Change IRI -> shortform convention in MolecularModelJsonRenderer

From cmung...@gmail.com on January 21, 2014 16:08:27

MolecularModelJsonRenderer has:

{{{
// TODO - fix for individuals
private String getId(OWLNamedObject i) {
return graph.getIdentifier(i).replaceAll(":", "_");
}
}}}

This is a bit of an unholy mix of the graph objects IRI -> ID mapping plus an ad-hoc replacement.

The translation should make use of:

http://geneontology.org/contexts/core.jsonld

And where multiple shortenings are possible, an explicit prefix should be preferred over @base.

In practical terms, this means:

• GO class URLs are shortened to normal OBO-style IDs, e.g. GO:nnnnnnn
• All other class URLs are encoded likewise
• The model IRIs and individual IRIs are shortened to a standard <db>:<prefix> type ID, e.g. gomodel:XYZ-nnn-nnn-nnn
  

Original issue: http://code.google.com/p/owltools/issues/detail?id=89

Inspect MolecularModelJsonRenderer and the linked Gene Ontology core.jsonld context to understand the existing graph identifier conversion. Verify the desired shortening rules for GO classes, other classes, models, and individuals, including explicit-prefix precedence; done means the renderer emits those standard IDs instead of ad-hoc colon replacement.