Examples with Taxon ubic.gemma.model.genome.Taxon used on opensource projects

Example 71 with Taxon

use of ubic.gemma.model.genome.Taxon in project Gemma by PavlidisLab.

the class GeneSetServiceImpl method getUsersGeneGroups.

@Override
@Transactional(readOnly = true)
public Collection<GeneSet> getUsersGeneGroups(boolean privateOnly, Long taxonId, boolean sharedPublicOnly) {
    Taxon tax = null;
    if (taxonId != null) {
        tax = taxonService.load(taxonId);
        if (tax == null) {
            throw new IllegalArgumentException("No such taxon with id=" + taxonId);
        }
    }
    Collection<GeneSet> geneSets;
    if (privateOnly) {
        // gets all groups user can see (includes: owned by user, shared with user & public)
        geneSets = this.loadAll(tax);
        // this filtering is to filter out public sets
        try {
            if (!geneSets.isEmpty()) {
                geneSets.retainAll(securityService.choosePrivate(geneSets));
            }
        } catch (AccessDeniedException e) {
        // okay, they just aren't allowed to see those.
        }
    } else if (sharedPublicOnly) {
        // gets all groups shared with the user and all groups owned by the user, except public ones
        geneSets = this.loadMySharedGeneSets(tax);
    } else {
        geneSets = this.loadAll(tax);
    }
    return geneSets;
}

Example 72 with Taxon

use of ubic.gemma.model.genome.Taxon in project Gemma by PavlidisLab.

the class GeneSetServiceImpl method getTaxon.

@Override
@Transactional(readOnly = true)
public Taxon getTaxon(GeneSet geneSet) {
    if (geneSet == null)
        return null;
    Taxon tmpTax;
    tmpTax = geneSetDao.getTaxon(geneSet.getId());
    // check top-level parent
    while (tmpTax != null && tmpTax.getParentTaxon() != null) {
        tmpTax = tmpTax.getParentTaxon();
    }
    return tmpTax;
}

Example 73 with Taxon

use of ubic.gemma.model.genome.Taxon in project Gemma by PavlidisLab.

the class DataUpdater method addAffyExonArrayData.

/**
 * Use when we want to avoid downloading the CEL files etc. For example if GEO doesn't have them and we ran
 * apt-probeset-summarize ourselves. Must be single-platform
 *
 * @param ee                  ee
 * @param pathToAptOutputFile file
 */
public void addAffyExonArrayData(ExpressionExperiment ee, String pathToAptOutputFile) throws IOException {
    Collection<ArrayDesign> ads = experimentService.getArrayDesignsUsed(ee);
    if (ads.size() > 1) {
        throw new IllegalArgumentException("Can't handle experiments with more than one platform when passing APT output file");
    }
    ArrayDesign ad = ads.iterator().next();
    ad = arrayDesignService.thaw(ad);
    ee = experimentService.thawLite(ee);
    Taxon primaryTaxon = ad.getPrimaryTaxon();
    ArrayDesign targetPlatform = this.prepareTargetPlatformForExonArrays(primaryTaxon);
    AffyPowerToolsProbesetSummarize apt = new AffyPowerToolsProbesetSummarize();
    Collection<RawExpressionDataVector> vectors = apt.processData(ee, pathToAptOutputFile, targetPlatform);
    if (vectors.isEmpty()) {
        throw new IllegalStateException("No vectors were returned for " + ee);
    }
    experimentService.replaceRawVectors(ee, vectors);
    if (!targetPlatform.equals(ad)) {
        AuditEventType eventType = ExpressionExperimentPlatformSwitchEvent.Factory.newInstance();
        auditTrailService.addUpdateEvent(ee, eventType, "Switched in course of updating vectors using AffyPowerTools (from " + ad.getShortName() + " to " + targetPlatform.getShortName() + ")");
    }
    this.audit(ee, "Data vector input from APT output file " + pathToAptOutputFile + " on " + targetPlatform, true);
    this.postprocess(ee);
}

Example 74 with Taxon

use of ubic.gemma.model.genome.Taxon in project Gemma by PavlidisLab.

the class DataUpdater method addAffyExonArrayData.

/**
 * Replaces any existing "preferred" data. Must be a single-platform study
 *
 * @param ee ee
 * @param ad ad
 */
// Possible external use
@SuppressWarnings({ "unused", "WeakerAccess" })
public void addAffyExonArrayData(ExpressionExperiment ee, ArrayDesign ad) {
    RawDataFetcher f = new RawDataFetcher();
    Collection<LocalFile> files = f.fetch(ee.getAccession().getAccession());
    if (files.isEmpty()) {
        throw new RuntimeException("Data was apparently not available");
    }
    ad = arrayDesignService.thaw(ad);
    ee = experimentService.thawLite(ee);
    Taxon primaryTaxon = ad.getPrimaryTaxon();
    ArrayDesign targetPlatform = this.prepareTargetPlatformForExonArrays(primaryTaxon);
    assert !targetPlatform.getCompositeSequences().isEmpty();
    AffyPowerToolsProbesetSummarize apt = new AffyPowerToolsProbesetSummarize();
    Collection<RawExpressionDataVector> vectors = apt.processExonArrayData(ee, targetPlatform, files);
    if (vectors.isEmpty()) {
        throw new IllegalStateException("No vectors were returned for " + ee);
    }
    ee = experimentService.replaceRawVectors(ee, vectors);
    if (!targetPlatform.equals(ad)) {
        AuditEventType eventType = ExpressionExperimentPlatformSwitchEvent.Factory.newInstance();
        auditTrailService.addUpdateEvent(ee, eventType, "Switched in course of updating vectors using AffyPowerTools (from " + ad.getShortName() + " to " + targetPlatform.getShortName() + ")");
    }
    this.audit(ee, "Data vector computation from CEL files using AffyPowerTools for " + targetPlatform, true);
    this.postprocess(ee);
}

Example 75 with Taxon

use of ubic.gemma.model.genome.Taxon 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;
}