ASAP CRN Cloud Platform data QC app

An app that allows you to QC your data

Table of Contents

1. About the app
   • Built With
2. Getting Started
   • Prerequisites
   • Installation
3. Usage
4. Contact
5. Acknowledgments

About the app

Welcome to the ASAP CRN metadata QC app. This is an application intended to make easier the burden of harmonizing the data to ASAP CRN standards.

In the future this may also assign ASAP CRN IDs.

The intended workflow is as follow:

• upload csvs to to the app ( clinical tab)

(back to top)

Built With

Here I summarise the main software we have used to build the app

• 

• 

• 

(back to top)

Getting Started

Try it out deployed via [streamlit] (https://asap-meta-qc.streamlit.app/) Here, I summarise some points to efficiently use the app.

• To perform clinical data QC and then visualise, please make sure you QC and upload the sample manifest for your samples
• If your are QC ing several sample manifests at a time, please refresh the app between sample manifests. The app makes use of something called streamlit session state to propagate data across apps, you need to release the cache between sample manifests first.
• You can only visualise your data if both the sample manifest and the clinical data have been QCed. Otherwise an error message will pop up

Prerequisites

• Docker installed
• Python3.9 or higher

Installation

If you wanted to run this app locally and play with it, it should be ass simple as:

1. Clone the github repository

git clone git@github.com:ergonyc/asap_sc_collect.git 

2. Make sure you have access to some paths hard coded within the app not added on the github remote

3. Build the docker container that contains the app

docker build -t <docker-container-name> .

4. Run the docker container on a port

docker run -d -p 8080:8080 <docker-container-name>

5. Alternatively, you can also build virtual environment, then run the streamlit app locally

streamlit run app.py

(back to top)

Usage

Load your metadata tables, and generate a report

(back to top)

Contributing

Contributions are what make the open source community such an amazing place to learn, inspire, and create. Any contributions you make are greatly appreciated.

If you have a suggestion that would make this better, please fork the repo and create a pull request. Thanks again!

1. Fork the Project
2. Create your Feature Branch (git checkout -b feature/AmazingFeature)
3. Commit your Changes (git commit -m 'Add some AmazingFeature')
4. Push to the Branch (git push origin feature/AmazingFeature)
5. Open a Pull Request

(back to top)

License

Distributed under the MIT License. See LICENSE.txt for more information.

(back to top)

Contact

Also email me on henrie@datatecnica.com

Project Link: [TBD]

(back to top)

Acknowledgments

This would not be possible without help of the Data Tecnica team, specially Alejandro Martinez, and the similar GP2 tool

• DtI
• [ASAP CRN]

(back to top)