From c0f35e8a698c213a1986ce0893fc7a8e4569cf7a Mon Sep 17 00:00:00 2001
From: kfilippopolitis <kostasfilippop@gmail.com>
Date: Thu, 14 Sep 2023 14:56:09 +0300
Subject: [PATCH] Added Documentation for the validation of a pathology folder.

---
 README.md | 39 ++++++++++++++++++++++++++++++++++++++-
 1 file changed, 38 insertions(+), 1 deletion(-)

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-[![codecov](https://codecov.io/gh/madgik/mipdb/branch/main/graph/badge.svg?token=BGF1OU23JA)](https://codecov.io/gh/madgik/mipdb)
+# mipdb [![codecov](https://codecov.io/gh/madgik/mipdb/branch/main/graph/badge.svg?token=BGF1OU23JA)](https://codecov.io/gh/madgik/mipdb)
+
+mipdb is a tool for managing and validating pathology data. This README provides guidance on how to get started with mipdb.
+
+## Prerequisites
+
+Before you begin, ensure you have met the following requirements:
+
+- **python**
+- **pip**
+
+## Installation
+
+You can easily install mipdb using `pip`:
+
+```bash
+pip install mipdb
+```
+
+## Usage
+
+### Validating a Pathology Folder
+
+**Command**: `mipdb validate-folder <folder_path>`
+
+**Description**:
+- The command first validates the `CDEsMetadata.json` file, if it follows the [CDEsMetadata Requirements](https://github.com/HBPMedical/mip-deployment/blob/master/documentation/NewDataRequirements.md#cdesmetadata-requirements).
+- It then validates every CSV file in the folder against the defined Common Data Elements (CDEs) of the pathology and the [CSV File Requirements](https://github.com/HBPMedical/mip-deployment/blob/master/documentation/NewDataRequirements.md#csv-file-requirements).
+
+**Note**: You can nest multiple pathology folders within a parent folder, and the `validate-folder` command will automatically iterate through each pathology folder.
+
+**Examples**:
+```bash
+  mipdb validate-folder /home/user/data/dementia
+```
+```bash
+  mipdb validate-folder /home/user/data
+```
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