Installation

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).

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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

1. Clone the repository:

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

2. 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.

3. Activate the environment:

   source ../pat2vec_env/bin/activate

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Installation on Windows

1. Clone the repository:

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

2. Run the installation script: This script sets up the Python virtual environment.

   cd pat2vec
   install.bat

3. Activate the environment:

   pat2vec_env\Scripts\activate

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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: