public void processRequest() throws Exception {
FormProcessor fp = new FormProcessor(request);
int itemId = fp.getInt(ITEM_ID);
ItemDAO idao = new ItemDAO(sm.getDataSource());
ItemFormMetadataDAO ifmdao = new ItemFormMetadataDAO(sm.getDataSource());
CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
CRFDAO cdao = new CRFDAO(sm.getDataSource());
if (itemId == 0) {
addPageMessage("Please choose an item first.");
forwardPage(Page.ITEM_DETAIL);
return;
}
ItemBean item = (ItemBean) idao.findByPK(itemId);
ArrayList versions = idao.findAllVersionsByItemId(item.getId());
ArrayList versionItems = new ArrayList();
// finds each item metadata for each version
for (int i = 0; i < versions.size(); i++) {
Integer versionId = (Integer) versions.get(i);
CRFVersionBean version = (CRFVersionBean) cvdao.findByPK(versionId.intValue());
if (versionId != null && versionId.intValue() > 0) {
ItemFormMetadataBean imfBean =
ifmdao.findByItemIdAndCRFVersionId(item.getId(), versionId.intValue());
imfBean.setCrfVersionName(version.getName());
CRFBean crf = (CRFBean) cdao.findByPK(version.getCrfId());
imfBean.setCrfName(crf.getName());
versionItems.add(imfBean);
}
}
request.setAttribute(VERSION_ITEMS, versionItems);
request.setAttribute(ITEM_BEAN, item);
forwardPage(Page.ITEM_DETAIL);
}
@Override
public void processRequest() throws Exception {
resetPanel();
panel.setStudyInfoShown(false);
panel.setOrderedData(true);
panel.setSubmitDataModule(false);
panel.setExtractData(false);
panel.setCreateDataset(false);
setToPanel(resword.getString("create_CRF"), respage.getString("br_create_new_CRF_entering"));
setToPanel(
resword.getString("create_CRF_version"), respage.getString("br_create_new_CRF_uploading"));
setToPanel(
resword.getString("revise_CRF_version"), respage.getString("br_if_you_owner_CRF_version"));
setToPanel(
resword.getString("CRF_spreadsheet_template"),
respage.getString("br_download_blank_CRF_spreadsheet_from"));
setToPanel(
resword.getString("example_CRF_br_spreadsheets"),
respage.getString("br_download_example_CRF_instructions_from"));
FormProcessor fp = new FormProcessor(request);
// checks which module the requests are from, manage or admin
String module = fp.getString(MODULE);
request.setAttribute(MODULE, module);
int crfId = fp.getInt(CRF_ID);
if (crfId == 0) {
addPageMessage(respage.getString("please_choose_a_CRF_to_view"));
forwardPage(Page.CRF_LIST);
} else {
CRFDAO cdao = new CRFDAO(sm.getDataSource());
CRFVersionDAO vdao = new CRFVersionDAO(sm.getDataSource());
CRFBean crf = (CRFBean) cdao.findByPK(crfId);
ArrayList<CRFVersionBean> versions = (ArrayList<CRFVersionBean>) vdao.findAllByCRF(crfId);
crf.setVersions(versions);
// Collection<RuleSetBean> items =
// getRuleSetService().getRuleSetsByCrf(crf);
Collection<TableColumnHolder> items = populate(crf, versions);
TableFacade tableFacade = createTableFacade("rules", request);
tableFacade.setItems(items); // set the items
tableFacade.setExportTypes(response, CSV, JEXCEL);
tableFacade.setStateAttr("restore");
Limit limit = tableFacade.getLimit();
if (limit.isExported()) {
export(tableFacade);
// return null; // In Spring returning null tells the controller
// not to do anything.
}
String html = html(tableFacade);
request.setAttribute("rules", html); // Set the Html in the
// request for the JSP.
request.setAttribute(CRF, crf);
forwardPage(Page.VIEW_CRF);
}
}
private void validateStudy6(FormProcessor fp, Validator v) {
v.addValidation(
"medlineIdentifier",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"url",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"urlDescription",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
errors = v.validate();
study.setMedlineIdentifier(fp.getString("medlineIdentifier"));
study.setResultsReference(fp.getBoolean("resultsReference"));
study.setUrl(fp.getString("url"));
study.setUrlDescription(fp.getString("urlDescription"));
// request.setAttribute("interventions",session.getAttribute(
// "interventions"));
if (!errors.isEmpty()) {
request.setAttribute("formMessages", errors);
}
}
/** Finds all the studies */
@Override
public void processRequest() throws Exception {
StudyDAO sdao = new StudyDAO(sm.getDataSource());
ArrayList studies = (ArrayList) sdao.findAll();
// find all parent studies
ArrayList parents = (ArrayList) sdao.findAllParents();
ArrayList displayStudies = new ArrayList();
for (int i = 0; i < parents.size(); i++) {
StudyBean parent = (StudyBean) parents.get(i);
ArrayList children = (ArrayList) sdao.findAllByParent(parent.getId());
DisplayStudyBean displayStudy = new DisplayStudyBean();
displayStudy.setParent(parent);
displayStudy.setChildren(children);
displayStudies.add(displayStudy);
}
FormProcessor fp = new FormProcessor(request);
EntityBeanTable table = fp.getEntityBeanTable();
ArrayList allStudyRows = DisplayStudyRow.generateRowsFromBeans(displayStudies);
String[] columns = {
resword.getString("name"),
resword.getString("unique_identifier"),
resword.getString("OID"),
resword.getString("principal_investigator"),
resword.getString("facility_name"),
resword.getString("date_created"),
resword.getString("status"),
resword.getString("actions")
};
table.setColumns(new ArrayList(Arrays.asList(columns)));
table.hideColumnLink(2);
table.hideColumnLink(6);
table.setQuery("ListStudy", new HashMap());
table.addLink(resword.getString("create_a_new_study"), "CreateStudy");
table.setRows(allStudyRows);
table.computeDisplay();
request.setAttribute("table", table);
// request.setAttribute("studies", studies);
session.setAttribute("fromListSite", "no");
resetPanel();
panel.setStudyInfoShown(false);
panel.setOrderedData(true);
setToPanel(resword.getString("in_the_application"), "");
if (parents.size() > 0) {
setToPanel(resword.getString("studies"), new Integer(parents.size()).toString());
}
if (studies.size() > 0) {
setToPanel(
resword.getString("sites"), new Integer(studies.size() - parents.size()).toString());
}
forwardPage(Page.STUDY_LIST);
}
public void processRequest() throws Exception {
String action = request.getParameter("action");
FormProcessor fp = new FormProcessor(request);
int classId = fp.getInt("id");
if (classId == 0) {
addPageMessage("Please choose a subject group class to remove.");
forwardPage(Page.SUBJECT_GROUP_CLASS_LIST_SERVLET);
} else {
StudyGroupClassDAO sgcdao = new StudyGroupClassDAO(sm.getDataSource());
StudyGroupDAO sgdao = new StudyGroupDAO(sm.getDataSource());
SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource());
if (action.equalsIgnoreCase("confirm")) {
StudyGroupClassBean sgcb = (StudyGroupClassBean) sgcdao.findByPK(classId);
if (sgcb.getStatus().equals(Status.DELETED)) {
addPageMessage("This subject group class has been deleted already.");
forwardPage(Page.SUBJECT_GROUP_CLASS_LIST_SERVLET);
return;
}
ArrayList groups = sgdao.findAllByGroupClass(sgcb);
for (int i = 0; i < groups.size(); i++) {
StudyGroupBean sg = (StudyGroupBean) groups.get(i);
ArrayList subjectMaps = sgmdao.findAllByStudyGroupClassAndGroup(sgcb.getId(), sg.getId());
sg.setSubjectMaps(subjectMaps);
}
session.setAttribute("group", sgcb);
session.setAttribute("studyGroups", groups);
forwardPage(Page.REMOVE_SUBJECT_GROUP_CLASS);
} else if (action.equalsIgnoreCase("submit")) {
StudyGroupClassBean group = (StudyGroupClassBean) session.getAttribute("group");
group.setStatus(Status.DELETED);
group.setUpdater(ub);
sgcdao.update(group);
ArrayList subjectMaps = sgmdao.findAllByStudyGroupClassId(group.getId());
for (int i = 0; i < subjectMaps.size(); i++) {
SubjectGroupMapBean sgmb = (SubjectGroupMapBean) subjectMaps.get(i);
sgmb.setStatus(Status.DELETED);
sgmb.setUpdater(ub);
sgmdao.update(sgmb);
}
addPageMessage("This subject group class was removed successfully.");
forwardPage(Page.SUBJECT_GROUP_CLASS_LIST_SERVLET);
} else {
addPageMessage("No action specified.");
forwardPage(Page.SUBJECT_GROUP_CLASS_LIST_SERVLET);
}
}
}
@Override
protected void processRequest() throws Exception {
FormProcessor fp = new FormProcessor(request);
DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(sm.getDataSource());
int noteId = fp.getInt(NOTE_ID, true);
DiscrepancyNoteBean note = (DiscrepancyNoteBean) dndao.findByPK(noteId);
String entityType = note.getEntityType();
UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
ArrayList notes = dndao.findAllEntityByPK(note.getEntityType(), noteId);
Date lastUpdatedDate = note.getCreatedDate();
UserAccountBean lastUpdator = (UserAccountBean) udao.findByPK(note.getOwnerId());
for (int i = 0; i < notes.size(); i++) {
DiscrepancyNoteBean n = (DiscrepancyNoteBean) notes.get(i);
int pId = n.getParentDnId();
if (pId == 0) {
note = n;
note.setLastUpdator((UserAccountBean) udao.findByPK(n.getOwnerId()));
note.setLastDateUpdated(n.getCreatedDate());
lastUpdatedDate = note.getLastDateUpdated();
lastUpdator = note.getLastUpdator();
}
}
for (int i = 0; i < notes.size(); i++) {
DiscrepancyNoteBean n = (DiscrepancyNoteBean) notes.get(i);
int pId = n.getParentDnId();
if (pId > 0) {
note.getChildren().add(n);
if (!n.getCreatedDate().before(lastUpdatedDate)) {
lastUpdatedDate = n.getCreatedDate();
lastUpdator = (UserAccountBean) udao.findByPK(n.getOwnerId());
note.setLastUpdator(lastUpdator);
note.setLastDateUpdated(lastUpdatedDate);
note.setResolutionStatusId(n.getResolutionStatusId());
note.setResStatus(ResolutionStatus.get(n.getResolutionStatusId()));
}
}
}
note.setNumChildren(note.getChildren().size());
note.setDisType(DiscrepancyNoteType.get(note.getDiscrepancyNoteTypeId()));
logger.info("Just set Note: " + note.getCrfName() + " column " + note.getColumn());
request.setAttribute(DIS_NOTE, note);
forwardPage(Page.VIEW_SINGLE_NOTE);
}
private boolean updateStudy2(FormProcessor fp) {
study.setOldStatus(study.getStatus());
study.setStatus(Status.get(fp.getInt("statusId")));
