Java tutorial
/* * 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.admin.AuditEventBean; import org.akaza.openclinica.bean.admin.CRFBean; import org.akaza.openclinica.bean.admin.StudyEventAuditBean; import org.akaza.openclinica.bean.core.DataEntryStage; 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.StudyUserRoleBean; import org.akaza.openclinica.bean.login.UserAccountBean; import org.akaza.openclinica.bean.managestudy.*; import org.akaza.openclinica.bean.service.*; import org.akaza.openclinica.bean.submit.*; import org.akaza.openclinica.control.SpringServletAccess; import org.akaza.openclinica.control.core.SecureController; import org.akaza.openclinica.control.form.FormProcessor; import org.akaza.openclinica.control.submit.CreateNewStudyEventServlet; import org.akaza.openclinica.control.submit.SubmitDataServlet; import org.akaza.openclinica.dao.admin.AuditEventDAO; import org.akaza.openclinica.dao.admin.CRFDAO; import org.akaza.openclinica.dao.hibernate.StudyParameterValueDao; import org.akaza.openclinica.dao.login.UserAccountDAO; import org.akaza.openclinica.dao.managestudy.*; import org.akaza.openclinica.dao.service.StudyParameterValueDAO; import org.akaza.openclinica.dao.submit.*; import org.akaza.openclinica.domain.datamap.StudyParameterValue; import org.akaza.openclinica.service.crfdata.HideCRFManager; import org.akaza.openclinica.service.managestudy.StudySubjectService; import org.akaza.openclinica.view.Page; import org.akaza.openclinica.web.InsufficientPermissionException; import org.akaza.openclinica.web.bean.DisplayStudyEventRow; import org.akaza.openclinica.web.bean.EntityBeanTable; import org.apache.commons.lang.StringUtils; import org.springframework.web.context.support.WebApplicationContextUtils; import javax.sql.DataSource; import java.net.URLEncoder; import java.util.*; /** * @author jxu * * Processes 'view subject' request */ public class ViewStudySubjectServlet extends SecureController { // The study subject has an existing discrepancy note related to their // person id; this // value will be saved as a request attribute public final static String HAS_UNIQUE_ID_NOTE = "hasUniqueIDNote"; // The study subject has an existing discrepancy note related to their date // of birth; this // value will be saved as a request attribute public final static String HAS_DOB_NOTE = "hasDOBNote"; // The study subject has an existing discrepancy note related to their // Gender; this // value will be saved as a request attribute public final static String HAS_GENDER_NOTE = "hasGenderNote"; // The study subject has an existing discrepancy note related to their // Enrollment Date; this // value will be saved as a request attribute public final static String HAS_ENROLLMENT_NOTE = "hasEnrollmentNote"; // request attribute for a discrepancy note public final static String UNIQUE_ID_NOTE = "uniqueIDNote"; // request attribute for a discrepancy note public final static String DOB_NOTE = "dOBNote"; // request attribute for a discrepancy note public final static String GENDER_NOTE = "genderNote"; // request attribute for a discrepancy note public final static String ENROLLMENT_NOTE = "enrollmentNote"; public final static String COMMON = "common"; /** * Checks whether the user has the right permission to proceed function */ @Override public void mayProceed() throws InsufficientPermissionException { // YW 10-18-2007, if a study subject with passing parameter does not // belong to user's studies, it can not be viewed // mayAccess(); getEventCrfLocker().unlockAllForUser(ub.getId()); if (ub.isSysAdmin()) { return; } if (SubmitDataServlet.mayViewData(ub, currentRole)) { return; } addPageMessage(respage.getString("no_have_correct_privilege_current_study") + " " + respage.getString("change_study_contact_sysadmin")); throw new InsufficientPermissionException(Page.LIST_STUDY_SUBJECTS, resexception.getString("not_study_director"), "1"); } public