Example usage for org.jdom2 Document getRootElement

List of usage examples for org.jdom2 Document getRootElement

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Introduction

In this page you can find the example usage for org.jdom2 Document getRootElement.

Prototype

public Element getRootElement()

Source Link

Document

This will return the root Element for this Document

Usage

From source file:edu.unc.lib.deposit.normalize.Proquest2N3BagJob.java

License:Apache License

private void normalizePackage(File packageDir, Model model, Bag depositBag) {

    // Generate a uuid for the main object
    PID primaryPID = new PID("uuid:" + UUID.randomUUID());
    Resource primaryResource;/*  w ww  .j  a  v  a 2  s  . c o  m*/

    // Identify the important files from the deposit
    File dataFile = null, contentFile = null, attachmentDir = null;

    File[] files = packageDir.listFiles();
    for (File file : files) {
        if (file.isDirectory()) {
            attachmentDir = file;
        } else if (file.getName().endsWith(DATA_SUFFIX)) {
            dataFile = file;
        } else {
            contentFile = file;
        }
    }

    long lastModified = -1;
    File zipFile = new File(packageDir.getAbsolutePath() + ".zip");
    try (ZipFile zip = new ZipFile(zipFile)) {
        ZipArchiveEntry entry = zip.getEntry(contentFile.getName());
        lastModified = entry.getTime();
    } catch (IOException e) {
        log.error("Failed to read zip file located at {}.zip", packageDir.getAbsolutePath(), e);
    }

    if (lastModified == -1) {
        lastModified = zipFile.lastModified();
    }

    DateTime modified = new DateTime(lastModified, DateTimeZone.UTC);

    // Deserialize the data document
    SAXBuilder builder = new SAXBuilder();
    Element dataRoot = null;
    Document mods = null;
    try {

        Document dataDocument = builder.build(dataFile);
        dataRoot = dataDocument.getRootElement();

        // Transform the data into MODS and store it to its final resting place
        mods = extractMods(primaryPID, dataRoot, modified);
    } catch (TransformerException e) {
        failJob(e, Type.NORMALIZATION, "Failed to transform metadata to MODS");
    } catch (Exception e) {
        failJob(e, Type.NORMALIZATION, "Unable to deserialize the metadata file");
    }

    // Detect if there are any attachments
    List<?> attachmentElements = dataRoot.getChild("DISS_content").getChildren("DISS_attachment");

    if (attachmentElements == null || attachmentElements.size() == 0) {

        // Simple object with the content as its source data
        primaryResource = populateSimple(model, primaryPID, contentFile);
    } else {
        String title = mods.getRootElement().getChild("titleInfo", MODS_V3_NS).getChildText("title",
                MODS_V3_NS);

        // Has attachments, so it is an aggregate
        primaryResource = populateAggregate(model, primaryPID, attachmentElements, attachmentDir, contentFile,
                title);
    }

    // Store primary resource as child of the deposit
    depositBag.add(primaryResource);

    // Add the data file as a metadata datastream of the primary object
    setSourceMetadata(model, primaryResource, dataFile);

    // Capture other metadata, like embargoes
    setEmbargoUntil(model, primaryResource, dataRoot);

    // Creation date for the content file
    model.add(primaryResource, cdrprop(model, dateCreated), modified.toString(), XSDDatatype.XSDdateTime);
}

From source file:edu.unc.lib.deposit.normalize.VocabularyEnforcementJob.java

License:Apache License

@Override
public void runJob() {
    Model model = getWritableModel();/*from ww w .j  a va2 s .c  o  m*/

    // Get the list of all objects being ingested in this job
    List<String> resourcePIDs = new ArrayList<>();
    Bag deposit = model.getBag(getDepositPID().getURI());
    walkChildrenDepthFirst(deposit, resourcePIDs, true);

    SAXBuilder sb = new SAXBuilder(new XMLReaderSAX2Factory(false));

    // Vocabulary mappings need to be resolved against the destination since they are not in the hierarchy yet
    PID destinationPID = new PID(getDepositStatus().get(DepositField.containerId.name()));

    for (String resourcePID : resourcePIDs) {
        PID pid = new PID(resourcePID);
        File modsFile = new File(getDescriptionDir(), pid.getUUID() + ".xml");

        // Check if the resource has a description
        if (modsFile.exists()) {
            try {
                Document modsDoc = sb.build(modsFile);

