package src;

import java.io.ByteArrayInputStream;
import java.util.Iterator;

import org.biomoby.client.*;
import org.biomoby.shared.*;
import org.biomoby.shared.data.*;
import org.biomoby.shared.datatypes.MobyObject;
import org.biomoby.shared.parser.MobyJob;
import org.biomoby.shared.parser.MobyPackage;

public class TestGetAffyprobesetIdsForAGILocuscode {
	 
	public static void main(String[] args) throws Exception{

		if (args.length != 2) {
		    System.err.println ("Usage: java TestGetAffyprobesetIdsForAGILocuscode [<AGI_LocusCode> [<service-endpoint>]]\n");
		    System.exit (1);
		}
		
		String agiLocusCode = "AT2G44490";
		String serviceEndPoint =  "http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl";
		
		Central worker = new CentralImpl();
		
	    // Make template for finding services
        MobyService service = new MobyService();
        service.setURL(serviceEndPoint);
        service.setName("getAffyProbesetIdsForAgiLocusCode");
        service.setAuthority("ssg.uab.edu");
        
        MobyDataObject input = new MobyDataObject("Object", agiLocusCode);
        input.setId(agiLocusCode);
        input.setPrimaryNamespace(new MobyNamespace("AGI_LocusCode"));
        System.out.println("Finding services matching template: "+service.getName());
        
        MobyService[] validServices = worker.findService(service);
        
        // Make sure we have a service to run for this input
	    if(validServices == null || validServices.length == 0){
		System.err.println("Could not find any valid services");
	    }
	    else{
		System.out.println("Found some services");
	    }
	    
	    MobyRequest request = new MobyRequest(worker);
	    request.setDebugMode(true);
	    request.setService(validServices[0]);
	    request.setInput(input);
	   
	    MobyContentInstance responses = request.invokeService();
	    
	    //System.out.println(responses.toXML());
	    
	    // Process responses
	    // The service invocation may have had many requests, there is a response
	    // object for each request
	    Iterator i = responses.keySet().iterator();
	    while(i.hasNext()){
                MobyDataJob responseObjects = responses.get(i.next());
                // The response for a request may have many objects
                Iterator i2 = responseObjects.values().iterator();
                while(i2.hasNext()){
                	MobyDataInstance responseObject = (MobyDataInstance)i2.next();
                	//The response objects may either be simple data, or data sets
                	if(responseObject instanceof MobyDataObject){
                		System.out.println("Plain simple instance is "+((MobyDataInstance)responseObject).toXML());
                	}
                	else if(responseObject instanceof MobyDataObjectSet){
                			System.out.println("Found a collection:");
                			MobyDataObject[] simples = ((MobyDataObjectSet) responseObject).getElementInstances();
			        for(int j = 0; j < simples.length; j++){
			        	// Print results probe set ids
			        	System.out.println("Object type:" + simples[j].getName());
			        	System.out.println("Probeset Id:" + simples[j].getId());
			        	
			        	//Print XML formatted result set XML 
			        	System.out.println("  Member instance is \n"+simples[j].toXML());
			        }
		         }
                	else{
                		System.out.println("Found funky data!" + responseObject);
                	}
                }
	    	}	    
    	}
}