[VIVO-1342] Use XML parser to generate valid GraphML files
This commit is contained in:
Graham Triggs
parent
38b95ccbd5
commit
9df0f009ed
2 changed files with 402 additions and 373 deletions
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@ -2,6 +2,8 @@
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package edu.cornell.mannlib.vitro.webapp.visualization.coauthorship;
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import java.io.OutputStreamWriter;
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import java.io.StringWriter;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.List;
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@ -16,44 +18,76 @@ import edu.cornell.mannlib.vitro.webapp.visualization.collaborationutils.Collabo
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import edu.cornell.mannlib.vitro.webapp.visualization.collaborationutils.CollaboratorComparator;
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import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.Collaboration;
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import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.Collaborator;
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import org.w3c.dom.Document;
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import org.w3c.dom.Element;
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import javax.xml.parsers.DocumentBuilder;
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import javax.xml.parsers.DocumentBuilderFactory;
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import javax.xml.parsers.ParserConfigurationException;
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import javax.xml.transform.OutputKeys;
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import javax.xml.transform.Transformer;
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import javax.xml.transform.TransformerConfigurationException;
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import javax.xml.transform.TransformerException;
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import javax.xml.transform.TransformerFactory;
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import javax.xml.transform.dom.DOMSource;
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import javax.xml.transform.stream.StreamResult;
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public class CoAuthorshipGraphMLWriter {
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private StringBuilder coAuthorshipGraphMLContent;
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private final String GRAPHML_HEADER = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
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+ " <graphml xmlns=\"http://graphml.graphdrawing.org/xmlns\"\n"
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+ " xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"\n"
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+ " xsi:schemaLocation=\"http://graphml.graphdrawing.org/xmlns\n"
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+ " http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd\">\n\n";
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private final String GRAPHML_FOOTER = "</graphml>";
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private final String GRAPHML_NS = "http://graphml.graphdrawing.org/xmlns";
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public CoAuthorshipGraphMLWriter(CollaborationData visVOContainer) {
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coAuthorshipGraphMLContent = createCoAuthorshipGraphMLContent(visVOContainer);
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}
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private StringBuilder createCoAuthorshipGraphMLContent(
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CollaborationData coAuthorshipData) {
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private StringBuilder createCoAuthorshipGraphMLContent(CollaborationData coAuthorshipData) {
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StringBuilder graphMLContent = new StringBuilder();
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graphMLContent.append(GRAPHML_HEADER);
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try {
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DocumentBuilderFactory docFactory = DocumentBuilderFactory.newInstance();
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docFactory.setNamespaceAware(true);
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DocumentBuilder docBuilder = docFactory.newDocumentBuilder();
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/*
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* We are side-effecting "graphMLContent" object in this method since creating
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* another String object to hold key definition data will be redundant & will
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* not serve the purpose.
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* */
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generateKeyDefinitionContent(coAuthorshipData, graphMLContent);
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// root elements
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Document doc = docBuilder.newDocument();
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doc.setXmlVersion("1.0");
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Element rootElement = doc.createElementNS(GRAPHML_NS, "graphml");
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doc.appendChild(rootElement);
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/*
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* Used to generate graph content. It will contain both the nodes & edge information.
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* We are side-effecting "graphMLContent".
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* */
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generateGraphContent(coAuthorshipData, graphMLContent);
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/*
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* We are side-effecting "graphMLContent" object in this method since creating
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* another String object to hold key definition data will be redundant & will
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* not serve the purpose.
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* */
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generateKeyDefinitionContent(coAuthorshipData, rootElement);
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graphMLContent.append(GRAPHML_FOOTER);
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/*
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* Used to generate graph content. It will contain both the nodes & edge information.
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* We are side-effecting "graphMLContent".
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* */
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generateGraphContent(coAuthorshipData, rootElement);
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DOMSource source = new DOMSource(doc);
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TransformerFactory transFactory = TransformerFactory.newInstance();
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Transformer transformer = transFactory.newTransformer();
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transformer.setOutputProperty(OutputKeys.ENCODING, "UTF-8");
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transformer.setOutputProperty(OutputKeys.INDENT, "yes");
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StringWriter writer = new StringWriter();
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StreamResult result = new StreamResult(writer);
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transformer.transform(source, result);
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graphMLContent.append(writer.toString());
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} catch (TransformerConfigurationException e) {
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throw new IllegalStateException("XML error generating GraphML", e);
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} catch (TransformerException e) {
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throw new IllegalStateException("XML error generating GraphML", e);
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} catch (ParserConfigurationException e) {
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throw new IllegalStateException("XML error generating GraphML", e);
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}
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return graphMLContent;
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}
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@ -62,118 +96,109 @@ public class CoAuthorshipGraphMLWriter {
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return coAuthorshipGraphMLContent;
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}
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private void generateGraphContent(CollaborationData coAuthorshipData,
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StringBuilder graphMLContent) {
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private void generateGraphContent(CollaborationData coAuthorshipData, Element rootElement) {
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Document doc = rootElement.getOwnerDocument();
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graphMLContent.append("\n<graph edgedefault=\"undirected\">\n");
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Element graph = doc.createElementNS(GRAPHML_NS, "graph");
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graph.setAttribute("edgedefault", "undirected");
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rootElement.appendChild(graph);
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if (coAuthorshipData.getCollaborators() != null
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&& coAuthorshipData.getCollaborators().size() > 0) {
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generateNodeSectionContent(coAuthorshipData, graphMLContent);
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if (coAuthorshipData.getCollaborators() != null && coAuthorshipData.getCollaborators().size() > 0) {
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generateNodeSectionContent(coAuthorshipData, graph);
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}
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if (coAuthorshipData.getCollaborations() != null
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&& coAuthorshipData.getCollaborations().size() > 0) {
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generateEdgeSectionContent(coAuthorshipData, graphMLContent);
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if (coAuthorshipData.getCollaborations() != null && coAuthorshipData.getCollaborations().size() > 0) {
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generateEdgeSectionContent(coAuthorshipData, graph);
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}
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graphMLContent.append("</graph>\n");
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}
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private void generateEdgeSectionContent(CollaborationData coAuthorshipData,
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StringBuilder graphMLContent) {
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private void generateEdgeSectionContent(CollaborationData coAuthorshipData, Element graphElement) {
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Document doc = graphElement.getOwnerDocument();
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graphMLContent.append("<!-- edges -->\n");
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Set<Collaboration> edges = coAuthorshipData.getCollaborations();
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graphElement.appendChild(doc.createComment("edges"));
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Set<Collaboration> edges = coAuthorshipData.getCollaborations();
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List<Collaboration> orderedEdges = new ArrayList<Collaboration>(edges);
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Collections.sort(orderedEdges, new CollaborationComparator());
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for (Collaboration currentEdge : orderedEdges) {
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/*
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* This method actually creates the XML code for a single Collaboration.
