List of usage examples for org.apache.wicket.markup.html.form.upload FileUpload getMD5
public byte[] getMD5()
From source file:au.org.theark.core.web.component.customfieldupload.CustomFieldUploadStep1.java
License:Open Source License
private void saveFileInMemory() { // Set study in context Long studyId = (Long) SecurityUtils.getSubject().getSession() .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID); Study study = iArkCommonService.getStudy(studyId); // Retrieve file and store as Blob in database // TODO: AJAX-ified and asynchronous and hit database FileUpload fileUpload = fileUploadField.getFileUpload(); containerForm.getModelObject().setFileUpload(fileUpload); InputStream inputStream = null; BufferedOutputStream outputStream = null; File temp = null;//from w w w . j a v a 2 s. co m try { // Copy all the contents of the file upload to a temp file (to read multiple times)... inputStream = containerForm.getModelObject().getFileUpload().getInputStream(); // Create temp file temp = File.createTempFile("customFieldUploadBlob", ".tmp"); containerForm.getModelObject().setTempFile(temp); // Delete temp file when program exits (just in case manual delete fails later) temp.deleteOnExit(); // Write to temp file outputStream = new BufferedOutputStream(new FileOutputStream(temp)); IOUtils.copy(inputStream, outputStream); } catch (IOException ioe) { log.error("IOException " + ioe.getMessage()); // Something failed, so there is temp file is not valid (step 2 should check for null) temp.delete(); temp = null; containerForm.getModelObject().setTempFile(temp); } finally { if (inputStream != null) { try { inputStream.close(); } catch (IOException e) { log.error("Unable to close inputStream: " + e.getMessage()); } } if (outputStream != null) { try { outputStream.flush(); outputStream.close(); } catch (IOException e) { log.error("Unable to close outputStream: " + e.getMessage()); } } } // Set details of Upload object containerForm.getModelObject().getUpload().setStudy(study); String filename = containerForm.getModelObject().getFileUpload().getClientFileName(); String fileFormatName = filename.substring(filename.lastIndexOf('.') + 1).toUpperCase(); FileFormat fileFormat = new 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()); wizardForm.setFileName(fileUpload.getClientFileName()); }
From source file:au.org.theark.lims.web.component.biospecimenupload.BiospecimenUploadStep1.java
License:Open Source License
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 {//from w ww.j a va 2s . c o m iArkCommonService.createUpload(containerForm.getModelObject().getUpload()); } catch (Exception e) { error("There is a problem during the upload process."); getWizardForm().onError(target, null); } }
From source file:au.org.theark.lims.web.component.biospecimenupload.form.DetailForm.java
License:Open Source License
@Override protected void onSave(Form<UploadVO> containerForm, AjaxRequestTarget target) { // Implement Save/Update if (containerForm.getModelObject().getUpload().getId() == null) { setMultiPart(true); // multipart required for file uploads // Set study in context Long studyId = (Long) SecurityUtils.getSubject().getSession() .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID); Study study = iArkCommonService.getStudy(studyId); // TODO: AJAX-ified and asynchronous and hit database FileUpload fileUpload = fileUploadField.getFileUpload(); Payload payload = iArkCommonService.createPayload(fileUpload.getBytes()); containerForm.getModelObject().getUpload().setPayload(payload); // Set details of Upload object containerForm.getModelObject().getUpload().setStudy(study); byte[] byteArray = fileUpload.getMD5(); String checksum = getHex(byteArray); containerForm.getModelObject().getUpload().setChecksum(checksum); containerForm.getModelObject().getUpload().setFilename(fileUpload.getClientFileName()); // Save//from www . j a v a 2s .c om containerForm.getModelObject().getUpload().setArkFunction(arkFunction); containerForm.getModelObject().getUpload() .setUploadStatus(iArkCommonService.getUploadStatusFor(Constants.UPLOAD_STATUS_COMPLETED)); try { iArkCommonService.createUpload(containerForm.getModelObject().getUpload()); } catch (Exception e) { error("There is a problem during the upload process."); processErrors(target); } this.info("Subject upload " + containerForm.getModelObject().getUpload().getFilename() + " was created successfully"); processErrors(target); } else { // Update containerForm.getModelObject().getUpload().setArkFunction(arkFunction); iArkCommonService.updateUpload(containerForm.getModelObject().getUpload()); this.info("Subject upload " + containerForm.getModelObject().getUpload().getFilename() + " was updated successfully"); processErrors(target); } onSavePostProcess(target); /* * TODO:(CE) To handle Business and System Exceptions here */ }
