Java tutorial
/******************************************************************************* * 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.biospecimenupload; import java.util.ArrayList; import java.util.Date; import java.util.List; import org.apache.shiro.SecurityUtils; import org.apache.wicket.ajax.AjaxRequestTarget; import org.apache.wicket.markup.html.form.ChoiceRenderer; import org.apache.wicket.markup.html.form.DropDownChoice; import org.apache.wicket.markup.html.form.Form; import org.apache.wicket.markup.html.form.upload.FileUpload; import org.apache.wicket.markup.html.form.upload.FileUploadField; import org.apache.wicket.model.Model; import org.apache.wicket.model.PropertyModel; import org.apache.wicket.model.StringResourceModel; import org.apache.wicket.spring.injection.annot.SpringBean; import au.org.theark.core.Constants; import au.org.theark.core.model.study.entity.DelimiterType; import au.org.theark.core.model.study.entity.Payload; import au.org.theark.core.model.study.entity.Study; import au.org.theark.core.model.study.entity.UploadType; 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.web.component.biospecimenupload.form.WizardForm; /** * The first step of this wizard. */ public class BiospecimenUploadStep1 extends AbstractWizardStepPanel { private static final long serialVersionUID = -3267334731280446472L; public java.util.Collection<String> validationMessages = null; @SpringBean(name = au.org.theark.core.Constants.ARK_COMMON_SERVICE) private IArkCommonService<Void> iArkCommonService; private Form<UploadVO> containerForm; private DropDownChoice<Study> studyDdc; private FileUploadField fileUploadField; // private UploadProgressBar uploadProgressBar; private DropDownChoice<DelimiterType> delimiterTypeDdc; private WizardForm wizardForm; private DropDownChoice<UploadType> uploadTypeDdc; public BiospecimenUploadStep1(String id) { super(id); initialiseDetailForm(); } public BiospecimenUploadStep1(String id, Form<UploadVO> containerForm, WizardForm wizardForm) { super(id, "Step 1/5: Select data file to upload", "Select the file containing data, the Study and the specified delimiter, click Next to continue."); this.containerForm = containerForm; this.setWizardForm(wizardForm); initialiseDetailForm(); } private void initialiseDropDownChoices() { // Initialise Drop Down Choices java.util.Collection<DelimiterType> delimiterTypeCollection = iArkCommonService.getDelimiterTypes(); ChoiceRenderer<DelimiterType> choiceRenderer = new ChoiceRenderer<DelimiterType>(Constants.NAME, Constants.ID); delimiterTypeDdc = new DropDownChoice<DelimiterType>(Constants.UPLOADVO_UPLOAD_DELIMITER_TYPE, (List<DelimiterType>) delimiterTypeCollection, choiceRenderer); // Set to default delimiterType containerForm.getModelObject().getUpload() .setDelimiterType(iArkCommonService.getDelimiterType(new Long(1)));//TODO: This looks hardcoded...please check different types java.util.Collection<UploadType> uploadTypeCollection = iArkCommonService.getUploadTypesForLims(); ChoiceRenderer uploadTypeRenderer = new ChoiceRenderer(Constants.UPLOAD_TYPE_NAME, Constants.UPLOAD_TYPE_ID); uploadTypeDdc = new DropDownChoice<UploadType>(Constants.UPLOADVO_UPLOAD_UPLOAD_TYPE, (List) uploadTypeCollection, uploadTypeRenderer); List<Study> studyListForUser = new ArrayList<Study>(0); Long sessionStudyId = (Long) SecurityUtils.getSubject().getSession() .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID); Study study = null; if (sessionStudyId != null) { study = iArkCommonService.getStudy(sessionStudyId); studyListForUser.add(study); } ChoiceRenderer<Study> studyRenderer = new ChoiceRenderer<Study>(Constants.NAME, Constants.ID); PropertyModel<Study> pModel = new PropertyModel<Study>(containerForm.getModelObject(), "upload.study"); studyDdc = new DropDownChoice<Study>(Constants.UPLOADVO_UPLOAD_STUDY, pModel, (List<Study>) studyListForUser, studyRenderer); containerForm.getModelObject().getUpload().setUploadType(iArkCommonService.getDefaultUploadType()); } public void initialiseDetailForm() { // Set up field on form here // progress bar for upload // uploadProgressBar = new UploadProgressBar("progress", // ajaxSimpleUploadForm); // fileUpload for payload fileUploadField = new FileUploadField(Constants.UPLOADVO_UPLOAD_FILENAME); // Initialise Drop Down Choices initialiseDropDownChoices(); attachValidators(); addComponents(); } protected void attachValidators() { // Field validation here studyDdc.setRequired(true) .setLabel(new StringResourceModel("error.study.required", this, new Model<String>("Study"))); fileUploadField.setRequired(true) .setLabel(new StringResourceModel("error.filename.required", this, new Model<String>("Filename"))); delimiterTypeDdc.setRequired(true).setLabel( new StringResourceModel("error.delimiterType.required", this, new Model<String>("Delimiter"))); } private void addComponents() { // Add components here add(studyDdc); add(fileUploadField); add(delimiterTypeDdc); add(uploadTypeDdc); } @Override public void handleWizardState(AbstractWizardForm<?> form, AjaxRequestTarget target) { } @Override public void onStepOutNext(AbstractWizardForm<?> form, AjaxRequestTarget target) { saveFileInMemory(target); } public void setWizardForm(WizardForm wizardForm) { this.wizardForm = wizardForm; } public WizardForm getWizardForm() { return wizardForm; } private void saveFileInMemory(AjaxRequestTarget target) { // Retrieve file and store as Blob in database // TODO: AJAX-ified and asynchronous and hit database FileUpload fileUpload = fileUploadField.getFileUpload(); containerForm.getModelObject().setFileUpload(fileUpload); Payload payload = iArkCommonService.createPayload(fileUpload.getBytes()); containerForm.getModelObject().getUpload().setPayload(payload); // Set details of Upload object containerForm.getModelObject().getUpload().setStudy(studyDdc.getModelObject()); String filename = containerForm.getModelObject().getFileUpload().getClientFileName(); String fileFormatName = filename.substring(filename.lastIndexOf('.') + 1).toUpperCase(); au.org.theark.core.model.study.entity.FileFormat fileFormat = new au.org.theark.core.model.study.entity.FileFormat(); fileFormat = iArkCommonService.getFileFormatByName(fileFormatName); containerForm.getModelObject().getUpload().setFileFormat(fileFormat); byte[] byteArray = fileUpload.getMD5(); String checksum = getHex(byteArray); containerForm.getModelObject().getUpload().setChecksum(checksum); containerForm.getModelObject().getUpload().setFilename(fileUpload.getClientFileName()); containerForm.getModelObject().getUpload().setStartTime(new Date(System.currentTimeMillis())); containerForm.getModelObject().setUploadType( uploadTypeDdc.getModelObject() == null ? "Unknown" : uploadTypeDdc.getModelObject().getName()); containerForm.getModelObject().getUpload().setArkFunction( iArkCommonService.getArkFunctionByName(Constants.FUNCTION_KEY_VALUE_BIOSPECIMEN_UPLOAD)); wizardForm.setFileName(fileUpload.getClientFileName()); containerForm.getModelObject().getUpload() .setUploadStatus(iArkCommonService.getUploadStatusFor(Constants.UPLOAD_STATUS_AWAITING_VALIDATION)); try { iArkCommonService.createUpload(containerForm.getModelObject().getUpload()); } catch (Exception e) { error("There was a problem during the upload process."); getWizardForm().onError(target, null); } } }