au.org.theark.lims.web.component.bioupload.BioUploadStep4.java Source code

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Here is the source code for au.org.theark.lims.web.component.bioupload.BioUploadStep4.java

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/*******************************************************************************
 * Copyright (c) 2011  University of Western Australia. All rights reserved.
 * 
 * This file is part of The Ark.
 * 
 * The Ark is free software; 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.
 * 
 * The Ark 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 this program.  If not, see <http://www.gnu.org/licenses/>.
 ******************************************************************************/
package au.org.theark.lims.web.component.bioupload;

import java.io.InputStream;
import java.util.List;

import org.apache.shiro.SecurityUtils;
import org.apache.shiro.subject.Subject;
import org.apache.wicket.ajax.AjaxRequestTarget;
import org.apache.wicket.markup.html.form.Form;
import org.apache.wicket.spring.injection.annot.SpringBean;

import au.org.theark.core.service.IArkCommonService;
import au.org.theark.core.vo.UploadVO;
import au.org.theark.core.web.form.AbstractWizardForm;
import au.org.theark.core.web.form.AbstractWizardStepPanel;
import au.org.theark.lims.job.BioSpecimenCustomDataUploadExecutor;
import au.org.theark.lims.job.StudyDataUploadExecutor;
import au.org.theark.lims.service.ILimsService;
import au.org.theark.lims.util.SubjectUploadReport;
import au.org.theark.lims.web.component.bioupload.form.WizardForm;

public class BioUploadStep4 extends AbstractWizardStepPanel {
    private static final long serialVersionUID = 2971945948091031160L;
    private Form<UploadVO> containerForm;
    private WizardForm wizardForm;

    @SpringBean(name = au.org.theark.core.Constants.ARK_COMMON_SERVICE)
    private IArkCommonService iArkCommonService;

    @SpringBean(name = au.org.theark.core.Constants.STUDY_SERVICE)
    private ILimsService iLimsService;

    public BioUploadStep4(String id, Form<UploadVO> containerForm, WizardForm wizardForm) {
        super(id, "Step 4/5: Confirm Upload",
                "Data will now be written to the database, click Next to continue, otherwise click Cancel.");
        this.containerForm = containerForm;
        this.wizardForm = wizardForm;
        initialiseDetailForm();
    }

    private void initialiseDetailForm() {
    }

    @Override
    public void handleWizardState(AbstractWizardForm<?> form, AjaxRequestTarget target) {
    }

    @Override
    public void onStepInNext(AbstractWizardForm<?> form, AjaxRequestTarget target) {
        form.getNextButton().setEnabled(true);
        target.add(form.getNextButton());

        form.getArkExcelWorkSheetAsGrid().setVisible(false);
        target.add(form.getArkExcelWorkSheetAsGrid());
    }

    @Override
    public void onStepOutNext(AbstractWizardForm<?> form, AjaxRequestTarget target) {
        form.getNextButton().setEnabled(false);
        target.add(form.getNextButton());
        // Filename seems to be lost from model when moving between steps in wizard?  is this a symptom of something greater?
        containerForm.getModelObject().getUpload().setFilename(wizardForm.getFileName());

        String fileFormat = containerForm.getModelObject().getUpload().getFileFormat().getName();
        char delimiterChar = containerForm.getModelObject().getUpload().getDelimiterType().getDelimiterCharacter();
        try {
            List<String> uidsToUpload = containerForm.getModelObject().getUidsToUpload();
            //log.info("________________________________________________________" + "about to try passing list of uids is of size " + uidsToUpload.size() );
            InputStream inputStream = containerForm.getModelObject().getFileUpload().getInputStream();
            long size = containerForm.getModelObject().getFileUpload().getSize();
            Long uploadId = containerForm.getModelObject().getUpload().getId();
            String report = generateInitialUploadReport();

            Subject currentUser = SecurityUtils.getSubject();
            Long studyId = (Long) currentUser.getSession()
                    .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);

            if (containerForm.getModelObject().getUpload().getUploadType().getName()
                    .equalsIgnoreCase("Subject Demographic Data")) {
                StudyDataUploadExecutor task = new StudyDataUploadExecutor(iArkCommonService, iLimsService,
                        inputStream, uploadId, //null user
                        studyId, fileFormat, delimiterChar, size, report, uidsToUpload);
                task.run();
            } else if (containerForm.getModelObject().getUpload().getUploadType().getName()
                    .equalsIgnoreCase("Study-specific (custom) Data")) {
                BioSpecimenCustomDataUploadExecutor task = new BioSpecimenCustomDataUploadExecutor(
                        iArkCommonService, iLimsService, inputStream, uploadId, //null user
                        studyId, fileFormat, delimiterChar, size, report, uidsToUpload);
                task.run();
            }

        } catch (Exception e1) {
            // TODO Auto-generated catch block
            e1.printStackTrace();
        }
    }

    public String generateInitialUploadReport() {
        SubjectUploadReport subjectUploadReport = new SubjectUploadReport();
        subjectUploadReport.appendDetails(containerForm.getModelObject().getUpload());
        return subjectUploadReport.getReport().toString();
    }

}