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

Example 51 with Document

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

the class PathwayReaderBiopax3 method main.

public static void main(String[] args) {
    try {
        // usual testing pathway
        Document document = XmlUtil.readXML(new File("C:\\dan\\reactome biopax\\Reactome3_189445.owl"));
        // infinite recursion between pathway steps
        // http://www.pathwaycommons.org/pc/webservice.do?cmd=get_record_by_cpath_id&version=2.0&q=826249&output=biopax
        // Document document = XmlUtil.readXML(new File("C:\\dan\\reactome biopax\\recursive.owl"));
        PathwayReaderBiopax3 pathwayReader = new PathwayReaderBiopax3(new RDFXMLContext());
        System.out.println("starting parsing");
        PathwayModel pathwayModel = pathwayReader.parse(document.getRootElement(), true);
        System.out.println("ending parsing");
        pathwayModel.reconcileReferences(null);
        System.out.println(pathwayModel.show(false));
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
}

Example 52 with Document

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

the class OptXmlReader method stringToXML.

public static Element stringToXML(String xmlString) {
    try {
        StringReader reader = new StringReader(xmlString);
        SAXBuilder builder = new SAXBuilder();
        Document sDoc = builder.build(reader);
        Element root = sDoc.getRootElement();
        return root;
    } catch (JDOMException e) {
        e.printStackTrace();
        throw new RuntimeException("source document is not well-formed\n" + e.getMessage());
    } catch (IOException e) {
        e.printStackTrace();
        throw new RuntimeException("Unable to read source document\n" + e.getMessage());
    }
}

Example 53 with Document

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

the class PathwayXMLHelper method getElementPathString.

private static String getElementPathString(Element childElement) {
    StringBuffer buffer = new StringBuffer();
    Element element = childElement;
    while (element != null) {
        if (buffer.length() == 0) {
            buffer.append(element.getName());
        } else {
            buffer.insert(0, element.getName() + "/");
        }
        Parent parent = element.getParent();
        if (parent instanceof Element) {
            element = (Element) parent;
        } else if (parent instanceof Document) {
            return buffer.toString();
        } else {
            return buffer.toString();
        }
    }
    return buffer.toString();
}

Example 54 with Document

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

the class PathwayEntryReader method main.

public static void main(String[] args) {
    try {
        Document document = XmlUtil.readXML(new File("C:\\dan\\reactome biopax\\PathwayCommons.xml"));
        PathwayEntryReader pathwayReader = new PathwayEntryReader();
        System.out.println("starting parsing");
        PathwayEntryModel pathwayModel = pathwayReader.parse(document.getRootElement());
        System.out.println("ending parsing");
        System.out.println(pathwayModel.show(true));
        System.out.println("Summary: ");
        System.out.println("   " + pathwayModel.getPathwayEntryObjects().size() + " elements.");
        System.out.println("   " + pathwayReader.numDuplicates + " duplicates.");
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
}

Example 55 with Document

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

the class PathwayBiopax3Test method main.

public static void main(String[] args) {
    try {
        // sbpax: http://www.signaling-gateway.org/molecule/query?afcsid=A000037&type=sbPAXExport
        // items within items
        // Document document = XmlUtil.readXML(new File("C:\\dan\\reactome biopax\\sbpax3fullexample.xml"));
        // biopax with URI-like IDs and resources
        // http://www.pathwaycommons.org/pc2/get?uri=HTTP:%2F%2FWWW.REACTOME.ORG%2FBIOPAX/48887%23PATHWAY1076_1_9606
        // sbpax3_uri_id.xml
        Document document = XmlUtil.readXML(new File("C:\\dan\\reactome biopax\\biopax3_no_id.xml"));
        // Document document = XmlUtil.readXML(new File("C:\\dan\\reactome biopax\\SBPax3.owl"));
        // Document document = XmlUtil.readXML(new File("C:\\dan\\reactome biopax\\Reactome3_189445.owl"));
        PathwayReaderBiopax3 pathwayReader = new PathwayReaderBiopax3(new RDFXMLContext());
        PathwayModel pathwayModel = pathwayReader.parse(document.getRootElement(), true);
        // System.out.print(pathwayModel.show(true));
        pathwayModel.reconcileReferences(null);
        bioModelToXML(pathwayModel);
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
}