Examples with Namespace org.jdom.Namespace used on opensource projects

Example 46 with Namespace

use of org.jdom.Namespace in project vcell by virtualcell.

the class XmlHelper method XMLToDocument.

/**
 * Insert the method's description here.
 * Creation date: (2/7/2006 4:45:26 PM)
 * @return cbit.vcell.document.VCDocument
 * @param xmlString java.lang.String
 */
public static VCDocument XMLToDocument(VCLogger vcLogger, String xmlString) throws Exception {
    VCDocument doc = null;
    XMLSource xmlSource = new XMLSource(xmlString);
    // some overhead.
    org.jdom.Element rootElement = xmlSource.getXmlDoc().getRootElement();
    String xmlType = rootElement.getName();
    if (xmlType.equals(XMLTags.VcmlRootNodeTag)) {
        // For now, assuming that <vcml> element has only one child (biomodel, mathmodel or geometry).
        // Will deal with multiple children of <vcml> Element when we get to model composition.
        java.util.List<?> childElementList = rootElement.getChildren();
        // assuming first child is the biomodel, mathmodel or geometry.
        Element modelElement = (Element) childElementList.get(0);
        xmlType = modelElement.getName();
    }
    if (xmlType.equals(XMLTags.BioModelTag)) {
        doc = XmlHelper.XMLToBioModel(xmlSource);
    } else if (xmlType.equals(XMLTags.MathModelTag)) {
        doc = XmlHelper.XMLToMathModel(xmlSource);
    } else if (xmlType.equals(XMLTags.GeometryTag)) {
        doc = XmlHelper.XMLToGeometry(xmlSource);
    } else if (xmlType.equals(XMLTags.SbmlRootNodeTag)) {
        Namespace namespace = rootElement.getNamespace(XMLTags.SBML_SPATIAL_NS_PREFIX);
        boolean bIsSpatial = (namespace == null) ? false : true;
        doc = XmlHelper.importSBML(vcLogger, xmlSource, bIsSpatial);
    } else if (xmlType.equals(XMLTags.CellmlRootNodeTag)) {
        doc = XmlHelper.importMathCellML(vcLogger, xmlSource);
    } else {
        // unknown XML format
        throw new RuntimeException("unsupported XML format, first element tag is <" + rootElement.getName() + ">");
    }
    return doc;
}

Example 47 with Namespace

use of org.jdom.Namespace in project vcell by virtualcell.

the class XmlHelper method XMLToImage.

static VCImage XMLToImage(String xmlString, boolean printKeys) throws XmlParseException {
    Namespace ns = Namespace.getNamespace(XMLTags.VCML_NS);
    if (xmlString == null || xmlString.length() == 0) {
        throw new XmlParseException("Invalid xml for Image: " + xmlString);
    }
    // default parser and no validation
    Element root = (XmlUtil.stringToXML(xmlString, null)).getRootElement();
    Element extentElement = root.getChild(XMLTags.ExtentTag, ns);
    Element imageElement = root.getChild(XMLTags.ImageTag, ns);
    // Element extentElement = root.getChild(XMLTags.ExtentTag);
    // Element imageElement = root.getChild(XMLTags.ImageTag);
    XmlReader reader = new XmlReader(printKeys, ns);
    Extent extent = reader.getExtent(extentElement);
    VCImage vcImage = reader.getVCImage(imageElement, extent);
    vcImage.refreshDependencies();
    return vcImage;
}

Example 48 with Namespace

use of org.jdom.Namespace in project vcell by virtualcell.

the class XmlHelper method XMLToSimTask.

