Example usage for org.apache.commons.collections ListUtils removeAll

Introduction

In this page you can find the example usage for org.apache.commons.collections ListUtils removeAll.

Prototype

public static List removeAll(Collection collection, Collection remove) 

Source Link

Document

Removes the elements in remove from collection.

Usage

From source file:org.kuali.rice.krad.devtools.datadictionary.ReloadingDataDictionary.java

public void urlContentChanged(final URL url) {
    LOG.info("reloading dictionary configuration for " + url.toString());
    try {/*from  w ww  .  ja  v a2  s  .  c o  m*/
        InputStream urlStream = url.openStream();
        InputStreamResource resource = new InputStreamResource(urlStream);

        List<String> beforeReloadBeanNames = Arrays.asList(ddBeans.getBeanDefinitionNames());

        int originalValidationMode = xmlReader.getValidationMode();
        xmlReader.setValidationMode(XmlBeanDefinitionReader.VALIDATION_XSD);
        xmlReader.loadBeanDefinitions(resource);
        xmlReader.setValidationMode(originalValidationMode);

        List<String> afterReloadBeanNames = Arrays.asList(ddBeans.getBeanDefinitionNames());

        List<String> addedBeanNames = ListUtils.removeAll(afterReloadBeanNames, beforeReloadBeanNames);
        String namespace = KRADConstants.DEFAULT_NAMESPACE;
        if (urlToNamespaceMapping.containsKey(url.toString())) {
            namespace = urlToNamespaceMapping.get(url.toString());
        }

        ddIndex.addBeanNamesToNamespace(namespace, addedBeanNames);

        performDictionaryPostProcessing(true);
    } catch (Exception e) {
        LOG.info("Exception in dictionary hot deploy: " + e.getMessage(), e);
    }
}

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From source file:ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDaoImpl.java

@Override
public Map<Long, Collection<DifferentialExpressionAnalysisValueObject>> getAnalysesByExperimentIds(
        Collection<Long> expressionExperimentIds, int offset, int limit) {

    /*/*w  ww. j  a  v  a2 s .com*/
     * There are three cases to consider: the ids are experiments; the ids are experiment subsets; the ids are
     * experiments that have subsets.
     */
    Map<Long, Collection<DifferentialExpressionAnalysisValueObject>> r = new HashMap<>();

    Map<Long, Collection<Long>> arrayDesignsUsed = CommonQueries
            .getArrayDesignsUsedEEMap(expressionExperimentIds, this.getSessionFactory().getCurrentSession());

    /*
     * Fetch analyses of experiments or subsets.
     */
    //noinspection unchecked
    Collection<DifferentialExpressionAnalysis> hits = this.getSessionFactory().getCurrentSession().createQuery(
            "select distinct a from DifferentialExpressionAnalysis a join fetch a.experimentAnalyzed e join"
                    + " fetch a.resultSets rs join fetch rs.hitListSizes where e.id in (:eeids)")
            .setParameterList("eeids", expressionExperimentIds).setFirstResult(offset)
            .setMaxResults(limit > 0 ? limit : -1).list();

    /*
     * FIXME the above query yields a warning
     * "firstResult/maxResults specified with collection fetch; applying in memory!"
     */

    Map<Long, Collection<FactorValue>> ee2fv = new HashMap<>();
    List<Object[]> fvs;

    if (!hits.isEmpty()) {
        // factor values for the experiments.
        //noinspection unchecked
        fvs = this.getSessionFactory().getCurrentSession().createQuery("select distinct ee.id, fv from "
                + "ExpressionExperiment"
                + " ee join ee.bioAssays ba join ba.sampleUsed bm join bm.factorValues fv where ee.id in (:ees)")
                .setParameterList("ees", expressionExperimentIds).list();
        this.addFactorValues(ee2fv, fvs);

        // also get factor values for subsets - those not found yet.
        Collection<Long> used = new HashSet<>();
        for (DifferentialExpressionAnalysis a : hits) {
            used.add(a.getExperimentAnalyzed().getId());
        }

        List probableSubSetIds = ListUtils.removeAll(used, ee2fv.keySet());
        if (!probableSubSetIds.isEmpty()) {
            //noinspection unchecked
            fvs = this.getSessionFactory().getCurrentSession().createQuery("select distinct ee.id, fv from "
                    + "ExpressionExperimentSubSet"
                    + " ee join ee.bioAssays ba join ba.sampleUsed bm join bm.factorValues fv where ee.id in (:ees)")
                    .setParameterList("ees", probableSubSetIds).list();
            this.addFactorValues(ee2fv, fvs);
        }

