use of org.akaza.openclinica.dao.submit.ItemDAO in project OpenClinica by OpenClinica.
the class DataEntryServlet method getAllDisplayBeans.
/**
* Retrieve the DisplaySectionBean which will be used to display the Event CRF Section on the JSP, and also is used to controll processRequest.
* @param request TODO
*/
protected ArrayList getAllDisplayBeans(HttpServletRequest request) throws Exception {
EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF);
ArrayList sections = new ArrayList();
HttpSession session = request.getSession();
StudyBean study = (StudyBean) session.getAttribute("study");
SectionDAO sdao = new SectionDAO(getDataSource());
ItemDataDAO iddao = new ItemDataDAO(getDataSource(), locale);
// ALL_SECTION_BEANS
ArrayList<SectionBean> allSectionBeans = (ArrayList<SectionBean>) request.getAttribute(ALL_SECTION_BEANS);
for (int j = 0; j < allSectionBeans.size(); j++) {
SectionBean sb = allSectionBeans.get(j);
DisplaySectionBean section = new DisplaySectionBean();
section.setEventCRF(ecb);
if (sb.getParentId() > 0) {
SectionBean parent = (SectionBean) sdao.findByPK(sb.getParentId());
sb.setParent(parent);
}
section.setSection(sb);
CRFVersionDAO cvdao = new CRFVersionDAO(getDataSource());
CRFVersionBean cvb = (CRFVersionBean) cvdao.findByPK(ecb.getCRFVersionId());
section.setCrfVersion(cvb);
CRFDAO cdao = new CRFDAO(getDataSource());
CRFBean cb = (CRFBean) cdao.findByPK(cvb.getCrfId());
section.setCrf(cb);
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(getDataSource());
EventDefinitionCRFBean edcb = edcdao.findByStudyEventIdAndCRFVersionId(study, ecb.getStudyEventId(), cvb.getId());
section.setEventDefinitionCRF(edcb);
// setup DAO's here to avoid creating too many objects
ItemDAO idao = new ItemDAO(getDataSource());
ItemFormMetadataDAO ifmdao = new ItemFormMetadataDAO(getDataSource());
iddao = new ItemDataDAO(getDataSource(), locale);
// get all the display item beans
ArrayList displayItems = getParentDisplayItems(false, sb, edcb, idao, ifmdao, iddao, false, request);
LOGGER.debug("222 just ran get parent display, has group " + " FALSE has ungrouped FALSE");
// now sort them by ordinal
Collections.sort(displayItems);
// now get the child DisplayItemBeans
for (int i = 0; i < displayItems.size(); i++) {
DisplayItemBean dib = (DisplayItemBean) displayItems.get(i);
dib.setChildren(getChildrenDisplayItems(dib, edcb, request));
if (shouldLoadDBValues(dib)) {
LOGGER.trace("should load db values is true, set value");
dib.loadDBValue();
}
displayItems.set(i, dib);
}
section.setItems(displayItems);
sections.add(section);
}
return sections;
}
use of org.akaza.openclinica.dao.submit.ItemDAO in project OpenClinica by OpenClinica.
the class DataEntryServlet method isEachRequiredFieldFillout.
protected boolean isEachRequiredFieldFillout(HttpServletRequest request) {
HttpSession session = request.getSession();
EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF);
DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(getDataSource());
// need to update this method to accomodate dynamics, tbh
ItemDataDAO iddao = new ItemDataDAO(getDataSource(), locale);
ItemDAO idao = new ItemDAO(getDataSource());
ItemFormMetadataDAO itemFormMetadataDao = new ItemFormMetadataDAO(getDataSource());
// Below code will iterate all shown and hidden required fields/items in a crf version and verify if the data field is filled up with value or if not , then it is a hidden field with no show rule triggered for the item.
