/*
* OpenClinica is distributed under the
* GNU Lesser General Public License (GNU LGPL).
* For details see: http://www.openclinica.org/license
* copyright 2003-2012 Akaza Research
*/
package org.akaza.openclinica.control.submit;
import java.text.DateFormat;
import java.text.MessageFormat;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Locale;
import javax.servlet.http.HttpSession;
import org.akaza.openclinica.bean.admin.CRFBean;
import org.akaza.openclinica.bean.core.DiscrepancyNoteType;
import org.akaza.openclinica.bean.core.NumericComparisonOperator;
import org.akaza.openclinica.bean.core.ResolutionStatus;
import org.akaza.openclinica.bean.core.Role;
import org.akaza.openclinica.bean.core.Status;
import org.akaza.openclinica.bean.core.SubjectEventStatus;
import org.akaza.openclinica.bean.login.UserAccountBean;
import org.akaza.openclinica.bean.managestudy.DiscrepancyNoteBean;
import org.akaza.openclinica.bean.managestudy.StudyBean;
import org.akaza.openclinica.bean.managestudy.StudyEventBean;
import org.akaza.openclinica.bean.managestudy.StudyEventDefinitionBean;
import org.akaza.openclinica.bean.managestudy.StudySubjectBean;
import org.akaza.openclinica.bean.submit.CRFVersionBean;
import org.akaza.openclinica.bean.submit.EventCRFBean;
import org.akaza.openclinica.bean.submit.ItemBean;
import org.akaza.openclinica.bean.submit.ItemDataBean;
import org.akaza.openclinica.bean.submit.SectionBean;
import org.akaza.openclinica.bean.submit.SubjectBean;
import org.akaza.openclinica.control.core.SecureController;
import org.akaza.openclinica.control.form.FormDiscrepancyNotes;
import org.akaza.openclinica.control.form.FormProcessor;
import org.akaza.openclinica.control.form.Validator;
import org.akaza.openclinica.core.EmailEngine;
import org.akaza.openclinica.core.form.StringUtil;
import org.akaza.openclinica.dao.admin.CRFDAO;
import org.akaza.openclinica.dao.login.UserAccountDAO;
import org.akaza.openclinica.dao.managestudy.DiscrepancyNoteDAO;
import org.akaza.openclinica.dao.managestudy.StudyDAO;
import org.akaza.openclinica.dao.managestudy.StudyEventDAO;
import org.akaza.openclinica.dao.managestudy.StudyEventDefinitionDAO;
import org.akaza.openclinica.dao.managestudy.StudySubjectDAO;
import org.akaza.openclinica.dao.submit.CRFVersionDAO;
import org.akaza.openclinica.dao.submit.EventCRFDAO;
import org.akaza.openclinica.dao.submit.ItemDAO;
import org.akaza.openclinica.dao.submit.ItemDataDAO;
import org.akaza.openclinica.dao.submit.SectionDAO;
import org.akaza.openclinica.dao.submit.SubjectDAO;
import org.akaza.openclinica.i18n.core.LocaleResolver;
import org.akaza.openclinica.view.Page;
import org.akaza.openclinica.web.InsufficientPermissionException;
import org.akaza.openclinica.web.SQLInitServlet;
import org.apache.commons.lang.StringUtils;
/**
* Create a discrepancy note for a data entity
*
* @author jxu
*
*/
public class CreateDiscrepancyNoteServlet extends SecureController {
Locale locale;
// < ResourceBundleresexception,respage;
public static final String DIS_TYPES = "discrepancyTypes";
public static final String RES_STATUSES = "resolutionStatuses";
public static final String ENTITY_ID = "id";
public static final String SUBJECT_ID = "subjectId";
public static final String ITEM_ID = "itemId";
public static final String IS_GROUP_ITEM = "isGroup";
public static final String PARENT_ID = "parentId";// parent note id
public static final String ENTITY_TYPE = "name";
public static final String ENTITY_COLUMN = "column";
public static final String ENTITY_FIELD = "field";
public static final String DIS_NOTE = "discrepancyNote";
public static final String WRITE_TO_DB = "writeToDB";
public static final String IS_REASON_FOR_CHANGE = "isRfc";
public static final String PRESET_RES_STATUS = "strResStatus";
public static final String CAN_MONITOR = "canMonitor";
public static final String NEW_NOTE = "new";
public static final String RES_STATUS_ID = "resStatusId";
public static final String ERROR_FLAG = "errorFlag";// use to determine
// discrepany note type,
// whether a note's item
// has validation error
// or not
public static final String USER_ACCOUNTS = "userAccounts"; // use to provide
// a list of user
// accounts
public static final String USER_ACCOUNT_ID = "strUserAccountId"; // use to
// provide a
// single user
// id, to whom
// the query
// is
// assigned,
// tbh 02/2009
public static final String SUBMITTED_USER_ACCOUNT_ID = "userAccountId";
public static final String PRESET_USER_ACCOUNT_ID = "preUserAccountId";
public static final String EMAIL_USER_ACCOUNT = "sendEmail";
public static final String WHICH_RES_STATUSES = "whichResStatus";
public static final String EVENT_CRF_ID = "eventCRFId";
public static final String PARENT_ROW_COUNT = "rowCount";
public String exceptionName = resexception.getString("no_permission_to_create_discrepancy_note");
public String noAccessMessage = respage.getString("you_may_not_create_discrepancy_note") + respage.getString("change_study_contact_sysadmin");
public static final String FLAG_DISCREPANCY_RFC ="flagDNRFC";
/*
* (non-Javadoc)
*
* @see org.akaza.openclinica.control.core.SecureController#mayProceed()
*/
@Override
protected void mayProceed() throws InsufficientPermissionException {
checkStudyLocked(Page.MENU_SERVLET, respage.getString("current_study_locked"));
locale = LocaleResolver.getLocale(request);
if (SubmitDataServlet.mayViewData(ub, currentRole)) {
return;
}
addPageMessage(noAccessMessage);
throw new InsufficientPermissionException(Page.MENU, exceptionName, "1");
}
@Override
protected void processRequest() throws Exception {
FormProcessor fp = new FormProcessor(request);
DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(sm.getDataSource());
List<DiscrepancyNoteType> types = DiscrepancyNoteType.list;
request.setAttribute(DIS_TYPES, types);
request.setAttribute(RES_STATUSES, ResolutionStatus.list);
boolean writeToDB = fp.getBoolean(WRITE_TO_DB, true); //this should be set based on a new property of DisplayItemBean
boolean isReasonForChange = fp.getBoolean(IS_REASON_FOR_CHANGE);
int entityId = fp.getInt(ENTITY_ID);
// subjectId has to be added to the database when disc notes area saved
// as entity_type 'subject'
int subjectId = fp.getInt(SUBJECT_ID);
int itemId = fp.getInt(ITEM_ID);
String entityType = fp.getString(ENTITY_TYPE);
String field = fp.getString(ENTITY_FIELD);
String column = fp.getString(ENTITY_COLUMN);
int parentId = fp.getInt(PARENT_ID);
//patch for repeating groups and RFC on empty fields
int isGroup = fp.getInt(IS_GROUP_ITEM);
// request.setAttribute(IS_GROUP_ITEM, new Integer(isGroup));
int eventCRFId = fp.getInt(EVENT_CRF_ID);
request.setAttribute(EVENT_CRF_ID, new Integer(eventCRFId));
int rowCount = fp.getInt(PARENT_ROW_COUNT);
// run only once: try to recalculate writeToDB
if (!StringUtils.isBlank(entityType) && "itemData".equalsIgnoreCase(entityType)
&& isGroup !=0 && eventCRFId != 0 ){
// request.setAttribute(PARENT_ROW_COUNT, new Integer(eventCRFId));
int ordinal_for_repeating_group_field = calculateOrdinal( isGroup, field,eventCRFId,rowCount);
int writeToDBStatus = isWriteToDB( isGroup, field, entityId,itemId, ordinal_for_repeating_group_field, eventCRFId);
writeToDB = (writeToDBStatus == -1)? false : (( writeToDBStatus==1)? true:writeToDB);
}
boolean isInError = fp.getBoolean(ERROR_FLAG);
boolean isNew = fp.getBoolean(NEW_NOTE);
request.setAttribute(NEW_NOTE, isNew ? "1" : "0");
String strResStatus = fp.getString(PRESET_RES_STATUS);
if (!strResStatus.equals("")) {
request.setAttribute(PRESET_RES_STATUS, strResStatus);
}
String monitor = fp.getString("monitor");
String enterData = fp.getString("enterData");
request.setAttribute("enterData", enterData);
boolean enteringData = false;
if (enterData != null && "1".equalsIgnoreCase(enterData)) {
// variables are not set in JSP, so not from viewing data and from
// entering data
request.setAttribute(CAN_MONITOR, "1");
request.setAttribute("monitor", monitor);
enteringData = true;
} else if ("1".equalsIgnoreCase(monitor)) {// change to allow user to
// enter note for all items,
// not just blank items
request.setAttribute(CAN_MONITOR, "1");
request.setAttribute("monitor", monitor);
} else {
request.setAttribute(CAN_MONITOR, "0");
}
if ("itemData".equalsIgnoreCase(entityType) && enteringData) {
request.setAttribute("enterItemData", "yes");
}
DateFormat dateFormatter = DateFormat.getDateInstance(DateFormat.DEFAULT, locale);
int preUserId = 0;
if (!StringUtils.isBlank(entityType)) {
if ("itemData".equalsIgnoreCase(entityType)||"itemdata".equalsIgnoreCase(entityType)) {
ItemBean item = (ItemBean) new ItemDAO(sm.getDataSource()).findByPK(itemId);
ItemDataBean itemData = (ItemDataBean) new ItemDataDAO(sm.getDataSource()).findByPK(entityId);
request.setAttribute("entityValue", itemData.getValue());
request.setAttribute("entityName", item.getName());
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
EventCRFBean ec = (EventCRFBean) ecdao.findByPK(itemData.getEventCRFId());
preUserId = ec.getOwnerId();
} else if ("studySub".equalsIgnoreCase(entityType)) {
StudySubjectBean ssub = (StudySubjectBean) new StudySubjectDAO(sm.getDataSource()).findByPK(entityId);
SubjectBean sub = (SubjectBean)new SubjectDAO(sm.getDataSource()).findByPK(ssub.getSubjectId());
preUserId = ssub.getOwnerId();
if (!StringUtils.isBlank(column)) {
if ("enrollment_date".equalsIgnoreCase(column)) {
if (ssub.getEnrollmentDate() != null) {
request.setAttribute("entityValue", dateFormatter.format(ssub.getEnrollmentDate()));
} else {
request.setAttribute("entityValue", resword.getString("N/A"));
}
request.setAttribute("entityName", resword.getString("enrollment_date"));
} else if ("gender".equalsIgnoreCase(column)) {
request.setAttribute("entityValue", sub.getGender() + "");
request.setAttribute("entityName", resword.getString("gender"));
} else if ("date_of_birth".equalsIgnoreCase(column)) {
if (sub.getDateOfBirth() != null) {
request.setAttribute("entityValue", dateFormatter.format(sub.getDateOfBirth()));
} else {
request.setAttribute("entityValue", resword.getString("N/A"));
}
request.setAttribute("entityName", resword.getString("date_of_birth"));
} else if ("unique_identifier".equalsIgnoreCase(column)) {
if (sub.getUniqueIdentifier() != null) {
request.setAttribute("entityValue", sub.getUniqueIdentifier());
}
request.setAttribute("entityName", resword.getString("unique_identifier"));
}
}
} else if ("subject".equalsIgnoreCase(entityType)) {
SubjectBean sub = (SubjectBean) new SubjectDAO(sm.getDataSource()).findByPK(entityId);
preUserId = sub.getOwnerId();
if (!StringUtils.isBlank(column)) {
if ("gender".equalsIgnoreCase(column)) {
request.setAttribute("entityValue", sub.getGender() + "");
request.setAttribute("entityName", resword.getString("gender"));
} else if ("date_of_birth".equalsIgnoreCase(column)) {
if (sub.getDateOfBirth() != null) {
request.setAttribute("entityValue", dateFormatter.format(sub.getDateOfBirth()));
}
request.setAttribute("entityName", resword.getString("date_of_birth"));
} else if ("unique_identifier".equalsIgnoreCase(column)) {
request.setAttribute("entityValue", sub.getUniqueIdentifier());
request.setAttribute("entityName", resword.getString("unique_identifier"));
}
}