if (StringUtil.isBlank(fp.getString(INPUT_VER_DATE))) {
study.setProtocolDateVerification(null);
} else {
study.setProtocolDateVerification(fp.getDate(INPUT_VER_DATE));
}
study.setDatePlannedStart(fp.getDate(INPUT_START_DATE));
if (StringUtil.isBlank(fp.getString(INPUT_END_DATE))) {
study.setDatePlannedEnd(null);
} else {
study.setDatePlannedEnd(fp.getDate(INPUT_END_DATE));
}
study.setPhase(fp.getString("phase"));
if (fp.getInt("genetic") == 1) {
study.setGenetic(true);
} else {
study.setGenetic(false);
}
String interventional = resadmin.getString("interventional");
return interventional.equalsIgnoreCase(study.getProtocolType());
}
private StudyBean createStudyBean(FormProcessor fp) {
StudyBean newStudy = study;
newStudy.setId(fp.getInt("studyId"));
newStudy.setName(fp.getString("name"));
newStudy.setOfficialTitle(fp.getString("officialTitle"));
newStudy.setIdentifier(fp.getString("uniqueProId"));
newStudy.setSecondaryIdentifier(fp.getString("secondProId"));
newStudy.setPrincipalInvestigator(fp.getString("prinInvestigator"));
newStudy.setSummary(fp.getString("description"));
newStudy.setProtocolDescription(fp.getString("protocolDescription"));
newStudy.setSponsor(fp.getString("sponsor"));
newStudy.setCollaborators(fp.getString("collaborators"));
return newStudy;
}
private Date getInputEndDate() {
/*
* if (fp.getString(INPUT_ENDDATE_PREFIX + "Date").equals("")) { return
* fp.getDateTime(INPUT_STARTDATE_PREFIX); } else { return
* fp.getDateTime(INPUT_ENDDATE_PREFIX); }
*/
return fp.getDateTime(INPUT_ENDDATE_PREFIX);
}
@Override
protected void processRequest() throws Exception {
UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
FormProcessor fp = new FormProcessor(request);
int userId = fp.getInt(ARG_USERID);
UserAccountBean u = (UserAccountBean) udao.findByPK(userId);
String message;
if (!u.isActive() || u.getAccountNonLocked()) {
message = respage.getString("the_specified_user_not_exits");
} else {
u.setUpdater(ub);
SecurityManager sm =
((SecurityManager)
SpringServletAccess.getApplicationContext(context).getBean("securityManager"));
String password = sm.genPassword();
String passwordHash = sm.encrytPassword(password, getUserDetails());
u.setPasswd(passwordHash);
u.setPasswdTimestamp(null);
u.setAccountNonLocked(Boolean.TRUE);
u.setStatus(Status.AVAILABLE);
u.setLockCounter(0);
udao.update(u);
if (udao.isQuerySuccessful()) {
message = respage.getString("the_user_has_been_unlocked");
try {
sendRestoreEmail(u, password);
} catch (Exception e) {
message += respage.getString("however_was_error_sending_user_email_regarding");
}
} else {
message = respage.getString("the_user_could_not_be_deleted_due_database_error");
}
}
addPageMessage(message);
forwardPage(Page.LIST_USER_ACCOUNTS_SERVLET);
}
private void validateStudy1(FormProcessor fp, Validator v) {
v.addValidation("name", Validator.NO_BLANKS);
v.addValidation("uniqueProId", Validator.NO_BLANKS);
v.addValidation("description", Validator.NO_BLANKS);
v.addValidation("prinInvestigator", Validator.NO_BLANKS);
v.addValidation("sponsor", Validator.NO_BLANKS);
v.addValidation(
"secondProId",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"collaborators",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
1000);
v.addValidation(
"protocolDescription",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
1000);
errors = v.validate();
if (fp.getString("name").trim().length() > 100) {
Validator.addError(errors, "name", resexception.getString("maximum_lenght_name_100"));
}
if (fp.getString("uniqueProId").trim().length() > 30) {
Validator.addError(
errors, "uniqueProId", resexception.getString("maximum_lenght_unique_protocol_30"));
}
if (fp.getString("description").trim().length() > 255) {
Validator.addError(
errors, "description", resexception.getString("maximum_lenght_brief_summary_255"));
}
if (fp.getString("prinInvestigator").trim().length() > 255) {
Validator.addError(
errors,
"prinInvestigator",
resexception.getString("maximum_lenght_principal_investigator_255"));
}
if (fp.getString("sponsor").trim().length() > 255) {
Validator.addError(errors, "sponsor", resexception.getString("maximum_lenght_sponsor_255"));
}
if (fp.getString("officialTitle").trim().length() > 255) {
Validator.addError(
errors, "officialTitle", resexception.getString("maximum_lenght_official_title_255"));
}
study = createStudyBean(fp);
}
/** Override processRequest in super class */
@Override
public void processRequest() throws Exception {
FormProcessor fp = new FormProcessor(request);
int current = fp.getInt("current");
int previous = fp.getInt("previous");
int currOrdinal = fp.getInt("currentOrdinal");
int prevOrdinal = fp.getInt("previousOrdinal");
int definitionId = fp.getInt("id");
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
increase(current, previous, currOrdinal, prevOrdinal, definitionId, edcdao);
request.setAttribute("id", new Integer(definitionId).toString());
forwardPage(Page.VIEW_EVENT_DEFINITION_SERVLET);
}
private void validateStudy3(boolean isInterventional, Validator v, FormProcessor fp) {
v.addValidation("purpose", Validator.NO_BLANKS);
for (int i = 0; i < 10; i++) {
String type = fp.getString("interType" + i);
String name = fp.getString("interName" + i);
if (!StringUtil.isBlank(type) && StringUtil.isBlank(name)) {
v.addValidation("interName", Validator.NO_BLANKS);
request.setAttribute(
"interventionError", respage.getString("name_cannot_be_blank_if_type"));
break;
}
if (!StringUtil.isBlank(name) && StringUtil.isBlank(type)) {
v.addValidation("interType", Validator.NO_BLANKS);
request.setAttribute(
"interventionError", respage.getString("name_cannot_be_blank_if_name"));
break;
}
}
updateStudy3(isInterventional, fp);
}
private void validateStudy4(FormProcessor fp, Validator v) {
v.addValidation(
"conditions",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
500);
v.addValidation(
"keywords",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"eligibility",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
500);
errors = v.validate();
if (fp.getInt("expectedTotalEnrollment") <= 0) {
Validator.addError(
errors,
"expectedTotalEnrollment",
respage.getString("expected_total_enrollment_must_be_a_positive_number"));
}
study.setConditions(fp.getString("conditions"));
study.setKeywords(fp.getString("keywords"));
study.setEligibility(fp.getString("eligibility"));
study.setGender(fp.getString("gender"));
study.setAgeMax(fp.getString("ageMax"));
study.setAgeMin(fp.getString("ageMin"));
study.setHealthyVolunteerAccepted(fp.getBoolean("healthyVolunteerAccepted"));
study.setExpectedTotalEnrollment(fp.getInt("expectedTotalEnrollment"));
request.setAttribute("facRecruitStatusMap", CreateStudyServlet.facRecruitStatusMap);
}
@Override
protected void processRequest() throws Exception {
FormProcessor fp = new FormProcessor(request);
String triggerName = fp.getString("tname");
String gName = fp.getString("gname");
String finalGroupName = "";
if ("".equals(gName) || "0".equals(gName)) {
finalGroupName = groupName;
} else { // should equal 1
finalGroupName = groupImportName;
}
String deleteMe = fp.getString("del");
scheduler = getScheduler();
Trigger trigger = scheduler.getTrigger(triggerName, finalGroupName);
try {
// System.out.println("found delete key: "+deleteMe);
// System.out.println("found is sys admin: "+ub.isSysAdmin());
// System.out.println("found is tech admin: "+ub.isTechAdmin());
if (("y".equals(deleteMe)) && (ub.isSysAdmin())) {
scheduler.deleteJob(triggerName, finalGroupName);
// set return message here
System.out.println("deleted job: " + triggerName);
addPageMessage(
"The following job "
+ triggerName
+ " and its corresponding Trigger have been deleted from the system.");
} else {
if (scheduler.getTriggerState(triggerName, finalGroupName) == Trigger.STATE_PAUSED) {
scheduler.resumeTrigger(triggerName, finalGroupName);
// trigger.setPriority(Trigger.DEFAULT_PRIORITY);
System.out.println("-- resuming trigger! " + triggerName + " " + finalGroupName);
addPageMessage(
"This trigger "
+ triggerName
+ " has been resumed and will continue to run until paused or deleted.");
// set message here
} else {
scheduler.pauseTrigger(triggerName, finalGroupName);
// trigger.setPriority(Trigger.STATE_PAUSED);
System.out.println("-- pausing trigger! " + triggerName + " " + finalGroupName);
addPageMessage(
"This trigger "
+ triggerName
+ " has been paused, and will not run again until it is restored.");
// set message here
}
}
} catch (NullPointerException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
// all validation done on JSP side
// forward back to view job servlet here
// set a message
if ("".equals(gName) || "0".equals(gName)) {
forwardPage(Page.VIEW_JOB_SERVLET);
} else {
forwardPage(Page.VIEW_IMPORT_JOB_SERVLET);
}
}
protected void processRequest() throws Exception {
UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
FormProcessor fp = new FormProcessor(request);
int userId = fp.getInt(ARG_USERID);
int action = fp.getInt(ARG_ACTION);
UserAccountBean u = (UserAccountBean) udao.findByPK(userId);
String message;
if (!u.isActive()) {
message = respage.getString("the_specified_user_not_exits");
} else if (!EntityAction.contains(action)) {
message = respage.getString("the_specified_action_on_the_user_is_invalid");
} else if (!EntityAction.get(action).equals(EntityAction.DELETE)
&& !EntityAction.get(action).equals(EntityAction.RESTORE)) {
message = respage.getString("the_specified_action_is_not_allowed");
} else {
EntityAction desiredAction = EntityAction.get(action);
u.setUpdater(ub);
if (desiredAction.equals(EntityAction.DELETE)) {
udao.delete(u);
if (udao.isQuerySuccessful()) {
message = respage.getString("the_user_has_been_deleted");
// YW 07-31-2007 << for feature that deletion doesn't need email the deleted user.
