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.bioupload; 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.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.bioupload.form.WizardForm; /** * The first step of this wizard. */ public class BioUploadStep1 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 FileUploadField fileUploadField; private DropDownChoice<DelimiterType> delimiterTypeDdc; private DropDownChoice<UploadType> uploadTypeDdc; private WizardForm wizardForm; public BioUploadStep1(String id) { super(id); initialiseDetailForm(); } public BioUploadStep1(String id, Form<UploadVO> containerForm, WizardForm wizardForm) { super(id, "Step 1/5: Select data file to upload", "Select the file containing data, the file type and the specified delimiter, click Next to continue."); this.containerForm = containerForm; this.setWizardForm(wizardForm); initialiseDetailForm(); } @SuppressWarnings({ "unchecked" }) private void initialiseDropDownChoices() { java.util.Collection<DelimiterType> delimiterTypeCollection = iArkCommonService.getDelimiterTypes(); ChoiceRenderer delimiterTypeRenderer = new ChoiceRenderer( au.org.theark.lims.web.Constants.DELIMITER_TYPE_NAME, au.org.theark.lims.web.Constants.DELIMITER_TYPE_ID); delimiterTypeDdc = new DropDownChoice<DelimiterType>( au.org.theark.lims.web.Constants.UPLOADVO_UPLOAD_DELIMITER_TYPE, (List) delimiterTypeCollection, delimiterTypeRenderer); containerForm.getModelObject().getUpload() .setDelimiterType(iArkCommonService.getDelimiterType(new Long(1))); java.util.Collection<UploadType> uploadTypeCollection = iArkCommonService.getUploadTypesForLims(); ChoiceRenderer uploadTypeRenderer = new ChoiceRenderer(au.org.theark.lims.web.Constants.UPLOAD_TYPE_NAME, au.org.theark.lims.web.Constants.UPLOAD_TYPE_ID); uploadTypeDdc = new DropDownChoice<UploadType>(au.org.theark.lims.web.Constants.UPLOADVO_UPLOAD_UPLOAD_TYPE, (List) uploadTypeCollection, uploadTypeRenderer); //containerForm.getModelObject().getUpload().setUploadType(iArkCommonService.getDefaultUploadType()); } public void initialiseDetailForm() { fileUploadField = new FileUploadField(au.org.theark.lims.web.Constants.UPLOADVO_UPLOAD_FILENAME); initialiseDropDownChoices(); attachValidators(); addComponents(); } protected void attachValidators() { 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"))); uploadTypeDdc.setRequired(true) .setLabel(new StringResourceModel("error.uploadType.required", this, new Model<String>("Upload"))); } private void addComponents() { 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) { Long studyId = (Long) SecurityUtils.getSubject().getSession() .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID); Study study = iArkCommonService.getStudy(studyId); FileUpload fileUpload = fileUploadField.getFileUpload(); containerForm.getModelObject().setFileUpload(fileUpload); Payload payload = iArkCommonService.createPayload(fileUpload.getBytes()); containerForm.getModelObject().getUpload().setPayload(payload); 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); byte[] byteArray = fileUpload.getMD5(); String checksum = getHex(byteArray); containerForm.getModelObject().getUpload().setStudy(study); containerForm.getModelObject().getUpload().setFileFormat(fileFormat); containerForm.getModelObject().getUpload().setChecksum(checksum); containerForm.getModelObject().getUpload().setFilename(filename); containerForm.getModelObject().getUpload().setStartTime(new Date(System.currentTimeMillis())); if (containerForm.getModelObject().getUpload().getUploadType() != null) { if (containerForm.getModelObject().getUpload().getUploadType().getName() .equalsIgnoreCase("Biospecimen Custom Data")) { containerForm.getModelObject().getUpload().setArkFunction( iArkCommonService.getArkFunctionByName(Constants.FUNCTION_KEY_VALUE_BIOSPECIMEN)); } else if (containerForm.getModelObject().getUpload().getUploadType().getName() .equalsIgnoreCase("Biocollection Custom Data")) { //containerForm.getModelObject().getUpload().setArkFunction(iArkCommonService.getArkFunctionByName(Constants.FUNCTION_KEY_VALUE_LIMS_COLLECTION)); containerForm.getModelObject().getUpload().setArkFunction( iArkCommonService.getArkFunctionByName(Constants.FUNCTION_KEY_VALUE_LIMS_CUSTOM_FIELD)); } else { log.error("\n\n\n\n\n\n\n\n\n\n\n uploadType unrecognized"); } //containerForm.getModelObject().getUpload().setArkFunction(iArkCommonService.getArkFunctionByName(Constants.FUNCTION_KEY_VALUE_SUBJECT_UPLOAD)); log.info("\n\n\n\n\n\n\n\n\n\n\n\n upload type = " + containerForm.getModelObject().getUpload().getUploadType().getName()); } else { log.error("\n\n\n\n\n\n\n\n\n\n\n uploadType is null"); } wizardForm.setFileName(filename); 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); } } }