Java tutorial
/* * OpenClinica is distributed under the * GNU Lesser General Public License (GNU LGPL). * For details see: http://www.openclinica.org/license * copyright 2003-2011 Akaza Research */ package org.akaza.openclinica.control.submit; import java.io.File; import java.text.DateFormat; import java.text.SimpleDateFormat; import java.util.ArrayList; import java.util.Collections; import java.util.Date; import java.util.HashMap; import java.util.Iterator; import java.util.LinkedList; import java.util.List; import java.util.Locale; import java.util.Map; import java.util.Set; import java.util.TreeSet; import javax.servlet.ServletConfig; import javax.servlet.ServletContext; import javax.servlet.ServletException; import javax.servlet.http.HttpServletRequest; import javax.servlet.http.HttpServletResponse; import javax.servlet.http.HttpSession; import javax.sql.DataSource; import org.apache.commons.beanutils.BeanUtils; import org.akaza.openclinica.bean.admin.AuditBean; import org.akaza.openclinica.bean.admin.CRFBean; import org.akaza.openclinica.bean.core.AuditableEntityBean; import org.akaza.openclinica.bean.core.DataEntryStage; import org.akaza.openclinica.bean.core.EntityBean; import org.akaza.openclinica.bean.core.ItemDataType; import org.akaza.openclinica.bean.core.NullValue; import org.akaza.openclinica.bean.core.NumericComparisonOperator; import org.akaza.openclinica.bean.core.ResolutionStatus; import org.akaza.openclinica.bean.core.Status; import org.akaza.openclinica.bean.core.SubjectEventStatus; import org.akaza.openclinica.bean.core.Utils; import org.akaza.openclinica.bean.login.StudyUserRoleBean; import org.akaza.openclinica.bean.login.UserAccountBean; import org.akaza.openclinica.bean.managestudy.DiscrepancyNoteBean; import org.akaza.openclinica.bean.managestudy.EventDefinitionCRFBean; 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.DisplayItemBean; import org.akaza.openclinica.bean.submit.DisplayItemGroupBean; import org.akaza.openclinica.bean.submit.DisplayItemWithGroupBean; import org.akaza.openclinica.bean.submit.DisplaySectionBean; import org.akaza.openclinica.bean.submit.DisplayTableOfContentsBean; 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.ItemFormMetadataBean; import org.akaza.openclinica.bean.submit.ItemGroupBean; import org.akaza.openclinica.bean.submit.ItemGroupMetadataBean; import org.akaza.openclinica.bean.submit.ResponseOptionBean; import org.akaza.openclinica.bean.submit.ResponseSetBean; import org.akaza.openclinica.bean.submit.SCDItemDisplayInfo; import org.akaza.openclinica.bean.submit.SectionBean; import org.akaza.openclinica.bean.submit.SubjectBean; import org.akaza.openclinica.control.SpringServletAccess; import org.akaza.openclinica.control.core.CoreSecureController; import org.akaza.openclinica.control.form.DiscrepancyValidator; import org.akaza.openclinica.control.form.FormDiscrepancyNotes; import org.akaza.openclinica.control.form.FormProcessor; import org.akaza.openclinica.control.form.RuleValidator; import org.akaza.openclinica.control.form.ScoreItemValidator; import org.akaza.openclinica.control.form.Validation; import org.akaza.openclinica.control.form.Validator; import org.akaza.openclinica.control.managestudy.ViewNotesServlet; import org.akaza.openclinica.core.SecurityManager; import org.akaza.openclinica.core.SessionManager; import org.akaza.openclinica.core.form.StringUtil; import org.akaza.openclinica.dao.admin.AuditDAO; 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.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.