Add ability to tailor report messages from SPARQL checks

[dosumis]

It's hard to make the name of a SPARQL check clear enough to communicate the nature of an error and we shouldn't expect all editors to be able understand SPARQL. For this reason, it would be good to have a way to specify some error text to return when the SPARQL. This could work via a simple TSV table of SPARQL queries and error messages. Test fail in Make could echo the warning & write it to the report log.

[balhoff]

You can do this directly in the SPARQL query with a little more effort when writing the query. I experimented with this in one query for GO, but haven't gone in to improve any of the others yet: https://github.com/geneontology/go-ontology/blob/8b673eb97a9c82a9ad0d24a0f02a7d8ea6717d46/src/sparql/duplicate-synonym-violation.sparql#L69

[matentzn]

@balhoff How would we make that work in a ROBOT report setting? Ideally, all our checks should move to ROBOT report, even the custom ones in ODK, and they require the entity, property, value variables to be bound to...

I still prefer the documentation based approach. We should be able to create PURLs for all custom ODK checks, and create a way to looking them up with a click on them.

What do you think? I mean I definitely do not want to block more reasonable approaches - whatever is best for the curators..

[balhoff]

@matentzn I hadn't thought about robot report. We use those queries with robot verify.

[cmungall]

I like this

A pattern I quite like is CONSTRUCT or SELECTing into a defined validation data model, e.g. the SHACL one

On Fri, Jan 21, 2022 at 9:49 AM Jim Balhoff @.***> wrote:

You can do this directly in the SPARQL query with a little more effort when writing the query. I experimented with this in one query for GO, but haven't gone in to improve any of the others yet: https://github.com/geneontology/go-ontology/blob/8b673eb97a9c82a9ad0d24a0f02a7d8ea6717d46/src/sparql/duplicate-synonym-violation.sparql#L69

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[matentzn]

@balhoff do you have any further thought on this? Do you see robot verify to live side-by-side rebot report indefinitely? I was hoping to be able to build custom profiles I could share around, but the advantage of that over verify are minor.. If you had the choice, would you have all ROBOT verify queries spit out human readable error messages and ditch the idea of mapping it to ROBOT report? Or perhaps, use the ?value column of ROBOT report for a detailed message?