Example usage for javax.xml.bind JAXBContext createUnmarshaller

List of usage examples for javax.xml.bind JAXBContext createUnmarshaller

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Introduction

In this page you can find the example usage for javax.xml.bind JAXBContext createUnmarshaller.

Prototype

public abstract Unmarshaller createUnmarshaller() throws JAXBException;

Source Link

Document

Create an Unmarshaller object that can be used to convert XML data into a java content tree.

Usage

From source file:org.cbio.portal.pipelines.foundation.FoundationFileTasklet.java

/**
 * Extract the case data from source xml file by root tag
 * @param xmlFile/* w  w w .  j  a  va2  s .c  o m*/
 * @return
 * @throws JAXBException
 * @throws IOException
 * @throws ParserConfigurationException
 * @throws SAXException 
 */
private List<CaseType> extractFileCaseData(File xmlFile)
        throws JAXBException, IOException, ParserConfigurationException, SAXException {
    List<CaseType> newCases = new ArrayList();

    // get the document root and determine how to unmarshal document
    Document document = DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(xmlFile);
    Element root = document.getDocumentElement();
    if (root.getNodeName().equals("ClientCaseInfo")) {
        // unmarshal document with root tag = ClientCaseInfo
        JAXBContext context = JAXBContext.newInstance(ClientCaseInfoType.class);
        Unmarshaller jaxbUnmarshaller = context.createUnmarshaller();
        ClientCaseInfoType cci = (ClientCaseInfoType) jaxbUnmarshaller.unmarshal(root);
        newCases.addAll(cci.getCases().getCase());
    } else {
        // unmarshal document with root tag = ResultsReport
        JAXBContext context = JAXBContext.newInstance(ResultsReportType.class);
        Unmarshaller jaxbUnmarshaller = context.createUnmarshaller();
        ResultsReportType rrt = (ResultsReportType) jaxbUnmarshaller.unmarshal(root);
        newCases.add(new CaseType(rrt.getVariantReport()));
    }

    return newCases;
}

From source file:eu.over9000.skadi.io.PersistenceHandler.java

public PersistenceHandler() {
    try {/*from w  w  w . ja  va 2 s. co  m*/
        final JAXBContext context = JAXBContext.newInstance(StateContainer.class);
        this.marshaller = context.createMarshaller();
        this.unmarshaller = context.createUnmarshaller();
        this.marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);

    } catch (final JAXBException e) {
        LOGGER.error("exception construction persistence handler", e);
    }
}

From source file:com.github.lindenb.jvarkit.tools.blast.BlastFilterJS.java

@Override
protected Collection<Throwable> call(String inputName) throws Exception {

    final CompiledScript compiledScript;
    Unmarshaller unmarshaller;/*from www  .  j a  va  2s.c  o  m*/
    Marshaller marshaller;
    try {
        compiledScript = super.compileJavascript();

        JAXBContext jc = JAXBContext.newInstance("gov.nih.nlm.ncbi.blast");

        unmarshaller = jc.createUnmarshaller();
        marshaller = jc.createMarshaller();

        XMLInputFactory xmlInputFactory = XMLInputFactory.newFactory();
        xmlInputFactory.setProperty(XMLInputFactory.IS_NAMESPACE_AWARE, Boolean.TRUE);
        xmlInputFactory.setProperty(XMLInputFactory.IS_COALESCING, Boolean.TRUE);
        xmlInputFactory.setProperty(XMLInputFactory.IS_REPLACING_ENTITY_REFERENCES, Boolean.TRUE);
        xmlInputFactory.setProperty(XMLInputFactory.IS_SUPPORTING_EXTERNAL_ENTITIES, Boolean.FALSE);
        marshaller.setProperty(Marshaller.JAXB_FRAGMENT, true);
        marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);

        PrintWriter pw = openFileOrStdoutAsPrintWriter();
        XMLOutputFactory xof = XMLOutputFactory.newFactory();
        xof.setProperty(XMLOutputFactory.IS_REPAIRING_NAMESPACES, Boolean.FALSE);
        XMLEventWriter w = xof.createXMLEventWriter(pw);

        StreamSource src = null;
        if (inputName == null) {
            LOG.info("Reading stdin");
            src = new StreamSource(stdin());
        } else {
            LOG.info("Reading file " + inputName);
            src = new StreamSource(new File(inputName));
        }

        XMLEventReader r = xmlInputFactory.createXMLEventReader(src);

        XMLEventFactory eventFactory = XMLEventFactory.newFactory();

