@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());
}
/*
* (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
}
@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);
}
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;
}
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;
}