From source file:au.org.theark.lims.web.component.bioupload.BioUploadStep1.java
License:Open Source License
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 {/*from www. j a v a 2s .c om*/ 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 is a problem during the upload process."); getWizardForm().onError(target, null); } }
From source file:au.org.theark.phenotypic.web.component.phenodataupload.PhenoDataUploadStep1.java
License:Open Source License
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())); containerForm.getModelObject().getUpload().setArkFunction( iArkCommonService.getArkFunctionByName(Constants.FUNCTION_KEY_VALUE_FIELD_DATA_UPLOAD)); wizardForm.setFileName(filename);//from ww w . j av a 2 s . co m containerForm.getModelObject().getUpload() .setUploadStatus(iArkCommonService.getUploadStatusFor(Constants.UPLOAD_STATUS_COMPLETED)); //TODO analyse how many times this is saved and where it should be saved try { iArkCommonService.createUpload(containerForm.getModelObject().getUpload()); containerForm.getModelObject().setPreviousStepOutCompleted(true); } catch (Exception e) { // TODO Auto-generated catch block error("There is a problem during the upload process."); getWizardForm().onError(target, null); } }
From source file:au.org.theark.study.web.component.attachments.form.DetailForm.java
License:Open Source License
@Override protected void onSave(Form<SubjectVO> containerForm, AjaxRequestTarget target) { LinkSubjectStudy linkSubjectStudy = null; Long studyId = (Long) SecurityUtils.getSubject().getSession() .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID); Study study = iArkCommonService.getStudy(studyId); Long sessionPersonId = (Long) SecurityUtils.getSubject().getSession() .getAttribute(au.org.theark.core.Constants.PERSON_CONTEXT_ID); String userId = SecurityUtils.getSubject().getPrincipal().toString(); try {// w ww. ja v a 2s . c om linkSubjectStudy = iArkCommonService.getSubject(sessionPersonId, study); containerForm.getModelObject().getSubjectFile().setLinkSubjectStudy(linkSubjectStudy); // Implement Save/Update if (containerForm.getModelObject().getSubjectFile().getId() == null) { // required for file uploads setMultiPart(true); // Retrieve file and store as Blob in database // TODO: AJAX-ified and asynchronous and hit database FileUpload fileSubjectFile = fileSubjectFileField.getFileUpload(); try { containerForm.getModelObject().getSubjectFile() .setPayload(IOUtils.toByteArray(fileSubjectFile.getInputStream())); } catch (IOException e) { log.error("IOException trying to convert inputstream" + e); } byte[] byteArray = fileSubjectFile.getMD5(); String checksum = getHex(byteArray); // Set details of ConsentFile object containerForm.getModelObject().getSubjectFile().setChecksum(checksum); containerForm.getModelObject().getSubjectFile().setFilename(fileSubjectFile.getClientFileName()); containerForm.getModelObject().getSubjectFile().setUserId(userId); // Save iStudyService.create(containerForm.getModelObject().getSubjectFile()); this.info("Attachment " + containerForm.getModelObject().getSubjectFile().getFilename() + " was created successfully"); // processErrors(target); } else { FileUpload fileSubjectFile = fileSubjectFileField.getFileUpload(); try { containerForm.getModelObject().getSubjectFile() .setPayload(IOUtils.toByteArray(fileSubjectFile.getInputStream())); } catch (IOException e) { log.error("IOException trying to convert inputstream" + e); } byte[] byteArray = fileSubjectFile.getMD5(); String checksum = getHex(byteArray); // Set details of ConsentFile object //containerForm.getModelObject().getSubjectFile().setChecksum(checksum); containerForm.getModelObject().getSubjectFile().setFilename(fileSubjectFile.getClientFileName()); containerForm.getModelObject().getSubjectFile().setUserId(userId); // Update