ArrayList<ItemFormMetadataBean> shownRequiredAllItemsInCrfVersion = itemFormMetadataDao.findAllItemsRequiredAndShownByCrfVersionId(ecb.getCRFVersionId());
ArrayList<ItemFormMetadataBean> hiddenRequiredAllItemsInCrfVersion = itemFormMetadataDao.findAllItemsRequiredAndHiddenByCrfVersionId(ecb.getCRFVersionId());
ItemGroupMetadataDAO<String, ArrayList> igdao = new ItemGroupMetadataDAO<String, ArrayList>(dataSource);
ArrayList<ItemDataBean> itemdatas = null;
for (ItemFormMetadataBean shownItemMeta : shownRequiredAllItemsInCrfVersion) {
ItemGroupMetadataBean igBean = (ItemGroupMetadataBean) igdao.findByItemAndCrfVersion(shownItemMeta.getItemId(), ecb.getCRFVersionId());
// verifies if the group that the item belongs to is not hidden.
if (igBean != null && igBean.isShowGroup()) {
itemdatas = iddao.findAllByEventCRFIdAndItemId(ecb.getId(), shownItemMeta.getItemId());
if (itemdatas == null || itemdatas.size() == 0)
return false;
for (ItemDataBean itemdata : itemdatas) {
System.out.println(itemdata.getItemId() + " : " + itemdata.getValue());
if ((itemdata.getValue() == null || itemdata.getValue().equals("") || itemdata.getValue().trim().length() == 0) && dndao.findNumExistingNotesForItem(itemdata.getId()) < 1) {
return false;
}
}
}
ArrayList<DynamicsItemFormMetadataBean> dynamicsItemFormMetadataBeans = null;
for (ItemFormMetadataBean hiddenItemMeta : hiddenRequiredAllItemsInCrfVersion) {
itemdatas = iddao.findAllByEventCRFIdAndItemId(ecb.getId(), hiddenItemMeta.getItemId());
dynamicsItemFormMetadataBeans = getItemMetadataService().getDynamicsItemFormMetadataDao().findByItemAndEventCrfShown(ecb, hiddenItemMeta.getItemId());
if (itemdatas.size() == 0 && dynamicsItemFormMetadataBeans.size() > 0) {
return false;
}
for (ItemDataBean itemdata : itemdatas) {
if ((itemdata.getValue() == null || itemdata.getValue().equals("") || itemdata.getValue().trim().length() == 0) && dndao.findNumExistingNotesForItem(itemdata.getId()) < 1 && dynamicsItemFormMetadataBeans.size() > 0) {
return false;
}
}
}
}
// had to change the query below to allow for hidden items here, tbh 04/2010
ArrayList allFilled = iddao.findAllBlankRequiredByEventCRFId(ecb.getId(), ecb.getCRFVersionId());
int numNotes = 0;
if (!allFilled.isEmpty()) {
LOGGER.trace("allFilled is not empty");
FormDiscrepancyNotes fdn = (FormDiscrepancyNotes) session.getAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME);
HashMap idNotes = fdn.getIdNotes();
for (int i = 0; i < allFilled.size(); i++) {
ItemDataBean idb = (ItemDataBean) allFilled.get(i);
int exsitingNotes = dndao.findNumExistingNotesForItem(idb.getId());
if (exsitingNotes > 0) {
LOGGER.trace("has existing note");
numNotes++;
} else if (idNotes.containsKey(idb.getId())) {
LOGGER.trace("has note in session");
numNotes++;
}
}
LOGGER.trace("numNotes allFilled.size:" + numNotes + " " + allFilled.size());
if (numNotes >= allFilled.size()) {
LOGGER.trace("all required are filled out");
return true;
} else {
LOGGER.debug("numNotes < allFilled.size() " + numNotes + ": " + allFilled.size());
return false;
}
}
return true;
}
use of org.akaza.openclinica.dao.submit.ItemDAO in project OpenClinica by OpenClinica.
the class ImportSpringJob method processData.
/*
* processData, a method which should take in all XML files, check to see if they were imported previously, ? insert
* them into the database if not, and return a message which will go to audit and to the end user.
