org.sc.probro.servlets.TextQueryServlet.java Source code

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Here is the source code for org.sc.probro.servlets.TextQueryServlet.java

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/*
   Copyright 2010 Massachusetts General Hospital
    
   Licensed under the Apache License, Version 2.0 (the "License");
   you may not use this file except in compliance with the License.
   You may obtain a copy of the License at
    
   http://www.apache.org/licenses/LICENSE-2.0
    
   Unless required by applicable law or agreed to in writing, software
   distributed under the License is distributed on an "AS IS" BASIS,
   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
   See the License for the specific language governing permissions and
   limitations under the License.
*/
package org.sc.probro.servlets;

import java.io.File;
import java.io.IOException;
import java.io.PrintWriter;
import java.net.URLDecoder;
import java.util.Arrays;
import java.util.Map;
import java.util.Set;
import java.util.TreeSet;

import javax.servlet.ServletException;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;

import org.eclipse.jetty.util.log.Log;
import org.json.JSONArray;
import org.json.JSONException;
import org.json.JSONObject;
import org.json.JSONStringer;
import org.sc.probro.Broker;
import org.sc.probro.BrokerProperties;
import org.sc.probro.SearchResult;
import org.sc.probro.UserCredentials;
import org.sc.probro.exceptions.BadRequestException;
import org.sc.probro.exceptions.BrokerException;
import org.sc.probro.lucene.ProteinSearcher;

public class TextQueryServlet extends BrokerServlet {

    private String luceneIndexPath;

    public TextQueryServlet(BrokerProperties props) {
        super(props);
        luceneIndexPath = props.getLuceneIndex();
    }

    public void init() throws ServletException {
        super.init();
    }

    public void destroy() {
        super.destroy();
    }

    private String renderHitAsHTML(SearchResult obj) {
        StringBuilder sb = new StringBuilder();
        sb.append("<tr>");
        sb.append(String.format("<td>%s</td>", obj.id));
        sb.append(String.format("<td>%s</td>", obj.response_type));

        sb.append("<td><table>");
        for (String desc : obj.description) {
            sb.append(String.format("<tr><td>%s</td></tr>", desc));
        }
        sb.append("</table></td>");

        sb.append("<td><table>");
        for (String acc : obj.accession) {
            sb.append(String.format("<tr><td>%s</td></tr>", acc));
        }
        sb.append("</table></td>");

        sb.append("</tr>");
        return sb.toString();
    }

    protected void doGet(HttpServletRequest request, HttpServletResponse response)
            throws ServletException, IOException {

        try {
            String searchTerm = getRequiredParam(request, "search", String.class);
            String contentType = getContentType(request);
            String[] ontologies = getOptionalParam(request, "ontology_id", String[].class);
            UserCredentials user = new UserCredentials();

            Broker broker = getBroker();
            try {
                SearchResult[] results = broker.query(user, searchTerm, ontologies);

                response.setStatus(HttpServletResponse.SC_OK);
                response.setContentType(contentType);

                if (contentType.equals(CONTENT_TYPE_JSON)) {

                    JSONStringer stringer = new JSONStringer();
                    stringer.array();
                    for (SearchResult res : results) {
                        res.stringJSON(stringer);
                    }
                    stringer.endArray();

                    response.getWriter().println(stringer.toString());

                } else if (contentType.equals(CONTENT_TYPE_HTML)) {

                    PrintWriter writer = response.getWriter();
                    writer.println("<table>");
                    writer.println("<tr>" + "<th>ID</th>" + "<th>Type</th>" + "<th>Descriptions</th>"
                            + "<th>Accessions</th>" + "</tr>");
                    for (SearchResult res : results) {
                        writer.println(renderHitAsHTML(res));
                    }
                    writer.println("</table>");

                } else {
                    throw new BadRequestException(String.format("Unsupported content type: %s", contentType));
                }

            } catch (JSONException e) {
                throw new BrokerException(e);

            } finally {
                broker.close();
            }

        } catch (BrokerException e) {
            handleException(response, e);
            return;
        }

    }

    protected void doPost(HttpServletRequest request, HttpServletResponse response)
            throws ServletException, IOException {

        handleException(response,
                new BrokerException(HttpServletResponse.SC_METHOD_NOT_ALLOWED, String.format("POST not allowed.")));
    }

}