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Java GO-CAM validator

Java code for validating GO-CAMs against the shex schema can be found in the minerva-core project at https://github.com/geneontology/minerva and can be accessed via the Minerva command line utility as seen in https://github.com/geneontology/minerva/blob/master/build-cli.sh

You can run it like this:

  • git clone https://github.com/geneontology/minerva.git
  • cd minerva
  • git checkout dev
  • ./build-cli.sh
  • cd minerva-cli/
  • bin/minerva-cli.sh --validate-go-cams -s ../../shapes/go-cam-shapes.shex -m ../../shapes/go-cam-shapes.shapeMap -f ../../test_ttl/go_cams/should_pass/ -r ./shape_report_shouldpass.txt -expand -travis
  • bin/minerva-cli.sh --validate-go-cams -s ../../shapes/go-cam-shapes.shex -m ../../shapes/go-cam-shapes.shapeMap -f ../../test_ttl/go_cams/should_fail/ -r ./shape_report_shouldfail.txt -expand -travis -shouldfail
  • fix the paths accordingly. If you leave out the -s and -m options, it will download the schema and shapemap files from this repository.

It will:

  • Enrich each GO-CAM with subclass relations linking instances to root classes
  • then validate the resulting RDF models against the go-cam-shapes.shex schema using the go-cam-shapes.shapeMap shape map to look up the appropriate focus nodes.
  • It will show errors if the ttl files in the should_pass directories do not validate or if the ttl files in the should_fail directories do validate.