id int64 1 49k | buggy stringlengths 34 37.5k | fixed stringlengths 2 37k |
|---|---|---|
8,901 | super("AccessDenied", "Access Denied", "Entity", entity, HttpResponseStatus.FORBIDDEN);
}
public AccessDeniedException(String entityType, String entity)
{
super("AccessDenied", "Access Denied", entityType, entity, HttpResponseStatus.FORBIDDEN);
<BUG>}
public AccessDeniedException(Throwable ex)</BUG>
{
super("Access Den... | public AccessDeniedException(String entityType, String entity, BucketLogData logData)
super("AccessDenied", "Access Denied", entityType, entity, HttpResponseStatus.FORBIDDEN, logData);
public AccessDeniedException(Throwable ex)
|
8,902 | public class WalrusException extends EucalyptusCloudException {
String message;
String code;
HttpResponseStatus errStatus;
String resourceType;
<BUG>String resource;
public WalrusException()</BUG>
{
super();
}
| BucketLogData logData;
public WalrusException()
|
8,903 | super( "Bucket Not Empty" );
}
public BucketNotEmptyException(String bucket)
{
super("BucketNotEmpty", "The bucket you tried to delete is not empty.", "Bucket", bucket, HttpResponseStatus.CONFLICT);
<BUG>}
public BucketNotEmptyException(Throwable ex)</BUG>
{
super("Bucket Not Empty", ex);
}
| public BucketNotEmptyException(String bucket, BucketLogData logData)
super("BucketNotEmpty", "The bucket you tried to delete is not empty.", "Bucket", bucket, HttpResponseStatus.CONFLICT, logData);
public BucketNotEmptyException(Throwable ex)
|
8,904 | super( "No Such Entity" );
}
public NoSuchEntityException(String entityName)
{
super("NoSuchEntity", "The specified entity was not found", "Entity", entityName, HttpResponseStatus.NOT_FOUND);
<BUG>}
public NoSuchEntityException(Throwable ex)</BUG>
{
super("No Such Entity", ex);
}
| public NoSuchEntityException(String entityName, BucketLogData logData)
super("NoSuchEntity", "The specified entity was not found", "Entity", entityName, HttpResponseStatus.NOT_FOUND, logData);
public NoSuchEntityException(Throwable ex)
|
8,905 | super("EntityTooLarge", "Your proposed upload exceeds the maximum allowed object size.", "Entity", entity, HttpResponseStatus.BAD_REQUEST);
}
public EntityTooLargeException(String entityType, String entity)
{
super("EntityTooLarge", "Your proposed upload exceeds the maximum allowed object size.", entityType, entity, Ht... | public EntityTooLargeException(String entityType, String entity, BucketLogData logData)
super("EntityTooLarge", "Your proposed upload exceeds the maximum allowed object size.", entityType, entity, HttpResponseStatus.BAD_REQUEST, logData);
public EntityTooLargeException(Throwable ex)
|
8,906 | return this.factory.register(super.build(target));
}
@Override
public JGroupsTransportBuilder configure(OperationContext context, ModelNode model) throws OperationFailedException {
this.lockTimeout = LOCK_TIMEOUT.resolveModelAttribute(context, model).asLong();
<BUG>this.channel = ModelNodes.asString(CHANNEL.resolveMode... | this.channel = ModelNodes.optionalString(CHANNEL.resolveModelAttribute(context, model)).orElse(null);
|
8,907 | import org.jboss.dmr.ModelNode;
import org.jboss.msc.service.ServiceBuilder;
import org.jboss.msc.service.ServiceTarget;
import org.jboss.msc.value.InjectedValue;
public class FileStoreBuilder extends StoreBuilder {
<BUG>private final InjectedValue<PathManager> pathManager = new InjectedValue<>();
private volatile Sing... | private final String containerName;
private volatile SingleFileStoreConfigurationBuilder builder;
|
8,908 | public PersistenceConfiguration getValue() {
this.builder.location(this.pathManager.getValue().resolveRelativePathEntry(this.relativePath, this.relativeTo));
return super.getValue();
}
@Override
<BUG>StoreConfigurationBuilder<?, ?> createStore(OperationContext context, ModelNode model) throws OperationFailedException {... | this.relativePath = ModelNodes.optionalString(RELATIVE_PATH.resolveModelAttribute(context, model)).orElse(InfinispanExtension.SUBSYSTEM_NAME + File.separatorChar + this.containerName);
|
8,909 | package org.jboss.as.clustering.infinispan.subsystem;
import static org.jboss.as.clustering.infinispan.subsystem.BackupForResourceDefinition.Attribute.CACHE;
<BUG>import static org.jboss.as.clustering.infinispan.subsystem.BackupForResourceDefinition.Attribute.SITE;
import org.infinispan.configuration.cache.BackupForCon... | import java.util.Optional;
import org.infinispan.configuration.cache.BackupForConfiguration;
|
8,910 | BackupForBuilder(PathAddress cacheAddress) {
super(CacheComponent.BACKUP_FOR, cacheAddress);
}
@Override
public Builder<BackupForConfiguration> configure(OperationContext context, ModelNode model) throws OperationFailedException {
<BUG>String site = ModelNodes.asString(SITE.resolveModelAttribute(context, model));
if (... | Optional<String> site = ModelNodes.optionalString(SITE.resolveModelAttribute(context, model));
if (site.isPresent()) {
this.builder.remoteSite(site.get()).remoteCache(CACHE.resolveModelAttribute(context, model).asString());
|
8,911 | super(address);
this.mode = mode;
}
@Override
public Builder<Configuration> configure(OperationContext context, ModelNode model) throws OperationFailedException {
<BUG>Mode mode = ModelNodes.asEnum(ClusteredCacheResourceDefinition.Attribute.MODE.resolveModelAttribute(context, model), Mode.class);
ClusteringConfiguratio... | Mode mode = ModelNodes.asEnum(MODE.resolveModelAttribute(context, model), Mode.class);
ClusteringConfigurationBuilder builder = new ConfigurationBuilder().clustering().cacheMode(mode.apply(this.mode));