iStudyService.update(containerForm.getModelObject().getSubjectFile(), checksum); this.info("Attachment " + containerForm.getModelObject().getSubjectFile().getFilename() + " was updated successfully"); } processErrors(target); onSavePostProcess(target); AjaxButton deleteButton = (AjaxButton) arkCrudContainerVO.getEditButtonContainer().get("delete"); deleteButton.setEnabled(false); } catch (EntityNotFoundException e) { this.error("The record you tried to update is no longer available in the system"); } catch (ArkSystemException e) { this.error("Saving the file attachment failed. Please contact The Ark administrator."); } processErrors(target); }
From source file:au.org.theark.study.web.component.consent.form.DetailForm.java
License:Open Source License
private void createConsentFile() throws ArkSystemException { FileUpload fileSubjectFile = fileUploadField.getFileUpload(); if (fileSubjectFile != null) { LinkSubjectStudy linkSubjectStudy = null; Long studyId = (Long) SecurityUtils.getSubject().getSession() .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID); Study study = iArkCommonService.getStudy(studyId); Long sessionPersonId = (Long) SecurityUtils.getSubject().getSession() .getAttribute(au.org.theark.core.Constants.PERSON_CONTEXT_ID); try {/* ww w. ja v a 2 s . c o m*/ linkSubjectStudy = iArkCommonService.getSubject(sessionPersonId, study); containerForm.getModelObject().getSubjectFile().setLinkSubjectStudy(linkSubjectStudy); containerForm.getModelObject().getSubjectFile() .setPayload(IOUtils.toByteArray(fileSubjectFile.getInputStream())); byte[] byteArray = fileSubjectFile.getMD5(); String checksum = getHex(byteArray); // Set details of Consent File object containerForm.getModelObject().getSubjectFile() .setStudyComp(containerForm.getModelObject().getConsent().getStudyComp()); containerForm.getModelObject().getSubjectFile() .setComments(containerForm.getModelObject().getConsent().getComments()); containerForm.getModelObject().getSubjectFile().setChecksum(checksum); containerForm.getModelObject().getSubjectFile().setFilename(fileSubjectFile.getClientFileName()); containerForm.getModelObject().getSubjectFile() .setUserId(SecurityUtils.getSubject().getPrincipals().getPrimaryPrincipal().toString()); // Save iStudyService.create(containerForm.getModelObject().getSubjectFile()); this.info("Consent file: " + containerForm.getModelObject().getSubjectFile().getFilename() + " was created successfully"); } catch (IOException ioe) { log.error("Failed to save the uploaded file: " + ioe); } catch (EntityNotFoundException e) { log.error(e.getMessage()); } } }
From source file:au.org.theark.study.web.component.correspondence.form.DetailForm.java
License:Open Source License
@Override protected void onSave(Form<CorrespondenceVO> containerForm, AjaxRequestTarget target) { CorrespondenceVO correspondenceVO = containerForm.getModelObject(); if (correspondenceVO.getCorrespondence().getId() == null) { if ((correspondenceVO.getWorkRequest() == null && correspondenceVO.getBillableItemType() != null)) { this.error("Work request must be set if a billable item type is specified"); processErrors(target);//from w ww. ja v a 2 s . c om return; } if (correspondenceVO.getWorkRequest() != null && correspondenceVO.getBillableItemType() == null) { this.error("Billable item type must be set if a work request is specified"); processErrors(target); return; } } if (containerForm.getModelObject().getWorkRequest() != null && containerForm.getModelObject().getBillableItemType() != null) { BillableItem billableItem = createAutomatedBillableItem(); containerForm.getModelObject().getCorrespondence().setBillableItem(billableItem); } Long personSessionId = (Long) SecurityUtils.getSubject().getSession() .getAttribute(au.org.theark.core.Constants.PERSON_CONTEXT_ID); // get the person and set it on the correspondence object try { // set the Person in context //Person person = studyService.getPerson(personSessionId); // set the Study in context Long studyId = (Long) SecurityUtils.getSubject().getSession() .