Examples with CharacteristicValueObject ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObject used on opensource projects

Example 16 with CharacteristicValueObject

use of ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObject in project Gemma by PavlidisLab.

the class SearchServiceImpl method filterByTaxon.

/**
 * @param excludeWithoutTaxon if true: If the SearchResults have no "getTaxon" method then the results will get
 *                            filtered out Results with no taxon associated will also get removed.
 */
private void filterByTaxon(SearchSettings settings, Collection<SearchResult> results, boolean excludeWithoutTaxon) {
    if (settings.getTaxon() == null) {
        return;
    }
    Collection<SearchResult> toRemove = new HashSet<>();
    Taxon t = settings.getTaxon();
    if (results == null)
        return;
    for (SearchResult sr : results) {
        Object o = sr.getResultObject();
        try {
            Taxon currentTaxon;
            if (o instanceof ExpressionExperiment) {
                ExpressionExperiment ee = (ExpressionExperiment) o;
                currentTaxon = expressionExperimentService.getTaxon(ee);
            } else if (o instanceof ExpressionExperimentSet) {
                ExpressionExperimentSet ees = (ExpressionExperimentSet) o;
                currentTaxon = ees.getTaxon();
            } else if (o instanceof Gene) {
                Gene gene = (Gene) o;
                currentTaxon = gene.getTaxon();
            } else if (o instanceof GeneSet) {
                GeneSet geneSet = (GeneSet) o;
                currentTaxon = geneSetService.getTaxon(geneSet);
            } else if (o instanceof CharacteristicValueObject) {
                CharacteristicValueObject charVO = (CharacteristicValueObject) o;
                currentTaxon = taxonDao.findByCommonName(charVO.getTaxon());
            } else {
                Method m = o.getClass().getMethod("getTaxon");
                currentTaxon = (Taxon) m.invoke(o);
            }
            if (currentTaxon == null || !currentTaxon.getId().equals(t.getId())) {
                if (currentTaxon == null) {
                    // Sanity check for bad data in db (could happen if EE has no samples). Can happen that
                    // searchResults have a vaild getTaxon method
                    // but the method returns null (shouldn't make it this far)
                    SearchServiceImpl.log.debug("Object has getTaxon method but it returns null. Obj is: " + o);
                }
                toRemove.add(sr);
            }
        } catch (SecurityException | IllegalArgumentException | InvocationTargetException | IllegalAccessException e) {
            throw new RuntimeException(e);
        } catch (NoSuchMethodException e) {
            /*
                 * In case of a programming error where the results don't have a taxon at all, we assume we should
                 * filter them out but issue a warning.
                 */
            if (excludeWithoutTaxon) {
                toRemove.add(sr);
                SearchServiceImpl.log.warn("No getTaxon method for: " + o.getClass() + ".  Filtering from results. Error was: " + e);
            }
        }
    }
    results.removeAll(toRemove);
}

Example 17 with CharacteristicValueObject

use of ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObject in project Gemma by PavlidisLab.

the class GeneController method loadGeneDetails.

/**
 * AJAX used for gene page
 */
public GeneValueObject loadGeneDetails(Long geneId) {
    // return geneCoreService.loadGeneDetails( geneId );
    GeneValueObject gvo = geneCoreService.loadGeneDetails(geneId);
    Collection<EvidenceValueObject<? extends PhenotypeAssociation>> collEVO = phenotypeAssociationManagerService.findEvidenceByGeneId(geneId, new HashSet<String>(), new EvidenceFilter(gvo.getTaxonId(), false, null));
    Iterator<EvidenceValueObject<? extends PhenotypeAssociation>> iter = collEVO.iterator();
    Collection<CharacteristicValueObject> collFilteredDVO = new HashSet<>();
    while (iter.hasNext()) {
        EvidenceValueObject evo = iter.next();
        if (!evo.isHomologueEvidence())
            collFilteredDVO.addAll(evo.getPhenotypes());
    }
    gvo.setPhenotypes(collFilteredDVO);
    gvo.setNumGoTerms(this.findGOTerms(geneId).size());
    return gvo;
}