|
8,912 | public class JGroupsTransportServiceHandler implements ResourceServiceHandler {
@Override
public void installServices(OperationContext context, ModelNode model) throws OperationFailedException {
PathAddress containerAddress = context.getCurrentAddress().getParent();
String name = containerAddress.getLastElement().getVa... | String channel = ModelNodes.optionalString(CHANNEL.resolveModelAttribute(context, model)).orElse(null);
|
8,913 | }
@Override
public void removeServices(OperationContext context, ModelNode model) throws OperationFailedException {
PathAddress containerAddress = context.getCurrentAddress().getParent();
String name = containerAddress.getLastElement().getValue();
<BUG>String channel = ModelNodes.asString(CHANNEL.resolveModelAttribute(... | String channel = ModelNodes.optionalString(CHANNEL.resolveModelAttribute(context, model)).orElse(null);
|
8,914 | import static org.jboss.as.clustering.infinispan.subsystem.StoreResourceDefinition.Attribute.PASSIVATION;
import static org.jboss.as.clustering.infinispan.subsystem.StoreResourceDefinition.Attribute.PRELOAD;
import static org.jboss.as.clustering.infinispan.subsystem.StoreResourceDefinition.Attribute.PROPERTIES;
import ... | import java.util.Properties;
import org.infinispan.configuration.cache.AsyncStoreConfiguration;
|
8,915 | ;
}
@Override
public Builder<PersistenceConfiguration> configure(OperationContext context, ModelNode model) throws OperationFailedException {
this.storeBuilder = this.createStore(context, model);
<BUG>this.storeBuilder.persistence().passivation(PASSIVATION.resolveModelAttribute(context, model).asBoolean());
this.storeB... | Properties properties = new Properties();
ModelNodes.optionalPropertyList(PROPERTIES.resolveModelAttribute(context, model)).ifPresent(list -> list.forEach(property -> properties.setProperty(property.getName(), property.getValue().asString())));
this.storeBuilder.fetchPersistentState(FETCH_STATE.resolveModelAttribute(co... |
8,916 | import java.util.stream.Collectors;</BUG>
import org.jboss.dmr.ModelNode;
import org.jboss.dmr.Property;
import org.jboss.modules.ModuleIdentifier;
public class ModelNodes {
<BUG>@Deprecated
public static String asString(ModelNode value) {
return optionalString(value).orElse(null);
}
@Deprecated
public static String as... | package org.jboss.as.clustering.dmr;
import java.util.List;
import java.util.Optional;
import java.util.OptionalDouble;
import java.util.OptionalInt;
import java.util.OptionalLong;
|
8,917 | ServiceBuilder<SiteConfiguration> builder = super.build(target);
return (this.factory != null) ? this.factory.register(builder) : builder;
}
@Override
public Builder<SiteConfiguration> configure(OperationContext context, ModelNode model) throws OperationFailedException {
<BUG>String channel = ModelNodes.asString(CHANNE... | String channel = ModelNodes.optionalString(CHANNEL.resolveModelAttribute(context, model)).orElse(null);
|
8,918 | new ModuleBuilder(CacheContainerComponent.MODULE.getServiceName(address), MODULE).configure(context, model).build(target).install();
new GlobalConfigurationBuilder(address).configure(context, model).build(target).install();
CacheContainerBuilder containerBuilder = new CacheContainerBuilder(address).configure(context, m... | ModelNodes.optionalString(JNDI_NAME.resolveModelAttribute(context, model)).map(jndiName -> ContextNames.bindInfoFor(JndiNameFactory.parse(jndiName).getAbsoluteName())).ifPresent(aliasBinding -> bindingBuilder.alias(aliasBinding));
|
8,919 | public static final String DELETE_ACTION_HISTORY_RESULT;
public static final String DELETE_ACTION_PLUGIN;
public static final String DELETE_ALERT;
public static final String DELETE_ALERT_CTIME;
public static final String DELETE_ALERT_LIFECYCLE;
<BUG>public static final String DELETE_ALERT_SEVERITY;
public static final ... | [DELETED] |
8,920 | public static final String INSERT_ACTION_PLUGIN;
public static final String INSERT_ACTION_PLUGIN_DEFAULT_PROPERTIES;
public static final String INSERT_ALERT;
public static final String INSERT_ALERT_CTIME;
public static final String INSERT_ALERT_LIFECYCLE;
<BUG>public static final String INSERT_ALERT_SEVERITY;
public st... | [DELETED] |
8,921 | public static final String SELECT_ALERT_CTIME_START;
public static final String SELECT_ALERT_CTIME_START_END;
public static final String SELECT_ALERT_LIFECYCLE_END;
public static final String SELECT_ALERT_LIFECYCLE_START;
public static final String SELECT_ALERT_LIFECYCLE_START_END;
<BUG>public static final String SELEC... | [DELETED] |
8,922 | DELETE_ALERT = "DELETE FROM " + keyspace + ".alerts " + "WHERE tenantId = ? AND alertId = ? ";
DELETE_ALERT_CTIME = "DELETE FROM " + keyspace + ".alerts_ctimes "
+ "WHERE tenantId = ? AND ctime = ? AND alertId = ? ";
DELETE_ALERT_LIFECYCLE = "DELETE FROM " + keyspace + ".alerts_lifecycle "
+ "WHERE tenantId = ? AND sta... | [DELETED] |
8,923 | INSERT_ALERT = "INSERT INTO " + keyspace + ".alerts " + "(tenantId, alertId, payload) VALUES (?, ?, ?) ";
INSERT_ALERT_CTIME = "INSERT INTO " + keyspace + ".alerts_ctimes "
+ "(tenantId, alertId, ctime) VALUES (?, ?, ?) ";
INSERT_ALERT_LIFECYCLE = "INSERT INTO " + keyspace + ".alerts_lifecycle "
+ "(tenantId, alertId, ... | [DELETED] |
8,924 | + "WHERE tenantId = ? AND status = ? AND stime <= ? ";
SELECT_ALERT_LIFECYCLE_START = "SELECT alertId FROM " + keyspace + ".alerts_lifecycle "
+ "WHERE tenantId = ? AND status = ? AND stime >= ? ";
SELECT_ALERT_LIFECYCLE_START_END = "SELECT alertId FROM " + keyspace + ".alerts_lifecycle "
