Java Code Examples for org.apache.commons.io.FileUtils#contentEquals()

@Test
public void writeOutput() {
	BaseDistributionAtReadPosition test= new BaseDistributionAtReadPosition();
	BaseDistributionMetricCollection result = test.gatherBaseQualities (TAGGED_FILE, "XC");
	File tempReportFile=getTempReportFile();

       result.writeOutput(tempReportFile);

	boolean testSuccess=false;
	try {
		testSuccess=FileUtils.contentEquals(tempReportFile, OUTPUT_EXPECTED_RESULT);
	} catch (IOException e) {
		e.printStackTrace();
	}

	Assert.assertTrue(testSuccess);
	tempReportFile.delete();

}
 

@Test
public void testDoWork () {
	BaseDistributionAtReadPosition test= new BaseDistributionAtReadPosition();
	File tempReportFile=getTempReportFile();
	test.INPUT=TAGGED_FILE;
	test.TAG="XC";
	test.OUTPUT=tempReportFile;
	test.doWork();

	boolean testSuccess=false;
	try {
		testSuccess=FileUtils.contentEquals(tempReportFile, OUTPUT_EXPECTED_RESULT);
	} catch (IOException e) {
		e.printStackTrace();
	}

	Assert.assertTrue(testSuccess);
	tempReportFile.delete();

}
 

public List<File> load(String artifact, Collection<String> excludes, File destPath)
    throws RepositoryException, IOException {
  List<File> libs = new LinkedList<>();

  if (StringUtils.isNotBlank(artifact)) {
    libs = load(artifact, excludes);

    for (File srcFile : libs) {
      File destFile = new File(destPath, srcFile.getName());
      if (!destFile.exists() || !FileUtils.contentEquals(srcFile, destFile)) {
        FileUtils.copyFile(srcFile, destFile);
        logger.debug("copy {} to {}", srcFile.getAbsolutePath(), destPath);
      }
    }
  }
  return libs;
}
 

public void execute() {
    checkParams();
    File file1 = new File(firstFile);
    if (!file1.exists()) {
        throw new BuildException("The file " + firstFile + "does not exist");
    }
    File file2 = new File(secondFile);
    if (!file2.exists()) {
        throw new BuildException("The file " + secondFile
                + "does not exist");
    }

    try {
        if (!FileUtils.contentEquals(file1, file2)) {
            throw new BuildException(
                    "The two input files are not equal in content");
        }
    } catch (IOException e) {
        throw new BuildException(
                "IOException while trying to compare content of files: "
                        + e.getMessage());
    }
}
 

@Test
    public void testDoWork () {
    	ReduceGtf r = new ReduceGtf();
    	r.GTF=GTF_FILE5;
    	r.SEQUENCE_DICTIONARY=SD;
    	File o = getTempReportFile("ReduceGtf", ".reduced.gtf.gz");
    	// File o2 = getTempReportFile("ReduceGtf", ".reduced.gtf");
    	o.deleteOnExit();
    	// o2.deleteOnExit();
    	//r.OUTPUT=GTF_FILE5_REDUCED;
    	r.OUTPUT=o;
    	r.ENHANCE_GTF=true;
    	int ret = r.doWork();
    	Assert.assertTrue(ret==0);
//    	r.OUTPUT=o2;
//    	int ret2 = r.doWork();
//    	Assert.assertTrue(ret2==0);


    	try {
			boolean t1 = FileUtils.contentEquals(o, GTF_FILE5_REDUCED);
			Assert.assertTrue(t1);
		} catch (IOException e) {
			e.printStackTrace();
		}


    }
 

@Test
public void testBytesReceived() throws IOException
{
  long blockSize = 1500;
  int noOfBlocks = (int)((testMeta.dataFile.length() / blockSize) + (((testMeta.dataFile.length() % blockSize) == 0) ?
      0 : 1));

  testMeta.blockReader.beginWindow(1);

  for (int i = 0; i < noOfBlocks; i++) {
    BlockMetadata.FileBlockMetadata blockMetadata = new BlockMetadata.FileBlockMetadata(
        testMeta.dataFile.getAbsolutePath(), i, i * blockSize,
        i == noOfBlocks - 1 ? testMeta.dataFile.length() : (i + 1) * blockSize,
        i == noOfBlocks - 1, i - 1);
    testMeta.blockReader.blocksMetadataInput.process(blockMetadata);
  }

  testMeta.blockReader.endWindow();