                // Update the MODS document to use approved terms when possible if the vocabularies support remapping
                log.debug("Updating document terms for {} within destination {}", pid, destinationPID);
                boolean modified = updateDocumentTerms(destinationPID, modsDoc.getRootElement());

                // Update the mods document if it was changed
                if (modified) {
                    try (FileOutputStream fos = new FileOutputStream(modsFile)) {
                        new XMLOutputter(Format.getPrettyFormat()).output(modsDoc.getDocument(), fos);
                    }
                }

                // Capture any invalid affiliations as relations
                log.debug("Adding invalid terms for {} within destination {}", pid, destinationPID);
                addInvalidTerms(pid, destinationPID, modsDoc.getRootElement(), model);

            } catch (JDOMException | IOException e) {
                log.error("Failed to parse description file {}", modsFile.getAbsolutePath(), e);
            }
        }
    }
}

From source file:edu.unc.lib.dl.util.VocabularyHelperManager.java

License:Apache License

/**
 * Returns the authoritative vocabulary forms for selected fields from the given document using all applicable
 * helpers for the specified object. Terms are grouped by vocabulary URI.
 *
 * @param pid/*w w  w. j  av a2  s. c  o m*/
 * @param doc
 * @return
 */
public Map<String, List<List<String>>> getAuthoritativeForms(PID pid, Document doc) {
    return getAuthoritativeForms(pid, doc.getRootElement());
}

From source file:edu.unc.lib.dl.xml.DepartmentOntologyUtil.java

License:Apache License

/**
 * Parses a SKOS XML vocabulary located at filePath and populates a lookup index labels and alternative labels
 * referencing the authoritative version.
 *
 * @param ontologyURL/*from   w  ww .  j  a  v a2 s .c o  m*/
 * @throws Exception
 */
private void parseVocabulary(byte[] content) throws Exception {
    departments = new HashMap<String, DepartmentConcept>();

    log.debug("Parsing and building Department vocabulary from {}", getVocabularyURI());

    SAXBuilder sb = new SAXBuilder(new XMLReaderSAX2Factory(false));
    Document skosDoc = sb.build(new ByteArrayInputStream(content));

    // Extract all of the concepts and store them to an index
    List<?> concepts = skosDoc.getRootElement().getChildren("Concept", SKOS_NS);
    Map<String, DepartmentConcept> tempDepts = new HashMap<String, DepartmentConcept>(concepts.size());
    for (Object conceptObj : concepts) {
        DepartmentConcept dept = new DepartmentConcept((Element) conceptObj);
        tempDepts.put(cleanLabel(dept.getIdentifier()), dept);
    }

    // Expand out all the alternative labels into an index and resolve references
    for (Iterator<Entry<String, DepartmentConcept>> deptIt = tempDepts.entrySet().iterator(); deptIt
            .hasNext();) {
        Entry<String, DepartmentConcept> deptEntry = deptIt.next();

        DepartmentConcept dept = deptEntry.getValue();

        // Check if this concept should be ignored in favor of a preferred concept
        if (dept.prefLabel != null) {
            if (departments.containsKey(dept.prefLabel)) {
                // The preferred concept has already been indexed, grab extra labels from this concept and reindex pref
                DepartmentConcept prefDept = departments.get(dept.prefLabel);
                prefDept.merge(dept);
                addLabels(prefDept);
            } else {
                // Since the preferred concept isn't indexed yet, just need to merge labels into it
                DepartmentConcept prefDept = tempDepts.get(dept.prefLabel);
                if (prefDept == null) {
                    log.warn("Preferred label {} referencing a concept which is not present", dept.prefLabel);
                } else {
                    prefDept.merge(dept);
                }
            }
            continue;
        }

        String identifier = cleanLabel(dept.identifier);
        if (departments.containsKey(identifier)
                && dept.identifier.equals(departments.get(identifier).identifier)) {
            log.error("Illegal state, multiple concepts share the identifier {}, ignoring duplicate",
                    identifier);
        } else {
            departments.put(identifier, dept);
        }

        addLabels(dept);
    }
}

From source file:edu.utep.cs.jasg.Frontend.java

License:Open Source License

/** Parse build XML file. Returns a String array with the following content:
 *       [0] = target module name/*from w w  w . j  a v a  2  s.  com*/
 *       [1] = target module main scanner specification file
 *       [2] = target module main parser specification file
 * */
public String[] parseBuildFile(String filePath) {
    String[] result = { "", "", "" };

    if (Files.exists(Paths.get(filePath))) {

        try {
            SAXBuilder builder = new SAXBuilder();
            Document doc = (Document) builder.build(filePath);
            Element root = doc.getRootElement();

            if (root != null) {
                List<Element> propertyList = root.getChildren("property");
                Iterator<Element> propertiesIterator = propertyList.iterator();

