/*
* OpenClinica is distributed under the
* GNU Lesser General Public License (GNU LGPL).
* For details see: http://www.openclinica.org/license
* copyright 2003-2005 Akaza Research
*/
package org.akaza.openclinica.control.managestudy;
import org.akaza.openclinica.bean.core.SubjectEventStatus;
import org.akaza.openclinica.bean.login.StudyUserRoleBean;
import org.akaza.openclinica.bean.login.UserAccountBean;
import org.akaza.openclinica.bean.managestudy.DisplayStudyEventBean;
import org.akaza.openclinica.bean.managestudy.DisplayStudySubjectBean;
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.StudyGroupClassBean;
import org.akaza.openclinica.bean.managestudy.StudySubjectBean;
import org.akaza.openclinica.bean.service.StudyParameterValueBean;
import org.akaza.openclinica.bean.submit.EventCRFBean;
import org.akaza.openclinica.bean.submit.SubjectGroupMapBean;
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.submit.AddNewSubjectServlet;
import org.akaza.openclinica.dao.managestudy.EventDefinitionCRFDAO;
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.StudyGroupClassDAO;
import org.akaza.openclinica.dao.managestudy.StudyGroupDAO;
import org.akaza.openclinica.dao.managestudy.StudySubjectDAO;
import org.akaza.openclinica.dao.service.StudyParameterValueDAO;
import org.akaza.openclinica.dao.submit.EventCRFDAO;
import org.akaza.openclinica.dao.submit.SubjectGroupMapDAO;
import org.akaza.openclinica.i18n.core.LocaleResolver;
import org.akaza.openclinica.view.Page;
import org.akaza.openclinica.web.bean.DisplayStudySubjectRow;
import org.akaza.openclinica.web.bean.EntityBeanTable;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Locale;
import javax.sql.DataSource;
/**
* @author jxu
*/
public abstract class ListStudySubjectServlet extends SecureController {
// Shaoyu Su
Locale locale;
// BWP Issue 3195, 3330 <<
public static String SUBJECT_PAGE_NUMBER = "ebl_page";
public static String PAGINATING_QUERY = "paginatingQuery";
public static String FILTER_KEYWORD = "ebl_filterKeyword";
public static String SEARCH_SUBMITTED = "submitted";
// >>
// < ResourceBundleresword;
@Override
public void processRequest() throws Exception {
FormProcessor fp = new FormProcessor(request);
locale = LocaleResolver.getLocale(request);
// < resword =
// ResourceBundle.getBundle("org.akaza.openclinica.i18n.words",locale);
// BWP 3098 << close the info side panel and show icons
request.setAttribute("closeInfoShowIcons", true);
// >>
// BWP 3195, 3330 : designed to address pagination issues
String pageNumber = fp.getString(SUBJECT_PAGE_NUMBER);
StringBuilder paginatingQuery = new StringBuilder("");
String filterKeyword = fp.getString(FILTER_KEYWORD);
String tmpSearch = fp.getString(SEARCH_SUBMITTED);
boolean searchSubmitted =
!(tmpSearch == null || "".equalsIgnoreCase(tmpSearch)) && !"".equalsIgnoreCase(filterKeyword) && !"+".equalsIgnoreCase(filterKeyword);
if (pageNumber != null && !"".equalsIgnoreCase(pageNumber)) {
int tempNum = 0;
try {
tempNum = Integer.parseInt(pageNumber);
} catch (NumberFormatException nfe) {
// tempNum is already initialized to 0
}
if (tempNum > 0) {
paginatingQuery = new StringBuilder(SUBJECT_PAGE_NUMBER).append("=").append(pageNumber);
paginatingQuery.append("&ebl_paginated=1");
}
}
// URL encode the search keyword, since it will be a parameter in the
// URL
String filterKeywordURLEncode = java.net.URLEncoder.encode(filterKeyword, "UTF-8");
if (searchSubmitted) {
paginatingQuery.append("&ebl_sortColumnInd=0&submitted=1&ebl_sortAscending=1&ebl_filtered=1");
paginatingQuery.append("&").append(FILTER_KEYWORD).append("=").append(filterKeywordURLEncode);
}
request.setAttribute(PAGINATING_QUERY, paginatingQuery.toString());
StudyDAO stdao = new StudyDAO(sm.getDataSource());
StudySubjectDAO sdao = new StudySubjectDAO(sm.getDataSource());
StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource());
StudyGroupClassDAO sgcdao = new StudyGroupClassDAO(sm.getDataSource());
StudyGroupDAO sgdao = new StudyGroupDAO(sm.getDataSource());
StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
// YW << update study parameters of current study.
// "collectDob" and "genderRequired" are set as the same as the parent
// study
// tbh, also add the params "subjectPersonIdRequired",
// "subjectIdGeneration", "subjectIdPrefixSuffix"
int parentStudyId = currentStudy.getParentStudyId();
ArrayList studyGroupClasses = new ArrayList();
ArrayList allDefs = new ArrayList();
// allDefs holds the list of study event definitions used in the table,
// tbh
if (parentStudyId > 0) {
StudyBean parentStudy = (StudyBean) stdao.findByPK(parentStudyId);
studyGroupClasses = sgcdao.findAllActiveByStudy(parentStudy);
allDefs = seddao.findAllActiveByStudy(parentStudy);
} else {
parentStudyId = currentStudy.getId();
studyGroupClasses = sgcdao.findAllActiveByStudy(currentStudy);
allDefs = seddao.findAllActiveByStudy(currentStudy);
}
StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
StudyParameterValueBean parentSPV = spvdao.findByHandleAndStudy(parentStudyId, "collectDob");
currentStudy.getStudyParameterConfig().setCollectDob(parentSPV.getValue());
parentSPV = spvdao.findByHandleAndStudy(parentStudyId, "genderRequired");
currentStudy.getStudyParameterConfig().setGenderRequired(parentSPV.getValue());
parentSPV = spvdao.findByHandleAndStudy(parentStudyId, "subjectPersonIdRequired");
currentStudy.getStudyParameterConfig().setSubjectPersonIdRequired(parentSPV.getValue());
parentSPV = spvdao.findByHandleAndStudy(parentStudyId, "subjectIdGeneration");
currentStudy.getStudyParameterConfig().setSubjectIdGeneration(parentSPV.getValue());
parentSPV = spvdao.findByHandleAndStudy(parentStudyId, "subjectIdPrefixSuffix");
currentStudy.getStudyParameterConfig().setSubjectIdPrefixSuffix(parentSPV.getValue());
// YW >>
// for all the study groups for each group class
for (int i = 0; i < studyGroupClasses.size(); i++) {
StudyGroupClassBean sgc = (StudyGroupClassBean) studyGroupClasses.get(i);
ArrayList groups = sgdao.findAllByGroupClass(sgc);
sgc.setStudyGroups(groups);
}
request.setAttribute("studyGroupClasses", studyGroupClasses);
// information for the event tabs
session.setAttribute("allDefsArray", allDefs);
session.setAttribute("allDefsNumber", new Integer(allDefs.size()));
session.setAttribute("groupSize", new Integer(studyGroupClasses.size()));
// find all the subjects in current study
ArrayList subjects = sdao.findAllByStudyId(currentStudy.getId());
ArrayList<DisplayStudySubjectBean> displayStudySubs = new ArrayList<DisplayStudySubjectBean>();
// BEGIN LOOPING THROUGH SUBJECTS
for (int i = 0; i < subjects.size(); i++) {
StudySubjectBean studySub = (StudySubjectBean) subjects.get(i);
ArrayList groups = (ArrayList) sgmdao.findAllByStudySubject(studySub.getId());
ArrayList subGClasses = new ArrayList();
for (int j = 0; j < studyGroupClasses.size(); j++) {
StudyGroupClassBean sgc = (StudyGroupClassBean) studyGroupClasses.get(j);
boolean hasClass = false;
for (int k = 0; k < groups.size(); k++) {
SubjectGroupMapBean sgmb = (SubjectGroupMapBean) groups.get(k);
if (sgmb.getGroupClassName().equalsIgnoreCase(sgc.getName())) {
subGClasses.add(sgmb);
hasClass = true;
break;
}
}
if (!hasClass) {