} else if ("studyEvent".equalsIgnoreCase(entityType)) {
StudyEventBean se = (StudyEventBean)new StudyEventDAO(sm.getDataSource()).findByPK(entityId);
preUserId = se.getOwnerId();
if (!StringUtils.isBlank(column)) {
if ("location".equalsIgnoreCase(column)) {
request.setAttribute("entityValue", se.getLocation().equals("") || se.getLocation() == null ? resword.getString("N/A") : se.getLocation());
request.setAttribute("entityName", resword.getString("location"));
} else if ("start_date".equalsIgnoreCase(column)) {
if (se.getDateStarted() != null) {
request.setAttribute("entityValue", dateFormatter.format(se.getDateStarted()));
} else {
request.setAttribute("entityValue", resword.getString("N/A"));
}
request.setAttribute("entityName", resword.getString("start_date"));
} else if ("end_date".equalsIgnoreCase(column)) {
if (se.getDateEnded() != null) {
request.setAttribute("entityValue", dateFormatter.format(se.getDateEnded()));
} else {
request.setAttribute("entityValue", resword.getString("N/A"));
}
request.setAttribute("entityName", resword.getString("end_date"));
}
}
} else if ("eventCrf".equalsIgnoreCase(entityType)) {
EventCRFBean ec = (EventCRFBean) new EventCRFDAO(sm.getDataSource()).findByPK(entityId);
preUserId = ec.getOwnerId();
if (!StringUtils.isBlank(column)) {
if ("date_interviewed".equals(column)) {
if (ec.getDateInterviewed() != null) {
request.setAttribute("entityValue", dateFormatter.format(ec.getDateInterviewed()));
} else {
request.setAttribute("entityValue", resword.getString("N/A"));
}
request.setAttribute("entityName", resword.getString("date_interviewed"));
} else if ("interviewer_name".equals(column)) {
request.setAttribute("entityValue", ec.getInterviewerName());
request.setAttribute("entityName", resword.getString("interviewer_name"));
}
}
}
}
// finds all the related notes
ArrayList notes = (ArrayList) dndao.findAllByEntityAndColumn(entityType, entityId, column);
DiscrepancyNoteBean parent = new DiscrepancyNoteBean();
if (parentId > 0) {
dndao.setFetchMapping(true);
parent = (DiscrepancyNoteBean) dndao.findByPK(parentId);
if (parent.isActive()) {
request.setAttribute("parent", parent);
}
dndao.setFetchMapping(false);
}
FormDiscrepancyNotes newNotes = (FormDiscrepancyNotes) session.getAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME);
if (newNotes == null) {
newNotes = new FormDiscrepancyNotes();
}
boolean isNotesExistInSession = (!newNotes.getNotes(field).isEmpty())? true : (!newNotes.getNotes(eventCRFId+"_"+field).isEmpty())? true:false;
if (!notes.isEmpty() || isNotesExistInSession) {
request.setAttribute("hasNotes", "yes");
} else {
request.setAttribute("hasNotes", "no");
logger.debug("has notes:" + "no");
}
//only for adding a new thread
if (currentRole.getRole().equals(Role.RESEARCHASSISTANT) || currentRole.getRole().equals(Role.RESEARCHASSISTANT2) || currentRole.getRole().equals(Role.INVESTIGATOR)) {
ArrayList<ResolutionStatus> resStatuses = new ArrayList<ResolutionStatus>();
resStatuses.add(ResolutionStatus.OPEN);
resStatuses.add(ResolutionStatus.RESOLVED);
request.setAttribute(RES_STATUSES, resStatuses);
List<DiscrepancyNoteType> types2 = new ArrayList<DiscrepancyNoteType>(DiscrepancyNoteType.list);
types2.remove(DiscrepancyNoteType.QUERY);
request.setAttribute(DIS_TYPES, types2);
request.setAttribute(WHICH_RES_STATUSES, "22");
} else if(currentRole.getRole().equals(Role.MONITOR)){
ArrayList<ResolutionStatus> resStatuses = new ArrayList();
resStatuses.add(ResolutionStatus.OPEN);
resStatuses.add(ResolutionStatus.UPDATED);
resStatuses.add(ResolutionStatus.CLOSED);
request.setAttribute(RES_STATUSES, resStatuses);
request.setAttribute(WHICH_RES_STATUSES, "1");
ArrayList<DiscrepancyNoteType> types2 = new ArrayList<DiscrepancyNoteType>();
types2.add(DiscrepancyNoteType.QUERY);
request.setAttribute(DIS_TYPES, types2);
} else {//Role.STUDYDIRECTOR Role.COORDINATOR
List<ResolutionStatus> resStatuses = new ArrayList<ResolutionStatus>(ResolutionStatus.list);
resStatuses.remove(ResolutionStatus.NOT_APPLICABLE);
request.setAttribute(RES_STATUSES, resStatuses); ;
request.setAttribute(WHICH_RES_STATUSES, "2");
}
if (!fp.isSubmitted()) {
DiscrepancyNoteBean dnb = new DiscrepancyNoteBean();
if (subjectId > 0) {
// BWP: this doesn't seem correct, because the SubjectId should
// be the id for
// the SubjectBean, different from StudySubjectBean
StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
StudySubjectBean ssub = (StudySubjectBean) ssdao.findByPK(subjectId);
dnb.setSubjectName(ssub.getName());
dnb.setSubjectId(ssub.getId());
dnb.setStudySub(ssub);
StudyDAO studyDAO = new StudyDAO(sm.getDataSource());
int parentStudyForSubject = 0;
StudyBean studyBeanSub = (StudyBean) studyDAO.findByPK(ssub.getStudyId());
if (null != studyBeanSub) {
parentStudyForSubject = studyBeanSub.getParentStudyId();
}
if (ssub.getStudyId() != currentStudy.getId() && currentStudy.getId() != parentStudyForSubject) {
addPageMessage(noAccessMessage);
throw new InsufficientPermissionException(Page.MENU_SERVLET, exceptionName, "1");
}
}
if (itemId > 0) {
ItemBean item = (ItemBean) new ItemDAO(sm.getDataSource()).findByPK(itemId);
dnb.setEntityName(item.getName());
request.setAttribute("item", item);
}
dnb.setEntityType(entityType);
dnb.setColumn(column);
dnb.setEntityId(entityId);
dnb.setField(field);
dnb.setParentDnId(parent.getId());
dnb.setCreatedDate(new Date());
// When a user is performing Data Entry, Initial Data Entry or
// Double Data Entry and
// have not received any validation warnings or messages for a
// particular item,
// they will see Annotation as the default type in the Add
// Discrepancy note window.
// When a user is performing Data Entry, Initial Data Entry or
// Double Data Entry and they
// have received a validation warning or message for a particular
// item,
// they can click on the flag and the default type should be Failed
// Validation Check
// When a user is viewing a CRF and they click on the flag icon, the
// default type should be query.
// when the type is query, we should also get the user id for the
// person who completed data entry
/* Mantis issue: tbh 08/31/2009
* 0004092: CRCs and Investigators allowed to close a Query
CRCs and Investigators are allowed to choose Closed for a Query. they are also allowed to choose New.
They should only be allowed to choose Updated or Resolution Proposed.
*/
// above extra business rule here, tbh
if (parent.getId() == 0 || isNew) {// no parent, new note thread
if (enteringData) {
if (isInError) {
dnb.setDiscrepancyNoteTypeId(DiscrepancyNoteType.FAILEDVAL.getId());
} else {
dnb.setDiscrepancyNoteTypeId(DiscrepancyNoteType.ANNOTATION.getId());
dnb.setResolutionStatusId(ResolutionStatus.NOT_APPLICABLE.getId());
// >> tbh WHO bug: set an assigned user for the parent
// note
// dnb.setAssignedUser(ub);
// dnb.setAssignedUserId(ub.getId());
// << tbh 08/2009
}
if (isReasonForChange) {
dnb.setDiscrepancyNoteTypeId(DiscrepancyNoteType.REASON_FOR_CHANGE.getId());
dnb.setResolutionStatusId(ResolutionStatus.NOT_APPLICABLE.getId());
}
// << tbh 02/2010, trumps failed evaluation error checks
// can we put this in admin editing
request.setAttribute("autoView", "0");
// above set to automatically open up the user panel
} else {
// when the user is a CRC and is adding a note to the thread
// it should default to Resolution Proposed,
// and the assigned should be the user who logged the query,
// NOT the one who is proposing the solution, tbh 02/2009
// if (currentRole.getRole().equals(Role.COORDINATOR)) {
// dnb.setDiscrepancyNoteTypeId(DiscrepancyNoteType.
// REASON_FOR_CHANGE.getId());
// request.setAttribute("autoView", "1");
// // above set to automatically open up the user panel
// } else {
dnb.setDiscrepancyNoteTypeId(DiscrepancyNoteType.QUERY.getId());
// remove this option for CRCs and Investigators
//if (currentRole.getRole().equals(Role.RESEARCHASSISTANT) && currentStudy.getId() != currentStudy.getParentStudyId()
if (currentRole.getRole().equals(Role.RESEARCHASSISTANT) || currentRole.getRole().equals(Role.RESEARCHASSISTANT2)
|| currentRole.getRole().equals(Role.INVESTIGATOR)) {
request.setAttribute("autoView", "0");
} else {
request.setAttribute("autoView", "1");
dnb.setAssignedUserId(preUserId);
}
// above set to automatically open up the user panel
// }
}
}
else if (parent.getDiscrepancyNoteTypeId() > 0) {
dnb.setDiscrepancyNoteTypeId(parent.getDiscrepancyNoteTypeId());
// if it is a CRC then we should automatically propose a
// solution, tbh
// adding second rule here, tbh 08/2009
if ((currentRole.getRole().equals(Role.RESEARCHASSISTANT) || currentRole.getRole().equals(Role.RESEARCHASSISTANT2)) && currentStudy.getId() != currentStudy.getParentStudyId()) {
dnb.setResolutionStatusId(ResolutionStatus.RESOLVED.getId());
request.setAttribute("autoView", "0");
// hide the panel, tbh
} else {
dnb.setResolutionStatusId(ResolutionStatus.UPDATED.getId());
}
}
dnb.setOwnerId(parent.getOwnerId());
String detailedDes = fp.getString("strErrMsg");
if (detailedDes != null) {
dnb.setDetailedNotes(detailedDes);
logger.debug("found strErrMsg: " + fp.getString("strErrMsg"));
}
// #4346 TBH 10/2009
//If the data entry form has not been saved yet, collecting info from parent page.
dnb = getNoteInfo(dnb);// populate note infos
if (dnb.getEventName() == null || dnb.getEventName().equals("")) {
if (!fp.getString("eventName").equals("")){
dnb.setEventName(fp.getString("eventName"));
}else{
dnb.setEventName(getStudyEventDefinition(eventCRFId).getName());
}
}
if (dnb.getEventStart() == null) {
if (fp.getDate("eventDate")!=null){
dnb.setEventStart(fp.getDate("eventDate"));
}else{
dnb.setEventStart(getStudyEvent(eventCRFId).getDateStarted());
}
}
if (dnb.getCrfName() == null || dnb.getCrfName().equals("")) {
if(!fp.getString("crfName").equals("")){
dnb.setCrfName(fp.getString("crfName"));
}else{
dnb.setCrfName(getCrf(eventCRFId).getName());
}
}
// // #4346 TBH 10/2009
request.setAttribute(DIS_NOTE, dnb);
request.setAttribute("unlock", "0");
request.setAttribute(WRITE_TO_DB, writeToDB ? "1" : "0");//this should go from UI & here
ArrayList userAccounts = this.generateUserAccounts(ub.getActiveStudyId(), subjectId);
request.setAttribute(USER_ACCOUNTS, userAccounts);
// ideally should be only two cases
if ((currentRole.getRole().equals(Role.RESEARCHASSISTANT) || currentRole.getRole().equals(Role.RESEARCHASSISTANT2)) && currentStudy.getId() != currentStudy.getParentStudyId()) { // assigning back to OP, tbh
request.setAttribute(USER_ACCOUNT_ID, Integer.valueOf(parent.getOwnerId()).toString());
logger.debug("assigned owner id: " + parent.getOwnerId());
} else if (dnb.getEventCRFId() > 0) {
logger.debug("found a event crf id: " + dnb.getEventCRFId());
EventCRFDAO eventCrfDAO = new EventCRFDAO(sm.getDataSource());
EventCRFBean eventCrfBean = new EventCRFBean();
eventCrfBean = (EventCRFBean) eventCrfDAO.findByPK(dnb.getEventCRFId());
request.setAttribute(USER_ACCOUNT_ID, Integer.valueOf(eventCrfBean.getOwnerId()).toString());
logger.debug("assigned owner id: " + eventCrfBean.getOwnerId());
} else {
// the end case
}
// set the user account id for the user who completed data entry
forwardPage(Page.ADD_DISCREPANCY_NOTE);
} else {
FormDiscrepancyNotes noteTree = (FormDiscrepancyNotes) session.getAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME);
FormDiscrepancyNotes noteTree_RFC_REPEAT = (FormDiscrepancyNotes) session.getAttribute(FLAG_DISCREPANCY_RFC);;
if(noteTree_RFC_REPEAT == null)
noteTree_RFC_REPEAT = new FormDiscrepancyNotes();
if (noteTree == null) {
noteTree = new FormDiscrepancyNotes();
logger.debug("No note tree initailized in session");
}
Validator v = new Validator(request);
String description = fp.getString("description");
int typeId = fp.getInt("typeId");
int assignedUserAccountId = fp.getInt(SUBMITTED_USER_ACCOUNT_ID);
int resStatusId = fp.getInt(RES_STATUS_ID);
String detailedDes = fp.getString("detailedDes");
int sectionId = fp.getInt("sectionId");
DiscrepancyNoteBean note = new DiscrepancyNoteBean();
v.addValidation("description", Validator.NO_BLANKS);
v.addValidation("description", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 255);
v.addValidation("detailedDes", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 1000);
v.addValidation("typeId", Validator.NO_BLANKS);
HashMap errors = v.validate();
note.setDescription(description);
note.setDetailedNotes(detailedDes);
note.setOwner(ub);
note.setOwnerId(ub.getId());
note.setCreatedDate(new Date());
note.setResolutionStatusId(resStatusId);
note.setDiscrepancyNoteTypeId(typeId);
note.setParentDnId(parent.getId());
if (typeId != DiscrepancyNoteType.ANNOTATION.getId() && typeId != DiscrepancyNoteType.FAILEDVAL.getId()
&& typeId != DiscrepancyNoteType.REASON_FOR_CHANGE.getId()) {
if (assignedUserAccountId > 0) {
note.setAssignedUserId(assignedUserAccountId);
logger.debug("^^^ found assigned user id: " + assignedUserAccountId);
} else {
// a little bit of a workaround, should ideally be always from
// the form
note.setAssignedUserId(parent.getOwnerId());
logger.debug("found user assigned id, in the PARENT OWNER ID: " + parent.getOwnerId() + " note that user assgined id did not work: "
+ assignedUserAccountId);
}
}
note.setField(field);
if (DiscrepancyNoteType.ANNOTATION.getId() == note.getDiscrepancyNoteTypeId()) {
updateStudyEvent(entityType, entityId);
updateStudySubjectStatus(entityType, entityId);
}
if (DiscrepancyNoteType.ANNOTATION.getId() == note.getDiscrepancyNoteTypeId()
|| DiscrepancyNoteType.REASON_FOR_CHANGE.getId() == note.getDiscrepancyNoteTypeId()) {
note.setResStatus(ResolutionStatus.NOT_APPLICABLE);
note.setResolutionStatusId(ResolutionStatus.NOT_APPLICABLE.getId());
}
if (DiscrepancyNoteType.FAILEDVAL.getId() == note.getDiscrepancyNoteTypeId()
|| DiscrepancyNoteType.QUERY.getId() == note.getDiscrepancyNoteTypeId()) {
if (ResolutionStatus.NOT_APPLICABLE.getId() == note.getResolutionStatusId()) {
Validator.addError(errors, RES_STATUS_ID, restext.getString("not_valid_res_status"));
}
}
if (!parent.isActive()) {
note.setEntityId(entityId);
note.setEntityType(entityType);
note.setColumn(column);
} else {
note.setEntityId(parent.getEntityId());
note.setEntityType(parent.getEntityType());
if (!StringUtils.isBlank(parent.getColumn())) {
note.setColumn(parent.getColumn());
} else {
note.setColumn(column);
}
note.setParentDnId(parent.getId());
}
note.setStudyId(currentStudy.getId());
note = getNoteInfo(note);// populate note infos
request.setAttribute(DIS_NOTE, note);
request.setAttribute(WRITE_TO_DB, writeToDB ? "1" : "0");//this should go from UI & here
