Code for conversion of Tree of Life from xml source to csv dataset using jsoup

TreeOfLifeEval.java

public static void main(String[] args) {

    DataSet linkSet = new DataSet();
    linkSet.getHeaders().setHeaders("source_node_id", "target_node_id");

    DataSet nodeSet = new DataSet();
    nodeSet.getHeaders().setHeaders("node_id", "node_name", "child_nodes", "leaf_node", "tolorg_link", "extinct", "confidence", "phylesis");

    try {
        Connection connection = HttpConnection.connect("http://tolweb.org/");
        connection.process("tolskeletaldump.xml", "application/xml");
        connection.parser(new Parser(new XmlTreeBuilder()));

        Document document = connection.response().parse();
        Elements elements = document.select("node[id]");

        for(Element element : elements) {
            DataTuple tuple = new DataTuple();
            tuple.setRecord("source_node_id", element.parent().parent().attr("id"));
            tuple.setRecord("target_node_id", element.attr("id"));
            linkSet.getStore().addTuple(tuple);
            
            DataTuple nodeTuple = new DataTuple();
            String nodeName = element.getElementsByTag("name").first().ownText();
            if(StringUtils.containsAny(nodeName, ','))
                nodeName = TextUtils.encloseQuotes(nodeName);
            if(StringUtils.isAllLowerCase(nodeName))
                nodeName = StringUtils.leftSub(nodeName, 1) + StringUtils.snip(nodeName, 1, 0);
            if(StringUtils.isBlank(nodeName))
                nodeName = "none";
            
            nodeTuple.setRecord("node_id", element.attr("id"));
            nodeTuple.setRecord("node_name", nodeName);
            nodeTuple.setRecord("child_nodes", element.attr("childcount"));
            nodeTuple.setRecord("leaf_node", element.attr("leaf"));
            nodeTuple.setRecord("tolorg_link", element.attr("haspage"));
            nodeTuple.setRecord("extinct", element.attr("extinct"));
            nodeTuple.setRecord("confidence", element.attr("confidence"));
            nodeTuple.setRecord("phylesis", element.attr("phylesis"));
            nodeSet.getStore().addTuple(nodeTuple);
        }
    } catch (IOException e) {
        e.printStackTrace();
    }

    nodeSet.getStore().updateTuples("tolorg_link", s -> "2".equals(s), s -> "1");
    nodeSet.getStore().updateTuples("extinct", s -> "2".equals(s), s -> "1");

    linkSet.getConfig().setDelimiter(",");
    StorageUtils.flushDataSet("treeoflife_links.csv", linkSet);

    nodeSet.getConfig().setDelimiter(",");
    StorageUtils.flushDataSet("treeoflife_nodes.csv", nodeSet);
}