Dev #326
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Dev #326
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Can run from the minerva command line as it sits. Most likely not useful code once we are done here. Could run it off a branch or merge it in and consider removing it later. or just leave it in.. not harmful. example from minerva-cli --update-gene-product-types -i /Users/bgood/Documents/GitHub/noctua-models/models/ -o /Users/bgood/test/typed_master/ -n /Users/bgood/gocam_ontology/neo_full_nov20_2019.owl -c /Users/bgood/gocam_ontology/catalog-no-import.xml
rather than always downloading from the repo.
Types added to gene nodes will now work for the reasoner and validation but will not be saved in the models. Note that this increases the overall dependency on the presence of GOLR as this is where the types come from.
…asses from classes to expand with golr
travis_mode is used only for go_shapes to fail when something is wrong. This change allows the shex validation to run when the OWL validation succeeds - and when we are expecting a failure. if we want to separate owl and shex validation and use this kind of set up we would want to introduce another yet another parameter to indicate travis-owl travis-shex travis-both ... currently equates to travis-shex
This will eliminate the addition and saving of GP types while still using them during OWL inference and shex validation. (they are gathered dynamically from golr, added to temporary models, and then discarded).
…pes-for-problem-nodes adding information on the shapes that do match troublesome nodes.
add id to order by for #235
fix ordering for model search
…h-response fix search result for users and groups
currently skipping over all nice error handling...
This is a sparql-based version of closing the shape.
In JSON response, will look the same as other shex violations except will show the intended range shapes for the misused property as owl:Nothing like this:
"intended-range-shapes": [
"owl:Nothing"
]
Performance go shapes199
addressing shape inheritance issue
…re-exact not exactly exact match.. but this should work better so lets try it.
think this should fix issue #311
…s-search-taxa changing routes for search service
…location change ontojournal location As requested elsewhere.
fixes problem detected in #313 resulting from lack of inference step applied to go-lego including neo. That found that PR_000000001 was equivalent to CHEBI_36080 . All reference in minerva code now use the chebi uri.
changing all root protein to chebi reference
Somehow.. I think the re-use of the go-cam's IRI as the IRI for the schema ontology confused the system. Following a GPAD export, the go-cam model had nothing in it except for all of the object property assertions from the original imported go-lego ontology. Taking that out stabilized my system locally.
seems jdk.internal.org.jline.utils exists on my java but not on travis. Yay!
#316 (comment) also removing unused method addTaxonToDatabaseWithOWL (which was astonishingly slow compared to the RDF version of the same method that replaced it..)
have tbox in manager when loading model from blazegraph
This ought to go into that config file and not get spread all over.. Someday. Regarding: #316 (comment)
removing /tmp/blazegraph.jnl references
…eo-setup minor update - now assumes pre-merged tbox ontology
…n-report-318 Add title to shex validation report 318
pretty dumb. should work now. (also sneaking in an option to report some reasoning results on the models tested. add --reasoner_report to see).
…n-report-318 fixing title printing to file..
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Catch |
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People have been testing for a while, ready to do. |
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readying master branch for noctua upgrade. Encapsulates many changes.