mzTab Validator Webapplication

This project provides a validator implementation for the mzTab 1.0 standard and for the current mzTab-M 2.0 standard for metabolomics.

Using the LIFS Web application

The mzTab validator webapplication is hosted here. For programmatic usage of the validation service, the REST API description is available here.

Building the project from the command-line

In order to build the project and run the unit tests, execute the following command from a terminal:

./mvnw install

Running the Web Application for Development

./mvnw spring-boot:run

Running the Web Application for Validation

The web-application is based on Spring-Boot, Thymeleaf, jQuery, jQuery Datatables and Bootstrap 4. The target folder holds all necessary dependencies and resources as a stand-alone, executable JAR file that can be run as follows (please replace <VERSION> with the correct one)

./mztab-validator-webapp-<VERSION>.jar

This will start the application with a default configuration, running on http port 8083. The application can then be accessed from your web browser at

http://localhost:8083/mztabvalidator

Building the Web Application Docker Image

If you want to run the web application as a docker container, you can build it as follows:

./mvnw -Pdocker install

This will build a Docker container for the webapplication and will make it locally available to be run by docker.

docker image ls
REPOSITORY                    TAG                 IMAGE ID            CREATED             SIZE
isas/mztab-validator-webapp   1.0.8-SNAPSHOT      b87d4683db50        About an hour ago   472MB

Please note that the base image we use is quite large (for details, see web/Dockerfile), but also includes monitoring utilities and automatic scaling and limiting of the internal JVMs memory based on the amount of memory allocated for the container by Docker.

To run the web application as a Docker container, type in the following (replacing <VERSION> with the current project version, i.e. the TAG version displayed by docker image ls):

docker run -it --rm --name mztabvalidator -p 8080:8083 -m 150M isas/mztab-validator-webapp:<VERSION>

References

This project is based on and uses code that was developed for the original jmzTab project:

Qing-Wei Xu et al., Proteomics 2014; Jun;14(11):1328-32. PDF File. PubMed record.

It uses the new reader / writer and validator APIs of the jmztab-m reference implementation