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.ItemFormMetadataDAO; import org.akaza.openclinica.dao.submit.ItemGroupDAO; import org.akaza.openclinica.dao.submit.SectionDAO; import org.akaza.openclinica.dao.submit.SubjectDAO; import org.akaza.openclinica.domain.rule.RuleSetBean; import org.akaza.openclinica.domain.rule.action.RuleActionRunBean.Phase; import org.akaza.openclinica.exception.OpenClinicaException; import org.akaza.openclinica.i18n.core.LocaleResolver; import org.akaza.openclinica.i18n.util.ResourceBundleProvider; import org.akaza.openclinica.logic.expressionTree.ExpressionTreeHelper; import org.akaza.openclinica.logic.rulerunner.MessageContainer.MessageType; import org.akaza.openclinica.logic.score.ScoreCalculator; import org.akaza.openclinica.service.DiscrepancyNoteThread; import org.akaza.openclinica.service.DiscrepancyNoteUtil; import org.akaza.openclinica.service.crfdata.DynamicsMetadataService; import org.akaza.openclinica.service.crfdata.InstantOnChangeService; import org.akaza.openclinica.service.crfdata.SimpleConditionalDisplayService; import org.akaza.openclinica.service.crfdata.front.InstantOnChangeFrontStrGroup; import org.akaza.openclinica.service.crfdata.front.InstantOnChangeFrontStrParcel; import org.akaza.openclinica.service.rule.RuleSetServiceInterface; import org.akaza.openclinica.view.Page; import org.akaza.openclinica.view.form.DataEntryInputGenerator; import org.akaza.openclinica.view.form.FormBeanUtil; import org.akaza.openclinica.web.InconsistentStateException; import org.akaza.openclinica.web.InsufficientPermissionException; import org.apache.commons.lang.StringEscapeUtils; import org.apache.commons.lang.StringUtils; import org.apache.commons.lang.text.StrSubstitutor; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.mail.javamail.JavaMailSenderImpl; /** * @author ssachs */ public abstract class DataEntryServlet extends CoreSecureController { private static final Logger LOGGER = LoggerFactory.getLogger(DataEntryServlet.class); Locale locale; // < ResourceBundleresmessage,restext,resexception,respage; // these inputs come from the form, from another JSP via POST, // or from another JSP via GET // e.g. InitialDataEntry?eventCRFId=123§ionId=234 public static final String INPUT_EVENT_CRF_ID = "eventCRFId"; public static final String INPUT_SECTION_ID = "sectionId"; // these inputs are used when other servlets redirect you here // this is most typically the case when the user enters data and clicks the // "Previous" or "Next" button public static final String INPUT_EVENT_CRF = "event"; public static final String INPUT_SECTION = "section"; /** * A bean used to indicate that servlets to which this servlet forwards should ignore any parameters, in particular the "submitted" parameter which controls * FormProcessor.isSubmitted. If an attribute with this name is set in the request, the servlet to which this servlet forwards should consider * fp.isSubmitted to always return false. */ public static final String INPUT_IGNORE_PARAMETERS = "ignore"; /** * A bean used to indicate that we are not validating inputs, that is, that the user is "confirming" values which did not validate properly the first time. * If an attribute with this name is set in the request, this servlet should not perform any validation on the form inputs. */ public static final String INPUT_CHECK_INPUTS = "checkInputs"; /** * The name of the form input on which users write annotations. */ public static final String INPUT_ANNOTATIONS = "annotations"; /** * The name of the attribute in the request which hold the preset annotations form value. */ public static final String BEAN_ANNOTATIONS = "annotations"; // names of submit buttons in the JSP public static final String RESUME_LATER = "submittedResume"; public static final String GO_PREVIOUS = "submittedPrev"; public static final String GO_NEXT = "submittedNext"; public static final String BEAN_DISPLAY = "section"; public static final String TOC_DISPLAY = "toc"; // from // TableOfContentServlet // these inputs are displayed on the table of contents and // are used to edit Event CRF properties public static final String INPUT_INTERVIEWER = "interviewer"; public static final String INPUT_INTERVIEW_DATE = "interviewDate"; public static final String INTERVIEWER_NAME_NOTE = "InterviewerNameNote"; public static final String INTERVIEWER_DATE_NOTE = "InterviewerDateNote"; public static final String INPUT_TAB = "tabId"; public static final String INPUT_MARK_COMPLETE = "markComplete"; public