ArrayList userAccounts = this.generateUserAccounts(ub.getActiveStudyId(), subjectId);
request.setAttribute(USER_ACCOUNT_ID, Integer.valueOf(note.getAssignedUserId()).toString());
// formality more than anything else, we should go to say the note
// is done
Role r = currentRole.getRole();
if (r.equals(Role.MONITOR) || r.equals(Role.INVESTIGATOR) || r.equals(Role.RESEARCHASSISTANT) || r.equals(Role.RESEARCHASSISTANT2) || r.equals(Role.COORDINATOR)) { // investigator
request.setAttribute("unlock", "1");
logger.debug("set UNLOCK to ONE");
} else {
request.setAttribute("unlock", "0");
logger.debug("set UNLOCK to ZERO");
}
request.setAttribute(USER_ACCOUNTS, userAccounts);
if (errors.isEmpty()) {
if (!writeToDB) {
noteTree.addNote(field, note);
noteTree.addIdNote(note.getEntityId(), field);
noteTree_RFC_REPEAT.addNote(EVENT_CRF_ID+"_"+field, note);
noteTree_RFC_REPEAT.addIdNote(note.getEntityId(), field);
//-> catcher // FORM_DISCREPANCY_NOTES_NAME
session.setAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME, noteTree);
session.setAttribute(FLAG_DISCREPANCY_RFC, noteTree_RFC_REPEAT);
//
/*Setting a marker to check later while saving administrative edited data. This is needed to make
* sure the system flags error while changing data for items which already has a DiscrepanyNote*/
manageReasonForChangeState(session, eventCRFId+"_"+field);
forwardPage(Page.ADD_DISCREPANCY_NOTE_DONE);
} else {
// if not creating a new thread(note), update exsiting notes
// if necessary
//if ("itemData".equalsIgnoreCase(entityType) && !isNew) {
int pdnId = note!=null?note.getParentDnId():0;
if(pdnId > 0) {
logger.debug("Create:find parent note for item data:" + note.getEntityId());
DiscrepancyNoteBean pNote = (DiscrepancyNoteBean) dndao.findByPK(pdnId);
logger.debug("setting DN owner id: " + pNote.getOwnerId());
note.setOwnerId(pNote.getOwnerId());
if (note.getDiscrepancyNoteTypeId() == pNote.getDiscrepancyNoteTypeId()) {
if (note.getResolutionStatusId() != pNote.getResolutionStatusId()) {
pNote.setResolutionStatusId(note.getResolutionStatusId());
dndao.update(pNote);
}
if (note.getAssignedUserId() != pNote.getAssignedUserId()) {
pNote.setAssignedUserId(note.getAssignedUserId());
if(pNote.getAssignedUserId()>0) {
dndao.updateAssignedUser(pNote);
} else {
dndao.updateAssignedUserToNull(pNote);
}
}
}
}
note = (DiscrepancyNoteBean) dndao.create(note);
dndao.createMapping(note);
request.setAttribute(DIS_NOTE, note);
if (note.getParentDnId() == 0) {
// see issue 2659 this is a new thread, we will create
// two notes in this case,
// This way one can be the parent that updates as the
// status changes, but one also stays as New.
note.setParentDnId(note.getId());
note = (DiscrepancyNoteBean) dndao.create(note);
dndao.createMapping(note);
}
/*Setting a marker to check later while saving administrative edited data. This is needed to make
* sure the system flags error while changing data for items which already has a DiscrepanyNote*/
//session.setAttribute(DataEntryServlet.NOTE_SUBMITTED, true);
//session.setAttribute(DataEntryServlet.NOTE_SUBMITTED, true);
// String field_id_for_RFC_hash = buildDiscrepancyNoteIdForRFCHash(eventCRFId,entityId, isGroup, field, ordinal_for_repeating_group_field);
String field_id_for_RFC_hash = eventCRFId+"_"+field;
manageReasonForChangeState(session, field_id_for_RFC_hash);
logger.debug("found resolution status: " + note.getResolutionStatusId());
String email = fp.getString(EMAIL_USER_ACCOUNT);
logger.debug("found email: " + email);
if (note.getAssignedUserId() > 0 && "1".equals(email.trim()) && DiscrepancyNoteType.QUERY.getId() == note.getDiscrepancyNoteTypeId()) {
logger.debug("++++++ found our way here: " + note.getDiscrepancyNoteTypeId() + " id number and " + note.getDisType().getName());
// generate email for user here
StringBuffer message = new StringBuffer();
// generate message here
UserAccountDAO userAccountDAO = new UserAccountDAO(sm.getDataSource());
ItemDAO itemDAO = new ItemDAO(sm.getDataSource());
ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
ItemBean item = new ItemBean();
ItemDataBean itemData = new ItemDataBean();
SectionBean section = new SectionBean();
StudyDAO studyDAO = new StudyDAO(sm.getDataSource());
UserAccountBean assignedUser = (UserAccountBean) userAccountDAO.findByPK(note.getAssignedUserId());
String alertEmail = assignedUser.getEmail();
message.append(MessageFormat.format(respage.getString("mailDNHeader"), assignedUser.getFirstName(),assignedUser.getLastName()));
message.append("<A HREF='" + SQLInitServlet.getField("sysURL.base")
+ "ViewNotes?module=submit&listNotes_f_discrepancyNoteBean.user=" + assignedUser.getName()
+ "&listNotes_f_entityName=" + note.getEntityName()
+ "'>" + SQLInitServlet.getField("sysURL.base") + "</A><BR/>");
message.append(respage.getString("you_received_this_from"));
StudyBean study = (StudyBean) studyDAO.findByPK(note.getStudyId());
SectionDAO sectionDAO = new SectionDAO(sm.getDataSource());
if ("itemData".equalsIgnoreCase(entityType)) {
itemData = (ItemDataBean) iddao.findByPK(note.getEntityId());
item = (ItemBean) itemDAO.findByPK(itemData.getItemId());
if (sectionId > 0) {
section = (SectionBean) sectionDAO.findByPK(sectionId);
} else {
//Todo section should be initialized when sectionId = 0
}
}
message.append(respage.getString("email_body_separator"));
message.append(respage.getString("disc_note_info"));