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID); Study study = iArkCommonService.getStudy(studyId); LinkSubjectStudy lss = studyService.getSubjectLinkedToStudy(personSessionId, study); containerForm.getModelObject().getCorrespondence().setLss(lss); //containerForm.getModelObject().getCorrespondence().setStudy(study); if (containerForm.getModelObject().getCorrespondence().getId() == null) { // store correspondence file attachment if (fileUploadField != null && fileUploadField.getFileUpload() != null) { FileUpload fileUpload = fileUploadField.getFileUpload(); byte[] byteArray = fileUpload.getMD5(); String checksum = getHex(byteArray); containerForm.getModelObject().getCorrespondence().setAttachmentPayload(fileUpload.getBytes()); containerForm.getModelObject().getCorrespondence() .setAttachmentFilename(fileUpload.getClientFileName()); containerForm.getModelObject().getCorrespondence().setAttachmentChecksum(checksum); } // save studyService.create(containerForm.getModelObject().getCorrespondence()); this.info("Correspondence was successfully added and linked to subject: " + lss.getSubjectUID()); processErrors(target); } else { // store correspondence file attachment String checksum = null; if (fileUploadField != null && fileUploadField.getFileUpload() != null) { // retrieve file and store as Blob in database FileUpload fileUpload = fileUploadField.getFileUpload(); byte[] byteArray = fileUpload.getMD5(); checksum = getHex(byteArray); containerForm.getModelObject().getCorrespondence().setAttachmentPayload(fileUpload.getBytes()); containerForm.getModelObject().getCorrespondence() .setAttachmentFilename(fileUpload.getClientFileName()); // containerForm.getModelObject().getCorrespondence().setAttachementChecksum(checksum); } studyService.update(containerForm.getModelObject().getCorrespondence(), checksum); this.info("Correspondence was successfully updated and linked to subject: " + lss.getSubjectUID()); processErrors(target); } // invoke backend to persist the correspondence workTrackingContainer.setVisible(false); onSavePostProcess(target); } catch (EntityNotFoundException ex) { ex.printStackTrace(); } catch (ArkSystemException ex) { ex.printStackTrace(); } }
From source file:au.org.theark.study.web.component.subjectUpload.SubjectUploadStep1.java
License:Open Source License
private void saveFileInMemory() { 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().set; containerForm.getModelObject().getUpload().setFileFormat(fileFormat); containerForm.getModelObject().getUpload().setChecksum(checksum); containerForm.getModelObject().getUpload().setFilename(filename); containerForm.getModelObject().getUpload().setStartTime(new Date(System.currentTimeMillis())); containerForm.getModelObject().getUpload().setArkFunction( iArkCommonService.getArkFunctionByName(Constants.FUNCTION_KEY_VALUE_STUDY_STUDY_DATA_UPLOAD)); wizardForm.setFileName(filename);/* w ww . j a va 2 s . c o m*/ containerForm.getModelObject().getUpload() .setUploadStatus(iArkCommonService.getUploadStatusFor(Constants.UPLOAD_STATUS_AWAITING_VALIDATION)); //Move to step 2 to add the file type validation // iArkCommonService.createUpload(containerForm.getModelObject().getUpload()); }
From source file:de.inren.frontend.storehouse.ActionPanel.java
License:Apache License
private void addUpload() { // Add one file input field FileUploadField fileUploadField = new FileUploadField("fileInput"); final Form progressUploadForm = new Form("restore") { @Override// ww w . ja v a 2 s . co m protected void onSubmit() { final List<FileUpload> uploads = fileUploadField.getFileUploads(); if (uploads != null) { for (FileUpload upload : uploads) { try { String digest = storehouseService.doImport(upload.getInputStream(), upload.getMD5()); Picture picture = new Picture(); picture.setDigest(digest); picture.setFilename(upload.getClientFileName()); picture = pictureService.savePicture(picture); Folder srcFolder = ActionPanel.this.getModel().getObject(); folderService.insertIntoFolder(srcFolder, picture); PageParameters parameters = new PageParameters(); parameters.add("id", srcFolder.getId()); throw new RestartResponseException(FileManagerPage.class, parameters); } catch (Exception e) { throw new IllegalStateException("Unable to restore data.", e); } } } }; }; // set this form to multipart mode (allways needed for uploads!) progressUploadForm.setMultiPart(true); progressUploadForm.add(fileUploadField); progressUploadForm.add(new UploadProgressBar("progress", progressUploadForm, fileUploadField)); add(progressUploadForm); }