Alpha Version This pipeline is currently in Alpha testing and issues could appear during data processing, use at your own risk. Feedback and suggestions are welcome!
Epi_Helper was created to help local health departments in MI quickly and easily create communicable disease surveillance reports from MDSS output csv data files. The tool includes two parts:
- Query Assistant - remembers the case status and investigation status settings for groups of reportable diseases of interest. Guides the user through MDSS report queries
- Automated Pipeline - intakes MDSS-generated csv files, extracts relevent disease data, cleans & preprocesses, then inputs data into a master dataset.csv
The pipeline is dynamic in that the user creates a config file to select case and investigation status settings for groups of reportable diseases. The Query Assistant checks MDSS output csv files case and investigation status metadata against the config file, and rejects csv files that do not match the config settings for that particular group of diseases.
The output dataset.csv is optimized for use in PowerBI. Once PowerBI is configured to generate surveillance reports from output Epi_Helper data, the user only has to refresh PowerBI after generating dataset.csv for each new surveillance data period moving forward
Epi_helper is designed for 5-year MDSS surveillance reports, and has only been tested on Kent County data.
View the Epi_Helper Guidebook
Starting on the main Epi_Helper GitHub page, click the down arrow on the green "<>Code" button, then click "Download ZIP" Create a new file folder in your working directory for Epi_Helper to live in, then extract all files from the newly downloaded Epi_Helper ZIP into it
The repository utilizes code licensed under the terms of the Apache Software License and therefore is licensed under ASL v2 or later.
This source code in this repository is free: you can redistribute it and/or modify it under the terms of the Apache Software License version 2, or (at your option) any later version.
This source code in this repository is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache Software License for more details.
You should have received a copy of the Apache Software License along with this program. If not, see http://www.apache.org/licenses/LICENSE-2.0.html
The source code forked from other open source projects will inherit its license.
This repository contains only non-sensitive, publicly available data and information.
This repository is not a source of government records, but is a copy to increase collaboration and collaborative potential. All government records will be published through the Kent County Health Department website.
- The project expects a
config.jsonfile in the working directory. - This project relies on tkinter and is only tested on Windows.
Special thanks to @H3MMY for their highly specialized assistance with the packaging of Epi_Helper