Examples with XMLOutputter org.jdom.output.XMLOutputter used on opensource projects

Example 31 with XMLOutputter

use of org.jdom.output.XMLOutputter in project vcell by virtualcell.

the class RulebasedTransformer method compareOperations.

private static void compareOperations(Element eTheirs, Element eOurs) {
    XMLOutputter outp = new XMLOutputter();
    Set<String> theirOperations = new HashSet<String>();
    Set<String> ourOperations = new HashSet<String>();
    Element le = eTheirs.getChild("ListOfOperations", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
    List<Element> children = new ArrayList<Element>();
    children = le.getChildren();
    for (Element e : children) {
        String s = outp.outputString(e);
        s = s.replace("xmlns=\"http://www.sbml.org/sbml/level3\"", "");
        s = s.replaceAll("\\s+", "");
        if (theirOperations.add(s) == false) {
            System.out.println("Duplicate their operation: " + s);
        }
        System.out.println(s);
    }
    le = eOurs.getChild("ListOfOperations");
    children = le.getChildren();
    for (Element e : children) {
        String s = outp.outputString(e);
        s = s.replace(".0", "");
        s = s.replaceAll("\\s+", "");
        if (ourOperations.add(s) == false) {
            System.out.println("Duplicate our operation: " + s);
        }
        System.out.println(s);
    }
    List<String> theirUnmatched = new ArrayList<String>();
    for (String their : theirOperations) {
        if (!ourOperations.contains(their)) {
            theirUnmatched.add(their);
        }
    }
    List<String> ourUnmatched = new ArrayList<String>();
    for (String our : ourOperations) {
        if (!theirOperations.contains(our)) {
            ourUnmatched.add(our);
        }
    }
    if (!theirUnmatched.isEmpty() || !ourUnmatched.isEmpty()) {
        String s1 = "theirs: ";
        String s2 = "ours  : ";
        for (String their : theirUnmatched) {
            s1 += their + "' ";
        }
        for (String our : ourUnmatched) {
            s2 += our + "' ";
        }
        throw new RuntimeException("Operations not matching for rule\n" + s1 + "\n" + s2 + "\n");
    } else {
        System.out.println("Operations matching for rule");
    }
}

Example 32 with XMLOutputter

use of org.jdom.output.XMLOutputter in project vcell by virtualcell.

the class RulebasedTransformer method parseObservablesBngOutput.

private void parseObservablesBngOutput(SimulationContext simContext, BNGOutput bngOutput) {
    Model model = simContext.getModel();
    Document bngNFSimXMLDocument = bngOutput.getNFSimXMLDocument();
    bngRootElement = bngNFSimXMLDocument.getRootElement();
    Element modelElement = bngRootElement.getChild("model", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
    Element listOfObservablesElement = modelElement.getChild("ListOfObservables", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
    XMLOutputter outp = new XMLOutputter();
    String sTheirs = outp.outputString(listOfObservablesElement);
    sTheirs = sTheirs.replace("xmlns=\"http://www.sbml.org/sbml/level3\"", "");
    // System.out.println("==================== Their Observables ===================================================================");
    // System.out.println(sTheirs);
    // System.out.println("=======================================================================================");
    saveAsText("c:\\TEMP\\ddd\\theirObservables.txt", sTheirs);
// sTheirs = sTheirs.replaceAll("\\s+","");
}

Example 33 with XMLOutputter

use of org.jdom.output.XMLOutputter in project vcell by virtualcell.

the class ExportRawTimeSeriesToVFrapOp method exportToVFRAP.