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* "graphMLContent" is being side-effected.
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* */
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getEdgeContent(graphMLContent, currentEdge);
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getEdgeContent(graphElement, currentEdge);
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}
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}
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private void getEdgeContent(StringBuilder graphMLContent, Collaboration currentEdge) {
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private void getEdgeContent(Element graphElement, Collaboration currentEdge) {
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Document doc = graphElement.getOwnerDocument();
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graphMLContent.append("<edge "
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+ "id=\"" + currentEdge.getCollaborationID() + "\" "
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+ "source=\"" + currentEdge.getSourceCollaborator()
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.getCollaboratorID() + "\" "
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+ "target=\"" + currentEdge.getTargetCollaborator()
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.getCollaboratorID() + "\" "
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+ ">\n");
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Element edge = doc.createElementNS(GRAPHML_NS, "edge");
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edge.setAttribute("id", String.valueOf(currentEdge.getCollaborationID()));
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edge.setAttribute("source", String.valueOf(currentEdge.getSourceCollaborator().getCollaboratorID()));
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edge.setAttribute("target", String.valueOf(currentEdge.getTargetCollaborator().getCollaboratorID()));
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graphElement.appendChild(edge);
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graphMLContent.append("\t<data key=\"collaborator1\">"
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+ currentEdge.getSourceCollaborator().getCollaboratorName()
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+ "</data>\n");
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Element collaborator1 = doc.createElementNS(GRAPHML_NS, "data");
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collaborator1.setAttribute("key", "collaborator1");
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collaborator1.setTextContent(currentEdge.getSourceCollaborator().getCollaboratorName());
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edge.appendChild(collaborator1);
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graphMLContent.append("\t<data key=\"collaborator2\">"
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+ currentEdge.getTargetCollaborator().getCollaboratorName()
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+ "</data>\n");
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Element collaborator2 = doc.createElementNS(GRAPHML_NS, "data");
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collaborator2.setAttribute("key", "collaborator2");
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collaborator2.setTextContent(currentEdge.getTargetCollaborator().getCollaboratorName());
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edge.appendChild(collaborator2);
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graphMLContent.append("\t<data key=\"number_of_coauthored_works\">"
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+ currentEdge.getNumOfCollaborations()
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+ "</data>\n");
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Element works = doc.createElementNS(GRAPHML_NS, "data");
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works.setAttribute("key", "number_of_coauthored_works");
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works.setTextContent(String.valueOf(currentEdge.getNumOfCollaborations()));
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edge.appendChild(works);
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if (currentEdge.getEarliestCollaborationYearCount() != null) {
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/*
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* There is no clean way of getting the map contents in java even though
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* we are sure to have only one entry on the map. So using the for loop.
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* */
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for (Map.Entry<String, Integer> publicationInfo
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: currentEdge.getEarliestCollaborationYearCount().entrySet()) {
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for (Map.Entry<String, Integer> publicationInfo : currentEdge.getEarliestCollaborationYearCount().entrySet()) {
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graphMLContent.append("\t<data key=\"earliest_collaboration\">"
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+ publicationInfo.getKey()
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+ "</data>\n");
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Element earliest = doc.createElementNS(GRAPHML_NS, "data");
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earliest.setAttribute("key", "earliest_collaboration");
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earliest.setTextContent(publicationInfo.getKey());
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edge.appendChild(earliest);
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graphMLContent.append("\t<data key=\"num_earliest_collaboration\">"
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+ publicationInfo.getValue()
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+ "</data>\n");
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Element earliestCount = doc.createElementNS(GRAPHML_NS, "data");
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earliestCount.setAttribute("key", "num_earliest_collaboration");
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earliestCount.setTextContent(publicationInfo.getValue().toString());
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edge.appendChild(earliestCount);
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}
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}
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if (currentEdge.getLatestCollaborationYearCount() != null) {
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for (Map.Entry<String, Integer> publicationInfo : currentEdge.getLatestCollaborationYearCount().entrySet()) {
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Element latest = doc.createElementNS(GRAPHML_NS, "data");
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latest.setAttribute("key", "latest_collaboration");
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latest.setTextContent(publicationInfo.getKey());
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edge.appendChild(latest);
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for (Map.Entry<String, Integer> publicationInfo
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: currentEdge.getLatestCollaborationYearCount().entrySet()) {
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graphMLContent.append("\t<data key=\"latest_collaboration\">"
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+ publicationInfo.getKey()
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+ "</data>\n");
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graphMLContent.append("\t<data key=\"num_latest_collaboration\">"
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+ publicationInfo.getValue()
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+ "</data>\n");
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Element latestCount = doc.createElementNS(GRAPHML_NS, "data");
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latestCount.setAttribute("key", "num_latest_collaboration");
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latestCount.setTextContent(publicationInfo.getValue().toString());
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edge.appendChild(latestCount);
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}
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}
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if (currentEdge.getUnknownCollaborationYearCount() != null) {
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graphMLContent.append("\t<data key=\"num_unknown_collaboration\">"
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+ currentEdge.getUnknownCollaborationYearCount()
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+ "</data>\n");
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Element unknown = doc.createElementNS(GRAPHML_NS, "data");
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unknown.setAttribute("key", "num_unknown_collaboration");
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unknown.setTextContent(String.valueOf(currentEdge.getUnknownCollaborationYearCount()));
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edge.appendChild(unknown);
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}
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graphMLContent.append("</edge>\n");
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}
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private void generateNodeSectionContent(CollaborationData coAuthorshipData,
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StringBuilder graphMLContent) {
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private void generateNodeSectionContent(CollaborationData coAuthorshipData, Element graphElement) {
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Document doc = graphElement.getOwnerDocument();
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graphMLContent.append("<!-- nodes -->\n");
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graphElement.appendChild(doc.createComment("nodes"));
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Collaborator egoNode = coAuthorshipData.getEgoCollaborator();
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Set<Collaborator> authorNodes = coAuthorshipData.getCollaborators();
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@ -184,142 +209,130 @@ public class CoAuthorshipGraphMLWriter {
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* of the co-author vis. Ego should always come first.
