zxliu/ReAPR-Automatic-Program-Repair-via-Retrieval-Augmented-Large-Language-Models

package org.jboss.as.testsuite.integration.ejb.exception; /* * JBoss, Home of Professional Open Source. * Copyright (c) 2011, Red Hat, Inc., and individual contributors * as indicated by the @author tags. See the copyright.txt file in the * distribution for a full listing of individual contributors. * * This is ...

package org.jboss.as.testsuite.integration.ejb.packaging.multimodule; /* * JBoss, Home of Professional Open Source. * Copyright 2011, Red Hat, Inc., and individual contributors * as indicated by the @author tags. See the copyright.txt file in the * distribution for a full listing of individual contributors. * * ...

package org.jboss.as.testsuite.integration.ejb.security; /* * JBoss, Home of Professional Open Source. * Copyright (c) 2011, Red Hat, Inc., and individual contributors * as indicated by the @author tags. See the copyright.txt file in the * distribution for a full listing of individual contributors. * * This is f...

package org.jboss.as.testsuite.integration.ejb.security.lifecycle; /* * JBoss, Home of Professional Open Source. * Copyright (c) 2011, Red Hat, Inc., and individual contributors * as indicated by the @author tags. See the copyright.txt file in the * distribution for a full listing of individual contributors. * *...

package org.jboss.as.testsuite.integration.ejb.stateful.remove; /* * JBoss, Home of Professional Open Source. * Copyright 2011, Red Hat, Inc., and individual contributors * as indicated by the @author tags. See the copyright.txt file in the * distribution for a full listing of individual contributors. * * This i...

package org.jboss.as.testsuite.integration.ejb.view.basic; /* * JBoss, Home of Professional Open Source. * Copyright 2011, Red Hat, Inc., and individual contributors * as indicated by the @author tags. See the copyright.txt file in the * distribution for a full listing of individual contributors. * * This is fre...

package org.jboss.as.testsuite.integration.ejb.view.duplicateview; /* * JBoss, Home of Professional Open Source. * Copyright (c) 2011, Red Hat, Inc., and individual contributors * as indicated by the @author tags. See the copyright.txt file in the * distribution for a full listing of individual contributors. * *...

package org.jboss.as.testsuite.integration.weld.ejb.constructor; /* * JBoss, Home of Professional Open Source * Copyright 2010, Red Hat Inc., and individual contributors as indicated * by the @authors tag. See the copyright.txt in the distribution for a * full listing of individual contributors. * * This is free...

package org.jboss.as.testsuite.integration.weld.ejb.inheritance; /* * JBoss, Home of Professional Open Source * Copyright 2010, Red Hat Inc., and individual contributors as indicated * by the @authors tag. See the copyright.txt in the distribution for a * full listing of individual contributors. * * This is free...

package org.jboss.as.testsuite.integration.weld.ejb.injection; /* * JBoss, Home of Professional Open Source * Copyright 2010, Red Hat Inc., and individual contributors as indicated * by the @authors tag. See the copyright.txt in the distribution for a * full listing of individual contributors. * * This is free s...

package org.jboss.as.testsuite.integration.weld.ejb.interceptor.binding; /* * JBoss, Home of Professional Open Source * Copyright 2010, Red Hat Inc., and individual contributors as indicated * by the @authors tag. See the copyright.txt in the distribution for a * full listing of individual contributors. * * This...

package org.jboss.as.testsuite.integration.weld.ejb.interceptor.exceptions; /* * JBoss, Home of Professional Open Source * Copyright 2010, Red Hat Inc., and individual contributors as indicated * by the @authors tag. See the copyright.txt in the distribution for a * full listing of individual contributors. * * T...

package org.jboss.as.testsuite.integration.weld.ejb.interceptor.interceptorsOrderWithExclusions; /* * JBoss, Home of Professional Open Source * Copyright 2010, Red Hat, Inc. and/or its affiliates, and individual * contributors by the @authors tag. See the copyright.txt in the * distribution for a full listing of i...

