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Added Documentation for the validation of a pathology folder.
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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) | ||
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mipdb is a tool for managing and validating pathology data. This README provides guidance on how to get started with mipdb. | ||
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## Prerequisites | ||
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Before you begin, ensure you have met the following requirements: | ||
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- **python** | ||
- **pip** | ||
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## Installation | ||
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You can easily install mipdb using `pip`: | ||
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```bash | ||
pip install mipdb | ||
``` | ||
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## Usage | ||
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### Validating a Pathology Folder | ||
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**Command**: `mipdb validate-folder <folder_path>` | ||
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**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). | ||
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**Note**: You can nest multiple pathology folders within a parent folder, and the `validate-folder` command will automatically iterate through each pathology folder. | ||
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**Examples**: | ||
```bash | ||
mipdb validate-folder /home/user/data/dementia | ||
``` | ||
```bash | ||
mipdb validate-folder /home/user/data | ||
``` |