add action to check conformance with "GPAD ShEx" on each change

[balhoff]

Need to check performance of this on various-sized models.

[balhoff]

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.

[balhoff]

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).

[balhoff]

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

[balhoff]

@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

[kltm]

@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?

[balhoff]

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

[kltm]

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',