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*
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* */
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getNodeContent(graphMLContent, egoNode);
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getNodeContent(graphElement, egoNode);
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List<Collaborator> orderedAuthorNodes = new ArrayList<Collaborator>(authorNodes);
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orderedAuthorNodes.remove(egoNode);
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Collections.sort(orderedAuthorNodes, new CollaboratorComparator());
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for (Collaborator currNode : orderedAuthorNodes) {
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/*
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* We have already printed the Ego Collaborator info.
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* */
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if (currNode != egoNode) {
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getNodeContent(graphMLContent, currNode);
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getNodeContent(graphElement, currNode);
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}
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}
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}
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private void getNodeContent(StringBuilder graphMLContent, Collaborator node) {
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private void getNodeContent(Element graphElement, Collaborator collaborator) {
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Document doc = graphElement.getOwnerDocument();
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ParamMap individualProfileURLParams =
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new ParamMap(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY,
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node.getCollaboratorURI());
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new ParamMap(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY, collaborator.getCollaboratorURI());
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String profileURL = UrlBuilder.getUrl(VisualizationFrameworkConstants.INDIVIDUAL_URL_PREFIX,
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individualProfileURLParams);
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String profileURL = UrlBuilder.getUrl(VisualizationFrameworkConstants.INDIVIDUAL_URL_PREFIX, individualProfileURLParams);
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graphMLContent.append("<node id=\"" + node.getCollaboratorID() + "\">\n");
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graphMLContent.append("\t<data key=\"url\">" + node.getCollaboratorURI() + "</data>\n");
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graphMLContent.append("\t<data key=\"label\">" + node.getCollaboratorName() + "</data>\n");
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Element node = doc.createElementNS(GRAPHML_NS, "node");
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node.setAttribute("id", String.valueOf(collaborator.getCollaboratorID()));
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graphElement.appendChild(node);
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Element url = doc.createElementNS(GRAPHML_NS, "data");
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url.setAttribute("key", "url");
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url.setTextContent(collaborator.getCollaboratorURI());
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node.appendChild(url);
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Element label = doc.createElementNS(GRAPHML_NS, "data");
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label.setAttribute("key", "label");
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label.setTextContent(collaborator.getCollaboratorName());
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node.appendChild(label);
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if (profileURL != null) {
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graphMLContent.append("\t<data key=\"profile_url\">" + profileURL + "</data>\n");
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Element profile = doc.createElementNS(GRAPHML_NS, "data");
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profile.setAttribute("key", "profile_url");
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profile.setTextContent(profileURL);
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node.appendChild(profile);
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}
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Element works = doc.createElementNS(GRAPHML_NS, "data");
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works.setAttribute("key", "number_of_authored_works");
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works.setTextContent(String.valueOf(collaborator.getNumOfActivities()));
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node.appendChild(works);
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graphMLContent.append("\t<data key=\"number_of_authored_works\">"
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+ node.getNumOfActivities()
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+ "</data>\n");
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if (node.getEarliestActivityYearCount() != null) {
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if (collaborator.getEarliestActivityYearCount() != null) {
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/*
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* There is no clean way of getting the map contents in java even though
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* we are sure to have only one entry on the map. So using the for loop.
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* I am feeling dirty just about now.