public static SimulationTask XMLToSimTask(String xmlString) throws XmlParseException, ExpressionException {
    Namespace ns = Namespace.getNamespace(XMLTags.VCML_NS);
    try {
        if (xmlString == null || xmlString.length() == 0) {
            throw new XmlParseException("Invalid xml for Simulation: " + xmlString);
        }
        // default parser and no validation
        Element root = (XmlUtil.stringToXML(xmlString, null)).getRootElement();
        if (!root.getName().equals(SimulationTask_tag)) {
            throw new RuntimeException("expecting top level element to be " + SimulationTask_tag);
        }
        int taskId = Integer.parseInt(root.getAttributeValue(TaskId_attr));
        int jobIndex = Integer.parseInt(root.getAttributeValue(JobIndex_attr));
        boolean isPowerUser = false;
        if (root.getAttributeValue(powerUser_attr) != null) {
            isPowerUser = Boolean.parseBoolean(root.getAttributeValue(powerUser_attr));
        }
        String computeResource = root.getChildTextTrim(ComputeResource_tag, ns);
        List<?> children = root.getChildren(FieldFunctionIdentifierSpec_tag, ns);
        ArrayList<FieldDataIdentifierSpec> fdisArrayList = new ArrayList<FieldDataIdentifierSpec>();
        for (Object child : children) {
            if (child instanceof Element) {
                String fdisText = ((Element) child).getTextTrim();
                FieldDataIdentifierSpec fdis = FieldDataIdentifierSpec.fromCSVString(fdisText);
                fdisArrayList.add(fdis);
            }
        }
        FieldDataIdentifierSpec[] fdisArray = fdisArrayList.toArray(new FieldDataIdentifierSpec[0]);
        Element simElement = root.getChild(XMLTags.SimulationTag, ns);
        Element mdElement = root.getChild(XMLTags.MathDescriptionTag, ns);
        Element geomElement = root.getChild(XMLTags.GeometryTag, ns);
        XmlReader reader = new XmlReader(true, ns);
        Geometry geom = null;
        if (geomElement != null) {
            geom = reader.getGeometry(geomElement);
        }
        MathDescription md = reader.getMathDescription(mdElement, geom);
        Simulation sim = reader.getSimulation(simElement, md);
        sim.refreshDependencies();
        SimulationJob simJob = new SimulationJob(sim, jobIndex, fdisArray);
        SimulationTask simTask = new SimulationTask(simJob, taskId, computeResource, isPowerUser);
        return simTask;
    } catch (Exception pve) {
        pve.printStackTrace();
        throw new XmlParseException("Unable to parse simulation string.", pve);
    }
}

Example 49 with Namespace

use of org.jdom.Namespace in project vcell by virtualcell.

the class SEDMLExporter method getSEDMLFile.

public String getSEDMLFile(String sPath, String sBaseFileName, boolean bForceVCML, boolean bHasDataOnly, boolean bFromOmex) {
    // Create an SEDMLDocument and create the SEDMLModel from the document, so that other details can be added to it in translateBioModel()
    SEDMLDocument sedmlDocument = new SEDMLDocument(this.sedmlLevel, this.sedmlVersion);
    // sedmlDocument.getSedMLModel().setAdditionalNamespaces(Arrays.asList(new Namespace[] {
    // Namespace.getNamespace(SEDMLTags.SBML_NS_PREFIX, SEDMLTags.SBML_NS_L2V4)
    // }));
    final String SBML_NS = "http://www.sbml.org/sbml/level3/version1/core";
    final String SBML_NS_PREFIX = "sbml";
    final String VCML_NS = "http://sourceforge.net/projects/vcell/vcml";
    final String VCML_NS_PREFIX = "vcml";
    List<Namespace> nsList = new ArrayList<>();
    Namespace ns = Namespace.getNamespace(SEDMLTags.MATHML_NS_PREFIX, SEDMLTags.MATHML_NS);
    nsList.add(ns);
    ns = Namespace.getNamespace(SBML_NS_PREFIX, SBML_NS);
    nsList.add(ns);
    ns = Namespace.getNamespace(VCML_NS_PREFIX, VCML_NS);
    nsList.add(ns);
    sedmlModel = sedmlDocument.getSedMLModel();
    sedmlModel.setAdditionalNamespaces(nsList);
    translateBioModelToSedML(sPath, sBaseFileName, bForceVCML, bHasDataOnly, bFromOmex);
    // write SEDML document into SEDML writer, so that the SEDML str can be retrieved
    return sedmlDocument.writeDocumentToString();
}

Example 50 with Namespace

use of org.jdom.Namespace in project vcell by virtualcell.

the class SEDMLReader method getSedDocument.

