List of usage examples for org.apache.commons.io FileUtils openInputStream
public static FileInputStream openInputStream(File file) throws IOException
new FileInputStream(file). From source file:de.haber.xmind2latex.XMindToLatexExporter.java
/** * @param xMindSource the xMindSource to set, must not be null * /*from www . j a va 2s .c om*/ * @throws ZipException if a given XMind file may not be extracted. * @throws IOException */ private InputStream setxMindSourceInputStream(File xMindSource) throws ZipException, IOException { Preconditions.checkNotNull(xMindSource); File usedFile = xMindSource; if (!usedFile.exists()) { throw new FileNotFoundException("The given input file " + xMindSource + " does not exist!"); } if (usedFile.getName().endsWith(".xmind")) { ZipFile zip = new ZipFile(usedFile); FileHeader fh = zip.getFileHeader("content.xml"); return zip.getInputStream(fh); } else { return FileUtils.openInputStream(usedFile); } }
From source file:net.nicholaswilliams.java.teamcity.plugin.buildNumber.PluginConfigurationServiceDefault.java
protected void loadConfiguration() { PluginConfigurationServiceDefault.logger.info("Loading the plugin configuration from the XML file."); FileInputStream stream = null; try {// www . j ava2 s .c o m stream = FileUtils.openInputStream(this.configFile); this.configuration = this.newDigester().parse(stream); } catch (IOException e) { throw new FatalBeanException("Could not read plugin configuration XML file", e); } catch (SAXException e) { throw new FatalBeanException("Could not parse plugin configuration XML", e); } catch (ParserConfigurationException e) { throw new FatalBeanException("Could not configure the configuration XML parser", e); } finally { try { if (stream != null) stream.close(); } catch (IOException e) { PluginConfigurationServiceDefault.logger.warn("Failed to close configuration XML file.", e); } } }
From source file:com.google.refine.model.medadata.ProjectMetadata.java
@Override public void loadFromFile(File metadataFile) { InputStream targetStream = null; try {/* w w w. j ava 2 s . c o m*/ targetStream = FileUtils.openInputStream(metadataFile); } catch (IOException e) { logger.error(ExceptionUtils.getStackTrace(e)); } loadFromStream(targetStream); }
From source file:com.edgenius.core.repository.SimpleRepositoryServiceImpl.java
public List<FileNode> getAllSpaceNodes(ITicket ticket, String type, String spaceUname, boolean withResource) throws RepositoryException { if (!ticket.isAllowRead()) { String error = "Workspace has not read permission " + ticket.getSpacename(); log.warn(error);/* w w w .j a v a 2 s .co m*/ throw new RepositoryException("Permission denied: " + error); } CrWorkspace crW = getCrWorkspace(ticket); List<CrFileNode> nodes = crFileNodeDAO.getSpaceNodes(type, spaceUname); List<FileNode> list = new ArrayList<FileNode>(); //retrieve all geniuswiki:file nodes under this identifier for (Iterator<CrFileNode> iter = nodes.iterator(); iter.hasNext();) { CrFileNode fileNode = iter.next(); //copy geniuswiki:file history as well FileNode my = FileNode.copyPersistToNode(fileNode); //copy geniuswiki:filenode->nt:resource node as well if (withResource) { File file = new File(FileUtil.getFullPath(homeDir, crW.getSpaceUuid(), fileNode.getNodeType(), fileNode.getIdentifierUuid(), fileNode.getNodeUuid(), Integer.valueOf(fileNode.getVersion()).toString(), SimpleRepositoryServiceImpl.DEFAULT_FILE_NAME)); try { my.setFile(FileUtils.openInputStream(file)); } catch (IOException e) { log.warn("Failed get node " + file.getAbsolutePath() + " with error " + e); } } list.add(my); } return list; }
From source file:com.evolveum.midpoint.report.impl.ReportManagerImpl.java
@Override public InputStream getReportOutputData(String reportOutputOid, OperationResult parentResult) { Task task = taskManager.createTaskInstance(REPORT_OUTPUT_DATA); OperationResult result = parentResult.createSubresult(REPORT_OUTPUT_DATA); result.addParam("oid", reportOutputOid); InputStream reportData = null; try {/*from w w w. jav a 2s. co m*/ ReportOutputType reportOutput = modelService .getObject(ReportOutputType.class, reportOutputOid, null, task, result).asObjectable(); String filePath = reportOutput.getFilePath(); if (StringUtils.isEmpty(filePath)) { parentResult.recordFatalError("Report output file path is not defined."); return null; } File file = new File(filePath); reportData = FileUtils.openInputStream(file); result.recordSuccessIfUnknown(); } catch (Exception e) { LOGGER.trace("Cannot read the report data : {}", e.getMessage()); result.recordFatalError("Cannot read the report data.", e); } finally { result.computeStatusIfUnknown(); } return reportData; }
