Examples with SearchResultDisplayObject ubic.gemma.core.search.SearchResultDisplayObject used on opensource projects

Example 6 with SearchResultDisplayObject

use of ubic.gemma.core.search.SearchResultDisplayObject in project Gemma by PavlidisLab.

the class GeneSearchServiceImpl method addEntryForAllResults.

/**
 * Get a list of SearchResultDisplayObjects that summarise all the results found (one per taxon), so at front end
 * user can "select all"
 *
 * @param query          query
 * @param genes          genes
 * @param geneSets       gene sets
 * @param phenotypeSrDos phenotype display objects
 * @param srDos          display objects
 * @return list of search result display objects
 */
private List<SearchResultDisplayObject> addEntryForAllResults(String query, Collection<SearchResultDisplayObject> genes, Collection<SearchResultDisplayObject> geneSets, List<SearchResultDisplayObject> srDos, List<SearchResultDisplayObject> phenotypeSrDos) {
    List<SearchResultDisplayObject> summaryResultEntries = new ArrayList<>();
    // if >1 result, add a group whose members are all genes returned from search
    if ((genes.size() + geneSets.size() + srDos.size()) > 1) {
        Map<Long, Set<Long>> geneIdsByTaxonId = new HashMap<>();
        // add every individual gene to the set
        for (SearchResultDisplayObject srDo : genes) {
            if (!geneIdsByTaxonId.containsKey(srDo.getTaxonId())) {
                geneIdsByTaxonId.put(srDo.getTaxonId(), new HashSet<Long>());
            }
            Long id = (srDo.getResultValueObject() instanceof GeneValueObject) ? ((GeneValueObject) srDo.getResultValueObject()).getId() : new Long(-1);
            if (id != -1) {
                geneIdsByTaxonId.get(srDo.getTaxonId()).add(id);
            }
        }
        // if there's a group, get the number of members
        this.updateGeneIdsByTaxonId(geneSets, geneIdsByTaxonId);
        this.updateGeneIdsByTaxonId(srDos, geneIdsByTaxonId);
        this.updateGeneIdsByTaxonId(phenotypeSrDos, geneIdsByTaxonId);
        // make an entry for each taxon
        Long taxonId;
        Taxon taxon;
        for (Map.Entry<Long, Set<Long>> entry : geneIdsByTaxonId.entrySet()) {
            taxonId = entry.getKey();
            assert taxonId != null;
            taxon = taxonService.load(taxonId);
            // don't make groups for 1 gene
            if (taxon != null && entry.getValue().size() > 1) {
                FreeTextGeneResultsValueObject byTaxFtVo = new FreeTextGeneResultsValueObject("All " + taxon.getCommonName() + " results for '" + query + "'", "All " + taxon.getCommonName() + " genes found for your query", taxon.getId(), taxon.getCommonName(), entry.getValue(), query);
                summaryResultEntries.add(new SearchResultDisplayObject(byTaxFtVo));
            }
        }
    }
    return summaryResultEntries;
}

Example 7 with SearchResultDisplayObject

use of ubic.gemma.core.search.SearchResultDisplayObject in project Gemma by PavlidisLab.

the class GeneSearchServiceImpl method getGOGroupResults.

/**
 * updates goSets & srDos with GO results
 *
 * @param query query
 * @param taxon taxon
 * @return list of search result display objects
 */
private List<SearchResultDisplayObject> getGOGroupResults(String query, Taxon taxon) {
    StopWatch timer = new StopWatch();
    timer.start();
    List<SearchResultDisplayObject> srDos = new ArrayList<>();
    if (taxon != null) {
        if (query.toUpperCase().startsWith("GO")) {
            GeneSearchServiceImpl.log.debug("Getting results from geneSetSearch.findByGoId for GO prefixed query: " + query);
            GeneSet goSet = geneSetSearch.findByGoId(query, taxon);
            if (goSet != null && goSet.getMembers() != null && goSet.getMembers().size() > 0) {
                SearchResultDisplayObject sdo = this.makeGoGroupSearchResult(goSet, query, query, taxon);
                srDos.add(sdo);
            }
        } else {
            GeneSearchServiceImpl.log.debug("Getting results from geneSetSearch.findByGoTermName for " + query);
            for (GeneSet geneSet : geneSetSearch.findByGoTermName(query, taxon, GeneSearchServiceImpl.MAX_GO_TERMS_TO_PROCESS, GeneSearchServiceImpl.MAX_GO_GROUP_SIZE)) {
                // (should probably do this check elsewhere in case it speeds things up)
                if (geneSet.getMembers() != null && geneSet.getMembers().size() != 0) {
                    SearchResultDisplayObject sdo = this.makeGoGroupSearchResult(geneSet, null, query, taxon);
                    srDos.add(sdo);
                }
            }
        }
    } else {
        // taxon is null, search without taxon as a constraint and bag up the results based on taxon
        GeneSearchServiceImpl.log.debug("getting results from geneSetSearch.findByGoId for GO prefixed query: " + query + " with null taxon");
        if (query.toUpperCase().startsWith("GO")) {
            GeneSet goSet = geneSetSearch.findByGoId(query, null);
            if (goSet == null) {
                return srDos;
            }
            // this gene set has genes from all the different taxons, organize them
            Collection<GeneSet> taxonSpecificSets = this.organizeMultiTaxaSetIntoTaxonSpecificSets(goSet);
            for (GeneSet taxonGeneSet : taxonSpecificSets) {
                if (taxonGeneSet != null && taxonGeneSet.getMembers() != null && taxonGeneSet.getMembers().size() > 0) {
                    SearchResultDisplayObject sdo = this.makeGoGroupSearchResult(taxonGeneSet, query, query, taxonGeneSet.getMembers().iterator().next().getGene().getTaxon());
                    srDos.add(sdo);
                }
            }
        } else {
            GeneSearchServiceImpl.log.debug("getting results from geneSetSearch.findByGoTermName for " + query + " with null taxon");
            for (GeneSet geneSet : geneSetSearch.findByGoTermName(query, null, GeneSearchServiceImpl.MAX_GO_TERMS_TO_PROCESS, GeneSearchServiceImpl.MAX_GO_GROUP_SIZE)) {
                // geneSet will have genes from different taxons inside, organize them.
                Collection<GeneSet> taxonSpecificSets = this.organizeMultiTaxaSetIntoTaxonSpecificSets(geneSet);
                for (GeneSet taxonGeneSet : taxonSpecificSets) {
                    if (geneSet.getMembers() != null && taxonGeneSet.getMembers().size() != 0) {
                        SearchResultDisplayObject sdo = this.makeGoGroupSearchResult(taxonGeneSet, null, query, taxonGeneSet.getMembers().iterator().next().getGene().getTaxon());
                        srDos.add(sdo);
                    }
                }
            }
        }
    }
    Collections.sort(srDos);
    if (timer.getTime() > 500)
        GeneSearchServiceImpl.log.info("GO search: " + srDos.size() + " results in " + timer.getTime() + "ms");
    return srDos;
}

