[MOBY-l] java xml parsing

[Paul Gordon]

If you are using MobyRequest, the getOutput will return a Vector with 
one element (corresponding to the one response).  This element is a 
MobySimpleDataInstance array of length one.  The MobySimpleDataInstance 
will just contain the genbank-flatfile tag and its nested contents.  
Unfortunately, for now this is as far as the autoparsing goes.  
Hopefully soon
MobySimpleDataInstance will soon give you its constituent members as 
other MobySimpleDataInstances, down to the primitives of the ontology. 

But for now, you can parse the XML response in an XML parser (determined 
by Java using the runtime libraries available) and run an XPath.  I 
haven't tried to compile the following code, but it should give you an 
idea of how to parse robustly (given that your XML object 
genbank-flatfile is not attributed to the MOBY namespace):

import javax.xml.parsers.*;
import org.w3c.dom.*;
import org.apache.xpath.XPathAPI; // xpath statement execution env

try{
  // Insert your code to get the XML string

  // Get a parser and parse the document
 DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
 DocumentBuilder docBuilder = dbf.newDocumentBuilder();
 Document document=docBuilder.parse(new 
java.io.StringBufferInputStream(xmlString));
 Element mobyPayload = document.getDocumentElement();

  // Now run the XPath statement that will be used fetch data from the 
server response   
  Node idAttr = XPathAPI.selectSingleNode(mobyPayload, 
"//genbank-flatfile/@id");
  if(idAttr != null){
        System.out.println("Output of XPath was " + idAttr.getNodeValue());
  }
}
catch(TransformerException te){
  // Insert your favourite death scene here
}
catch(ParserConfigurationException){
  // Ditto
}
catch(org.xml.sax.SAXException saxe){
  // Ditto
}
catch(java.io.IOException ioe){
  //Ditto
}


Benjamin Good wrote:

> Say I have a Query response like this
>
> "<?xml version='1.0' encoding='UTF-8'?>"+
>        "<moby:MOBY xmlns:moby='http://www.biomoby.org/moby' 
> xmlns='http://www.biomoby.org/moby'>"+
>        "<moby:mobyContent 
> moby:authority='illuminae.com'><moby:serviceNotes>This is provided by 
> SeqHound</moby:serviceNotes>"+
>                "<moby:mobyData moby:queryID='1'>"+
>                    "<moby:Simple moby:articleName=''>" +
>                    "<genbank-flatfile namespace='NCBI_gi' 
> id='111076'><![CDATA[LOCUS D31461 32 aa linear   ROD 30-MAY-1997"+
>        "DEFINITION  T-cell receptor delta chain BDN7, thymus - mouse 
> (fragment)."+
>        "ACCESSION   D31461"+
>        "PID         g111076"+
>        "ORIGIN"+
>         "       1 atyfcalmer vsrrgapdkl vfgqgtqvtv ep"+
>        "//]]></genbank-flatfile></moby:Simple>"+
>                "</moby:mobyData>"+
>                "</moby:mobyContent></moby:MOBY>";      
> Any suggestions regarding the best way to extract the gi id or the 
> CDATA ?  It seems there are many options, just wondering if the Java 
> group has already settled on an approach.
>
> thanks
> -Ben
>
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