  List<Object> messages = testMeta.messageSink.collectedTuples;
  long totatBytesReceived = 0;

  File outputFile = new File(testMeta.output + "/reader_test_data.csv");
  FileOutputStream outputStream = new FileOutputStream(outputFile);

  for (Object message : messages) {
    @SuppressWarnings("unchecked")
    AbstractBlockReader.ReaderRecord<Slice> msg = (AbstractBlockReader.ReaderRecord<Slice>)message;
    totatBytesReceived += msg.getRecord().length;
    outputStream.write(msg.getRecord().buffer);
  }
  outputStream.close();

  Assert.assertEquals("number of bytes", testMeta.dataFile.length(), totatBytesReceived);
  FileUtils.contentEquals(testMeta.dataFile, outputFile);
}
 

private void copyJarEntryTrimmingBasePath(JarFile jarFile,
        ZipEntry jarEntry, String basePath, File outputDirectory) {
    String fullPath = jarEntry.getName();
    String relativePath = fullPath
            .substring(fullPath.toLowerCase(Locale.ENGLISH)
                    .indexOf(basePath.toLowerCase(Locale.ENGLISH))
                    + basePath.length());
    File target = new File(outputDirectory, relativePath);
    try {
        if (target.exists()) {
            File tempFile = File.createTempFile(fullPath, null);
            FileUtils.copyInputStreamToFile(
                    jarFile.getInputStream(jarEntry), tempFile);
            if (!FileUtils.contentEquals(tempFile, target)) {
                FileUtils.forceDelete(target);
                FileUtils.moveFile(tempFile, target);
            } else {
                tempFile.delete();
            }
        } else {
            FileUtils.copyInputStreamToFile(
                    jarFile.getInputStream(jarEntry), target);
        }
    } catch (IOException e) {
        throw new UncheckedIOException(String.format(
                "Failed to extract jar entry '%s' from jarFile '%s'",
                jarEntry, outputDirectory), e);
    }
}
 

public synchronized void copyLocalDependency(String srcPath, File destPath)
    throws IOException {
  if (StringUtils.isBlank(srcPath)) {
    return;
  }

  File srcFile = new File(srcPath);
  File destFile = new File(destPath, srcFile.getName());

  if (!destFile.exists() || !FileUtils.contentEquals(srcFile, destFile)) {
    FileUtils.copyFile(srcFile, destFile);
    logger.debug("copy {} to {}", srcFile.getAbsolutePath(), destPath);
  }
}
 

/****
 * Checks if the DDL file is same for stat1 and stat2
 * @param stat1
 * @param stat2
 * @return true if the files are same
 */
public static boolean isDDLFileSame(GFXDSnapshotExportStat stat1, GFXDSnapshotExportStat stat2)  {
  File ddlFile1  = new File(stat1.getFileName());
  File ddlFile2 = new File(stat2.getFileName());
  try {
    return FileUtils.contentEquals(ddlFile1, ddlFile2);
  }catch (Exception e) {
    GemFireXDDataExtractorImpl.logInfo("Exception occurred while comparing the DDL", e);
  }
  return false;
}
 

/****
 * Checks if the DDL file is same for stat1 and stat2
 * @param stat1
 * @param stat2
 * @return true if the files are same
 */
public static boolean isDDLFileSame(GFXDSnapshotExportStat stat1, GFXDSnapshotExportStat stat2)  {
  File ddlFile1  = new File(stat1.getFileName());
  File ddlFile2 = new File(stat2.getFileName());
  try {
    return FileUtils.contentEquals(ddlFile1, ddlFile2);
  }catch (Exception e) {
    GemFireXDDataExtractorImpl.logInfo("Exception occurred while comparing the DDL", e);
  }
  return false;
}
 