package org.jboss.as.testsuite.integration.weld.ejb.interceptor.packaging; /* * JBoss, Home of Professional Open Source * Copyright 2010, Red Hat Inc., and individual contributors as indicated * by the @authors tag. See the copyright.txt in the distribution for a * full listing of individual contributors. * * Th...

package org.jboss.as.testsuite.integration.weld.ejb.packaging.warlib; /* * JBoss, Home of Professional Open Source * Copyright 2010, Red Hat Inc., and individual contributors as indicated * by the @authors tag. See the copyright.txt in the distribution for a * full listing of individual contributors. * * This is...

public final PathEntry getPathEntry(String pathName) { synchronized (pathEntries) { PathEntry pathEntry = pathEntries.get(pathName); if (pathEntry == null) { throw MESSAGES.pathEntryNotFound(pathName); } return pathEntry; } } f...

public boolean isGNULongNameEntry() { return linkFlag == LF_GNUTYPE_LONGNAME && name.toString().equals(GNU_LONGLINK); }

public boolean isGNULongNameEntry() { return linkFlag == LF_GNUTYPE_LONGNAME && name.equals(GNU_LONGLINK); }

public boolean evaluate(T object) { Boolean result = iTransformer.transform(object); if (result == null) { throw new FunctorException( "Transformer must return an instanceof Boolean, it was a null object"); } return result; }

public boolean evaluate(T object) { Boolean result = iTransformer.transform(object); if (result == null) { throw new FunctorException( "Transformer must return an instanceof Boolean, it was a null object"); } return result.booleanValue(); }

protected void prepare() { final Configuration hbConfig = HBaseConfiguration.create(); Map<String, Object> conf = (Map<String, Object>) map.get(options.configKey); if(conf == null){ LOG.info("HBase configuration not found using key '" + options.configKey + "'"); LOG.i...

String invalidLocaleString(String unparsed); /* * JBoss, Home of Professional Open Source. * Copyright 2011, Red Hat, Inc., and individual contributors * as indicated by the @author tags. See the copyright.txt file in the * distribution for a full listing of individual contributors. * * This is free software; yo...

public void handleReport(final MessageSeverity severity, final String message) { Logger.Level level; switch (severity) { case ERROR: level = Logger.Level.ERROR; break; case WARN: level = Logger.Level.WARN; break; case INFO: ...

public class InherritanceAnnOnlyCheckSLSB extends ParentAnnOnlyCheck implements SimpleAuthorizationRemote { /* * JBoss, Home of Professional Open Source. * Copyright (c) 2011, Red Hat, Inc., and individual contributors * as indicated by the @author tags. See the copyright.txt file in the * distribution for a full ...

public Archive<?> createAuxiliaryArchive() { JavaArchive archive = ShrinkWrap.create(JavaArchive.class, "arquillian-testenricher-msc.jar"); archive.addAsServiceProvider(RemoteLoadableExtension.class, MSCEnricherRemoteExtension.class); archive.addPackage(MSCTestEnricher.class.getPackage()); ...

public Archive<?> createAuxiliaryArchive() { JavaArchive archive = ShrinkWrap.create(JavaArchive.class, "arquillian-testenricher-msc.jar"); archive.addAsServiceProvider(RemoteLoadableExtension.class, MSCEnricherRemoteExtension.class); archive.addPackage(MSCEnricherExtension.class.getPackage(...

protected void initModel(Resource rootResource, ManagementResourceRegistration rootRegistration) { // TODO maybe make creating of empty nodes part of the MNR description Resource managementResource = Resource.Factory.create(); // TODO - Can we get a Resource direct from CoreManagementResourceDefinit...

public void setMessageListenerInterfaceName(String messageListenerInterfaceName) { if (messageListenerInterfaceName == null || messageListenerInterfaceName.isEmpty()) { throw new IllegalArgumentException("Cannot set null or empty string as message listener interface"); } this.mes...