static ArrayList<DisplayStudyEventBean> getDisplayStudyEventsForStudySubject(StudySubjectBean studySub, DataSource ds, UserAccountBean ub, StudyUserRoleBean currentRole) { StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(ds); StudyEventDAO sedao = new StudyEventDAO(ds); EventCRFDAO ecdao = new EventCRFDAO(ds); EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(ds); StudySubjectDAO ssdao = new StudySubjectDAO(ds); StudyDAO sdao = new StudyDAO(ds); ArrayList events = sedao.findAllByStudySubject(studySub); ArrayList displayEvents = new ArrayList(); for (int i = 0; i < events.size(); i++) { StudyEventBean event = (StudyEventBean) events.get(i); StudySubjectBean studySubject = (StudySubjectBean) ssdao.findByPK(event.getStudySubjectId()); StudyEventDefinitionBean sed = (StudyEventDefinitionBean) seddao .findByPK(event.getStudyEventDefinitionId()); event.setStudyEventDefinition(sed); // find all active crfs in the definition StudyBean study = (StudyBean) sdao.findByPK(studySubject.getStudyId()); ArrayList eventDefinitionCRFs = (ArrayList) edcdao.findAllActiveByEventDefinitionId(study, sed.getId()); ArrayList eventCRFs = ecdao.findAllByStudyEvent(event); // construct info needed on view study event page DisplayStudyEventBean de = new DisplayStudyEventBean(); de.setStudyEvent(event); de.setDisplayEventCRFs(getDisplayEventCRFs(ds, eventCRFs, eventDefinitionCRFs, ub, currentRole, event.getSubjectEventStatus(), study)); ArrayList al = getUncompletedCRFs(ds, eventDefinitionCRFs, eventCRFs, event.getSubjectEventStatus()); populateUncompletedCRFsWithCRFAndVersions(ds, al); de.setUncompletedCRFs(al); de.setMaximumSampleOrdinal(sedao.getMaxSampleOrdinal(sed, studySubject)); Status status = de.getStudyEvent().getStatus(); if (status == Status.AVAILABLE || status == Status.AUTO_DELETED) displayEvents.add(de); // event.setEventCRFs(createAllEventCRFs(eventCRFs, // eventDefinitionCRFs)); } return displayEvents; } @Override public void processRequest() throws Exception { SubjectDAO sdao = new SubjectDAO(sm.getDataSource()); StudySubjectDAO subdao = new StudySubjectDAO(sm.getDataSource()); CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource()); FormProcessor fp = new FormProcessor(request); int studySubId = fp.getInt("id", true);// studySubjectId String from = fp.getString("from"); int parentStudyId = currentStudy.getParentStudyId() > 0 ? currentStudy.getParentStudyId() : currentStudy.getId(); StudyParameterValueDao studyParameterValueDao = (StudyParameterValueDao) SpringServletAccess .getApplicationContext(context).getBean("studyParameterValueDao"); StudyParameterValue parentSPV = studyParameterValueDao.findByStudyIdParameter(parentStudyId, "subjectIdGeneration"); currentStudy.getStudyParameterConfig().setSubjectIdGeneration(parentSPV.getValue()); String module = fp.getString(MODULE); request.setAttribute(MODULE, module); // if coming from change crf version -> display message String crfVersionChangeMsg = fp.getString("isFromCRFVersionChange"); if (crfVersionChangeMsg != null && !crfVersionChangeMsg.equals("")) { addPageMessage(crfVersionChangeMsg); } if (studySubId == 0) { addPageMessage(respage.getString("please_choose_a_subject_to_view")); forwardPage(Page.LIST_STUDY_SUBJECTS); } else { if (!StringUtils.isBlank(from)) { request.setAttribute("from", from); // form ListSubject or // ListStudySubject } else { request.setAttribute("from", ""); } StudySubjectBean studySub = (StudySubjectBean) subdao.findByPK(studySubId); request.setAttribute("studySub", studySub); request.setAttribute("originatingPage", URLEncoder.encode("ViewStudySubject?id=" + studySub.getId(), "UTF-8")); int studyId = studySub.getStudyId(); int subjectId = studySub.getSubjectId(); StudyDAO studydao = new StudyDAO(sm.getDataSource()); StudyBean study = (StudyBean) studydao.findByPK(studyId); // Check if this