+ "WHERE tenantId = ? AND stat... | [DELETED] |
8,925 | import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
<BUG>import java.util.stream.Collectors;
import javax.ejb.EJB;</BUG>
import javax.ejb.Local;
import javax.ejb.Stateless;
import javax.ejb.TransactionAttribute;
| import javax.annotation.PostConstruct;
import javax.ejb.EJB;
|
8,926 | import org.hawkular.alerts.api.model.trigger.Trigger;
import org.hawkular.alerts.api.services.ActionsService;
import org.hawkular.alerts.api.services.AlertsCriteria;
import org.hawkular.alerts.api.services.AlertsService;
import org.hawkular.alerts.api.services.DefinitionsService;
<BUG>import org.hawkular.alerts.api.ser... | import org.hawkular.alerts.api.services.PropertiesService;
import org.hawkular.alerts.engine.impl.IncomingDataManagerImpl.IncomingData;
|
8,927 | import com.datastax.driver.core.Session;
import com.google.common.util.concurrent.Futures;
@Local(AlertsService.class)
@Stateless
@TransactionAttribute(value = TransactionAttributeType.NOT_SUPPORTED)
<BUG>public class CassAlertsServiceImpl implements AlertsService {
private final MsgLogger msgLog = MsgLogger.LOGGER;
pr... | private static final String CRITERIA_NO_QUERY_SIZE = "hawkular-alerts.criteria-no-query-size";
private static final String CRITERIA_NO_QUERY_SIZE_ENV = "CRITERIA_NO_QUERY_SIZE";
private static final String CRITERIA_NO_QUERY_SIZE_DEFAULT = "200";
private int criteriaNoQuerySize;
|
8,928 | log.debug("Adding " + alerts.size() + " alerts");
}
PreparedStatement insertAlert = CassStatement.get(session, CassStatement.INSERT_ALERT);
PreparedStatement insertAlertTrigger = CassStatement.get(session, CassStatement.INSERT_ALERT_TRIGGER);
PreparedStatement insertAlertCtime = CassStatement.get(session, CassStatement... | [DELETED] |
8,929 | futures.add(session.executeAsync(insertAlertTrigger.bind(a.getTenantId(),
a.getAlertId(),
a.getTriggerId())));
futures.add(session.executeAsync(insertAlertCtime.bind(a.getTenantId(),
a.getAlertId(), a.getCtime())));
<BUG>futures.add(session.executeAsync(insertAlertStatus.bind(a.getTenantId(),
a.getAlertId(),
a.getStatu... | [DELETED] |
8,930 | for (Row row : rsAlerts) {
String payload = row.getString("payload");
Alert alert = JsonUtil.fromJson(payload, Alert.class, thin);
alerts.add(alert);
}
<BUG>}
} catch (Exception e) {
msgLog.errorDatabaseException(e.getMessage());
throw e;
}
return preparePage(alerts, pager);</BUG>
}
| [DELETED] |
8,931 | for (Alert a : alertsToDelete) {
String id = a.getAlertId();
List<ResultSetFuture> futures = new ArrayList<>();
futures.add(session.executeAsync(deleteAlert.bind(tenantId, id)));
futures.add(session.executeAsync(deleteAlertCtime.bind(tenantId, a.getCtime(), id)));
<BUG>futures.add(session.executeAsync(deleteAlertSeveri... | [DELETED] |
8,932 | private Alert updateAlertStatus(Alert alert) throws Exception {
if (alert == null || alert.getAlertId() == null || alert.getAlertId().isEmpty()) {
throw new IllegalArgumentException("AlertId must be not null");
}
try {
<BUG>PreparedStatement deleteAlertStatus = CassStatement.get(session,
CassStatement.DELETE_ALERT_STAT... | [DELETED] |
8,933 | PreparedStatement insertAlertLifecycle = CassStatement.get(session,
CassStatement.INSERT_ALERT_LIFECYCLE);
PreparedStatement updateAlert = CassStatement.get(session,
CassStatement.UPDATE_ALERT);
List<ResultSetFuture> futures = new ArrayList<>();
<BUG>for (Status statusToDelete : EnumSet.complementOf(EnumSet.of(alert.ge... | [DELETED] |
8,934 | String category = null;
Collection<String> categories = null;
String triggerId = null;
Collection<String> triggerIds = null;
Map<String, String> tags = null;
<BUG>boolean thin = false;
public EventsCriteria() {</BUG>
super();
}
public Long getStartTime() {
| Integer criteriaNoQuerySize = null;
public EventsCriteria() {
|
8,935 | }
@Override
public String toString() {
return "EventsCriteria [startTime=" + startTime + ", endTime=" + endTime + ", eventId=" + eventId
+ ", eventIds=" + eventIds + ", category=" + category + ", categories=" + categories + ", triggerId="
<BUG>+ triggerId + ", triggerIds=" + triggerIds + ", tags=" + tags + ", thin=" + ... | public void addTag(String name, String value) {
if (null == tags) {
tags = new HashMap<>();
|
8,936 | import org.bedework.calsvci.RestoreIntf.FixAliasResult;
import org.bedework.dumprestore.dump.Dump;
import org.bedework.dumprestore.restore.Restore;
import org.bedework.indexer.BwIndexCtlMBean;
import org.bedework.util.jmx.ConfBase;
<BUG>import org.bedework.util.jmx.MBeanUtil;
import org.bedework.util.timezones.DateTime... | import org.bedework.util.misc.Util;
import org.bedework.util.timezones.DateTimeUtil;
|
8,937 | implements BwDumpRestoreMBean {
private static final String confuriPname = "org.bedework.bwengine.confuri";
private List<AliasInfo> externalSubs;
private Map<String, AliasEntry> aliasInfo = new HashMap<>();
private boolean allowRestore;
<BUG>private boolean fixAliases;
private String curSvciOwner;</BUG>
private CalSvcI... | private boolean newDumpFormat;
private String curSvciOwner;
|
8,938 | public void endTransaction() throws CalFacadeException {
colCache.flush();
}
@Override
public void principalChanged() throws CalFacadeException {
<BUG>colCache.flushAccess(this);
}</BUG>
@Override
public CollectionSynchInfo getSynchInfo(final String path,
final String token) throws CalFacadeException {
| colCache.clear();
|
8,939 | void setAllowRestore(boolean val);
@MBeanInfo("Set true to enable restores")
boolean getAllowRestore();