private ContextManager initializeContextManager(final ArquillianConfig config, final Map<String, Object> properties) { final ContextManagerBuilder builder = new ContextManagerBuilder(); final DeploymentUnit depUnit = config.getDeploymentUnit(); final XBundle bundle = depUnit....

public void deploy(DeploymentPhaseContext phaseContext) throws DeploymentUnitProcessingException { DeploymentUnit depUnit = phaseContext.getDeploymentUnit(); ContextActivator activator = depUnit.getAttachment(ContextActivator.ATTACHMENT_KEY); XBundle bundle = depUnit.getAttachment(OSGiConsta...

public void deploy(final DeploymentPhaseContext phaseContext) throws DeploymentUnitProcessingException { DeploymentUnit depUnit = phaseContext.getDeploymentUnit(); Deployment deployment = depUnit.getAttachment(OSGiConstants.DEPLOYMENT_KEY); XBundle bundle = depUnit.getAttachment(OSGiConstan...

private BundleContext getSystemContext(OperationContext context) { ServiceController<?> controller = context.getServiceRegistry(false).getService(Services.SYSTEM_CONTEXT); return controller != null ? (BundleContext)controller.getValue() : null; }

private BundleContext getSystemContext(OperationContext context) { ServiceController<?> controller = context.getServiceRegistry(false).getService(Services.FRAMEWORK_CREATE); return controller != null ? (BundleContext)controller.getValue() : null; }

public static void addService(ServiceTarget serviceTarget) { EchoService service = new EchoService(); ServiceBuilder<Echo> serviceBuilder = serviceTarget.addService(SERVICE_NAME, service); serviceBuilder.addDependency(Services.SYSTEM_CONTEXT, BundleContext.class, service.injectedBundleContex...

public static void addService(ServiceTarget serviceTarget) { EchoService service = new EchoService(); ServiceBuilder<Echo> serviceBuilder = serviceTarget.addService(SERVICE_NAME, service); serviceBuilder.addDependency(Services.FRAMEWORK_ACTIVE, BundleContext.class, service.injectedBundleCont...

public DuplicateSampleAbscissaException(double abscissa, int i1, int i2) { super("Abscissa {0} is duplicated at both indices {1} and {2}", new Object[] { Double.valueOf(abscissa), Integer.valueOf(i1), Integer.valueOf(i2) }); }

public DuplicateSampleAbscissaException(double abscissa, int i1, int i2) { super("Abscissa {0} is duplicated at both indices {1} and {2}", abscissa, i1, i2); }

public LegendreGaussIntegrator(final int n, final int defaultMaximalIterationCount) throws IllegalArgumentException { super(defaultMaximalIterationCount); switch(n) { case 2 : abscissas = ABSCISSAS_2; weights = WEIGHTS_2; break; case 3 : ...

protected void verifyIterationCount() throws IllegalArgumentException { super.verifyIterationCount(); // at most 32 bisection refinements due to higher order divider if (maximalIterationCount > 32) { throw MathRuntimeException.createIllegalArgumentException( "...

protected void verifyIterationCount() throws IllegalArgumentException { super.verifyIterationCount(); // at most 64 bisection refinements if (maximalIterationCount > 64) { throw MathRuntimeException.createIllegalArgumentException( "invalid iteration limits: mi...

protected void checkResultComputed() throws IllegalStateException { if (!resultComputed) { throw MathRuntimeException.createIllegalStateException("no result available", null); } }

protected void checkResultComputed() throws IllegalStateException { if (!resultComputed) { throw MathRuntimeException.createIllegalStateException("no result available"); } }

public double solve(final UnivariateRealFunction f, final double min, final double max) throws MaxIterationsExceededException, FunctionEvaluationException { clearResult(); verifyInterval(min, max); double ret = Double.NaN; ...

public double value(double x) throws FunctionEvaluationException { try { return cumulativeProbability(x) - p; } catch (MathException ex) { throw new FunctionEvaluationException(x, ex.getPattern(), ex.getArguments(), ex); ...