static final String VALUE_YES = "Yes"; // these are only for use with ACTION_START_INITIAL_DATA_ENTRY public static final String INPUT_EVENT_DEFINITION_CRF_ID = "eventDefinitionCRFId"; public static final String INPUT_CRF_VERSION_ID = "crfVersionId"; public static final String INPUT_STUDY_EVENT_ID = "studyEventId"; public static final String INPUT_SUBJECT_ID = "subjectId"; public static final String GO_EXIT = "submittedExit"; public static final String GROUP_HAS_DATA = "groupHasData"; public static final String HAS_DATA_FLAG = "hasDataFlag"; // See the session variable in DoubleDataEntryServlet public static final String DDE_PROGESS = "doubleDataProgress"; public static final String INTERVIEWER_NAME = "interviewer_name"; public static final String DATE_INTERVIEWED = "date_interviewed"; public static final String NOTE_SUBMITTED = "note_submitted"; public static final String SECTION_BEAN = "section_bean"; public static final String ALL_SECTION_BEANS = "all_section_bean"; public static final String EVENT_DEF_CRF_BEAN = "event_def_crf_bean"; public static final String ALL_ITEMS_LIST = "all_items_list"; /** * Session attribute, and will be followed by crf_version_id */ public static final String CV_INSTANT_META = "cvInstantMeta"; private DataSource dataSource; @Override public void init(ServletConfig config) throws ServletException { super.init(config); try { ServletContext context = getServletContext(); SessionManager sm = new SessionManager(SpringServletAccess.getApplicationContext(context)); dataSource = sm.getDataSource(); } catch (Exception ne) { ne.printStackTrace(); } } @Override public DataSource getDataSource() { return dataSource; } /* * (non-Javadoc) * @see org.akaza.openclinica.control.core.SecureController#mayProceed() */ @Override protected abstract void mayProceed(HttpServletRequest request, HttpServletResponse response) throws InsufficientPermissionException; /* * locale = LocaleResolver.getLocale(request); //< resmessage = ResourceBundle.getBundle("org.akaza.openclinica.i18n.page_messages" ,locale); //< restext = * ResourceBundle.getBundle("org.akaza.openclinica.i18n.notes",locale); //< resexception =ResourceBundle.getBundle("org.akaza.openclinica.i18n.exceptions" * ,locale); */ /* * (non-Javadoc) * @see org.akaza.openclinica.control.core.SecureController#processRequest() */ private String getSectionFirstFieldId(int sectionId) { ItemDAO itemDAO = new ItemDAO(getDataSource()); List<ItemBean> items = itemDAO.findAllBySectionId(sectionId); if (!items.isEmpty()) { return new Integer(items.get(0).getId()).toString(); } return ""; } private void logMe(String message) { // System.out.println(message); LOGGER.trace(message); } @Override protected void processRequest(HttpServletRequest request, HttpServletResponse response) throws Exception { //JN:The following were the the global variables, moved as local. locale = LocaleResolver.getLocale(request); EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); SectionBean sb = (SectionBean) request.getAttribute(SECTION_BEAN); ItemDataDAO iddao = new ItemDataDAO(getDataSource(), locale); HttpSession session = request.getSession(); StudyBean currentStudy = (StudyBean) session.getAttribute("study"); StudyUserRoleBean currentRole = (StudyUserRoleBean) session.getAttribute("userRole"); SectionDAO sdao = new SectionDAO(getDataSource()); /** * Determines whether the form was submitted. Calculated once in processRequest. The reason we don't use the normal means to determine if the form was * submitted (ie FormProcessor.isSubmitted) is because when we use forwardPage, Java confuses the inputs from the just-processed form with the inputs for * the forwarded-to page. This is a problem since frequently we're forwarding from one (submitted) section to the next (unsubmitted) section. If we use the * normal means, Java will always think that the unsubmitted section is, in fact, submitted. This member is guaranteed to be calculated before * shouldLoadDBValues() is called. */ boolean isSubmitted = false; boolean