void setFixAliases(boolean val);
@MBeanInfo("Set true to fix aliases - false to list only")
<BUG>boolean getFixAliases();
@MBeanInfo("Restores the data from the DataIn path")</BUG>
String restoreData();
@MBeanInfo("S... | void setNewDumpFormat(boolean val);
@MBeanInfo("Set true to dump in new format - not for production use yet")
boolean getNewDumpFormat();
@MBeanInfo("Restores the data from the DataIn path")
|
8,940 | package org.jetbrains.plugins.gradle.importing.wizard.adjust;
<BUG>import com.intellij.ide.util.projectWizard.WizardContext;
import com.intellij.openapi.util.Pair;</BUG>
import com.intellij.ui.components.JBScrollPane;
import com.intellij.ui.treeStructure.Tree;
import com.intellij.util.containers.HashMap;
| import com.intellij.openapi.options.ConfigurationException;
import com.intellij.openapi.util.Pair;
|
8,941 | import com.intellij.openapi.util.Pair;</BUG>
import com.intellij.ui.components.JBScrollPane;
import com.intellij.ui.treeStructure.Tree;
import com.intellij.util.containers.HashMap;
import org.jetbrains.annotations.NotNull;
<BUG>import org.jetbrains.plugins.gradle.importing.model.GradleDependency;
import org.jetbrains.p... | package org.jetbrains.plugins.gradle.importing.wizard.adjust;
import com.intellij.ide.util.projectWizard.WizardContext;
import com.intellij.openapi.options.ConfigurationException;
import com.intellij.openapi.util.Pair;
import org.jetbrains.plugins.gradle.importing.model.*;
|
8,942 | ));
}
Map<GradleEntity, Pair<String, Collection<GradleProjectStructureNode>>> entity2nodes
= new HashMap<GradleEntity, Pair<String, Collection<GradleProjectStructureNode>>>();
int counter = 0;
<BUG>DefaultMutableTreeNode root = buildNode(project, entity2nodes, counter++);
for (GradleModule module : project.getModules()... | List<GradleModule> modules = new ArrayList<GradleModule>(project.getModules());
Collections.sort(modules, Named.COMPARATOR);
for (GradleModule module : modules) {
|
8,943 | package org.jetbrains.plugins.gradle.importing.model;
<BUG>import org.jetbrains.annotations.NotNull;
public interface Named {
@NotNull</BUG>
String getName();
void setName(@NotNull String name);
| import java.util.Comparator;
Comparator<Named> COMPARATOR = new Comparator<Named>() {
@Override
public int compare(Named o1, Named o2) {
return o1.getName().compareTo(o2.getName());
}
};
@NotNull
|
8,944 | import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.security.DigestOutputStream;
import java.security.MessageDigest;
<BUG>import java.security.NoSuchAlgorithmException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;</BUG>
public final class ... | import java.text.DateFormat;
import java.util.Date;
import java.util.List;
|
8,945 | package org.jboss.as.patching.runner;
<BUG>import org.jboss.as.boot.DirectoryStructure;
import org.jboss.as.patching.LocalPatchInfo;</BUG>
import org.jboss.as.patching.PatchInfo;
import org.jboss.as.patching.PatchLogger;
import org.jboss.as.patching.PatchMessages;
| import static org.jboss.as.patching.runner.PatchUtils.generateTimestamp;
import org.jboss.as.patching.CommonAttributes;
import org.jboss.as.patching.LocalPatchInfo;
|
8,946 | private static final String PATH_DELIMITER = "/";
public static final byte[] NO_CONTENT = PatchingTask.NO_CONTENT;
enum Element {
ADDED_BUNDLE("added-bundle"),
ADDED_MISC_CONTENT("added-misc-content"),
<BUG>ADDED_MODULE("added-module"),
BUNDLES("bundles"),</BUG>
CUMULATIVE("cumulative"),
DESCRIPTION("description"),
MIS... | APPLIES_TO_VERSION("applies-to-version"),
BUNDLES("bundles"),
|
8,947 | final int count = reader.getAttributeCount();
for (int i = 0; i < count; i++) {
final String value = reader.getAttributeValue(i);
final Attribute attribute = Attribute.forName(reader.getAttributeLocalName(i));
switch (attribute) {
<BUG>case APPLIES_TO_VERSION:
builder.addAppliesTo(value);
break;</BUG>
case RESULTING_VE... | [DELETED] |
8,948 | final StringBuilder path = new StringBuilder();
for(final String p : item.getPath()) {
path.append(p).append(PATH_DELIMITER);
}
path.append(item.getName());
<BUG>writer.writeAttribute(Attribute.PATH.name, path.toString());
if(type != ModificationType.REMOVE) {</BUG>
writer.writeAttribute(Attribute.HASH.name, bytesToHex... | if (item.isDirectory()) {
writer.writeAttribute(Attribute.DIRECTORY.name, "true");
if(type != ModificationType.REMOVE) {
|
8,949 | package org.jboss.as.patching;
import org.jboss.as.controller.OperationFailedException;
import org.jboss.as.patching.runner.PatchingException;
import org.jboss.logging.Messages;
import org.jboss.logging.annotations.Message;
<BUG>import org.jboss.logging.annotations.MessageBundle;
import java.io.IOException;</BUG>
impor... | import org.jboss.logging.annotations.Cause;
import java.io.IOException;
|
8,950 | import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.DataInputStream;
import java.io.DataOutputStream;
import java.io.IOException;
<BUG>import java.nio.file.Path;
import java.util.Random;
import org.junit.Before;
</BUG>
import org.junit.Test;
| import java.nio.file.Paths;
import org.junit.After;
|
8,951 | package net.java.sip.communicator.plugin.otr;
<BUG>import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;</BUG>
import java.security.KeyFactory;
import java.security.KeyPair;
import java.security.KeyPairGenerator;
| [DELETED] |
8,952 | {
e.printStackTrace();
return null;
}
}
<BUG>private String getSessionNS(SessionID sessionID, String function)
{
try
{
return "net.java.sip.comunicator.plugin.otr."
+ URLEncoder.encode(sessionID.toString(), "UTF-8") + "."
