BundleInfo.java

package net.sourceforge.seqware.pipeline.bundle;

import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import org.xml.sax.SAXException;

/**
 * <p>
 * BundleInfo class.
 * </p>
 * 
 * @author boconnor
 * @version $Id: $Id
 */
public class BundleInfo {

    private ArrayList<WorkflowInfo> workflows = new ArrayList<>();
    private File metadata = null;

    /**
     * <p>
     * parseFromFile.
     * </p>
     * 
     * @param metadata
     *            a {@link java.io.File} object.
     */
    public void parseFromFile(File metadata) {

        try {

            DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
            DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
            Document doc = dBuilder.parse(metadata);
            doc.getDocumentElement().normalize();

            NodeList nList = doc.getElementsByTagName("workflow");

            for (int temp = 0; temp < nList.getLength(); temp++) {

                Node nNode = nList.item(temp);
                if (nNode.getNodeType() == Node.ELEMENT_NODE) {

                    Element eElement = (Element) nNode;

                    String templatePath = null;
                    NodeList nodes = eElement.getElementsByTagName("workflow_template");
                    if (nodes.getLength() > 0) {
                        templatePath = nodes.item(0).getAttributes().getNamedItem("path").getNodeValue();
                    }

                    String classesPath = null;
                    if (null != eElement.getElementsByTagName("classes").item(0)) {
                        classesPath = eElement.getElementsByTagName("classes").item(0).getAttributes().getNamedItem("path").getNodeValue();
                    }

                    String configPath = eElement.getElementsByTagName("config").item(0).getAttributes().getNamedItem("path").getNodeValue();

                    String computeReq = eElement.getElementsByTagName("requirements").item(0).getAttributes().getNamedItem("compute")
                            .getNodeValue();
                    String memReq = eElement.getElementsByTagName("requirements").item(0).getAttributes().getNamedItem("memory")
                            .getNodeValue();
                    String networkReq = eElement.getElementsByTagName("requirements").item(0).getAttributes().getNamedItem("network")
                            .getNodeValue();

                    String workflowEngineReq = null;
                    if (null != eElement.getElementsByTagName("requirements").item(0).getAttributes().getNamedItem("workflow_engine")) {
                        workflowEngineReq = eElement.getElementsByTagName("requirements").item(0).getAttributes()
                                .getNamedItem("workflow_engine").getNodeValue();
                    }
                    String workflowTypeReq = null;
                    if (null != eElement.getElementsByTagName("requirements").item(0).getAttributes().getNamedItem("workflow_type")) {
                        workflowTypeReq = eElement.getElementsByTagName("requirements").item(0).getAttributes()
                                .getNamedItem("workflow_type").getNodeValue();
                    }
                    String workflowClass = null;
                    if (null != eElement.getElementsByTagName("workflow_class").item(0)) {
                        workflowClass = eElement.getElementsByTagName("workflow_class").item(0).getAttributes().getNamedItem("path")
                                .getNodeValue();
                    }

                    WorkflowInfo wi = new WorkflowInfo();
                    wi.setName(eElement.getAttribute("name"));
                    wi.setVersion(eElement.getAttribute("version"));
                    wi.setDescription(getTagValue("description", eElement));
                    wi.setTemplatePath(templatePath);
                    wi.setConfigPath(configPath);
                    wi.setComputeReq(computeReq);
                    wi.setMemReq(memReq);
                    wi.setNetworkReq(networkReq);
                    wi.setClassesDir(classesPath);
                    wi.setBaseDir(eElement.getAttribute("basedir"));
                    wi.setWorkflowSqwVersion(eElement.getAttribute("seqware_version"));
                    wi.setWorkflowClass(workflowClass);
                    wi.setWorkflowEngine(workflowEngineReq);
                    wi.setWorkflowType(workflowTypeReq);

                    workflows.add(wi);
                    this.metadata = metadata;
                }
            }

        } catch (SAXException | IOException | ParserConfigurationException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }

    }

    public File parsedFrom() {
        return metadata;
    }

    /**
     * <p>
     * getWorkflowInfo.
     * </p>
     * 
     * @return a {@link java.util.ArrayList} object.
     */
    public ArrayList<WorkflowInfo> getWorkflowInfo() {
        return workflows;
    }

    /**
     * <p>
     * Setter for the field <code>workflows</code>.
     * </p>
     * 
     * @param workflows
     *            a {@link java.util.ArrayList} object.
     */
    public void setWorkflows(ArrayList<WorkflowInfo> workflows) {
        this.workflows = workflows;
    }

    private static String getTagValue(String sTag, Element eElement) {
        NodeList nlList = eElement.getElementsByTagName(sTag).item(0).getChildNodes();
        Node nValue = (Node) nlList.item(0);
        return nValue.getNodeValue();
    }

}