    }

    /*
     * Subsets of those same experiments (there might not be any)
     */
    //noinspection unchecked
    List<DifferentialExpressionAnalysis> analysesOfSubsets = this.getSessionFactory().getCurrentSession()
            .createQuery("select distinct a from " + "ExpressionExperimentSubSet"
                    + " ee, DifferentialExpressionAnalysis a" + " join ee.sourceExperiment see "
                    + " join fetch a.experimentAnalyzed eeanalyzed where see.id in (:eeids) and ee=eeanalyzed")
            .setParameterList("eeids", expressionExperimentIds).list();

    if (!analysesOfSubsets.isEmpty()) {
        hits.addAll(analysesOfSubsets);

        Collection<Long> experimentSubsetIds = new HashSet<>();
        for (DifferentialExpressionAnalysis a : analysesOfSubsets) {
            ExpressionExperimentSubSet subset = (ExpressionExperimentSubSet) a.getExperimentAnalyzed();
            experimentSubsetIds.add(subset.getId());
        }

        // factor value information for the subset. The key output is the ID of the subset, not of the source
        // experiment.
        //noinspection unchecked
        fvs = this.getSessionFactory().getCurrentSession().createQuery("select distinct ee.id, fv from "
                + "ExpressionExperimentSubSet"
                + " ee join ee.bioAssays ba join ba.sampleUsed bm join bm.factorValues fv where ee.id in (:ees)")
                .setParameterList("ees", experimentSubsetIds).list();
        this.addFactorValues(ee2fv, fvs);
    }

    // postprocesss...
    if (hits.isEmpty()) {
        return r;
    }
    Collection<DifferentialExpressionAnalysisValueObject> summaries = this.convertToValueObjects(hits,
            arrayDesignsUsed, ee2fv);

    for (DifferentialExpressionAnalysisValueObject an : summaries) {

        Long bioAssaySetId;
        if (an.getSourceExperiment() != null) {
            bioAssaySetId = an.getSourceExperiment();
        } else {
            bioAssaySetId = an.getBioAssaySetId();
        }
        if (!r.containsKey(bioAssaySetId)) {
            r.put(bioAssaySetId, new ArrayList<DifferentialExpressionAnalysisValueObject>());
        }
        r.get(bioAssaySetId).add(an);
    }

    return r;

}

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From source file:ubic.gemma.persistence.util.CommonQueries.java

/**
 * @param ees     experiments//from w  w w .j  a va  2 s . c  o  m
 * @param session session
 * @return map of experiment to collection of array design ids. If any of the ids given are for subsets, then the
 * key in the return value will be for the subset, not the source experiment (so it is consistent with the
 * input)
 */
public static Map<Long, Collection<Long>> getArrayDesignsUsedEEMap(Collection<Long> ees, Session session) {
    Map<Long, Collection<Long>> ee2ads = new HashMap<>();

    if (ees == null || ees.isEmpty())
        return ee2ads;

    final String eeAdQuery = "select distinct ee.id,ad.id from ExpressionExperiment as ee inner join "
            + "ee.bioAssays b inner join b.arrayDesignUsed ad where ee.id in (:ees)";

    org.hibernate.Query queryObject = session.createQuery(eeAdQuery);
    queryObject.setParameterList("ees", ees);
    queryObject.setReadOnly(true);
    queryObject.setFlushMode(FlushMode.MANUAL);

    List<?> qr = queryObject.list();
    ee2ads = CommonQueries.addAllAds(ee2ads, qr);

    if (ee2ads.size() < ees.size()) {
        // ids might be invalid, but also might be subsets. Note that the output key is for the subset, not the
        // source.
        String subsetQuery = "select distinct ees.id,ad.id from ExpressionExperimentSubSet as ees join ees.sourceExperiment ee "
                + " join ee.bioAssays b join b.arrayDesignUsed ad where ees.id in (:ees)";
        //noinspection unchecked
        Collection<Long> possibleEEsubsets = ListUtils.removeAll(ees, ee2ads.keySet());
        // note: CollectionUtils.removeAll has a bug.

        qr = session.createQuery(subsetQuery).setParameterList("ees", possibleEEsubsets).list();
        ee2ads = CommonQueries.addAllAds(ee2ads, qr);
    }

    return ee2ads;
}

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