+ function;</BUG>
}
| private List<ScOtrEngineListener> listeners =
new Vector<ScOtrEngineListener>();
public void addListener(ScOtrEngineListener l)
|
8,953 | OtrActivator.bundleContext.getService(ref);
service.openURL(OtrActivator.resourceService
.getI18NString("plugin.otr.authbuddydialog.HELP_URI"));
}
public OtrPolicy getContactPolicy(Contact contact)
<BUG>{
String id = getSessionNS(getSessionID(contact), "policy");
if (id == null || id.length() < 1)
return getGlobalPolic... | int policy = this.configurator.getPropertyInt(getSessionID(contact) + "policy", -1);
|
8,954 | return null;
}
Object b64PubKey = OtrActivator.configService.getProperty(idPubKey);</BUG>
if (b64PubKey == null)
<BUG>return null;
X509EncodedKeySpec publicKeySpec =
new X509EncodedKeySpec(Base64.decode((String) b64PubKey));</BUG>
PublicKey publicKey;
PrivateKey privateKey;
KeyFactory keyFactory;
| PKCS8EncodedKeySpec privateKeySpec = new PKCS8EncodedKeySpec(b64PrivKey);
byte[] b64PubKey = this.configurator.getPropertyBytes(accountID + ".publicKey");
X509EncodedKeySpec publicKeySpec = new X509EncodedKeySpec(b64PubKey);
|
8,955 | if (specificAnnotationSettings == null || selectedIonTypes.keySet().contains(Ion.IonType.PEPTIDE_FRAGMENT_ION) && specificAnnotationSettings.getFragmentIonTypes().contains(PeptideFragmentIon.A_ION)) {
int subType = PeptideFragmentIon.A_ION;
ArrayList<Ion> ions = ionsMap.get(subType);
if (ions == null) {
if (neutralLoss... | ions = new ArrayList<Ion>(neutralLossesCombinations.length);
|
8,956 | if (specificAnnotationSettings == null || selectedIonTypes.keySet().contains(Ion.IonType.PEPTIDE_FRAGMENT_ION) && specificAnnotationSettings.getFragmentIonTypes().contains(PeptideFragmentIon.B_ION)) {
int subType = PeptideFragmentIon.B_ION;
ArrayList<Ion> ions = ionsMap.get(subType);
if (ions == null) {
if (neutralLoss... | ions = new ArrayList<Ion>(neutralLossesCombinations.length);
|
8,957 | ions = new ArrayList<Ion>(1);
}
ionsMap.put(subType, ions);
}
if (neutralLossesCombinations != null) {
<BUG>for (ArrayList<NeutralLoss> losses : neutralLossesCombinations) {
ions.add(new PeptideFragmentIon(subType, faa, forwardMass - getLossesMass(losses), losses));
</BUG>
}
| for (NeutralLossCombination losses : neutralLossesCombinations) {
ions.add(new PeptideFragmentIon(subType, faa, forwardMass - losses.getMass(), losses.getNeutralLossCombination()));
|
8,958 | if (specificAnnotationSettings == null || selectedIonTypes.keySet().contains(Ion.IonType.PEPTIDE_FRAGMENT_ION) && specificAnnotationSettings.getFragmentIonTypes().contains(PeptideFragmentIon.C_ION)) {
int subType = PeptideFragmentIon.C_ION;
ArrayList<Ion> ions = ionsMap.get(subType);
if (ions == null) {
if (neutralLoss... | ions = new ArrayList<Ion>(neutralLossesCombinations.length);
|
8,959 | if (specificAnnotationSettings == null || selectedIonTypes.keySet().contains(Ion.IonType.PEPTIDE_FRAGMENT_ION) && specificAnnotationSettings.getFragmentIonTypes().contains(PeptideFragmentIon.X_ION)) {
int subType = PeptideFragmentIon.X_ION;
ArrayList<Ion> ions = ionsMap.get(subType);
if (ions == null) {
if (neutralLoss... | ions = new ArrayList<Ion>(neutralLossesCombinations.length);
|
8,960 | if (specificAnnotationSettings == null || selectedIonTypes.keySet().contains(Ion.IonType.PEPTIDE_FRAGMENT_ION) && specificAnnotationSettings.getFragmentIonTypes().contains(PeptideFragmentIon.Y_ION)) {
int subType = PeptideFragmentIon.Y_ION;
ArrayList<Ion> ions = ionsMap.get(subType);
if (ions == null) {
if (neutralLoss... | ions = new ArrayList<Ion>(neutralLossesCombinations.length);
|
8,961 |
ions.add(new PeptideFragmentIon(subType, faa, rewindMass + 2 * Atom.H.getMonoisotopicMass() - getLossesMass(losses), losses));
}</BUG>
} else {
<BUG>ions.add(new PeptideFragmentIon(subType, faa, rewindMass + 2 * Atom.H.getMonoisotopicMass(), null));
</BUG>
}
}
if (specificAnnotationSettings == null || selectedIonTypes... | ions = new ArrayList<Ion>(1);
ionsMap.put(subType, ions);
if (neutralLossesCombinations != null) {
for (NeutralLossCombination losses : neutralLossesCombinations) {
ions.add(new PeptideFragmentIon(subType, faa, rewindMass + h2 - losses.getMass(), losses.getNeutralLossCombination()));
ions.add(new PeptideFragmentIon(sub... |
8,962 | if (specificAnnotationSettings == null || selectedIonTypes.keySet().contains(Ion.IonType.PEPTIDE_FRAGMENT_ION) && specificAnnotationSettings.getFragmentIonTypes().contains(PeptideFragmentIon.Z_ION)) {
int subType = PeptideFragmentIon.Z_ION;
ArrayList<Ion> ions = ionsMap.get(subType);
if (ions == null) {
if (neutralLoss... | ions = new ArrayList<Ion>(neutralLossesCombinations.length);
|
8,963 | ions = new ArrayList<Ion>(1);
}
ionsMap.put(subType, ions);
}
if (neutralLossesCombinations != null) {
<BUG>for (ArrayList<NeutralLoss> losses : neutralLossesCombinations) {
ions.add(new PeptideFragmentIon(subType, faa, rewindMass - Atom.N.getMonoisotopicMass() - getLossesMass(losses), losses));
</BUG>
}
| for (NeutralLossCombination losses : neutralLossesCombinations) {
ions.add(new PeptideFragmentIon(subType, faa, rewindMass - Atom.N.getMonoisotopicMass() - losses.getMass(), losses.getNeutralLossCombination()));
|
8,964 | ArrayList<Ion> ions = ionsMap.get(subType);