public void exportToVFRAP(File vfrapFile, ImageTimeSeries<UShortImage> imageTimeSeries, ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    Xmlproducer vcellXMLProducer = new Xmlproducer(false);
    boolean bSaveCompressed = true;
    ImageDataset imageData = new ImageDataset(imageTimeSeries.getAllImages(), imageTimeSeries.getImageTimeStamps(), imageTimeSeries.getSizeZ());
    Element root = new Element(MicroscopyXMLTags.FRAPStudyTag);
    Element next = new Element(MicroscopyXMLTags.FRAPDataTag);
    root.addContent(next);
    Element imageDataXML = MicroscopyXmlproducer.getXML(imageData, vcellXMLProducer, clientTaskStatusSupport, bSaveCompressed);
    next.addContent(imageDataXML);
    java.io.FileOutputStream fileOutStream = new java.io.FileOutputStream(vfrapFile);
    BufferedOutputStream bufferedStream = new BufferedOutputStream(fileOutStream);
    // XmlUtil.writeXmlToStream(root, false, bufferedStream);
    XMLOutputter xmlOut = new XMLOutputter(Format.getPrettyFormat());
    xmlOut.getFormat().setTextMode(Format.TextMode.PRESERVE);
    xmlOut.output(root, bufferedStream);
    bufferedStream.flush();
    fileOutStream.flush();
    fileOutStream.close();
}

Example 34 with XMLOutputter

use of org.jdom.output.XMLOutputter in project vcell by virtualcell.

the class BiomodelsDB_TestSuite method writeSupportedModelsReport.

public static Document writeSupportedModelsReport(File supportInfoDir, File saveSupportedXMLPathname) throws Exception {
    if (!supportInfoDir.isDirectory()) {
        throw new IllegalArgumentException("File " + supportInfoDir.getAbsolutePath() + " must be a directory.");
    }
    File[] xmlReportFiles = supportInfoDir.listFiles(new FileFilter() {

        public boolean accept(File pathname) {
            if (pathname.isFile()) {
                if (pathname.getName().endsWith("_report.xml")) {
                    return true;
                }
            }
            return false;
        }
    });
    Document supportedDocument = new Document(new Element("Supported_BioModelsNet"));
    List<Element> supportedElements = new ArrayList<Element>();
    for (int i = 0; i < xmlReportFiles.length; i++) {
        byte[] xmlBytes = new byte[(int) xmlReportFiles[i].length()];
        FileInputStream fis = new FileInputStream(xmlReportFiles[i]);
        BufferedInputStream bis = new BufferedInputStream(fis);
        DataInputStream dis = new DataInputStream(bis);
        dis.readFully(xmlBytes);
        dis.close();
        Document document = XmlUtil.stringToXML(new String(xmlBytes), null);
        Element bioModelElement = document.getRootElement().getChild(BioModelsNetPanel.BIOMODELINFO_ELEMENT_NAME);
        Attribute supportedAttribute = bioModelElement.getAttribute(BioModelsNetPanel.SUPPORTED_ATTRIBUTE_NAME);
        if (supportedAttribute.getBooleanValue()) {
            Element newBioModelElement = new Element(BioModelsNetPanel.BIOMODELINFO_ELEMENT_NAME);
            @SuppressWarnings("unchecked") List<Attribute> attrList = bioModelElement.getAttributes();
            Iterator<Attribute> iterAttr = attrList.iterator();
            while (iterAttr.hasNext()) {
                newBioModelElement.setAttribute((Attribute) iterAttr.next().clone());
            }
            supportedElements.add(newBioModelElement);
        }
    }
    // Collections.sort(supportedElements, new ElementComparer());
    Element root = supportedDocument.getRootElement();
    for (Element e : supportedElements) {
        root.addContent(e);
    }
    if (saveSupportedXMLPathname != null) {
        try (FileWriter fw = new FileWriter(saveSupportedXMLPathname.getAbsolutePath())) {
            Format format = Format.getPrettyFormat();
            XMLOutputter out = new XMLOutputter(format);
            out.output(supportedDocument, fw);
        }
    }
    return supportedDocument;
}

Example 35 with XMLOutputter

use of org.jdom.output.XMLOutputter in project yamcs-studio by yamcs.

the class XMLUtil method getXMLOutputter.

/**
 * Create and configure an XMLOutputter object.
 *
 * @param prettyFormat
 * @return the XMLOutputter
 */
private static XMLOutputter getXMLOutputter(boolean prettyFormat) {
    Format format = Format.getRawFormat();
    if (prettyFormat)
        // $NON-NLS-1$
        format.setIndent("  ");
    // Always use Unix-style line endings.
    format.setLineSeparator("\n");
    XMLOutputter xmlOutputter = new XMLOutputter();
    xmlOutputter.setFormat(format);
    return xmlOutputter;
}