*/
private ArrayList<String> processData(File[] dest, DataSource dataSource, ResourceBundle respage, ResourceBundle resword, UserAccountBean ub, StudyBean studyBean, File destDirectory, TriggerBean triggerBean, RuleSetServiceInterface ruleSetService) throws Exception {
StringBuffer msg = new StringBuffer();
StringBuffer auditMsg = new StringBuffer();
Mapping myMap = new Mapping();
String propertiesPath = CoreResources.PROPERTIES_DIR;
new File(propertiesPath + File.separator + "ODM1-3-0.xsd");
File xsdFile2 = new File(propertiesPath + File.separator + "ODM1-2-1.xsd");
// @pgawade 18-April-2011 Fix for issue 8394
String ODM_MAPPING_DIR_path = CoreResources.ODM_MAPPING_DIR;
myMap.loadMapping(ODM_MAPPING_DIR_path + File.separator + "cd_odm_mapping.xml");
Unmarshaller um1 = new Unmarshaller(myMap);
ODMContainer odmContainer = new ODMContainer();
// File("log.txt")));
for (File f : dest) {
// >> tbh
boolean fail = false;
// all whitespace, one or more times
String regex = "\\s+";
// replace with underscores
String replacement = "_";
String pattern = "yyyy" + File.separator + "MM" + File.separator + "dd" + File.separator + "HHmmssSSS" + File.separator;
SimpleDateFormat sdfDir = new SimpleDateFormat(pattern);
String generalFileDir = sdfDir.format(new java.util.Date());
File logDestDirectory = new File(destDirectory + File.separator + generalFileDir + f.getName().replaceAll(regex, replacement) + ".log.txt");
if (!logDestDirectory.isDirectory()) {
logger.debug("creating new dir: " + logDestDirectory.getAbsolutePath());
logDestDirectory.mkdirs();
}
File newFile = new File(logDestDirectory, "log.txt");
// FileOutputStream out = new FileOutputStream(new
// File(logDestDirectory, "log.txt"));
// BufferedWriter out = null;
// wrap the below in a try-catch?
BufferedWriter out = new BufferedWriter(new FileWriter(newFile));
// << tbh 06/2010
if (f != null) {
String firstLine = "<P>" + f.getName() + ": ";
msg.append(firstLine);
out.write(firstLine);
auditMsg.append(firstLine);
} else {
msg.append("<P>" + respage.getString("unreadable_file") + ": ");
out.write("<P>" + respage.getString("unreadable_file") + ": ");
auditMsg.append("<P>" + respage.getString("unreadable_file") + ": ");
}
try {
// schemaValidator.validateAgainstSchema(f, xsdFile);
odmContainer = (ODMContainer) um1.unmarshal(new FileReader(f));
logger.debug("Found crf data container for study oid: " + odmContainer.getCrfDataPostImportContainer().getStudyOID());
logger.debug("found length of subject list: " + odmContainer.getCrfDataPostImportContainer().getSubjectData().size());
} catch (Exception me1) {
// fail against one, try another
try {
schemaValidator.validateAgainstSchema(f, xsdFile2);
// for backwards compatibility, we also try to validate vs
// 1.2.1 ODM 06/2008
odmContainer = (ODMContainer) um1.unmarshal(new FileReader(f));
} catch (Exception me2) {
// not sure if we want to report me2
MessageFormat mf = new MessageFormat("");
mf.applyPattern(respage.getString("your_xml_is_not_well_formed"));
Object[] arguments = { me1.getMessage() };
msg.append(mf.format(arguments) + "<br/>");
auditMsg.append(mf.format(arguments) + "<br/>");
// break here with an exception
logger.error("found an error with XML: " + msg.toString());
// continue looping
continue;
}
}
// next: check, then import
List<String> errors = getImportCRFDataService(dataSource).validateStudyMetadata(odmContainer, studyBean.getId());
// the user could be in any study ...