if (ions == null) {
ions = new ArrayList<Ion>();
ionsMap.put(subType, ions);
}
<BUG>for (ArrayList<NeutralLoss> losses : neutralLossesCombinations) {
ions.add(new TagFragmentIon(subType, aa, subaa, forwardMass - Atom.C.getMonoisotopicMass() - Atom.O.getMonoisotopicMass() - g... | for (NeutralLossCombination losses : neutralLossesCombinations) {
ions.add(new TagFragmentIon(subType, aa, subaa, forwardMass - co - losses.getMass(), losses.getNeutralLossCombination(), massOffset));
|
8,965 | ions = ionsMap.get(subType);
if (ions == null) {
ions = new ArrayList<Ion>();
ionsMap.put(subType, ions);
}
<BUG>for (ArrayList<NeutralLoss> losses : neutralLossesCombinations) {
ions.add(new TagFragmentIon(subType, aa, subaa, forwardMass + Atom.N.getMonoisotopicMass() + 3 * Atom.H.getMonoisotopicMass() - getLossesMas... | [DELETED] |
8,966 | ArrayList<Ion> ions = ionsMap.get(subType);
if (ions == null) {
ions = new ArrayList<Ion>();
ionsMap.put(subType, ions);
}
<BUG>for (ArrayList<NeutralLoss> losses : neutralLossesCombinations) {
ions.add(new TagFragmentIon(subType, aa, subaa, forwardMass - Atom.C.getMonoisotopicMass() - Atom.O.getMonoisotopicMass() - g... | for (NeutralLossCombination losses : neutralLossesCombinations) {
ions.add(new TagFragmentIon(subType, aa, subaa, forwardMass - co - losses.getMass(), losses.getNeutralLossCombination(), massOffset));
|
8,967 | ions = ionsMap.get(subType);
if (ions == null) {
ions = new ArrayList<Ion>();
ionsMap.put(subType, ions);
}
<BUG>for (ArrayList<NeutralLoss> losses : neutralLossesCombinations) {
ions.add(new TagFragmentIon(subType, aa, subaa, forwardMass - getLossesMass(losses), losses, massOffset));
</BUG>
}
| for (NeutralLossCombination losses : neutralLossesCombinations) {
ions.add(new TagFragmentIon(subType, aa, subaa, forwardMass - losses.getMass(), losses.getNeutralLossCombination(), massOffset));
|
8,968 | ArrayList<Ion> ions = ionsMap.get(subType);
if (ions == null) {
ions = new ArrayList<Ion>();
ionsMap.put(subType, ions);
}
<BUG>for (ArrayList<NeutralLoss> losses : neutralLossesCombinations) {
ions.add(new TagFragmentIon(subType, aa, subaa, rewindMass + Atom.C.getMonoisotopicMass() + 2 * Atom.O.getMonoisotopicMass() ... | ions.add(immoniumIon);
ionsMap = result.get(Ion.IonType.RELATED_ION.index);
if (ionsMap == null) {
ionsMap = new HashMap<Integer, ArrayList<Ion>>();
result.put(Ion.IonType.RELATED_ION.index, ionsMap);
ArrayList<RelatedIon> relatedIons = RelatedIon.getRelatedIons(aminoAcid);
for (RelatedIon tempRelated : relatedIons) {
... |
8,969 | ArrayList<Ion> ions = ionsMap.get(subType);
if (ions == null) {
ions = new ArrayList<Ion>();
ionsMap.put(subType, ions);
}
<BUG>for (ArrayList<NeutralLoss> losses : neutralLossesCombinations) {
ions.add(new TagFragmentIon(subType, aa, subaa, rewindMass + Atom.C.getMonoisotopicMass() + 2 * Atom.O.getMonoisotopicMass() ... | for (NeutralLossCombination losses : neutralLossesCombinations) {
ions.add(new TagFragmentIon(subType, aa, subaa, forwardMass - co - losses.getMass(), losses.getNeutralLossCombination(), massOffset));
subType = TagFragmentIon.B_ION;
|
8,970 | ions = ionsMap.get(subType);
if (ions == null) {
ions = new ArrayList<Ion>();
ionsMap.put(subType, ions);
}
<BUG>for (ArrayList<NeutralLoss> losses : neutralLossesCombinations) {
ions.add(new TagFragmentIon(subType, aa, subaa, rewindMass - Atom.N.getMonoisotopicMass() + Atom.O.getMonoisotopicMass() - getLossesMass(los... | [DELETED] |
8,971 | package com.compomics.util.experiment.biology.ions;
import com.compomics.util.experiment.biology.NeutralLoss;
import com.compomics.util.experiment.biology.Ion;
import com.compomics.util.pride.CvTerm;
<BUG>import java.util.ArrayList;
public class PeptideFragmentIon extends Ion {</BUG>
static final long serialVersionUID ... | import java.util.Collections;
public class PeptideFragmentIon extends Ion {
|
8,972 | public static final int B_ION = 1;
public static final int C_ION = 2;
public static final int X_ION = 3;
public static final int Y_ION = 4;
public static final int Z_ION = 5;
<BUG>private ArrayList<NeutralLoss> neutralLosses;
</BUG>
private int number = -1;
private int subType;
private CvTerm cvTerm = null;
| private NeutralLoss[] neutralLosses;
|
8,973 | public String getNameWithNumber() {
return getSubTypeAsString() + getNumber() + getNeutralLossesAsString();
}
@Override
public CvTerm getPrideCvTerm() {
<BUG>if (cvTerm != null) {
return cvTerm;
}</BUG>
switch (subType) {
| if (cvTerm == null) {
|
8,974 | private Semaphore proteinsMutex;
private ArrayList<ModificationMatch> modifications = null;
private ArrayList<VariantMatch> variants = null;
private HashMap<String, HashMap<Integer, ArrayList<Variant>>> variantsMap = null;
public final static String MODIFICATION_LOCALIZATION_SEPARATOR = "-ATAA-";
<BUG>public final stat... | public final static char MODIFICATION_SEPARATOR_CHAR = '_';
public Peptide() {
|
8,975 | ArrayList<Integer> possibleTypes = new ArrayList<Integer>();
possibleTypes.add(PROTON);
return possibleTypes;
}
@Override
<BUG>public ArrayList<NeutralLoss> getNeutralLosses() {
switch (subType) {
case PROTON:
return new ArrayList<NeutralLoss>(); // If you see a neutral loss of a proton, call Gell-Mann and Zweig