/**
 * Updates certificates from temporary working directory to production and
 * restarts services.
 * 
 * @return true if update was successful. false if update was aborted due to
 *         some error (perhaps permissions issue.)
 */
private boolean updateCertificates() {
	if (!compare(tomcatCertFN) || !compare(idpCertFN)) {
		facesMessages.add(FacesMessage.SEVERITY_ERROR,
				"Certificates and private keys should match. Certificate update aborted.");
		return false;
	}
	String tempDirFN = appConfiguration.getTempCertDir();
	String dirFN = appConfiguration.getCertDir();
	File certDir = new File(dirFN);
	File tempDir = new File(tempDirFN);
	if (tempDirFN == null || dirFN == null || !certDir.isDirectory() || !tempDir.isDirectory()) {
		facesMessages.add(FacesMessage.SEVERITY_ERROR, "Certificate update aborted due to filesystem error");
		return false;
	} else {
		File[] files = tempDir.listFiles();
		for (File file : files) {
			try {
				if (file.isFile()
						&& !FileUtils.contentEquals(file, new File(dirFN + File.separator + file.getName()))) {
					FileHelper.copy(file, new File(dirFN + File.separator + file.getName()));
					this.wereAnyChanges = true;
				}
			} catch (IOException e) {
				facesMessages.add(FacesMessage.SEVERITY_FATAL,
						"Certificate update failed. Certificates may have been corrupted. Please contact a Gluu administrator for help.");
				log.error("Error occured on certificates update:", e);
			}
		}
	}
	return true;
}
 

@Override
protected boolean compare(File baselineFile, File comparisonFile) {
    try {
        return FileUtils.contentEquals(baselineFile, comparisonFile);
    } catch (IOException e) {
        throw new TransformationUtilityException("An exception has happened when comparing files", e);
    }
}
 

@Test
public void testDoWorkDualOrganism () throws IOException {

	File outFile = File.createTempFile("SelectCellsByNumTranscripts.", ".cellBarcodes");
	File outFileMinReads = File.createTempFile("SelectCellsByNumTranscripts.", ".minReads");
	outFile.deleteOnExit();
	outFileMinReads.deleteOnExit();

	List<String> organisms = Arrays.asList("HUMAN", "MOUSE");
	SelectCellsByNumTranscripts s = new SelectCellsByNumTranscripts();
	s.INPUT=this.DUAL_ORGANISM_BAM;
	s.ORGANISM=organisms;
	s.MIN_TRANSCRIPTS_PER_CELL=100;
	s.OUTPUT=outFile;
	s.MIN_READS_PER_CELL=null;
	s.OUTPUT_INTERIM_CELLS=outFileMinReads;
	s.READ_MQ=0;
	s.METRICS = File.createTempFile("SelectCellsByNumTranscripts.", ".metrics");
	s.METRICS.deleteOnExit();
	int success = s.doWork();

	try {
		boolean t1 = FileUtils.contentEquals(outFileMinReads, DUAL_ORGANISM_BAM_EXPECTED_CB_100_READS);
		boolean t2 = FileUtils.contentEquals(outFile, DUAL_ORGANISM_BAM_EXPECTED_CB_100_TRANSCRIPTS);
		Assert.assertTrue(t1);
		Assert.assertTrue(t2);
	} catch (IOException e) {
		e.printStackTrace();
	}

	Assert.assertEquals(0, success);

}
 

public boolean areImagesOfShaderResultsIdentical(
    File referenceShaderResultFile,
    File variantShaderResultFile) throws IOException {

  //noinspection deprecation: OK in this class.
  File reference = getUnderlyingImageFileFromShaderJobResultFile(referenceShaderResultFile);
  //noinspection deprecation: OK in this class.
  File variant = getUnderlyingImageFileFromShaderJobResultFile(variantShaderResultFile);

  LOGGER.info("Comparing: {} and {}.", reference, variant);
  boolean identical = FileUtils.contentEquals(reference, variant);
  LOGGER.info("Identical? {}", identical);

  return identical;
}
 

protected boolean checkContentEquals(File expected, String actual) throws IOException, CoreException {
	File actualContent = EFS.getStore(makeLocalPathAbsolute(actual)).toLocalFile(EFS.NONE, null);
	return FileUtils.contentEquals(expected, actualContent);
}
 

public static boolean hierarchieEquals(File root1,File root2) throws IOException {
    File[] files1 = root1.listFiles();
    File[] files2 = root2.listFiles();
    if(files1.length != files2.length) {
        return false;
    }
    
    Map<String,File> mapFiles2 = new HashMap<>();
    for(File f : files2) {
        mapFiles2.put(f.getName(), f);
    }
    
    for(File f1 : files1) {
        if(!mapFiles2.containsKey(f1.getName())) {
            return false;
        }
        
