styling	Bootstrap 5 · SCSS · Sass CLI
Front-end libs	DataTables · Highcharts · Quill · Select2 · SweetAlert2
Package manager	npm (front-end) · Composer (PHP)
Database	MySQL
Runtime	Docker / Docker Compose (php:8.1-apache)

Getting started (Docker)

1) Clone the repository

git clone https://github.com/auri-gabriel/thoth.git
cd thoth

2) Install PHP dependencies

composer install

3) Install Node.js dependencies

npm install

4) Build CSS

npm run build-css

5) Configure application files

cp application/config/database_sample.php application/config/database.php
cp application/config/config_sample.php application/config/config.php

Optionally edit these files to match your local database settings.

6) Start containers

docker compose up --build

Application URL: http://localhost:8080

7) Initialize the database

docker exec -i <mysql_container_name> mysql -uthoth -pthoth thoth < docs/database/thoth.sql

Replace <mysql_container_name> with your actual container name (for example, thoth-db-1).

8) Session directory permissions (if needed)

If you get session path/permission errors:

mkdir -p application/cache/sessions
chmod 777 application/cache/sessions

9) Default credentials

Check the database seed data (or ask your admin) for available default users.

10) Stop containers

docker compose down -v

11) Xdebug (optional)

Xdebug is installed in the web container and is disabled by default.

Start the stack with debug mode enabled:

XDEBUG_MODE=debug,develop docker compose up --build

Then set a breakpoint in VS Code and start listening on port 9003.

Because xdebug.start_with_request=trigger, only requests with a trigger will start debugging. Use one of these:

Cookie: XDEBUG_TRIGGER=1

Query string: ?XDEBUG_TRIGGER=1

For coverage commands, use:

XDEBUG_MODE=coverage docker compose run --rm web composer test:coverage

Troubleshooting

• If login fails, confirm the SQL import was executed successfully.
• If sessions do not persist, verify application/cache/sessions exists and is writable.
• If containers fail to start, run docker compose logs to inspect service errors.
• If styles look broken, make sure you ran npm run build-css after installing dependencies.

Contributing

Contributions are welcome. See contributing.md for contribution guidelines.

Contributors

License

This project is licensed under the MIT License. See license.txt for details.

Contact

For questions or support, open an issue in this repository: auri-gabriel/thoth.