defau... | [DELETED] |
8,976 | return RelatedIon.getPossibleSubtypes();
default:
throw new UnsupportedOperationException("Not supported yet.");
}
}
<BUG>public abstract ArrayList<NeutralLoss> getNeutralLosses();
</BUG>
public boolean hasNeutralLosses() {
switch (type) {
case PEPTIDE_FRAGMENT_ION:
| public abstract NeutralLoss[] getNeutralLosses();
|
8,977 | public boolean hasNeutralLosses() {
switch (type) {
case PEPTIDE_FRAGMENT_ION:
case TAG_FRAGMENT_ION:
case PRECURSOR_ION:
<BUG>ArrayList<NeutralLoss> neutralLosses = getNeutralLosses();
return neutralLosses != null && !neutralLosses.isEmpty();
</BUG>
default:
| NeutralLoss[] neutralLosses = getNeutralLosses();
return neutralLosses != null && neutralLosses.length > 0;
|
8,978 | return "Unknown ion type";
default:
throw new UnsupportedOperationException("No name for ion type " + type + ".");
}
}
<BUG>public static Ion getGenericIon(IonType ionType, int subType, ArrayList<NeutralLoss> neutralLosses) {
</BUG>
switch (ionType) {
case ELEMENTARY_ION:
return new ElementaryIon("new ElementaryIon", 0... | public static Ion getGenericIon(IonType ionType, int subType, NeutralLoss[] neutralLosses) {
|
8,979 | possibleTypes.add(TRYPTOPHAN);
possibleTypes.add(TYROSINE);
return possibleTypes;
}
@Override
<BUG>public ArrayList<NeutralLoss> getNeutralLosses() {
return new ArrayList<NeutralLoss>(0);
</BUG>
}
| [DELETED] |
8,980 | import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.fs.StorageType;
import org.apache.hadoop.hdfs.protocol.DSQuotaExceededException;
import org.apache.hadoop.hdfs.protocol.HdfsConstants;
<BUG>import org.apache.hadoop.hdfs.protocol.NSQuotaExceededException;
import org.apach... | import org.apache.hadoop.hdfs.protocol.QuotaByStorageTypeExceededException;
import org.apache.hadoop.hdfs.protocol.QuotaExceededException;
|
8,981 | timeWarp = new OwnLabel(getFormattedTimeWrap(), skin, "warp");
timeWarp.setName("time warp");
Container wrapWrapper = new Container(timeWarp);
wrapWrapper.width(60f * GlobalConf.SCALE_FACTOR);
wrapWrapper.align(Align.center);
<BUG>VerticalGroup timeGroup = new VerticalGroup().align(Align.left).space(3 * GlobalConf.SCAL... | VerticalGroup timeGroup = new VerticalGroup().align(Align.left).columnAlign(Align.left).space(3 * GlobalConf.SCALE_FACTOR).padTop(3 * GlobalConf.SCALE_FACTOR);
|
8,982 | focusListScrollPane.setFadeScrollBars(false);
focusListScrollPane.setScrollingDisabled(true, false);
focusListScrollPane.setHeight(tree ? 200 * GlobalConf.SCALE_FACTOR : 100 * GlobalConf.SCALE_FACTOR);
focusListScrollPane.setWidth(160);
}
<BUG>VerticalGroup objectsGroup = new VerticalGroup().align(Align.left).space(3 *... | VerticalGroup objectsGroup = new VerticalGroup().align(Align.left).columnAlign(Align.left).space(3 * GlobalConf.SCALE_FACTOR);
|
8,983 | headerGroup.addActor(expandIcon);
headerGroup.addActor(detachIcon);
addActor(headerGroup);
expandIcon.setChecked(expanded);
}
<BUG>public void expand() {
</BUG>
if (!expandIcon.isChecked()) {
expandIcon.setChecked(true);
}
| public void expandPane() {
|
8,984 | </BUG>
if (!expandIcon.isChecked()) {
expandIcon.setChecked(true);
}
}
<BUG>public void collapse() {
</BUG>
if (expandIcon.isChecked()) {
expandIcon.setChecked(false);
}
| headerGroup.addActor(expandIcon);
headerGroup.addActor(detachIcon);
addActor(headerGroup);
expandIcon.setChecked(expanded);
public void expandPane() {
public void collapsePane() {
|
8,985 | });
playstop.addListener(new TextTooltip(txt("gui.tooltip.playstop"), skin));
TimeComponent timeComponent = new TimeComponent(skin, ui);
timeComponent.initialize();
CollapsiblePane time = new CollapsiblePane(ui, txt("gui.time"), timeComponent.getActor(), skin, true, playstop);
<BUG>time.align(Align.left);
mainActors.ad... | time.align(Align.left).columnAlign(Align.left);
mainActors.add(time);
|
8,986 | panes.put(visualEffectsComponent.getClass().getSimpleName(), visualEffects);
ObjectsComponent objectsComponent = new ObjectsComponent(skin, ui);
objectsComponent.setSceneGraph(sg);
objectsComponent.initialize();
CollapsiblePane objects = new CollapsiblePane(ui, txt("gui.objects"), objectsComponent.getActor(), skin, fal... | objects.align(Align.left).columnAlign(Align.left);
mainActors.add(objects);
|
8,987 | if (Constants.desktop) {
MusicComponent musicComponent = new MusicComponent(skin, ui);
musicComponent.initialize();
Actor[] musicActors = MusicActorsManager.getMusicActors() != null ? MusicActorsManager.getMusicActors().getActors(skin) : null;
CollapsiblePane music = new CollapsiblePane(ui, txt("gui.music"), musicCompo... | music.align(Align.left).columnAlign(Align.left);
mainActors.add(music);
|
8,988 | package com.intellij.ide.favoritesTreeView;
import com.intellij.ide.SelectInManager;
import com.intellij.ide.SelectInTarget;
<BUG>import com.intellij.ide.impl.ContentManagerWatcher;
import com.intellij.openapi.actionSystem.ActionManager;</BUG>
import com.intellij.openapi.actionSystem.DefaultActionGroup;
import com.inte... | import com.intellij.openapi.actionSystem.ActionGroup;
import com.intellij.openapi.actionSystem.ActionManager;
|
8,989 | ToolWindowManager toolWindowManager = ToolWindowManager.getInstance(myCurrentProject);