if (errors != null) {
if (errors.size() > 0) {
out.write("<P>Errors:<br/>");
for (String error : errors) {
out.write(error + "<br/>");
}
out.write("</P>");
// fail = true;
// forwardPage(Page.IMPORT_CRF_DATA);
// break here with an exception
// throw new Exception("Your XML in the file " + f.getName()
// + " was well formed, but generated metadata errors: " +
// errors.toString());
// msg.append("Your XML in the file " + f.getName() +
// " was well formed, but generated metadata errors: " +
// errors.toString());
MessageFormat mf = new MessageFormat("");
mf.applyPattern(respage.getString("your_xml_in_the_file"));
Object[] arguments = { f.getName(), errors.size() };
auditMsg.append(mf.format(arguments) + "<br/>");
msg.append(mf.format(arguments) + "<br/>");
auditMsg.append("You can see the log file <a href='" + SQLInitServlet.getField("sysURL.base") + "ViewLogMessage?n=" + generalFileDir + f.getName() + "&tn=" + triggerBean.getName() + "&gn=1'>here</a>.<br/>");
msg.append("You can see the log file <a href='" + SQLInitServlet.getField("sysURL.base") + "ViewLogMessage?n=" + generalFileDir + f.getName() + "&tn=" + triggerBean.getName() + "&gn=1'>here</a>.<br/>");
// auditMsg.append("Your XML in the file " + f.getName() +
// " was well formed, but generated " + errors.size() +
// " metadata errors." + "<br/>");
out.close();
continue;
} else {
msg.append(respage.getString("passed_study_check") + "<br/>");
msg.append(respage.getString("passed_oid_metadata_check") + "<br/>");
auditMsg.append(respage.getString("passed_study_check") + "<br/>");
auditMsg.append(respage.getString("passed_oid_metadata_check") + "<br/>");
}
}
ImportCRFInfoContainer importCrfInfo = new ImportCRFInfoContainer(odmContainer, dataSource);
// validation errors, the same as in the ImportCRFDataServlet. DRY?
List<EventCRFBean> eventCRFBeans = getImportCRFDataService(dataSource).fetchEventCRFBeans(odmContainer, ub);
ArrayList<Integer> permittedEventCRFIds = new ArrayList<Integer>();
Boolean eventCRFStatusesValid = getImportCRFDataService(dataSource).eventCRFStatusesValid(odmContainer, ub);
List<DisplayItemBeanWrapper> displayItemBeanWrappers = new ArrayList<DisplayItemBeanWrapper>();
HashMap<String, String> totalValidationErrors = new HashMap<String, String>();
HashMap<String, String> hardValidationErrors = new HashMap<String, String>();
// The following map is used for setting the EventCRF status post import.
HashMap<Integer, String> importedCRFStatuses = getImportCRFDataService(dataSource).fetchEventCRFStatuses(odmContainer);
// -- does the event already exist? if not, fail
if (eventCRFBeans == null) {
fail = true;
msg.append(respage.getString("no_event_status_matching"));
out.write(respage.getString("no_event_status_matching"));
out.close();
continue;
} else if (!eventCRFBeans.isEmpty()) {
logger.debug("found a list of eventCRFBeans: " + eventCRFBeans.toString());
for (EventCRFBean eventCRFBean : eventCRFBeans) {
DataEntryStage dataEntryStage = eventCRFBean.getStage();
Status eventCRFStatus = eventCRFBean.getStatus();
logger.debug("Event CRF Bean: id " + eventCRFBean.getId() + ", data entry stage " + dataEntryStage.getName() + ", status " + eventCRFStatus.getName());
if (eventCRFStatus.equals(Status.AVAILABLE) || dataEntryStage.equals(DataEntryStage.INITIAL_DATA_ENTRY) || dataEntryStage.equals(DataEntryStage.INITIAL_DATA_ENTRY_COMPLETE) || dataEntryStage.equals(DataEntryStage.DOUBLE_DATA_ENTRY_COMPLETE) || dataEntryStage.equals(DataEntryStage.DOUBLE_DATA_ENTRY)) {
permittedEventCRFIds.add(new Integer(eventCRFBean.getId()));
} else {
// break out here with an exception
// throw new
// Exception("Your listed Event CRF in the file " +
// f.getName() +
// " does not exist, or has already been locked for import."
