Merging xml file using java NodeList

Question

I\'m trying to merge two xml files as shown below but i can\'t able to get the desired output please help me thank you

Java code:

DocumentBuilderFac         


        

Answer 1

This solution is for files where you need to iterate and verify something before to merge.

file1.xml:

    
    
        
            07402
            irreversible
            15666
            07756
        
        
    03063
    irreversible
    00916
    04712

file2.xml:

    
    
        00001
        polyphosphate polyphosphohydrolase
         Polyphosphate + n H2O <=> (n+1) Oligophosphate
    
    
        00002
        Reduced ferredoxin:dinitrogen oxidoreductase (ATP-hydrolysing)
         16 ATP + 16 H2O + 8 Reduced ferredoxin <=> 8 e- + 16 Orthophosphate + 16 ADP + 8 Oxidized ferredoxin
        
    
        03063
        cephalosporin-C:2-oxoglutarate aminotransferase
         Cephalosporin C + 2-Oxoglutarate <=> (7R)-7-(5-Carboxy-5-oxopentanoyl)aminocephalosporinate + D-Glutamate
    
    
        07402
        (7R)-7-(4-carboxybutanamido)cephalosporanate amidohydrolase
         (7R)-7-(4-Carboxybutanamido)cephalosporanate + H2O <=> 7-Aminocephalosporanic acid + Glutarate
      

Result.xml

    

    
        07402
        irreversible
        15666
        07756
    (7R)-7-(4-carboxybutanamido)cephalosporanate amidohydrolase
 (7R)-7-(4-Carboxybutanamido)cephalosporanate + H2O <=> 7-Aminocephalosporanic acid + Glutarate

    
        03063
        irreversible
        00916
        04712
    cephalosporin-C:2-oxoglutarate aminotransferase
 Cephalosporin C + 2-Oxoglutarate <=> (7R)-7-(5-Carboxy-5-oxopentanoyl)aminocephalosporinate + D-Glutamate

Java program to do this:

import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.StringWriter;
import java.io.Writer;

import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.transform.OutputKeys;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;

import org.w3c.dom.Document;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;

public class MergeXML {

    public static void main(String[] args) {
        MergeXML m = new MergeXML();
        try {
            DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();

            DocumentBuilder db;

            db = dbf.newDocumentBuilder();

            Document secondaryMetabolismXML = db
                    .parse(new File("/home/bioinfo/workspace/teste/src/file1.xml"));
            Document generalMetabolismXML = db
                    .parse(new File("/home/bioinfo/workspace/teste/src/file2.xml"));

            NodeList secondaryReactions = secondaryMetabolismXML.getElementsByTagName("reaction");
            NodeList generalReactions = generalMetabolismXML.getElementsByTagName("reaction");

            for (int s = 0; s < secondaryReactions.getLength(); s++) {
                Node secondaryReaction = secondaryReactions.item(s);
                for (int g = 0; g < generalReactions.getLength(); g++) {
                    Node generalReaction = generalReactions.item(g);
                    if (getChildrenByNodeName(secondaryReaction, "ID").getTextContent()
                            .equals(getChildrenByNodeName(generalReaction, "ID").getTextContent())) {
                        if (getChildrenByNodeName(generalReaction, "reactionName") != null) {
                            secondaryReaction.appendChild(secondaryMetabolismXML
                                    .importNode(getChildrenByNodeName(generalReaction, "reactionName"), true));
                        }
                        if (getChildrenByNodeName(generalReaction, "reactionAlternativeName") != null) {
                            secondaryReaction.appendChild(secondaryMetabolismXML.importNode(
                                    getChildrenByNodeName(generalReaction, "reactionAlternativeName"), true));
                        }
                        if (getChildrenByNodeName(generalReaction, "reactionDescription") != null) {
                            secondaryReaction.appendChild(secondaryMetabolismXML
                                    .importNode(getChildrenByNodeName(generalReaction, "reactionDescription"), true));
                        }
                    }
                }
            }
            TransformerFactory tFactory = TransformerFactory.newInstance();
            Transformer transformer = tFactory.newTransformer();
            transformer.setOutputProperty(OutputKeys.INDENT, "yes");

            DOMSource source = new DOMSource(secondaryMetabolismXML);
            StreamResult result = new StreamResult(new StringWriter());
            transformer.transform(source, result);

            Writer output = new BufferedWriter(
                    new FileWriter("/home/bioinfo/workspace/teste/src/Result.xml"));
            String xmlOutput = result.getWriter().toString();
            output.write(xmlOutput);
            output.close();

        } catch (Exception e) {
            e.printStackTrace();
        }

    }

    /**
     * Returns a node child when you have a match with a given node name
     * 
     * @param node
     * @param nodeName
     * @return
     */
    public static Node getChildrenByNodeName(Node node, String nodeName) {
        for (Node childNode = node.getFirstChild(); childNode != null;) {
            Node nextChild = childNode.getNextSibling();
            if (childNode.getNodeName().equalsIgnoreCase(nodeName)) {
                return childNode;
            }
            childNode = nextChild;
        }
        return null;
    }
}