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* */
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for (Map.Entry<String, Integer> publicationInfo
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: node.getEarliestActivityYearCount().entrySet()) {
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for (Map.Entry<String, Integer> publicationInfo : collaborator.getEarliestActivityYearCount().entrySet()) {
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Element earliest = doc.createElementNS(GRAPHML_NS, "data");
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earliest.setAttribute("key", "earliest_publication");
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earliest.setTextContent(publicationInfo.getKey());
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node.appendChild(earliest);
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graphMLContent.append("\t<data key=\"earliest_publication\">"
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+ publicationInfo.getKey()
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+ "</data>\n");
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graphMLContent.append("\t<data key=\"num_earliest_publication\">"
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+ publicationInfo.getValue()
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+ "</data>\n");
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Element earliestCount = doc.createElementNS(GRAPHML_NS, "data");
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earliestCount.setAttribute("key", "num_earliest_publication");
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earliestCount.setTextContent(publicationInfo.getValue().toString());
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node.appendChild(earliestCount);
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}
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}
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if (node.getLatestActivityYearCount() != null) {
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if (collaborator.getLatestActivityYearCount() != null) {
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for (Map.Entry<String, Integer> publicationInfo : collaborator.getLatestActivityYearCount().entrySet()) {
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Element latest = doc.createElementNS(GRAPHML_NS, "data");
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latest.setAttribute("key", "latest_publication");
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latest.setTextContent(publicationInfo.getKey());
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node.appendChild(latest);
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for (Map.Entry<String, Integer> publicationInfo
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: node.getLatestActivityYearCount().entrySet()) {
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graphMLContent.append("\t<data key=\"latest_publication\">"
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+ publicationInfo.getKey()
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+ "</data>\n");
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graphMLContent.append("\t<data key=\"num_latest_publication\">"
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+ publicationInfo.getValue()
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+ "</data>\n");
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Element latestCount = doc.createElementNS(GRAPHML_NS, "data");
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latestCount.setAttribute("key", "num_latest_publication");
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latestCount.setTextContent(publicationInfo.getValue().toString());
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node.appendChild(latestCount);
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}
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}
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if (node.getUnknownActivityYearCount() != null) {
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graphMLContent.append("\t<data key=\"num_unknown_publication\">"
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+ node.getUnknownActivityYearCount()
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+ "</data>\n");
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if (collaborator.getUnknownActivityYearCount() != null) {
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Element unknown = doc.createElementNS(GRAPHML_NS, "data");
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unknown.setAttribute("key", "num_unknown_publication");
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unknown.setTextContent(String.valueOf(collaborator.getUnknownActivityYearCount()));
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node.appendChild(unknown);
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}
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graphMLContent.append("</node>\n");
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}
|
||||
|
||||
private void generateKeyDefinitionContent(CollaborationData visVOContainer,
|
||||
StringBuilder graphMLContent) {
|
||||
|
||||
private void generateKeyDefinitionContent(CollaborationData visVOContainer, Element rootElement) {
|
||||
/*
|
||||
* Generate the key definition content for node.
|
||||
* */
|
||||
getKeyDefinitionFromSchema(visVOContainer.getNodeSchema(), graphMLContent);
|
||||
getKeyDefinitionFromSchema(visVOContainer.getNodeSchema(), rootElement);
|
||||
|
||||
/*
|
||||
* Generate the key definition content for edge.
|
||||
* */
|
||||
getKeyDefinitionFromSchema(visVOContainer.getEdgeSchema(), graphMLContent);
|
||||
getKeyDefinitionFromSchema(visVOContainer.getEdgeSchema(), rootElement);
|
||||
|
||||
|
||||
}
|
||||
|
||||
private void getKeyDefinitionFromSchema(Set<Map<String, String>> schema,
|
||||
StringBuilder graphMLContent) {
|
||||
private void getKeyDefinitionFromSchema(Set<Map<String, String>> schema, Element rootElement) {
|
||||
Document doc = rootElement.getOwnerDocument();
|
||||
|
||||
for (Map<String, String> currentNodeSchemaAttribute : schema) {
|
||||
Element key = doc.createElementNS(GRAPHML_NS, "key");
|
||||
|
||||
graphMLContent.append("\n<key ");
|
||||
|
||||
for (Map.Entry<String, String> currentAttributeKey
|
||||
: currentNodeSchemaAttribute.entrySet()) {
|
||||
|
||||
graphMLContent.append(currentAttributeKey.getKey()
|
||||
+ "=\"" + currentAttributeKey.getValue()
|
||||
+ "\" ");
|
||||
|
||||
for (Map.Entry<String, String> currentAttributeKey : currentNodeSchemaAttribute.entrySet()) {
|
||||
key.setAttribute(currentAttributeKey.getKey(), currentAttributeKey.getValue());
|
||||
}
|
||||
|
||||
if (currentNodeSchemaAttribute.containsKey("default")) {
|
||||
|
||||
graphMLContent.append(">\n");
|
||||
graphMLContent.append("<default>");
|
||||
graphMLContent.append(currentNodeSchemaAttribute.get("default"));
|
||||
graphMLContent.append("</default>\n");
|
||||
graphMLContent.append("</key>\n");
|
||||
|
||||
} else {
|
||||
graphMLContent.append("/>\n");
|
||||
Element def = doc.createElementNS(GRAPHML_NS, "default");
|
||||
def.setTextContent(currentNodeSchemaAttribute.get("default"));
|
||||
key.appendChild(def);
|
||||
}
|
||||
|
||||
rootElement.appendChild(key);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -2,6 +2,7 @@
|
|||
|
||||
package edu.cornell.mannlib.vitro.webapp.visualization.coprincipalinvestigator;
|
||||
|
||||
import java.io.StringWriter;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Collections;
|
||||
import java.util.List;
|
||||
|
|
@ -16,6 +17,20 @@ import edu.cornell.mannlib.vitro.webapp.visualization.collaborationutils.Collabo
|
|||
import edu.cornell.mannlib.vitro.webapp.visualization.collaborationutils.CollaboratorComparator;
|
||||
import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.Collaboration;
|
||||
import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.Collaborator;
|
||||
import org.w3c.dom.Document;
|
||||
import org.w3c.dom.Element;
|
||||
|
||||
import javax.xml.parsers.DocumentBuilder;
|
||||
import javax.xml.parsers.DocumentBuilderFactory;
|
||||
import javax.xml.parsers.ParserConfigurationException;
|
||||
import javax.xml.transform.OutputKeys;
|
||||
import javax.xml.transform.Transformer;
|
||||
import javax.xml.transform.TransformerConfigurationException;
|
||||
import javax.xml.transform.TransformerException;
|
||||
import javax.xml.transform.TransformerFactory;
|
||||
import javax.xml.transform.dom.DOMSource;
|
||||
import javax.xml.transform.stream.StreamResult;
|
||||
|
||||
/**
|
||||
* @author bkoniden
|
||||
* Deepak Konidena
|
||||
|
|
@ -24,38 +39,57 @@ public class CoPIGraphMLWriter {
|
|||
|
||||
private StringBuilder coPIGraphMLContent;
|
||||
|
||||
private final String GRAPHML_HEADER = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
|
||||
+ " <graphml xmlns=\"http://graphml.graphdrawing.org/xmlns\"\n"
|
||||
+ " xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"\n"
|
||||
+ " xsi:schemaLocation=\"http://graphml.graphdrawing.org/xmlns\n"
|
||||
+ " http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd\">\n\n";
|
||||
|
||||
private final String GRAPHML_FOOTER = "</graphml>";
|
||||
private final String GRAPHML_NS = "http://graphml.graphdrawing.org/xmlns";
|
||||
|
||||
public CoPIGraphMLWriter(CollaborationData coPIData) {
|
||||
coPIGraphMLContent = createCoPIGraphMLContent(coPIData);
|
||||
}
|
||||
|
||||
private StringBuilder createCoPIGraphMLContent(CollaborationData coPIData) {
|
||||
|
||||
StringBuilder graphMLContent = new StringBuilder();
|
||||
|
||||
graphMLContent.append(GRAPHML_HEADER);
|
||||
try {
|
||||
DocumentBuilderFactory docFactory = DocumentBuilderFactory.newInstance();
|
||||
docFactory.setNamespaceAware(true);
|
||||
DocumentBuilder docBuilder = docFactory.newDocumentBuilder();
|
||||
|
||||
/*
|
||||
* We are side-effecting "graphMLContent" object in this method since creating
|
||||
* another String object to hold key definition data will be redundant & will
|
||||
* not serve the purpose.