StudySubject would be accessed from the Current Study if (studySub.getStudyId() != currentStudy.getId()) { if (currentStudy.getParentStudyId() > 0) { addPageMessage(respage.getString("no_have_correct_privilege_current_study") + " " + respage.getString("change_active_study_or_contact")); forwardPage(Page.MENU_SERVLET); return; } else { // The SubjectStudy is not belong to currentstudy and current study is not a site. Collection sites = studydao.findOlnySiteIdsByStudy(currentStudy); if (!sites.contains(study.getId())) { addPageMessage(respage.getString("no_have_correct_privilege_current_study") + " " + respage.getString("change_active_study_or_contact")); forwardPage(Page.MENU_SERVLET); return; } } } // If the study subject derives from a site, and is being viewed // from a parent study, // then the study IDs will be different. However, since each note is // saved with the specific // study ID, then its study ID may be different than the study // subject's ID. boolean subjectStudyIsCurrentStudy = studyId == currentStudy.getId(); boolean isParentStudy = study.getParentStudyId() < 1; // Get any disc notes for this subject : studySubId DiscrepancyNoteDAO discrepancyNoteDAO = new DiscrepancyNoteDAO(sm.getDataSource()); List<DiscrepancyNoteBean> allNotesforSubject = new ArrayList<DiscrepancyNoteBean>(); // These methods return only parent disc notes if (subjectStudyIsCurrentStudy && isParentStudy) { allNotesforSubject = discrepancyNoteDAO.findAllSubjectByStudyAndId(study, subjectId); allNotesforSubject.addAll(discrepancyNoteDAO.findAllStudySubjectByStudyAndId(study, studySubId)); } else { if (!isParentStudy) { StudyBean stParent = (StudyBean) studydao.findByPK(study.getParentStudyId()); allNotesforSubject = discrepancyNoteDAO.findAllSubjectByStudiesAndSubjectId(stParent, study, subjectId); allNotesforSubject.addAll(discrepancyNoteDAO .findAllStudySubjectByStudiesAndStudySubjectId(stParent, study, studySubId)); } else { allNotesforSubject = discrepancyNoteDAO.findAllSubjectByStudiesAndSubjectId(currentStudy, study, subjectId); allNotesforSubject.addAll(discrepancyNoteDAO .findAllStudySubjectByStudiesAndStudySubjectId(currentStudy, study, studySubId)); } } if (!allNotesforSubject.isEmpty()) { setRequestAttributesForNotes(allNotesforSubject); } SubjectBean subject = (SubjectBean) sdao.findByPK(subjectId); if (currentStudy.getStudyParameterConfig().getCollectDob().equals("2")) { Date dob = subject.getDateOfBirth(); if (dob != null) { Calendar cal = Calendar.getInstance(); cal.setTime(dob); int year = cal.get(Calendar.YEAR); request.setAttribute("yearOfBirth", new Integer(year)); } else { request.setAttribute("yearOfBirth", ""); } } request.setAttribute("subject", subject); /* * StudyDAO studydao = new StudyDAO(sm.getDataSource()); StudyBean * study = (StudyBean) studydao.findByPK(studyId); */ // YW 11-26-2007 << StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource()); if (isParentStudy) { study.getStudyParameterConfig() .setCollectDob(spvdao.findByHandleAndStudy(studyId, "collectDob").getValue()); } else { study.getStudyParameterConfig().setCollectDob( spvdao.findByHandleAndStudy(study.getParentStudyId(), "collectDob").getValue()); } // YW >> request.setAttribute("subjectStudy", study); if (study.getParentStudyId() > 0) {// this is a site,find parent StudyBean parentStudy2 = (StudyBean) studydao.findByPK(study.getParentStudyId()); request.setAttribute("parentStudy", parentStudy2); } else { request.setAttribute("parentStudy", new StudyBean()); } ArrayList children = (ArrayList) sdao.findAllChildrenByPK(subjectId); request.setAttribute("children", children); // find study events StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource()); StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource()); StudySubjectService studySubjectService = (StudySubjectService) WebApplicationContextUtils .getWebApplicationContext(getServletContext()).getBean("studySubjectService"); List<DisplayStudyEventBean> displayEvents = studySubjectService .getDisplayStudyEventsForStudySubject(studySub, ub, currentRole); List<DisplayStudyEventBean> tempList = new ArrayList<>(); for (DisplayStudyEventBean displayEvent : displayEvents) { if (!displayEvent.getStudyEvent().getStudyEventDefinition().getType().equals(COMMON)) { tempList.add(displayEvent); } } displayEvents = new ArrayList(tempList); for (int i = 0; i < displayEvents.size(); i++) { DisplayStudyEventBean decb = displayEvents.get(i); if (!(currentRole.isDirector() || currentRole.isCoordinator()) && decb.getStudyEvent().getSubjectEventStatus().isLocked()) { decb.getStudyEvent().setEditable(false); } } if (currentStudy.getParentStudyId() > 0) { HideCRFManager hideCRFManager = HideCRFManager.createHideCRFManager(); for (DisplayStudyEventBean displayStudyEventBean : displayEvents) { hideCRFManager.removeHiddenEventCRF(displayStudyEventBean); } } EntityBeanTable table = fp.getEntityBeanTable(); table.setSortingIfNotExplicitlySet(1, false);// sort by start // date, desc ArrayList allEventRows = DisplayStudyEventRow.generateRowsFromBeans(displayEvents); String[] columns = { resword.getString("event") + " (" + resword.getString("occurrence_number") + ")", resword.getString("start_date1"), resword.getString("status"), resword.getString("event_actions"), resword.getString("CRFs") }; table.setColumns(new ArrayList(Arrays.asList(columns))); table.hideColumnLink(4); table.hideColumnLink(5); if (!"removed".equalsIgnoreCase(studySub.getStatus().getName()) && !"auto-removed".equalsIgnoreCase(studySub.getStatus().getName())) { if (currentStudy.getStatus().isAvailable() && !currentRole.getRole().equals(Role.MONITOR)) { table.addLink(resword.getString("add_new"), "CreateNewStudyEvent?" + CreateNewStudyEventServlet.INPUT_STUDY_SUBJECT_ID_FROM_VIEWSUBJECT + "=" + studySub.getId()); } } HashMap args = new HashMap(); args.put("id", new Integer(studySubId).toString()); table.setQuery("ViewStudySubject", args); table.setRows(allEventRows); table.computeDisplay(); request.setAttribute("table", table); SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource()); ArrayList groupMaps = (ArrayList) sgmdao.findAllByStudySubject(studySubId); request.setAttribute("groups", groupMaps); // find audit log for events AuditEventDAO aedao = new AuditEventDAO(sm.getDataSource()); ArrayList logs = aedao.findEventStatusLogByStudySubject(studySubId); // logger.warning("^^^ retrieved logs"); UserAccountDAO udao = new UserAccountDAO(sm.getDataSource()); ArrayList eventLogs = new ArrayList(); // logger.warning("^^^ starting to iterate"); for (int i = 0; i < logs.size(); i++) { AuditEventBean avb = (AuditEventBean) logs.get(i); StudyEventAuditBean sea = new StudyEventAuditBean(); sea.setAuditEvent(avb); StudyEventBean se = (StudyEventBean) sedao.findByPK(avb.getEntityId()); StudyEventDefinitionBean sed = (StudyEventDefinitionBean) seddao .findByPK(se.getStudyEventDefinitionId()); sea.setDefinition(sed); String old = avb.getOldValue().trim(); try { if (!StringUtils.isBlank(old)) { SubjectEventStatus oldStatus = SubjectEventStatus.get(new Integer(old).intValue()); sea.setOldSubjectEventStatus(oldStatus); } String newValue = avb.getNewValue().trim(); if (!StringUtils.isBlank(newValue)) { SubjectEventStatus newStatus = SubjectEventStatus.get(new Integer(newValue).intValue()); sea.setNewSubjectEventStatus(newStatus); } } catch (NumberFormatException e) { e.printStackTrace(); } UserAccountBean updater = (UserAccountBean) udao.findByPK(avb.getUserId()); sea.setUpdater(updater); eventLogs.add(sea); } request.setAttribute("eventLogs", eventLogs); String errorData = request.getParameter("errorData"); if (StringUtils.isNotEmpty(errorData)) request.setAttribute("errorData", errorData); String participateStatus = getParticipateStatus(parentStudyId); request.setAttribute("participateStatus", participateStatus); forwardPage(Page.VIEW_STUDY_SUBJECT); } } /** * Each of the event CRFs with its corresponding CRFBean. Then generates a * list of DisplayEventCRFBeans, one for each event CRF. * * @param eventCRFs * The list of event CRFs for this study event. * @param eventDefinitionCRFs * The list of event definition CRFs for this study event. * @return The list of DisplayEventCRFBeans for this study event. */ public static ArrayList getDisplayEventCRFs(DataSource ds, ArrayList eventCRFs, ArrayList eventDefinitionCRFs, UserAccountBean ub, StudyUserRoleBean currentRole, SubjectEventStatus status, StudyBean study) { ArrayList answer = new ArrayList(); // HashMap definitionsById = new HashMap(); int i; /* * for (i = 0; i < eventDefinitionCRFs.size(); i++) { * EventDefinitionCRFBean edc = (EventDefinitionCRFBean) * eventDefinitionCRFs.get(i); definitionsById.put(new * Integer(edc.getStudyEventDefinitionId()), edc); } */ StudyEventDAO sedao = new StudyEventDAO(ds); CRFDAO cdao = new CRFDAO(ds); CRFVersionDAO cvdao = new CRFVersionDAO(ds); FormLayoutDAO fldao = new FormLayoutDAO(ds); ItemDataDAO iddao = new ItemDataDAO(ds); EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(ds); for (i = 0; i < eventCRFs.size(); i++) { EventCRFBean ecb = (EventCRFBean) eventCRFs.get(i); // populate the event CRF with its crf bean int crfVersionId = ecb.getCRFVersionId(); int formLayoutId = ecb.getFormLayoutId(); CRFBean cb = cdao.findByLayoutId(formLayoutId); ecb.setCrf(cb); CRFVersionBean cvb = (CRFVersionBean) cvdao.findByPK(crfVersionId); ecb.setCrfVersion(cvb); FormLayoutBean flb = (FormLayoutBean) fldao.findByPK(formLayoutId); ecb.setFormLayout(flb); // then get the definition so we can call // DisplayEventCRFBean.setFlags int studyEventId = ecb.getStudyEventId(); int studyEventDefinitionId = sedao.getDefinitionIdFromStudyEventId(studyEventId); // EventDefinitionCRFBean edc = (EventDefinitionCRFBean) // definitionsById.get(new Integer( // studyEventDefinitionId)); // fix problem of the above code(commented out), find the correct // edc, note that on definitionId can be related to multiple // eventdefinitioncrfBeans EventDefinitionCRFBean edc = edcdao.findByStudyEventDefinitionIdAndCRFId(study, studyEventDefinitionId, cb.getId()); // below added 092007 tbh // rules updated 112007 tbh if (status.equals(SubjectEventStatus.LOCKED) || status.equals(SubjectEventStatus.SKIPPED) || status.equals(SubjectEventStatus.STOPPED)) { ecb.setStage(DataEntryStage.LOCKED); // we need to set a SED-wide flag here, because other edcs // in this event can be filled in and change the status, tbh } else if (status.equals(SubjectEventStatus.INVALID)) { ecb.setStage(DataEntryStage.LOCKED); } else if (!cb.getStatus().equals(Status.AVAILABLE)) { ecb.setStage(DataEntryStage.LOCKED); } else if (!cvb.getStatus().equals(Status.AVAILABLE)) { ecb.setStage(DataEntryStage.LOCKED); } // above added 092007-102007 tbh // TODO need to refactor since this is similar to other code, tbh if (edc != null) { // System.out.println("edc is not null, need to set flags"); DisplayEventCRFBean dec = new DisplayEventCRFBean(); dec.setEventDefinitionCRF(edc); // System.out.println("edc.isDoubleEntry()" + // edc.isDoubleEntry() + ecb.getId()); dec.setFlags(ecb, ub, currentRole, edc.isDoubleEntry()); if (dec.isLocked()) { // System.out.println("*** found a locked DEC: // "+edc.getCrfName()); } ArrayList idata = iddao.findAllByEventCRFId(ecb.getId()); if (!idata.isEmpty()) { // consider an event crf started only if item data get // created answer.add(dec); } } } return answer; } /** * Finds all the event definitions for which no event CRF exists - which is * the list of event definitions with uncompleted event CRFs. * * @param eventDefinitionCRFs * All of the event definition CRFs for this study event. * @param eventCRFs * All of the event CRFs for this study event. * @return The list of event definitions for which no event CRF exists. */ public static ArrayList getUncompletedCRFs(DataSource ds, ArrayList eventDefinitionCRFs, ArrayList eventCRFs, SubjectEventStatus status) { int i; HashMap completed = new HashMap(); HashMap startedButIncompleted = new HashMap(); ArrayList answer = new ArrayList(); /** * A somewhat non-standard algorithm is used here: let answer = empty; * foreach event definition ED, set isCompleted(ED) = false foreach * event crf EC, set isCompleted(EC.getEventDefinition()) = true foreach * event definition ED, if (!isCompleted(ED)) { answer += ED; } return * answer; This algorithm is guaranteed to find all the event * definitions for which no event CRF exists. * * The motivation for using this algorithm is reducing the number of * database hits. * * -jun-we have to add more CRFs here: the event CRF which dones't have * item data yet */ for (i = 0; i < eventDefinitionCRFs.size(); i++) { EventDefinitionCRFBean edcrf = (EventDefinitionCRFBean) eventDefinitionCRFs.get(i); completed.put(new Integer(edcrf.getCrfId()), Boolean.FALSE); startedButIncompleted.put(new Integer(edcrf.getCrfId()), new EventCRFBean()); } CRFVersionDAO cvdao = new CRFVersionDAO(ds); ItemDataDAO iddao = new ItemDataDAO(ds); for (i = 0; i < eventCRFs.size(); i++) { EventCRFBean ecrf = (EventCRFBean) eventCRFs.get(i); // System.out.println("########event crf id:" + ecrf.getId()); int crfId = cvdao.getCRFIdFromCRFVersionId(ecrf.getCRFVersionId()); ArrayList idata = iddao.findAllByEventCRFId(ecrf.getId()); if (!idata.isEmpty()) {// this crf has data already completed.put(new Integer(crfId), Boolean.TRUE); } else {// event crf got created, but no data entered // System.out.println("added one into startedButIncompleted" + ecrf.getId()); startedButIncompleted.put(new Integer(crfId), ecrf); } } // TODO possible relation to 1689 here, tbh for (i = 0; i < eventDefinitionCRFs.size(); i++) { DisplayEventDefinitionCRFBean dedc = new DisplayEventDefinitionCRFBean(); EventDefinitionCRFBean edcrf = (EventDefinitionCRFBean) eventDefinitionCRFs.get(i); dedc.setEdc(edcrf); // below added tbh, 112007 to fix bug 1943 if (status.equals(SubjectEventStatus.LOCKED)) { dedc.setStatus(Status.LOCKED); } Boolean b = (Boolean) completed.get(new Integer(edcrf.getCrfId())); EventCRFBean ev = (EventCRFBean) startedButIncompleted.get(new Integer(edcrf.getCrfId())); if (b == null || !b.booleanValue()) { dedc.setEventCRF(ev); answer.add(dedc); } } return answer; } public static void populateUncompletedCRFsWithCRFAndVersions(DataSource ds, ArrayList uncompletedEventDefinitionCRFs) { CRFDAO cdao = new CRFDAO(ds); CRFVersionDAO cvdao = new CRFVersionDAO(ds); int size = uncompletedEventDefinitionCRFs.size(); for (int i = 0; i < size; i++) { DisplayEventDefinitionCRFBean dedcrf = (DisplayEventDefinitionCRFBean) uncompletedEventDefinitionCRFs .get(i); CRFBean cb = (CRFBean) cdao.findByPK(dedcrf.getEdc().getCrfId()); dedcrf.getEdc().setCrf(cb); ArrayList theVersions = (ArrayList) cvdao.findAllActiveByCRF(dedcrf.getEdc().getCrfId()); ArrayList versions = new ArrayList(); HashMap<String, CRFVersionBean> crfVersionIds = new HashMap<String, CRFVersionBean>(); for (int j = 0; j < theVersions.size(); j++) { CRFVersionBean crfVersion = (CRFVersionBean) theVersions.get(j); crfVersionIds.put(String.valueOf(crfVersion.getId()), crfVersion); } if (!dedcrf.getEdc().getSelectedVersionIds().equals("")) { String[] kk = dedcrf.getEdc().getSelectedVersionIds().split(","); for (String string : kk) { if (crfVersionIds.get(string) != null) { versions.add(crfVersionIds.get(string)); } } } else { versions = theVersions; } dedcrf.getEdc().setVersions(versions); uncompletedEventDefinitionCRFs.set(i, dedcrf); } } /* * //Returns an array list which contain all completed eventcrf and * uncompleted * * private