public double value(double x) throws FunctionEvaluationException { try { return cumulativeProbability(x) - p; } catch (MathException ex) { throw new FunctionEvaluationException(ex, x, ex.getPattern(), ex.getArguments()); ...

public EstimationException(String specifier, Object[] parts) { super(specifier, parts); } }

public EstimationException(String specifier, Object ... parts) { super(specifier, parts); } }

public void estimate(EstimationProblem problem) throws EstimationException { initializeEstimate(problem); // work matrices double[] grad = new double[parameters.length]; RealVectorImpl bDecrement = new RealVectorImpl(parameters.length); double[] bDecrementDa...

public CardanEulerSingularityException(boolean isCardan) { super(isCardan ? "Cardan angles singularity" : "Euler angles singularity", null); }

public CardanEulerSingularityException(boolean isCardan) { super(isCardan ? "Cardan angles singularity" : "Euler angles singularity"); }

public MatrixIndexException(final String pattern, final Object[] arguments) { super(pattern, arguments); } }

public MatrixIndexException(final String pattern, final Object ... arguments) { super(pattern, arguments); } }

public NonSquareMatrixException(final int rows, final int columns) { super("a {0}x{1} matrix was provided instead of a square matrix", new Object[] { rows, columns }); }

public NonSquareMatrixException(final int rows, final int columns) { super("a {0}x{1} matrix was provided instead of a square matrix", rows, columns); }

public NotPositiveDefiniteMatrixException() { super("not positive definite matrix", null); }

public NotPositiveDefiniteMatrixException() { super("not positive definite matrix"); }

public NotSymmetricMatrixException() { super("not symmetric matrix", null); }

public NotSymmetricMatrixException() { super("not symmetric matrix"); }

public SingularMatrixException() { super("matrix is singular", null); }

public SingularMatrixException() { super("matrix is singular"); }

public void setInterpolatedTime(final double time) { try { // initialize the search with the complete steps table int iMin = 0; final StepInterpolator sMin = steps.get(iMin); double tMin = 0.5 * (sMin.getPreviousTime() + sMin.getCurrentTime()); int iMax = steps.size() - 1; fi...

public void testConstructorPatternArgumentsCause(){ String pattern = "a {0}x{1} matrix cannot be a rotation matrix"; Object[] arguments = { Integer.valueOf(6), Integer.valueOf(4) }; String inMsg = "inner message"; Exception cause = new Exception(inMsg); ConvergenceException e...

public void testConstructorPatternArgumentsCause(){ String pattern = "a {0}x{1} matrix cannot be a rotation matrix"; Object[] arguments = { Integer.valueOf(6), Integer.valueOf(4) }; String inMsg = "inner message"; Exception cause = new Exception(inMsg); MathConfigurationExcep...

public void testComplexConstructor(){ MaxIterationsExceededException ex = new MaxIterationsExceededException(1000000, "Continued fraction convergents failed to converge for value {0}", new Object[] { Double.valueOf(1234567) }); assertNull(ex.getCause()); ...

public void testComplexConstructor(){ MaxIterationsExceededException ex = new MaxIterationsExceededException(1000000, "Continued fraction convergents failed to converge for value {0}", 1234567); assertNull(ex.getCause()); assertNotNull(ex.getMessag...

public void testConstructorMessage(){ String msg = "message"; MatrixIndexException ex = new MatrixIndexException(msg, null); assertEquals(msg, ex.getMessage()); }

public void testConstructorMessage(){ String msg = "message"; MatrixIndexException ex = new MatrixIndexException(msg); assertEquals(msg, ex.getMessage()); }

protected void splitLU(RealMatrix lu, double[][] lowerData, double[][] upperData) throws InvalidMatrixException { if (!lu.isSquare() || lowerData.length != lowerData[0].length || upperData.length != upperData[0].length || lowerData.length != upperData.length || lowerData.l...

