MIPDB Installation and Usage Guide

mipdb is a tool to validate datasets for the MIP platform.

Prerequisites

Before you begin, ensure you have met the following requirements:

• Python 3.8
• pip

Installation Steps

1. Update Package List:

   sudo apt update

2. Install Python 3.8:

   sudo apt install python3.8

3. Verify Python 3.8 Installation:

   python3.8 --version

4. Install pip for Python 3.8:

   sudo apt install python3-pip

5. Verify pip Installation:

   python3.8 -m pip --version

6. Install mipdb Using pip:

   python3.8 -m pip install mipdb

Setting Up PATH

7. Update PATH to Include Local Binary Directory:

   Run this command to dynamically fetch the user base path and update the PATH environment variable:

   export PATH="$PATH:$(python3.8 -m site --user-base)/bin"

   To make this change permanent, add this line to your ~/.bashrc or ~/.profile file:

   echo 'export PATH="$PATH:$(python3.8 -m site --user-base)/bin"' >> ~/.bashrc
   source ~/.bashrc

   or

   echo 'export PATH="$PATH:$(python3.8 -m site --user-base)/bin"' >> ~/.profile
   source ~/.profile

Usage

Validating a Pathology Folder

Command:

mipdb validate-folder <folder_path>

Description:

• The command enforces the following requirements:
  • First, the metadata file itself is validated.
  • Secondly, the CSV files in the folder are validated against the metadata.
• You can nest multiple pathology folders within a parent folder, and the validate-folder command will automatically iterate through each pathology folder.

• The folder has to comply with these requirements: https://github.com/HBPMedical/mip-deployment/blob/master/doc/NewDataRequirements.md

Examples:

mipdb validate-folder /home/user/data/dementia
mipdb validate-folder /home/user/data