mipdb

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

Prerequisites

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

• python3.10
• pip

Installation

You can easily install mipdb using pip on python3.10:

python3.10 -m pip install mipdb

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 csvs in the folder are validated against the metadata.

Note: You can nest multiple pathology folders within a parent folder, and the validate-folder command will automatically iterate through each pathology folder.

Examples:

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

  mipdb validate-folder /home/user/data