        SimpleBindings bindings = new SimpleBindings();
        while (r.hasNext()) {
            XMLEvent evt = r.peek();
            switch (evt.getEventType()) {
            case XMLEvent.START_ELEMENT: {
                StartElement sE = evt.asStartElement();
                Hit hit = null;
                JAXBElement<Hit> jaxbElement = null;
                if (sE.getName().getLocalPart().equals("Hit")) {
                    jaxbElement = unmarshaller.unmarshal(r, Hit.class);
                    hit = jaxbElement.getValue();
                } else {
                    w.add(r.nextEvent());
                    break;
                }

                if (hit != null) {

                    bindings.put("hit", hit);

                    boolean accept = super.evalJavaScriptBoolean(compiledScript, bindings);

                    if (accept) {
                        marshaller.marshal(jaxbElement, w);
                        w.add(eventFactory.createCharacters("\n"));
                    }
                }

                break;
            }
            case XMLEvent.SPACE:
                break;
            default: {
                w.add(r.nextEvent());
                break;
            }
            }
            r.close();
        }
        w.flush();
        w.close();
        pw.flush();
        pw.close();
        return RETURN_OK;
    } catch (Exception err) {
        return wrapException(err);
    } finally {

    }
}

From source file:com.spend.spendService.MainPage.java

private SearchEngines getSearchEnginesFromXml() {
    try {//from   ww  w.j a  v  a2s  .c o  m
        File file = new File("SearchEngines.xml");
        JAXBContext jaxbContext = JAXBContext.newInstance(SearchEngines.class);

        Unmarshaller jaxbUnmarshaller = jaxbContext.createUnmarshaller();
        SearchEngines searchEngineList = (SearchEngines) jaxbUnmarshaller.unmarshal(file);
        return searchEngineList;

    } catch (JAXBException e) {
        e.printStackTrace();
    }
    return null;
}

From source file:org.fcrepo.auth.oauth.integration.api.ContainerWrapper.java

public void start() throws Exception {

    final JAXBContext context = JAXBContext.newInstance(WebAppConfig.class);
    final Unmarshaller u = context.createUnmarshaller();
    final WebAppConfig o = (WebAppConfig) u.unmarshal(getClass().getResource(this.configLocation));

    final URI uri = URI.create("http://localhost:" + port + "/");

    final Map<String, String> initParams = new HashMap<String, String>();

    server = GrizzlyWebContainerFactory.create(uri, initParams);

    // create a "root" web application
    final WebappContext wac = new WebappContext(o.displayName(), "");

    for (final ContextParam p : o.contextParams()) {
        wac.addContextInitParameter(p.name(), p.value());
    }/* www.j  av a  2s  .co m*/

    for (final Listener l : o.listeners) {
        wac.addListener(l.className());
    }

    for (final Servlet s : o.servlets) {
        final ServletRegistration servlet = wac.addServlet(s.servletName(), s.servletClass());

        final Collection<ServletMapping> mappings = o.servletMappings(s.servletName());
        for (final ServletMapping sm : mappings) {
            servlet.addMapping(sm.urlPattern());
        }
        for (final InitParam p : s.initParams()) {
            servlet.setInitParameter(p.name(), p.value());
        }
    }

    for (final Filter f : o.filters) {
        final FilterRegistration filter = wac.addFilter(f.filterName(), f.filterClass());

        final Collection<FilterMapping> mappings = o.filterMappings(f.filterName());
        for (final FilterMapping sm : mappings) {
            final String urlPattern = sm.urlPattern();
            final String servletName = sm.servletName();
            if (urlPattern != null) {
                filter.addMappingForUrlPatterns(null, urlPattern);
            } else {
                filter.addMappingForServletNames(null, servletName);
            }

        }
        for (final InitParam p : f.initParams()) {
            filter.setInitParameter(p.name(), p.value());
        }
    }

    wac.deploy(server);

    final URL webXml = this.getClass().getResource("/web.xml");
    logger.error(webXml.toString());

    logger.debug("started grizzly webserver endpoint at " + server.getHttpHandler().getName());
}

From source file:org.fcrepo.integration.auth.oauth.api.ContainerWrapper.java

public void start() throws Exception {

    final JAXBContext context = JAXBContext.newInstance(WebAppConfig.class);
    final Unmarshaller u = context.createUnmarshaller();
    final WebAppConfig o = (WebAppConfig) u.unmarshal(getClass().getResource(this.configLocation));

    final URI uri = URI.create("http://localhost:" + port + "/");

    final Map<String, String> initParams = new HashMap<>();

    server = GrizzlyWebContainerFactory.create(uri, initParams);

    // create a "root" web application
    final WebappContext wac = new WebappContext(o.displayName(), "");

    for (final ContextParam p : o.contextParams()) {
        wac.addContextInitParameter(p.name(), p.value());
    }/*  w w w.  ja  va 2  s.c  o  m*/

    for (final Listener l : o.listeners) {
        wac.addListener(l.className());
    }

    for (final Servlet s : o.servlets) {
        final ServletRegistration servlet = wac.addServlet(s.servletName(), s.servletClass());

        final Collection<ServletMapping> mappings = o.servletMappings(s.servletName());
        for (final ServletMapping sm : mappings) {
            servlet.addMapping(sm.urlPattern());
        }
        for (final InitParam p : s.initParams()) {
            servlet.setInitParameter(p.name(), p.value());
        }
    }

    for (final Filter f : o.filters) {
        final FilterRegistration filter = wac.addFilter(f.filterName(), f.filterClass());

        final Collection<FilterMapping> mappings = o.filterMappings(f.filterName());
        for (final FilterMapping sm : mappings) {
            final String urlPattern = sm.urlPattern();
            final String servletName = sm.servletName();
            if (urlPattern != null) {
                filter.addMappingForUrlPatterns(null, urlPattern);
            } else {
                filter.addMappingForServletNames(null, servletName);
            }

