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

Example 86 with Namespace

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

the class XMLUtils method getNamespacesWithPrefixes.

public Map<Namespace, String> getNamespacesWithPrefixes(Document doc) {
    Map<Namespace, Element> n2El = getElementNamespaces(doc);
    Map<Namespace, String> rc = new HashMap<Namespace, String>();
    for (Namespace ns : n2El.keySet()) {
        String s = null;
        // ideally we use the existing prefix in the model element
        if (ns.getPrefix().length() > 0) {
            rc.put(ns, ns.getPrefix());
        // else we use the namespace to generate a prefix
        } else if ((s = getNCNameFromNSURL(ns)) != null) {
            rc.put(ns, s);
        // else a last resort we sjust use the element name as a prefix
        // and
        // hope this will get matched to a namespace in the model.
        } else {
            rc.put(ns, n2El.get(ns).getName());
        }
    }
    return rc;
}

Example 87 with Namespace

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

the class AnatomicalStructure method getCompartmentGoTerms.

public static HashMap<String, AnatomicalStructure> getCompartmentGoTerms(String sbmlText) {
    HashMap<String, AnatomicalStructure> compartmentAnatomyMap = new HashMap<String, AnatomicalStructure>();
    Namespace sbmlNamespace = Namespace.getNamespace("http://www.sbml.org/sbml/level2");
    Namespace rdfNamespace = Namespace.getNamespace("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
    Namespace bioqualifierNamespace = Namespace.getNamespace("http://biomodels.net/biology-qualifiers/");
    Element rootSBML = (XmlUtil.stringToXML(sbmlText, null)).getRootElement();
    Element sbmlModelElement = rootSBML.getChild("model", sbmlNamespace);
    Element listOfCompartments = sbmlModelElement.getChild("listOfCompartments", sbmlNamespace);
    List<Element> compartmentElementList = listOfCompartments.getChildren("compartment", sbmlNamespace);
    for (Element compartmentElement : compartmentElementList) {
        AnatomicalStructure anatomicalStructure = null;
        String compartmentID = compartmentElement.getAttributeValue("id");
        String goPrefix = "http://www.geneontology.org/#GO:";
        String compartmentOutside = compartmentElement.getAttributeValue("outside");
        Element annotationElement = compartmentElement.getChild("annotation", sbmlNamespace);
        if (annotationElement != null) {
            Element rdfElement = annotationElement.getChild("RDF", rdfNamespace);
            Element descriptionElement = rdfElement.getChild("Description", rdfNamespace);
            Element isElement = descriptionElement.getChild("is", bioqualifierNamespace);
            if (isElement == null) {
                isElement = descriptionElement.getChild("isVersionOf", bioqualifierNamespace);
            }
            if (isElement != null) {
                Element bagElement = isElement.getChild("Bag", rdfNamespace);
                Element liElement = bagElement.getChild("li", rdfNamespace);
                String compartmentRdfResource = liElement.getAttributeValue("resource", rdfNamespace);
                if (compartmentRdfResource.startsWith(goPrefix)) {
                    String GoTerm = compartmentRdfResource.substring(goPrefix.length(), compartmentRdfResource.length());
                    anatomicalStructure = AnatomicalStructure.fromGOTerm(GoTerm);
                }
                if (compartmentOutside != null) {
                    System.out.println(compartmentOutside + "," + compartmentID);
                }
            }
            compartmentAnatomyMap.put(compartmentID, anatomicalStructure);
        }
    }
    return compartmentAnatomyMap;
}

Example 88 with Namespace

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

the class XmlHelper method XMLToGeometry.

static Geometry XMLToGeometry(XMLSource xmlSource, boolean printkeys) throws XmlParseException {
    Geometry geometry = null;
    if (xmlSource == null) {
        throw new XmlParseException("Invalid xml for Geometry.");
    }
    Document xmlDoc = xmlSource.getXmlDoc();
    // NOTES:
    // * The root element can be <Biomodel> (old-style vcml) OR <vcml> (new-style vcml)
    // * With the old-style vcml, the namespace was " "
    // * With the new-style vcml, there is an intermediate stage where the namespace for <vcml> root
    // was set to "http://sourceforge.net/projects/VCell/version0.4" for some models and
    // "http://sourceforge.net/projects/vcell/vcml" for some models; and the namespace for child element
    // <biomdel>, etc. was " "
    // * The final new-style vcml has (should have) the namespace "http://sourceforge.net/projects/vcell/vcml"
    // for <vcml> and all children elements.
    // The code below attempts to take care of this situation.
    Element root = xmlDoc.getRootElement();
    Namespace ns = null;
    if (root.getName().equals(XMLTags.VcmlRootNodeTag)) {
        // NEW WAY - with xml string containing xml declaration, vcml element, namespace, etc ...
        ns = root.getNamespace();
        Element geoRoot = root.getChild(XMLTags.GeometryTag, ns);
        if (geoRoot == null) {
            geoRoot = root.getChild(XMLTags.GeometryTag);
            // geoRoot was null, so obtained the <Geometry> element with namespace " ";
            // Re-set the namespace so that the correct XMLReader constructor is invoked.
            ns = null;
        }
        root = geoRoot;
    }
    // else - root is assumed to be old-style vcml with <Geometry> as root.
    // common for both new-style (with xml declaration, vcml element, etc) and old-style (geometry is root)
    // If namespace is null, xml is the old-style xml with geometry as root, so invoke XMLReader without namespace argument.
    XmlReader reader = null;
    if (ns == null) {
        reader = new XmlReader(printkeys);
    } else {
        reader = new XmlReader(printkeys, ns);
    }
    geometry = reader.getGeometry(root);
    geometry.refreshDependencies();
    return geometry;
}

Example 89 with Namespace

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

the class XmlHelper method XMLToMathModel.

static MathModel XMLToMathModel(XMLSource xmlSource, boolean printkeys) throws XmlParseException {
    MathModel mathModel = null;
    if (xmlSource == null) {
        throw new XmlParseException("Invalid xml for Geometry.");
    }
    Document xmlDoc = xmlSource.getXmlDoc();
    // NOTES:
    // * The root element can be <Biomodel> (old-style vcml) OR <vcml> (new-style vcml)
    // * With the old-style vcml, the namespace was " "
    // * With the new-style vcml, there is an intermediate stage where the namespace for <vcml> root
    // was set to "http://sourceforge.net/projects/VCell/version0.4" for some models and
    // "http://sourceforge.net/projects/vcell/vcml" for some models; and the namespace for child element
    // <biomdel>, etc. was " "
    // * The final new-style vcml has (should have) the namespace "http://sourceforge.net/projects/vcell/vcml"
    // for <vcml> and all children elements.
    // The code below attempts to take care of this situation.
    Element root = xmlDoc.getRootElement();
    Namespace ns = null;
    if (root.getName().equals(XMLTags.VcmlRootNodeTag)) {
        // NEW WAY - with xml string containing xml declaration, vcml element, namespace, etc ...
        ns = root.getNamespace();
        Element mathRoot = root.getChild(XMLTags.MathModelTag, ns);
        if (mathRoot == null) {
            mathRoot = root.getChild(XMLTags.MathModelTag);
            // mathRoot was null, so obtained the <Mathmodel> element with namespace " ";
            // Re-set the namespace so that the correct XMLReader constructor is invoked.
            ns = null;
        }
        root = mathRoot;
    }
    // else - root is assumed to be old-style vcml with <Mathmodel> as root.
    // common for both new-style (with xml declaration, vcml element, etc) and old-style (mathmodel is root)
    // If namespace is null, xml is the old-style xml with mathmodel as root, so invoke XMLReader without namespace argument.
    XmlReader reader = null;
    if (ns == null) {
        reader = new XmlReader(printkeys);
    } else {
        reader = new XmlReader(printkeys, ns);
    }
    mathModel = reader.getMathModel(root);
    mathModel.refreshDependencies();
    return mathModel;
}

Example 90 with Namespace

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

the class XmlHelper method XMLToBioModel.

public static BioModel XMLToBioModel(XMLSource xmlSource, boolean printkeys, ModelUnitSystem forcedModelUnitSystem) throws XmlParseException {
    // long l0 = System.currentTimeMillis();
    BioModel bioModel = null;
    if (xmlSource == null) {
        throw new XmlParseException("Invalid xml for Biomodel.");
    }
    Document xmlDoc = xmlSource.getXmlDoc();
    // NOTES:
    // * The root element can be <Biomodel> (old-style vcml) OR <vcml> (new-style vcml)
    // * With the old-style vcml, the namespace was " "
    // * With the new-style vcml, there is an intermediate stage where the namespace for <vcml> root
    // was set to "http://sourceforge.net/projects/VCell/version0.4" for some models and
    // "http://sourceforge.net/projects/vcell/vcml" for some models; and the namespace for child element
    // <biomdel>, etc. was " "
    // * The final new-style vcml has (should have) the namespace "http://sourceforge.net/projects/vcell/vcml"
    // for <vcml> and all children elements.
    // The code below attempts to take care of this situation.
    Element root = xmlDoc.getRootElement();
    Namespace ns = null;
    if (root.getName().equals(XMLTags.VcmlRootNodeTag)) {
        // NEW WAY - with xml string containing xml declaration, vcml element, namespace, etc ...
        ns = root.getNamespace();
        Element bioRoot = root.getChild(XMLTags.BioModelTag, ns);
        if (bioRoot == null) {
            bioRoot = root.getChild(XMLTags.BioModelTag);
            // bioRoot was null, so obtained the <Biomodel> element with namespace " ";
            // Re-set the namespace so that the correct XMLReader constructor is invoked.
            ns = null;
        }
        root = bioRoot;
    }
    // else - root is assumed to be old-style vcml with <Biomodel> as root.
    // common for both new way (with xml declaration, vcml element, etc) and existing way (biomodel is root)
    // If namespace is null, xml is the old-style xml with biomodel as root, so invoke XMLReader without namespace argument.
    XmlReader reader = null;
    VCellSoftwareVersion vCellSoftwareVersion = null;
    if (ns == null) {
        reader = new XmlReader(printkeys);
    } else {
        reader = new XmlReader(printkeys, ns);
        vCellSoftwareVersion = VCellSoftwareVersion.fromString(root.getAttributeValue(XMLTags.SoftwareVersionAttrTag, ns));
    }
    if (forcedModelUnitSystem != null) {
        reader.setForcedModelUnitSystem(forcedModelUnitSystem);
    }
    bioModel = reader.getBioModel(root, vCellSoftwareVersion);
    // long l1 = System.currentTimeMillis();
    bioModel.refreshDependencies();
    return bioModel;
}