/*
//YW 07-26-2007 << catch exception (eg. timeout) and inform users.
try {
sendDeleteEmail(u);
} catch (Exception e) {
message += " However, there has been an error sending the user an email regarding this deletion.";
}
*/
// YW >>
} else {
message = respage.getString("the_user_could_not_be_deleted_due_database_error");
}
} else {
SecurityManager sm = SecurityManager.getInstance();
String password = sm.genPassword();
String passwordHash = sm.encrytPassword(password);
u.setPasswd(passwordHash);
u.setPasswdTimestamp(null);
udao.restore(u);
if (udao.isQuerySuccessful()) {
message = respage.getString("the_user_has_been_restored");
try {
sendRestoreEmail(u, password);
} catch (Exception e) {
message += respage.getString("however_was_error_sending_user_email_regarding");
}
} else {
message = respage.getString("the_user_could_not_be_deleted_due_database_error");
}
}
}
addPageMessage(message);
forwardPage(Page.LIST_USER_ACCOUNTS_SERVLET);
}
@Override
public void processRequest() throws Exception {
resetPanel();
panel.setStudyInfoShown(false);
panel.setOrderedData(true);
FormProcessor fp = new FormProcessor(request);
// checks which module the requests are from
String module = fp.getString(MODULE);
// keep the module in the session
session.setAttribute(MODULE, module);
String action = request.getParameter("action");
CRFVersionBean version = (CRFVersionBean) session.getAttribute("version");
File xsdFile = new File(SpringServletAccess.getPropertiesDir(context) + "ODM1-3-0.xsd");
File xsdFile2 = new File(SpringServletAccess.getPropertiesDir(context) + "ODM1-2-1.xsd");
if (StringUtil.isBlank(action)) {
logger.info("action is blank");
request.setAttribute("version", version);
forwardPage(Page.IMPORT_CRF_DATA);
}
if ("confirm".equalsIgnoreCase(action)) {
String dir = SQLInitServlet.getField("filePath");
if (!(new File(dir)).exists()) {
logger.info("The filePath in datainfo.properties is invalid " + dir);
addPageMessage(respage.getString("filepath_you_defined_not_seem_valid"));
forwardPage(Page.IMPORT_CRF_DATA);
}
// All the uploaded files will be saved in filePath/crf/original/
String theDir = dir + "crf" + File.separator + "original" + File.separator;
if (!(new File(theDir)).isDirectory()) {
(new File(theDir)).mkdirs();
logger.info("Made the directory " + theDir);
}
// MultipartRequest multi = new MultipartRequest(request, theDir, 50 * 1024 * 1024);
File f = null;
try {
f = uploadFile(theDir, version);
} catch (Exception e) {
logger.warn("*** Found exception during file upload***");
e.printStackTrace();
}
if (f == null) {
forwardPage(Page.IMPORT_CRF_DATA);
}
// TODO
// validation steps
// 1. valid xml - validated by file uploader below
// LocalConfiguration config = LocalConfiguration.getInstance();
// config.getProperties().setProperty(
// "org.exolab.castor.parser.namespaces",
// "true");
// config
// .getProperties()
// .setProperty("org.exolab.castor.sax.features",
// "http://xml.org/sax/features/validation,
// http://apache.org/xml/features/validation/schema,
// http://apache.org/xml/features/validation/schema-full-checking");
// // above sets to validate against namespace
Mapping myMap = new Mapping();
String propertiesPath = CoreResources.PROPERTIES_DIR;
myMap.loadMapping(propertiesPath + File.separator + "cd_odm_mapping.xml");
Unmarshaller um1 = new Unmarshaller(myMap);
// um1.addNamespaceToPackageMapping("http://www.cdisc.org/ns/odm/v1.3"
// ,
// "ODMContainer");
boolean fail = false;
ODMContainer odmContainer = new ODMContainer();
try {
// schemaValidator.validateAgainstSchema(f, xsdFile);
// utf-8 compliance, tbh 06/2009
InputStreamReader isr = new InputStreamReader(new FileInputStream(f), "UTF-8");
odmContainer = (ODMContainer) um1.unmarshal(isr);
System.out.println(
"Found crf data container for study oid: "
+ odmContainer.getCrfDataPostImportContainer().getStudyOID());
System.out.println(
"found length of subject list: "
+ odmContainer.getCrfDataPostImportContainer().getSubjectData().size());
// 2. validates against ODM 1.3
// check it all below, throw an exception and route to a
// different
// page if not working
// TODO this block of code needs the xerces serializer in order
// to
// work
// StringWriter myWriter = new StringWriter();
// Marshaller m1 = new Marshaller(myWriter);
//
// m1.setProperty("org.exolab.castor.parser.namespaces",
// "true");
// m1
// .setProperty("org.exolab.castor.sax.features",
// "http://xml.org/sax/features/validation,
// http://apache.org/xml/features/validation/schema,
// http://apache.org/xml/features/validation/schema-full-checking
// ");
//
// m1.setMapping(myMap);
// m1.setNamespaceMapping("",
// "http://www.cdisc.org/ns/odm/v1.3");
// m1.setSchemaLocation("http://www.cdisc.org/ns/odm/v1.3
// ODM1-3.xsd");
// m1.marshal(odmContainer);
// if you havent thrown it, you wont throw it here
addPageMessage(respage.getString("passed_xml_validation"));
} catch (Exception me1) {
me1.printStackTrace();
// expanding it to all exceptions, but hoping to catch Marshal
// Exception or SAX Exceptions
logger.info("found exception with xml transform");
//
logger.info("trying 1.2.1");
try {
schemaValidator.validateAgainstSchema(f, xsdFile2);
// for backwards compatibility, we also try to validate vs
// 1.2.1 ODM 06/2008
InputStreamReader isr = new InputStreamReader(new FileInputStream(f), "UTF-8");
odmContainer = (ODMContainer) um1.unmarshal(isr);
} 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()};
addPageMessage(mf.format(arguments));
//
// addPageMessage("Your XML is not well-formed, and does not
// comply with the ODM 1.3 Schema. Please check it, and try
// again. It returned the message: "
// + me1.getMessage());
// me1.printStackTrace();
forwardPage(Page.IMPORT_CRF_DATA);
// you can't really wait to forward because then you throw
// NPEs
// in the next few parts of the code
}
}
// TODO need to output further here
// 2.a. is the study the same one that the user is in right now?
// 3. validates against study metadata
// 3.a. is that study subject in that study?
// 3.b. is that study event def in that study?
// 3.c. is that site in that study?
// 3.d. is that crf version in that study event def?
// 3.e. are those item groups in that crf version?
// 3.f. are those items in that item group?
List<String> errors =
getImportCRFDataService().validateStudyMetadata(odmContainer, ub.getActiveStudyId());
if (errors != null) {
// add to session
// forward to another page
logger.info(errors.toString());
for (String error : errors) {
addPageMessage(error);
}
if (errors.size() > 0) {
// fail = true;
forwardPage(Page.IMPORT_CRF_DATA);
} else {
addPageMessage(respage.getString("passed_study_check"));
addPageMessage(respage.getString("passed_oid_metadata_check"));
}
}
System.out.println("passed error check");
// TODO ADD many validation steps before we get to the
// session-setting below
// 4. is the event in the correct status to accept data import?
// -- scheduled, data entry started, completed
// (and the event should already be created)
// (and the event should be independent, ie not affected by other
// events)
List<EventCRFBean> eventCRFBeans =
getImportCRFDataService().fetchEventCRFBeans(odmContainer, ub);
ArrayList<Integer> permittedEventCRFIds = new ArrayList<Integer>();
logger.info("found a list of eventCRFBeans: " + eventCRFBeans.toString());
List<DisplayItemBeanWrapper> displayItemBeanWrappers =
new ArrayList<DisplayItemBeanWrapper>();
HashMap<String, String> totalValidationErrors = new HashMap<String, String>();
HashMap<String, String> hardValidationErrors = new HashMap<String, String>();
System.out.println("found event crfs " + eventCRFBeans.size());
// -- does the event already exist? if not, fail
if (!eventCRFBeans.isEmpty()) {
for (EventCRFBean eventCRFBean : eventCRFBeans) {
DataEntryStage dataEntryStage = eventCRFBean.getStage();
Status eventCRFStatus = eventCRFBean.getStatus();
logger.info(
"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)) {
// actually want the negative
// was status == available and the stage questions, but
// when you are at 'data entry complete' your status is
// set to 'unavailable'.
// >> tbh 09/2008
// HOWEVER, when one event crf is removed and the rest
// are good, what happens???
// need to create a list and inform that one is blocked
// and the rest are not...
//
permittedEventCRFIds.add(new Integer(eventCRFBean.getId()));
} else {
// fail = true;
// addPageMessage(respage.getString(
// "the_event_crf_not_correct_status"));
// forwardPage(Page.IMPORT_CRF_DATA);
}
}
// so that we don't repeat this following message
// did we exclude all the event CRFs? if not, pass, else fail
if (eventCRFBeans.size() >= permittedEventCRFIds.size()) {
addPageMessage(respage.getString("passed_event_crf_status_check"));
} else {
fail = true;
addPageMessage(respage.getString("the_event_crf_not_correct_status"));
}
// do they all have to have the right status to move
// forward? answer from bug tracker = no
// 5. do the items contain the correct data types?
// 6. are all the related OIDs present?
// that is to say, do we chain all the way down?
// this is covered by the OID Metadata Check
// 7. do the edit checks pass?
// only then can we pass on to VERIFY_IMPORT_SERVLET
// do we overwrite?
// XmlParser xp = new XmlParser();
// List<HashMap<String, String>> importedData =
// xp.getData(f);
// now we generate hard edit checks, and have to set that to the
// screen. get that from the service, generate a summary bean to
// set to either
// page in the workflow, either verifyImport.jsp or import.jsp
try {
List<DisplayItemBeanWrapper> tempDisplayItemBeanWrappers =
new ArrayList<DisplayItemBeanWrapper>();
tempDisplayItemBeanWrappers =
getImportCRFDataService()
.lookupValidationErrors(
request,
odmContainer,
ub,
totalValidationErrors,
hardValidationErrors,
permittedEventCRFIds);
System.out.println(
"generated display item bean wrappers " + tempDisplayItemBeanWrappers.size());
System.out.println("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?
