Example usage for org.jdom2.input SAXBuilder SAXBuilder

List of usage examples for org.jdom2.input SAXBuilder SAXBuilder

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Introduction

In this page you can find the example usage for org.jdom2.input SAXBuilder SAXBuilder.

Prototype

public SAXBuilder()

Source Link

Document

Creates a new JAXP-based SAXBuilder.

Usage

From source file:edu.kit.iks.cryptographicslib.framework.controller.StartController.java

License:MIT License

@Override
public void loadView() {
    this.view = new JPanel(new GridBagLayout());
    this.view.setName("start-controller-view");

    SAXBuilder saxBuilder = new SAXBuilder();

    // obtain file object
    InputStream is = this.getClass().getResourceAsStream("/start/startResources.xml");

    try {//from   w w  w  .  ja  v a 2  s  .c o m
        // converted file to document object
        Document document = saxBuilder.build(is);

        // get root node from xml
        this.startResources = document.getRootElement();
    } catch (JDOMException | IOException e) {
        Logger.error(e);
    }

    // Add welcome view and its layout
    GridBagConstraints welcomeViewLayout = new GridBagConstraints();
    welcomeViewLayout.fill = GridBagConstraints.HORIZONTAL;
    welcomeViewLayout.gridy = 0;
    welcomeViewLayout.weighty = 0.95f;
    this.welcomeView = new WelcomeView();
    this.view.add(this.welcomeView, welcomeViewLayout);

    String path = startResources.getChild("welcomeImage").getAttributeValue("path");

    GridBagConstraints imgConstraint = new GridBagConstraints();
    imgConstraint.gridx = 0;
    imgConstraint.gridy = 1;
    imgConstraint.insets = new Insets(0, 0, 50, 0);
    ImageView imageToSet = new ImageView(path);
    this.view.add(imageToSet, imgConstraint);

    // Add timeline view and its layout
    GridBagConstraints timelineViewLayout = new GridBagConstraints();
    timelineViewLayout.fill = GridBagConstraints.HORIZONTAL;
    timelineViewLayout.weightx = 1.0f;
    timelineViewLayout.weighty = 0.05f;
    timelineViewLayout.gridy = 2;
    this.timelineView = new TimelineView(visualizationInfos);
    this.view.add(this.timelineView, timelineViewLayout);

    // Add event handlers
    for (VisualizationButtonView button : this.timelineView.getButtons()) {
        button.addActionListener(new ActionListener() {

            @Override
            public void actionPerformed(ActionEvent e) {
                VisualizationButtonView button = (VisualizationButtonView) e.getSource();
                StartController.this.presentPopoverAction(button.getVisualizationInfo(), button);
            }

        });
    }

    this.view.validate();
}

From source file:edu.kit.trufflehog.model.configdata.SettingsDataModel.java

License:Open Source License

/**
 * <p>//w  ww . j av a 2s.  c o m
 *     Loads all settings found on the hard drive into memory.
 * </p>
 */
public void load() {
    settingsMap.clear();

    try {
        // Set up the XML parser
        SAXBuilder saxBuilder = new SAXBuilder();
        Document document = saxBuilder.build(settingsFile);
        Element rootElement = document.getRootElement();

        if (!checkHead(rootElement.getChild("head"))) {
            logger.error("Settings file does not match specified type");
            return;
        }

        // Get the "data" elements of the xml file
        Element data = rootElement.getChild("data");

        // Parse through all entries and add them to the map
        List<Element> entries = data.getChildren();
        entries.stream().forEach(entry -> {
            // Get the type, key and value. The type has to be specified as the whole class name, otherwise
            // it is set to java.lang.Object
            String type = entry.getAttribute("type").getValue();
            Class typeClass;
            try {
                typeClass = Class.forName(type);
            } catch (ClassNotFoundException e) {
                logger.error("Specified type class does not exist, setting the type class to java.lang.Object",
                        e);
                typeClass = Object.class;
            }
            String key = entry.getChild("key").getValue();
            String value = entry.getChild("value").getValue();

            // Finally add the data to the map
            addToMap(typeClass, key, value);
        });
    } catch (JDOMException | IOException e) {
        logger.error("Error while parsing the " + CONFIG_FILE_NAME + " file", e);
    }
}

From source file:edu.kit.trufflehog.model.configdata.SettingsDataModel.java

License:Open Source License

/**
 * <p>//w  w  w  .  j a v a 2 s  .co m
 *     Updates the settings xml file with the current value.
 * </p>
 *
 * @param typeClass The type of the value (i.e. String, Integer or Boolean are examples)
 * @param key The key mapped to the value, classic key value mapping.
 * @param oldValue The old value that should be updated.
 * @param newValue The new value, that should overwrite the old value.
 */
private synchronized void updateSettingsFile(final Class typeClass, final String key, final String oldValue,
        final String newValue) {
    // synchronized because this always runs in its own thread

    try {
        SAXBuilder saxBuilder = new SAXBuilder();
        Document document = saxBuilder.build(settingsFile);

