org.spee.sbweb.controller.SBWebController.java Source code

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Here is the source code for org.spee.sbweb.controller.SBWebController.java

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package org.spee.sbweb.controller;

import gui.sequencebundle.JSequenceBundle;

import java.io.File;
import java.io.IOException;
import java.io.StringReader;
import java.util.Date;
import java.util.Timer;
import java.util.TimerTask;

import javax.servlet.ServletContext;
import javax.validation.Valid;

import org.spee.sbweb.model.AlvisModel;
import org.springframework.stereotype.Controller;
import org.springframework.ui.Model;
import org.springframework.validation.BindingResult;
import org.springframework.web.bind.annotation.ModelAttribute;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.context.ServletContextAware;

import alvis.Alvis;
import alvis.AlvisDataModel;
import alvis.algorithm.ParseAlignmentTask;
import alvis.algorithm.ParseAlignmentTask.AlignmentParserResults;

/**
 *
 * @author Roland Schwarz <rfs32@cam.ac.uk>
 */
@Controller
@RequestMapping(value = "/")
public class SBWebController implements ServletContextAware {

    private ServletContext servletContext;

    // value of milliseconds in one minute
    private static final int MINS_IN_MS = 60 * 1000;
    // time in milliseconds
    private static final int TIME_TO_CHECK_IMAGE_FOLDER = 60 * MINS_IN_MS;
    private static final int IMAGE_LIFETIME = 60 * MINS_IN_MS;

    @RequestMapping(method = RequestMethod.GET)
    public String viewSequenceBundleConfig(Model model) {
        return "index";
    }

    @RequestMapping(method = RequestMethod.POST)
    public String processSequenceBundleConfig(@ModelAttribute("userForm") @Valid AlvisModel alvisModel,
            BindingResult bindingResult, Model model) {

        if (bindingResult.hasErrors()) {
            return "AlvisInput";
        }
        System.setProperty("java.awt.headless", "true");
        JSequenceBundle jsb = new JSequenceBundle(null, null, alvisModel);

        // process sequences
        if (alvisModel.getSequences().trim().isEmpty()) {
            alvisModel.setErrorMessage("No sequences to render!");
            return ("AlvisError");
        }
        ParseAlignmentTask alignmentParser = new ParseAlignmentTask(new StringReader(alvisModel.getSequences()),
                Alvis.AlignmentFormat.FASTA, AlvisDataModel.AlignmentType.AminoAcid, null);
        AlignmentParserResults alignmentResults;
        try {
            alignmentResults = alignmentParser.parse();
            jsb.setAlignment(alignmentResults.alignment);
            // SequenceAlphabet.AMINOACIDS;
            // AbstractLegendRenderer lr =
            // AbstractLegendRenderer.createAAIndexLegendRenderer(SequenceBundleConfig.AlignmentType.valueOf(alvisModel.getAlignmentType()))
            // ;
            // jsb.setLegendRenderer(lr);
        } catch (Exception ex) {
            alvisModel.setErrorMessage(ex.getMessage());
            return ("AlvisError");
        }

        jsb.setBundleConfig(alvisModel);

        File tmpFile;
        try {
            File folder = new File(servletContext.getRealPath("/images"));
            tmpFile = File.createTempFile("alvis", ".png", folder);
            jsb.renderPNGToFile(tmpFile, 300);
            alvisModel.setTempFile(tmpFile);
            alvisModel.setWebPath(servletContext.getContextPath() + "/images/" + tmpFile.getName());

            // alvisModel.setWebPath(servletContext.getContextPath("/") +
            // "/images/" + tmpFile.getName());
        } catch (IOException ex) {
            alvisModel.setErrorMessage(ex.getMessage());
            return ("AlvisError");
        }

        // do stuff
        return "SBWebResult";
    }

    @RequestMapping(value = "/ezviz", method = { RequestMethod.GET })
    public String seqStatus() {
        return "EzViz";
    }

    @Override
    public void setServletContext(ServletContext servletContext) {
        this.servletContext = servletContext;
        System.out.println(
                "SBWebControler.java - ServletContext: images - " + this.servletContext.getRealPath("/images"));
        System.out.println("SBWebControler.java - ServletContext: root - " + this.servletContext.getRealPath("/"));

        Timer t = new Timer();
        CronJobs mTask = new CronJobs();

        t.scheduleAtFixedRate(mTask, 0, TIME_TO_CHECK_IMAGE_FOLDER);

    }

    class CronJobs extends TimerTask {
        // private static final int HOUR_THRESHOLD = 1 * 60 * 60 * 1000;
        private final File folder = new File(servletContext.getRealPath("/resources/images"));

        public CronJobs() {
            // Some stuffs
        }

        private void cleanImageFiles(final File folder) {
            for (final File fileEntry : folder.listFiles()) {
                if (fileEntry.isDirectory()) {
                    cleanImageFiles(fileEntry);
                } else {
                    long diff = new Date().getTime() - fileEntry.lastModified();
                    if (diff > IMAGE_LIFETIME) {
                        fileEntry.delete();
                    }
                }
            }
        }

        @Override
        public void run() {
            final File folder = new File(servletContext.getRealPath("/resources/images"));
            // create an image folder if one doens't already exist
            if (!folder.exists()) {
                System.out.println("SBWebControler.java: creating temporay image directory" + folder.toString());
                folder.mkdir();
            }
            Date date = new Date();
            System.out.println("Cleaning image folder: " + date.toString());
            cleanImageFiles(folder);
        }

    }

    // @InitBinder
    // public void initBinder(WebDataBinder dataBinder) {
    // dataBinder.setRequiredFields(new String[] {"sequence", "cellWidth",
    // "cellHeight", "maxBundleWidth", "tangL", "tangR", "horizontalExtent",
    // "offsetY", "conservationThreshold",
    // "minAlphaPerThread", "maxAlphaTotal"});
    //
    // dataBinder.registerCustomEditor(String.class, new
    // StringTrimmerEditor(false));
    //
    // }
}