ArrayList createAllEventCRFs(ArrayList eventCRFs, ArrayList * eventDefinitionCRFs) { CRFDAO cdao = new CRFDAO(sm.getDataSource()); * CRFVersionDAO vdao = new CRFVersionDAO(sm.getDataSource()); HashMap * crfIdMap = new HashMap(); ArrayList evs = new ArrayList(); for (int i = * 0; i < eventDefinitionCRFs.size(); i++) { EventDefinitionCRFBean edc = * (EventDefinitionCRFBean) eventDefinitionCRFs.get(i); crfIdMap.put(new * Integer(edc.getCrfId()), Boolean.FALSE); } * * for (int i = 0; i < eventCRFs.size(); i++) { EventCRFBean eventCRF = * (EventCRFBean) eventCRFs.get(i); logger.info("\nstage:" + * eventCRF.getStage().getName()); CRFBean crf = * cdao.findByVersionId(eventCRF.getCRFVersionId()); CRFVersionBean cVersion = * (CRFVersionBean) vdao.findByPK(eventCRF.getCRFVersionId()); * eventCRF.setCrf(crf); eventCRF.setCrfVersion(cVersion); * evs.add(eventCRF); * * if (crfIdMap.containsKey(new Integer(crf.getId()))) { crfIdMap.put(new * Integer(crf.getId()), Boolean.TRUE);//already has // entry for this // * crf } }//for * * //find those crfs which are not started yet(stage=uncompleted) Set keys = * crfIdMap.keySet(); Iterator it = keys.iterator(); while (it.hasNext()) { * Integer crfId = (Integer) it.next(); if (crfIdMap.containsKey(crfId) && * crfIdMap.get(crfId).equals(Boolean.FALSE)) { EventCRFBean ec = new * EventCRFBean(); CRFBean crf1 = (CRFBean) cdao.findByPK(crfId.intValue()); * ArrayList versions = vdao.findAllByCRFId(crfId.intValue()); * crf1.setVersions(versions); ec.setCrf(crf1); * * logger.info("\nstage:" + ec.getStage().getName()); evs.add(ec); } * }//while * * return evs; } * */ @Override protected String getAdminServlet() { if (ub.isSysAdmin()) { return SecureController.ADMIN_SERVLET_CODE; } else { return ""; } } /** * Current User may access a requested study subject in the current user's * studies * * @author ywang 10-18-2007 */ public void mayAccess() throws InsufficientPermissionException { FormProcessor fp = new FormProcessor(request); StudySubjectDAO subdao = new StudySubjectDAO(sm.getDataSource()); int studySubId = fp.getInt("id", true); if (studySubId > 0) { if (!entityIncluded(studySubId, ub.getName(), subdao, sm.getDataSource())) { addPageMessage(respage.getString("required_study_subject_not_belong")); throw new InsufficientPermissionException(Page.MENU, resexception.getString("entity_not_belong_studies"), "1"); } } } private void setRequestAttributesForNotes(List<DiscrepancyNoteBean> discBeans) { for (DiscrepancyNoteBean discrepancyNoteBean : discBeans) { if ("unique_identifier".equalsIgnoreCase(discrepancyNoteBean.getColumn())) { request.setAttribute(HAS_UNIQUE_ID_NOTE, "yes"); request.setAttribute(UNIQUE_ID_NOTE, discrepancyNoteBean); } else if ("date_of_birth".equalsIgnoreCase(discrepancyNoteBean.getColumn())) { request.setAttribute(HAS_DOB_NOTE, "yes"); request.setAttribute(DOB_NOTE, discrepancyNoteBean); } else if ("enrollment_date".equalsIgnoreCase(discrepancyNoteBean.getColumn())) { request.setAttribute(HAS_ENROLLMENT_NOTE, "yes"); request.setAttribute(ENROLLMENT_NOTE, discrepancyNoteBean); } else if ("gender".equalsIgnoreCase(discrepancyNoteBean.getColumn())) { request.setAttribute(HAS_GENDER_NOTE, "yes"); request.setAttribute(GENDER_NOTE, discrepancyNoteBean); } } } private void addDiscrepancyNotesFromChildStudies(List<DiscrepancyNoteBean> discBeans, int parentStudyId, int subjectId, int studySubId, StudyDAO studyDAO, DiscrepancyNoteDAO discrepancyNoteDAO) { if (discBeans == null || discBeans.isEmpty() || studyDAO == null || discrepancyNoteDAO == null) { return; } ArrayList<StudyBean> childStudies = (ArrayList) studyDAO.findAllByParent(parentStudyId); for (StudyBean studyBean : childStudies) { discBeans.addAll(discrepancyNoteDAO.findAllSubjectByStudyAndId(studyBean, subjectId)); discBeans.addAll(discrepancyNoteDAO.findAllStudySubjectByStudyAndId(studyBean, studySubId)); } } }