Example usage for java.nio.file.attribute PosixFilePermission GROUP

Introduction

In this page you can find the example usage for java.nio.file.attribute PosixFilePermission GROUP_READ.

Prototype

PosixFilePermission GROUP_READ

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Document

Read permission, group.

Usage

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  .  j a  v  a2s .co  m
 * @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:sce.ProcessExecutor.java

/**
 * File Permissions using File and PosixFilePermission
 *
 * @throws IOException/*from www  . j a v a  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:org.roda.core.storage.fedora.FedoraStorageService.java

private static FileAttribute<Set<PosixFilePermission>> getTempDirFilePermissions() {
    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_EXECUTE);
    return PosixFilePermissions.asFileAttribute(perms);
}

From source file:edu.utah.bmi.ibiomes.lite.IBIOMESLiteManager.java

/**
 * Copy file that will displayed in Jmol
 * @param doc XML document/*from w  ww . j  av a  2 s  .  co  m*/
 * @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;
}

From source file:org.eclipse.cdt.arduino.core.internal.board.ArduinoManager.java

private static Set<PosixFilePermission> toPerms(int mode) {
    Set<PosixFilePermission> perms = new HashSet<>();
    if ((mode & 0400) != 0) {
        perms.add(PosixFilePermission.OWNER_READ);
    }//from w w w.  j  av  a 2s.  c  o m
    if ((mode & 0200) != 0) {
        perms.add(PosixFilePermission.OWNER_WRITE);
    }
    if ((mode & 0100) != 0) {
        perms.add(PosixFilePermission.OWNER_EXECUTE);
    }
    if ((mode & 0040) != 0) {
        perms.add(PosixFilePermission.GROUP_READ);
    }
    if ((mode & 0020) != 0) {
        perms.add(PosixFilePermission.GROUP_WRITE);
    }
    if ((mode & 0010) != 0) {
        perms.add(PosixFilePermission.GROUP_EXECUTE);
    }
    if ((mode & 0004) != 0) {
        perms.add(PosixFilePermission.OTHERS_READ);
    }
    if ((mode & 0002) != 0) {
        perms.add(PosixFilePermission.OTHERS_WRITE);
    }
    if ((mode & 0001) != 0) {
        perms.add(PosixFilePermission.OTHERS_EXECUTE);
    }
    return perms;
}

Example usage for java.nio.file.attribute PosixFilePermission GROUP_READ

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