cirad.cgh.vcf2fasta.Vcf2fastaUI.java Source code

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Here is the source code for cirad.cgh.vcf2fasta.Vcf2fastaUI.java

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/*******************************************************************************
 * Copyright (C) 2016 <CIRAD>
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Affero General Public License, version 3 as
 * published by the Free Software Foundation.
 *
 * 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.
 *
 * See <http://www.gnu.org/licenses/gpl-3.0.html> for details about
 * GNU Affero General Public License V3.
 *
 * Contributors:
 *     Anestis Gkanogiannis <ganoyan@gmail.com>
 *******************************************************************************/
package cirad.cgh.vcf2fasta;

import java.io.File;
import java.lang.reflect.Method;
import java.util.ArrayList;
import java.util.List;
import java.util.UUID;

import javax.servlet.annotation.WebServlet;

import org.apache.commons.configuration.XMLConfiguration;
import org.apache.commons.configuration.tree.xpath.XPathExpressionEngine;
import org.apache.commons.io.Charsets;
import org.apache.commons.io.FileUtils;

import com.vaadin.annotations.Title;
import com.vaadin.annotations.VaadinServletConfiguration;
import com.vaadin.server.VaadinRequest;
import com.vaadin.server.VaadinServlet;

import cirad.cgh.vcf2fasta.beans.Vcf2fastaInputBean;
import cirad.cgh.vcf2fasta.listeners.SubmitClickListener;
import cirad.cgh.vcf2fasta.view.Vcf2fastaForm;

import com.vaadin.ui.Panel;
import com.vaadin.ui.UI;
import com.vaadin.ui.VerticalLayout;

//@Theme("tests-valo")
@Title("Vcf2fasta")
//@PreserveOnRefresh
public class Vcf2fastaUI extends UI {

    private XMLConfiguration config;

    private Vcf2fastaForm vcf2fastaForm;

    private Vcf2fastaRunner vcf2fastaRunner;

    @WebServlet(value = "/*", asyncSupported = true)
    @VaadinServletConfiguration(productionMode = false, ui = Vcf2fastaUI.class)
    public static class Vcf2fastaServlet extends VaadinServlet {
    }

    public XMLConfiguration getConfig() {
        return config;
    }

    private XMLConfiguration initConfig() {
        System.out.println("INIT");
        try {
            File base = this.getSession().getService().getBaseDirectory();
            File webinf = new File(base, "WEB-INF");
            File tmp = new File(base, "tmp");
            if (!tmp.exists())
                tmp.mkdirs();

            XMLConfiguration config = new XMLConfiguration(new File(webinf, "config.xml"));

            config.setProperty("base", base.getAbsolutePath());

            config.setExpressionEngine(new XPathExpressionEngine());

            return config;
        } catch (Exception e) {
            e.printStackTrace();
            return null;
        }
    }

    @Override
    protected void init(VaadinRequest request) {
        config = initConfig();

        Panel mainPanel = new Panel("Vcf2fasta");

        VerticalLayout layout = new VerticalLayout();
        layout.setMargin(true);
        mainPanel.setContent(layout);

        vcf2fastaForm = new Vcf2fastaForm(this, config);
        vcf2fastaForm.setFormSubmitHandler(getSubmitClickListener(this));

        layout.addComponent(vcf2fastaForm);

        setTheme("tests-valo-reindeer");
        //setTheme("tests-valo-facebook");
        //setTheme("tests-valo-metro");

        setContent(mainPanel);
    }

    @Override
    protected void refresh(VaadinRequest request) {
        System.out.println("refresh");
    }

    private SubmitClickListener<Vcf2fastaInputBean> getSubmitClickListener(final Vcf2fastaUI vcf2fastaUI) {
        return new SubmitClickListener<Vcf2fastaInputBean>() {

            @Override
            public void onSubmit(Vcf2fastaInputBean vcf2fastaInputBean) {
                System.out.println(vcf2fastaInputBean.getAnalysis());
                System.out.println(vcf2fastaInputBean.getAccession());
                System.out.println(vcf2fastaInputBean.getContig());
                System.out.println(vcf2fastaInputBean.getInterval());

                vcf2fastaForm.vcf2fastaStart();

                vcf2fastaRunner = new Vcf2fastaRunner(vcf2fastaUI, vcf2fastaInputBean);
                Thread t = new Thread(vcf2fastaRunner);
                t.start();
            }

        };
    }

    public void vcf2fastaStop() {
        if (vcf2fastaRunner != null)
            vcf2fastaRunner.vcf2fastaStop();
    }

    public void vcf2fastaEnd(String vcf2fastaResultURLcc, Vcf2fastaInputBean vcf2fastaInputBean) {
        //UUID uuid = UUID.randomUUID();
        try {
            String vcf2fastaResultTxt = Utils.getTextFromURL(vcf2fastaResultURLcc);
            if (vcf2fastaResultTxt != null) {
                //String vcf2fastaResultFileName = "tmp." + uuid + ".fasta";
                String vcf2fastaResultFileName = vcf2fastaInputBean.getAnalysis().replaceAll("\\s+", "_")
                        + vcf2fastaInputBean.getAccession() + "_" + vcf2fastaInputBean.getContig() + "_"
                        + vcf2fastaInputBean.getInterval() + ".fasta";
                File vcf2fastaResultFile = new File(new File(new File(config.getString("base")), "tmp"),
                        vcf2fastaResultFileName);
                vcf2fastaResultFile.deleteOnExit();
                FileUtils.writeStringToFile(vcf2fastaResultFile, vcf2fastaResultTxt, Charsets.UTF_8);
                String vcf2fastaResultURL = UI.getCurrent().getPage().getLocation().toString() + "tmp/"
                        + vcf2fastaResultFileName;

                List<String[]> links = new ArrayList<String[]>();
                links.add(new String[] { "Download result fasta file.", vcf2fastaResultURL });

                vcf2fastaForm.drawResult(links);
            }

            vcf2fastaForm.vcf2fastaEnd();
        } catch (Exception e) {
            e.printStackTrace();
            vcf2fastaForm.vcf2fastaEnd();
        }
    }

}