fail = true;
logger.debug("threw a NPE after calling lookup validation errors");
addPageMessage(respage.getString("an_error_was_thrown_while_validation_errors"));
System.out.println("threw the null pointer at line 323, import");
// npe1.printStackTrace();
} catch (OpenClinicaException oce1) {
fail = true;
logger.debug(
"threw an OCE after calling lookup validation errors "
+ oce1.getOpenClinicaMessage());
addPageMessage(oce1.getOpenClinicaMessage());
System.out.println("threw the openclinica message at line 327, import");
}
} else {
fail = true;
addPageMessage(respage.getString("no_event_crfs_matching_the_xml_metadata"));
}
// for (HashMap<String, String> crfData : importedData) {
// DisplayItemBeanWrapper displayItemBeanWrapper =
// testing(request,
// crfData);
// displayItemBeanWrappers.add(displayItemBeanWrapper);
// errors = displayItemBeanWrapper.getValidationErrors();
//
// }
if (fail) {
System.out.println("failed here - forwarding...");
forwardPage(Page.IMPORT_CRF_DATA);
} else {
addPageMessage(respage.getString("passing_crf_edit_checks"));
session.setAttribute("importedData", displayItemBeanWrappers);
session.setAttribute("validationErrors", totalValidationErrors);
session.setAttribute("hardValidationErrors", hardValidationErrors);
// above are updated 'statically' by the method that originally
// generated the wrappers; soon the only thing we will use
// wrappers for is the 'overwrite' flag
System.out.println("found total validation errors: " + totalValidationErrors.size());
logger.debug("+++ content of total validation errors: " + totalValidationErrors.toString());
SummaryStatsBean ssBean =
getImportCRFDataService()
.generateSummaryStatsBean(odmContainer, displayItemBeanWrappers);
session.setAttribute("summaryStats", ssBean);
// will have to set hard edit checks here as well
session.setAttribute(
"subjectData", odmContainer.getCrfDataPostImportContainer().getSubjectData());
System.out.println("did not fail - forwarding...");
forwardPage(Page.VERIFY_IMPORT_SERVLET);
}
}
}
@Override
public void processRequest() throws Exception {
CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
FormProcessor fp = new FormProcessor(request);
int versionId = fp.getInt("id", true);
String module = fp.getString("module");
request.setAttribute("module", module);
String action = fp.getString("action");
if (versionId == 0) {
addPageMessage(respage.getString("please_choose_a_CRF_version_to_remove"));
forwardPage(Page.CRF_LIST_SERVLET);
} else {
if (StringUtil.isBlank(action)) {
addPageMessage(respage.getString("no_action_specified"));
forwardPage(Page.CRF_LIST_SERVLET);
return;
}
CRFVersionBean version = (CRFVersionBean) cvdao.findByPK(versionId);
SectionDAO secdao = new SectionDAO(sm.getDataSource());
EventCRFDAO evdao = new EventCRFDAO(sm.getDataSource());
// find all event crfs by version id
ArrayList eventCRFs = evdao.findUndeletedWithStudySubjectsByCRFVersion(versionId);
if ("confirm".equalsIgnoreCase(action)) {
request.setAttribute("versionToRemove", version);
request.setAttribute("eventCRFs", eventCRFs);
forwardPage(Page.REMOVE_CRF_VERSION);
} else {
logger.info("submit to remove the crf version");
// version
version.setStatus(Status.DELETED);
version.setUpdater(ub);
version.setUpdatedDate(new Date());
cvdao.update(version);
// added below tbh 092007, seems that we don't remove the event
// crfs in the second pass
for (int ii = 0; ii < eventCRFs.size(); ii++) {
EventCRFBean ecbean = (EventCRFBean) eventCRFs.get(ii);
ecbean.setStatus(Status.AUTO_DELETED);
ecbean.setUpdater(ub);
ecbean.setUpdatedDate(new Date());
evdao.update(ecbean);
}
// added above tbh 092007, to fix task
// all sections
ArrayList sections = secdao.findAllByCRFVersionId(version.getId());
for (int j = 0; j < sections.size(); j++) {
SectionBean section = (SectionBean) sections.get(j);
if (!section.getStatus().equals(Status.DELETED)) {
section.setStatus(Status.AUTO_DELETED);
section.setUpdater(ub);
section.setUpdatedDate(new Date());
secdao.update(section);
}
}
// all item data related to event crfs
ItemDataDAO idao = new ItemDataDAO(sm.getDataSource());
for (int i = 0; i < eventCRFs.size(); i++) {
EventCRFBean eventCRF = (EventCRFBean) eventCRFs.get(i);
if (!eventCRF.getStatus().equals(Status.DELETED)) {
eventCRF.setStatus(Status.AUTO_DELETED);
eventCRF.setUpdater(ub);
eventCRF.setUpdatedDate(new Date());
evdao.update(eventCRF);
ArrayList items = idao.findAllByEventCRFId(eventCRF.getId());
for (int j = 0; j < items.size(); j++) {
ItemDataBean item = (ItemDataBean) items.get(j);
if (!item.getStatus().equals(Status.DELETED)) {
item.setStatus(Status.AUTO_DELETED);
item.setUpdater(ub);
item.setUpdatedDate(new Date());
idao.update(item);
}
}
}
}
addPageMessage(
respage.getString("the_CRF")
+ version.getName()
+ " "
+ respage.getString("has_been_removed_succesfully"));
forwardPage(Page.CRF_LIST_SERVLET);
}
}
}
@Override
public void processRequest() throws Exception {
resetPanel();
FormProcessor fp = new FormProcessor(request);
Validator v = new Validator(request);
int studyId = fp.getInt("id");
studyId = studyId == 0 ? fp.getInt("studyId") : studyId;
String action = fp.getString("action");
StudyDAO sdao = new StudyDAO(sm.getDataSource());
boolean isInterventional = false;
study = (StudyBean) sdao.findByPK(studyId);
if (study.getId() != currentStudy.getId()) {
addPageMessage(
respage.getString("not_current_study")
+ respage.getString("change_study_contact_sysadmin"));
forwardPage(Page.MENU_SERVLET);
return;
}
study.setId(studyId);
StudyConfigService scs = new StudyConfigService(sm.getDataSource());
study = scs.setParametersForStudy(study);
request.setAttribute("studyToView", study);
request.setAttribute("studyId", studyId + "");
request.setAttribute("studyPhaseMap", CreateStudyServlet.studyPhaseMap);
ArrayList statuses = Status.toStudyUpdateMembersList();
statuses.add(Status.PENDING);
request.setAttribute("statuses", statuses);
String interventional = resadmin.getString("interventional");
isInterventional = interventional.equalsIgnoreCase(study.getProtocolType());
request.setAttribute("isInterventional", isInterventional ? "1" : "0");
String protocolType = study.getProtocolTypeKey();
// A. Hamid. 5001
if (study.getParentStudyId() > 0) {
StudyBean parentStudy = (StudyBean) sdao.findByPK(study.getParentStudyId());
request.setAttribute("parentStudy", parentStudy);
}
ArrayList interventionArray = new ArrayList();
if (isInterventional) {
interventionArray = parseInterventions((study));
setMaps(isInterventional, interventionArray);
} else {
setMaps(isInterventional, interventionArray);
}
if (!action.equals("submit")) {
// First Load First Form
if (study.getDatePlannedStart() != null) {
fp.addPresetValue(INPUT_START_DATE, local_df.format(study.getDatePlannedStart()));
}
if (study.getDatePlannedEnd() != null) {
fp.addPresetValue(INPUT_END_DATE, local_df.format(study.getDatePlannedEnd()));
}
if (study.getProtocolDateVerification() != null) {
fp.addPresetValue(INPUT_VER_DATE, local_df.format(study.getProtocolDateVerification()));
}
setPresetValues(fp.getPresetValues());
// first load 2nd form
}
if (study == null) {
addPageMessage(respage.getString("please_choose_a_study_to_edit"));
forwardPage(Page.STUDY_LIST_SERVLET);
return;
}
if (action.equals("submit")) {
validateStudy1(fp, v);
validateStudy2(fp, v);
validateStudy3(isInterventional, v, fp);
validateStudy4(fp, v);
validateStudy5(fp, v);
validateStudy6(fp, v);
confirmWholeStudy(fp, v);
request.setAttribute("studyToView", study);
if (!errors.isEmpty()) {
System.out.println("found errors : " + errors.toString());
request.setAttribute("formMessages", errors);
forwardPage(Page.UPDATE_STUDY_NEW);
} else {
study.setProtocolType(protocolType);
submitStudy(study);
addPageMessage(respage.getString("the_study_has_been_updated_succesfully"));
ArrayList pageMessages = (ArrayList) request.getAttribute(PAGE_MESSAGE);
session.setAttribute("pageMessages", pageMessages);
response.sendRedirect(request.getContextPath() + "/pages/studymodule");
// forwardPage(Page.MANAGE_STUDY_MODULE);
}
} else {
forwardPage(Page.UPDATE_STUDY_NEW);
}
}
private void updateStudy3(boolean isInterventional, FormProcessor fp) {
study.setPurpose(fp.getString("purpose"));
ArrayList interventionArray = new ArrayList();
if (isInterventional) {
study.setAllocation(fp.getString("allocation"));
study.setMasking(fp.getString("masking"));
study.setControl(fp.getString("control"));
study.setAssignment(fp.getString("assignment"));
study.setEndpoint(fp.getString("endpoint"));
StringBuffer interventions = new StringBuffer();
for (int i = 0; i < 10; i++) {
String type = fp.getString("interType" + i);
String name = fp.getString("interName" + i);
if (!StringUtil.isBlank(type) && !StringUtil.isBlank(name)) {
InterventionBean ib =
new InterventionBean(fp.getString("interType" + i), fp.getString("interName" + i));
interventionArray.add(ib);
interventions.append(ib.toString()).append(",");
}
}
study.setInterventions(interventions.toString());
} else { // type = observational
study.setDuration(fp.getString("duration"));
study.setSelection(fp.getString("selection"));
study.setTiming(fp.getString("timing"));
}
request.setAttribute("interventions", interventionArray);
}
@Override
protected void processRequest() throws Exception {
checkStudyLocked(Page.LIST_STUDY_SUBJECTS, respage.getString("current_study_locked"));
panel.setStudyInfoShown(false);
fp = new FormProcessor(request);
FormDiscrepancyNotes discNotes = null;
int studySubjectId = fp.getInt(INPUT_STUDY_SUBJECT_ID_FROM_VIEWSUBJECT);
// input from manage subject matrix, user has specified definition id
int studyEventDefinitionId = fp.getInt(INPUT_STUDY_EVENT_DEFINITION);
// TODO: make this sensitive to permissions
StudySubjectDAO sdao = new StudySubjectDAO(sm.getDataSource());
StudySubjectBean ssb;
if (studySubjectId <= 0) {
ssb = (StudySubjectBean) request.getAttribute(INPUT_STUDY_SUBJECT);
} else {
// YW 11-08-2007, << a new study event could not be added if its
// study subject has been removed
ssb = (StudySubjectBean) sdao.findByPK(studySubjectId);
Status s = ssb.getStatus();
if ("removed".equalsIgnoreCase(s.getName()) || "auto-removed".equalsIgnoreCase(s.getName())) {
addPageMessage(
resword.getString("study_event")
+ resterm.getString("could_not_be")
+ resterm.getString("added")
+ "."