                //Get module name
                String moduleName = root.getAttributeValue("name");
                if (moduleName != null)
                    result[0] = moduleName;

                //Get specification name properties
                while (propertiesIterator.hasNext()) {
                    Element property = propertiesIterator.next();
                    String propertyName = property.getAttributeValue("name");
                    String propertyValue = property.getAttributeValue("value");

                    if (propertyName != null) {
                        //Get scanner name
                        if (propertyName.equals("scannerName")) {
                            if (propertyValue != null)
                                result[1] = propertyValue;
                        }
                        //Get scanner name
                        else if (propertyName.equals("parserName")) {
                            if (propertyValue != null)
                                result[2] = propertyValue;
                        }
                    }
                }
            }
        } catch (IOException io) {
            System.out.println(io.getMessage());
        } catch (JDOMException jdomex) {
            System.out.println(jdomex.getMessage());
        }
    }
    return result;
}

From source file:edu.utep.cs.jasg.specificationGenerator.XMLParser.java

License:Open Source License

/** Parser XML file. */
public void parse(String filePath) {
    if (Files.exists(Paths.get(filePath)) && DOMValidateDTD.validateXML(filePath)) {
        try {//from   w ww.ja va2 s .c o m
            SAXBuilder builder = new SAXBuilder();
            Document doc = (Document) builder.build(filePath);
            Element root = doc.getRootElement();

            nameSpace = root.getChild("nameSpace").getText();

            //TODO: should I replace all files? Like compiling new files
            //check existing name spaces
            if (!Files.exists(Paths.get(workspace + File.separator + nameSpace))) {
                fileFactory.createDirectory(nameSpace);
            }

            specificationGenerator = new SpecificationGenerator(fileFactory, nameSpace);

            //get root element declarations
            Element parserElement = root.getChild("parser");

            Element scannerElement = root.getChild("scanner");

            Element ASTNodeElement = root.getChild("AST");

            Element ASTBehaviorElement = root.getChild("ASTBehavior");

            //parse root elements (document specifications)
            if (parserElement != null)
                parseRootElement("parser", parserElement);

            if (scannerElement != null)
                parseRootElement("scanner", scannerElement);

            if (ASTNodeElement != null)
                parseRootElement("AST", ASTNodeElement);

            if (ASTBehaviorElement != null)
                parseRootElement("ASTBehavior", ASTBehaviorElement);

        } catch (IOException io) {
            System.out.println(io.getMessage());
        } catch (JDOMException jdomex) {
            System.out.println(jdomex.getMessage());

        }
    }
}

From source file:edu.wisc.ssec.adapter.NetCDFFile.java

License:Open Source License

public static NetCDFFile makeUnion(String filename, String other) throws Exception {
    Object obj = new Object();
    URL url = obj.getClass().getResource("/edu/wisc/ssec/mcidasv/data/hydra/resources/union.ncml");
    SAXBuilder builder = new SAXBuilder(false);
    Document doc = null;

    try {/*from   w  ww  .j a va2 s .c  o m*/
        doc = builder.build(url);
    } catch (Exception e) {
        e.printStackTrace();
    }
    Element root = doc.getRootElement();

    List list = root.getChildren();

    list = ((Element) list.get(1)).getChildren();

    org.jdom2.Attribute attr1 = (org.jdom2.Attribute) (((Element) list.get(0)).getAttributes()).get(0);
    attr1.setValue(filename);

    org.jdom2.Attribute attr2 = (org.jdom2.Attribute) (((Element) list.get(1)).getAttributes()).get(0);
    attr2.setValue(other);

    XMLOutputter xmlOut = new XMLOutputter();
    String newStr = xmlOut.outputString(doc);
    ByteArrayInputStream is = new ByteArrayInputStream(newStr.getBytes());
    return new NetCDFFile(is);
}

