tmfev/ths-tools repository overview

⁠THS-Tools

⁠Note - Obsolete Release

This software product has no longer been maintained in the TMF Docker Hub since 2020. The latest versions in the form of docker-compose are continuously made available at ths-greifswald.de⁠.

For questions and suggestions, please contact us⁠.

⁠About

The ths-tools docker image combines the tools E-PIX, gPAS and gICS. "THS" is the German abbreviaton for a Trusted Third Party (TTP). Read our publication (link below) for details.

⁠Available Images

tmfev/ths-tools:2020-02-20

tmfev/ths-tools:latest

⁠Image Structure

The ths-tools docker image bases on the mosaicgreifswald/wildfly image (latest), which was extended with a mysql database and the necessary deployments for the three tools. After successful start of the container, the database is prepared and initialised. Afterwards the wildfly starts and publishes the EAR- and WAR-files.

For more flexibility and ease of use, it is possible to access the MySQL Database, to mount a folder of the host-system as database volume

⁠Installation

docker run -p 8080:8080 tmfev/ths-tools:latest

⁠Using the Web-Interface

• after the container successfully started, open your web-browser and visit the specific tool page

http://your-ip:8080/gics-web

http://your-ip:8080/gpas-web

http://your-ip:8080/epix-web

⁠Accessing the gICS MySQL Database

• In order to access the database the port 3306 has to be published.

• Change the run command to docker run -p 8080:8080 -p 3306:3306 tmfev/ths-tools:latest

• Database credentials for gPAS: user=gpas_user, password=gpas_password

• Database credentials for E-PIX: user=epix_user, password=epix_password

• Database credentials for gICS: user=gics_user, password=gics_password

⁠Custom database initialisation

• Use a volume to initialise your gics database with demo data or domain configurations. Simply put your sql-files into a separate folder within your host-system and provide the respective volume as follows

docker run -p 8080:8080 -v /your/path/to/sqls:/entrypoint-mysql-initfiles tmfev/ths-tools:latest

⁠Docker-External data storage

• Use a volume to store the database contents outside of docker and within your host file system

docker run -p 8080:8080 -v /your/absolute/path:/entrypoint-mysql-data tmfev/ths-tools:latest

⁠More Information

Concept and implementation:

• Lars Geidel (Backend)
• Arne Blumentritt (Frontend)
• Ronny Schuldt (Docker)

Please cite our publications:

• MOSAIC--A Modular Approach to Data Management in Epidemiological Studies. (http://dx.doi.org/10.3414/ME14-01-0133⁠)
• A workflow-driven approach to integrate generic software modules in a Trusted Third Party. (http://dx.doi.org/10.1186/s12967-015-0545-6⁠)
• MAGIC: once upon a time in consent management—a FHIR® tale (https://doi.org/10.1186/s12967-018-1631-3⁠)
• Assessment of scalability and performance of the record linkage tool E-PIX® in managing multi-million patients in research projects at a large university hospital in Germany (https://doi.org/10.1186/s12967-020-02257-4⁠)

For more info visit

• https://ths-greifswald.de⁠ or check out our live demos from
• https://demo.ths-greifswald.de⁠

⁠License

This Software was developed by the University Medicine Greifswald. It it licensed under AGPLv3 and initially provided by the DFG-funded MOSAIC-Project (grant number HO 1937/2-1). Selected functionalities of gICS were developed as part of the MAGIC Project (funded by the DFG HO 1937/5-1).