message.append(respage.getString("email_body_separator"));
message.append(MessageFormat.format(respage.getString("mailDNParameters1"), note.getDescription(), note.getDetailedNotes(), ub.getName()));
message.append(respage.getString("email_body_separator"));
message.append(respage.getString("entity_information"));
message.append(respage.getString("email_body_separator"));
message.append(MessageFormat.format(respage.getString("mailDNParameters2"), study.getName(), note.getSubjectName()));
if (!("studySub".equalsIgnoreCase(entityType)
|| "subject".equalsIgnoreCase(entityType))) {
message.append(MessageFormat.format(respage.getString("mailDNParameters3"), note.getEventName()));
if (!"studyEvent".equalsIgnoreCase(note.getEntityType())) {
message.append(MessageFormat.format(respage.getString("mailDNParameters4"), note.getCrfName()));
if (!"eventCrf".equalsIgnoreCase(note.getEntityType())) {
if (sectionId > 0) {
message.append(MessageFormat.format(respage.getString("mailDNParameters5"), section.getName()));
}
message.append(MessageFormat.format(respage.getString("mailDNParameters6"), item.getName()));
}
}
}
message.append(respage.getString("email_body_separator"));
message.append(MessageFormat.format(respage.getString("mailDNThanks"), study.getName()));
message.append(respage.getString("email_body_separator"));
message.append(respage.getString("disclaimer"));
message.append(respage.getString("email_body_separator"));
message.append(respage.getString("email_footer"));
String emailBodyString = message.toString();
sendEmail(alertEmail.trim(), EmailEngine.getAdminEmail(), MessageFormat.format(respage.getString("mailDNSubject"),study.getName(), note.getEntityName()), emailBodyString, true, null,
null, true);
} else {
logger.debug("did not send email, but did save DN");
}
// addPageMessage(
// "Your discrepancy note has been saved into database.");
addPageMessage(respage.getString("note_saved_into_db"));
addPageMessage(respage.getString("page_close_automatically"));
forwardPage(Page.ADD_DISCREPANCY_NOTE_SAVE_DONE);
}
} else {
if(parentId>0) {
if(note.getResolutionStatusId() == ResolutionStatus.NOT_APPLICABLE.getId()) {
request.setAttribute("autoView", "0");
}
}else {
if(note.getDiscrepancyNoteTypeId() == DiscrepancyNoteType.QUERY.getId()) {
request.setAttribute("autoView", "1");
} else {
request.setAttribute("autoView", "0");
}
}
setInputMessages(errors);
forwardPage(Page.ADD_DISCREPANCY_NOTE);
}
}
}
/**
* Constructs a url for creating new note on 'view note list' page
*
* @param note
* @param preset
* @return
*/
public static String getAddChildURL(DiscrepancyNoteBean note, ResolutionStatus preset, boolean toView) {
ArrayList<String> arguments = new ArrayList<String>();
arguments.add(ENTITY_TYPE + "=" + note.getEntityType());
arguments.add(ENTITY_ID + "=" + note.getEntityId());
arguments.add(WRITE_TO_DB + "=" + "1");
arguments.add("monitor" + "=" + 1);// of course, when resolving a note,
// we have monitor privilege
if (preset.isActive()) {
arguments.add(PRESET_RES_STATUS + "=" + String.valueOf(preset.getId()));
}
if (toView) {
// BWP 3/19/2009 3166: <<
String columnValue = "".equalsIgnoreCase(note.getColumn()) ? "value" : note.getColumn();
// >>
arguments.add(ENTITY_COLUMN + "=" + columnValue);
arguments.add(SUBJECT_ID + "=" + note.getSubjectId());
arguments.add(ITEM_ID + "=" + note.getItemId());
String queryString = StringUtil.join("&", arguments);
return "ViewDiscrepancyNote?" + queryString;
} else {
arguments.add(PARENT_ID + "=" + note.getId());
String queryString = StringUtil.join("&", arguments);
return "CreateDiscrepancyNote?" + queryString;
}
}
/**
* Pulls the note related information from database according to note type
*
* @param note
*/
private void updateStudySubjectStatus(String entityType, int entityId) {
if ("itemData".equalsIgnoreCase(entityType)) {
int itemDataId = entityId;
ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
ItemDataBean itemData = (ItemDataBean) iddao.findByPK(itemDataId);
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
StudyEventDAO svdao = new StudyEventDAO(sm.getDataSource());
StudySubjectDAO studySubjectDAO = new StudySubjectDAO(sm.getDataSource());
EventCRFBean ec = (EventCRFBean) ecdao.findByPK(itemData.getEventCRFId());
StudyEventBean event = (StudyEventBean) svdao.findByPK(ec.getStudyEventId());
StudySubjectBean studySubject = (StudySubjectBean) studySubjectDAO.findByPK(event.getStudySubjectId());
if (studySubject.getStatus() != null && studySubject.getStatus().equals(Status.SIGNED)) {
studySubject.setStatus(Status.AVAILABLE);
studySubject.setUpdater(ub);
studySubject.setUpdatedDate(new Date());
studySubjectDAO.update(studySubject);
}
if (ec.isSdvStatus()) {
studySubject.setStatus(Status.AVAILABLE);
studySubject.setUpdater(ub);
studySubject.setUpdatedDate(new Date());
studySubjectDAO.update(studySubject);
ec.setSdvStatus(false);
ec.setSdvUpdateId(ub.getId());
ecdao.update(ec);
}
}
}
private ArrayList generateUserAccounts(int studyId, int subjectId) {
UserAccountDAO userAccountDAO = new UserAccountDAO(sm.getDataSource());
StudyDAO studyDAO = new StudyDAO(sm.getDataSource());
StudyBean subjectStudy = studyDAO.findByStudySubjectId(subjectId);
// study id, tbh 03/2009
ArrayList userAccounts = new ArrayList();
if (currentStudy.getParentStudyId() > 0) {
userAccounts = userAccountDAO.findAllUsersByStudyOrSite(studyId, currentStudy.getParentStudyId(), subjectId);
