Example usage for java.util Collection clear

List of usage examples for java.util Collection clear

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Introduction

In this page you can find the example usage for java.util Collection clear.

Prototype

void clear();

Source Link

Document

Removes all of the elements from this collection (optional operation).

Usage

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

@Override
public Collection<BioAssaySet> findExperimentsWithAnalyses(Gene gene) {

    StopWatch timer = new StopWatch();
    timer.start();/*w w w  . j a  v  a 2 s . c  om*/

    Collection<CompositeSequence> probes = CommonQueries.getCompositeSequences(gene,
            this.getSessionFactory().getCurrentSession());
    Collection<BioAssaySet> result = new HashSet<>();
    if (probes.size() == 0) {
        return result;
    }

    if (timer.getTime() > 1000) {
        AbstractDao.log.info("Find probes: " + timer.getTime() + " ms");
    }
    timer.reset();
    timer.start();

    /*
     * Note: this query misses ExpressionExperimentSubSets. The native query was implemented because HQL was always
     * constructing a constraint on SubSets. See bug 2173.
     */
    final String queryToUse = "select e.ID from ANALYSIS a inner join INVESTIGATION e ON a.EXPERIMENT_ANALYZED_FK = e.ID "
            + "inner join BIO_ASSAY ba ON ba.EXPRESSION_EXPERIMENT_FK=e.ID "
            + " inner join BIO_MATERIAL bm ON bm.ID=ba.SAMPLE_USED_FK inner join TAXON t ON bm.SOURCE_TAXON_FK=t.ID "
            + " inner join COMPOSITE_SEQUENCE cs ON ba.ARRAY_DESIGN_USED_FK =cs.ARRAY_DESIGN_FK where cs.ID in "
            + " (:probes) and t.ID = :taxon";

    Taxon taxon = gene.getTaxon();

    int batchSize = 1000;
    Collection<CompositeSequence> batch = new HashSet<>();
    for (CompositeSequence probe : probes) {
        batch.add(probe);

        if (batch.size() == batchSize) {
            this.fetchExperimentsTestingGeneNativeQuery(batch, result, queryToUse, taxon);
            batch.clear();
        }
    }

    if (!batch.isEmpty()) {
        this.fetchExperimentsTestingGeneNativeQuery(batch, result, queryToUse, taxon);
    }

    if (timer.getTime() > 1000) {
        AbstractDao.log.info("Find experiments: " + timer.getTime() + " ms");
    }

    return result;
}

From source file:org.openmrs.module.webservices.rest.web.resource.impl.BaseDelegatingResource.java

/**
 * @see org.openmrs.module.webservices.rest.web.resource.api.Converter#setProperty(java.lang.Object,
 *      java.lang.String, java.lang.Object)
 *//*from   w  w w  . j  a v  a  2 s  .  c  om*/
@Override
public void setProperty(Object instance, String propertyName, Object value) throws ConversionException {
    if (propertiesIgnoredWhenUpdating.contains(propertyName)) {
        return;
    }
    try {
        DelegatingResourceHandler<? extends T> handler;

        try {
            handler = getResourceHandler((T) instance);
        } catch (Exception e) {
            // this try/catch isn't really needed because of java erasure behaviour at run time.
            // but I'm putting in here just in case
            handler = this;
        }

        // try to find a @PropertySetter-annotated method
        Method annotatedSetter = findSetterMethod(handler, propertyName);
        if (annotatedSetter != null) {
            Type expectedType = annotatedSetter.getGenericParameterTypes()[1];
            value = ConversionUtil.convert(value, expectedType);
            annotatedSetter.invoke(handler, instance, value);
            return;
        }

        // we need the generic type of this property, not just the class
        Method setter = PropertyUtils.getPropertyDescriptor(instance, propertyName).getWriteMethod();
        value = ConversionUtil.convert(value, setter.getGenericParameterTypes()[0]);

        if (value instanceof Collection) {
            //We need to handle collections in a way that Hibernate can track.
            Collection<?> newCollection = (Collection<?>) value;
            Object oldValue = PropertyUtils.getProperty(instance, propertyName);
            if (oldValue instanceof Collection) {
                Collection collection = (Collection) oldValue;
                collection.clear();
                collection.addAll(newCollection);
            } else {
                PropertyUtils.setProperty(instance, propertyName, value);
            }
        } else {
            PropertyUtils.setProperty(instance, propertyName, value);
        }
    } catch (Exception ex) {
        throw new ConversionException(propertyName + " on " + instance.getClass(), ex);
    }
}

From source file:org.malaguna.cmdit.service.reflection.HibernateProxyUtils.java

@SuppressWarnings("unchecked")
private Collection<?> deepLoadCollection(Collection collection, Collection guideObj) {
    Collection result = null;/*w  w w.  j a  v  a2s.co  m*/

    if (guideObj != null && !guideObj.isEmpty() && collection != null && !collection.isEmpty()) {

        try {
            if (collection instanceof PersistentSet) {
                result = new HashSet();
            } else if (collection instanceof PersistentList) {
                result = new ArrayList();
            } else {
                result = collection.getClass().newInstance();
            }

            //Recuperar primera instancia del guideObj y usarlo como siguiente guideObj
            Object collGuideObj = guideObj.iterator().next();
            for (Object aux : collection) {
                result.add(deepLoad(aux, collGuideObj));
            }

            collection.clear();
            collection.addAll(result);

        } catch (Throwable e) {
            e.printStackTrace();
        }
    }

    return collection;
}

From source file:org.grails.datastore.mapping.core.AbstractSession.java

private void executePendings(Collection<Runnable> pendings) {
    try {/*  w w  w  .j av a 2 s . co m*/
        for (Runnable pending : pendings) {
            pending.run();
        }
    } catch (RuntimeException e) {
        exceptionOccurred = true;
        throw e;
    }
    pendings.clear();
}

From source file:cn.vlabs.duckling.vwb.service.login.UMT2LoginAction.java

private void addUserToSiteByCheckFlag(Collection<Principal> currentPrincipals, String userName,
        String displayName) {//from  w ww  . ja  va 2s. c o m
    if (currentPrincipals != null) {
        boolean existInSite = false;
        for (Principal p : currentPrincipals) {
            if (p instanceof GroupPrincipal) {
                existInSite = true;
                break;
            }
        }
        if (!existInSite) {
            String checkValue = getVwbcontext().getProperty(Attributes.CHECK_SITE_FOR_USER);
            IUserService userS = VWBContainerImpl.findContainer().getUserService();
            if (checkValue != null && Attributes.CHECK_SITE_FOR_USER_ADD.equals(checkValue)) {
                userS.addUserToGroup(getVwbcontext().getVO(), "root", userName);
                currentPrincipals.clear();
                currentPrincipals.addAll(userS.getUserPrincipal(userName, getVwbcontext().getVO()));

            } else if (Attributes.CHECK_SITE_FOR_USER_APPLY.equals(checkValue)) {
                userS.applyUserToVo(getVwbcontext().getVO(), userName, displayName, null);
                currentPrincipals.clear();
                currentPrincipals.addAll(userS.getUserPrincipal(userName, getVwbcontext().getVO()));
            }
        }

    }

}

From source file:de.hybris.platform.servicelayer.media.impl.DefaultMediaPermissionServiceIntegrationTest.java

/**
 * Test method for/*w w w  .j av a 2 s .  com*/
 * {@link de.hybris.platform.servicelayer.media.impl.DefaultMediaPermissionService#setDeniedPrincipals(MediaModel, Collection)}
 * .
 */
@Test
public void testSetDeniedPrincipals() {
    Collection<PrincipalModel> deniedPrincipals = mediaPermissionService.getDeniedPrincipals(testMediaItem);
    Assert.assertTrue(CollectionUtils.isEmpty(deniedPrincipals));

    //create new user and assign proper permission
    final UserModel testUser = modelService.create(UserModel.class);
    testUser.setUid("testGroup");
    testUser.setName("Testgroup");
    modelService.save(testUser);

    final Collection<PrincipalModel> principalsToBeSet = new HashSet<PrincipalModel>();
    principalsToBeSet.add(userService.getCurrentUser());
    principalsToBeSet.add(testUser);

    //update the denied principals list. Expected result - 2 denied principals
    mediaPermissionService.setDeniedPrincipals(testMediaItem, principalsToBeSet);

    deniedPrincipals = mediaPermissionService.getDeniedPrincipals(testMediaItem);
    Assert.assertTrue(deniedPrincipals.size() == 2);
    Assert.assertTrue(deniedPrincipals.contains(userService.getCurrentUser()));
    Assert.assertTrue(deniedPrincipals.contains(testUser));

    principalsToBeSet.clear();
    //update the denied principals list. Expected result - empty list (no denied principals)
    mediaPermissionService.setDeniedPrincipals(testMediaItem, principalsToBeSet);

    deniedPrincipals = mediaPermissionService.getDeniedPrincipals(testMediaItem);
    Assert.assertTrue(CollectionUtils.isEmpty(deniedPrincipals));

}

From source file:de.uniba.wiai.kinf.pw.projects.lillytab.reasoner.tbox.RBox.java

private void addSubSuper() {
    final Collection<Map.Entry<R, R>> addList = new HashSet<>();

    for (Map.Entry<R, R> invEntry : MultiMapEntryIterable.decorate(_subRoles.entrySet())) {
        if (!_superRoles.containsValue(invEntry.getValue(), invEntry.getKey())) {
            addList.add(invEntry);/* www  .j a v a 2s. com*/
        }
    }
    for (Map.Entry<R, R> addItem : addList) {
        _superRoles.put(addItem.getKey(), addItem.getValue());
    }

    addList.clear();
    for (Map.Entry<R, R> invEntry : MultiMapEntryIterable.decorate(_superRoles.entrySet())) {
        if (!_subRoles.containsValue(invEntry.getValue(), invEntry.getKey())) {
            addList.add(invEntry);
        }
    }
    for (Map.Entry<R, R> addItem : addList) {
        _subRoles.put(addItem.getKey(), addItem.getValue());
    }
}