        }
        for (final InitParam p : f.initParams()) {
            filter.setInitParameter(p.name(), p.value());
        }
    }

    wac.deploy(server);

    final URL webXml = this.getClass().getResource("/web.xml");
    logger.error(webXml.toString());

    logger.debug("started grizzly webserver endpoint at " + server.getHttpHandler().getName());
}

From source file:org.jasig.portlet.courses.dao.xml.MockCoursesSectionDao.java

@Override
public TermList getTermList(PortletRequest request) {
    try {//from w  w w .  j a v  a 2 s .c om
        JAXBContext jaxbContext = JAXBContext.newInstance(TermsAndCourses.class);
        Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
        this.summary = (TermsAndCourses) unmarshaller.unmarshal(mockData.getInputStream());
    } catch (IOException e) {
        log.error("Failed to read mock data for TermList", e);
    } catch (JAXBException e) {
        log.error("Failed to unmarshall mock data for TermList", e);
    }
    return summary.getTermList();
}

From source file:com.intuit.tank.script.TankXmlUploadBean.java

public void processScript(InputStream inputStream, String fileName) throws Exception {
    try {//from  ww  w.  j a  v a  2  s  .c  o  m
        ScriptDao dao = new ScriptDao();
        JAXBContext ctx = JAXBContext.newInstance(ScriptTO.class.getPackage().getName());
        ScriptTO scriptTo = (ScriptTO) ctx.createUnmarshaller().unmarshal(inputStream);
        Script script = ScriptServiceUtil.transferObjectToScript(scriptTo);
        if (script.getId() > 0) {
            Script existing = dao.findById(script.getId());
            if (existing == null) {
                LOG.error("Error updating script: Script passed with unknown id.");
                messages.error("Script " + fileName + " passed with unknown id.");
                return;
            }
            if (!existing.getName().equals(script.getName())) {
                LOG.error("Error updating script: Cannot change the name of an existing Script.");
                messages.error("Cannot change the name of an existing script.");
                return;
            }
            if (!security.isAdmin() && !security.isOwner(script)) {
                LOG.error("Error updating script: Cannot change the name of an existing Script.");
                messages.error("You do not have rights to modify " + script.getName() + ".");
                return;
            }
        } else {
            script.setCreator(identity.getUser().getId());
        }
        script = dao.saveOrUpdate(script);
        messages.info("Script " + script.getName() + " from file " + fileName + " has been added.");
        scriptEvent.fire(new ModifiedScriptMessage(script, this));
    } catch (Exception e) {
        LOG.error("Error unmarshalling script: " + e.getMessage() + " from file " + fileName, e);
        messages.error("Error unmarshalling script: " + e.toString() + " from file " + fileName);
    }
}

From source file:org.jasig.portlet.campuslife.dao.ScreenScrapingService.java

/**
 * Deserialize a menu from the provided XML.
 * /*from w ww.  j  av a2s .  c  o m*/
 * @param xml
 * @return
 * @throws JAXBException
 */
protected T deserializeItem(String xml) throws JAXBException {

    final JAXBContext jc = JAXBContext.newInstance(getPackageName());
    final Unmarshaller u = jc.createUnmarshaller();

    @SuppressWarnings("unchecked")
    final T menu = (T) u.unmarshal(IOUtils.toInputStream(xml));
    return menu;
}

From source file:se.vgregion.domain.infrastructure.webservice.RestCalendarEventsRepository.java

private CalendarEvents extractCalendarEvents(InputStream bis) throws IOException, JAXBException {
    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    byte[] buf = new byte[4096];
    int n;//from  w  w  w .  j  a  va  2s  .  c om
    while ((n = bis.read(buf)) != -1) {
        baos.write(buf, 0, n);
    }

    String inUtf8 = new String(baos.toByteArray(), "UTF-8");
    String inIso8859 = new String(baos.toByteArray(), "ISO-8859-1");
    int numberSwedishCharactersFromUtf8 = StringUtils.countMatches(inUtf8, "")
            + StringUtils.countMatches(inUtf8, "") + StringUtils.countMatches(inUtf8, "");
    int numberSwedishCharactersFromIso8859 = StringUtils.countMatches(inIso8859, "")
            + StringUtils.countMatches(inIso8859, "") + StringUtils.countMatches(inIso8859, "");

    String toUse;
    if (numberSwedishCharactersFromIso8859 > numberSwedishCharactersFromUtf8) {
        toUse = inIso8859;
    } else {
        toUse = inUtf8;
    }

    JAXBContext jaxbContext = JAXBContext.newInstance(CalendarEvents.class);
    return (CalendarEvents) jaxbContext.createUnmarshaller().unmarshal(new StringReader(toUse));
}