hasGroup = false; EventCRFDAO ecdao = null; FormProcessor fp = new FormProcessor(request); logMe("Enterting DataEntry Servlet" + System.currentTimeMillis()); EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(getDataSource()); FormDiscrepancyNotes discNotes; panel.setStudyInfoShown(false); String age = ""; UserAccountBean ub = (UserAccountBean) request.getSession().getAttribute(USER_BEAN_NAME); String instantAtt = CV_INSTANT_META + ecb.getCRFVersionId(); //for 11958: repeating groups rows appear if validation returns to the same section int isFirstTimeOnSection = fp.getInt("isFirstTimeOnSection"); request.setAttribute("isFirstTimeOnSection", isFirstTimeOnSection + ""); if (fp.getString(GO_EXIT).equals("") && !isSubmitted && fp.getString("tabId").equals("") && fp.getString("sectionId").equals("")) { //HashMap unavailableCRF = getUnavailableCRFList(); if (getCrfLocker().isLocked(ecb.getId())) { int userId = getCrfLocker().getLockOwner(ecb.getId()); UserAccountDAO udao = new UserAccountDAO(getDataSource()); UserAccountBean ubean = (UserAccountBean) udao.findByPK(userId); addPageMessage(resword.getString("CRF_unavailable") + " " + ubean.getName() + " " + resword.getString("Currently_entering_data") + " " + resword.getString("Leave_the_CRF"), request); forwardPage(Page.LIST_STUDY_SUBJECTS_SERVLET, request, response); } else { getCrfLocker().lock(ecb.getId(), ub.getId()); } } if (!ecb.isActive()) { throw new InconsistentStateException(Page.LIST_STUDY_SUBJECTS_SERVLET, resexception.getString("event_not_exists")); } logMe("Enterting DataEntry Get the status/number of item discrepancy notes" + System.currentTimeMillis()); // Get the status/number of item discrepancy notes DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(getDataSource()); ArrayList<DiscrepancyNoteBean> allNotes = new ArrayList<DiscrepancyNoteBean>(); List<DiscrepancyNoteBean> eventCrfNotes = new ArrayList<DiscrepancyNoteBean>(); List<DiscrepancyNoteThread> noteThreads = new ArrayList<DiscrepancyNoteThread>(); // BWP: this try block is not necessary try { dndao = new DiscrepancyNoteDAO(getDataSource()); allNotes = dndao.findAllTopNotesByEventCRF(ecb.getId()); eventCrfNotes = dndao.findOnlyParentEventCRFDNotesFromEventCRF(ecb); if (!eventCrfNotes.isEmpty()) { allNotes.addAll(eventCrfNotes); } logMe("Entering DataEntry Create disc note threads out of the various notes" + System.currentTimeMillis()); // Create disc note threads out of the various notes DiscrepancyNoteUtil dNoteUtil = new DiscrepancyNoteUtil(); noteThreads = dNoteUtil.createThreadsOfParents(allNotes, getDataSource(), currentStudy, null, -1, true); // variables that provide values for the CRF discrepancy note header int updatedNum = 0; int openNum = 0; int closedNum = 0; int resolvedNum = 0; int notAppNum = 0; DiscrepancyNoteBean tempBean; for (DiscrepancyNoteThread dnThread : noteThreads) { /* * 3014: do not count parent beans, only the last child disc note of the thread. */ tempBean = dnThread.getLinkedNoteList().getLast(); if (tempBean != null) { if (ResolutionStatus.UPDATED.equals(tempBean.getResStatus())) { updatedNum++; } else if (ResolutionStatus.OPEN.equals(tempBean.getResStatus())) { openNum++; } else if (ResolutionStatus.CLOSED.equals(tempBean.getResStatus())) { // if (dn.getParentDnId() > 0){ closedNum++; // } } else if (ResolutionStatus.RESOLVED.equals(tempBean.getResStatus())) { // if (dn.getParentDnId() > 0){ resolvedNum++; // } } else if (ResolutionStatus.NOT_APPLICABLE.equals(tempBean.getResStatus())) { notAppNum++; } } } logMe("Entering DataEntry Create disc note threads out of the various notes DONE" + System.currentTimeMillis()); request.setAttribute("updatedNum", updatedNum + ""); request.setAttribute("openNum", openNum + ""); request.setAttribute("closedNum", closedNum + ""); request.setAttribute("resolvedNum", resolvedNum + ""); request.setAttribute("notAppNum", notAppNum + ""); String fromViewNotes = fp.getString("fromViewNotes"); if (fromViewNotes != null && "1".equals(fromViewNotes)) { request.setAttribute("fromViewNotes", fromViewNotes); } logMe("Entering