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

Example 1 with ExpressionExperimentSetValueObject

use of ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject 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;
}

Example 2 with ExpressionExperimentSetValueObject

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

the class ExpressionExperimentSetController method updateUserAndSessionGroups.

/**
 * AJAX Updates the session group and user database groups.
 */
public Collection<ExpressionExperimentSetValueObject> updateUserAndSessionGroups(Collection<ExpressionExperimentSetValueObject> vos) {
    Collection<ExpressionExperimentSetValueObject> updatedSets = new HashSet<>();
    Collection<ExpressionExperimentSetValueObject> databaseCollection = new HashSet<>();
    Collection<SessionBoundExpressionExperimentSetValueObject> sessionCollection = new HashSet<>();
    for (ExpressionExperimentSetValueObject experimentSetValueObject : vos) {
        if (experimentSetValueObject instanceof SessionBoundExpressionExperimentSetValueObject) {
            sessionCollection.add((SessionBoundExpressionExperimentSetValueObject) experimentSetValueObject);
        } else {
            databaseCollection.add(experimentSetValueObject);
        }
    }
    sessionCollection = this.updateSessionGroups(sessionCollection);
    databaseCollection = this.update(databaseCollection);
    updatedSets.addAll(sessionCollection);
    updatedSets.addAll(databaseCollection);
    return updatedSets;
}

Example 3 with ExpressionExperimentSetValueObject

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

the class ExpressionExperimentSetController method getExpressionExperimentSetFromRequest.

/**
 * @throws IllegalArgumentException if a matching EE can't be loaded
 */
private ExpressionExperimentSetValueObject getExpressionExperimentSetFromRequest(HttpServletRequest request) {
    ExpressionExperimentSetValueObject set;
    Long id;
    if (request.getParameter("id") != null) {
        try {
            id = Long.parseLong(request.getParameter("id"));
        } catch (NumberFormatException e) {
            throw new IllegalArgumentException("You must provide a valid numerical identifier");
        }
        set = expressionExperimentSetService.loadValueObjectById(id);
        if (set == null) {
            throw new IllegalArgumentException("Unable to access experiment set with id=" + id);
        }
    } else {
        throw new IllegalArgumentException("You must provide an id");
    }
    return set;
}

Example 4 with ExpressionExperimentSetValueObject

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

the class ExpressionExperimentSetController method showExpressionExperimentSet.

@RequestMapping(value = "/showExpressionExperimentSet.html", method = RequestMethod.GET)
public ModelAndView showExpressionExperimentSet(HttpServletRequest request, HttpServletResponse response) {
    ModelAndView mav = new ModelAndView("expressionExperimentSet.detail");
    StopWatch timer = new StopWatch();
    timer.start();
    ExpressionExperimentSetValueObject eesvo = this.getExpressionExperimentSetFromRequest(request);
    mav.addObject("eeSetId", eesvo.getId());
    mav.addObject("eeSetName", eesvo.getName());
    if (timer.getTime() > 200) {
        log.info("Show experiment set was slow: id=" + eesvo.getId() + " " + timer.getTime() + "ms");
    }
    return mav;
}

Example 5 with ExpressionExperimentSetValueObject

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

the class ExpressionExperimentSetDaoImpl method fetchValueObjects.

/**
 * @param ids,      if null fetch all.
 * @param loadEEIds whether the returned value object should have the ExpressionExperimentIds collection populated.
 *                  This might be a useful information, but loading the IDs takes slightly longer, so for larger amount of
 *                  EESets this might want to be avoided.
 * @return EE set VOs
 */
private Collection<ExpressionExperimentSetValueObject> fetchValueObjects(Collection<Long> ids, boolean loadEEIds) {
    Map<Long, ExpressionExperimentSetValueObject> vo = new LinkedHashMap<>();
    Query queryObject = this.getLoadValueObjectsQueryString(ids);
    List<?> list = queryObject.list();
    for (Object object : list) {
        Object[] res = (Object[]) object;
        Long eeId = (Long) res[0];
        assert eeId != null;
        ExpressionExperimentSetValueObject v;
        if (vo.containsKey(eeId)) {
            v = vo.get(eeId);
        } else {
            v = new ExpressionExperimentSetValueObject(eeId);
            vo.put(eeId, v);
        }
        v.setName((String) res[1]);
        v.setDescription((String) res[2]);
        v.setTaxonName((String) res[3]);
        v.setTaxonId((Long) res[4]);
        /*
             * FIXME this is not adequate because these are not security filtered, so the count could be too high for
             * the current user. We can avoid a lot of problems by not putting private data sets in public EE sets.
             */
        v.setSize(((Long) res[5]).intValue());
        // Add experiment ids
        if (loadEEIds) {
            v.setExpressionExperimentIds(this.getExperimentIdsInSet(eeId));
        }
        vo.put(eeId, v);
    }
    Collection<ExpressionExperimentSetValueObject> result = vo.values();
    this.populateAnalysisInformation(result);
    return result;
}