Web app to manage CAIPP Core systems and data.

A lightweight, customizable web system built with Flask for managing the operations of the LSUHSC-CAIPP Bioinformatics and Modeling Cores (Core B and Core C). CoreSystemsApp centralizes order management, invoicing, inventory, and reporting behind a role-based access system, with safe database operations across client-side logic, server-side processing, and API communication.

Table of Contents

• Features
• Setup
• Roles and Access
• Web App
  • Login
  • Core B
  • Core C
  • Dashboards
• Reader
• PdfWriter
• Development
• License

Features

• Role-based authentication (Admin, User, Core B, Core C) with a super-admin tier
• Core B: order tracking, PI management, and itemized invoice PDF generation with discounts
• Core C: antibody stock, mouse stock, predefined antibody panels, and supply inventory
• Fuzzy search and filtering across records
• CSV export on every major table
• Orders and Invoice analytics dashboards
• BioRender license billing support

Setup

Python version required: 3.14.5

Create an environment with:

python3 -m venv <venv_name>

or for a specific Python version:

python3.14 -m venv <venv_name>

Activate the environment:

source <venv_name>/bin/activate

Install requirements:

pip install -r requirements.txt

The application uses SQLite by default for user credentials (configurable via the DATABASE_URI environment variable) and connects to MySQL databases for Core B and Core C data using the JSON credential files in db_config/. See Database Configuration details in each core's README.

Roles and Access

Access is governed by a role system enforced through a custom login_required decorator. Roles are:

• Admin — manage users, including creating and deleting other admins (super-admin can do all)
• User — base authenticated access
• Core B — access to the Bioinformatics and Modeling order/invoice system
• Core C — access to the antibody, mouse, and panel systems

Only super admins (Admin + Core B + Core C) can add and delete users through the Authentication/Admin panel.

Web App

The app is divided into sections based on access level and function.

Login

Each user logs in to an account tied to specific roles that determine what they can access. The login system uses Flask-Login with custom role checks. After login, users are routed to the appropriate core based on their roles.

Core B

Order and invoice system for the Bioinformatics and Modeling Core. Handles service orders, PI records, and invoice PDF generation.

For details see CoreB.

Core C

Antibody sharing and tracking system, including antibody stock, mouse stock, predefined panels, and supply inventory.

For details see CoreC.

Dashboards

Core B includes Orders and Invoice analytics dashboards that summarize order and billing data into KPIs and charts (BioRender entries are reported separately). Dashboards are generated server-side with matplotlib and rendered into the app.

PdfWriter

Fills invoice PDF templates from a dictionary of data, populating a predefined invoice form to produce a completed invoice document.

Development

Linting and formatting use Ruff (Python), HTMLHint (templates), and Stylelint (CSS). Common tasks are available through the Makefile:

make setup      # install Python + Node dependencies
make run        # run the Flask app
make lint       # lint Python with Ruff
make lint-html  # lint HTML templates
make lint-css   # lint CSS
make format     # format Python with Ruff

Tests run with pytest:

python -m pytest

License

This project is licensed under the GNU General Public License v3.0 — see the LICENSE file for details.