Examples with BibliographicReferenceValueObject ubic.gemma.model.common.description.BibliographicReferenceValueObject used on opensource projects

Example 6 with BibliographicReferenceValueObject

use of ubic.gemma.model.common.description.BibliographicReferenceValueObject in project Gemma by PavlidisLab.

the class BibliographicReferenceServiceImpl method search.

@Override
@Transactional(readOnly = true)
public List<BibliographicReferenceValueObject> search(SearchSettingsValueObject settings) {
    SearchSettings ss = SearchSettingsImpl.bibliographicReferenceSearch(settings.getQuery());
    // noinspection unchecked
    List<BibliographicReference> resultEntities = (List<BibliographicReference>) searchService.search(ss, BibliographicReference.class);
    List<BibliographicReferenceValueObject> results = new ArrayList<>();
    // only return associations with the selected entity types.
    for (BibliographicReference entity : resultEntities) {
        BibliographicReferenceValueObject vo = new BibliographicReferenceValueObject(entity);
        if (settings.getSearchPhenotypes() || settings.getSearchBibrefs()) {
            this.populateBibliographicPhenotypes(vo);
            if (!vo.getBibliographicPhenotypes().isEmpty() || settings.getSearchBibrefs()) {
                results.add(vo);
            }
        }
        if (settings.getSearchExperiments() || settings.getSearchBibrefs()) {
            this.populateRelatedExperiments(entity, vo);
            if (!vo.getExperiments().isEmpty() || settings.getSearchBibrefs()) {
                results.add(vo);
            }
        }
        if (settings.getSearchBibrefs() && !settings.getSearchPhenotypes() && !settings.getSearchExperiments()) {
            results.add(vo);
        }
    }
    return results;
}

Example 7 with BibliographicReferenceValueObject

use of ubic.gemma.model.common.description.BibliographicReferenceValueObject in project Gemma by PavlidisLab.

the class PhenotypeController method findBibliographicReference.

/**
 * Finds bibliographic reference with the given pubmed id.
 *
 * @return bibliographic reference with the given pubmed id
 */
public Collection<BibliographicReferenceValueObject> findBibliographicReference(String pubMedId, Long evidenceId) {
    BibliographicReferenceValueObject valueObject = this.phenotypeAssociationManagerService.findBibliographicReference(pubMedId);
    // Contain at most 1 element.
    ArrayList<BibliographicReferenceValueObject> valueObjects = new ArrayList<>(1);
    if (valueObject != null) {
        valueObjects.add(valueObject);
    }
    return valueObjects;
}

Example 8 with BibliographicReferenceValueObject

use of ubic.gemma.model.common.description.BibliographicReferenceValueObject in project Gemma by PavlidisLab.

the class SearchServiceImpl method expressionExperimentSearch.

/**
 * A general search for expression experiments. This search does both an database search and a compass search.
 * A problem with this is that we cap the number of results that can be returned. This could be a limitation for
 * applications like building data set groups. Thus MAX_CHARACTERISTIC_SEARCH_RESULTS should not be too low.
 *
 * @return {@link Collection}
 */
private Collection<SearchResult> expressionExperimentSearch(final SearchSettings settings) {
    StopWatch watch = this.startTiming();
    SearchServiceImpl.log.info("Starting search for " + settings.getQuery() + " in taxon: " + settings.getTaxon());
    Collection<SearchResult> results = new HashSet<>();
    if (settings.getUseDatabase()) {
        results.addAll(this.databaseExpressionExperimentSearch(settings));
        if (watch.getTime() > 1000)
            SearchServiceImpl.log.info("Expression Experiment database search for '" + settings + "' took " + watch.getTime() + " ms, " + results.size() + " hits.");
        watch.reset();
        watch.start();
    }
    if (settings.getUseIndices() && results.size() < SearchServiceImpl.MAX_CHARACTERISTIC_SEARCH_RESULTS) {
        results.addAll(this.compassExpressionSearch(settings));
        if (watch.getTime() > 1000)
            SearchServiceImpl.log.info("Expression Experiment index search for '" + settings + "' took " + watch.getTime() + " ms, " + results.size() + " hits.");
        watch.reset();
        watch.start();
    }
    if (results.size() < SearchServiceImpl.MAX_CHARACTERISTIC_SEARCH_RESULTS) {
        /*
             * Try a more thorough search. This is slower; calls to ontologySearchAnnotatedObject take a long time
             */
        if (settings.getUseCharacteristics()) {
            results.addAll(this.characteristicExpressionExperimentSearch(settings));
        }
        if (watch.getTime() > 1000)
            SearchServiceImpl.log.info("Expression Experiment ontology search for '" + settings + "' took " + watch.getTime() + " ms, " + results.size() + " hits.");
        watch.reset();
        watch.start();
    }
    /*
         * Find data sets that match the platform
         */
    if (results.size() == 0) {
        Collection<SearchResult> matchingPlatforms = this.arrayDesignSearch(settings, null);
        for (SearchResult adRes : matchingPlatforms) {
            if (adRes.getResultObject() instanceof ArrayDesign) {
                ArrayDesign ad = (ArrayDesign) adRes.getResultObject();
                Collection<ExpressionExperiment> expressionExperiments = this.arrayDesignService.getExpressionExperiments(ad);
                if (expressionExperiments.size() > 0)
                    results.addAll(this.dbHitsToSearchResult(expressionExperiments, null));
            }
        }
        if (watch.getTime() > 1000)
            SearchServiceImpl.log.info("Expression Experiment platform search for '" + settings + "' took " + watch.getTime() + " ms, " + results.size() + " hits.");
        watch.reset();
        watch.start();
    }
    if (results.size() == 0) {
        /*
             * Search for bib refs
             */
        List<BibliographicReferenceValueObject> bibrefs = bibliographicReferenceService.search(settings.getQuery());
        if (!bibrefs.isEmpty()) {
            Collection<BibliographicReference> refs = new HashSet<>();
            Collection<SearchResult> r = this.compassBibliographicReferenceSearch(settings);
            for (SearchResult searchResult : r) {
                refs.add((BibliographicReference) searchResult.getResultObject());
            }
            Map<BibliographicReference, Collection<ExpressionExperiment>> relatedExperiments = this.bibliographicReferenceService.getRelatedExperiments(refs);
            for (Entry<BibliographicReference, Collection<ExpressionExperiment>> e : relatedExperiments.entrySet()) {
                results.addAll(this.dbHitsToSearchResult(e.getValue(), null));
            }
            if (watch.getTime() > 1000)
                SearchServiceImpl.log.info("Expression Experiment publication search for '" + settings + "' took " + watch.getTime() + " ms, " + results.size() + " hits.");
            watch.reset();
            watch.start();
        }
    }
    watch.stop();
    if (watch.getTime() > 1000)
        SearchServiceImpl.log.info("Expression Experiment search for '" + settings + "' took " + watch.getTime() + " ms, " + results.size() + " hits.");
    return results;
}