tranSMART-dataquality

This repository contains the developmental part of Cornelius Knopp's master thesis. This encompasses all the project data needed to build a dataquality-Plugin in tranSMART using the SmartR framework.

Build the plugin

Alternative 1: build .war manually

To use these contents, simply copy the SmartR folder into the SmartR folder of your tranSMART binaries.
Afterwards one has to build the .war-file using Grails.

Alternative 2: use UMG-internal GitLab-CI/CD Pipeline

THIS APPROACH DOES ONLY WORK WITH VALID CREDENTIALS FOR GWDG-GITLAB!

• Step 1: create a personal GitLab branch in each of the following Repositories [1]
  • transmart-data
  • Rmodules
  • transmart-core-db
  • transmartApp
  • SmartR
• Step 2: copy/move the plugin files into the SmartR-Repository [2]
• Step 3: modify .gitlab-ci.yml File
  • replace branch "master" by your personal branch name
• Step 4: start the CI/CD Pipeline (if not triggered automatically)
• Step 5: Start the tranSMART-server by using the tm_umg-Repository from GWDG-GitLab [3]
  • clone tm_umg-Repository
  • switch to your (local) personal branch
  • modify .env according to tm_umg-README --> replace WAR_BRANCH by personal branch name
  • start the server via docker-compose up -d

---

[1] https://gitlab.gwdg.de/medinf/AGITF/transmart
[2] https://gitlab.gwdg.de/medinf/AGITF/transmart/SmartR
[3] https://gitlab.gwdg.de/medinf/AGITF/tm_umg