subGClasses.add(new SubjectGroupMapBean());
}
}
ArrayList subEvents = new ArrayList();
// find all events order by definition ordinal
ArrayList events = sedao.findAllByStudySubject(studySub);
for (int j = 0; j < allDefs.size(); j++) {
StudyEventDefinitionBean sed = (StudyEventDefinitionBean) allDefs.get(j);
boolean hasDef = false;
// StudyEventBean first = (StudyEventBean) events.get(0);
// whack idea to try and set things right with the code
// below, tbh
// below needs to change, we need to reach into the list and
// pick the next one, tbh
// int blankid = first.getId();
// logger.info("...set blank to "+blankid);
for (int k = 0; k < events.size(); k++) {
StudyEventBean se = (StudyEventBean) events.get(k);
if (se.getStudyEventDefinitionId() == sed.getId()) {
se.setStudyEventDefinition(sed);
// logger.info(">>>found assigned id "+sed.getId()+" sed
// name: "+sed.getName()+" "+se.getId());
subEvents.add(se);
hasDef = true;
}
}
if (!hasDef) {
StudyEventBean blank = new StudyEventBean();
blank.setSubjectEventStatus(SubjectEventStatus.NOT_SCHEDULED);
blank.setStudyEventDefinitionId(sed.getId());
// how can we set the following:
// logger.info("...resetting blank id: "+blank.getId()+" to
// "+blankid);
// blank.setId(blankid);
blank.setStudyEventDefinition(sed);
// logger.info(">>>blank id: "+blank.getId());
// logger.info(">>>found unassigned id "+sed.getId()+" sed
// name: "+sed.getName()+" ");
subEvents.add(blank);
}
}
// logger.info("subevents size after all adds: "+subEvents.size());
// reorganize the events and find the repeating ones
// subEvents:[aa bbb cc d ee]
// finalEvents:[a(2) b(3) c(2) d e(2)]
int prevDefId = 0;
int currDefId = 0;
ArrayList finalEvents = new ArrayList();
int repeatingNum = 1;
int count = 0;
StudyEventBean event = new StudyEventBean();
// begin looping through subject events
for (int j = 0; j < subEvents.size(); j++) {
StudyEventBean se = (StudyEventBean) subEvents.get(j);
currDefId = se.getStudyEventDefinitionId();
if (currDefId != prevDefId) {// find a new event
if (repeatingNum > 1) {
event.setRepeatingNum(repeatingNum);
repeatingNum = 1;
}
finalEvents.add(se); // add current event to final
event = se;
count++;
// logger.info("event id? "+event.getId());
} else {// repeating event
repeatingNum++;
event.getRepeatEvents().add(se);
// logger.info("repeating size:" +
// event.getStudySubjectId()+
// event.getRepeatEvents().size());
if (j == subEvents.size() - 1) {
event.setRepeatingNum(repeatingNum);
repeatingNum = 1;
}
}
prevDefId = currDefId;
}
// end looping through subject events
DisplayStudySubjectBean dssb = new DisplayStudySubjectBean();
// logger.info("final events size: "+finalEvents.size());
dssb.setStudyEvents(finalEvents);
dssb.setStudySubject(studySub);
dssb.setStudyGroups(subGClasses);
displayStudySubs.add(dssb);
}
// END LOOPING THROUGH SUBJECTS
// Set a subject property to determine whether to show a signed-type
// icon (electronic signature)
// in the JSP view or not
// Get all event crfs by studyevent id; then use
// EventDefinitionCRFDAO.isRequired to
// determine whether any uncompleted CRFs are required.