+ respage.getString("study_subject_has_been_deleted"));
request.setAttribute("id", new Integer(studySubjectId).toString());
forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
}
// YW >>
request.setAttribute(INPUT_REQUEST_STUDY_SUBJECT, "no");
}
// running this crashes the server, or so we think...instead, let's grab a count
// or remove it altogether tbh 10/2009
// ArrayList subjects = sdao.findAllActiveByStudyOrderByLabel(currentStudy);
// TODO: make this sensitive to permissions
StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
StudyBean studyWithEventDefinitions = currentStudy;
if (currentStudy.getParentStudyId() > 0) {
studyWithEventDefinitions = new StudyBean();
studyWithEventDefinitions.setId(currentStudy.getParentStudyId());
}
// find all active definitions with CRFs
ArrayList eventDefinitions = seddao.findAllActiveByStudy(studyWithEventDefinitions);
// EventDefinitionCRFDAO edcdao = new
// EventDefinitionCRFDAO(sm.getDataSource());
// ArrayList definitionsWithCRF = new ArrayList();
// for (int i=0; i<eventDefinitions.size(); i++) {
// StudyEventDefinitionBean sed =
// (StudyEventDefinitionBean)eventDefinitions.get(i);
// logger.info("StudyEventDefinition name[" + sed.getName() + "]");
// ArrayList edcs = edcdao.findAllByEventDefinitionId(sed.getId());
// if (!edcs.isEmpty()) {
// definitionsWithCRF.add(sed);
// }
// }
// Collections.sort(definitionsWithCRF);
Collections.sort(eventDefinitions);
/*
* ArrayList eventDefinitionsScheduled = new ArrayList(); for (int i =
* 0; i < eventDefinitions.size(); i++) { StudyEventDefinitionBean sed =
* (StudyEventDefinitionBean) eventDefinitions.get(i); if
* (sed.getType().equalsIgnoreCase("scheduled")) {
* eventDefinitionsScheduled.add(sed); } }
*/
// all definitions will appear in scheduled event creation box-11/26/05
ArrayList eventDefinitionsScheduled = eventDefinitions;
if (!fp.isSubmitted()) {
// StudyEventDAO sed = new StudyEventDAO(sm.getDataSource());
// sed.updateSampleOrdinals_v092();
HashMap presetValues = new HashMap();
// YW 08-16-2007 << set default as blank for time
presetValues.put(INPUT_STARTDATE_PREFIX + "Hour", new Integer(-1));
presetValues.put(INPUT_STARTDATE_PREFIX + "Minute", new Integer(-1));
presetValues.put(INPUT_STARTDATE_PREFIX + "Half", new String(""));
presetValues.put(INPUT_ENDDATE_PREFIX + "Hour", new Integer(-1));
presetValues.put(INPUT_ENDDATE_PREFIX + "Minute", new Integer(-1));
presetValues.put(INPUT_ENDDATE_PREFIX + "Half", new String(""));
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
presetValues.put(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Hour", new Integer(-1));
presetValues.put(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Minute", new Integer(-1));
presetValues.put(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Half", new String(""));
presetValues.put(INPUT_ENDDATE_PREFIX_SCHEDULED[i] + "Hour", new Integer(-1));
presetValues.put(INPUT_ENDDATE_PREFIX_SCHEDULED[i] + "Minute", new Integer(-1));
presetValues.put(INPUT_ENDDATE_PREFIX_SCHEDULED[i] + "Half", new String(""));
}
// SimpleDateFormat sdf = new SimpleDateFormat("MM/dd/yyyy");
// example of taking the above line and transferring to i18n on the
// below line, tbh
String dateValue = local_df.format(new Date(System.currentTimeMillis()));
presetValues.put(INPUT_STARTDATE_PREFIX + "Date", dateValue);
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
presetValues.put(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Date", dateValue);
// location
presetValues.put(INPUT_SCHEDULED_LOCATION[i], currentStudy.getFacilityCity());
presetValues.put(this.DISPLAY_SCHEDULED[i], "none");
}
presetValues.put(INPUT_LOCATION, currentStudy.getFacilityCity()); // defualt
if (ssb != null && ssb.isActive()) {
presetValues.put(INPUT_STUDY_SUBJECT, ssb);
String requestStudySubject = (String) request.getAttribute(INPUT_REQUEST_STUDY_SUBJECT);
if (requestStudySubject != null) {
presetValues.put(INPUT_REQUEST_STUDY_SUBJECT, requestStudySubject);
dateValue = local_df.format(new Date());
presetValues.put(INPUT_STARTDATE_PREFIX + "Date", dateValue);
}
}
if (studyEventDefinitionId > 0) {
StudyEventDefinitionBean sed =
(StudyEventDefinitionBean) seddao.findByPK(studyEventDefinitionId);
presetValues.put(INPUT_STUDY_EVENT_DEFINITION, sed);
}
// tbh
logger.info("set preset values: " + presetValues.toString());
System.out.println("set preset values: " + presetValues.toString());
logger.info("found def.w.CRF list, size " + eventDefinitions.size());
// tbh
setPresetValues(presetValues);
ArrayList subjects = new ArrayList();
setupBeans(subjects, eventDefinitions);
discNotes = new FormDiscrepancyNotes();
session.setAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME, discNotes);
request.setAttribute("eventDefinitionsScheduled", eventDefinitionsScheduled);
setInputMessages(new HashMap());
forwardPage(Page.CREATE_NEW_STUDY_EVENT);
} else {
// tbh
// String dateCheck = (String)request.getAttribute("startDate");
// String endCheck = (String)request.getAttribute("endDate");
// logger.info(dateCheck+"; "+endCheck);
String dateCheck2 = request.getParameter("startDate");
String endCheck2 = request.getParameter("endDate");
logger.info(dateCheck2 + "; " + endCheck2);
// YW, 3-12-2008, 2220 fix <<
String strEnd = fp.getDateTimeInputString(INPUT_ENDDATE_PREFIX);
String strEndScheduled[] = new String[ADDITIONAL_SCHEDULED_NUM];
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
strEndScheduled[i] = fp.getDateTimeInputString(INPUT_ENDDATE_PREFIX_SCHEDULED[i]);
}
Date start = getInputStartDate();
Date end = null;
Date[] startScheduled = new Date[ADDITIONAL_SCHEDULED_NUM];
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
startScheduled[i] = getInputStartDateScheduled(i);
}
Date[] endScheduled = new Date[ADDITIONAL_SCHEDULED_NUM];
// YW >>
// for (java.util.Enumeration enu = request.getAttributeNames();
// enu.hasMoreElements() ;) {
// logger.info(">>> found "+enu.nextElement().toString());
// }
// tbh
discNotes =
(FormDiscrepancyNotes)
session.getAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME);
if (discNotes == null) {
discNotes = new FormDiscrepancyNotes();
session.setAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME, discNotes);
}
DiscrepancyValidator v = new DiscrepancyValidator(request, discNotes);
v.addValidation(INPUT_STARTDATE_PREFIX, Validator.IS_DATE_TIME);
v.alwaysExecuteLastValidation(INPUT_STARTDATE_PREFIX);
if (!strEnd.equals("")) {
v.addValidation(INPUT_ENDDATE_PREFIX, Validator.IS_DATE_TIME);
v.alwaysExecuteLastValidation(INPUT_ENDDATE_PREFIX);
}
v.addValidation(
INPUT_STUDY_EVENT_DEFINITION,
Validator.ENTITY_EXISTS_IN_STUDY,
seddao,
studyWithEventDefinitions);
// v.addValidation(INPUT_STUDY_SUBJECT, Validator.ENTITY_EXISTS_IN_STUDY, sdao, currentStudy);
// removed tbh 11/2009
v.addValidation(INPUT_LOCATION, Validator.NO_BLANKS);
v.addValidation(INPUT_STUDY_SUBJECT_LABEL, Validator.NO_BLANKS);
v.addValidation(
INPUT_LOCATION,
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
2000);
v.alwaysExecuteLastValidation(INPUT_LOCATION);
boolean hasScheduledEvent = false;
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
if (!StringUtil.isBlank(fp.getString(this.INPUT_STUDY_EVENT_DEFINITION_SCHEDULED[i]))) {
// logger.info("has scheduled definition******");
v.addValidation(
this.INPUT_STUDY_EVENT_DEFINITION_SCHEDULED[i],
Validator.ENTITY_EXISTS_IN_STUDY,
seddao,
studyWithEventDefinitions);
v.addValidation(INPUT_SCHEDULED_LOCATION[i], Validator.NO_BLANKS);
v.addValidation(
INPUT_SCHEDULED_LOCATION[i],
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
2000);
v.alwaysExecuteLastValidation(INPUT_SCHEDULED_LOCATION[i]);
v.addValidation(INPUT_STARTDATE_PREFIX_SCHEDULED[i], Validator.IS_DATE_TIME);
v.alwaysExecuteLastValidation(INPUT_STARTDATE_PREFIX_SCHEDULED[i]);
if (!strEndScheduled[i].equals("")) {
v.addValidation(INPUT_ENDDATE_PREFIX_SCHEDULED[i], Validator.IS_DATE_TIME);
v.alwaysExecuteLastValidation(INPUT_ENDDATE_PREFIX_SCHEDULED[i]);
}
hasScheduledEvent = true;
fp.addPresetValue(DISPLAY_SCHEDULED[i], "all");
} else {
fp.addPresetValue(DISPLAY_SCHEDULED[i], "none");
}
}
HashMap errors = v.validate();
// logger.info("v is not null *****");
String location = resword.getString("location");
// don't allow user to use the default value 'Location' since
// location
// is a required field
if (!StringUtil.isBlank(fp.getString(INPUT_LOCATION))
&& fp.getString(INPUT_LOCATION).equalsIgnoreCase(location)) {
Validator.addError(errors, INPUT_LOCATION, restext.getString("not_a_valid_location"));
}
StudyEventDefinitionBean definition =
(StudyEventDefinitionBean) seddao.findByPK(fp.getInt(INPUT_STUDY_EVENT_DEFINITION));
// StudySubjectBean studySubject = (StudySubjectBean)
// sdao.findByPK(fp.getInt(INPUT_STUDY_SUBJECT));
// sdao.findByLabelAndStudy(label, study)
StudySubjectBean studySubject =
(StudySubjectBean)
sdao.findByLabelAndStudy(fp.getString(INPUT_STUDY_SUBJECT_LABEL), currentStudy);
// >> 4358 tbh, 11/2009
// what if we are sent here from AddNewSubjectServlet.java??? we need to get that study
// subject bean
if (request.getAttribute(INPUT_STUDY_SUBJECT) != null) {
studySubject = (StudySubjectBean) request.getAttribute(INPUT_STUDY_SUBJECT);
}
// << tbh
if (studySubject.getLabel() == "") {
// add an error here, tbh
System.out.println("tripped the error here 20091109");
Validator.addError(
errors,
INPUT_STUDY_SUBJECT,
respage.getString("must_enter_subject_ID_for_identifying"));
}
if (!subjectMayReceiveStudyEvent(sm.getDataSource(), definition, studySubject)) {
Validator.addError(
errors,
INPUT_STUDY_EVENT_DEFINITION,
restext.getString("not_added_since_event_not_repeating"));
}
ArrayList<StudyEventDefinitionBean> definitionScheduleds =
new ArrayList<StudyEventDefinitionBean>();
int[] scheduledDefinitionIds = new int[ADDITIONAL_SCHEDULED_NUM];
if (hasScheduledEvent) {
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
int pk = fp.getInt(INPUT_STUDY_EVENT_DEFINITION_SCHEDULED[i]);
if (pk > 0) {
StudyEventDefinitionBean sedb = (StudyEventDefinitionBean) seddao.findByPK(pk);
System.out.println(
"scheduled def:"
+ pk
+ " "
+ INPUT_STUDY_EVENT_DEFINITION_SCHEDULED[i]
+ " "
+ sedb.getName());
definitionScheduleds.add(sedb);
scheduledDefinitionIds[i] = pk;
if (!subjectMayReceiveStudyEvent(sm.getDataSource(), sedb, studySubject)) {
Validator.addError(
errors,
INPUT_STUDY_EVENT_DEFINITION_SCHEDULED[i],
restext.getString("not_added_since_event_not_repeating"));
}
} else {
definitionScheduleds.add(new StudyEventDefinitionBean());
}
}
}
// YW, 3-12-2008, 2220 fix >>
if (!"".equals(strEnd)
&& !errors.containsKey(INPUT_STARTDATE_PREFIX)
&& !errors.containsKey(INPUT_ENDDATE_PREFIX)) {
end = getInputEndDate();
if (!fp.getString(INPUT_STARTDATE_PREFIX + "Date")
.equals(fp.getString(INPUT_ENDDATE_PREFIX + "Date"))) {
if (end.before(start)) {
Validator.addError(
errors,
INPUT_ENDDATE_PREFIX,
resexception.getString("input_provided_not_occure_after_previous_start_date_time"));
}
} else {
// if in same date, only check when both had time entered
if (fp.timeEntered(INPUT_STARTDATE_PREFIX) && fp.timeEntered(INPUT_ENDDATE_PREFIX)) {
if (end.before(start) || end.equals(start)) {
Validator.addError(
errors,
INPUT_ENDDATE_PREFIX,
resexception.getString(
"input_provided_not_occure_after_previous_start_date_time"));
}
}
}
}
String prevStartPrefix = INPUT_STARTDATE_PREFIX;
Set<Integer> pickedSeds = new TreeSet<Integer>();
pickedSeds.add(studyEventDefinitionId);
HashMap<Integer, Integer> scheduledSeds = new HashMap<Integer, Integer>();
scheduledSeds.put(studyEventDefinitionId, -1);
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
if (scheduledDefinitionIds[i] > 0
&& !errors.containsKey(INPUT_STARTDATE_PREFIX_SCHEDULED[i])
&& !errors.containsKey(INPUT_ENDDATE_PREFIX_SCHEDULED[i])) {
if (scheduledSeds.containsKey(scheduledDefinitionIds[i])) {
int prevStart = scheduledSeds.get(scheduledDefinitionIds[i]);
prevStartPrefix =
prevStart == -1
? INPUT_STARTDATE_PREFIX
: INPUT_STARTDATE_PREFIX_SCHEDULED[prevStart];
Date prevStartDate =
prevStart == -1
? this.getInputStartDate()
: this.getInputStartDateScheduled(
Integer.parseInt(
prevStartPrefix.charAt(prevStartPrefix.length() - 1) + ""));
if (fp.getString(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Date")
.equals(fp.getString(prevStartPrefix + "Date"))) {
// if in same day, only check when both have time
// inputs.
