@Override
protected void onSearch(AjaxRequestTarget target) {
target.add(feedbackPanel);
// Set study in context
Long studyId =
(Long)
SecurityUtils.getSubject()
.getSession()
.getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
// Get a list of all Fields for the Study in context
Study study = iArkCommonService.getStudy(studyId);
Upload searchUpload = getModelObject().getUpload();
searchUpload.setStudy(study);
searchUpload.setArkFunction(
iArkCommonService.getArkFunctionByName(Constants.FUNCTION_KEY_VALUE_DATA_DICTIONARY));
Collection<Upload> uploadCollection = iArkCommonService.searchUploads(searchUpload);
if (uploadCollection != null && uploadCollection.size() == 0) {
this.info("Uploads with the specified criteria does not exist in the system.");
target.add(feedbackPanel);
}
getModelObject().setUploadCollection(uploadCollection);
listView.removeAll();
arkCrudContainerVO.getSearchResultPanelContainer().setVisible(true);
target.add(arkCrudContainerVO.getSearchResultPanelContainer());
}
public AffectionContainerPanel(String id, WebMarkupContainer arkContextMarkup) {
super(id);
this.arkContextMarkup = arkContextMarkup;
cpModel = new CompoundPropertyModel<AffectionVO>(new AffectionVO());
sessionStudyID =
(Long) SecurityUtils.getSubject().getSession().getAttribute(Constants.STUDY_CONTEXT_ID);
if (sessionStudyID != null) {
study = iArkCommonService.getStudy(sessionStudyID);
}
Long subjectSessionID =
(Long) SecurityUtils.getSubject().getSession().getAttribute(Constants.PERSON_CONTEXT_ID);
try {
linkSubjectStudy = iArkCommonService.getSubject(subjectSessionID, study);
} catch (EntityNotFoundException e) {
e.printStackTrace();
}
containerForm = new ContainerForm("containerForm", cpModel);
containerForm.add(initialiseFeedBackPanel());
containerForm.add(initialiseDetailPanel());
containerForm.add(initialiseSearchResults());
containerForm.add(initialiseSearchPanel());
add(containerForm);
}
/*
* (non-Javadoc)
*
* @see au.org.theark.core.web.form.AbstractDetailForm#onSave(org.apache.wicket.markup.html.form.Form, org.apache.wicket.ajax.AjaxRequestTarget)
*/
@Override
protected void onSave(Form<CustomFieldGroupVO> containerForm, AjaxRequestTarget target) {
if (getModelObject().getCustomFieldGroup().getId() == null) {
// Create
ArkFunction arkFunction =
iArkCommonService.getArkFunctionByName(
au.org.theark.core.Constants.FUNCTION_KEY_VALUE_PHENO_COLLECTION);
Long studyId =
(Long)
SecurityUtils.getSubject()
.getSession()
.getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
Study study = iArkCommonService.getStudy(studyId);
getModelObject().getCustomFieldGroup().setArkFunction(arkFunction);
getModelObject().getCustomFieldGroup().setStudy(study);
try {
iPhenotypicService.createCustomFieldGroup(getModelObject());
initCustomFieldDataListPanel();
this.info("Data Set has been created successfully.");
} catch (EntityExistsException e) {
this.error("A Data Set with the same name already exisits. Please choose a unique one.");
} catch (ArkSystemException e) {
this.error("A System error occured. Please contact Administrator.");
}
} else {
try {
iPhenotypicService.updateCustomFieldGroup(getModelObject());
initCustomFieldDataListPanel();
this.info("Data Set has been updated successfully.");
} catch (EntityExistsException e) {
this.error("A Data Set with the same name already exisits. Please choose a unique one.");
e.printStackTrace();
} catch (ArkSystemException e) {
this.error("A System error occured. Please contact Administrator.");
e.printStackTrace();
}
}
target.add(
arkCrudContainerVO
.getWmcForCustomFieldDisplayListPanel()); // Repaint this List of Custom Field Displays
onSavePostProcess(target); // Post process
}
public void buildTabs(final WebMarkupContainer arkContextMarkup) {
ArkModule arkModule =
iArkCommonService.getArkModuleByName(au.org.theark.core.Constants.ARK_MODULE_PHENOTYPIC);
List<ArkFunction> arkFunctionList = iArkCommonService.getModuleFunction(arkModule);
for (final ArkFunction menuArkFunction : arkFunctionList) {
AbstractTab tab =
new AbstractTab(new StringResourceModel(menuArkFunction.getResourceKey(), this, null)) {
@Override
public Panel getPanel(final String panelId) {
return panelToReturn(menuArkFunction, panelId);
}
};
moduleSubTabsList.add(tab);
