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Pull Request description

feat: Add semantic validation with OBO parser

  • Implement OboParser for OBO file parsing
  • Add SemanticValidator for CV parameters and metrics
  • Support term definitions and relationship validation

Which issue this PR aims to resolve or fix?

Solve #10

How to test these changes

  • Ensure you have OBO files for testing
  • Run the SemanticValidator on provided OBO files
  • Verify that CV parameters and metrics are correctly validated
  • Check term definitions and relationship validation

Pull Request checklists

This PR is a:

  • bug-fix
  • new feature
  • maintenance

About this PR:

  • it includes tests.
  • the tests are executed on CI.
  • the tests generate log file(s) (path).
  • pre-commit hooks were executed locally.
  • this PR requires a project documentation update.

Author's checklist:

  • I have reviewed the changes and it contains no misspelling.
  • The code is well commented, especially in the parts that contain more
    complexity.
  • New and old tests passed locally.

Additional information

Reviewer's checklist

Copy and paste this template for your review's note:

## Reviewer's Checklist

- [ ] I managed to reproduce the problem locally from the `main` branch
- [ ] I managed to test the new changes locally
- [ ] I confirm that the issues mentioned were fixed/resolved.

@nilshoffmann nilshoffmann self-requested a review March 28, 2025 15:12
@nilshoffmann nilshoffmann self-assigned this Mar 28, 2025
@nilshoffmann nilshoffmann linked an issue Mar 28, 2025 that may be closed by this pull request
@nilshoffmann
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nilshoffmann commented Mar 28, 2025

@SanjayUG Thanks for the PR. I have pushed an update to the develop branch to fix the failing unit tests and have updated the CI workflow to automatically run builds & tests on PRs. So please rebase your fork / PR against the upstream develop branch and push again to trigger the CI build.

After that, you could move this effort forward and try to implement a OboParserTest and SemanticValidatorTest file below org.lifstools.jmzqc.semantic to implement UnitTests verifying the intended functionality of the OboParser and SemanticValidator classes.
In the next step, we would be looking to integrate the SemanticValidator class with the Converter class to combine JSON-schema-based validation and the semantic validation.

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Add semantic validation

2 participants