Installation and Setup Guide

This guide provides detailed instructions for installing and configuring pat2vec.

Requirements

Core Services:

CogStack: An operational instance for data retrieval.
Elasticsearch: The backend for CogStack.
MedCAT: For medical concept annotation.

Local Setup:

Python: Version 3.10 or higher.
Virtual Environment: Requires the python3-venv package (or equivalent for your OS).

Installation on Unix/Linux (Recommended)

The install_pat2vec.sh script automates the full setup.

Prerequisites

A MedCAT model pack (.zip file).
Your CogStack/Elasticsearch credentials.

Steps

Clone the repository:

git clone https://github.com/SamoraHunter/pat2vec.git
cd pat2vec

Run the installation script:
```
chmod +x install_pat2vec.sh
./install_pat2vec.sh
```
The script supports several options:
- --proxy: Use if you are behind a corporate proxy.
- --dev: Installs development dependencies (e.g., pytest).
- --force: Performs a clean installation, removing any existing environment.
Activate the environment:
```
source ../pat2vec_env/bin/activate
```

Installation on Windows

Clone the repository:

git clone https://github.com/SamoraHunter/pat2vec.git

Run the installation script: This script sets up the Python virtual environment.
```
cd pat2vec
install.bat
```
Activate the environment:
```
pat2vec_env\Scripts\activate
```

Post-Installation Configuration

After running the installation script, you must configure your environment.

1. Elasticsearch Credentials

Your credentials should be placed in a file named credentials.py in the parent directory of your pat2vec clone. The install_pat2vec.sh script automatically copies a template for you.

IMPORTANT: This file contains sensitive information and should never be committed to version control.

The structure should look like this: