DQA MDR-Connector

This repository provides python scripts to connect the MIRACUM metadata reposiory (MDR) with the MIRACUM DQA-tool.

It includes to basic functions:

• to download the MDR from the dataelement-hub
• to add DQA-specific information to dataelements that should be analyzed using the DQA-tool and to upload this information to the dataelement-hub

Installation

git clone https://github.com/miracum/dqa-mdr-connector.git
cd dqa-mdr-connector
pip install -e .

Or simply:

pip install git+https://github.com/miracum/dqa-mdr-connector.git

Usage

In your scripts, import the connector as follows:

MDR Download

import logging
from dqa_mdr_connector.get_mdr import GetMDR

if __name__ == "__main__":
    logging.basicConfig(level=logging.DEBUG)
    gm = GetMDR(
        output_folder="./",
        output_filename="mdr_download.csv",
        api_url="https://rest.demo.dataelementhub.de/v1/",
        bypass_auth=True,
        namespace_designation="test_mdr"
    )
    gm()

MDR Update

import os
from dqa_mdr_connector.update_mdr import UpdateMDR
import logging

if __name__ == "__main__":
    logging.basicConfig(level=logging.DEBUG)
    um = UpdateMDR(
        csv_file=os.path.join(
            os.path.dirname(__file__),
            "mdr.csv"
        ),
        separator=";",
        api_url="https://rest.demo.dataelementhub.de/v1/",
        api_auth_url="https://auth.dev.osse-register.de/auth/realms/dehub-demo/protocol/openid-connect/token",
        namespace_designation="test_mdr",
        namespace_definition="This is an awesome testing namespace."
    )
    um()

More Infos

• about the MIRACUM DQA-tool: https://gitlab.miracum.org/miracum/dqa/miracumdqa
• about MIRACUM: https://www.miracum.org/
• about the Medical Informatics Initiative: https://www.medizininformatik-initiative.de/index.php/de