Example 8 with SearchResultDisplayObject

use of ubic.gemma.core.search.SearchResultDisplayObject in project Gemma by PavlidisLab.

the class GeneSearchServiceImpl method getPhenotypeAssociationSearchResults.

/**
 * updates goSets & srDos with GO results
 *
 * @param query query
 * @param taxon taxon
 * @return list of search result display objects
 */
private List<SearchResultDisplayObject> getPhenotypeAssociationSearchResults(String query, Taxon taxon) {
    List<SearchResultDisplayObject> phenotypeSrDos = new ArrayList<>();
    // if taxon==null then it grabs results for all taxons
    Collection<GeneSetValueObject> geneSets = geneSetSearch.findByPhenotypeName(query, taxon);
    for (GeneSetValueObject geneSet : geneSets) {
        // (should probably do this check elsewhere in case it speeds things up)
        if (geneSet.getGeneIds() != null && geneSet.getGeneIds().size() != 0) {
            SearchResultDisplayObject sdo = this.makePhenotypeAssociationGroupSearchResult(geneSet, query, taxon);
            phenotypeSrDos.add(sdo);
        // phenotypeSets.add( geneSet );
        }
    }
    Collections.sort(phenotypeSrDos);
    return phenotypeSrDos;
}

Example 9 with SearchResultDisplayObject

use of ubic.gemma.core.search.SearchResultDisplayObject in project Gemma by PavlidisLab.

the class GeneSearchServiceImpl method setUserOwnedForGeneSets.

private void setUserOwnedForGeneSets(Collection<SearchResultDisplayObject> geneSets, Map<Long, Boolean> isSetOwnedByUser) {
    if (SecurityUtil.isUserLoggedIn()) {
        for (SearchResultDisplayObject srDo : geneSets) {
            Long id = (srDo.getResultValueObject() instanceof DatabaseBackedGeneSetValueObject) ? ((GeneSetValueObject) srDo.getResultValueObject()).getId() : new Long(-1);
            srDo.setUserOwned(isSetOwnedByUser.get(id));
        }
    }
}

Example 10 with SearchResultDisplayObject

use of ubic.gemma.core.search.SearchResultDisplayObject in project Gemma by PavlidisLab.

the class ExpressionExperimentSearchServiceImpl method getAllTaxonExperimentGroup.

@Override
public List<SearchResultDisplayObject> getAllTaxonExperimentGroup(Long taxonId) {
    List<SearchResultDisplayObject> setResults = new LinkedList<>();
    Taxon taxon = taxonService.load(taxonId);
    Collection<ExpressionExperimentSet> sets = expressionExperimentSetService.findByName("Master set for " + taxon.getCommonName().toLowerCase());
    SearchResultDisplayObject newSRDO;
    for (ExpressionExperimentSet set : sets) {
        expressionExperimentSetService.thaw(set);
        if (set.getTaxon().getId().equals(taxonId)) {
            ExpressionExperimentSetValueObject eevo = expressionExperimentSetService.loadValueObject(set);
            newSRDO = new SearchResultDisplayObject(eevo);
            newSRDO.setUserOwned(securityService.isPrivate(set));
            ((ExpressionExperimentSetValueObject) newSRDO.getResultValueObject()).setIsPublic(securityService.isPublic(set));
            setResults.add(newSRDO);
        }
    }
    Collections.sort(setResults);
    return setResults;
}