}
ArkAjaxTabbedPanel moduleTabbedPanel =
new ArkAjaxTabbedPanel(Constants.PHENOTYPIC_SUBMENU, moduleSubTabsList);
add(moduleTabbedPanel);
}
@SuppressWarnings("unchecked")
private void setSelectedCustomFieldsFromFile() {
if (fileUploadField.getFileUpload() != null) {
ArkFunction arkFunction =
iArkCommonService.getArkFunctionByName(
au.org.theark.core.Constants.FUNCTION_KEY_VALUE_PHENO_COLLECTION);
Long studyId =
(Long)
SecurityUtils.getSubject()
.getSession()
.getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
Study study = iArkCommonService.getStudy(studyId);
ArrayList<CustomField> selectedCustomFields =
(ArrayList<CustomField>)
iArkCommonService.matchCustomFieldsFromInputFile(
fileUploadField.getFileUpload(), study, arkFunction);
cpModel.getObject().setSelectedCustomFields(selectedCustomFields);
}
initCustomFieldPalette();
arkCrudContainerVO.getDetailPanelFormContainer().addOrReplace(customFieldPalette);
}
/** @param id */
public SubjectSubMenuTab(String id, WebMarkupContainer arkContextMarkup) {
super(id);
this.arkContextMarkup = arkContextMarkup;
new ArrayList<ITab>();
buildTabs();
Long sessionStudyId =
(Long)
SecurityUtils.getSubject()
.getSession()
.getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
Study study = iArkCommonService.getStudy(sessionStudyId);
childStudy = study.getParentStudy() != null && (study != study.getParentStudy());
}
public void initialiseDetailForm() {
phoneIdTxtFld = new TextField<String>("phoneVo.phone.id");
areaCodeTxtFld = new TextField<String>("phoneVo.phone.areaCode");
phoneNumberTxtFld = new TextField<String>("phoneVo.phone.phoneNumber");
source = new TextField<String>("phoneVo.phone.source");
commentsTxtArea = new TextArea<String>("phoneVo.phone.comment");
dateReceivedDp =
new DateTextField("phoneVo.phone.dateReceived", au.org.theark.core.Constants.DD_MM_YYYY);
ArkDatePicker datePicker = new ArkDatePicker();
datePicker.bind(dateReceivedDp);
dateReceivedDp.add(datePicker);
List<PhoneStatus> phoneStatusSourceList = iArkCommonService.getPhoneStatus();
ChoiceRenderer<PhoneStatus> phoneStatusRenderer =
new ChoiceRenderer<PhoneStatus>(Constants.NAME, Constants.ID);
phoneStatusChoice =
new DropDownChoice<PhoneStatus>(
"phoneVo.phone.phoneStatus", phoneStatusSourceList, phoneStatusRenderer);
List<YesNo> yesNoListSource = iArkCommonService.getYesNoList();
ChoiceRenderer<YesNo> yesNoRenderer = new ChoiceRenderer<YesNo>(Constants.NAME, Constants.ID);
silentModeChoice =
new DropDownChoice<YesNo>("phoneVo.phone.silentMode", yesNoListSource, yesNoRenderer);
List<PhoneType> phoneTypeList = iArkCommonService.getListOfPhoneType();
ChoiceRenderer<PhoneType> defaultChoiceRenderer =
new ChoiceRenderer<PhoneType>(Constants.NAME, Constants.ID);
phoneTypeChoice =
new DropDownChoice<PhoneType>(
"phoneVo.phone.phoneType", phoneTypeList, defaultChoiceRenderer);
phoneTypeChoice.add(new ArkDefaultFormFocusBehavior());
addDetailFormComponents();
attachValidators();
}
protected boolean prerenderContextCheck() {
Long sessionPersonId =
(Long)
SecurityUtils.getSubject()
.getSession()
.getAttribute(au.org.theark.core.Constants.PERSON_CONTEXT_ID);
Long sessionStudyId =
(Long)
SecurityUtils.getSubject()
.getSession()
.getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
boolean contextLoaded = false;
if ((sessionStudyId != null) && (sessionPersonId != null)) {
String sessionPersonType =
(String)
SecurityUtils.getSubject()
.getSession()
.getAttribute(au.org.theark.core.Constants.PERSON_TYPE);
if (sessionPersonType.equals(au.org.theark.core.Constants.PERSON_CONTEXT_TYPE_SUBJECT)) {
LinkSubjectStudy lss;
try {
Study study = iArkCommonService.getStudy(sessionStudyId);
lss = iArkCommonService.getSubject(sessionPersonId, study);
contextLoaded = true;
} catch (EntityNotFoundException e) {
log.error(e.getMessage());
}
if (contextLoaded) {
arkCrudContainerVO.getDetailPanelContainer().setVisible(true);
}
}
}
return contextLoaded;
}
@SuppressWarnings("unchecked")
private void initDropDownChoice() {
// Initialise any drop-downs
java.util.Collection<FileFormat> fileFormatCollection = iArkCommonService.getFileFormats();
CompoundPropertyModel<CustomFieldUploadVO> uploadCpm = cpmModel;
PropertyModel<Upload> uploadPm = new PropertyModel<Upload>(uploadCpm, Constants.UPLOAD);