} else if (subjectStudy.getParentStudyId() > 0) {
userAccounts = userAccountDAO.findAllUsersByStudyOrSite(subjectStudy.getId(), subjectStudy.getParentStudyId(), subjectId);
} else {
userAccounts = userAccountDAO.findAllUsersByStudyOrSite(studyId, 0, subjectId);
}
return userAccounts;
}
private void updateStudyEvent(String entityType, int entityId) {
if ("itemData".equalsIgnoreCase(entityType)) {
int itemDataId = entityId;
ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
ItemDataBean itemData = (ItemDataBean) iddao.findByPK(itemDataId);
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
StudyEventDAO svdao = new StudyEventDAO(sm.getDataSource());
EventCRFBean ec = (EventCRFBean) ecdao.findByPK(itemData.getEventCRFId());
StudyEventBean event = (StudyEventBean) svdao.findByPK(ec.getStudyEventId());
if (event.getSubjectEventStatus().equals(SubjectEventStatus.SIGNED)) {
event.setSubjectEventStatus(SubjectEventStatus.COMPLETED);
event.setUpdater(ub);
event.setUpdatedDate(new Date());
svdao.update(event);
}
} else if ("eventCrf".equalsIgnoreCase(entityType)) {
int eventCRFId = entityId;
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
StudyEventDAO svdao = new StudyEventDAO(sm.getDataSource());
EventCRFBean ec = (EventCRFBean) ecdao.findByPK(eventCRFId);
StudyEventBean event = (StudyEventBean) svdao.findByPK(ec.getStudyEventId());
if (event.getSubjectEventStatus().equals(SubjectEventStatus.SIGNED)) {
event.setSubjectEventStatus(SubjectEventStatus.COMPLETED);
event.setUpdater(ub);
event.setUpdatedDate(new Date());
svdao.update(event);
}
}
}
private void manageReasonForChangeState(HttpSession session, String itemDataBeanId) {
@SuppressWarnings("unchecked")
HashMap<String, Boolean> noteSubmitted = (HashMap<String, Boolean>) session.getAttribute(DataEntryServlet.NOTE_SUBMITTED);
if (noteSubmitted == null) {
noteSubmitted = new HashMap<String, Boolean>();
}
noteSubmitted.put(itemDataBeanId, Boolean.TRUE);
session.setAttribute(DataEntryServlet.NOTE_SUBMITTED, noteSubmitted);
}
/*
* @return 0 - not defined; 1 - yes, -1 - no
*
*/
private int isWriteToDB(int isGroup, String field, int item_data_id,
int item_id, int ordinal_for_repeating_group_field, int event_crf_id){
if ( item_data_id > 0 && isGroup==-1){//non repeating group; coming from showItemInput.jsp
return 1;
}
else if ( item_data_id < 0 && isGroup==-1){//non repeating group; coming from showItemInput.jsp
return -1;
}
else if ( isGroup==1){// repeating group;
//initial data entry or if template cell is empty (last row)
if ( item_data_id < 0 ){ return -1;}
if ( item_data_id > 0 ){
// first row IG_TEST__GROUP1_6727_0input320
// row without X IG_TEST__GROUP1_6727_manual1input320
// row with X IG_TEST__GROUP1_6727_1input320
if (field.contains("_0input") || field.contains("manual")){
//get ordinal
ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource(), locale);
boolean isExistInDB = iddao.isItemExists(item_id,ordinal_for_repeating_group_field,event_crf_id);
return (isExistInDB)? 1: -1;
}
else if (field.contains("input")){
return -1;
}
}
}
return 0;
}
public int calculateOrdinal(int isGroup, String field_name, int event_crf_id, int rowCount){
// first row IG_TEST__GROUP1_6727_0input320
// row without X IG_TEST__GROUP1_6727_manual1input320
// row with X IG_TEST__GROUP1_6727_1input320
int ordinal = 0;
int start = -1;int end=-1;
if ( isGroup == -1){ return 1;}
if (field_name.contains("_0input")) { return 1;}
try{
if ( field_name.contains("manual")){
start = field_name.indexOf("manual")+5;
end = field_name.indexOf("input");
if ( start == 4 || end == -1){ return 0;}
ordinal = Integer.valueOf(field_name.substring(start+1, end));
return ordinal+1;
}else{
//get max ordinal from DB
ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource(), locale);
//IG_TEST__GROUP1_6727_manual1input320
String[] field_name_items=field_name.split("_");
String group_oid = field_name.substring(0, field_name.indexOf(field_name_items[field_name_items.length-1])-1);
int maxOrdinal = iddao.getMaxOrdinalForGroupByGroupOID(group_oid, event_crf_id);
//get ordinal from field
end = field_name.indexOf("input");
start = field_name.lastIndexOf("_");
if ( end == -1 || start ==-1){ return 0;}
ordinal = Integer.valueOf(field_name.substring(start+1, end));
return ordinal+maxOrdinal+rowCount;
}
}catch(NumberFormatException e){
//DO NOTHING
}
return ordinal;
}
private StudyEventBean getStudyEvent(int eventCRFId) {
StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
StudyEventBean event = (StudyEventBean) sedao.findByPK(getEventCrf(eventCRFId).getStudyEventId());
return event;
}
private StudyEventDefinitionBean getStudyEventDefinition(int eventCRFId) {
StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
StudyEventDefinitionBean sed = (StudyEventDefinitionBean) seddao.findByPK(getStudyEvent(eventCRFId).getStudyEventDefinitionId());
return sed;
}
private CRFBean getCrf(int eventCRFId) {
CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
CRFDAO cdao = new CRFDAO(sm.getDataSource());
CRFVersionBean cv = (CRFVersionBean) cvdao.findByPK(getEventCrf(eventCRFId).getCRFVersionId());
CRFBean c = (CRFBean) cdao.findByPK(cv.getCrfId());
return c;
}
private EventCRFBean getEventCrf(int eventCRFId) {
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
EventCRFBean ec = (EventCRFBean) ecdao.findByPK(eventCRFId);
return ec;
}
}