// );
MessageFormat mf = new MessageFormat("");
mf.applyPattern(respage.getString("your_listed_crf_in_the_file"));
Object[] arguments = { f.getName() };
msg.append(mf.format(arguments) + "<br/>");
auditMsg.append(mf.format(arguments) + "<br/>");
out.write(mf.format(arguments) + "<br/>");
out.close();
continue;
}
}
if (eventCRFBeans.size() >= permittedEventCRFIds.size()) {
msg.append(respage.getString("passed_event_crf_status_check") + "<br/>");
auditMsg.append(respage.getString("passed_event_crf_status_check") + "<br/>");
} else {
fail = true;
msg.append(respage.getString("the_event_crf_not_correct_status") + "<br/>");
auditMsg.append(respage.getString("the_event_crf_not_correct_status") + "<br/>");
}
// create a 'fake' request to generate the validation errors
// here, tbh 05/2009
MockHttpServletRequest request = new MockHttpServletRequest();
// Locale locale = new Locale("en-US");
request.addPreferredLocale(locale);
try {
List<DisplayItemBeanWrapper> tempDisplayItemBeanWrappers = new ArrayList<DisplayItemBeanWrapper>();
tempDisplayItemBeanWrappers = getImportCRFDataService(dataSource).lookupValidationErrors(request, odmContainer, ub, totalValidationErrors, hardValidationErrors, permittedEventCRFIds);
logger.debug("size of total validation errors: " + totalValidationErrors.size());
displayItemBeanWrappers.addAll(tempDisplayItemBeanWrappers);
} catch (NullPointerException npe1) {
// what if you have 2 event crfs but the third is a fake?
npe1.printStackTrace();
fail = true;
logger.debug("threw a NPE after calling lookup validation errors");
msg.append(respage.getString("an_error_was_thrown_while_validation_errors") + "<br/>");
auditMsg.append(respage.getString("an_error_was_thrown_while_validation_errors") + "<br/>");
out.write(respage.getString("an_error_was_thrown_while_validation_errors") + "<br/>");
logger.debug("=== threw the null pointer, import ===");
} catch (OpenClinicaException oce1) {
fail = true;
logger.error("threw an OCE after calling lookup validation errors " + oce1.getOpenClinicaMessage());
msg.append(oce1.getOpenClinicaMessage() + "<br/>");
// auditMsg.append(oce1.getOpenClinicaMessage() + "<br/>");
out.write(oce1.getOpenClinicaMessage() + "<br/>");
}
} else if (!eventCRFStatusesValid) {
fail = true;
msg.append(respage.getString("the_event_crf_not_correct_status"));
out.write(respage.getString("the_event_crf_not_correct_status"));
out.close();
continue;
} else {
// fail = true;
// break here with an exception
msg.append(respage.getString("no_event_crfs_matching_the_xml_metadata") + "<br/>");
// auditMsg.append(respage.getString("no_event_crfs_matching_the_xml_metadata")
// + "<br/>");
out.write(respage.getString("no_event_crfs_matching_the_xml_metadata") + "<br/>");
// throw new Exception(msg.toString());
out.close();
continue;
}
ArrayList<SubjectDataBean> subjectData = odmContainer.getCrfDataPostImportContainer().getSubjectData();
if (!hardValidationErrors.isEmpty()) {
String messageHardVals = triggerService.generateHardValidationErrorMessage(subjectData, hardValidationErrors, false);
// byte[] messageHardValsBytes = messageHardVals.getBytes();
out.write(messageHardVals);
msg.append(respage.getString("file_generated_hard_validation_error"));
// here we create a file and append the data, tbh 06/2010
fail = true;
} else {
if (!totalValidationErrors.isEmpty()) {
String totalValErrors = triggerService.generateHardValidationErrorMessage(subjectData, totalValidationErrors, false);
out.write(totalValErrors);
// here we also append data to the file, tbh 06/2010
}
String validMsgs = triggerService.generateValidMessage(subjectData, totalValidationErrors);
out.write(validMsgs);
// third place to append data to the file? tbh 06/2010
}
// << tbh 05/2010, bug #5110, leave off the detailed reports
out.close();
if (fail) {
// forwardPage(Page.IMPORT_CRF_DATA);
// break here with an exception
// throw new Exception("Problems encountered with file " +
// f.getName() + ": " + msg.toString());
MessageFormat mf = new MessageFormat("");
mf.applyPattern(respage.getString("problems_encountered_with_file"));
Object[] arguments = { f.getName(), msg.toString() };
msg = new StringBuffer(mf.format(arguments) + "<br/>");
out.close();
auditMsg.append("You can see the log file <a href='" + SQLInitServlet.getField("sysURL.base") + "ViewLogMessage?n=" + generalFileDir + f.getName() + "&tn=" + triggerBean.getName() + "&gn=1'>here</a>.<br/>");
msg.append("You can see the log file <a href='" + SQLInitServlet.getField("sysURL.base") + "ViewLogMessage?n=" + generalFileDir + f.getName() + "&tn=" + triggerBean.getName() + "&gn=1'>here</a>.<br/>");
// ": " + msg.toString() + "<br/>");
continue;
} else {
msg.append(respage.getString("passing_crf_edit_checks") + "<br/>");
auditMsg.append(respage.getString("passing_crf_edit_checks") + "<br/>");
// session.setAttribute("importedData",
// displayItemBeanWrappers);
// session.setAttribute("validationErrors",
// totalValidationErrors);
// session.setAttribute("hardValidationErrors",
// hardValidationErrors);
// above are to be sent to the user, but what kind of message
// can we make of them here?
// if hard validation errors are present, we only generate one
// table
// otherwise, we generate the other two: validation errors and
// valid data
logger.debug("found total validation errors: " + totalValidationErrors.size());
SummaryStatsBean ssBean = getImportCRFDataService(dataSource).generateSummaryStatsBean(odmContainer, displayItemBeanWrappers, importCrfInfo);
// msg.append("===+");
// the above is a special key that we will use to split the
// message into two parts
// a shorter version for the audit and
// a longer version for the email
msg.append(triggerService.generateSummaryStatsMessage(ssBean, respage) + "<br/>");
// session.setAttribute("summaryStats", ssBean);
// will have to set hard edit checks here as well
// session.setAttribute("subjectData",
// ArrayList<SubjectDataBean> subjectData =
// odmContainer.getCrfDataPostImportContainer().getSubjectData();
// forwardPage(Page.VERIFY_IMPORT_SERVLET);
// instead of forwarding, go ahead and save it all, sending a
// message at the end
msg.append(triggerService.generateSkippedCRFMessage(importCrfInfo, resword) + "<br/>");
// setup ruleSets to run if applicable
List<ImportDataRuleRunnerContainer> containers = this.ruleRunSetup(dataSource, studyBean, ub, ruleSetService, odmContainer);
CrfBusinessLogicHelper crfBusinessLogicHelper = new CrfBusinessLogicHelper(dataSource);
for (DisplayItemBeanWrapper wrapper : displayItemBeanWrappers) {
boolean resetSDV = false;
int eventCrfBeanId = -1;
EventCRFBean eventCrfBean = new EventCRFBean();
logger.debug("right before we check to make sure it is savable: " + wrapper.isSavable());
if (wrapper.isSavable()) {
ArrayList<Integer> eventCrfInts = new ArrayList<Integer>();
logger.debug("wrapper problems found : " + wrapper.getValidationErrors().toString());
itemDataDao.setFormatDates(false);
for (DisplayItemBean displayItemBean : wrapper.getDisplayItemBeans()) {
eventCrfBeanId = displayItemBean.getData().getEventCRFId();
eventCrfBean = (EventCRFBean) eventCrfDao.findByPK(eventCrfBeanId);
logger.debug("found value here: " + displayItemBean.getData().getValue());
logger.debug("found status here: " + eventCrfBean.getStatus().getName());
ItemDataBean itemDataBean = new ItemDataBean();
itemDataBean = itemDataDao.findByItemIdAndEventCRFIdAndOrdinal(displayItemBean.getItem().getId(), eventCrfBean.getId(), displayItemBean.getData().getOrdinal());
if (wrapper.isOverwrite() && itemDataBean.getStatus() != null) {
logger.debug("just tried to find item data bean on item name " + displayItemBean.getItem().getName());
if (!itemDataBean.getValue().equals(displayItemBean.getData().getValue()))
resetSDV = true;
itemDataBean.setUpdatedDate(new Date());
itemDataBean.setUpdater(ub);
itemDataBean.setValue(displayItemBean.getData().getValue());
// set status?
itemDataDao.update(itemDataBean);
logger.debug("updated: " + itemDataBean.getItemId());
// need to set pk here in order to create dn
displayItemBean.getData().setId(itemDataBean.getId());
} else {
resetSDV = true;
itemDataDao.create(displayItemBean.getData());
logger.debug("created: " + displayItemBean.getData().getItemId());
ItemDataBean itemDataBean2 = itemDataDao.findByItemIdAndEventCRFIdAndOrdinal(displayItemBean.getItem().getId(), eventCrfBean.getId(), displayItemBean.getData().getOrdinal());
logger.debug("found: id " + itemDataBean2.getId() + " name " + itemDataBean2.getName());
displayItemBean.getData().setId(itemDataBean2.getId());
}
ItemDAO idao = new ItemDAO(dataSource);
ItemBean ibean = (ItemBean) idao.findByPK(displayItemBean.getData().getItemId());
logger.debug("*** checking for validation errors: " + ibean.getName());
String itemOid = displayItemBean.getItem().getOid() + "_" + wrapper.getStudyEventRepeatKey() + "_" + displayItemBean.getData().getOrdinal() + "_" + wrapper.getStudySubjectOid();
if (wrapper.getValidationErrors().containsKey(itemOid)) {
ArrayList messageList = (ArrayList) wrapper.getValidationErrors().get(itemOid);
for (int iter = 0; iter < messageList.size(); iter++) {
String message = (String) messageList.get(iter);
DiscrepancyNoteBean parentDn = createDiscrepancyNote(ibean, message, eventCrfBean, displayItemBean, null, ub, dataSource, studyBean);
createDiscrepancyNote(ibean, message, eventCrfBean, displayItemBean, parentDn.getId(), ub, dataSource, studyBean);
logger.debug("*** created disc note with message: " + message);
// displayItemBean);
}
}
// Update CRF status
if (!eventCrfInts.contains(new Integer(eventCrfBean.getId()))) {
String eventCRFStatus = importedCRFStatuses.get(new Integer(eventCrfBean.getId()));
if (eventCRFStatus != null && eventCRFStatus.equals(DataEntryStage.INITIAL_DATA_ENTRY.getName()) && eventCrfBean.getStatus().isAvailable()) {
crfBusinessLogicHelper.markCRFStarted(eventCrfBean, ub);
} else {
crfBusinessLogicHelper.markCRFComplete(eventCrfBean, ub);
}
logger.debug("*** just updated event crf bean: " + eventCrfBean.getId());
eventCrfInts.add(new Integer(eventCrfBean.getId()));
}
}
itemDataDao.setFormatDates(true);
// Reset the SDV status if item data has been changed or added
if (eventCrfBean != null && resetSDV)
eventCrfDao.setSDVStatus(false, ub.getId(), eventCrfBean.getId());
}
}
// msg.append("===+");
msg.append(respage.getString("data_has_been_successfully_import") + "<br/>");
auditMsg.append(respage.getString("data_has_been_successfully_import") + "<br/>");
// MessageFormat mf = new MessageFormat("");
String linkMessage = respage.getString("you_can_review_the_data") + SQLInitServlet.getField("sysURL.base") + respage.getString("you_can_review_the_data_2") + SQLInitServlet.getField("sysURL.base") + respage.getString("you_can_review_the_data_3") + generalFileDir + f.getName() + "&tn=" + triggerBean.getFullName() + "&gn=1" + respage.getString("you_can_review_the_data_4") + "<br/>";
// mf.applyPattern(respage.getString("you_can_review_the_data"));
// Object[] arguments = {
// SQLInitServlet.getField("sysURL.base"),
// SQLInitServlet.getField("sysURL.base"), f.getName() };
msg.append(linkMessage);
auditMsg.append(linkMessage);
// was here but is now moved up, tbh
// String finalLine =
// "<p>You can review the entered data <a href='" +
// SQLInitServlet.getField("sysURL.base") +
// "ListStudySubjects'>here</a>.";
// >> tbh additional message
// "you can review the validation messages here" <-- where
// 'here' is a link to view an external file
// i.e. /ViewExternal?n=file_name.txt
// << tbh 06/2010
// msg.append(finalLine);
// auditMsg.append(finalLine);
auditMsg.append(this.runRules(studyBean, ub, containers, ruleSetService, ExecutionMode.SAVE));
}
}
// end for loop
// is the writer still not closed? try to close it
ArrayList<String> retList = new ArrayList<String>();
retList.add(msg.toString());
retList.add(auditMsg.toString());
// msg.toString();
return retList;
}
use of org.akaza.openclinica.dao.submit.ItemDAO in project OpenClinica by OpenClinica.
the class OpenRosaXmlGenerator method buildInstance.