boolean schStartTime = fp.timeEntered(INPUT_STARTDATE_PREFIX_SCHEDULED[i]);
boolean startTime = fp.timeEntered(prevStartPrefix);
if (schStartTime && startTime) {
if (startScheduled[i].before(prevStartDate)) {
Validator.addError(
errors,
INPUT_STARTDATE_PREFIX_SCHEDULED[i],
resexception.getString(
"input_provided_not_occure_after_previous_start_date_time"));
}
}
} else {
if (startScheduled[i].before(prevStartDate)) {
Validator.addError(
errors,
INPUT_STARTDATE_PREFIX_SCHEDULED[i],
resexception.getString(
"input_provided_not_occure_after_previous_start_date_time"));
}
}
}
scheduledSeds.put(scheduledDefinitionIds[i], i);
if (!strEndScheduled[i].equals("")) {
endScheduled[i] = fp.getDateTime(INPUT_ENDDATE_PREFIX_SCHEDULED[i]);
String prevEndPrefix =
i > 0 ? INPUT_ENDDATE_PREFIX_SCHEDULED[i - 1] : INPUT_ENDDATE_PREFIX;
if (!fp.getString(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Date")
.equals(fp.getString(prevEndPrefix + "Date"))) {
if (endScheduled[i].before(startScheduled[i])) {
Validator.addError(
errors,
INPUT_ENDDATE_PREFIX_SCHEDULED[i],
resexception.getString(
"input_provided_not_occure_after_previous_start_date_time"));
}
} else {
// if in same date, only check when both had time
// entered
if (fp.timeEntered(INPUT_STARTDATE_PREFIX_SCHEDULED[i])
&& fp.timeEntered(INPUT_ENDDATE_PREFIX_SCHEDULED[i])) {
if (endScheduled[i].before(startScheduled[i])
|| endScheduled[i].equals(startScheduled[i])) {
Validator.addError(
errors,
INPUT_ENDDATE_PREFIX_SCHEDULED[i],
resexception.getString(
"input_provided_not_occure_after_previous_start_date_time"));
}
}
}
}
}
}
// YW >>
System.out.println("we have errors; number of this; " + errors.size());
if (!errors.isEmpty()) {
logger.info("we have errors; number of this; " + errors.size());
System.out.println(
"found request study subject: " + fp.getString(INPUT_REQUEST_STUDY_SUBJECT));
addPageMessage(respage.getString("errors_in_submission_see_below"));
setInputMessages(errors);
fp.addPresetValue(INPUT_STUDY_EVENT_DEFINITION, definition);
fp.addPresetValue(INPUT_STUDY_SUBJECT, studySubject);
fp.addPresetValue(INPUT_STUDY_SUBJECT_LABEL, fp.getString(INPUT_STUDY_SUBJECT_LABEL));
fp.addPresetValue(INPUT_REQUEST_STUDY_SUBJECT, fp.getString(INPUT_REQUEST_STUDY_SUBJECT));
fp.addPresetValue(INPUT_LOCATION, fp.getString(INPUT_LOCATION));
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
fp.addPresetValue(INPUT_SCHEDULED_LOCATION[i], fp.getString(INPUT_SCHEDULED_LOCATION[i]));
}
String prefixes[] = new String[2 + 2 * ADDITIONAL_SCHEDULED_NUM];
prefixes[0] = INPUT_STARTDATE_PREFIX;
prefixes[1] = INPUT_ENDDATE_PREFIX;
int b = ADDITIONAL_SCHEDULED_NUM + 2;
for (int i = 2; i < b; ++i) {
prefixes[i] = INPUT_STARTDATE_PREFIX_SCHEDULED[i - 2];
}
for (int i = b; i < ADDITIONAL_SCHEDULED_NUM + b; ++i) {
prefixes[i] = INPUT_ENDDATE_PREFIX_SCHEDULED[i - b];
}
fp.setCurrentDateTimeValuesAsPreset(prefixes);
if (hasScheduledEvent) {
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
fp.addPresetValue(
INPUT_STUDY_EVENT_DEFINITION_SCHEDULED[i], definitionScheduleds.get(i));
}
}
setPresetValues(fp.getPresetValues());
ArrayList subjects = new ArrayList();
setupBeans(subjects, eventDefinitions);
request.setAttribute("eventDefinitionsScheduled", eventDefinitionsScheduled);
forwardPage(Page.CREATE_NEW_STUDY_EVENT);
} else {
System.out.println("error is empty");
StudyEventDAO sed = new StudyEventDAO(sm.getDataSource());
StudyEventBean studyEvent = new StudyEventBean();
studyEvent.setStudyEventDefinitionId(definition.getId());
studyEvent.setStudySubjectId(studySubject.getId());
// YW 08-17-2007 <<
if ("-1".equals(getInputStartHour())
&& "-1".equals(getInputStartMinute())
&& "".equals(getInputStartHalf())) {
studyEvent.setStartTimeFlag(false);
} else {
studyEvent.setStartTimeFlag(true);
}
// YW >>
studyEvent.setDateStarted(start);
// comment to find bug 1389, tbh
logger.info("found start date: " + local_df.format(start));
Date startScheduled2[] = new Date[ADDITIONAL_SCHEDULED_NUM];
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
startScheduled2[i] = getInputStartDateScheduled(i);
}
// tbh
// YW, 3-12-2008, 2220 fix <<
if (!"".equals(strEnd)) {
// YW >>
if ("-1".equals(getInputEndHour())
&& "-1".equals(getInputEndMinute())
&& "".equals(getInputEndHalf())) {
studyEvent.setEndTimeFlag(false);
} else {
studyEvent.setEndTimeFlag(true);
}
studyEvent.setDateEnded(end);
}
studyEvent.setOwner(ub);
studyEvent.setStatus(Status.AVAILABLE);
studyEvent.setLocation(fp.getString(INPUT_LOCATION));
studyEvent.setSubjectEventStatus(SubjectEventStatus.SCHEDULED);
// ArrayList subjectsExistingEvents =
// sed.findAllByStudyAndStudySubjectId(currentStudy,
// studySubject.getId());
studyEvent.setSampleOrdinal(sed.getMaxSampleOrdinal(definition, studySubject) + 1);
studyEvent = (StudyEventBean) sed.create(studyEvent);
if (!studyEvent.isActive()) {
throw new OpenClinicaException(restext.getString("event_not_created_in_database"), "2");
}
addPageMessage(
restext.getString("X_event_wiht_definition")
+ definition.getName()
+ restext.getString("X_and_subject")
+ studySubject.getName()
+ respage.getString("X_was_created_succesfully"));
// save discrepancy notes into DB
FormDiscrepancyNotes fdn =
(FormDiscrepancyNotes)
session.getAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME);
DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(sm.getDataSource());
String[] eventFields = {INPUT_LOCATION, INPUT_STARTDATE_PREFIX, INPUT_ENDDATE_PREFIX};
for (String element : eventFields) {
AddNewSubjectServlet.saveFieldNotes(
element, fdn, dndao, studyEvent.getId(), "studyEvent", currentStudy);
}
// logger.info("here ok 3333333333333333");
if (hasScheduledEvent) {
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
// should only do the following process if user inputs a
// scheduled event,
// which is scheduledDefinitionIds[i] > 0
if (scheduledDefinitionIds[i] > 0) {
if (subjectMayReceiveStudyEvent(
sm.getDataSource(), definitionScheduleds.get(i), studySubject)) {
StudyEventBean studyEventScheduled = new StudyEventBean();
studyEventScheduled.setStudyEventDefinitionId(scheduledDefinitionIds[i]);
studyEventScheduled.setStudySubjectId(studySubject.getId());
// YW 11-14-2007
if ("-1".equals(fp.getString(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Hour"))
&& "-1".equals(fp.getString(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Minute"))
&& "".equals(fp.getString(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Half"))) {
studyEventScheduled.setStartTimeFlag(false);
} else {
studyEventScheduled.setStartTimeFlag(true);
}
// YW >>
studyEventScheduled.setDateStarted(startScheduled[i]);
// YW, 3-12-2008, 2220 fix<<
if (!"".equals(strEndScheduled[i])) {
endScheduled[i] = fp.getDateTime(INPUT_ENDDATE_PREFIX_SCHEDULED[i]);
if ("-1".equals(fp.getString(INPUT_ENDDATE_PREFIX_SCHEDULED[i] + "Hour"))
&& "-1".equals(fp.getString(INPUT_ENDDATE_PREFIX_SCHEDULED[i] + "Minute"))
&& "".equals(fp.getString(INPUT_ENDDATE_PREFIX_SCHEDULED[i] + "Half"))) {
studyEventScheduled.setEndTimeFlag(false);
} else {
studyEventScheduled.setEndTimeFlag(true);
}
}
studyEventScheduled.setDateEnded(endScheduled[i]);
// YW >>
studyEventScheduled.setOwner(ub);
studyEventScheduled.setStatus(Status.AVAILABLE);
studyEventScheduled.setLocation(fp.getString(INPUT_SCHEDULED_LOCATION[i]));
studyEvent.setSubjectEventStatus(SubjectEventStatus.SCHEDULED);
// subjectsExistingEvents =
// sed.findAllByStudyAndStudySubjectId(
// currentStudy,
// studySubject.getId());
studyEventScheduled.setSampleOrdinal(
sed.getMaxSampleOrdinal(definitionScheduleds.get(i), studySubject) + 1);
// System.out.println("create scheduled events");
studyEventScheduled = (StudyEventBean) sed.create(studyEventScheduled);
if (!studyEventScheduled.isActive()) {
throw new OpenClinicaException(
restext.getString("scheduled_event_not_created_in_database"), "2");
}
AddNewSubjectServlet.saveFieldNotes(
INPUT_SCHEDULED_LOCATION[i],
fdn,
dndao,
studyEventScheduled.getId(),
"studyEvent",
currentStudy);
// YW 3-12-2008, 2220 fix <<
AddNewSubjectServlet.saveFieldNotes(
INPUT_STARTDATE_PREFIX_SCHEDULED[i],
fdn,
dndao,
studyEventScheduled.getId(),
"studyEvent",
currentStudy);
AddNewSubjectServlet.saveFieldNotes(
INPUT_ENDDATE_PREFIX_SCHEDULED[i],
fdn,
dndao,
studyEventScheduled.getId(),
"studyEvent",
currentStudy);
// YW >>
} else {
addPageMessage(
restext.getString("scheduled_event_definition")
+ definitionScheduleds.get(i).getName()
+ restext.getString("X_and_subject")
+ studySubject.getName()
+ restext.getString("not_created_since_event_not_repeating")
+ restext.getString("event_type_already_exists"));
}
}
}
} // if
session.removeAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME);
request.setAttribute(
EnterDataForStudyEventServlet.INPUT_EVENT_ID, String.valueOf(studyEvent.getId()));
response.encodeRedirectURL("EnterDataForStudyEvent?eventId=" + studyEvent.getId());
forwardPage(Page.ENTER_DATA_FOR_STUDY_EVENT_SERVLET);
// we want to actually have url of entering data in browser, so
// redirecting
// response.sendRedirect(response.encodeRedirectURL(
// "EnterDataForStudyEvent?eventId="
// + studyEvent.getId()));
return;
}
}
}
/**
* Constructs study bean from request
*
* @param request
* @return
*/
private StudyBean createStudyBean() {
FormProcessor fp = new FormProcessor(request);
StudyBean study = (StudyBean) session.getAttribute("newStudy");
study.setName(fp.getString("name"));
study.setIdentifier(fp.getString("uniqueProId"));
study.setSecondaryIdentifier(fp.getString("secondProId"));
