gistfile1.txt

package org.zertz.genesearch.web.ajax;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.springframework.web.servlet.mvc.SimpleFormController;
import org.springframework.web.servlet.ModelAndView;
import org.springframework.web.servlet.view.AbstractView;
import org.springframework.core.io.Resource;

import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import java.util.*;
import java.io.*;

import net.sf.json.JSONObject;
import net.sf.json.JSONArray;

/*
 * Copyright 
 * 
 * Licensed under the 
 */

/**
 * <p/>
 * TODO: Add Description
 * </p>
 * Date: Dec 7, 2007
 *
 * @author Michael Jones.
 */
public class GeneSearch extends SimpleFormController {
    protected final Log logger = LogFactory.getLog(getClass());
    private Resource probeAnnotationResource;
    private Map<String, ProbeSetAnnotation> probe2annot = new HashMap<String, ProbeSetAnnotation>();

    public void init() throws IOException {
        BufferedReader in = new BufferedReader(new FileReader(probeAnnotationResource.getFile()));

        in.readLine(); //Remove header

        String line;
        while((line = in.readLine()) != null){
            String[] toks = line.split("\t");
            String probe = toks[0];
            String syn = toks[1];
            String id = toks[2];
            String desc = toks[3];
            String name = toks[4];

            ProbeSetAnnotation annot = new ProbeSetAnnotation(probe, name, Integer.parseInt(id), syn, desc);
            probe2annot.put(probe, annot);
        }

    }

    @Override
    protected ModelAndView onSubmit(Object command)  {
        return new ModelAndView(new JSONGeneSearchView((GeneSearchData)command));
    }

    @Override
    protected boolean isFormSubmission(HttpServletRequest request){
        return true;
    }

    class JSONGeneSearchView extends AbstractView {
        private GeneSearchData cmd;

        JSONGeneSearchView(GeneSearchData cmd) {
            this.cmd = cmd;
        }

        protected void renderMergedOutputModel(Map map, HttpServletRequest httpServletRequest,
                                               HttpServletResponse response) throws Exception {
            logger.debug("Building JSON");
            response.setHeader("Content-Disposition", "attachment; filename=test.json");
            response.setContentType("application/json; charset=utf-8");

            final PrintWriter writer = response.getWriter();

            List<String> probes = new ArrayList<String>(Arrays.asList(cmd.getProbes().split("\\s+")));

            JSONArray array = new JSONArray();
            Set<ProbeSetAnnotation> annotations = getProbeSetAnnotations(probes);
            logger.debug("Got annotations: " + annotations.size());
            for(ProbeSetAnnotation annot : annotations){
                logger.debug("Building JSON for " + annot.probeset);
                JSONObject item = new JSONObject();
                item.put("type", "probesets");
                item.put("label", annot.getProbeset());
                item.put("name", annot.getGeneName());
                item.put("entrez_gene_id", annot.getGeneID());
                item.put("synonyms", annot.getGeneSynonyms());
                item.put("description", annot.getDescription());
                array.put(item);
            }

            JSONObject jsonObj = new JSONObject();
            jsonObj.put("items", array);
            jsonObj.write(writer);
            writer.close();
            logger.debug("Done writing JSON");
        }
    }

    private Set<ProbeSetAnnotation> getProbeSetAnnotations(List<String> probes) {
        logger.debug("Getting probe annot : " + probes);
        Set<ProbeSetAnnotation> annots = new HashSet<ProbeSetAnnotation>(probes.size());
        for(String probe : probes){
            if(probe2annot.containsKey(probe))
                annots.add(probe2annot.get(probe));
        }
        return annots;
    }

    public Resource getProbeAnnotationResource() {
        return probeAnnotationResource;
    }

    public void setProbeAnnotationResource(Resource probeAnnotationResource) {
        this.probeAnnotationResource = probeAnnotationResource;
    }

    class ProbeSetAnnotation {
        private String probeset;
        private String geneName;
        private int geneID;
        private String geneSynonyms;
        private String description;

        ProbeSetAnnotation(String probeset, String geneName, int geneID, String geneSynonyms, String description) {
            this.probeset = probeset;
            this.geneName = geneName;
            this.geneID = geneID;
            this.geneSynonyms = geneSynonyms;
            this.description = description;
        }

        public String getProbeset() {
            return probeset;
        }

        public void setProbeset(String probeset) {
            this.probeset = probeset;
        }

        public String getGeneName() {
            return geneName;
        }

        public void setGeneName(String geneName) {
            this.geneName = geneName;
        }

        public int getGeneID() {
            return geneID;
        }

        public void setGeneID(int geneID) {
            this.geneID = geneID;
        }

        public String getGeneSynonyms() {
            return geneSynonyms;
        }

        public void setGeneSynonyms(String geneSynonyms) {
            this.geneSynonyms = geneSynonyms;
        }

        public String getDescription() {
            return description;
        }

        public void setDescription(String description) {
            this.description = description;
        }
    }
}