I've created a preliminary implementation of the ShEx checking part of this, which runs whenever a model is saved. It was a bit too slow using the shex-java library already used in Minerva, so I updated our Jena dependency to a version that comes with its own ShEx functionality (this is what I've been using to test the gpad-shapes schema on the command line). With that checker, performance seems reasonable. For a model on the larger side (http://noctua.geneontology.org/editor/graph/gomodel:MGI_MGI_88276) it adds about 2.5 seconds to the save time, but for a smaller model (http://noctua.geneontology.org/editor/graph/gomodel:YeastPathways_PWY3O-4105) it's much faster, 135 ms.

Next I'll add writing the conformance result into the model and then add this to dev.

I made a PR in #546. I also put the changes on the dev branch (which I reset, so may need to reset in existing checkouts).

@kltm hang on; need to deal with some test problems.

@kltm the dev branch is up to date with these changes. You will need to add something to the minerva command line options:

--gpad-shex gpad-shapes.shex --gpad-shape-map gpad-shapes.shapeMap

These files are currently on a branch in go-shapes:

• https://raw.githubusercontent.com/geneontology/go-shapes/gpad-shapes/shapes/gpad-shapes.shex
• https://raw.githubusercontent.com/geneontology/go-shapes/gpad-shapes/shapes/gpad-shapes.shapeMap

@balhoff Does this include a "surfacing" of the data (coming out in the API responses), or is this just adding the metadata to models on change?

Both—the surfacing seemed to happen without any specific effort on my part.

On noctua-dev, as a manual one-off on dev for gulpfile.js in noctua, I'm adding the last two lines here (after appropriately downloaded):

var minerva_opts_base = [
    'java',
    '-Xmx' + minerva_max_mem + 'G',
    '-cp', _select_minerva(),
    'org.geneontology.minerva.server.StartUpTool',
    '--use-golr-url-logging', // possibly unnecessary in non-lookup cases
    '--gpad-shex', '/tmp/gpad-shapes.shex',
    '--gpad-shape-map', '/tmp/gpad-shapes.shapeMap',

@kltm @tmushayahama I updated the PR and dev branch so that the property comes out as conforms-to-gpad rather than the full property IRI.

From 2024-07-25 workbenches call:

@balhoff
We need this metadata available via the search API, as well, so the SPARQL may need to be adjusted.

@vanaukenk @tmushayahama I've added the conformance value to the search API output.

The latest dev should now be active on noctua-dev.

I've tested this with a small model:

1. added standard annotations in the new UI
2. checked the icon on the Noctua landing page
3. added causal relations between functions; expanding anatomical extensions (i.e. CC part of cell, cell part of tissue) in both the graph editor and the VPE
4. checked the icon on the Noctua landing page

Seems to be working okay.