study.setSummary(fp.getString("description"));
study.setPrincipalInvestigator(fp.getString("prinInvestigator"));
study.setExpectedTotalEnrollment(fp.getInt("expectedTotalEnrollment"));
java.util.Date startDate = null;
java.util.Date endDate = null;
try {
local_df.setLenient(false);
startDate = local_df.parse(fp.getString("startDate"));
} catch (ParseException fe) {
startDate = study.getDatePlannedStart();
logger.info(fe.getMessage());
}
study.setDatePlannedStart(startDate);
try {
local_df.setLenient(false);
endDate = local_df.parse(fp.getString("endDate"));
} catch (ParseException fe) {
endDate = study.getDatePlannedEnd();
}
study.setDatePlannedEnd(endDate);
study.setFacilityCity(fp.getString("facCity"));
study.setFacilityContactDegree(fp.getString("facConDrgree"));
study.setFacilityName(fp.getString("facName"));
study.setFacilityContactEmail(fp.getString("facConEmail"));
study.setFacilityContactPhone(fp.getString("facConPhone"));
study.setFacilityContactName(fp.getString("facConName"));
study.setFacilityContactDegree(fp.getString("facConDegree"));
study.setFacilityCountry(fp.getString("facCountry"));
// study.setFacilityRecruitmentStatus(fp.getString("facRecStatus"));
study.setFacilityState(fp.getString("facState"));
study.setFacilityZip(fp.getString("facZip"));
study.setStatus(Status.get(fp.getInt("statusId")));
ArrayList parameters = study.getStudyParameters();
for (int i = 0; i < parameters.size(); i++) {
StudyParamsConfig scg = (StudyParamsConfig) parameters.get(i);
String value = fp.getString(scg.getParameter().getHandle());
logger.info("get value:" + value);
scg.getValue().setParameter(scg.getParameter().getHandle());
scg.getValue().setValue(value);
}
// YW 10-12-2007 <<
study
.getStudyParameterConfig()
.setInterviewerNameRequired(fp.getString("interviewerNameRequired"));
study
.getStudyParameterConfig()
.setInterviewerNameDefault(fp.getString("interviewerNameDefault"));
study.getStudyParameterConfig().setInterviewDateRequired(fp.getString("interviewDateRequired"));
study.getStudyParameterConfig().setInterviewDateDefault(fp.getString("interviewDateDefault"));
// YW >>
return study;
}
private void validateStudy5(FormProcessor fp, Validator v) {
if (!StringUtil.isBlank(fp.getString("facConEmail"))) {
v.addValidation("facConEmail", Validator.IS_A_EMAIL);
}
v.addValidation(
"facName",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"facCity",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"facState",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
20);
v.addValidation(
"facZip",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
64);
v.addValidation(
"facCountry",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
64);
v.addValidation(
"facConName",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"facConDegree",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"facConPhone",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"facConEmail",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
errors = v.validate();
study.setFacilityCity(fp.getString("facCity"));
study.setFacilityContactDegree(fp.getString("facConDrgree"));
study.setFacilityName(fp.getString("facName"));
study.setFacilityContactEmail(fp.getString("facConEmail"));
study.setFacilityContactPhone(fp.getString("facConPhone"));
study.setFacilityContactName(fp.getString("facConName"));
study.setFacilityCountry(fp.getString("facCountry"));
study.setFacilityContactDegree(fp.getString("facConDegree"));
// newStudy.setFacilityRecruitmentStatus(fp.getString("facRecStatus"));
study.setFacilityState(fp.getString("facState"));
study.setFacilityZip(fp.getString("facZip"));
if (errors.isEmpty()) {
} else {
request.setAttribute("formMessages", errors);
request.setAttribute("facRecruitStatusMap", CreateStudyServlet.facRecruitStatusMap);
}
}
private void validateStudy2(FormProcessor fp, Validator v) {
v.addValidation(INPUT_START_DATE, Validator.IS_A_DATE);
if (!StringUtil.isBlank(fp.getString(INPUT_END_DATE))) {
v.addValidation(INPUT_END_DATE, Validator.IS_A_DATE);
}
if (!StringUtil.isBlank(fp.getString(INPUT_VER_DATE))) {
v.addValidation(INPUT_VER_DATE, Validator.IS_A_DATE);
}
errors = v.validate();
logger.info("has validation errors");
try {
local_df.parse(fp.getString(INPUT_START_DATE));
fp.addPresetValue(INPUT_START_DATE, local_df.format(fp.getDate(INPUT_START_DATE)));
} catch (ParseException pe) {
fp.addPresetValue(INPUT_START_DATE, fp.getString(INPUT_START_DATE));
}
try {
local_df.parse(fp.getString(INPUT_VER_DATE));
fp.addPresetValue(INPUT_VER_DATE, local_df.format(fp.getDate(INPUT_VER_DATE)));
} catch (ParseException pe) {
fp.addPresetValue(INPUT_VER_DATE, fp.getString(INPUT_VER_DATE));
}
try {
local_df.parse(fp.getString(INPUT_END_DATE));
fp.addPresetValue(INPUT_END_DATE, local_df.format(fp.getDate(INPUT_END_DATE)));
} catch (ParseException pe) {
fp.addPresetValue(INPUT_END_DATE, fp.getString(INPUT_END_DATE));
}
updateStudy2(fp);
setPresetValues(fp.getPresetValues());
}
public void processRequest() throws Exception {
StudyDAO sdao = new StudyDAO(sm.getDataSource());
FormProcessor fp = new FormProcessor(request);
int studyId = fp.getInt("id");
StudyBean study = (StudyBean) sdao.findByPK(studyId);
// find all sites
ArrayList sites = (ArrayList) sdao.findAllByParent(studyId);
// find all user and roles in the study, include ones in sites
UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
ArrayList userRoles = udao.findAllByStudyId(studyId);
// find all subjects in the study, include ones in sites
StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
ArrayList subjects = ssdao.findAllByStudy(study);
// find all events in the study, include ones in sites
StudyEventDefinitionDAO sefdao = new StudyEventDefinitionDAO(sm.getDataSource());
ArrayList definitions = sefdao.findAllByStudy(study);
String action = request.getParameter("action");
if (studyId == 0) {
addPageMessage("Please choose a study to restore.");
forwardPage(Page.STUDY_LIST_SERVLET);
} else {
if ("confirm".equalsIgnoreCase(action)) {
request.setAttribute("studyToRestore", study);
request.setAttribute("sitesToRestore", sites);
request.setAttribute("userRolesToRestore", userRoles);
request.setAttribute("subjectsToRestore", subjects);
request.setAttribute("definitionsToRRestore", definitions);
forwardPage(Page.RESTORE_STUDY);
} else {
logger.info("submit to restore the study");
// change all statuses to unavailable
StudyDAO studao = new StudyDAO(sm.getDataSource());
study.setStatus(Status.AVAILABLE);
study.setUpdater(ub);
study.setUpdatedDate(new Date());
studao.update(study);
// remove all sites
for (int i = 0; i < sites.size(); i++) {
StudyBean site = (StudyBean) sites.get(i);
site.setStatus(Status.AVAILABLE);
site.setUpdater(ub);
site.setUpdatedDate(new Date());
sdao.update(site);
}
// remove all users and roles
for (int i = 0; i < userRoles.size(); i++) {
StudyUserRoleBean role = (StudyUserRoleBean) userRoles.get(i);
role.setStatus(Status.AVAILABLE);
role.setUpdater(ub);
role.setUpdatedDate(new Date());
udao.updateStudyUserRole(role, role.getUserName());
}
// remove all subjects
for (int i = 0; i < subjects.size(); i++) {
StudySubjectBean subject = (StudySubjectBean) subjects.get(i);
subject.setStatus(Status.AVAILABLE);
subject.setUpdater(ub);
subject.setUpdatedDate(new Date());
ssdao.update(subject);
}
// remove all study_group
StudyGroupDAO sgdao = new StudyGroupDAO(sm.getDataSource());
SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource());
ArrayList groups = sgdao.findAllByStudy(study);
for (int i = 0; i < groups.size(); i++) {
StudyGroupBean group = (StudyGroupBean) groups.get(i);
group.setStatus(Status.AVAILABLE);
group.setUpdater(ub);
group.setUpdatedDate(new Date());
sgdao.update(group);
// all subject_group_map
ArrayList subjectGroupMaps = sgmdao.findAllByStudyGroupId(group.getId());
for (int j = 0; j < subjectGroupMaps.size(); j++) {
SubjectGroupMapBean sgMap = (SubjectGroupMapBean) subjectGroupMaps.get(j);
sgMap.setStatus(Status.AVAILABLE);
sgMap.setUpdater(ub);
sgMap.setUpdatedDate(new Date());
sgmdao.update(sgMap);
}
}
// remove all event definitions and event
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
for (int i = 0; i < definitions.size(); i++) {
StudyEventDefinitionBean definition = (StudyEventDefinitionBean) definitions.get(i);
definition.setStatus(Status.AVAILABLE);
definition.setUpdater(ub);
definition.setUpdatedDate(new Date());
sefdao.update(definition);
ArrayList edcs = (ArrayList) edcdao.findAllByDefinition(definition.getId());
for (int j = 0; j < edcs.size(); j++) {
EventDefinitionCRFBean edc = (EventDefinitionCRFBean) edcs.get(j);
edc.setStatus(Status.AVAILABLE);
edc.setUpdater(ub);
edc.setUpdatedDate(new Date());
edcdao.update(edc);
}
ArrayList events = (ArrayList) sedao.findAllByDefinition(definition.getId());
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
for (int j = 0; j < events.size(); j++) {
StudyEventBean event = (StudyEventBean) events.get(j);
event.setStatus(Status.AVAILABLE);
event.setUpdater(ub);
event.setUpdatedDate(new Date());
sedao.update(event);
ArrayList eventCRFs = ecdao.findAllByStudyEvent(event);
ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
for (int k = 0; k < eventCRFs.size(); k++) {
EventCRFBean eventCRF = (EventCRFBean) eventCRFs.get(k);
eventCRF.setStatus(Status.AVAILABLE);
eventCRF.setUpdater(ub);
eventCRF.setUpdatedDate(new Date());
ecdao.update(eventCRF);
ArrayList itemDatas = iddao.findAllByEventCRFId(eventCRF.getId());
for (int a = 0; a < itemDatas.size(); a++) {