public double cost(double[] x) throws CostException { if (x[0] < 0) { throw new CostException("{0}", new Object[] { "oops"}); } else if (x[0] > 1) { throw new CostException(new RuntimeException("oops")); } else { ...

public double cost(double[] x) throws CostException { if (x[0] < 0) { throw new CostException("{0}", "oops"); } else if (x[0] > 1) { throw new CostException(new RuntimeException("oops")); } else { ret...

public double cost(double[] x) throws CostException { if (x[0] < 0) { throw new CostException("{0}", new Object[] { "oops"}); } else if (x[0] > 1) { throw new CostException(new RuntimeException("oops")); } else { ...

public double cost(double[] x) throws CostException { if (x[0] < 0) { throw new CostException("{0}", "oops"); } else if (x[0] > 1) { throw new CostException(new RuntimeException("oops")); } else { ret...

public Double getZ() { throw new MathRuntimeException("?", null); }

public Double getZ() { throw new MathRuntimeException("?"); }

SimpleAttributeDefinition SUFFIX = SimpleAttributeDefinitionBuilder.create("suffix", ModelType.STRING).build(); /* * JBoss, Home of Professional Open Source. * Copyright 2010, Red Hat, Inc., and individual contributors * as indicated by the @author tags. See the copyright.txt file in the * distribution for a full ...

public void add(VirtualFile file, InputStream is) throws Exception { String name = "JBOSS_HOME" + file.getPathName().substring(this.jbossHome.length()); this.add(is, name); }

public void add(VirtualFile file, InputStream is) throws Exception { String name = "JBOSS_HOME" + file.getPhysicalFile().getAbsolutePath().substring(this.jbossHome.length()); this.add(is, name); }

protected static final SimpleListAttributeDefinition VIRTUAL_SERVER = SimpleListAttributeDefinition.Builder.of(Constants.VIRTUAL_SERVER, new SimpleAttributeDefinitionBuilder(Constants.VIRTUAL_SERVER, ModelType.STRING, false)

protected static final SimpleListAttributeDefinition VIRTUAL_SERVER = new SimpleListAttributeDefinition.Builder(Constants.VIRTUAL_SERVER, new SimpleAttributeDefinitionBuilder(Constants.VIRTUAL_SERVER, ModelType.STRING, false)

protected static final SimpleListAttributeDefinition ALIAS = SimpleListAttributeDefinition.Builder.of(Constants.ALIAS, new SimpleAttributeDefinitionBuilder(Constants.ALIAS, ModelType.STRING, false)

protected static final SimpleListAttributeDefinition ALIAS = new SimpleListAttributeDefinition.Builder(Constants.ALIAS, new SimpleAttributeDefinitionBuilder(Constants.ALIAS, ModelType.STRING, false)

public void deploy(DeploymentPhaseContext phaseContext) throws DeploymentUnitProcessingException { final DeploymentUnit deploymentUnit = phaseContext.getDeploymentUnit(); if (!DeploymentTypeMarker.isType(DeploymentType.WAR, deploymentUnit)) { return; // Skip non web deployments }...

public void start(StartContext context) throws StartException { SingletonProvider.initialize(new TCCLSingletonProvider()); }

public void start(StartContext context) throws StartException { SingletonProvider.initialize(new ModuleGroupSingletonProvider()); }

Object convertValue(Object value, TypeDescriptor typeDescriptor) throws EvaluationException; /* * Copyright 2002-2009 the original author or authors. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of th...

private TypedValue createNewInstance(ExpressionState state) throws EvaluationException { Object[] arguments = new Object[getChildCount() - 1]; Class<?>[] argumentTypes = new Class[getChildCount() - 1]; for (int i = 0; i < arguments.length; i++) { TypedValue childValue = getChild(i + 1).getValueInternal(state)...

public BooleanTypedValue getValueInternal(ExpressionState state) throws EvaluationException { try { boolean value = state.convertValue(getChild(0).getValueInternal(state), BOOLEAN_TYPE_DESCRIPTOR); return BooleanTypedValue.forValue(!value); } catch (SpelException see) { see.setPosition(getChild(0).getCh...

