re-enabling regeneration of the tribble index if it's out of date. Also moved the class that can detect text in the log4j stream (useful in testing to make sure appropriate messages are generated).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3480 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron
parent
f0c379dde8
commit
8ec091d6d2
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@ -170,19 +170,17 @@ public class TribbleRMDTrackBuilder extends PluginManager<FeatureCodec> implemen
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// acquire a lock on the file
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boolean obtainedLock = lock.lock();
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try {
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// if the file exists, and we can read it, load the index from disk
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// check to see if the index file is out of date
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if (indexFile.exists() && indexFile.canRead() && obtainedLock && indexFile.lastModified() < inputFile.lastModified()) {
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logger.warn("Tribble index file " + indexFile + " is older than the track file " + inputFile + ", deleting and regenerating");
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indexFile.delete();
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}
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// if the file exists, and we can read it, load the index from disk (i.e. wasn't deleted in the last step).
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if (indexFile.exists() && indexFile.canRead() && obtainedLock) {
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// check to see if the index file is out of date
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if (indexFile.lastModified() < inputFile.lastModified())
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logger.warn("Tribble index file " + indexFile + " is older than the track file " + inputFile + ", this can lead to unexpected behavior");
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logger.info("Loading Tribble index from disk for file " + inputFile);
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return LinearIndex.createIndex(indexFile);
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}
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// else we need to create the index, and write it to disk if we can
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else
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return writeIndexToDisk(inputFile, codec, onDisk, indexFile, obtainedLock);
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return writeIndexToDisk(inputFile, codec, onDisk, indexFile, obtainedLock);
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}
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finally {
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lock.unlock();
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@ -1,6 +1,7 @@
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package org.broadinstitute.sting;
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import org.apache.log4j.*;
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import org.apache.log4j.spi.LoggingEvent;
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import org.junit.*;
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import java.io.BufferedReader;
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@ -139,4 +140,39 @@ public abstract class BaseTest {
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return temp.exists();
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}
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/**
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* this appender looks for a specific message in the log4j stream.
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* It can be used to verify that a specific message was generated to the logging system.
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*/
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public static class ValidationAppender extends AppenderSkeleton {
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private boolean foundString = false;
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private String targetString = "";
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public ValidationAppender(String target) {
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targetString = target;
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}
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@Override
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protected void append(LoggingEvent loggingEvent) {
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if (loggingEvent.getMessage().equals(targetString))
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foundString = true;
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}
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@Override
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public void close() {
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// do nothing
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}
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@Override
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public boolean requiresLayout() {
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return false;
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}
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public boolean foundString() {
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return foundString;
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}
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}
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}
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@ -33,9 +33,8 @@ import org.junit.Assert;
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import org.junit.Before;
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import org.junit.Test;
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import java.io.EOFException;
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import java.io.File;
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import java.io.IOException;
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import java.io.*;
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import java.nio.channels.FileChannel;
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import java.util.Map;
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@ -75,54 +74,135 @@ public class TribbleRMDTrackBuilderUnitTest extends BaseTest {
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}
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// test to make sure we delete the index and regenerate if it's out of date
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@Test
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public void testBuilderIndexOutOfDate() {
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Logger logger = Logger.getLogger(TribbleRMDTrackBuilder.class);
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ValidationAppender appender = new ValidationAppender("Tribble index file /humgen/gsa-hpprojects/GATK/data/Validation_Data/ROD_validation/newerTribbleTrack.vcf.idx is older than the track file /humgen/gsa-hpprojects/GATK/data/Validation_Data/ROD_validation/newerTribbleTrack.vcf, this can lead to unexpected behavior");
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logger.addAppender(appender);
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File vcfFile = new File(validationDataLocation + "/ROD_validation/newerTribbleTrack.vcf");
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File vcfFile = createOutofDateIndexFile(new File(validationDataLocation + "/ROD_validation/newerTribbleTrack.vcf"));
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try {
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builder.loadIndex(vcfFile,new VCFCodec(), true);
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} catch (IOException e) {
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e.printStackTrace();
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Assert.fail("IO exception unexpected" + e.getMessage());
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}
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// check to make sure the appender saw the target string
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Assert.assertTrue(appender.foundString());
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//System.err.println("index : " + new File(vcfFile + ".idx").lastModified());
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// System.err.println("vcf : " + vcfFile.lastModified());
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// make sure that we removed and updated the index
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Assert.assertTrue("VCF file index wasn't updated", new File(vcfFile + ".idx").lastModified() > vcfFile.lastModified());
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}
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// test to make sure we delete the index and regenerate if it's out of date
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@Test
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public void testBuilderIndexGoodDate() {
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Logger logger = Logger.getLogger(TribbleRMDTrackBuilder.class);
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File vcfFile = createCorrectDateIndexFile(new File(validationDataLocation + "/ROD_validation/newerTribbleTrack.vcf"));
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Long indexTimeStamp = new File(vcfFile.getAbsolutePath() + ".idx").lastModified();
