org.mskcc.cbio.portal.servlet.OncoPrintConverter.java Source code

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Here is the source code for org.mskcc.cbio.portal.servlet.OncoPrintConverter.java

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/*
 * Copyright (c) 2015 Memorial Sloan-Kettering Cancer Center.
 *
 * This library is distributed in the hope that it will be useful, but WITHOUT
 * ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS
 * FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder
 * is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no
 * obligations to provide maintenance, support, updates, enhancements or
 * modifications. In no event shall Memorial Sloan-Kettering Cancer Center be
 * liable to any party for direct, indirect, special, incidental or
 * consequential damages, including lost profits, arising out of the use of this
 * software and its documentation, even if Memorial Sloan-Kettering Cancer
 * Center has been advised of the possibility of such damage.
 */

/*
 * This file is part of cBioPortal.
 *
 * cBioPortal is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Affero General Public License as
 * published by the Free Software Foundation, either version 3 of the
 * License.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Affero General Public License for more details.
 *
 * You should have received a copy of the GNU Affero General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
*/

package org.mskcc.cbio.portal.servlet;

// imports
import org.mskcc.cbio.portal.util.XDebug;
import org.mskcc.cbio.portal.util.FileUploadRequestWrapper;

import javax.servlet.ServletContext;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServlet;
import javax.servlet.RequestDispatcher;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;

import org.apache.commons.fileupload.FileItem;
import org.mskcc.cbio.portal.util.XssRequestWrapper;
import org.owasp.validator.html.PolicyException;

import java.io.PrintWriter;
import java.io.IOException;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

/**
 * Servlet responsible for converting OncoPrint into SVG.
 */
public class OncoPrintConverter extends HttpServlet {

    private Pattern svgXPosPattern;

    /**
     * Initializes the servlet.
     *
     * @throws ServletException
     */
    public void init() throws ServletException {

        super.init();
        svgXPosPattern = Pattern.compile("( x=\"(\\d+)\")");
    }

    /**
     * Handles HTTP GET Request.
     *
     * @param httpServletRequest  HttpServletRequest
     * @param httpServletResponse HttpServletResponse
     * @throws ServletException
     */
    protected void doGet(HttpServletRequest httpServletRequest, HttpServletResponse httpServletResponse)
            throws ServletException, IOException {

        doPost(httpServletRequest, httpServletResponse);
    }

    /**
     * Handles the HTTP POST Request.
     *
     * @param httpServletRequest  HttpServletRequest
     * @param httpServletResponse HttpServletResponse
     * @throws ServletException
     */
    protected void doPost(HttpServletRequest httpServletRequest, HttpServletResponse httpServletResponse)
            throws ServletException, IOException {

        // setup a debug object 
        XDebug xdebug = new XDebug(httpServletRequest);
        xdebug.logMsg(this, "Attempting to parse request parameters.");

        String xml = "";
        String format = "";
        if (httpServletRequest instanceof FileUploadRequestWrapper) {

            // get instance of our request wrapper
            FileUploadRequestWrapper wrapper = (FileUploadRequestWrapper) httpServletRequest;

            // get format parameter
            format = wrapper.getParameter("format");

            // get xml parameter
            xml = wrapper.getParameter("xml");
        } else {
            httpServletRequest.getParameter("format");
            xml = httpServletRequest.getParameter("xml");

            // TODO - update antisamy.xml to support svg-xml
            if (httpServletRequest instanceof XssRequestWrapper) {
                xml = ((XssRequestWrapper) httpServletRequest).getRawParameter("xml");
            }

        }

        String xmlHeader = "<?xml version='1.0'?>";
        xml = xmlHeader + xml;
        if (!xml.contains("svg xmlns")) {
            xml = xml.replace("<svg", "<svg xmlns='http://www.w3.org/2000/svg' version='1.1'");
        }

        // sanity check
        //if (!format.equals("svg")) {
        //   forwardToErrorPage(getServletContext(), httpServletRequest, httpServletResponse, xdebug);
        //}

        // outta here
        convertToSVG(httpServletResponse, xml);
    }

    /**
     * Reflect given svg xml back to browser for saving.
     *
     * @param response HttpServletResponse
     * @param xml String
     */
    private void convertToSVG(HttpServletResponse response, String xml) throws ServletException {

        try {
            response.setContentType("application/svg+xml");
            PrintWriter writer = response.getWriter();
            try {
                writer.write(xml);
            } finally {
                writer.flush();
                writer.close();
            }
        } catch (IOException e) {
            throw new ServletException(e);
        }
    }

    /**
     * Method called when exception occurs.
     * 
     * @param servletContext ServletContext
     * @param request HttpServletRequest
     * @param response HttpServletResponse
     * @param xdebug XDebug
     */
    private static void forwardToErrorPage(ServletContext servletContext, HttpServletRequest request,
            HttpServletResponse response, XDebug xdebug) throws ServletException, IOException {

        request.setAttribute("xdebug_object", xdebug);
        RequestDispatcher dispatcher = servletContext.getRequestDispatcher("/WEB-INF/jsp/error.jsp");
        dispatcher.forward(request, response);
    }
}