Support using this as a library, rather than just as a command line tool

[electricsam]

I have a use case where I need to use the ArgoFormatChecker as part of a larger Java application. The current project does not lend itself well to this for the following reasons:

1. Use of System.exit() outside of the main class / method. This will kill any process using this library.
2. Abundant use of static variables makes this not thread safe
3. The shaded jar is problematic when being used as a dependency
4. Mixed use of log4j and slf4j. Consistent use of slf4j would allow for the use of different logging implementations in the containing application.

I've forked the project and created a branch that addresses these issues while still maintaining the ability of the shaded jar to work as a command line application. The branch is here: https://github.com/CI-CMG/ArgoFormatChecker/tree/file-checker-library

This branch also updates the code that writes the XML file to use JAXB classes generated from a XSD defined XML schema. I currently use this library to parse the output of the ArgoFormatChecker (https://github.com/CI-CMG/argo-file-check-xml/blob/1.0/src/main/resources/edu/colorado/cires/argonaut/xml/FileCheckResults.xsd).

I would be happy to discuss creating a pull request for these changes.

[electricsam]

I also made a change to put the file_checker_spec files in a dedicated jar. That jar is a dependency of file_checker_exec, avoiding the need to explicitly copy the spec files during the build. This made the project a multi-module build and the java build should be performed from the root of the repo.

I'm happy to discuss this change as well.

[YvanOceanops]

Hello @electricsam ,
Thank you very much, it is very interesting. Point 1 and 2 were on my to-do list so it is good if you have done the work! I also think the file_checker_spec in a dedicated jar is a good idea with the build from root of the repo should also ease the gitlab CI/CD workflow.
I have not look into details but the Python Wrapper and the "Argo toolbox API" (https://github.com/amrit-eu/Argo-Toolbox) may be impacted or at least improved with you changes.

Unfortunately, I'm not in charge anymore of the File Checker. So the POC will be @tcarval to discuss all of that.