ToolWindow toolWindow = toolWindowManager.registerToolWindow(ToolWindowId.FAVORITES_VIEW, getComponent(), ToolWindowAnchor.RIGHT);
toolWindow.setIcon(IconLoader.getIcon("/general/toolWindowFavorites.png"));
new ContentManagerWatcher(... | final ActionGroup favoritesActionsGroup = ((ActionGroup)ActionManager.getInstance().getAction(IdeActions.ADD_TO_FAVORITES));
|
8,990 | if (key.equals(myCurrentFavoritesList)){
setSelectedContent(content);
}
}
}
<BUG>favoritesActionsGroup.addSeparator();
favoritesActionsGroup.add(new AddToNewFavoritesListAction());</BUG>
}
});
}
| [DELETED] |
8,991 | import com.intellij.openapi.project.Project;
import com.intellij.openapi.vfs.VirtualFile;
import com.intellij.openapi.wm.ToolWindowId;
import com.intellij.openapi.wm.ToolWindowManager;
import com.intellij.psi.*;
<BUG>import com.intellij.psi.search.GlobalSearchScope;
import com.intellij.uiDesigner.compiler.Utils;
import... | import com.intellij.psi.util.PsiTreeUtil;
|
8,992 | if (vFile != null) {
final FileType fileType = FileTypeManager.getInstance().getFileTypeByFile(vFile);
if (StdFileTypes.GUI_DESIGNER_FORM.equals(fileType)) {
final PsiFile formFile = psiManager.findFile(vFile);
String text = formFile.getText();
<BUG>LwRootContainer container;
try {
container = Utils.getRootContainer(te... | String className;
className = Utils.getBoundClassName(text);
}
|
8,993 | container = Utils.getRootContainer(text, null);
}</BUG>
catch (Exception e) {
return null;
}
<BUG>final PsiClass classToBind = psiManager.findClass(container.getClassToBind(), GlobalSearchScope.allScope(project));
result.add(FormNode.constructFormNode(psiManager, classToBind, project, favoritesConfig));
}</BUG>
return... | if (vFile != null) {
final FileType fileType = FileTypeManager.getInstance().getFileTypeByFile(vFile);
if (StdFileTypes.GUI_DESIGNER_FORM.equals(fileType)) {
final PsiFile formFile = psiManager.findFile(vFile);
String text = formFile.getText();
String className;
try {
className = Utils.getBoundClassName(text);
|
8,994 | if(worldIn.getTileEntity(pos) != null){
TileEntity te = worldIn.getTileEntity(pos);
if(te.hasCapability(Capabilities.HEAT_HANDLER_CAPABILITY, null) && te.getCapability(Capabilities.HEAT_HANDLER_CAPABILITY, null).getTemp() >= -273D + mult){
te.getCapability(Capabilities.HEAT_HANDLER_CAPABILITY, null).addHeat(-mult);
}
<... | if(te.hasCapability(Capabilities.HEAT_HANDLER_CAPABILITY, null)){
te.getCapability(Capabilities.HEAT_HANDLER_CAPABILITY, null).addHeat(mult);
|
8,995 | public static double betterRound(double numIn, int decPlac){
double opOn = Math.round(numIn * Math.pow(10, decPlac)) / Math.pow(10D, decPlac);
return opOn;
}
public static double centerCeil(double numIn, int tiers){
<BUG>return ((numIn > 0) ? Math.ceil(numIn * tiers) : Math.floor(numIn * tiers)) / tiers;
</BUG>
}
publi... | return ((numIn > 0) ? Math.ceil(numIn * (double) tiers) : Math.floor(numIn * (double) tiers)) / (double) tiers;
|
8,996 | package com.Da_Technomancer.crossroads.API;
import com.Da_Technomancer.crossroads.API.DefaultStorageHelper.DefaultStorage;
import com.Da_Technomancer.crossroads.API.heat.DefaultHeatHandler;
import com.Da_Technomancer.crossroads.API.heat.IHeatHandler;
import com.Da_Technomancer.crossroads.API.magic.DefaultMagicHandler;
... | import com.Da_Technomancer.crossroads.API.rotary.DefaultAxleHandler;
import com.Da_Technomancer.crossroads.API.rotary.DefaultCogHandler;
import com.Da_Technomancer.crossroads.API.rotary.IAxleHandler;
import com.Da_Technomancer.crossroads.API.rotary.ICogHandler;
|
8,997 | import net.minecraftforge.common.capabilities.Capability;
import net.minecraftforge.common.capabilities.CapabilityInject;
import net.minecraftforge.common.capabilities.CapabilityManager;
public class Capabilities{
@CapabilityInject(IHeatHandler.class)
<BUG>public static Capability<IHeatHandler> HEAT_HANDLER_CAPABILITY ... | @CapabilityInject(IAxleHandler.class)
public static Capability<IAxleHandler> AXLE_HANDLER_CAPABILITY = null;
@CapabilityInject(ICogHandler.class)
public static Capability<ICogHandler> COG_HANDLER_CAPABILITY = null;
|
8,998 | public IEffect getMixEffect(Color col){
if(col == null){
return effect;
}
int top = Math.max(col.getBlue(), Math.max(col.getRed(), col.getGreen()));
<BUG>if(top < rand.nextInt(128) + 128){
return voidEffect;</BUG>
}
return effect;
}
| if(top != 255){
return voidEffect;
|
8,999 | import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.security.DigestOutputStream;
import java.security.MessageDigest;
<BUG>import java.security.NoSuchAlgorithmException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;</BUG>
public final class ... | import java.text.DateFormat;
import java.util.Date;
import java.util.List;
|
9,000 | package org.jboss.as.patching.runner;
<BUG>import org.jboss.as.boot.DirectoryStructure;
import org.jboss.as.patching.LocalPatchInfo;</BUG>
import org.jboss.as.patching.PatchInfo;
import org.jboss.as.patching.PatchLogger;
import org.jboss.as.patching.PatchMessages;
| import static org.jboss.as.patching.runner.PatchUtils.generateTimestamp;
import org.jboss.as.patching.CommonAttributes;
import org.jboss.as.patching.LocalPatchInfo;
|
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