PropertyModel<FileFormat> fileFormatPm =
new PropertyModel<FileFormat>(uploadPm, Constants.FILE_FORMAT);
ChoiceRenderer fileFormatRenderer =
new ChoiceRenderer(Constants.FILE_FORMAT_NAME, Constants.FILE_FORMAT_ID);
fileFormatDdc =
new DropDownChoice<FileFormat>(
Constants.UPLOADVO_UPLOAD_FILE_FORMAT,
fileFormatPm,
(List) fileFormatCollection,
fileFormatRenderer);
}
@Override
protected WebMarkupContainer initialiseSearchResults() {
searchResultsPanel =
new SearchResultListPanel(
"searchResults", arkContextMarkup, containerForm, arkCrudContainerVO);
searchResultsPanel.setOutputMarkupId(true);
affectionProvider =
new ArkDataProvider<AffectionVO, IArkDiseaseService>(iArkDiseaseService) {
private static final long serialVersionUID = 1L;
public int size() {
int count = service.getAffectionCount(containerForm.getModelObject());
return count;
}
public Iterator<? extends AffectionVO> iterator(int first, int count) {
List<AffectionVO> affectionVOs =
service.searchPageableAffections(containerForm.getModelObject(), first, count);
return affectionVOs.iterator();
}
};
affectionProvider.setModel(this.cpModel);
dataView = searchResultsPanel.buildDataView(affectionProvider);
dataView.setItemsPerPage(iArkCommonService.getRowsPerPage());
AjaxPagingNavigator pageNavigator =
new AjaxPagingNavigator("navigator", dataView) {
private static final long serialVersionUID = 1L;
@Override
protected void onAjaxEvent(AjaxRequestTarget target) {
target.add(searchResultsPanel);
}
};
resultsWmc.add(pageNavigator);
resultsWmc.add(dataView);
searchResultsPanel.add(resultsWmc);
arkCrudContainerVO.getSearchResultPanelContainer().add(searchResultsPanel);
return arkCrudContainerVO.getSearchResultPanelContainer();
}
private void initCustomFieldDataListPanel() {
cfdProvider.setCriteriaModel(
new PropertyModel<CustomFieldDisplay>(cpModel, "customFieldGroup"));
List<CustomField> selectedList =
iPhenotypicService.getCustomFieldsLinkedToCustomFieldGroup(
getModelObject().getCustomFieldGroup());
Boolean disableEditButton = false;
if (getModelObject().getCustomFieldGroup().getPublished()) {
for (CustomField customField : selectedList) {
if (customField.getCustomFieldHasData()) {
disableEditButton = true;
break;
}
}
}
CustomFieldDisplayListPanel cfdListPanel =
new CustomFieldDisplayListPanel(
"cfdListPanel", feedBackPanel, arkCrudContainerVO, disableEditButton);
cfdListPanel.setOutputMarkupId(true);
cfdListPanel.initialisePanel();
dataView = cfdListPanel.buildDataView(cfdProvider);
dataView.setItemsPerPage(iArkCommonService.getRowsPerPage());
AjaxPagingNavigator pageNavigator =
new AjaxPagingNavigator("cfDisplayNavigator", dataView) {
private static final long serialVersionUID = 1L;
@Override
protected void onAjaxEvent(AjaxRequestTarget target) {
target.add(arkCrudContainerVO.getWmcForCustomFieldDisplayListPanel());
}
};
cfdListPanel.addOrReplace(pageNavigator);
cfdListPanel.addOrReplace(dataView);
arkCrudContainerVO.getWmcForCustomFieldDisplayListPanel().addOrReplace(cfdListPanel);
}
/*
* (non-Javadoc)
*
* @see au.org.theark.core.web.form.AbstractDetailForm#onSave(org.apache.wicket.markup.html.form.Form, org.apache.wicket.ajax.AjaxRequestTarget)
*/
@Override
protected void onSave(Form<ContactVO> containerForm, AjaxRequestTarget target) {
// Persist the phone number to the backend, associate the person in context with the phone
// object
Long personSessionId =
(Long)
SecurityUtils.getSubject()
.getSession()
.getAttribute(au.org.theark.core.Constants.PERSON_CONTEXT_ID);
// Get the person and set it on the Phone object.
try {
boolean saveOk = true;
Person person = studyService.getPerson(personSessionId);
containerForm.getModelObject().getPhoneVo().getPhone().setPerson(person);
/*
// Make the area code mandatory only for landline phone (home/work) entries
String phType = containerForm.getModelObject().getPhone().getPhoneType().getName().toLowerCase();
if (!phType.equals("mobile")) {
// must be landline
if (containerForm.getModelObject().getPhone().getAreaCode() == null || containerForm.getModelObject().getPhone().getAreaCode().length() < 1) {
this.error("An area code must be entered for landline numbers");
saveOk = false;
}
}
*/
if (saveOk) {
// Ok to save...