        Element rootElement = document.getRootElement();

        // Get the "data" elements of the xml file
        Element data = rootElement.getChild("data");

        // Parse through all entries and find the right one
        List<Element> entries = data.getChildren();
        entries = entries.stream()
                .filter(entry -> entry.getAttribute("type").getValue().equals(typeClass.getName())
                        && entry.getChild("key").getValue().equals(key)
                        && entry.getChild("value").getValue().equals(oldValue))
                .collect(Collectors.toList());

        // Make sure we actually only found 1 entry
        if (entries.size() < 1) {
            logger.error("No entry was found for type: " + typeClass.getName() + ", key: " + key + ", value: "
                    + oldValue);
            return;
        } else if (entries.size() > 1) {
            logger.error("More than one entry was found for type: " + typeClass.getName() + ", key: " + key
                    + ", value: " + oldValue);
            return;
        }

        saveNewValue(typeClass, key, oldValue, newValue, document, entries.get(0));
    } catch (JDOMException | IOException e) {
        logger.error("Error updating the " + CONFIG_FILE_NAME + " file for key: " + key + " of type: "
                + typeClass.getName(), e);
    }
}

From source file:edu.pitt.apollo.runmanagerservice.methods.stage.StageExperimentMethod.java

License:Apache License

@Override
public void runApolloService() {

    XMLSerializer serializer = new XMLSerializer();
    XMLDeserializer deserializer = new XMLDeserializer();

    InfectiousDiseaseScenario baseScenario = idtes.getInfectiousDiseaseScenarioWithoutIntervention();
    // clear all set control strategies in base
    baseScenario.getInfectiousDiseaseControlStrategies().clear();

    List<SoftwareIdentification> modelIds = idtes.getInfectiousDiseaseTransmissionModelIds();
    try {/*from w w  w.j  ava  2  s.  co  m*/
        DataServiceAccessor dataServiceAccessor = new DataServiceAccessor();

        for (SoftwareIdentification modelId : modelIds) {

            // create a base scenario copy
            String baseXml = serializer.serializeObject(baseScenario);
            InfectiousDiseaseScenario baseScenarioCopy = deserializer.getObjectFromMessage(baseXml,
                    InfectiousDiseaseScenario.class);
            for (InfectiousDiseaseControlStrategy strategy : idtes.getInfectiousDiseaseControlStrategies()) {

                for (InfectiousDiseaseControlMeasure controlMeasure : strategy.getControlMeasures()) {
                    baseScenarioCopy.getInfectiousDiseaseControlStrategies().add(controlMeasure);
                }
            }

            List<SensitivityAnalysisSpecification> sensitivityAnalyses = idtes.getSensitivityAnalyses();
            for (SensitivityAnalysisSpecification sensitivityAnalysis : sensitivityAnalyses) {
                if (sensitivityAnalysis instanceof OneWaySensitivityAnalysisOfContinousVariableSpecification) {
                    OneWaySensitivityAnalysisOfContinousVariableSpecification owsaocv = (OneWaySensitivityAnalysisOfContinousVariableSpecification) sensitivityAnalysis;
                    double min = owsaocv.getMinimumValue();
                    double max = owsaocv.getMaximumValue();
                    double increment = (max - min) / owsaocv.getNumberOfDiscretizations().intValueExact();

                    String scenarioXML = serializer.serializeObject(baseScenarioCopy);

                    double val = min;
                    while (val <= max) {

                        String param = owsaocv.getUniqueApolloLabelOfParameter();

                        Document jdomDocument;
                        SAXBuilder jdomBuilder = new SAXBuilder();
                        try {
                            jdomDocument = jdomBuilder.build(
                                    new ByteArrayInputStream(scenarioXML.getBytes(StandardCharsets.UTF_8)));
                        } catch (JDOMException | IOException ex) {
                            ErrorUtils.reportError(runId,
                                    "Error inserting experiment run. Error was " + ex.getMessage(),
                                    authentication);
                            return;
                        }

                        Element e = jdomDocument.getRootElement();
                        List<Namespace> namespaces = e.getNamespacesInScope();