public BooleanTypedValue getValueInternal(ExpressionState state) throws EvaluationException { try { boolean value = (Boolean)state.convertValue(getChild(0).getValueInternal(state), BOOLEAN_TYPE_DESCRIPTOR); return BooleanTypedValue.forValue(!value); } catch (SpelException see) { see.setPosition(getChild...

protected String getBaseUrl() { final String address = injectedSocketBinding.getValue().getAddress().getHostAddress(); final int port = injectedSocketBinding.getValue().getPort(); if (injectedSocketBinding.getValue().getAddress() instanceof Inet4Address) { return "http://" + add...

protected String getBaseUrl() { final String address = injectedSocketBinding.getValue().getAddress().getHostAddress(); final int port = injectedSocketBinding.getValue().getAbsolutePort(); if (injectedSocketBinding.getValue().getAddress() instanceof Inet4Address) { return "http:/...

private URI extractSubSystemURI(String subsystem) { try { if (rootNode == null) { readRootNode(); } } catch (Exception e) { throw new RuntimeException(e); } if ("web".equals(subsystem)) { String socketBinding = rootNode...

package org.jboss.as.patching.installation; /* * JBoss, Home of Professional Open Source. * Copyright 2013, Red Hat, Inc., and individual contributors * as indicated by the @author tags. See the copyright.txt file in the * distribution for a full listing of individual contributors. * * This is free software; you...

private void checkManifest(Archive<?> archive, ModuleApplicationArchiveProcessor processor) { Node node = archive.get(MANIFEST); Assert.assertNotNull(node); Manifest mf = processor.getOrCreateManifest(archive); Attributes attributes = mf.getMainAttributes(); String value = a...

private void checkManifest(Archive<?> archive, ModuleApplicationArchiveProcessor processor) { Node node = archive.get(MANIFEST); Assert.assertNotNull(node); Manifest mf = ManifestUtils.getOrCreateManifest(archive); Attributes attributes = mf.getMainAttributes(); String value...

public void addEntries(ModelNode current, Context context) throws NamingException{ JndiViewOperation.this.addEntries(current, context); } }); } } ...

public static boolean waitFor(File file, int seconds) { int timeout = 0; int tick = 0; while (!file.exists()) { if (tick++ >= 10) { tick = 0; if (timeout++ > seconds) { return false; } } t...

public int hashCode() { return this.id.hashCode() ^ this.attribute.hashCode(); }

public int hashCode() { return this.id.hashCode(); }

public interface SessionManager<L> extends SessionIdentifierFactory, RouteLocator { /* * JBoss, Home of Professional Open Source. * Copyright 2013, Red Hat, Inc., and individual contributors * as indicated by the @author tags. See the copyright.txt file in the * distribution for a full listing of individual contri...

package org.jboss.as.ejb3.cache; /* * JBoss, Home of Professional Open Source. * Copyright 2007, Red Hat Middleware LLC, and individual contributors * as indicated by the @author tags. See the copyright.txt file in the * distribution for a full listing of individual contributors. * * This is free software; you ...

import org.jboss.as.ejb3.pool.Pool; /* * JBoss, Home of Professional Open Source. * Copyright (c) 2011, Red Hat, Inc., and individual contributors * as indicated by the @author tags. See the copyright.txt file in the * distribution for a full listing of individual contributors. * * This is free software; you can...

package org.jboss.as.ejb3.concurrency; /* * JBoss, Home of Professional Open Source. * Copyright 2010, Red Hat, Inc., and individual contributors * as indicated by the @author tags. See the copyright.txt file in the * distribution for a full listing of individual contributors. * * This is free software; you can ...

package org.jboss.as.ejb3.context.spi; /* * JBoss, Home of Professional Open Source * Copyright (c) 2010, JBoss Inc., and individual contributors as indicated * by the @authors tag. See the copyright.txt in the distribution for a * full listing of individual contributors. * * This is free software; you can redis...