From source file:edu.cornell.med.icb.goby.modes.TestReformatCompactReadsMode.java
/** * Validates that meta data are transfered by reformat. * The input file to this test was created with the following command: * goby 1g fasta-to-compact -k key1 -v value1 -k key2 -v value2 test-data/fastx-test-data/test-fastq-1.fq -o test-data/compact-reads/with-meta-data-input.compact-reads * * @throws IOException if there is a problem reading or writing to the files *//*from w ww . jav a 2 s . c om*/ @Test public void reformatTransferMetaData() throws IOException { final ReformatCompactReadsMode reformat = new ReformatCompactReadsMode(); final String inputFilename = "test-data/compact-reads/with-meta-data-input.compact-reads"; reformat.setInputFilenames(inputFilename); final String outputFilename = "test-results/with-meta-data-output.compact-reads"; reformat.setOutputFile(outputFilename); reformat.execute(); ReadsReader reader1 = new ReadsReader(inputFilename); for (Reads.ReadEntry it : reader1) { System.out.println(it.toString()); System.out.println(); } ReadsReader reader2 = new ReadsReader(outputFilename); for (Reads.ReadEntry it : reader2) { System.out.println(it.toString()); System.out.println(); } assertTrue(FileUtils.contentEquals(new File(inputFilename), new File(outputFilename))); final ReadsReader reader = new ReadsReader(FileUtils.openInputStream(new File(outputFilename))); assertTrue("There should be reads in this file", reader.hasNext()); final Reads.ReadEntry entry = reader.next(); assertNotNull("Entry should not be null", entry); Properties keyValuePairs = reader.getMetaData(); assertEquals("key/value pairs must match", "value1", keyValuePairs.get("key1")); assertEquals("key/value pairs must match", "value2", keyValuePairs.get("key2")); }
From source file:gov.nih.nci.caarray.application.project.FileUploadUtilsTest.java
@Test public void testUnpackFiles_SingleZip() throws Exception { CaArrayFile mockFile = mock(CaArrayFile.class); when(mockStorageFacade.openInputStream(any(URI.class), eq(false))) .thenReturn(FileUtils.openInputStream(File.createTempFile("aaa", "bbb"))); uploadUtils.unpackFiles(project, Lists.newArrayList(mockFile)); verify(mockStorageFacade).openInputStream(any(URI.class), eq(false)); }
From source file:edu.cornell.med.icb.goby.modes.CompactFileStatsMode.java
/** * Print statistics about a reads file in the Goby compact form. * * @param file The file to display statistics about * @throws IOException if the file cannot be read *//*from w ww. j a va2 s .c om*/ private void describeCompactReads(final File file) throws IOException { stream.printf("Compact reads filename = %s%n", file); // keep the read lengths for computing quantiles final DoubleArrayList readLengths = new DoubleArrayList(); int minLength = Integer.MAX_VALUE; int maxLength = Integer.MIN_VALUE; int numberOfIdentifiers = 0; int numberOfDescriptions = 0; int numberOfSequences = 0; int numberOfSequencePairs = 0; int numberOfQualityScores = 0; int numberOfQualityScorePairs = 0; long totalReadLength = 0; long totalReadLengthPair = 0; final DistinctIntValueCounterBitSet allQueryIndices = new DistinctIntValueCounterBitSet(); ReadsReader reader = null; boolean checkedForPaired = false; try { final long size = file.length(); reader = new ReadsReader(FileUtils.openInputStream(file)); for (final Reads.ReadEntry entry : reader) { final int readLength = entry.getReadLength(); for (int i = 0; i < entry.getMetaDataCount(); i++) { Reads.MetaData metaData = entry.getMetaData(i); stream.printf("meta-data key=%s value=%s%n", metaData.getKey(), metaData.getValue()); } // across this file allQueryIndices.observe(entry.getReadIndex()); totalReadLength += readLength; totalReadLengthPair += entry.getReadLengthPair(); // across all files numberOfReads++; numberOfDescriptions += entry.hasDescription() ? 1 : 0; cumulativeReadLength += readLength; if (verbose && entry.hasDescription()) { stream.println("Description found: " + entry.getDescription()); } numberOfIdentifiers += entry.hasReadIdentifier() ? 1 : 0; if (verbose && entry.hasReadIdentifier()) { stream.printf("Identifier found: %s / size=%,d%n", entry.getReadIdentifier(), readLength); } numberOfSequences += entry.hasSequence() && !entry.getSequence().isEmpty() ? 1 : 0; final boolean samplePaired = entry.hasSequencePair() && !entry.getSequencePair().isEmpty(); if (samplePaired) { numberOfSequencePairs += 1; } if (!checkedForPaired) { // Check only the very first entry. checkedForPaired = true; pairedSamples.add(samplePaired); } if (entry.hasQualityScores() && !entry.getQualityScores().isEmpty()) { numberOfQualityScores += 1; final int qualityLength = entry.getQualityScores().size(); minQualityLength = Math.min(minQualityLength, qualityLength); maxQualityLength = Math.max(maxQualityLength, qualityLength); } numberOfQualityScorePairs += entry.hasQualityScoresPair() && !entry.getQualityScoresPair().isEmpty() ? 1 : 0; // we only need to keep all the read lengths if quantiles are being computed if (computeQuantiles) { readLengths.add(readLength); } minLength = Math.min(minLength, readLength); maxLength = Math.max(maxLength, readLength); // adjust the min/max length of across all files minReadLength = Math.min(minReadLength, readLength); maxReadLength = Math.max(maxReadLength, readLength); } stream.printf("Average bytes per entry: %f%n", divide(size, allQueryIndices.count())); stream.printf("Average bytes per base: %f%n", divide(size, cumulativeReadLength)); } finally { if (reader != null) { reader.close(); } } final int numReadEntries = allQueryIndices.count(); stream.printf("Has identifiers = %s (%,d) %n", numberOfIdentifiers > 0, numberOfIdentifiers); stream.printf("Has descriptions = %s (%,d) %n", numberOfDescriptions > 0, numberOfDescriptions); stream.printf("Has sequences = %s (%,d) %n", numberOfSequences > 0, numberOfSequences); stream.printf("Has sequencePairs = %s (%,d) %n", numberOfSequencePairs > 0, numberOfSequencePairs); stream.printf("Has quality scores = %s (%,d) %n", numberOfQualityScores > 0, numberOfQualityScores); stream.printf("Has quality score Pairs = %s (%,d) %n", numberOfQualityScorePairs > 0, numberOfQualityScorePairs); stream.printf("Number of entries = %,d%n", numReadEntries); stream.printf("Min read length = %,d%n", numReadEntries > 0 ? minLength : 0); stream.printf("Max read length = %,d%n", numReadEntries > 0 ? maxLength : 0); stream.printf("Min quality length = %,d%n", numberOfQualityScores > 0 ? minQualityLength : 0); stream.printf("Max quality length = %,d%n", numberOfQualityScores > 0 ? maxQualityLength : 0); stream.printf("Avg read length = %,d%n", numReadEntries > 0 ? totalReadLength / numReadEntries : 0); stream.printf("Avg read pair length = %,d%n", numReadEntries > 0 ? totalReadLengthPair / numReadEntries : 0); // compute quantiles if (computeQuantiles) { final Percentile percentile = new Percentile(); final double[] increasingReadLengths = readLengths.toDoubleArray(); Arrays.sort(increasingReadLengths); stream.printf("Read length quantiles = [ "); for (int quantile = 1; quantile < numberOfQuantiles + 1; quantile++) { stream.printf("%,f ", percentile.evaluate(increasingReadLengths, quantile)); } stream.printf("]%n"); } }
From source file:com.cws.esolutions.security.dao.certmgmt.impl.CertificateManagerImpl.java
/** * @see com.cws.esolutions.security.dao.certmgmt.interfaces.ICertificateManager#applyCertificateRequest(String, File, File, String) *//* ww w. j a va 2 s. c om*/ public synchronized boolean applyCertificateRequest(final String commonName, final File certificateFile, final File keystoreFile, final String storePassword) throws CertificateManagementException { final String methodName = ICertificateManager.CNAME + "#applyCertificateRequest(final String commonName, final File certificateFile, final File keystoreFile, final String storePassword) throws CertificateManagementException"; if (DEBUG) { DEBUGGER.debug(methodName); DEBUGGER.debug("Value: {}", commonName); DEBUGGER.debug("Value: {}", certificateFile); DEBUGGER.debug("Value: {}", keystoreFile); } final File rootDirectory = certConfig.getRootDirectory(); final File certificateDirectory = FileUtils .getFile(certConfig.getCertificateDirectory() + "/" + commonName); final File storeDirectory = FileUtils.getFile(certConfig.getStoreDirectory() + "/" + commonName); if (DEBUG) { DEBUGGER.debug("rootDirectory: {}", rootDirectory); DEBUGGER.debug("certificateDirectory: {}", certificateDirectory); DEBUGGER.debug("storeDirectory: {}", storeDirectory); DEBUGGER.debug("certificateFile: {}", certificateFile); DEBUGGER.debug("keystoreFile: {}", keystoreFile); } boolean isComplete = false; FileInputStream certStream = null; FileOutputStream storeStream = null; FileInputStream keystoreInput = null; FileInputStream rootCertStream = null; FileInputStream intermediateCertStream = null; try { if (!(rootDirectory.exists())) { throw new CertificateManagementException( "Root certificate directory either does not exist or cannot be written to. Cannot continue."); } if (!(rootDirectory.canWrite())) { throw new CertificateManagementException( "Root certificate directory either does not exist or cannot be written to. Cannot continue."); } if (!(certConfig.getRootCertificateFile().exists())) { throw new CertificateManagementException("Root certificate file does not exist. Cannot continue."); } if (!(certConfig.getIntermediateCertificateFile().exists())) { throw new CertificateManagementException( "Intermediate certificate file does not exist. Cannot continue."); } if (!(storeDirectory.canWrite())) { throw new CertificateManagementException( "Keystore directory either does not exist or cannot be written to. Cannot continue."); } if (!(keystoreFile.canWrite())) { throw new CertificateManagementException( "Unable to write to applicable keystore. Cannot continue."); } keystoreInput = FileUtils.openInputStream(keystoreFile); certStream = FileUtils.openInputStream(certificateFile); if (DEBUG) { DEBUGGER.debug("keystoreInput: {}", keystoreInput); DEBUGGER.debug("certStream: {}", certStream); } KeyStore keyStore = KeyStore.getInstance(KeyStore.getDefaultType()); keyStore.load(keystoreInput, storePassword.toCharArray()); if (DEBUG) { DEBUGGER.debug("KeyStore: {}", keyStore); } Key privateKey = keyStore.getKey(commonName, storePassword.toCharArray()); CertificateFactory certFactory = CertificateFactory.getInstance(certConfig.getCertificateType()); if (DEBUG) { DEBUGGER.debug("CertificateFactory: {}", certFactory); } rootCertStream = FileUtils.openInputStream(FileUtils.getFile(certConfig.getRootCertificateFile())); intermediateCertStream = FileUtils .openInputStream(FileUtils.getFile(certConfig.getIntermediateCertificateFile())); if (DEBUG) { DEBUGGER.debug("rootCertStream: {}", rootCertStream); DEBUGGER.debug("intermediateCertStream: {}", intermediateCertStream); } X509Certificate[] responseCert = new X509Certificate[] { (X509Certificate) certFactory.generateCertificate(rootCertStream), (X509Certificate) certFactory.generateCertificate(intermediateCertStream), (X509Certificate) certFactory.generateCertificate(certStream) }; if (DEBUG) { DEBUGGER.debug("X509Certificate[]", (Object) responseCert); } storeStream = FileUtils.openOutputStream(keystoreFile); keyStore.setKeyEntry(commonName, privateKey, storePassword.toCharArray(), responseCert); keyStore.store(storeStream, storePassword.toCharArray()); isComplete = true; } catch (FileNotFoundException fnfx) { throw new CertificateManagementException(fnfx.getMessage(), fnfx); } catch (IOException iox) { throw new CertificateManagementException(iox.getMessage(), iox); } catch (NoSuchAlgorithmException nsax) { throw new CertificateManagementException(nsax.getMessage(), nsax); } catch (IllegalStateException isx) { throw new CertificateManagementException(isx.getMessage(), isx); } catch (KeyStoreException ksx) { throw new CertificateManagementException(ksx.getMessage(), ksx); } catch (CertificateException cx) { throw new CertificateManagementException(cx.getMessage(), cx); } catch (UnrecoverableKeyException ukx) { throw new CertificateManagementException(ukx.getMessage(), ukx); } finally { if (storeStream != null) { IOUtils.closeQuietly(storeStream); } if (intermediateCertStream != null) { IOUtils.closeQuietly(intermediateCertStream); } if (rootCertStream != null) { IOUtils.closeQuietly(rootCertStream); } if (certStream != null) { IOUtils.closeQuietly(certStream); } if (keystoreInput != null) { IOUtils.closeQuietly(keystoreInput); } } return isComplete; }
From source file:gov.nih.nci.caarray.application.project.FileUploadUtilsTest.java
@Test public void testUnpackFiles_MultipleZips() throws Exception { CaArrayFile mockFile = mock(CaArrayFile.class); CaArrayFile mockFile2 = mock(CaArrayFile.class); when(mockStorageFacade.openInputStream(any(URI.class), eq(false))).thenAnswer(new Answer<InputStream>() { @Override/*w w w . j a v a2 s. c o m*/ public InputStream answer(InvocationOnMock invocation) throws Throwable { return FileUtils.openInputStream(File.createTempFile("aaa", "bbb")); } }); uploadUtils.unpackFiles(project, Lists.newArrayList(mockFile, mockFile2)); verify(mockStorageFacade, times(2)).openInputStream(any(URI.class), eq(false)); }