ItemDataBean item = (ItemDataBean) itemDatas.get(a);
item.setStatus(Status.AVAILABLE);
item.setUpdater(ub);
item.setUpdatedDate(new Date());
iddao.update(item);
}
}
}
} // for definitions
DatasetDAO datadao = new DatasetDAO(sm.getDataSource());
ArrayList dataset = datadao.findAllByStudyId(study.getId());
for (int i = 0; i < dataset.size(); i++) {
DatasetBean data = (DatasetBean) dataset.get(i);
data.setStatus(Status.AVAILABLE);
data.setUpdater(ub);
data.setUpdatedDate(new Date());
datadao.update(data);
}
addPageMessage("This study has been restored successfully.");
forwardPage(Page.STUDY_LIST_SERVLET);
}
}
}
private String getInputEndMinute() {
return fp.getString(INPUT_ENDDATE_PREFIX + "Minute");
}
/**
* Validates the first section of study and save it into study bean
*
* @param request
* @param response
* @throws Exception
*/
private void confirmStudy() throws Exception {
Validator v = new Validator(request);
FormProcessor fp = new FormProcessor(request);
v.addValidation("name", Validator.NO_BLANKS);
v.addValidation("uniqueProId", Validator.NO_BLANKS);
v.addValidation("description", Validator.NO_BLANKS);
v.addValidation("prinInvestigator", Validator.NO_BLANKS);
if (!StringUtil.isBlank(fp.getString(INPUT_START_DATE))) {
v.addValidation(INPUT_START_DATE, Validator.IS_A_DATE);
}
if (!StringUtil.isBlank(fp.getString(INPUT_END_DATE))) {
v.addValidation(INPUT_END_DATE, Validator.IS_A_DATE);
}
if (!StringUtil.isBlank(fp.getString("facConEmail"))) {
v.addValidation("facConEmail", Validator.IS_A_EMAIL);
}
// v.addValidation("statusId", Validator.IS_VALID_TERM);
v.addValidation(
"secondProId",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"facName",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"facCity",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"facState",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
20);
v.addValidation(
"facZip",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
64);
v.addValidation(
"facCountry",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
64);
v.addValidation(
"facConName",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"facConDegree",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"facConPhone",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"facConEmail",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
errors = v.validate();
if (fp.getString("name").trim().length() > 100) {
Validator.addError(errors, "name", resexception.getString("maximum_lenght_name_100"));
}
if (fp.getString("uniqueProId").trim().length() > 30) {
Validator.addError(
errors, "uniqueProId", resexception.getString("maximum_lenght_unique_protocol_30"));
}
if (fp.getString("description").trim().length() > 255) {
Validator.addError(
errors, "description", resexception.getString("maximum_lenght_brief_summary_255"));
}
if (fp.getString("prinInvestigator").trim().length() > 255) {
Validator.addError(
errors,
"prinInvestigator",
resexception.getString("maximum_lenght_principal_investigator_255"));
}
if (fp.getInt("expectedTotalEnrollment") <= 0) {
Validator.addError(
errors,
"expectedTotalEnrollment",
respage.getString("expected_total_enrollment_must_be_a_positive_number"));
}
session.setAttribute("newStudy", createStudyBean());
if (errors.isEmpty()) {
logger.info("no errors");
forwardPage(Page.CONFIRM_CREATE_SUB_STUDY);
} else {
try {
local_df.parse(fp.getString(INPUT_START_DATE));
fp.addPresetValue(INPUT_START_DATE, local_df.format(fp.getDate(INPUT_START_DATE)));
} catch (ParseException pe) {
fp.addPresetValue(INPUT_START_DATE, fp.getString(INPUT_START_DATE));
}
try {
local_df.parse(fp.getString(INPUT_END_DATE));
fp.addPresetValue(INPUT_END_DATE, local_df.format(fp.getDate(INPUT_END_DATE)));
} catch (ParseException pe) {
fp.addPresetValue(INPUT_END_DATE, fp.getString(INPUT_END_DATE));
}
setPresetValues(fp.getPresetValues());
logger.info("has validation errors");
request.setAttribute("formMessages", errors);
// request.setAttribute("facRecruitStatusMap",
// CreateStudyServlet.facRecruitStatusMap);
request.setAttribute("statuses", Status.toActiveArrayList());
forwardPage(Page.CREATE_SUB_STUDY);
}
}
private String getInputEndHalf() {
return fp.getString(INPUT_ENDDATE_PREFIX + "Half");
}
@Override
public void processRequest() throws Exception {
FormProcessor fp = new FormProcessor(request);
String action = request.getParameter("action");
if (StringUtil.isBlank(action)) {
if (currentStudy.getParentStudyId() > 0) {
addPageMessage(respage.getString("you_cannot_create_site_itself_site"));
forwardPage(Page.SITE_LIST_SERVLET);
} else {
StudyBean newStudy = new StudyBean();
newStudy.setParentStudyId(currentStudy.getId());
// get default facility info from property file
newStudy.setFacilityName(SQLInitServlet.getField(CreateStudyServlet.FAC_NAME));
newStudy.setFacilityCity(SQLInitServlet.getField(CreateStudyServlet.FAC_CITY));
newStudy.setFacilityState(SQLInitServlet.getField(CreateStudyServlet.FAC_STATE));
newStudy.setFacilityCountry(SQLInitServlet.getField(CreateStudyServlet.FAC_COUNTRY));
newStudy.setFacilityContactDegree(
SQLInitServlet.getField(CreateStudyServlet.FAC_CONTACT_DEGREE));
newStudy.setFacilityContactEmail(
SQLInitServlet.getField(CreateStudyServlet.FAC_CONTACT_EMAIL));
newStudy.setFacilityContactName(
SQLInitServlet.getField(CreateStudyServlet.FAC_CONTACT_NAME));
newStudy.setFacilityContactPhone(
SQLInitServlet.getField(CreateStudyServlet.FAC_CONTACT_PHONE));
newStudy.setFacilityZip(SQLInitServlet.getField(CreateStudyServlet.FAC_ZIP));
ArrayList parentConfigs = currentStudy.getStudyParameters();
// logger.info("parentConfigs size:" + parentConfigs.size());
ArrayList configs = new ArrayList();
for (int i = 0; i < parentConfigs.size(); i++) {
StudyParamsConfig scg = (StudyParamsConfig) parentConfigs.get(i);
if (scg != null) {
// find the one that sub study can change
if (scg.getValue().getId() > 0 && scg.getParameter().isOverridable()) {
logger.info("parameter:" + scg.getParameter().getHandle());
logger.info("value:" + scg.getValue().getValue());
// YW 10-12-2007, set overridable study parameters
// for a site
if (scg.getParameter().getHandle().equalsIgnoreCase("interviewerNameRequired")) {
scg.getValue().setValue(fp.getString("interviewerNameRequired"));
} else if (scg.getParameter()
.getHandle()
.equalsIgnoreCase("interviewerNameDefault")) {
scg.getValue().setValue(fp.getString("interviewerNameDefault"));
} else if (scg.getParameter().getHandle().equalsIgnoreCase("interviewDateRequired")) {
scg.getValue().setValue(fp.getString("interviewDateRequired"));
} else if (scg.getParameter().getHandle().equalsIgnoreCase("interviewDateDefault")) {
scg.getValue().setValue(fp.getString("interviewDateDefault"));
}
// YW >>
configs.add(scg);
}
}
}
newStudy.setStudyParameters(configs);
// YW 10-12-2007 <<
newStudy
.getStudyParameterConfig()
.setInterviewerNameRequired(fp.getString("interviewerNameRequired"));
newStudy
.getStudyParameterConfig()
.setInterviewerNameDefault(fp.getString("interviewerNameDefault"));
newStudy
.getStudyParameterConfig()
.setInterviewDateRequired(fp.getString("interviewDateRequired"));
newStudy
.getStudyParameterConfig()
.setInterviewDateDefault(fp.getString("interviewDateDefault"));
// YW >>
session.setAttribute("newStudy", newStudy);
request.setAttribute("facRecruitStatusMap", CreateStudyServlet.facRecruitStatusMap);
request.setAttribute("statuses", Status.toActiveArrayList());
forwardPage(Page.CREATE_SUB_STUDY);
}
} else {
if ("confirm".equalsIgnoreCase(action)) {
confirmStudy();
} else if ("back".equalsIgnoreCase(action)) {
request.setAttribute("facRecruitStatusMap", CreateStudyServlet.facRecruitStatusMap);
request.setAttribute("statuses", Status.toActiveArrayList());
forwardPage(Page.CREATE_SUB_STUDY);
} else if ("submit".equalsIgnoreCase(action)) {
submitStudy();
}
}
}
private void confirmWholeStudy(FormProcessor fp, Validator v) {
errors = v.validate();
if (study.getStatus().isLocked()) {
study.getStudyParameterConfig().setDiscrepancyManagement("false");
} else {
study
.getStudyParameterConfig()
.setDiscrepancyManagement(fp.getString("discrepancyManagement"));
}
study.getStudyParameterConfig().setCollectDob(fp.getString("collectDob"));
study.getStudyParameterConfig().setGenderRequired(fp.getString("genderRequired"));
study
.getStudyParameterConfig()
.setInterviewerNameRequired(fp.getString("interviewerNameRequired"));
study
.getStudyParameterConfig()
.setInterviewerNameDefault(fp.getString("interviewerNameDefault"));
study.getStudyParameterConfig().setInterviewDateEditable(fp.getString("interviewDateEditable"));
study.getStudyParameterConfig().setInterviewDateRequired(fp.getString("interviewDateRequired"));
study
.getStudyParameterConfig()
.setInterviewerNameEditable(fp.getString("interviewerNameEditable"));
study.getStudyParameterConfig().setInterviewDateDefault(fp.getString("interviewDateDefault"));
study.getStudyParameterConfig().setSubjectIdGeneration(fp.getString("subjectIdGeneration"));
study
.getStudyParameterConfig()
.setSubjectPersonIdRequired(fp.getString("subjectPersonIdRequired"));
study.getStudyParameterConfig().setSubjectIdPrefixSuffix(fp.getString("subjectIdPrefixSuffix"));
study.getStudyParameterConfig().setPersonIdShownOnCRF(fp.getString("personIdShownOnCRF"));
study
.getStudyParameterConfig()
.setSecondaryLabelViewable(fp.getString("secondaryLabelViewable"));
study
.getStudyParameterConfig()
.setAdminForcedReasonForChange(fp.getString("adminForcedReasonForChange"));
if (!errors.isEmpty()) {
request.setAttribute("formMessages", errors);
}
}