String personType =
(String)
SecurityUtils.getSubject()
.getSession()
.getAttribute(au.org.theark.core.Constants.PERSON_TYPE);
if (personType != null
&& personType.equalsIgnoreCase(
au.org.theark.core.Constants.PERSON_CONTEXT_TYPE_SUBJECT)) {
Long studyId =
(Long)
SecurityUtils.getSubject()
.getSession()
.getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
Study study = iArkCommonService.getStudy(studyId);
LinkSubjectStudy subjectInContext =
iArkCommonService.getSubject(
personSessionId, study); // This is fetched basically to display the
// info
// message along with the Subject UID or Contact ID
if (containerForm.getModelObject().getPhoneVo().getPhone().getId() == null) {
studyService.create(containerForm.getModelObject().getPhoneVo().getPhone());
this.info(
"Phone number was added and linked to Subject UID: "
+ subjectInContext.getSubjectUID());
} else {
studyService.update(containerForm.getModelObject().getPhoneVo().getPhone());
this.info(
"Phone number was updated and linked to Subject UID: "
+ subjectInContext.getSubjectUID());
}
} else if (personType != null
&& personType.equalsIgnoreCase(
au.org.theark.core.Constants.PERSON_CONTEXT_TYPE_CONTACT)) {
// TODO: Contact Interface implementation
}
processErrors(target);
onSavePostProcess(target);
} else {
processErrors(target);
}
} catch (ArkUniqueException aue) {
this.error(aue.getMessage());
} catch (EntityNotFoundException e) {
this.error("The Subject/Participant is not available in the system anymore");
} catch (ArkSystemException e) {
this.error("A System Exception has occured please contact Support.");
}
}
public VelocityContext getBioCollectionLabelContext(BioCollection bioCollection) {
VelocityContext velocityContext = new VelocityContext();
LinkSubjectStudy linkSubjectStudy = null;
try {
linkSubjectStudy =
iArkCommonService.getSubjectByUID(
bioCollection.getLinkSubjectStudy().getSubjectUID(), bioCollection.getStudy());
} catch (EntityNotFoundException e) {
log.error(e.getMessage());
}
try {
bioCollection = iBioCollectionDao.getBioCollection(bioCollection.getId());
} catch (EntityNotFoundException e) {
log.error(e.getMessage());
}
String subjectUid = linkSubjectStudy.getSubjectUID();
// ArkFunction arkFunction =
// iArkCommonService.getArkFunctionByName(au.org.theark.core.Constants.FUNCTION_KEY_VALUE_LIMS_COLLECTION);
ArkFunction arkFunction =
iArkCommonService.getArkFunctionByName(
au.org.theark.core.Constants.FUNCTION_KEY_VALUE_LIMS_CUSTOM_FIELD);
// Custom field name "FAMILYID"
BioCollectionCustomFieldData bioCollectionCustomFieldData =
iBioCollectionDao.getBioCollectionCustomFieldData(bioCollection, arkFunction, "FAMILYID");
String familyId = bioCollectionCustomFieldData.getTextDataValue();
// Custom field name "ASRBNO"
bioCollectionCustomFieldData =
iBioCollectionDao.getBioCollectionCustomFieldData(bioCollection, arkFunction, "ASRBNO");
String asrbno = bioCollectionCustomFieldData.getTextDataValue();
String collectionDate = new String();
if (bioCollection.getCollectionDate() != null) {
collectionDate = simpleDateFormat.format(bioCollection.getCollectionDate());
}
String refDoctor = new String();
if (bioCollection.getRefDoctor() != null) {
refDoctor = bioCollection.getRefDoctor();
}
String dateOfBirth = new String();
if (bioCollection.getLinkSubjectStudy().getPerson().getDateOfBirth() != null) {
dateOfBirth =
simpleDateFormat.format(bioCollection.getLinkSubjectStudy().getPerson().getDateOfBirth());
}
String sex = new String();
if (bioCollection.getLinkSubjectStudy().getPerson().getGenderType() != null) {
sex = bioCollection.getLinkSubjectStudy().getPerson().getGenderType().getName();
}
String collectionID = bioCollection.getBiocollectionUid();
String subjectFirstName = linkSubjectStudy.getPerson().getFirstName();
String subjectLastName = linkSubjectStudy.getPerson().getLastName();
String initials = subjectFirstName.charAt(0) + "" + subjectLastName.charAt(0);
velocityContext.put("initials", initials);
velocityContext.put("firstName", subjectFirstName);
velocityContext.put("lastName", subjectLastName);
velocityContext.put("collectionID", collectionID);
velocityContext.put("subjectUid", subjectUid);
velocityContext.put("familyId", familyId);
velocityContext.put("asrbno", asrbno);
velocityContext.put("collectionDate", collectionDate);
velocityContext.put("refDoctor", refDoctor);
velocityContext.put("dateOfBirth", dateOfBirth);
velocityContext.put("sex", sex);
return velocityContext;
}
@Override
public void onStepInNext(AbstractWizardForm<?> form, AjaxRequestTarget target) {
try {
InputStream inputStream = containerForm.getModelObject().getFileUpload().getInputStream();
FileUpload fileUpload = containerForm.getModelObject().getFileUpload();