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try {
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builder.loadIndex(vcfFile,new VCFCodec(), true);
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} catch (IOException e) {
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e.printStackTrace();
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Assert.fail("IO exception unexpected" + e.getMessage());
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}
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//System.err.println("index : " + new File(vcfFile + ".idx").lastModified());
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//System.err.println("old : " + indexTimeStamp);
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// make sure that we removed and updated the index
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Assert.assertTrue("Fail: index file was modified", new File(vcfFile + ".idx").lastModified() == indexTimeStamp);
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}
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/**
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* create a temporary file and an associated out of date index file
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* @param tribbleFile the tribble file
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* @return a file pointing to the new tmp location, with out of date index
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*/
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private File createOutofDateIndexFile(File tribbleFile) {
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try {
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// first copy the tribble file to a temperary file
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File tmpFile = File.createTempFile("TribbleUnitTestFile","");
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logger.info("creating temp file " + tmpFile);
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// create a fake index, before we copy so it's out of date
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File tmpIndex = new File(tmpFile.getAbsolutePath() + ".idx");
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tmpIndex.deleteOnExit();
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// sleep, to make sure the timestamps are different
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Thread.sleep(1000);
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// copy the vcf (tribble) file to the tmp file location
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copyFile(tribbleFile,tmpFile);
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// sleep again, to make sure the timestamps are different (vcf vrs updated index file)
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Thread.sleep(1000);
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return tmpFile;
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} catch (IOException e) {
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Assert.fail("Fail: Unable to create temperary file");
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} catch (InterruptedException e) {
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Assert.fail("Fail: Somehow our thread got interupted");
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}
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return null;
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}
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/**
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* create a temporary file and an associated out of date index file
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* @param tribbleFile the tribble file
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* @return a file pointing to the new tmp location, with out of date index
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*/
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private File createCorrectDateIndexFile(File tribbleFile) {
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try {
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// first copy the tribble file to a temperary file
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File tmpFile = File.createTempFile("TribbleUnitTestFile","");
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logger.info("creating temp file " + tmpFile);
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// copy the vcf (tribble) file to the tmp file location
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copyFile(tribbleFile,tmpFile);
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// sleep again, to make sure the timestamps are different (vcf vrs updated index file)
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Thread.sleep(1000);
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// create a fake index, before we copy so it's out of date
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File tmpIndex = new File(tmpFile.getAbsolutePath() + ".idx");
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tmpIndex.deleteOnExit();
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// copy the vcf (tribble) file to the tmp file location
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copyFile(new File(tribbleFile + ".idx"),tmpIndex);
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return tmpFile;
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} catch (IOException e) {
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Assert.fail("Unable to create temperary file");
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} catch (InterruptedException e) {
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Assert.fail("Somehow our thread got interupted");
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}
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return null;
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}
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/**
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* copy a file, from http://www.exampledepot.com/egs/java.nio/File2File.html
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* @param srFile the source file
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* @param dtFile the destination file
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*/
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private static void copyFile(File srFile, File dtFile) {
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try {
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// Create channel on the source
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FileChannel srcChannel = new FileInputStream(srFile).getChannel();
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// Create channel on the destination
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FileChannel dstChannel = new FileOutputStream(dtFile).getChannel();
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// Copy file contents from source to destination
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dstChannel.transferFrom(srcChannel, 0, srcChannel.size());
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// Close the channels
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srcChannel.close();
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dstChannel.close();
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} catch (IOException e) {
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e.printStackTrace();
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Assert.fail("Unable to process copy " + e.getMessage());
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}
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}
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}
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/**
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* this appender looks for a specific message in the log4j stream.
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* It can be used to verify that a specific message was generated to the logging system.
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*/
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class ValidationAppender extends AppenderSkeleton {
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private boolean foundString = false;
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private String targetString = "";
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public ValidationAppender(String target) {
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targetString = target;
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}
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@Override
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protected void append(LoggingEvent loggingEvent) {
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if (loggingEvent.getMessage().equals(targetString))
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foundString = true;
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}
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@Override
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public void close() {
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// do nothing
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}
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@Override
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public boolean requiresLayout() {
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return false;
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}
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public boolean foundString() {
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return foundString;
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}
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}
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