|
||||
* */
|
||||
generateKeyDefinitionContent(coPIData, graphMLContent);
|
||||
// root elements
|
||||
Document doc = docBuilder.newDocument();
|
||||
doc.setXmlVersion("1.0");
|
||||
Element rootElement = doc.createElementNS(GRAPHML_NS, "graphml");
|
||||
doc.appendChild(rootElement);
|
||||
|
||||
/*
|
||||
* Used to generate graph content. It will contain both the nodes & edge information.
|
||||
* We are side-effecting "graphMLContent".
|
||||
* */
|
||||
generateGraphContent(coPIData, graphMLContent);
|
||||
/*
|
||||
* We are side-effecting "graphMLContent" object in this method since creating
|
||||
* another String object to hold key definition data will be redundant & will
|
||||
* not serve the purpose.
|
||||
* */
|
||||
generateKeyDefinitionContent(coPIData, rootElement);
|
||||
|
||||
graphMLContent.append(GRAPHML_FOOTER);
|
||||
/*
|
||||
* Used to generate graph content. It will contain both the nodes & edge information.
|
||||
* We are side-effecting "graphMLContent".
|
||||
* */
|
||||
generateGraphContent(coPIData, rootElement);
|
||||
|
||||
DOMSource source = new DOMSource(doc);
|
||||
TransformerFactory transFactory = TransformerFactory.newInstance();
|
||||
Transformer transformer = transFactory.newTransformer();
|
||||
transformer.setOutputProperty(OutputKeys.ENCODING, "UTF-8");
|
||||
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
|
||||
|
||||
StringWriter writer = new StringWriter();
|
||||
StreamResult result = new StreamResult(writer);
|
||||
transformer.transform(source, result);
|
||||
|
||||
graphMLContent.append(writer.toString());
|
||||
} catch (TransformerConfigurationException e) {
|
||||
throw new IllegalStateException("XML error generating GraphML", e);
|
||||
} catch (TransformerException e) {
|
||||
throw new IllegalStateException("XML error generating GraphML", e);
|
||||
} catch (ParserConfigurationException e) {
|
||||
throw new IllegalStateException("XML error generating GraphML", e);
|
||||
}
|
||||
|
||||
return graphMLContent;
|
||||
}
|
||||
|
|
@ -64,117 +98,111 @@ public class CoPIGraphMLWriter {
|
|||
return coPIGraphMLContent;
|
||||
}
|
||||
|
||||
private void generateGraphContent(CollaborationData coPIData,
|
||||
StringBuilder graphMLContent) {
|
||||
private void generateGraphContent(CollaborationData coPIData, Element rootElement) {
|
||||
Document doc = rootElement.getOwnerDocument();
|
||||
|
||||
graphMLContent.append("\n<graph edgedefault=\"undirected\">\n");
|
||||
Element graph = doc.createElementNS(GRAPHML_NS, "graph");
|
||||
graph.setAttribute("edgedefault", "undirected");
|
||||
rootElement.appendChild(graph);
|
||||
|
||||
if (coPIData.getCollaborators() != null & coPIData.getCollaborators().size() > 0) {
|
||||
generateNodeSectionContent(coPIData, graphMLContent);
|
||||
generateNodeSectionContent(coPIData, graph);
|
||||
}
|
||||
|
||||
if (coPIData.getCollaborations() != null & coPIData.getCollaborations().size() > 0) {
|
||||
generateEdgeSectionContent(coPIData, graphMLContent);
|
||||
generateEdgeSectionContent(coPIData, graph);
|
||||
}
|
||||
|
||||
graphMLContent.append("</graph>\n");
|
||||
}
|
||||
|
||||
private void generateEdgeSectionContent(CollaborationData coPIData,
|
||||
StringBuilder graphMLContent) {
|
||||
private void generateEdgeSectionContent(CollaborationData coPIData, Element graphElement) {
|
||||
Document doc = graphElement.getOwnerDocument();
|
||||
|
||||
graphMLContent.append("<!-- edges -->\n");
|
||||
graphElement.appendChild(doc.createComment("edges"));
|
||||
|
||||
Set<Collaboration> edges = coPIData.getCollaborations();
|
||||
|
||||
List<Collaboration> orderedEdges = new ArrayList<Collaboration>(edges);
|
||||
|
||||
Collections.sort(orderedEdges, new CollaborationComparator());
|
||||
|
||||
for (Collaboration currentEdge : orderedEdges) {
|
||||
|
||||
/*
|
||||
* This method actually creates the XML code for a single edge. "graphMLContent"
|
||||
* is being side-effected.