From source file:org.kuali.coeus.common.budget.impl.rate.BudgetRatesServiceImpl.java

protected void filterRates(Budget budget, Collection allAbstractInstituteRates,
        Collection filteredAbstractInstituteRates) {
    filteredAbstractInstituteRates.clear();
    Date personSalaryEffectiveDate = getBudgetPersonSalaryEffectiveDate(budget);
    filterInstituteRates(budget, allAbstractInstituteRates, filteredAbstractInstituteRates,
            personSalaryEffectiveDate);/*from w ww.j  a v  a 2 s.com*/
}

From source file:com.btoddb.fastpersitentqueue.InMemorySegmentMgr.java

private void loadPagedSegments() throws IOException {
    // read files and sort by their UUID name so they are in proper chronological order
    Collection<File> files = FileUtils.listFiles(pagingDirectory, TrueFileFilter.INSTANCE,
            TrueFileFilter.INSTANCE);//w ww .j a va  2  s  .  c om
    TreeSet<File> sortedFiles = new TreeSet<File>(new Comparator<File>() {
        @Override
        public int compare(File o1, File o2) {
            return new UUID(o1.getName()).compareTo(new UUID(o2.getName()));
        }
    });
    sortedFiles.addAll(files);

    // cleanup memory
    files.clear();

    assert 0 == numberOfActiveSegments.get();
    assert segments.isEmpty();

    segments.clear();

    for (File f : sortedFiles) {
        MemorySegment segment;
        // only load the segment's data if room in memory, otherwise just load its header
        if (numberOfActiveSegments.get() < maxNumberOfActiveSegments - 1) {
            segment = segmentSerializer.loadFromDisk(f.getName());
            segment.setStatus(MemorySegment.Status.READY);
            segment.setPushingFinished(true);

            assert segment.getNumberOfOnlineEntries() > 0;
            assert !segment.getQueue().isEmpty();

            numberOfActiveSegments.incrementAndGet();
        } else {
            segment = segmentSerializer.loadHeaderOnly(f.getName());
            segment.setStatus(MemorySegment.Status.OFFLINE);
            segment.setPushingFinished(true);

        }

        assert segment.isPushingFinished();
        assert segment.getNumberOfEntries() > 0;
        assert segment.getEntryListOffsetOnDisk() > 0;

        segments.add(segment);
        numberOfEntries.addAndGet(segment.getNumberOfEntries());
    }

    //        for (MemorySegment seg : segments) {
    //            if (seg.getStatus() == MemorySegment.Status.READY) {
    //                segmentSerializer.removePagingFile(seg);
    //            }
    //        }
}

From source file:de.hybris.platform.servicelayer.media.impl.DefaultMediaPermissionServiceIntegrationTest.java

/**
 * Test method for//from   w ww  . j  av  a2s .  c om
 * {@link de.hybris.platform.servicelayer.media.impl.DefaultMediaPermissionService#setPermittedPrincipals(MediaModel, Collection)}
 * .
 */
@Test
public void testSetPermittedPrincipals() {
    Collection<PrincipalModel> permittedPrincipals = mediaPermissionService
            .getPermittedPrincipals(testMediaItem);
    Assert.assertTrue(permittedPrincipals.size() == 1);
    Assert.assertTrue(permittedPrincipals.contains(userService.getCurrentUser()));

    //create new user and assign proper permission
    final UserModel testUser = modelService.create(UserModel.class);
    testUser.setUid("testGroup");
    testUser.setName("Testgroup");
    modelService.save(testUser);

    final Collection<PrincipalModel> principalsToBeSet = new HashSet<PrincipalModel>();
    principalsToBeSet.add(userService.getCurrentUser());
    principalsToBeSet.add(testUser);

    //update the permitted principals list. Expected result - 2 assigned principals
    mediaPermissionService.setPermittedPrincipals(testMediaItem, principalsToBeSet);

    permittedPrincipals = mediaPermissionService.getPermittedPrincipals(testMediaItem);
    Assert.assertTrue(permittedPrincipals.size() == 2);
    Assert.assertTrue(permittedPrincipals.contains(userService.getCurrentUser()));
    Assert.assertTrue(permittedPrincipals.contains(testUser));

    principalsToBeSet.clear();
    //update the permitted principals list. Expected result - empty list (no assigned principals)
    mediaPermissionService.setPermittedPrincipals(testMediaItem, principalsToBeSet);

    permittedPrincipals = mediaPermissionService.getPermittedPrincipals(testMediaItem);
    Assert.assertTrue(CollectionUtils.isEmpty(permittedPrincipals));
}