/*
	 * returns a SedML model given an Element of xml for a complete model non -
	 * api method
	 */
public SedML getSedDocument(Element sedRoot) throws XMLException {
    SedML sedDoc = null;
    SymbolRegistry.getInstance().addSymbolFactory(new SedMLSymbolFactory());
    try {
        Namespace sedNS = sedRoot.getNamespace();
        String verStr = sedRoot.getAttributeValue(SEDMLTags.VERSION_TAG);
        String lvlStr = sedRoot.getAttributeValue(SEDMLTags.LEVEL_TAG);
        if (verStr != null && lvlStr != null) {
            int sedVersion = Integer.parseInt(verStr);
            int sedLevel = Integer.parseInt(lvlStr);
            sedDoc = new SedML(sedLevel, sedVersion, sedNS);
        } else {
            sedDoc = new SedML(sedNS);
        }
        // Get additional namespaces if mentioned : mathml, sbml, etc.
        List additionalNamespaces = sedRoot.getAdditionalNamespaces();
        sedDoc.setAdditionalNamespaces(additionalNamespaces);
        // notes and annotations
        addNotesAndAnnotation(sedDoc, sedRoot);
        Iterator<Element> elementsIter = null;
        // models
        Element el = sedRoot.getChild(SEDMLTags.MODELS, sedNS);
        if (el != null) {
            List elementsList = el.getChildren();
            elementsIter = elementsList.iterator();
            while (elementsIter.hasNext()) {
                Element modelElement = elementsIter.next();
                if (modelElement.getName().equals(SEDMLTags.MODEL_TAG)) {
                    sedDoc.addModel(getModel(modelElement));
                }
            }
        }
        // simulations
        el = sedRoot.getChild(SEDMLTags.SIMS, sedNS);
        if (el != null) {
            List elementsList = el.getChildren();
            elementsIter = elementsList.iterator();
            while (elementsIter.hasNext()) {
                Element simElement = elementsIter.next();
                sedDoc.addSimulation(getSimulation(simElement));
            }
        }
        el = sedRoot.getChild(SEDMLTags.TASKS, sedNS);
        if (el != null) {
            List elementsList = el.getChildren();
            elementsIter = elementsList.iterator();
            while (elementsIter.hasNext()) {
                Element taskElement = elementsIter.next();
                if (taskElement.getName().equals(SEDMLTags.TASK_TAG)) {
                    sedDoc.addTask(getTask(taskElement));
                } else if (taskElement.getName().equals(SEDMLTags.REPEATED_TASK_TAG)) {
                    sedDoc.addTask(getRepeatedTask(taskElement));
                }
            }
        }
        el = sedRoot.getChild(SEDMLTags.DATAGENERATORS, sedNS);
        if (el != null) {
            List elementsList = el.getChildren();
            elementsIter = elementsList.iterator();
            while (elementsIter.hasNext()) {
                Element dataGenElement = elementsIter.next();
                if (dataGenElement.getName().equals(SEDMLTags.DATAGENERATOR_TAG)) {
                    sedDoc.addDataGenerator(getDataGenerator(dataGenElement));
                }
            }
        }
        el = sedRoot.getChild(SEDMLTags.OUTPUTS, sedNS);
        if (el != null) {
            List elementsList = el.getChildren();
            elementsIter = elementsList.iterator();
            while (elementsIter.hasNext()) {
                Element outputElement = elementsIter.next();
                if (outputElement.getName().equals(SEDMLTags.OUTPUT_P2D) || outputElement.getName().equals(SEDMLTags.OUTPUT_P3D) || outputElement.getName().equals(SEDMLTags.OUTPUT_REPORT)) {
                    sedDoc.addOutput(getOutput(outputElement));
                }
            }
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new XMLException("Error loading sed-ml document : " + e.getMessage());
    // return sedDoc;
    }
    return sedDoc;
}