        File f2 = mapFiles2.get(f1.getName());
        if(f1.isDirectory() && f2.isDirectory()) {
            if(!hierarchieEquals(f1,f2)) {
                return false;
            }
        }
        else if(f1.isFile() && f2.isFile()) {
            if(!FileUtils.contentEquals(f1, f2)) {
                return false;
            }
        }
        else {
            return false;
        }
        
        mapFiles2.remove(f1.getName());
    }
    
    if(!mapFiles2.isEmpty()) {
        return false;
    }
    
    return true;
}
 

@Test
public void readFileTest() throws IOException {
    TransformationOperation transformationOperation = getNewTestTransformationOperation().relative("pom.xml");
    File readFile = transformationOperation.getOrCreateReadFile(transformedAppFolder, transformationContext);
    FileUtils.contentEquals(new File(transformedAppFolder, "pom.xml"), readFile);
}
 

@Test
public void testDoWork() {
	DetectBeadSynthesisErrors gbse = new DetectBeadSynthesisErrors();

	File report = getTempReportFile("DetectBeadSynthesisErrorsTest", ".report");
	File stats = getTempReportFile("DetectBeadSynthesisErrorsTest", ".stats");
	File summary = getTempReportFile("DetectBeadSynthesisErrorsTest", ".summary");
	File cleanBAM = getTempReportFile("DetectBeadSynthesisErrorsTest", ".bam");

	report.deleteOnExit();
	stats.deleteOnExit();
	summary.deleteOnExit();
	cleanBAM.deleteOnExit();

	gbse.INPUT=Arrays.asList(TEST_INDEL);
	gbse.NUM_BARCODES=1000; // more than the BAM has.
	gbse.SUMMARY=summary;
    gbse.OUTPUT=cleanBAM;
	gbse.REPORT=report;
	gbse.OUTPUT_STATS=stats;

	// test custom command line validation
	gbse.MAX_BARCODE_ERRORS_IN_RAM=5;  // i want to test serialization/deserialization.

	int result = gbse.doWork();
	Assert.assertEquals(0, result);

	try {
		boolean t1 = FileUtils.contentEquals(report, EXPECTED_REPORT);
		boolean t2 = FileUtils.contentEquals(stats, EXPECTED_STATS);
		boolean t3 = FileUtils.contentEquals(summary, EXPECTED_SUMMARY);
		Assert.assertTrue(t1);
		Assert.assertTrue(t2);
		Assert.assertTrue(t3);
	} catch (IOException e) {
		e.printStackTrace();
	}

	// test BAM
	CompareBAMTagValues cbtv = new CompareBAMTagValues();
	cbtv.INPUT_1=EXPECTED_BAM;
	cbtv.INPUT_2=cleanBAM;
	List<String> tags = new ArrayList<>();
	tags.add("XC");
	cbtv.TAGS=tags;
	int r = cbtv.doWork();
	Assert.assertTrue(r==0);




}
 

public Boolean fileExistsAndHasTheGoodSize(String file) throws Exception {
    File dl = new File(FOLDER_PATH_GET + "/" + file);
    File or = new File(FOLDER_PATH_PUT + "/" + file);
    return (dl.exists() && FileUtils.contentEquals(dl, or));
}
 

/**
 * Compare each file in the example/results/ directory, to the corresponding file in the examples/
 * directory.
 *
 * @throws Exception on IO problems or file differences
 */
private void compareResults() throws Exception {
  IOHelper ioHelper = new IOHelper();
  File resultsDir = new File(resultsPath);
  for (File resultFile : resultsDir.listFiles()) {
    if (!resultFile.isFile()) {
      continue;
    }

    // Find the corresponding example file
    String examplePath = examplesPath + resultFile.getName();
    File exampleFile = new File(examplePath);
    if (!exampleFile.exists() || !exampleFile.isFile()) {
      throw new Exception(
          "Integration test file '"
              + resultsPath
              + resultFile.getName()
              + "' does not have a corresponding example file '"
              + examplePath
              + "'");
    }

    if (resultFile.getName().endsWith(".owl")) {
      // Compare OWL files using DiffOperation
      OWLOntology exampleOnt = ioHelper.loadOntology(exampleFile);
      OWLOntology resultOnt = ioHelper.loadOntology(resultFile);
      if (!DiffOperation.equals(exampleOnt, resultOnt)) {
        throw new Exception(
            "Integration test ontology '"
                + resultsPath
                + resultFile.getName()
                + "' is different from example ontology '"
                + examplePath
                + "'");
      }
    } else {
      // Compare all other files
      if (!FileUtils.contentEquals(exampleFile, resultFile)) {
        throw new Exception(
            "Integration test file '"
                + resultsPath
                + resultFile.getName()
                + "' is different from example file '"
                + examplePath
                + "'");
      }
    }
  }
}