String uploadType = containerForm.getModelObject().getUploadType();
log.info("so what is the upload type =" + uploadType);
String filename = containerForm.getModelObject().getFileUpload().getClientFileName();
String fileFormat = filename.substring(filename.lastIndexOf('.') + 1).toUpperCase();
char delimChar =
containerForm.getModelObject().getUpload().getDelimiterType().getDelimiterCharacter();
// Only allow csv, txt or xls
if (!(fileFormat.equalsIgnoreCase("CSV")
|| fileFormat.equalsIgnoreCase("TXT")
|| fileFormat.equalsIgnoreCase("XLS"))) {
throw new FileFormatException();
}
BiospecimenUploadValidator biospecimenUploadValidator =
new BiospecimenUploadValidator(
containerForm.getModelObject().getUpload().getStudy(),
iArkCommonService,
iLimsService,
iInventoryService);
if (uploadType.equalsIgnoreCase(Constants.UPLOAD_TYPE_FOR_LOCATION_UPLOADER)) {
validationMessages =
biospecimenUploadValidator.validateLocationFileFormat(containerForm.getModelObject());
} else { // TODO : i dont see biocollection uploader, so let's kill it in the database for now
validationMessages =
biospecimenUploadValidator.validateSubjectFileFormat(containerForm.getModelObject());
}
containerForm.getModelObject().setValidationMessages(validationMessages);
validationMessage = containerForm.getModelObject().getValidationMessagesAsString();
addOrReplace(new MultiLineLabel("multiLineLabel", validationMessage));
ArkExcelWorkSheetAsGrid arkExcelWorkSheetAsGrid =
new ArkExcelWorkSheetAsGrid(
"gridView",
inputStream,
fileFormat,
delimChar,
fileUpload,
iArkCommonService.getRowsPerPage());
arkExcelWorkSheetAsGrid.setOutputMarkupId(true);
WebMarkupContainer wizardDataGridKeyContainer =
new WebMarkupContainer("wizardDataGridKeyContainer");
wizardDataGridKeyContainer.setVisible(false);
wizardDataGridKeyContainer.setOutputMarkupId(true);
form.setArkExcelWorkSheetAsGrid(arkExcelWorkSheetAsGrid);
form.getWizardPanelFormContainer().addOrReplace(arkExcelWorkSheetAsGrid);
form.setArkExcelWorkSheetAsGrid(arkExcelWorkSheetAsGrid);
form.getWizardPanelFormContainer().addOrReplace(wizardDataGridKeyContainer);
target.add(form.getWizardPanelFormContainer());
containerForm.getModelObject().setValidationMessages(validationMessages);
validationMessage = containerForm.getModelObject().getValidationMessagesAsString();
addOrReplace(new MultiLineLabel("multiLineLabel", validationMessage));
if (validationMessage != null && validationMessage.length() > 0) {
this.containerForm
.getModelObject()
.getUpload()
.setUploadStatus(
iArkCommonService.getUploadStatusFor(
au.org.theark.lims.web.Constants.UPLOAD_STATUS_OF_ERROR_IN_FILE_VALIDATION));
this.containerForm
.getModelObject()
.getUpload()
.setFilename(
filename); // have to reset this because the container has the file name...luckily
// it never changes
iArkCommonService.updateUpload(this.containerForm.getModelObject().getUpload());
form.getNextButton().setEnabled(false);
target.add(form.getWizardButtonContainer());
downloadValMsgButton =
new ArkDownloadAjaxButton(
"downloadValMsg", "ValidationMessage", validationMessage, "txt") {
private static final long serialVersionUID = 1L;
@Override
protected void onError(AjaxRequestTarget target, Form<?> form) {
this.error("Unexpected Error: Download request could not be processed");
}
};
addOrReplace(downloadValMsgButton);
target.add(downloadValMsgButton);
}
} catch (IOException e) {
validationMessage =
"Error attempting to display the file. Please check the file and try again.";
addOrReplace(new MultiLineLabel("multiLineLabel", validationMessage));
form.getNextButton().setEnabled(false);
target.add(form.getWizardButtonContainer());
} catch (FileFormatException ffe) {
validationMessage =
"Error uploading file. You can only upload files of type: CSV (comma separated values), TXT (text), or XLS (Microsoft Excel file)";
addOrReplace(new MultiLineLabel("multiLineLabel", validationMessage));
form.getNextButton().setEnabled(false);
target.add(form.getWizardButtonContainer());
}
}
@SuppressWarnings({"serial", "unchecked"})
public void buildTabs() {
List<ITab> moduleSubTabsList = new ArrayList<ITab>();
ArkModule arkModule = iArkCommonService.getArkModuleByName(Constants.ARK_MODULE_SUBJECT);
List<ArkFunction> arkFunctionList =
iArkCommonService.getModuleFunction(
arkModule); // Gets a list of ArkFunctions for the given Module
for (final ArkFunction menuArkFunction : arkFunctionList) {
moduleSubTabsList.add(
new AbstractTab(new StringResourceModel(menuArkFunction.getResourceKey(), this, null)) {
@Override
public Panel getPanel(String panelId) {
Panel panelToReturn = null; // Set
if (menuArkFunction
.getName()
.equalsIgnoreCase(au.org.theark.core.Constants.FUNCTION_KEY_VALUE_SUBJECT)) {
processAuthorizationCache(