|
||||
* */
|
||||
getEdgeContent(graphMLContent, currentEdge);
|
||||
getEdgeContent(graphElement, currentEdge);
|
||||
}
|
||||
}
|
||||
|
||||
private void getEdgeContent(StringBuilder graphMLContent, Collaboration currentEdge) {
|
||||
private void getEdgeContent(Element graphElement, Collaboration currentEdge) {
|
||||
Document doc = graphElement.getOwnerDocument();
|
||||
|
||||
graphMLContent.append("<edge "
|
||||
+ "id=\"" + currentEdge.getCollaborationID() + "\" "
|
||||
+ "source=\"" + currentEdge.getSourceCollaborator()
|
||||
.getCollaboratorID() + "\" "
|
||||
+ "target=\"" + currentEdge.getTargetCollaborator()
|
||||
.getCollaboratorID() + "\" "
|
||||
+ ">\n");
|
||||
Element edge = doc.createElementNS(GRAPHML_NS, "edge");
|
||||
edge.setAttribute("id", String.valueOf(currentEdge.getCollaborationID()));
|
||||
edge.setAttribute("source", String.valueOf(currentEdge.getSourceCollaborator().getCollaboratorID()));
|
||||
edge.setAttribute("target", String.valueOf(currentEdge.getTargetCollaborator().getCollaboratorID()));
|
||||
graphElement.appendChild(edge);
|
||||
|
||||
graphMLContent.append("\t<data key=\"collaborator1\">"
|
||||
+ currentEdge.getSourceCollaborator().getCollaboratorName()
|
||||
+ "</data>\n");
|
||||
Element collaborator1 = doc.createElementNS(GRAPHML_NS, "data");
|
||||
collaborator1.setAttribute("key", "collaborator1");
|
||||
collaborator1.setTextContent(currentEdge.getSourceCollaborator().getCollaboratorName());
|
||||
edge.appendChild(collaborator1);
|
||||
|
||||
graphMLContent.append("\t<data key=\"collaborator2\">"
|
||||
+ currentEdge.getTargetCollaborator().getCollaboratorName()
|
||||
+ "</data>\n");
|
||||
Element collaborator2 = doc.createElementNS(GRAPHML_NS, "data");
|
||||
collaborator2.setAttribute("key", "collaborator2");
|
||||
collaborator2.setTextContent(currentEdge.getTargetCollaborator().getCollaboratorName());
|
||||
edge.appendChild(collaborator2);
|
||||
|
||||
graphMLContent.append("\t<data key=\"number_of_coinvestigated_grants\">"
|
||||
+ currentEdge.getNumOfCollaborations()
|
||||
+ "</data>\n");
|
||||
Element works = doc.createElementNS(GRAPHML_NS, "data");
|
||||
works.setAttribute("key", "number_of_coinvestigated_grants");
|
||||
works.setTextContent(String.valueOf(currentEdge.getNumOfCollaborations()));
|
||||
edge.appendChild(works);
|
||||
|
||||
if (currentEdge.getEarliestCollaborationYearCount() != null) {
|
||||
|
||||
/*
|
||||
* There is no clean way of getting the map contents in java even though
|
||||
* we are sure to have only one entry on the map. So using the for loop.
|
||||
* */
|
||||
for (Map.Entry<String, Integer> publicationInfo
|
||||
: currentEdge.getEarliestCollaborationYearCount().entrySet()) {
|
||||
for (Map.Entry<String, Integer> publicationInfo : currentEdge.getEarliestCollaborationYearCount().entrySet()) {
|
||||
|
||||
graphMLContent.append("\t<data key=\"earliest_collaboration\">"
|
||||
+ publicationInfo.getKey()
|
||||
+ "</data>\n");
|
||||
Element earliest = doc.createElementNS(GRAPHML_NS, "data");
|
||||
earliest.setAttribute("key", "earliest_collaboration");
|
||||
earliest.setTextContent(publicationInfo.getKey());
|
||||
edge.appendChild(earliest);
|
||||
|
||||
graphMLContent.append("\t<data key=\"num_earliest_collaboration\">"
|
||||
+ publicationInfo.getValue()
|
||||
+ "</data>\n");
|
||||
Element earliestCount = doc.createElementNS(GRAPHML_NS, "data");
|
||||
earliestCount.setAttribute("key", "num_earliest_collaboration");
|
||||
earliestCount.setTextContent(publicationInfo.getValue().toString());
|
||||
edge.appendChild(earliestCount);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
if (currentEdge.getLatestCollaborationYearCount() != null) {
|
||||
for (Map.Entry<String, Integer> publicationInfo : currentEdge.getLatestCollaborationYearCount().entrySet()) {
|
||||
Element latest = doc.createElementNS(GRAPHML_NS, "data");
|
||||
latest.setAttribute("key", "latest_collaboration");
|
||||
latest.setTextContent(publicationInfo.getKey());
|
||||
edge.appendChild(latest);
|
||||
|
||||
for (Map.Entry<String, Integer> publicationInfo
|
||||
: currentEdge.getLatestCollaborationYearCount().entrySet()) {
|
||||
|
||||
graphMLContent.append("\t<data key=\"latest_collaboration\">"
|
||||
+ publicationInfo.getKey()
|
||||
+ "</data>\n");
|
||||
|
||||
graphMLContent.append("\t<data key=\"num_latest_collaboration\">"
|
||||
+ publicationInfo.getValue()
|
||||
+ "</data>\n");
|
||||
Element latestCount = doc.createElementNS(GRAPHML_NS, "data");
|
||||
latestCount.setAttribute("key", "num_latest_collaboration");
|
||||
latestCount.setTextContent(publicationInfo.getValue().toString());
|
||||
edge.appendChild(latestCount);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
if (currentEdge.getUnknownCollaborationYearCount() != null) {
|
||||
|
||||
graphMLContent.append("\t<data key=\"num_unknown_collaboration\">"
|
||||
+ currentEdge.getUnknownCollaborationYearCount()
|
||||
+ "</data>\n");
|
||||
|
||||
Element unknown = doc.createElementNS(GRAPHML_NS, "data");
|
||||
unknown.setAttribute("key", "num_unknown_collaboration");
|
||||
unknown.setTextContent(String.valueOf(currentEdge.getUnknownCollaborationYearCount()));
|
||||
edge.appendChild(unknown);
|
||||
}
|
||||
|
||||
graphMLContent.append("</edge>\n");
|
||||
}
|
||||
|
||||
private void generateNodeSectionContent(CollaborationData coPIData, Element graphElement) {
|
||||
Document doc = graphElement.getOwnerDocument();
|
||||
|
||||
private void generateNodeSectionContent(CollaborationData coPIData,
|
||||
StringBuilder graphMLContent) {
|
||||
|
||||
graphMLContent.append("<!-- nodes -->\n");
|
||||
graphElement.appendChild(doc.createComment("nodes"));
|
||||
|
||||
Collaborator egoNode = coPIData.getEgoCollaborator();
|
||||
Set<Collaborator> piNodes = coPIData.getCollaborators();
|
||||
|
|
@ -185,7 +213,7 @@ public class CoPIGraphMLWriter {
|
|||
* of the co-pi vis. Ego should always come first.
