edu.vt.vbi.patric.portlets.CircosGenomeViewerPortlet.java Source code

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Here is the source code for edu.vt.vbi.patric.portlets.CircosGenomeViewerPortlet.java

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/**
 * ****************************************************************************
 * Copyright 2014 Virginia Polytechnic Institute and State University
 * <p/>
 * 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
 * <p/>
 * http://www.apache.org/licenses/LICENSE-2.0
 * <p/>
 * 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 edu.vt.vbi.patric.portlets;

import edu.vt.vbi.patric.beans.Genome;
import edu.vt.vbi.patric.circos.Circos;
import edu.vt.vbi.patric.circos.CircosData;
import edu.vt.vbi.patric.circos.CircosGenerator;
import edu.vt.vbi.patric.common.DataApiHandler;
import edu.vt.vbi.patric.common.SiteHelper;
import org.apache.commons.fileupload.FileItem;
import org.apache.commons.fileupload.FileUploadException;
import org.apache.commons.fileupload.disk.DiskFileItemFactory;
import org.apache.commons.fileupload.portlet.PortletFileUpload;
import org.apache.commons.lang.StringUtils;
import org.json.simple.JSONObject;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import javax.portlet.*;
import java.io.File;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;

public class CircosGenomeViewerPortlet extends GenericPortlet {

    CircosGenerator circosGenerator;

    private static final Logger LOGGER = LoggerFactory.getLogger(CircosGenomeViewerPortlet.class);

    @Override
    public void init(PortletConfig config) throws PortletException {
        String contextPath = config.getPortletContext().getRealPath(File.separator);
        String tmpPath = System.getProperty("shared_tmp",
                "/cid/share/deployment_software/patric/alpha/shared_tmp/");
        circosGenerator = new CircosGenerator(contextPath, tmpPath);
        super.init(config);
    }

    @Override
    protected void doView(RenderRequest request, RenderResponse response) throws PortletException, IOException {

        response.setContentType("text/html");

        SiteHelper.setHtmlMetaElements(request, response, "Circos Genome Viewer");
        response.setTitle("Circos Genome Viewer");

        DataApiHandler dataApi = new DataApiHandler(request);

        String actionUrl = "/portal/portal/patric/CircosGenomeViewer/CircosGenomeViewerWindow?action=1";
        String dataApiUrl = System.getProperty("dataapi.url", "https://www.patricbrc.org/api/");
        String genomeId = request.getParameter("context_id");
        Genome genome = dataApi.getGenome(genomeId);

        request.setAttribute("actionUrl", actionUrl);
        request.setAttribute("dataApiUrl", dataApiUrl);
        request.setAttribute("genome", genome);

        PortletRequestDispatcher prd = getPortletContext().getRequestDispatcher("/WEB-INF/jsp/circos_html.jsp");
        prd.include(request, response);
    }

    @SuppressWarnings("unchecked")
    public void serveResource(ResourceRequest request, ResourceResponse response)
            throws PortletException, IOException {

        String imageId = request.getParameter("imageId");
        String trackList = request.getParameter("trackList");
        JSONObject res = new JSONObject();
        res.put("success", true);
        res.put("imageId", imageId);
        res.put("trackList", trackList);

        PrintWriter writer = response.getWriter();
        res.writeJSONString(writer);
        writer.close();
    }

    public void processAction(ActionRequest request, ActionResponse response) throws PortletException, IOException {

        Map<String, Object> parameters = new LinkedHashMap<>();
        int fileCount = 0;

        try {
            List<FileItem> items = new PortletFileUpload(new DiskFileItemFactory()).parseRequest(request);
            for (FileItem item : items) {
                if (item.isFormField()) {
                    parameters.put(item.getFieldName(), item.getString());
                } else {
                    if (item.getFieldName().matches("file_(\\d+)$")) {
                        parameters.put("file_" + fileCount, item);
                        fileCount++;
                    }
                }
            }
        } catch (FileUploadException e) {
            LOGGER.error(e.getMessage(), e);
        }

        LOGGER.debug(parameters.toString());

        // Generate Circo Image
        CircosData circosData = new CircosData(request);
        Circos circosConf = circosGenerator.createCircosImage(circosData, parameters);

        if (circosConf != null) {
            String baseUrl = "https://" + request.getServerName();
            String redirectUrl = baseUrl
                    + "/portal/portal/patric/CircosGenomeViewer/CircosGenomeViewerWindow?action=b&cacheability=PAGE&imageId="
                    + circosConf.getUuid() + "&trackList=" + StringUtils.join(circosConf.getTrackList(), ",");

            LOGGER.trace("redirect: {}", redirectUrl);
            response.sendRedirect(redirectUrl);
        }
    }
}