au.org.theark.core.Constants.ARK_MODULE_SUBJECT, menuArkFunction);
panelToReturn =
new SubjectContainerPanel(
panelId, arkContextMarkup, null, null); // Note the constructor
} else if (menuArkFunction
.getName()
.equalsIgnoreCase(au.org.theark.core.Constants.FUNCTION_KEY_VALUE_PHONE)) {
processAuthorizationCache(
au.org.theark.core.Constants.ARK_MODULE_SUBJECT, menuArkFunction);
panelToReturn = new PhoneContainerPanel(panelId);
} else if (menuArkFunction
.getName()
.equalsIgnoreCase(au.org.theark.core.Constants.FUNCTION_KEY_VALUE_ADDRESS)) {
processAuthorizationCache(
au.org.theark.core.Constants.ARK_MODULE_SUBJECT, menuArkFunction);
panelToReturn = new AddressContainerPanel(panelId);
}
// Add contact panel
else if (menuArkFunction
.getName()
.equalsIgnoreCase(au.org.theark.core.Constants.FUNCTION_KEY_VALUE_CONTACT)) {
processAuthorizationCache(
au.org.theark.core.Constants.ARK_MODULE_SUBJECT, menuArkFunction);
panelToReturn = new ContactContainerPanel(panelId);
} else if (menuArkFunction
.getName()
.equalsIgnoreCase(au.org.theark.core.Constants.FUNCTION_KEY_VALUE_CONSENT)) {
processAuthorizationCache(
au.org.theark.core.Constants.ARK_MODULE_SUBJECT, menuArkFunction);
panelToReturn = new ConsentContainerPanel(panelId);
} else if (menuArkFunction
.getName()
.equalsIgnoreCase(au.org.theark.core.Constants.FUNCTION_KEY_VALUE_ATTACHMENT)) {
processAuthorizationCache(
au.org.theark.core.Constants.ARK_MODULE_SUBJECT, menuArkFunction);
panelToReturn = new AttachmentsContainerPanel(panelId);
} else if (menuArkFunction
.getName()
.equalsIgnoreCase(
au.org.theark.core.Constants.FUNCTION_KEY_VALUE_STUDY_STUDY_DATA_UPLOAD)) {
processAuthorizationCache(
au.org.theark.core.Constants.ARK_MODULE_SUBJECT, menuArkFunction);
panelToReturn = new SubjectUploadContainerPanel(panelId, menuArkFunction);
} else if (menuArkFunction
.getName()
.equalsIgnoreCase(
au.org.theark.core.Constants.FUNCTION_KEY_VALUE_SUBJECT_CORRESPONDENCE)) {
processAuthorizationCache(
au.org.theark.core.Constants.ARK_MODULE_SUBJECT, menuArkFunction);
panelToReturn = new CorrespondenceContainerPanel(panelId);
} else if (menuArkFunction
.getName()
.equalsIgnoreCase(
au.org.theark.core.Constants.FUNCTION_KEY_VALUE_SUBJECT_CUSTOM_FIELD)) {
processAuthorizationCache(
au.org.theark.core.Constants.ARK_MODULE_SUBJECT, menuArkFunction);
// useCustomFieldDisplay = true
panelToReturn =
new CustomFieldContainerPanel(
panelId,
true,
iArkCommonService.getArkFunctionByName(
au.org.theark.core.Constants.FUNCTION_KEY_VALUE_SUBJECT_CUSTOM_FIELD));
} else if (menuArkFunction
.getName()
.equalsIgnoreCase(
au.org.theark.core.Constants.FUNCTION_KEY_VALUE_SUBJECT_CUSTOM_DATA)) {
processAuthorizationCache(
au.org.theark.core.Constants.ARK_MODULE_SUBJECT, menuArkFunction);
panelToReturn = new SubjectCustomDataContainerPanel(panelId).initialisePanel();
} else if (menuArkFunction
.getName()
.equalsIgnoreCase(
au.org.theark.core.Constants
.FUNCTION_KEY_VALUE_SUBJECT_CUSTOM_FIELD_UPLOAD)) {
processAuthorizationCache(
au.org.theark.core.Constants.ARK_MODULE_SUBJECT, menuArkFunction);
panelToReturn =
new CustomFieldUploadContainerPanel(
panelId,
iArkCommonService.getArkFunctionByName(
au.org.theark.core.Constants.FUNCTION_KEY_VALUE_SUBJECT));
}
return panelToReturn;
}
@Override
public boolean isVisible() {
// Subject Upload only visible to parent studies
if (menuArkFunction
.getName()
.equalsIgnoreCase(
au.org.theark.core.Constants.FUNCTION_KEY_VALUE_STUDY_STUDY_DATA_UPLOAD)) {
return (!childStudy);
}
return true;
}
});
}
ArkAjaxTabbedPanel moduleTabbedPanel =
new ArkAjaxTabbedPanel(Constants.MENU_SUBJECT_SUBMENU, moduleSubTabsList);
add(moduleTabbedPanel);
}
/**
* @param iModel
* @return the pageableListView of Upload
*/
@SuppressWarnings("unchecked")
public PageableListView<Upload> buildPageableListView(IModel iModel) {
PageableListView<Upload> sitePageableListView =
new PageableListView<Upload>(
Constants.RESULT_LIST,
iModel,
iArkCommonService.getUserConfig(Constants.CONFIG_ROWS_PER_PAGE).getIntValue()) {
private static final long serialVersionUID = 1L;
@Override
protected void populateItem(final ListItem<Upload> item) {
Upload upload = item.getModelObject();
// The ID
if (upload.getId() != null) {
// Add the id component here
item.add(
new Label(
au.org.theark.phenotypic.web.Constants.UPLOADVO_UPLOAD_ID,
upload.getId().toString()));
} else {
item.add(new Label(au.org.theark.phenotypic.web.Constants.UPLOADVO_UPLOAD_ID, ""));
}
// / The filename
if (upload.getFilename() != null) {
// Add the id component here
item.add(
new Label(
au.org.theark.phenotypic.web.Constants.UPLOADVO_UPLOAD_FILENAME,
upload.getFilename()));
} else {
item.add(
new Label(au.org.theark.phenotypic.web.Constants.UPLOADVO_UPLOAD_FILENAME, ""));
}
// File Format