|
||||
*
|
||||
* */
|
||||
getNodeContent(graphMLContent, egoNode);
|
||||
getNodeContent(graphElement, egoNode);
|
||||
|
||||
List<Collaborator> orderedPINodes = new ArrayList<Collaborator>(piNodes);
|
||||
orderedPINodes.remove(egoNode);
|
||||
|
|
@ -194,131 +222,119 @@ public class CoPIGraphMLWriter {
|
|||
|
||||
|
||||
for (Collaborator currNode : orderedPINodes) {
|
||||
|
||||
/*
|
||||
* We have already printed the Ego Node info.
|
||||
* */
|
||||
if (currNode != egoNode) {
|
||||
|
||||
getNodeContent(graphMLContent, currNode);
|
||||
|
||||
getNodeContent(graphElement, currNode);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private void getNodeContent(StringBuilder graphMLContent, Collaborator node) {
|
||||
private void getNodeContent(Element graphElement, Collaborator collaborator) {
|
||||
Document doc = graphElement.getOwnerDocument();
|
||||
|
||||
ParamMap individualProfileURLParams = new ParamMap(
|
||||
VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY,
|
||||
node.getCollaboratorURI());
|
||||
VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY, collaborator.getCollaboratorURI());
|
||||
|
||||
String profileURL = UrlBuilder.getUrl(VisualizationFrameworkConstants.INDIVIDUAL_URL_PREFIX,
|
||||
individualProfileURLParams);
|
||||
String profileURL = UrlBuilder.getUrl(VisualizationFrameworkConstants.INDIVIDUAL_URL_PREFIX, individualProfileURLParams);
|
||||
|
||||
graphMLContent.append("<node id=\"" + node.getCollaboratorID() + "\">\n");
|
||||
graphMLContent.append("\t<data key=\"url\">" + node.getCollaboratorURI() + "</data>\n");
|
||||
graphMLContent.append("\t<data key=\"label\">" + node.getCollaboratorName() + "</data>\n");
|
||||
Element node = doc.createElementNS(GRAPHML_NS, "node");
|
||||
node.setAttribute("id", String.valueOf(collaborator.getCollaboratorID()));
|
||||
graphElement.appendChild(node);
|
||||
|
||||
Element url = doc.createElementNS(GRAPHML_NS, "data");
|
||||
url.setAttribute("key", "url");
|
||||
url.setTextContent(collaborator.getCollaboratorURI());
|
||||
node.appendChild(url);
|
||||
|
||||
Element label = doc.createElementNS(GRAPHML_NS, "data");
|
||||
label.setAttribute("key", "label");
|
||||
label.setTextContent(collaborator.getCollaboratorName());
|
||||
node.appendChild(label);
|
||||
|
||||
if (profileURL != null) {
|
||||
graphMLContent.append("\t<data key=\"profile_url\">" + profileURL + "</data>\n");
|
||||
Element profile = doc.createElementNS(GRAPHML_NS, "data");
|
||||
profile.setAttribute("key", "profile_url");
|
||||
profile.setTextContent(profileURL);
|
||||
node.appendChild(profile);
|
||||
}
|
||||
|
||||
Element works = doc.createElementNS(GRAPHML_NS, "data");
|
||||
works.setAttribute("key", "number_of_investigated_grants");
|
||||
works.setTextContent(String.valueOf(collaborator.getNumOfActivities()));
|
||||
node.appendChild(works);
|
||||
|
||||
graphMLContent.append("\t<data key=\"number_of_investigated_grants\">"
|
||||
+ node.getNumOfActivities()
|
||||
+ "</data>\n");
|
||||
|
||||
if (node.getEarliestActivityYearCount() != null) {
|
||||
|
||||
if (collaborator.getEarliestActivityYearCount() != null) {
|
||||
/*
|
||||
* There is no clean way of getting the map contents in java even though
|
||||
* we are sure to have only one entry on the map. So using the for loop.
|
||||
* I am feeling dirty just about now.
