Parsing Dom Document From Omim Restful Web Services

Question

[partha]

I am a beginner to web services can any one with experience please help me with the following:

I am writing a client trying to get information from OMIM RESTful web services. I am using a key OMIM provideds after registration. ( http://omim.org/help/api ) I am successful at getting connection to client. Also with the GET method I am able to fetch the required data into a DOM document. Further, I could successfuly write the entire DOM into a file on the local disk. However, I am unable to work with the DOM using the standard parsing functions available for DOM.

For example: I am able to get the root node with NodeList nl=doc.getDocumentElement()and print onto the console. But when I try to print the first child of the root node it returns null instead of expected child node.

Sample XML form: webservices -> DOM -> file

<?xml version="1.0" encoding="UTF-8" standalone="no"?><omim version="1.0">
<clinicalSynopsisList>
<clinicalSynopsis>
<mimNumber>100070</mimNumber>
<prefix>%</prefix>
<preferredTitle>AORTIC ANEURYSM, FAMILIAL ABDOMINAL, 1; AAA1</preferredTitle>
<oldFormat>
<Vascular>Abdominal aortic aneurysm; Generalized dilating diathesis;</Vascular>
<Misc>Estimated 11.6-fold increase among persons with an affected first-degree relative;</Misc>
<Inheritance>Autosomal dominant vs. recessive at an autosomal major locus or multifactorial; COL3A1 gene (120180.0004) mutations cause about 2%;</Inheritance>
</oldFormat>
</clinicalSynopsis>
</clinicalSynopsisList>
</omim>

Please find my code below:

String path="http://api.omim.org:8000/api/clinicalSynopsis?  mimNumber="+"100070"+"&include=clinicalSynopsis&format=xml&apiKey="+"<< xxxxx private key xxxxxxxxxx >> ";

              URL url = new URL(path);

              HttpURLConnection conn=(HttpURLConnection)url.openConnection();

              conn.setRequestMethod("GET");

              InputStream is = conn.getInputStream();

              DocumentBuilder docBuilder = DocumentBuilderFactory.newInstance().newDocumentBuilder();

              Document doc = docBuilder.parse(is);

              Source src= new DOMSource(doc);

              File file = new File("d:/text.xml");

              Result rs = new StreamResult(file);

              TransformerFactory tmf = TransformerFactory.newInstance();

              Transformer trnsfrmr = tmf.newTransformer();

              trnsfrmr.transform(src, rs);

              System.out.println("XML file is created successfully");

              System.out.println("The root element is :: "+doc.getDocumentElement().getNodeName());


              NodeList nl=doc.getDocumentElement().getChildNodes();

              System.out.println("child nodelist length::"+nl.getLength());


              System.out.println("First child node name :: "+doc.getDocumentElement().getFirstChild().getNodeName());

              System.out.println("Last child node name :: "+doc.getDocumentElement().getLastChild().getNodeName());

Output I got:- XML file is created successfully The root element is :: omim child nodelist length::3 First child node name :: #text Last child node name :: #text

In the output got the root node is “omim” and it has 3 children. but returns null when tried printing the first and last child name. Similarly getParent(), getChild(), getSibling() methods are not working for me.

Any help will be highly appreciated.

Thank you,

[Pierre Lindenbaum]

cross posted on SO: http://stackoverflow.com/questions/10551202

Answer 1

[Pierre Lindenbaum]

I cannot currently use the OMIM API , but the following java code should do the work. I think your problem is that you assume that the first child of an XML node is an ELEMENT, which is wrong, it seems to be a TEXT node containing a carriage return.

import java.net.URLEncoder;

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.Element;
import org.w3c.dom.Node;


public class Biostar44705
    {
    private static final String API_KEY="XXXXXXXX"; 
    private DocumentBuilder builder;
    private Transformer echoTransformer=null;

    private Biostar44705()throws Exception
        {
        DocumentBuilderFactory factory=DocumentBuilderFactory.newInstance();
        factory.setCoalescing(true);
        factory.setIgnoringComments(true);
        factory.setNamespaceAware(false);
        builder=factory.newDocumentBuilder();

        TransformerFactory trf=TransformerFactory.newInstance();
        this.echoTransformer =trf.newTransformer();
        this.echoTransformer .setOutputProperty(OutputKeys.INDENT, "yes");
        this.echoTransformer .setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
        }
    void get(int omimId)throws Exception
        {
        String uri="http://api.omim.org:8000/api/clinicalSynopsis?mimNumber="+omimId+
                "&include=clinicalSynopsis&format=xml&apiKey="+
                URLEncoder.encode(API_KEY,"UTF-8");
        Document dom=builder.parse(uri);
        Element root=dom.getDocumentElement();
        if(root==null) return;
        for(Node n1=root.getFirstChild();n1!=null;n1=n1.getNextSibling())
            {
            if(n1.getNodeType()!=Node.ELEMENT_NODE) continue;
            echoTransformer.transform(new DOMSource(n1),new StreamResult(System.out));
            break;
            }
        }
public static void main(String[] args) throws Exception
    {
    new Biostar44705().get(100070);
    }
}

[Jeremy Leipzig]

good lord Java is verbose. When are you going to switch to Groovy?

[Pierre Lindenbaum]

@Jeremy, well, for that simple problem I would use XSLT, not java

[Pierre Lindenbaum]

I'm sure Groovy is great, but if I use an exotic language, I'm afraid less people will be able to use/read it. Moreover, my code is standard and don't need any other depedencies but java itself.

Answer 2

[Damian Kao]

I would look into xslt (http://en.wikipedia.org/wiki/XSLT). Is XML the only output this service generates?