// method
/**
* @param model
* @param crfVersion
* @param crfSections
* @return
* @throws Exception
*/
private String buildInstance(Model model, FormLayoutBean formLayout, CRFVersionBean crfVersion, ArrayList<SectionBean> crfSections) throws Exception {
DocumentBuilderFactory docFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder build = docFactory.newDocumentBuilder();
Document doc = build.newDocument();
Element crfElement = doc.createElement(formLayout.getOid());
crfElement.setAttribute("id", formLayout.getOid());
doc.appendChild(crfElement);
crfElement.setAttributeNS("http://www.w3.org/2000/xmlns/", "xmlns:jr", "http://openrosa.org/javarosa");
for (SectionBean section : crfSections) {
Element sectionSubTitle = doc.createElement("SECTION_" + section.getId() + ".SUBTITLE");
Element sectionInstructions = doc.createElement("SECTION_" + section.getId() + ".INSTRUCTIONS");
Element sectionElm = doc.createElement("SECTION_" + section.getLabel().replaceAll("\\W", "_"));
crfElement.appendChild(sectionSubTitle);
crfElement.appendChild(sectionInstructions);
crfElement.appendChild(sectionElm);
}
ArrayList<ItemGroupBean> itemGroupBeans = getItemGroupBeansByFormLayout(formLayout);
for (ItemGroupBean itemGroupBean : itemGroupBeans) {
ItemGroupMetadataBean itemGroupMetadataBean = getItemGroupMetadataByGroup(itemGroupBean, crfVersion);
String repeatGroupMin = itemGroupMetadataBean.getRepeatNum().toString();
Boolean isrepeating = itemGroupMetadataBean.isRepeatingGroup();
Element groupElement = doc.createElement(itemGroupBean.getOid());
if (isrepeating) {
groupElement.setTextContent(repeatGroupMin);
groupElement.setAttribute("jr:template", "");
Element hiddenOrdinalItem = doc.createElement("OC.REPEAT_ORDINAL");
groupElement.appendChild(hiddenOrdinalItem);
}
crfElement.appendChild(groupElement);
idao = new ItemDAO(dataSource);
ArrayList<ItemBean> items = (ArrayList<ItemBean>) idao.findAllItemsByGroupIdOrdered(itemGroupBean.getId(), crfVersion.getId());
for (ItemBean item : items) {
ItemFormMetadataBean itemMetaData = getItemFormMetadata(item, crfVersion);
if (itemMetaData.getHeader() != null && !itemMetaData.getHeader().equals("")) {
Element header = doc.createElement(item.getOid() + ".HEADER");
groupElement.appendChild(header);
}
if (itemMetaData.getHeader() != null && !itemMetaData.getSubHeader().equals("")) {
Element subHeader = doc.createElement(item.getOid() + ".SUBHEADER");
groupElement.appendChild(subHeader);
}
Element question = doc.createElement(item.getOid());
groupElement.appendChild(question);
}
// end of item
}
// end of group
// add meta
Element meta = doc.createElement("meta");
// add instanceId
Element instanceId = doc.createElement("instanceID");
meta.appendChild(instanceId);
crfElement.appendChild(meta);
TransformerFactory transformFactory = TransformerFactory.newInstance();
Transformer transformer = transformFactory.newTransformer();
transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
StringWriter writer = new StringWriter();
StreamResult result = new StreamResult(writer);
DOMSource source = new DOMSource(doc);
transformer.transform(source, result);
return writer.toString();
}
use of org.akaza.openclinica.dao.submit.ItemDAO in project OpenClinica by OpenClinica.
the class OpenRosaXmlGenerator method getItemBean.
private ItemBean getItemBean(int itemId) {
ItemBean itemBean = null;
idao = new ItemDAO(dataSource);
itemBean = (ItemBean) idao.findByPK(itemId);
return itemBean;
}
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