AssaysHandler.java

package gov.nih.ncgc.bard.capextract.handler;

import gov.nih.ncgc.bard.capextract.CAPConstants;
import gov.nih.ncgc.bard.capextract.CapResourceHandlerRegistry;
import gov.nih.ncgc.bard.capextract.ICapResourceHandler;
import gov.nih.ncgc.bard.capextract.jaxb.Assays;
import gov.nih.ncgc.bard.capextract.jaxb.Link;

import java.io.IOException;
import java.math.BigInteger;
import java.util.List;

/**
 * A one line summary.
 *
 * @author Rajarshi Guha
 */
public class AssaysHandler extends CapResourceHandler implements ICapResourceHandler {

    public AssaysHandler() {
        super();
    }

    /**
     * Process a CAP entity that is located at some URL.
     *
     * @param url      The URL from which to retrieve the entity fron
     * @param resource The CAP resource that is meant to be processed. An implementing class
     *                 can choose to proceed or not based on this parameter.
     */
    public int process(String url, CAPConstants.CapResource resource) throws IOException {

	if (resource != CAPConstants.CapResource.ASSAYS) return CAPConstants.CAP_EXTRACT_LOAD_STATUS_FAILED;
	log.info("Processing " + resource);

	// get the Assays object here
	Assays assays = getResponse(url, resource);
	BigInteger n = assays.getCount();
	log.info("\tWill be processing " + n + " assays");
	List<Link> links = assays.getLink();
	for (Link link : links) {
	    String href = link.getHref();
	    String type = link.getType();
	    String title = link.getTitle();
	    log.info("\t" + title + "/" + type + "/ href = " + href);

	    // for now lets just handle a few specific assays
	    //            if (href.endsWith("/1640")) {
	    if (true) {
		ICapResourceHandler handler = CapResourceHandlerRegistry.getInstance().getHandler(CAPConstants.CapResource.ASSAY);
		if (handler != null) {		    
		    //start
		    setExtractionStatus(CAPConstants.CAP_STATUS_STARTED, href, 
			    CAPConstants.CapResource.ASSAY);
		    //process
		    handler.process(href, CAPConstants.CapResource.ASSAY);
		    //mark complete
		    setExtractionStatus(CAPConstants.CAP_STATUS_COMPLETE, href, 
			    CAPConstants.CapResource.ASSAY);
		}
	    }
	}
	return CAPConstants.CAP_EXTRACT_LOAD_STATUS_COMPLETE;
    }
}