if (upload.getFileFormat() != null) {
item.add(
new Label(
au.org.theark.phenotypic.web.Constants.UPLOADVO_UPLOAD_FILE_FORMAT,
upload.getFileFormat().getName()));
} else {
item.add(
new Label(
au.org.theark.phenotypic.web.Constants.UPLOADVO_UPLOAD_FILE_FORMAT, ""));
}
// UserId
if (upload.getUserId() != null) {
item.add(
new Label(
au.org.theark.phenotypic.web.Constants.UPLOADVO_UPLOAD_USER_ID,
upload.getUserId()));
} else {
item.add(
new Label(au.org.theark.phenotypic.web.Constants.UPLOADVO_UPLOAD_USER_ID, ""));
}
// Start time
if (upload.getStartTime() != null) {
item.add(
new Label(
au.org.theark.phenotypic.web.Constants.UPLOADVO_UPLOAD_START_TIME,
upload.getStartTime().toString()));
} else {
item.add(
new Label(au.org.theark.phenotypic.web.Constants.UPLOADVO_UPLOAD_START_TIME, ""));
}
// Finish time
if (upload.getFinishTime() != null) {
item.add(
new Label(
au.org.theark.phenotypic.web.Constants.UPLOADVO_UPLOAD_FINISH_TIME,
upload.getFinishTime().toString()));
} else {
item.add(
new Label(
au.org.theark.phenotypic.web.Constants.UPLOADVO_UPLOAD_FINISH_TIME, ""));
}
if (upload.getUploadStatus() != null
&& upload.getUploadStatus().getShortMessage() != null) {
item.add(
new Label(
au.org.theark.phenotypic.web.Constants.UPLOADVO_UPLOAD_UPLOAD_STATUS_NAME,
upload.getUploadStatus().getShortMessage()));
} else {
item.add(
new Label(
au.org.theark.phenotypic.web.Constants.UPLOADVO_UPLOAD_UPLOAD_STATUS_NAME,
""));
}
// Download file link button
item.add(buildDownloadButton(upload));
// Download upload report button
item.add(buildDownloadReportButton(upload));
item.add(buildDeleteUploadButton(upload));
// Delete the upload file
// item.add(buildDeleteButton(upload));
// For the alternative stripes
item.add(
new AttributeModifier(
"class",
new AbstractReadOnlyModel<String>() {
private static final long serialVersionUID = 1L;
@Override
public String getObject() {
return (item.getIndex() % 2 == 1) ? "even" : "odd";
}
}));
}
};
return sitePageableListView;
}
public StringBuffer uploadAndReportCustomDataFile(
InputStream inputStream,
long size,
String fileFormat,
char delimChar,
List<String> listOfUIDsToUpdate,
CustomFieldGroup customFieldGroup,
PhenoCollection phenoCollection,
boolean overwriteExisting)
throws FileFormatException, ArkSystemException {
List<PhenoCollection> phenoCollectionsWithTheirDataToInsert = new ArrayList<PhenoCollection>();
delimiterCharacter = delimChar;
uploadReport = new StringBuffer();
InputStream convertedInputStream;
if (fileFormat.equalsIgnoreCase(Constants.FileFormat.XLS.toString())) {
XLStoCSV xlsToCSV = new XLStoCSV(delimiterCharacter);
convertedInputStream = xlsToCSV.convertXlsInputStreamToCsv(inputStream);
} else {
convertedInputStream = inputStream;
}
InputStreamReader inputStreamReader = null;
CsvReader csvReader = null;
DecimalFormat decimalFormat = new DecimalFormat("0.00");
int subjectCount = 0;
long updateFieldsCount = 0L;
long insertFieldsCount = 0L;
long emptyDataCount = 0L;
try {
inputStreamReader = new InputStreamReader(convertedInputStream);
csvReader = new CsvReader(inputStreamReader, delimiterCharacter);
String[] stringLineArray;
List<LinkSubjectStudy> allSubjectWhichWillBeUpdated = null;
if (listOfUIDsToUpdate.size() > 0) {
allSubjectWhichWillBeUpdated =
iArkCommonService.getUniqueSubjectsWithTheseUIDs(study, listOfUIDsToUpdate);
} else {
allSubjectWhichWillBeUpdated = new ArrayList<LinkSubjectStudy>();
}
if (size <= 0) {
uploadReport.append(
"ERROR: The input size was not greater than 0. Actual length reported: ");
uploadReport.append(size);
uploadReport.append("\n");
throw new FileFormatException(
"The input size was not greater than 0. Actual length reported: " + size);
}
csvReader.readHeaders();
List<String> fieldNameCollection = Arrays.asList(csvReader.getHeaders());
ArkFunction phenoCustomFieldArkFunction =
iArkCommonService.getArkFunctionByName(
Constants.FUNCTION_KEY_VALUE_PHENO_COLLECTION); // ");
List<CustomFieldDisplay> cfdsThatWeNeed =
iArkCommonService.getCustomFieldDisplaysIn(
fieldNameCollection, study, phenoCustomFieldArkFunction, customFieldGroup);
// Paul has requested - in pheno we only insert List<PhenoData> dataThatWeHave =
// iArkCommonService.getCustomFieldDataFor(cfdsThatWeNeed, allSubjectWhichWillBeUpdated);
// read one line which contains potentially many custom fields
QuestionnaireStatus uploadingStatus =
iPhenotypicService.getPhenoCollectionStatusByName(
Constants.PHENO_COLLECTION_STATUS_UPLOADED);
while (csvReader.readRecord()) {
List<PhenoData> phenoDataToInsertForThisPhenoCollection = new ArrayList<PhenoData>();
log.info("reading record " + subjectCount);
stringLineArray = csvReader.getValues();
String subjectUID = stringLineArray[0];
String recordDate = stringLineArray[1];
