uk.ac.ebi.intact.widgets.webapp.servlet.cytoscape.CytoscapeServlet.java Source code

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Here is the source code for uk.ac.ebi.intact.widgets.webapp.servlet.cytoscape.CytoscapeServlet.java

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/**
 * Copyright 2009 The European Bioinformatics Institute, and others.
 *
 * 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 uk.ac.ebi.intact.widgets.webapp.servlet.cytoscape;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

import javax.servlet.ServletConfig;
import javax.servlet.ServletContext;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServlet;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import java.io.*;
import java.net.URLEncoder;

/**
 * Servlet used to export a JNLP file in order to laod Cytoscape as a web start.
 *
 * @author Prem Anand (prem@ebi.ac.uk)
 * @version $Id$
 * @since 0.9
 */
public class CytoscapeServlet extends HttpServlet {

    private static final Log log = LogFactory.getLog(CytoscapeServlet.class);

    public static final String DATA_URL = "intactDataURL";

    public static final String PARAM_QUERY = "query";
    public static final String PARAM_FORMAT = "format";
    public static final String PARAM_FILTER_NEGATIVE = "negative";
    public static final String PARAM_FILTER_SPOKE = "spoke";
    public static final String PARAM_ONTOLOGY_QUERY = "ontology";
    public static final String PARAM_SORT = "sort";
    public static final String PARAM_SORT_ASC = "asc";

    @Override
    public void init(ServletConfig config) throws ServletException {
        super.init(config);
    }

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

        String searchQuery = request.getParameter(PARAM_QUERY);
        String format = request.getParameter(PARAM_FORMAT);
        String negative = request.getParameter(PARAM_FILTER_NEGATIVE);
        String spoke = request.getParameter(PARAM_FILTER_SPOKE);
        String ontology = request.getParameter(PARAM_ONTOLOGY_QUERY);
        String sort = request.getParameter(PARAM_SORT);
        String asc = request.getParameter(PARAM_SORT_ASC);

        if (searchQuery == null) {
            throw new ServletException("Parameter '" + PARAM_QUERY + "' was expected");
        }
        if (log.isDebugEnabled())
            log.debug("Generating a JNLP file to start Cytoscape with query: " + searchQuery);

        searchQuery = encodeURL(searchQuery);
        if (log.isTraceEnabled())
            log.trace("Encoded query: " + searchQuery);

        final String serverContext = "http://" + request.getServerName() + ":" + request.getServerPort()
                + request.getContextPath();
        final String exportUrl = serverContext + "/export?query=" + searchQuery + "&format=" + format
                + "&negative=" + negative + "&spoke=" + spoke + "&ontology=" + ontology + "&sort="
                + sort + "&asc=" + asc;
        ;
        response.setContentType("application/x-java-jnlp-file");

        // Read the template cytoscape.jnlp from from WEB-INF directory.
        String filename = "/WEB-INF/cytoscape/cytoscape.jnlp";
        ServletContext context = getServletContext();
        InputStream is = context.getResourceAsStream(filename);

        PrintWriter writer = null;
        try {
            if (is != null) {
                BufferedReader reader = new BufferedReader(new InputStreamReader(is));
                writer = response.getWriter();
                String text = null;

                try {
                    if (log.isTraceEnabled())
                        log.trace("Starting JNLP export ...");

                    while ((text = reader.readLine()) != null) {
                        if (text.contains(DATA_URL)) {
                            text = text.replace(DATA_URL, exportUrl);
                        }

                        if (log.isTraceEnabled())
                            log.trace(text);

                        writer.println(text);
                        writer.flush();
                    }
                    if (log.isTraceEnabled())
                        log.trace("Completed JNLP export.");

                } finally {
                    reader.close();
                }
            }
        } finally {
            if (writer != null) {
                writer.close();
            }
            is.close();
        }
    }

    private static String encodeURL(String url) throws UnsupportedEncodingException {
        if (url == null) {
            throw new IllegalArgumentException("You must give a non null url");
        }
        return URLEncoder.encode(url, "UTF-8");
    }
}