|
||||
* */
|
||||
for (Map.Entry<String, Integer> publicationInfo
|
||||
: node.getEarliestActivityYearCount().entrySet()) {
|
||||
for (Map.Entry<String, Integer> publicationInfo : collaborator.getEarliestActivityYearCount().entrySet()) {
|
||||
Element earliest = doc.createElementNS(GRAPHML_NS, "data");
|
||||
earliest.setAttribute("key", "earliest_grant");
|
||||
earliest.setTextContent(publicationInfo.getKey());
|
||||
node.appendChild(earliest);
|
||||
|
||||
graphMLContent.append("\t<data key=\"earliest_grant\">"
|
||||
+ publicationInfo.getKey()
|
||||
+ "</data>\n");
|
||||
|
||||
graphMLContent.append("\t<data key=\"num_earliest_grant\">"
|
||||
+ publicationInfo.getValue()
|
||||
+ "</data>\n");
|
||||
Element earliestCount = doc.createElementNS(GRAPHML_NS, "data");
|
||||
earliestCount.setAttribute("key", "num_earliest_grant");
|
||||
earliestCount.setTextContent(publicationInfo.getValue().toString());
|
||||
node.appendChild(earliestCount);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
if (node.getLatestActivityYearCount() != null) {
|
||||
if (collaborator.getLatestActivityYearCount() != null) {
|
||||
for (Map.Entry<String, Integer> publicationInfo : collaborator.getLatestActivityYearCount().entrySet()) {
|
||||
Element latest = doc.createElementNS(GRAPHML_NS, "data");
|
||||
latest.setAttribute("key", "latest_grant");
|
||||
latest.setTextContent(publicationInfo.getKey());
|
||||
node.appendChild(latest);
|
||||
|
||||
for (Map.Entry<String, Integer> publicationInfo
|
||||
: node.getLatestActivityYearCount().entrySet()) {
|
||||
|
||||
graphMLContent.append("\t<data key=\"latest_grant\">"
|
||||
+ publicationInfo.getKey()
|
||||
+ "</data>\n");
|
||||
|
||||
graphMLContent.append("\t<data key=\"num_latest_grant\">"
|
||||
+ publicationInfo.getValue()
|
||||
+ "</data>\n");
|
||||
Element latestCount = doc.createElementNS(GRAPHML_NS, "data");
|
||||
latestCount.setAttribute("key", "num_latest_grant");
|
||||
latestCount.setTextContent(publicationInfo.getValue().toString());
|
||||
node.appendChild(latestCount);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
if (node.getUnknownActivityYearCount() != null) {
|
||||
|
||||
graphMLContent.append("\t<data key=\"num_unknown_grant\">"
|
||||
+ node.getUnknownActivityYearCount()
|
||||
+ "</data>\n");
|
||||
|
||||
if (collaborator.getUnknownActivityYearCount() != null) {
|
||||
Element unknown = doc.createElementNS(GRAPHML_NS, "data");
|
||||
unknown.setAttribute("key", "num_unknown_grant");
|
||||
unknown.setTextContent(String.valueOf(collaborator.getUnknownActivityYearCount()));
|
||||
node.appendChild(unknown);
|
||||
}
|
||||
|
||||
graphMLContent.append("</node>\n");
|
||||
}
|
||||
|
||||
private void generateKeyDefinitionContent(CollaborationData coPIData,
|
||||
StringBuilder graphMLContent) {
|
||||
private void generateKeyDefinitionContent(CollaborationData coPIData, Element rootElement) {
|
||||
/*
|
||||
* Generate the key definition content for node.
|
||||
* */
|
||||
getKeyDefinitionFromSchema(coPIData.getNodeSchema(), graphMLContent);
|
||||
getKeyDefinitionFromSchema(coPIData.getNodeSchema(), rootElement);
|
||||
|
||||
/*
|
||||
* Generate the key definition content for edge.
|
||||
* */
|
||||
getKeyDefinitionFromSchema(coPIData.getEdgeSchema(), graphMLContent);
|
||||
getKeyDefinitionFromSchema(coPIData.getEdgeSchema(), rootElement);
|
||||
}
|
||||
|
||||
private void getKeyDefinitionFromSchema(Set<Map<String, String>> schema,
|
||||
StringBuilder graphMLContent) {
|
||||
private void getKeyDefinitionFromSchema(Set<Map<String, String>> schema, Element rootElement) {
|
||||
Document doc = rootElement.getOwnerDocument();
|
||||
|
||||
for (Map<String, String> currentNodeSchemaAttribute : schema) {
|
||||
Element key = doc.createElementNS(GRAPHML_NS, "key");
|
||||
|
||||
graphMLContent.append("\n<key ");
|
||||
|
||||
for (Map.Entry<String, String> currentAttributeKey
|
||||
: currentNodeSchemaAttribute.entrySet()) {
|
||||
|
||||
graphMLContent.append(currentAttributeKey.getKey()
|
||||
+ "=\"" + currentAttributeKey.getValue()
|
||||
+ "\" ");
|
||||
|
||||
for (Map.Entry<String, String> currentAttributeKey : currentNodeSchemaAttribute.entrySet()) {
|
||||
key.setAttribute(currentAttributeKey.getKey(), currentAttributeKey.getValue());
|
||||
}
|
||||
|
||||
if (currentNodeSchemaAttribute.containsKey("default")) {
|
||||
|
||||
graphMLContent.append(">\n");
|
||||
graphMLContent.append("<default>");
|
||||
graphMLContent.append(currentNodeSchemaAttribute.get("default"));
|
||||
graphMLContent.append("</default>\n");
|
||||
graphMLContent.append("</key>\n");
|
||||
|
||||
} else {
|
||||
graphMLContent.append("/>\n");
|
||||
Element def = doc.createElementNS(GRAPHML_NS, "default");
|
||||
def.setTextContent(currentNodeSchemaAttribute.get("default"));
|
||||
key.appendChild(def);
|
||||
}
|
||||
|
||||
rootElement.appendChild(key);
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue