List of usage examples for java.nio.file Files setPosixFilePermissions
public static Path setPosixFilePermissions(Path path, Set<PosixFilePermission> perms) throws IOException
From source file:com.virtualparadigm.packman.processor.JPackageManager.java
public static boolean autorun(File autorunDir, Map<String, String> environmentVariableMap) { logger.info("PackageManager::autorun()"); boolean status = true; if (autorunDir != null && autorunDir.isDirectory()) { File[] autorunFiles = autorunDir.listFiles(); Arrays.sort(autorunFiles); String fileExtension = null; DefaultExecutor cmdExecutor = new DefaultExecutor(); // String sqlScriptFilePath = null; // Reader sqlScriptReader = null; // Properties sqlScriptProperties = null; for (File autorunFile : autorunFiles) { if (!autorunFile.isDirectory()) { try { fileExtension = FilenameUtils.getExtension(autorunFile.getAbsolutePath()); if (fileExtension != null) { if (fileExtension.equalsIgnoreCase("bat")) { logger.info(" executing autorun batch script: " + autorunFile.getAbsolutePath()); logger.info(" executing autorun environment: " + EnvironmentUtils.toStrings(environmentVariableMap)); cmdExecutor.execute(CommandLine.parse(autorunFile.getAbsolutePath()), environmentVariableMap); } else if (fileExtension.equalsIgnoreCase("sh")) { Set<PosixFilePermission> permissionSet = new HashSet<PosixFilePermission>(); permissionSet.add(PosixFilePermission.OWNER_READ); permissionSet.add(PosixFilePermission.OWNER_WRITE); permissionSet.add(PosixFilePermission.OWNER_EXECUTE); permissionSet.add(PosixFilePermission.OTHERS_READ); permissionSet.add(PosixFilePermission.OTHERS_WRITE); permissionSet.add(PosixFilePermission.OTHERS_EXECUTE); permissionSet.add(PosixFilePermission.GROUP_READ); permissionSet.add(PosixFilePermission.GROUP_WRITE); permissionSet.add(PosixFilePermission.GROUP_EXECUTE); Files.setPosixFilePermissions(Paths.get(autorunFile.toURI()), permissionSet); logger.info(" executing autorun shell script: " + autorunFile.getAbsolutePath()); logger.info(" executing autorun environment: " + EnvironmentUtils.toStrings(environmentVariableMap)); cmdExecutor.execute(CommandLine.parse(autorunFile.getAbsolutePath()), environmentVariableMap); } else if (fileExtension.equalsIgnoreCase("sql") || fileExtension.equalsIgnoreCase("ddl")) { logger.info(" executing autorun file: " + autorunFile.getAbsolutePath()); // look for properties file named same as script file for connection properties // sqlScriptFilePath = autorunFile.getAbsolutePath(); // sqlScriptProperties = PropertyLoader.loadProperties(sqlScriptFilePath.substring(0, sqlScriptFilePath.length()-3) + "properties"); // sqlScriptReader = new FileReader(autorunFile.getAbsolutePath()); } else if (fileExtension.equalsIgnoreCase("jar")) { logger.info(" executing autorun file: " + autorunFile.getAbsolutePath()); }/*ww w . j a v a2 s . c om*/ } } catch (Exception e) { logger.error("", e); e.printStackTrace(); } } } } return status; }
From source file:io.fabric8.kubernetes.client.ConfigTest.java
@Test public void honorClientAuthenticatorCommands() throws Exception { if (SystemUtils.IS_OS_WINDOWS) { System.setProperty(Config.KUBERNETES_KUBECONFIG_FILE, TEST_KUBECONFIG_EXEC_WIN_FILE); } else {/* w w w.j a va 2 s . c o m*/ Files.setPosixFilePermissions(Paths.get(TEST_TOKEN_GENERATOR_FILE), PosixFilePermissions.fromString("rwxrwxr-x")); System.setProperty(Config.KUBERNETES_KUBECONFIG_FILE, TEST_KUBECONFIG_EXEC_FILE); } Config config = Config.autoConfigure(null); assertNotNull(config); assertEquals("HELLO WORLD", config.getOauthToken()); }
From source file:org.apache.hadoop.yarn.server.security.CertificateLocalizationService.java
private void materializeInternalJWT(JWTSecurityMaterial material) throws IOException { FileUtils.writeStringToFile(material.getTokenLocation().toFile(), material.getToken()); if (service == ServiceType.NM) { Set<PosixFilePermission> materialPermissions = EnumSet.of(PosixFilePermission.OWNER_READ, PosixFilePermission.OWNER_WRITE, PosixFilePermission.OWNER_EXECUTE, PosixFilePermission.GROUP_READ, PosixFilePermission.GROUP_EXECUTE); Files.setPosixFilePermissions(material.getCertFolder(), materialPermissions); Files.setPosixFilePermissions(material.getTokenLocation(), materialPermissions); }/*from w ww. j a v a 2s . co m*/ }
From source file:edu.utah.bmi.ibiomes.lite.IBIOMESLiteManager.java
/** * Pull data files (pdb and images) for a given experiment * @param fileTreeXmlPath Path to XML file representing the project file tree * @param workflowXmlPath Path to XML file representing the experiment workflow * @param dataDirPath Path to directory used to store data files * @throws SAXException/*w w w. jav a2 s . com*/ * @throws IOException * @throws XPathExpressionException * @throws ParserConfigurationException * @throws TransformerException */ private void pullDataFilesForExperiment(String fileTreeXmlPath, String workflowXmlPath, String dataDirPath) throws SAXException, IOException, XPathExpressionException, ParserConfigurationException, TransformerException { if (outputToConsole) System.out.println("Copying analysis data files..."); DocumentBuilderFactory docFactory = DocumentBuilderFactory.newInstance(); DocumentBuilder docBuilder = docFactory.newDocumentBuilder(); Document fileTreeDoc = docBuilder.parse(fileTreeXmlPath); fileTreeDoc = Utils.normalizeXmlDoc(fileTreeDoc); Element fileTreeRootElt = (Element) fileTreeDoc.getDocumentElement().getChildNodes().item(0); String dirPath = fileTreeRootElt.getAttribute("absolutePath"); XPathReader xreader = new XPathReader(fileTreeDoc); //load XML representation of experiment workflow Document docWorkflow = docBuilder.parse(workflowXmlPath); docWorkflow = Utils.normalizeXmlDoc(docWorkflow); Element workflowRootElt = (Element) docWorkflow.getDocumentElement(); //find main structure for display in Jmol Element jmolElt = pullJmolFile(fileTreeDoc, fileTreeRootElt, xreader, dataDirPath, dirPath); if (jmolElt != null) workflowRootElt.appendChild(docWorkflow.importNode(jmolElt, true)); //find analysis data NodeList matchingFiles = (NodeList) xreader.read("//file[AVUs/AVU[@id='" + FileMetadata.FILE_CLASS + "' and text()='" + FileMetadata.FILE_CLASS_ANALYSIS.toUpperCase() + "']]", XPathConstants.NODESET); //add publication information //Element dirNode = (Element)fileTreeDoc.getDocumentElement().getFirstChild(); //dirNode.setAttribute("publisher", workflowRootElt.getAttribute("publisher")); //dirNode.setAttribute("publicationDate", workflowRootElt.getAttribute("publicationDate")); //analysis data if (matchingFiles != null && matchingFiles.getLength() > 0) { Element dataElt = docWorkflow.createElement("analysis"); workflowRootElt.appendChild(dataElt); Element imgElt = docWorkflow.createElement("images"); Element pdbElt = docWorkflow.createElement("structures"); Element csvElts = docWorkflow.createElement("spreadsheets"); Element otherDataElts = docWorkflow.createElement("unknowns"); dataElt.appendChild(imgElt); dataElt.appendChild(csvElts); dataElt.appendChild(pdbElt); dataElt.appendChild(otherDataElts); PlotGenerator plotTool = new PlotGenerator(); for (int f = 0; f < matchingFiles.getLength(); f++) { Element fileNode = (Element) matchingFiles.item(f); String dataFilePath = fileNode.getAttribute("absolutePath"); //copy file String dataFileNewName = dataFilePath.substring(dirPath.length() + 1) .replaceAll(PATH_FOLDER_SEPARATOR_REGEX, "_"); String dataFileDestPath = dataDirPath + PATH_FOLDER_SEPARATOR + dataFileNewName; Files.copy(Paths.get(dataFilePath), Paths.get(dataFileDestPath), StandardCopyOption.REPLACE_EXISTING); //set read permissions if (!Utils.isWindows()) { HashSet<PosixFilePermission> permissions = new HashSet<PosixFilePermission>(); permissions.add(PosixFilePermission.OWNER_READ); permissions.add(PosixFilePermission.OWNER_WRITE); permissions.add(PosixFilePermission.OWNER_EXECUTE); permissions.add(PosixFilePermission.GROUP_READ); permissions.add(PosixFilePermission.OTHERS_READ); Files.setPosixFilePermissions(Paths.get(dataFileDestPath), permissions); } //read file AVUs NodeList avuNodes = (NodeList) xreader.read("//file[@absolutePath='" + dataFilePath + "']/AVUs/AVU", XPathConstants.NODESET); MetadataAVUList avuList = new MetadataAVUList(); if (avuNodes != null) { for (int a = 0; a < avuNodes.getLength(); a++) { Element avuNode = (Element) avuNodes.item(a); avuList.add(new MetadataAVU(avuNode.getAttribute("id").toUpperCase(), avuNode.getFirstChild().getNodeValue())); } } //add reference in XML doc String description = avuList.getValue(FileMetadata.FILE_DESCRIPTION); String format = fileNode.getAttribute("format"); if (IBIOMESFileGroup.isJmolFile(format)) { Element jmolFileElt = docWorkflow.createElement("structure"); jmolFileElt.setAttribute("path", dataFileNewName); if (description != null && description.length() > 0) jmolFileElt.setAttribute("description", description); pdbElt.appendChild(jmolFileElt); } else if (format.equals(LocalFile.FORMAT_CSV)) { Element csvElt = docWorkflow.createElement("spreadsheet"); csvElt.setAttribute("path", dataFileNewName); if (description != null && description.length() > 0) csvElt.setAttribute("description", description); csvElts.appendChild(csvElt); //try to generate plot and save image try { String imgPath = dataFileNewName + "_plot.png"; String plotType = generatePlotForCSV(plotTool, dataFileDestPath, avuList, dataFileDestPath + "_plot", "png"); csvElt.setAttribute("plotPath", imgPath); if (outputToConsole) { if (plotType == null) plotType = ""; else plotType += " "; System.out.println("\t" + plotType + "plot generated for " + dataFileNewName); } } catch (Exception e) { if (outputToConsole) System.out.println( "Warning: Plot for '" + dataFileDestPath + "' could not be generated."); try { if (IBIOMESConfiguration.getInstance().isOutputErrorStackToConsole()) e.printStackTrace(); } catch (Exception e1) { } } } else if (IBIOMESFileGroup.isImageFile(format)) { Element imgFileElt = docWorkflow.createElement("image"); imgFileElt.setAttribute("path", dataFileNewName); if (description != null && description.length() > 0) imgFileElt.setAttribute("description", description); imgElt.appendChild(imgFileElt); } else { Element otherFileElt = docWorkflow.createElement("unknown"); otherFileElt.setAttribute("path", dataFileNewName); if (description != null && description.length() > 0) otherFileElt.setAttribute("description", description); imgElt.appendChild(otherDataElts); } } } //update XML files File outputXmlAvusFile = new File(fileTreeXmlPath); if (outputXmlAvusFile.exists()) outputXmlAvusFile.delete(); File outputXmlWorkflowFile = new File(workflowXmlPath); if (outputXmlWorkflowFile.exists()) outputXmlWorkflowFile.delete(); TransformerFactory transformerFactory = TransformerFactory.newInstance(); Transformer transformer = transformerFactory.newTransformer(); transformer.setOutputProperty(OutputKeys.INDENT, "yes"); transformer.setOutputProperty(OutputKeys.ENCODING, "ISO-8859-1"); transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "2"); DOMSource source = new DOMSource(fileTreeDoc); StreamResult result = null; result = new StreamResult(fileTreeXmlPath); transformer.transform(source, result); source = new DOMSource(docWorkflow); result = null; result = new StreamResult(outputXmlWorkflowFile); transformer.transform(source, result); }
From source file:com.twosigma.beaker.core.rest.PluginServiceLocatorRest.java
private void writePrivateFile(java.nio.file.Path path, String contents) throws IOException, InterruptedException { if (windows()) { String p = path.toString(); Thread.sleep(1000); // XXX unknown race condition try (PrintWriter out = new PrintWriter(p)) { out.print(contents);/* w w w . j a v a2 s. c om*/ } return; } if (Files.exists(path)) { Files.delete(path); } try (PrintWriter out = new PrintWriter(path.toFile())) { out.print(""); } Set<PosixFilePermission> perms = EnumSet.of(PosixFilePermission.OWNER_READ, PosixFilePermission.OWNER_WRITE); Files.setPosixFilePermissions(path, perms); // XXX why is this in a try block? try (PrintWriter out = new PrintWriter(path.toFile())) { out.print(contents); } }
From source file:sce.ProcessExecutor.java
/** * File Permissions using File and PosixFilePermission * * @throws IOException/*w w w .j a va 2 s .c o m*/ */ public void setFilePermissions() throws IOException { File file = new File("/Users/temp.txt"); //set application user permissions to 455 file.setExecutable(false); file.setReadable(false); file.setWritable(true); //change permission to 777 for all the users //no option for group and others file.setExecutable(true, false); file.setReadable(true, false); file.setWritable(true, false); //using PosixFilePermission to set file permissions 777 Set<PosixFilePermission> perms = new HashSet<>(); //add owners permission perms.add(PosixFilePermission.OWNER_READ); perms.add(PosixFilePermission.OWNER_WRITE); perms.add(PosixFilePermission.OWNER_EXECUTE); //add group permissions perms.add(PosixFilePermission.GROUP_READ); perms.add(PosixFilePermission.GROUP_WRITE); perms.add(PosixFilePermission.GROUP_EXECUTE); //add others permissions perms.add(PosixFilePermission.OTHERS_READ); perms.add(PosixFilePermission.OTHERS_WRITE); perms.add(PosixFilePermission.OTHERS_EXECUTE); Files.setPosixFilePermissions(Paths.get("/Users/pankaj/run.sh"), perms); }
From source file:de.decoit.visa.rdf.RDFManager.java
/** * Write the RDF model to a RDF/XML file. The output file will be created at * the specified location./* ww w .j a va 2 s. c o m*/ * * @param pFile File object with path and file name of the output file * @throws IOException */ public void writeRDF(Path pFile) throws IOException { OutputStream os = Files.newOutputStream(pFile, StandardOpenOption.CREATE, StandardOpenOption.WRITE, StandardOpenOption.TRUNCATE_EXISTING); writeRDF(os); Set<PosixFilePermission> attrSet = PosixFilePermissions.fromString("rwxrwxrwx"); Files.setPosixFilePermissions(pFile, attrSet); }
From source file:org.eclipse.cdt.arduino.core.internal.board.ArduinoManager.java
public static void downloadAndInstall(String url, String archiveFileName, Path installPath, IProgressMonitor monitor) throws IOException { Exception error = null;/*from w w w.j a va 2 s. c o m*/ for (int retries = 3; retries > 0 && !monitor.isCanceled(); --retries) { try { URL dl = new URL(url); Path dlDir = ArduinoPreferences.getArduinoHome().resolve("downloads"); //$NON-NLS-1$ Files.createDirectories(dlDir); Path archivePath = dlDir.resolve(archiveFileName); URLConnection conn = dl.openConnection(); conn.setConnectTimeout(10000); conn.setReadTimeout(10000); Files.copy(conn.getInputStream(), archivePath, StandardCopyOption.REPLACE_EXISTING); boolean isWin = Platform.getOS().equals(Platform.OS_WIN32); // extract ArchiveInputStream archiveIn = null; try { String compressor = null; String archiver = null; if (archiveFileName.endsWith("tar.bz2")) { //$NON-NLS-1$ compressor = CompressorStreamFactory.BZIP2; archiver = ArchiveStreamFactory.TAR; } else if (archiveFileName.endsWith(".tar.gz") || archiveFileName.endsWith(".tgz")) { //$NON-NLS-1$ //$NON-NLS-2$ compressor = CompressorStreamFactory.GZIP; archiver = ArchiveStreamFactory.TAR; } else if (archiveFileName.endsWith(".tar.xz")) { //$NON-NLS-1$ compressor = CompressorStreamFactory.XZ; archiver = ArchiveStreamFactory.TAR; } else if (archiveFileName.endsWith(".zip")) { //$NON-NLS-1$ archiver = ArchiveStreamFactory.ZIP; } InputStream in = new BufferedInputStream(new FileInputStream(archivePath.toFile())); if (compressor != null) { in = new CompressorStreamFactory().createCompressorInputStream(compressor, in); } archiveIn = new ArchiveStreamFactory().createArchiveInputStream(archiver, in); for (ArchiveEntry entry = archiveIn.getNextEntry(); entry != null; entry = archiveIn .getNextEntry()) { if (entry.isDirectory()) { continue; } // Magic file for git tarballs Path path = Paths.get(entry.getName()); if (path.endsWith("pax_global_header")) { //$NON-NLS-1$ continue; } // Strip the first directory of the path Path entryPath; switch (path.getName(0).toString()) { case "i586": case "i686": // Cheat for Intel entryPath = installPath.resolve(path); break; default: entryPath = installPath.resolve(path.subpath(1, path.getNameCount())); } Files.createDirectories(entryPath.getParent()); if (entry instanceof TarArchiveEntry) { TarArchiveEntry tarEntry = (TarArchiveEntry) entry; if (tarEntry.isLink()) { Path linkPath = Paths.get(tarEntry.getLinkName()); linkPath = installPath.resolve(linkPath.subpath(1, linkPath.getNameCount())); Files.deleteIfExists(entryPath); Files.createSymbolicLink(entryPath, entryPath.getParent().relativize(linkPath)); } else if (tarEntry.isSymbolicLink()) { Path linkPath = Paths.get(tarEntry.getLinkName()); Files.deleteIfExists(entryPath); Files.createSymbolicLink(entryPath, linkPath); } else { Files.copy(archiveIn, entryPath, StandardCopyOption.REPLACE_EXISTING); } if (!isWin && !tarEntry.isSymbolicLink()) { int mode = tarEntry.getMode(); Files.setPosixFilePermissions(entryPath, toPerms(mode)); } } else { Files.copy(archiveIn, entryPath, StandardCopyOption.REPLACE_EXISTING); } } } finally { if (archiveIn != null) { archiveIn.close(); } } return; } catch (IOException | CompressorException | ArchiveException e) { error = e; // retry } } // out of retries if (error instanceof IOException) { throw (IOException) error; } else { throw new IOException(error); } }
From source file:com.cloudbees.clickstack.util.Files2.java
/** * Update file and dir permissions.// w w w . j a v a 2 s . com * * @param path * @param filePermissions * @param dirPermissions * @throws RuntimeIOException */ private static void chmodOverwritePermissions(@Nonnull Path path, @Nonnull final Set<PosixFilePermission> filePermissions, @Nonnull final Set<PosixFilePermission> dirPermissions) throws RuntimeIOException { if (!Files.exists(path)) { throw new IllegalArgumentException("Given path " + path + " does not exist"); } SimpleFileVisitor<Path> setReadOnlyFileVisitor = new SimpleFileVisitor<Path>() { @Override public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException { if (Files.isDirectory(file)) { throw new IllegalStateException("No dir expected here: " + file); } else { Files.setPosixFilePermissions(file, filePermissions); } return super.visitFile(file, attrs); } @Override public FileVisitResult preVisitDirectory(Path dir, BasicFileAttributes attrs) throws IOException { Files.setPosixFilePermissions(dir, dirPermissions); return super.preVisitDirectory(dir, attrs); } }; try { Files.walkFileTree(path, setReadOnlyFileVisitor); } catch (IOException e) { throw new RuntimeIOException("Exception setting permissions file permissions to " + filePermissions + " and folder permissions to " + dirPermissions + " on " + path, e); } }
From source file:edu.utah.bmi.ibiomes.lite.IBIOMESLiteManager.java
/** * Copy file that will displayed in Jmol * @param doc XML document/* w ww.j a va 2s. c om*/ * @param rootElt Root element * @param xreader XPath reader for the document * @param dataDirPath Path to directory that contains analysis data * @param dirPath Path to experiment directory * @return XML element for Jmol data * @throws IOException */ private Element pullJmolFile(Document doc, Node rootElt, XPathReader xreader, String dataDirPath, String dirPath) throws IOException { Element jmolElt = doc.createElement("jmol"); String mainStructureRelPath = (String) xreader .read("ibiomes/directory/AVUs/AVU[@id='MAIN_3D_STRUCTURE_FILE']", XPathConstants.STRING); if (mainStructureRelPath != null && mainStructureRelPath.length() > 0) { String dataFileNewName = mainStructureRelPath.replaceAll(PATH_FOLDER_SEPARATOR_REGEX, "_"); String dataFileDestPath = dataDirPath + PATH_FOLDER_SEPARATOR + dataFileNewName; Files.copy(Paths.get(dirPath + PATH_FOLDER_SEPARATOR + mainStructureRelPath), Paths.get(dataFileDestPath), StandardCopyOption.REPLACE_EXISTING); //set read permissions if (!Utils.isWindows()) { Set<PosixFilePermission> permissions = new HashSet<PosixFilePermission>(); permissions.add(PosixFilePermission.OWNER_READ); permissions.add(PosixFilePermission.OWNER_WRITE); permissions.add(PosixFilePermission.OWNER_EXECUTE); permissions.add(PosixFilePermission.GROUP_READ); permissions.add(PosixFilePermission.OTHERS_READ); Files.setPosixFilePermissions(Paths.get(dataFileDestPath), permissions); } jmolElt.setAttribute("path", dataFileNewName); jmolElt.setAttribute("name", mainStructureRelPath); NodeList avuNodes = (NodeList) xreader.read("//file[@absolutePath='" + dirPath + PATH_FOLDER_SEPARATOR + mainStructureRelPath + "']/AVUs/AVU", XPathConstants.NODESET); MetadataAVUList avuList = parseMetadata(avuNodes); String description = avuList.getValue(FileMetadata.FILE_DESCRIPTION); if (description != null && description.length() > 0) jmolElt.setAttribute("description", description); rootElt.appendChild(jmolElt); return jmolElt; } else return null; }