org.strasa.web.updatestudy.view.GenotypicData.java Source code

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Here is the source code for org.strasa.web.updatestudy.view.GenotypicData.java

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/*
 * Data Management and Analysis (DMAS) - International Rice Research Institute 2013-2015
 * 
 *   DMAS is an opensource Data management and statistical analysis mainly for STRASA Project: you can redistribute it and/or modify
 *   it under the terms of the GNU General Public License as published by
 *   the Free Software Foundation, either version 3 of the License, or
 *   (at your option) any later version.
 *
 *  DMAS 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 General Public License for more details.
 *
 *  You should have received a copy of the GNU General Public License
 *   along with DMAS.  If not, see <http://www.gnu.org/licenses/>.
 * 
 * 
 * 
 */
package org.strasa.web.updatestudy.view;

import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.util.Date;
import java.util.List;

import org.apache.commons.io.input.ReaderInputStream;
import org.strasa.middleware.filesystem.manager.UserFileManager;
import org.strasa.middleware.manager.StudyFileManagerImpl;
import org.strasa.middleware.model.StudyFile;
import org.strasa.web.common.api.Encryptions;
import org.strasa.web.common.api.ProcessTabViewModel;
import org.strasa.web.uploadstudy.view.pojos.GenotypeFileModel;
import org.strasa.web.utilities.FileUtilities;
import org.zkoss.bind.BindContext;
import org.zkoss.bind.annotation.BindingParam;
import org.zkoss.bind.annotation.Command;
import org.zkoss.bind.annotation.ContextParam;
import org.zkoss.bind.annotation.ContextType;
import org.zkoss.bind.annotation.ExecutionArgParam;
import org.zkoss.bind.annotation.Init;
import org.zkoss.bind.annotation.NotifyChange;
import org.zkoss.zk.ui.Component;
import org.zkoss.zk.ui.event.UploadEvent;
import org.zkoss.zul.Messagebox;

public class GenotypicData {
    private StudyFileManagerImpl studyFileMan;

    private String dataType = "gd"; // genotypic data
    Integer studyid;
    private List<StudyFile> genotypicFiles;

    public GenotypicData() {
        // TODO Auto-generated constructor stub
    }

    @Init
    public void init(@ExecutionArgParam("uploadModel") ProcessTabViewModel model) {
        studyFileMan = new StudyFileManagerImpl();
        this.studyid = model.studyID;
        System.out.println("StudyId" + Integer.toString(model.studyID));
        try {
            setGenotypicFiles(studyFileMan.getFileByStudyIdAndDataType(model.studyID, dataType));
        } catch (IndexOutOfBoundsException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    }

    @NotifyChange("*")
    @Command("uploadGenotypeData")
    public void uploadGenotypeData(@ContextParam(ContextType.BIND_CONTEXT) BindContext ctx,
            @ContextParam(ContextType.VIEW) Component view) {

        UploadEvent event = (UploadEvent) ctx.getTriggerEvent();

        // System.out.println(event.getMedia().getStringData());

        String name = event.getMedia().getName();
        if (!name.endsWith(".txt")) {
            Messagebox.show("Error: File must be a text-based  format", "Upload Error", Messagebox.OK,
                    Messagebox.ERROR);
            return;
        }

        try {
            String filename = name + Encryptions.encryptStringToNumber(name, new Date().getTime());
            File tempGenoFile = File.createTempFile(filename, ".tmp");
            InputStream in = event.getMedia().isBinary() ? event.getMedia().getStreamData()
                    : new ReaderInputStream(event.getMedia().getReaderData());
            FileUtilities.uploadFile(tempGenoFile.getAbsolutePath(), in);

            GenotypeFileModel newGenotypeFile = new GenotypeFileModel(name, tempGenoFile);
            UserFileManager fileMan = new UserFileManager();
            fileMan.createNewFileFromUpload(1, studyid, newGenotypeFile.getName(), newGenotypeFile.getFilepath(),
                    "gd");
            setGenotypicFiles(studyFileMan.getFileByStudyIdAndDataType(studyid, dataType));
        } catch (IOException e1) {
            // TODO Auto-generated catch block
            e1.printStackTrace();
        }

    }

    @NotifyChange("*")
    @Command
    public void removeGenotypeFile(@BindingParam("model") StudyFile model) {

        new StudyFileManagerImpl().deleteRecord(model);
        setGenotypicFiles(studyFileMan.getFileByStudyIdAndDataType(studyid, dataType));
    }

    public List<StudyFile> getGenotypicFiles() {
        return genotypicFiles;
    }

    public void setGenotypicFiles(List<StudyFile> genotypicFiles) {
        this.genotypicFiles = genotypicFiles;
    }

    public String getDataType() {
        return dataType;
    }

    public void setDataType(String dataType) {
        this.dataType = dataType;
    }
}