gov.nih.nci.ispy.web.ajax.ReporterLookup.java Source code

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Here is the source code for gov.nih.nci.ispy.web.ajax.ReporterLookup.java

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/*L
 *  Copyright SAIC
 *
 *  Distributed under the OSI-approved BSD 3-Clause License.
 *  See http://ncip.github.com/i-spy/LICENSE.txt for details.
 */

package gov.nih.nci.ispy.web.ajax;

import gov.nih.nci.caintegrator.application.service.annotation.GeneExprAnnotationService;
import gov.nih.nci.caintegrator.enumeration.ArrayPlatformType;
import gov.nih.nci.ispy.service.annotation.GeneExprAnnotationServiceFactory;
import gov.nih.nci.ispy.web.helper.EnumHelper;

import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;

import org.json.simple.JSONArray;
import org.json.simple.JSONObject;

public class ReporterLookup {

    public ReporterLookup() {
    }

    /**
     * this ajax method looks up reporters using gexpannotation service
     * based on gene symbol and array platform. An addition parameter is 
     * provided so that the callback(javascript) knows where to put the collection
     * This last paramter is an id from the ui element.
     * NOTE: the id passed in WILL be used in the callback...make sure it is there!
     */
    public String lookup(String gene, String arrayPlatform, String uiElement) {
        Collection<String> reporters = new HashSet<String>();
        //set up geneCollection
        Collection<String> genes = new ArrayList<String>();
        genes.add(gene);
        //set up array platform by finding the appropriate type
        String[] uiString = arrayPlatform.split("#");
        String myClassName = uiString[0];
        String myValueName = uiString[1];
        Enum myType = EnumHelper.createType(myClassName, myValueName);

        if (myType instanceof ArrayPlatformType) {
            GeneExprAnnotationService gs = GeneExprAnnotationServiceFactory.getInstance();
            reporters = gs.getReporterNamesForGeneSymbols(genes, (ArrayPlatformType) myType);
        }
        /* reporterResultArray variable holds reporter objects like the result 
         * list of reporters (in its own array called reporterList), 
         * the results String, and the UIElement
        */
        JSONArray reporterResultArray = new JSONArray();
        JSONObject resultsObject = new JSONObject();

        JSONArray reporterList = new JSONArray();
        for (String reporter : reporters) {
            reporterList.add(reporter);
        }
        String results = "notFound";
        if (!reporterList.isEmpty()) {
            results = "found";
        }
        resultsObject.put("gene", gene);
        resultsObject.put("results", results);
        resultsObject.put("reporters", reporterList);
        resultsObject.put("elementId", uiElement);
        reporterResultArray.add(resultsObject);

        return reporterResultArray.toString();
    }

}