Examples with FreeTextExpressionExperimentResultsValueObject ubic.gemma.model.expression.experiment.FreeTextExpressionExperimentResultsValueObject used on opensource projects

Example 1 with FreeTextExpressionExperimentResultsValueObject

use of ubic.gemma.model.expression.experiment.FreeTextExpressionExperimentResultsValueObject in project Gemma by PavlidisLab.

the class ExpressionExperimentSearchServiceImpl method searchExperimentsAndExperimentGroups.

@Override
public List<SearchResultDisplayObject> searchExperimentsAndExperimentGroups(String query, Long taxonId) {
    List<SearchResultDisplayObject> displayResults = new LinkedList<>();
    // session-bound sets (not autogen sets until handling of large searches is fixed)
    if (StringUtils.isBlank(query)) {
        return this.searchExperimentsAndExperimentGroupBlankQuery(taxonId);
    }
    Map<Class<?>, List<SearchResult>> results = this.initialSearch(query, taxonId);
    List<SearchResultDisplayObject> experimentSets = this.getExpressionExperimentSetResults(results);
    List<SearchResultDisplayObject> experiments = this.getExpressionExperimentResults(results);
    if (experimentSets.isEmpty() && experiments.isEmpty()) {
        return displayResults;
    }
    /*
         * ALL RESULTS BY TAXON GROUPS
         */
    // if >1 result, add a group whose members are all experiments returned from search
    Map<Long, Set<Long>> eeIdsByTaxonId = new HashMap<>();
    // add every individual experiment to the set, grouped by taxon and also altogether.
    for (SearchResultDisplayObject srdo : experiments) {
        // group by the Parent Taxon, for things like salmonid - see bug 3286
        Long taxId;
        if (srdo.getParentTaxonId() != null) {
            taxId = srdo.getParentTaxonId();
        } else {
            taxId = srdo.getTaxonId();
        }
        if (!eeIdsByTaxonId.containsKey(taxId)) {
            eeIdsByTaxonId.put(taxId, new HashSet<Long>());
        }
        ExpressionExperimentValueObject eevo = (ExpressionExperimentValueObject) srdo.getResultValueObject();
        eeIdsByTaxonId.get(taxId).add(eevo.getId());
    }
    // for each group
    for (SearchResultDisplayObject eesSRO : experimentSets) {
        ExpressionExperimentSetValueObject set = (ExpressionExperimentSetValueObject) eesSRO.getResultValueObject();
        /*
             * This is security filtered.
             */
        Collection<Long> ids = EntityUtils.getIds(expressionExperimentSetService.getExperimentValueObjectsInSet(set.getId()));
        // to account for security filtering.
        set.setSize(ids.size());
        if (!eeIdsByTaxonId.containsKey(set.getTaxonId())) {
            eeIdsByTaxonId.put(set.getTaxonId(), new HashSet<Long>());
        }
        eeIdsByTaxonId.get(set.getTaxonId()).addAll(ids);
    }
    // make an entry for each taxon
    Long taxonId2;
    for (Map.Entry<Long, Set<Long>> entry : eeIdsByTaxonId.entrySet()) {
        taxonId2 = entry.getKey();
        Taxon taxon = taxonService.load(taxonId2);
        if (taxon != null && entry.getValue().size() > 0) {
            FreeTextExpressionExperimentResultsValueObject ftvo = new FreeTextExpressionExperimentResultsValueObject("All " + taxon.getCommonName() + " results for '" + query + "'", "All " + taxon.getCommonName() + " experiments found for your query", taxon.getId(), taxon.getCommonName(), entry.getValue(), query);
            int numWithDifferentialExpressionAnalysis = differentialExpressionAnalysisService.getExperimentsWithAnalysis(entry.getValue()).size();
            assert numWithDifferentialExpressionAnalysis <= entry.getValue().size();
            int numWithCoexpressionAnalysis = coexpressionAnalysisService.getExperimentsWithAnalysis(entry.getValue()).size();
            ftvo.setNumWithCoexpressionAnalysis(numWithCoexpressionAnalysis);
            ftvo.setNumWithDifferentialExpressionAnalysis(numWithDifferentialExpressionAnalysis);
            displayResults.add(new SearchResultDisplayObject(ftvo));
        }
    }
    displayResults.addAll(experimentSets);
    displayResults.addAll(experiments);
    if (displayResults.isEmpty()) {
        ExpressionExperimentSearchServiceImpl.log.info("No results for search: " + query);
    } else {
        ExpressionExperimentSearchServiceImpl.log.info("Results for search: " + query + " size=" + displayResults.size() + " entry0: " + ((SearchResultDisplayObject) (displayResults.toArray())[0]).getName() + " valueObject:" + ((SearchResultDisplayObject) (displayResults.toArray())[0]).getResultValueObject().toString());
    }
    return displayResults;
}