boolean isRequiredUncomplete = false;
for (DisplayStudySubjectBean subject : displayStudySubs) {
for (Iterator it = subject.getStudyEvents().iterator(); it.hasNext();) {
StudyEventBean event = (StudyEventBean) it.next();
if (event.getSubjectEventStatus() != null && event.getSubjectEventStatus().getId() == 3) {
// disallow the subject from signing any studies
subject.setStudySignable(false);
break;
} else {
// determine whether the subject has any required,
// uncompleted event CRFs
isRequiredUncomplete = eventHasRequiredUncompleteCRFs(event);
if (isRequiredUncomplete) {
subject.setStudySignable(false);
break;
}
}
}
}
fp = new FormProcessor(request);
EntityBeanTable table = fp.getEntityBeanTable();
ArrayList allStudyRows = DisplayStudySubjectRow.generateRowsFromBeans(displayStudySubs);
ArrayList columnArray = new ArrayList();
columnArray.add(resword.getString("study_subject_ID"));
columnArray.add(resword.getString("subject_status"));
columnArray.add(resword.getString("OID"));
columnArray.add(resword.getString("gender"));
// new
columnArray.add(resword.getString("secondary_ID"));
for (int i = 0; i < studyGroupClasses.size(); i++) {
StudyGroupClassBean sgc = (StudyGroupClassBean) studyGroupClasses.get(i);
columnArray.add(sgc.getName());
}
for (int i = 0; i < allDefs.size(); i++) {
StudyEventDefinitionBean sed = (StudyEventDefinitionBean) allDefs.get(i);
columnArray.add(sed.getName());
}
columnArray.add(resword.getString("actions"));
String columns[] = new String[columnArray.size()];
columnArray.toArray(columns);
// String[] columns = {"ID", "Subject Status", "Gender", "Enrollment
// Date",
// "Study Events", "Actions" };
table.setColumns(new ArrayList(Arrays.asList(columns)));
table.setQuery(getBaseURL(), new HashMap());
table.hideColumnLink(columnArray.size() - 1);
// table.addLink("Enroll a new subject",
// "javascript:leftnavExpand('addSubjectRowExpress');");
table.setRows(allStudyRows);
if (filterKeyword != null && !"".equalsIgnoreCase(filterKeyword)) {
table.setKeywordFilter(filterKeyword);
}
table.computeDisplay();
request.setAttribute("table", table);
// request.setAttribute("subjects", subjects);
String idSetting = currentStudy.getStudyParameterConfig().getSubjectIdGeneration();
// logger.info("subject id setting :" + idSetting);
// set up auto study subject id
if (idSetting.equals("auto editable") || idSetting.equals("auto non-editable")) {
//Shaoyu Su
//int nextLabel = ssdao.findTheGreatestLabel() + 1;
//request.setAttribute("label", new Integer(nextLabel).toString());
request.setAttribute("label", resword.getString("id_generated_Save_Add"));
}
FormDiscrepancyNotes discNotes = new FormDiscrepancyNotes();
session.setAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME, discNotes);
forwardPage(getJSP());
}
protected abstract String getBaseURL();
protected abstract Page getJSP();
private boolean eventHasRequiredUncompleteCRFs(StudyEventBean studyEvent) {
if (studyEvent == null)
return false;
EventCRFDAO eventCRFDAO = new EventCRFDAO(sm.getDataSource());
EventDefinitionCRFDAO eventDefinitionDAO = new EventDefinitionCRFDAO(sm.getDataSource());
List<EventCRFBean> crfBeans = new ArrayList<EventCRFBean>();
crfBeans.addAll(eventCRFDAO.findAllByStudyEvent(studyEvent));
// If the EventCRFBean has a completionStatusId of 0
// (indicating that it is not complete),
// then find
// out whether it's required. If so, then return from the method false.
for (EventCRFBean crfBean : crfBeans) {
if (crfBean != null && crfBean.getCompletionStatusId() == 0) {
if (eventDefinitionDAO.isRequiredInDefinition(crfBean.getCRFVersionId(), studyEvent)) {
return true;
}
}
}
return false;
}
public static DisplayStudyEventBean getDisplayStudyEventsForStudySubject(StudySubjectBean studySub, StudyEventBean event, DataSource ds,
UserAccountBean ub, StudyUserRoleBean currentRole, StudyBean study) {
StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(ds);
StudyEventDAO sedao = new StudyEventDAO(ds);
EventCRFDAO ecdao = new EventCRFDAO(ds);
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(ds);
StudyEventDefinitionBean sed = (StudyEventDefinitionBean) seddao.findByPK(event.getStudyEventDefinitionId());
event.setStudyEventDefinition(sed);
// find all active crfs in the definition
ArrayList eventDefinitionCRFs = edcdao.findAllActiveByEventDefinitionId(sed.getId());
ArrayList eventCRFs = ecdao.findAllByStudyEvent(event);
// construct info needed on view study event page
DisplayStudyEventBean de = new DisplayStudyEventBean();
de.setStudyEvent(event);
de.setDisplayEventCRFs(ViewStudySubjectServlet.getDisplayEventCRFs(ds, eventCRFs, eventDefinitionCRFs, ub, currentRole, event.getSubjectEventStatus(),
study));
ArrayList al = ViewStudySubjectServlet.getUncompletedCRFs(ds, eventDefinitionCRFs, eventCRFs, event.getSubjectEventStatus());
// ViewStudySubjectServlet.populateUncompletedCRFsWithCRFAndVersions(ds,
// al);
de.setUncompletedCRFs(al);
return de;
}
}