Date recordDate_asDate =
(recordDate.isEmpty() ? new Date() : simpleDateFormat.parse(recordDate));
LinkSubjectStudy subject =
getSubjectByUIDFromExistList(allSubjectWhichWillBeUpdated, subjectUID);
// log.info("get subject from list");
CustomField customField = null;
List<PhenoCollection> subjectExistingMatchingPhenoCollections =
iPhenotypicService.getSubjectMatchingPhenoCollections(
subject, customFieldGroup, recordDate_asDate);
PhenoCollection phenoCollectionIntoDB = new PhenoCollection();
if (subjectExistingMatchingPhenoCollections.size() == 0 || !overwriteExisting) {
phenoCollectionIntoDB.setDescription(phenoCollection.getDescription());
phenoCollectionIntoDB.setLinkSubjectStudy(subject);
// phenoCollectionIntoDB.setName(phenoCollection.getName());
phenoCollectionIntoDB.setQuestionnaire(customFieldGroup);
if (recordDate.isEmpty()) {
phenoCollectionIntoDB.setRecordDate(new Date());
} else {
phenoCollectionIntoDB.setRecordDate(recordDate_asDate);
}
phenoCollectionIntoDB.setStatus(
uploadingStatus); // TODO for this to be UPLOADED TYPE STATUS
} else {
if (subjectExistingMatchingPhenoCollections.size() == 1) {
recordDate_asDate =
(recordDate.isEmpty() ? new Date() : simpleDateFormat.parse(recordDate));
phenoCollectionIntoDB = subjectExistingMatchingPhenoCollections.get(0);
} else {
subjectCount++;
continue;
}
}
for (CustomFieldDisplay cfd : cfdsThatWeNeed) {
String theDataAsString = null;
customField = cfd.getCustomField();
if (csvReader.getIndex(cfd.getCustomField().getName()) < 0) {
for (String nameAsSeenInFile : fieldNameCollection) {
if (nameAsSeenInFile.equalsIgnoreCase(cfd.getCustomField().getName())) {
theDataAsString = csvReader.get(nameAsSeenInFile);
}
}
} else {
theDataAsString = csvReader.get(cfd.getCustomField().getName());
}
if (theDataAsString != null && !theDataAsString.isEmpty()) {
PhenoData dataToInsert = new PhenoData();
dataToInsert.setCustomFieldDisplay(cfd);
// as much as i disagree...pheno data isn't tied to subject....pheno collection is
// dataToInsert.setLinkSubjectStudy(subject);
setValue(customField, cfd, dataToInsert, theDataAsString);
boolean flag = true;
for (PhenoData phenoData : phenoCollectionIntoDB.getPhenoData()) {
if (phenoData.getCustomFieldDisplay().getId() == cfd.getId()) {
phenoData.setDateDataValue(dataToInsert.getDateDataValue());
phenoData.setErrorDataValue(dataToInsert.getErrorDataValue());
phenoData.setNumberDataValue(dataToInsert.getNumberDataValue());
phenoData.setTextDataValue(dataToInsert.getTextDataValue());
flag = false;
break;
}
}
if (flag) {
phenoDataToInsertForThisPhenoCollection.add(dataToInsert);
}
insertFieldsCount++;
} else {
emptyDataCount++;
}
}
phenoCollectionIntoDB.getPhenoData().addAll(phenoDataToInsertForThisPhenoCollection);
log.info(phenoCollectionIntoDB.toString());
phenoCollectionsWithTheirDataToInsert.add(phenoCollectionIntoDB);
subjectCount++;
}
log.info(
"finished message for "
+ subjectCount
+ "\n DATA inserts = "
+ insertFieldsCount
+ " phenocollections = "
+ phenoCollectionsWithTheirDataToInsert.size()
+ " amount of empty scells ="
+ emptyDataCount);
} catch (IOException ioe) {
uploadReport.append(
"SYSTEM ERROR: Unexpected I/O exception whilst reading the subject data file\n");
log.error("processMatrixSubjectFile IOException stacktrace:", ioe);
throw new ArkSystemException("Unexpected I/O exception whilst reading the subject data file");
} catch (Exception ex) {
uploadReport.append(
"SYSTEM ERROR: Unexpected exception whilst reading the subject data file\n");
log.error("processMatrixSubjectFile Exception stacktrace:", ex);
throw new ArkSystemException(
"Unexpected exception occurred when trying to process subject data file");
} finally {
uploadReport.append("Total file size: ");
uploadReport.append(decimalFormat.format(size / 1024.0 / 1024.0));
uploadReport.append(" MB");
uploadReport.append("\n");
if (csvReader != null) {
try {
csvReader.close();
} catch (Exception ex) {
log.error("Cleanup operation failed: csvRdr.close()", ex);
}
}
if (inputStreamReader != null) {
try {
inputStreamReader.close();
} catch (Exception ex) {
log.error("Cleanup operation failed: isr.close()", ex);
}
}
}
uploadReport.append("Processed ");
uploadReport.append(subjectCount);
uploadReport.append(" rows.");
uploadReport.append("\n");
uploadReport.append("Inserted ");
uploadReport.append(insertFieldsCount);
uploadReport.append(" rows of data.");
uploadReport.append("\n");
uploadReport.append("Updated ");
uploadReport.append(updateFieldsCount);
uploadReport.append(" rows of data.");
uploadReport.append("\n");
// TODO better exceptionhandling
iPhenotypicService.processPhenoCollectionsWithTheirDataToInsertBatch(
phenoCollectionsWithTheirDataToInsert, study);
return uploadReport;
}
