Health Database & Alchemy App

A Flask web application that extracts health/nutrition articles from markdown files, imports them into a SQLite database with full citation linking, and provides an alchemy-style interface for combining healing items into protocols.

Features

• Article Management: Browse, search, and view health/nutrition articles with full citation support
• Alchemy Builder: Combine healing items from different categories to create custom protocols
• Protocol Management: Create, edit, view, and delete user-created protocols
• Citation Linking: Granular citation linking at sentence, paragraph, and bullet-point level
• Full-Text Search: Search articles using SQLite FTS5

Project Structure

alchemy-app/
├── database/          # Database schema
├── parser/           # Markdown parsing modules
├── import/           # Data import scripts
├── app/              # Flask application
├── templates/        # Jinja2 templates
├── static/           # CSS, JS, images
├── requirements.txt  # Python dependencies
└── README.md         # This file

Setup

1. Install dependencies:

   pip install -r requirements.txt

2. Initialize the database:

   python -m import.import_articles --init --db health.db

3. Import articles:

   python -m import.import_articles --db health.db --articles ../site/source/_posts/Natural\ Healing

4. Run the Flask application:

   export FLASK_APP=app
   export FLASK_ENV=development
   flask run

   Or using Python:

   python run.py

Usage

Importing Articles

The import script scans the Natural Healing directory and parses all markdown files:

python -m import.import_articles --db health.db --articles ../site/source/_posts/Natural\ Healing

Options:

• --db: Database file path (default: health.db)
• --articles: Path to Natural Healing articles directory
• --init: Initialize database schema (run once)

Creating Protocols

1. Navigate to the Alchemy Builder page
2. Search and select items from the sidebar
3. Add items to your protocol
4. Enter a protocol name and description
5. Click "Create Protocol"

Viewing Protocols

• View all protocols on the Protocols page
• Click on a protocol to see its details and combined properties
• Edit or delete user-created protocols (predefined protocols are read-only)

Database Schema

The database includes the following main tables:

• articles - Main article information
• categories - Category hierarchy
• tags - Article tags
• citations - Citation/reference information
• content_blocks - Granular content units with citation links
• healing_properties - Healing properties with hierarchy
• treatments - Disease/symptom treatments
• composition_items - Chemical constituents
• synergistic_relationships - Synergistic combinations
• protocols - User-created and predefined protocols
• protocol_items - Items in protocols

API Endpoints

• GET /api/articles - Get all articles
• GET /api/article/<slug> - Get article by slug
• POST /api/protocol/create - Create a new protocol
• POST /api/protocol/<id>/add-item - Add item to protocol
• DELETE /api/protocol/<id>/remove-item/<item_id> - Remove item from protocol
• GET /api/protocol/<id>/combined - Get combined properties for protocol

Development

The application uses:

• Flask for the web framework
• SQLite for the database
• Jinja2 for templating
• python-frontmatter for parsing markdown frontmatter

License

See LICENSE file in the parent directory.