                        for (Namespace namespace : namespaces) {
                            if (namespace.getURI().contains("http://types.apollo.pitt.edu")) {
                                param = param.replaceAll("/", "/" + namespace.getPrefix() + ":");
                                param = param.replaceAll("\\[", "\\[" + namespace.getPrefix() + ":");
                                break;
                            }
                        }

                        XPathFactory xpf = XPathFactory.instance();
                        XPathExpression<Element> expr;
                        expr = xpf.compile(param, Filters.element(), null, namespaces);
                        List<Element> elements = expr.evaluate(jdomDocument);

                        for (Element element : elements) {
                            element.setText(Double.toString(val));
                        }

                        ByteArrayOutputStream baos = new ByteArrayOutputStream();
                        XMLOutputter xmlOutputter = new XMLOutputter();
                        xmlOutputter.output(jdomDocument, baos);

                        InfectiousDiseaseScenario newScenario = deserializer.getObjectFromMessage(
                                new String(baos.toByteArray()), InfectiousDiseaseScenario.class);

                        // new scenario is ready to be staged
                        RunSimulationMessage runSimulationMessage = new RunSimulationMessage();
                        runSimulationMessage.setAuthentication(authentication);
                        runSimulationMessage
                                .setSimulatorTimeSpecification(message.getSimulatorTimeSpecification());
                        runSimulationMessage.setSoftwareIdentification(modelId);
                        runSimulationMessage.setInfectiousDiseaseScenario(newScenario);

                        StageMethod stageMethod = new StageMethod(runSimulationMessage, runId);
                        InsertRunResult result = stageMethod.stage();
                        BigInteger newRunId = result.getRunId();

                        MethodCallStatus status = dataServiceAccessor.getRunStatus(newRunId, authentication);
                        if (status.getStatus().equals(MethodCallStatusEnum.FAILED)) {
                            ErrorUtils.reportError(runId,
                                    "Error inserting run in experiment with run ID " + runId + ""
                                            + ". Error was for inserting ID " + newRunId + " with message "
                                            + status.getMessage(),
                                    authentication);
                            return;
                        }

                        val += increment;
                    }
                }
            }
        }

        dataServiceAccessor.updateStatusOfRun(runId, MethodCallStatusEnum.TRANSLATION_COMPLETED,
                "All runs for this experiment have been translated", authentication);
    } catch (DeserializationException | IOException | SerializationException | RunManagementException ex) {
        ErrorUtils.reportError(runId, "Error inserting experiment run. Error was " + ex.getMessage(),
                authentication);
        return;
    }
}

From source file:edu.ucla.loni.server.ServerUtils.java

License:Open Source License

/**
 * Parse an XML file into a Document/*from  w  ww.  j  a v a 2 s . co  m*/
 */
public static Document readXML(File pipe) throws Exception {
    SAXBuilder builder = new SAXBuilder();
    Document doc = (Document) builder.build(pipe);

    return doc;
}

From source file:edu.ucla.loni.server.ServerUtils.java

License:Open Source License

/**
 * Parse an XML file into a Document/*from  ww  w .j  av  a2 s. co m*/
 */
public static Document readXML(InputStream stream) throws Exception {
    SAXBuilder builder = new SAXBuilder();
    Document doc = (Document) builder.build(stream);

    return doc;
}

From source file:edu.ucsd.crbs.cws.workflow.WorkflowFromAnnotatedVersionTwoFourMomlXmlFactory.java

License:Open Source License

/**
 * Returns the root element of parsed XML document
 *
 * @param in XML document to parse/* w ww.jav a 2s .  c o  m*/
 * @return Root element of document
 * @throws Exception If there is a problem parsing the document
 */
private Document getDocument(InputStream in) throws Exception {
    SAXBuilder builder = new SAXBuilder();
    builder.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
    return builder.build(in);
}

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;/*from  w ww . j av  a2 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.dl.fedora.JobForwardingJMSListener.java

License:Apache License

@Override
public void onMessage(Message message) {

    log.debug("Received message");

    // If no jobs are listening, ignore the message
    if (listenerJobs.size() == 0)
        return;//from   w w  w . jav  a2s  . co m

    if (message instanceof TextMessage) {
        try {
            TextMessage msg = (TextMessage) message;

            String messageBody = msg.getText();
            Document msgDoc = new SAXBuilder().build(new StringReader(messageBody));

            log.debug("Message contents:\n{}", messageBody);

            // This does not need to be synchronized because it is using CopyOnWriteArrayList
            for (ListenerJob listener : listenerJobs) {
                listener.onEvent(msgDoc);
            }

        } catch (Exception e) {
            log.error("onMessage failed", e);
        }
    } else {
        throw new IllegalArgumentException("Message must be of type TextMessage");
    }
}

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  2s. c  om
 *       [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;
}