From source file:edu.wisc.ssec.mcidasv.chooser.TDSRadarChooser.java

License:Open Source License

/**
 * Get  the radar collections for  the given server URL
 *
 * @param radarServerURL  server URL//ww  w.  j a  va 2 s  .  c o  m
 *
 * @return  a map of the collection names to URL
 */
private List getRadarCollections(String radarServerURL) {
    SAXBuilder builder;
    Document doc = null;
    XMLEntityResolver jaxp = new XMLEntityResolver(true);
    builder = jaxp.getSAXBuilder();
    List collections = new ArrayList();

    try {
        doc = builder.build(radarServerURL);
    } catch (JDOMException e) {
        userMessage("Invalid catalog");
    } catch (IOException e) {
        userMessage("Unable to open catalog");
    }

    org.jdom2.Element rootElem = doc.getRootElement();
    org.jdom2.Element serviceElem = readElements(rootElem, "service");
    String uriBase = serviceElem.getAttributeValue("base");
    org.jdom2.Element dsElem = readElements(rootElem, "dataset");
    String naming = "catalogRef";
    Namespace nss = rootElem.getNamespace("xlink");
    List children = dsElem.getChildren();
    for (int j = 0; j < children.size(); j++) {
        org.jdom2.Element child = (org.jdom2.Element) children.get(j);
        String childName = child.getName();
        if (childName.equals(naming)) {
            //String id   = child.getAttributeValue("ID");
            String desc = child.getAttributeValue("title", nss);
            String urlpath = child.getAttributeValue("href", nss);
            String[] c = radarServerURL.split(uriBase); //.replaceFirst("catalog.xml", "");
            String ul = c[0] + uriBase + urlpath;
            TwoFacedObject twoObj = new TwoFacedObject(desc, ul);
            collections.add(twoObj);
            //collections.put(desc, ul);
        }

    }

    return collections;
}

From source file:edu.wisc.ssec.mcidasv.data.hydra.NetCDFFile.java

License:Open Source License

public static NetCDFFile makeUnion(String filename, String other) throws Exception {
    Object obj = new Object();
    URL url = obj.getClass().getResource("/edu/wisc/ssec/mcidasv/data/hydra/resources/union.ncml");
    SAXBuilder builder = new SAXBuilder(false);
    Document doc = null;

    try {//w ww .  ja va2 s  .c o m
        doc = builder.build(url);
    } catch (Exception e) {
        e.printStackTrace();
    }
    Element root = doc.getRootElement();

    List list = root.getChildren();

    list = ((Element) list.get(1)).getChildren();

    org.jdom2.Attribute attr1 = (((Element) list.get(0)).getAttributes()).get(0);
    attr1.setValue(filename);

    org.jdom2.Attribute attr2 = (((Element) list.get(1)).getAttributes()).get(0);
    attr2.setValue(other);

    XMLOutputter xmlOut = new XMLOutputter();
    String newStr = xmlOut.outputString(doc);
    logger.trace("union string:\n{}", newStr);
    ByteArrayInputStream is = new ByteArrayInputStream(newStr.getBytes());
    return new NetCDFFile(is);
}

From source file:egovframework.rte.fdl.xml.AbstractXMLUtility.java

License:Apache License

/**
 *  Element // ww  w  .j  a v a 2s . com
 * 
 * @param doc - Document ?
 * @param addNDName -  ? Element
 * @param list -  Element 
 * @param path -  ? XML 
 * @throws TransformerException
 * @throws TransformerConfigurationException
 * @throws FileNotFoundException
 */
public void addElement(Document doc, String addNDName, List<?> list, String path)
        throws TransformerException, TransformerConfigurationException, FileNotFoundException, IOException {

    StreamResult sTResult = null;
    FileOutputStream fos = null;
    Element root = doc.getRootElement();

    addNode(root, addNDName, list);

    TransformerFactory transformerFactory = TransformerFactory.newInstance();
    Transformer serializer = transformerFactory.newTransformer();

    serializer.setOutputProperty(OutputKeys.ENCODING, "euc-kr");
    serializer.setOutputProperty(OutputKeys.INDENT, "yes");
    if (path != null) {
        fos = new FileOutputStream(path);
        sTResult = new StreamResult(fos);
        serializer.transform(new JDOMSource(doc), sTResult);
        fos.close();
    } else {
        fos = new FileOutputStream(savedPath + "addElement.xml");
        sTResult = new StreamResult(fos);
        serializer.transform(new JDOMSource(doc), sTResult);
        fos.close();
    }
}