Examples with SearchIndex ubic.basecode.ontology.search.SearchIndex used on opensource projects

Example 1 with SearchIndex

use of ubic.basecode.ontology.search.SearchIndex in project Gemma by PavlidisLab.

the class GeneOntologyServiceImpl method findTerm.

@Override
public Collection<OntologyTerm> findTerm(String queryString) {
    if (!this.isReady())
        return new HashSet<>();
    if (GeneOntologyServiceImpl.log.isDebugEnabled())
        GeneOntologyServiceImpl.log.debug("Searching Gene Ontology for '" + queryString + "'");
    // make sure we are all-inclusive
    queryString = queryString.trim();
    queryString = queryString.replaceAll("\\s+", " AND ");
    StopWatch timer = new StopWatch();
    timer.start();
    Collection<OntologyResource> rawMatches = new HashSet<>();
    for (SearchIndex index : this.indices) {
        rawMatches.addAll(OntologySearch.matchIndividuals(model, index, queryString));
    }
    if (timer.getTime() > 100) {
        GeneOntologyServiceImpl.log.info("Find " + rawMatches.size() + " raw go terms from " + queryString + ": " + timer.getTime() + " ms");
    }
    timer.reset();
    timer.start();
    /*
         * Required to make sure the descriptions are filled in.
         */
    Collection<OntologyTerm> matches = new HashSet<>();
    for (OntologyResource r : rawMatches) {
        if (StringUtils.isBlank(r.getUri()))
            continue;
        OntologyTerm termForURI = GeneOntologyServiceImpl.getTermForURI(r.getUri());
        if (termForURI == null) {
            GeneOntologyServiceImpl.log.warn("No term for : " + r);
            continue;
        }
        matches.add(termForURI);
    }
    if (timer.getTime() > 100) {
        GeneOntologyServiceImpl.log.info("Convert " + rawMatches.size() + " raw go terms to terms: " + timer.getTime() + " ms");
    }
    return matches;
}