Create studySubjDao.. ++++stuff" + System.currentTimeMillis()); StudySubjectDAO ssdao = new StudySubjectDAO(getDataSource()); StudySubjectBean ssb = (StudySubjectBean) ssdao.findByPK(ecb.getStudySubjectId()); // YW 11-07-2007, data entry could not be performed if its study subject // has been removed. // Notice: ViewSectionDataEntryServelet, ViewSectionDataEntryPreview, // PrintCRFServlet and PrintDataEntryServlet, have theirs own // processRequest Status s = ssb.getStatus(); if ("removed".equalsIgnoreCase(s.getName()) || "auto-removed".equalsIgnoreCase(s.getName())) { addPageMessage(respage.getString("you_may_not_perform_data_entry_on_a_CRF") + respage.getString("study_subject_has_been_deleted"), request); request.setAttribute("id", new Integer(ecb.getStudySubjectId()).toString()); session.removeAttribute(instantAtt); forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET, request, response); } // YW >> HashMap<String, String> newUploadedFiles = (HashMap<String, String>) session .getAttribute("newUploadedFiles"); if (newUploadedFiles == null) { newUploadedFiles = new HashMap<String, String>(); } request.setAttribute("newUploadedFiles", newUploadedFiles); if (!fp.getString("exitTo").equals("")) { request.setAttribute("exitTo", fp.getString("exitTo")); } //some EVENT CRF CHECK logMe("Entering some EVENT CRF CHECK" + System.currentTimeMillis()); if (!fp.getString(GO_EXIT).equals("")) { session.removeAttribute(GROUP_HAS_DATA); session.removeAttribute("to_create_crf"); session.removeAttribute("mayProcessUploading"); //Removing the user and EventCRF from the locked CRF List getCrfLocker().unlock(ecb.getId()); if (newUploadedFiles.size() > 0) { if (this.unloadFiles(newUploadedFiles)) { } else { String missed = ""; Iterator iter = newUploadedFiles.keySet().iterator(); while (iter.hasNext()) { missed += " " + newUploadedFiles.get(iter.next()); } addPageMessage(respage.getString("uploaded_files_not_deleted_or_not_exist") + ": " + missed, request); } } session.removeAttribute("newUploadedFiles"); addPageMessage(respage.getString("exit_without_saving"), request); // addPageMessage("You chose to exit the data entry page."); // changed bu jxu 03/06/2007- we should use redirection to go to // another servlet if (fromViewNotes != null && "1".equals(fromViewNotes)) { String viewNotesURL = (String) session.getAttribute("viewNotesURL"); if (viewNotesURL != null && viewNotesURL.length() > 0) { response.sendRedirect(response.encodeRedirectURL(viewNotesURL)); } return; } String fromResolvingNotes = fp.getString("fromResolvingNotes", true); String winLocation = (String) session.getAttribute(ViewNotesServlet.WIN_LOCATION); session.removeAttribute(instantAtt); if (!StringUtil.isBlank(fromResolvingNotes) && !StringUtil.isBlank(winLocation)) { response.sendRedirect(response.encodeRedirectURL(winLocation)); } else { if (!fp.getString("exitTo").equals("")) { response.sendRedirect(response.encodeRedirectURL(fp.getString("exitTo"))); } else response.sendRedirect(response.encodeRedirectURL("ListStudySubjects")); } // forwardPage(Page.SUBMIT_DATA_SERVLET); return; } logMe("Entering some EVENT CRF CHECK DONE" + System.currentTimeMillis()); // checks if the section has items in item group // for repeating items // hasGroup = getInputBeans(); hasGroup = checkGroups(fp, ecb); Boolean b = (Boolean) request.getAttribute(INPUT_IGNORE_PARAMETERS); isSubmitted = fp.isSubmitted() && b == null; // variable is used for fetching any null values like "not applicable" int eventDefinitionCRFId = 0; if (fp != null) { eventDefinitionCRFId = fp.getInt("eventDefinitionCRFId"); } StudyBean study = (StudyBean) session.getAttribute("study"); // constructs the list of items used on UI // tbh>> // logger.trace("trying event def crf id: "+eventDefinitionCRFId); logMe("Entering some EVENT DEF CRF CHECK " + System.currentTimeMillis()); if (eventDefinitionCRFId <= 0) { // TODO we have to get that id before we can continue EventDefinitionCRFBean edcBean = edcdao.findByStudyEventIdAndCRFVersionId(study, ecb.getStudyEventId(), ecb.getCRFVersionId()); eventDefinitionCRFId = edcBean.getId(); } logMe("Entering some EVENT DEF CRF CHECK DONE " + System.currentTimeMillis()); logMe("Entering some Study EVENT DEF CRF CHECK " + System.currentTimeMillis()); StudyEventDAO seDao = new StudyEventDAO(getDataSource()); EventDefinitionCRFBean edcBean = (EventDefinitionCRFBean) edcdao.findByPK(eventDefinitionCRFId); EventDefinitionCRFBean edcb = (EventDefinitionCRFBean) edcdao.findByPK(eventDefinitionCRFId); request.setAttribute(EVENT_DEF_CRF_BEAN, edcb);//JN:Putting the event_def_crf_bean in the request attribute. StudyEventBean studyEventBean = (StudyEventBean) seDao.findByPK(ecb.getStudyEventId()); edcBean.setId(eventDefinitionCRFId); StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(getDataSource()); StudyEventDefinitionBean studyEventDefinition = (StudyEventDefinitionBean) seddao .findByPK(edcBean.getStudyEventDefinitionId()); CRFVersionDAO cvdao = new CRFVersionDAO(getDataSource()); CRFVersionBean crfVersionBean = (CRFVersionBean) cvdao.findByPK(ecb.getCRFVersionId()); Phase phase2 = Phase.INITIAL_DATA_ENTRY; if (getServletPage(request).equals(Page.DOUBLE_DATA_ENTRY_SERVLET)) { phase2 = Phase.DOUBLE_DATA_ENTRY; } else if (getServletPage(request).equals(Page.ADMIN_EDIT_SERVLET)) { phase2 = Phase.ADMIN_EDITING; } logMe("Entering ruleSets::: CreateAndInitializeRuleSet:::" + Thread.currentThread()); logMe("Entering ruleSets::: CreateAndInitializeRuleSet:::" + Thread.currentThread() + "currentStudy?" + currentStudy + "studyEventDefinition" + studyEventDefinition + "crfVersionBean" + crfVersionBean + "studyEventBean" + studyEventBean + "ecb" + ecb); // List<RuleSetBean> ruleSets = createAndInitializeRuleSet(currentStudy, studyEventDefinition, crfVersionBean, studyEventBean, ecb, true, request, response); // boolean shouldRunRules = getRuleSetService(request).shouldRunRulesForRuleSets(ruleSets, phase2); logMe("Entering getDisplayBean:::::Thread::::" + Thread.currentThread()); DisplaySectionBean section = getDisplayBean(hasGroup, false, request, isSubmitted); //hasSCDItem has been initialized in getDisplayBean() which is online above VariableSubstitutionHelper.replaceVariables(section, study, ssb, studyEventDefinition, studyEventBean, dataSource); if (section.getSection().hasSCDItem()) { SimpleConditionalDisplayService cds0 = (SimpleConditionalDisplayService) SpringServletAccess .getApplicationContext(getServletContext()).getBean("simpleConditionalDisplayService"); section = cds0.initConditionalDisplays(section); } logMe("Entering Find out the id of the section's first field " + System.currentTimeMillis()); // 2790: Find out the id of the section's first field String firstFieldId = getSectionFirstFieldId(section.getSection().getId()); request.setAttribute("formFirstField", firstFieldId); // logger.trace("now trying event def crf id: "+eventDefinitionCRFId); // above is necessary to give us null values during DDE // ironically, this only covers vertical null value result sets // horizontal ones are covered in FormBeanUtil, tbh 112007 logMe("Entering displayItemWithGroups " + System.currentTimeMillis()); //@pgawade 30-May-2012 Fix for issue 13963 - added an extra parameter 'isSubmitted' to method createItemWithGroups List<DisplayItemWithGroupBean> displayItemWithGroups = createItemWithGroups(section, hasGroup, eventDefinitionCRFId, request, isSubmitted); logMe("Entering displayItemWithGroups end " + System.currentTimeMillis()); this.getItemMetadataService().updateGroupDynamicsInSection(displayItemWithGroups, section.getSection().getId(), ecb); section.setDisplayItemGroups(displayItemWithGroups); DisplayTableOfContentsBean toc = TableOfContentsServlet.getDisplayBeanWithShownSections(getDataSource(), (DisplayTableOfContentsBean) request.getAttribute(TOC_DISPLAY), (DynamicsMetadataService) SpringServletAccess.getApplicationContext(getServletContext()) .getBean("dynamicsMetadataService")); request.setAttribute(TOC_DISPLAY, toc); LinkedList<Integer> sectionIdsInToc = TableOfContentsServlet.sectionIdsInToc(toc); // why do we get previousSec and nextSec here, rather than in // getDisplayBeans? // so that we can use them in forwarding the user to the previous/next // section // if the validation was successful logMe("Entering displayItemWithGroups sdao.findPrevious " + System.currentTimeMillis()); int sIndex = TableOfContentsServlet.sectionIndexInToc(section.getSection(), toc, sectionIdsInToc); SectionBean previousSec = this.prevSection(section.getSection(), ecb, toc, sIndex); logMe("Entering displayItemWithGroups sdao.findPrevious end " + System.currentTimeMillis()); SectionBean nextSec = this.nextSection(section.getSection(), ecb, toc, sIndex); section.setFirstSection(!previousSec.isActive()); section.setLastSection(!nextSec.isActive()); // this is for generating side info panel // and the information panel under the Title SubjectDAO subjectDao = new SubjectDAO(getDataSource()); StudyDAO studydao = new StudyDAO(getDataSource()); SubjectBean subject = (SubjectBean) subjectDao.findByPK(ssb.getSubjectId()); // Get the study then the parent study logMe("Entering Get the study then the parent study " + System.currentTimeMillis()); if (study.getParentStudyId() > 0) { // this is a site,find parent StudyBean parentStudy = (StudyBean) studydao.findByPK(study.getParentStudyId()); request.setAttribute("studyTitle", parentStudy.getName()); request.setAttribute("siteTitle", study.getName()); } else { request.setAttribute("studyTitle", study.getName()); } logMe("Entering Get the study then the parent study end " + System.currentTimeMillis()); // Let us process the age if (currentStudy.getStudyParameterConfig().getCollectDob().equals("1")) { // YW 11-16-2007 erollment-date is used for calculating age. Date enrollmentDate = ssb.getEnrollmentDate(); age = Utils.getInstacne().processAge(enrollmentDate, subject.getDateOfBirth()); } //ArrayList beans = ViewStudySubjectServlet.getDisplayStudyEventsForStudySubject(ssb, getDataSource(), ub, currentRole); request.setAttribute("studySubject", ssb); request.setAttribute("subject", subject); //request.setAttribute("beans", beans); request.setAttribute("eventCRF", ecb); request.setAttribute("age", age); request.setAttribute("decryptedPassword", ((SecurityManager) SpringServletAccess.getApplicationContext(getServletContext()) .getBean("securityManager")).encrytPassword("root", getUserDetails())); // set up interviewer name and date fp.addPresetValue(INPUT_INTERVIEWER, ecb.getInterviewerName()); if (ecb.getDateInterviewed() != null) { DateFormat local_df = new SimpleDateFormat(resformat.getString("date_format_string"), ResourceBundleProvider.getLocale()); String idateFormatted = local_df.format(ecb.getDateInterviewed()); fp.addPresetValue(INPUT_INTERVIEW_DATE, idateFormatted); } else { fp.addPresetValue(INPUT_INTERVIEW_DATE, ""); } setPresetValues(fp.getPresetValues(), request); logMe("Entering Checks !submitted " + System.currentTimeMillis()); if (!isSubmitted) { // TODO: prevent data enterer from seeing results of first round of // data // entry, if this is second round // FLAG--SLOW HERE WHEN LOADING logMe("Entering Checks !submitted entered " + System.currentTimeMillis()); long t = System.currentTimeMillis(); request.setAttribute(BEAN_DISPLAY, section); request.setAttribute(BEAN_ANNOTATIONS, getEventCRFAnnotations(request)); session.setAttribute("shouldRunValidation", null); session.setAttribute("rulesErrors", null); session.setAttribute(DataEntryServlet.NOTE_SUBMITTED, null); discNotes = new FormDiscrepancyNotes(); // discNotes = (FormDiscrepancyNotes) session.getAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME); // if (discNotes == null) { // discNotes = new FormDiscrepancyNotes(); // } // << tbh 01/2010 section = populateNotesWithDBNoteCounts(discNotes, section, request); populateInstantOnChange(request.getSession(), ecb, section); LOGGER.debug( "+++ just ran populateNotes, printing field notes: " + discNotes.getFieldNotes().toString()); LOGGER.debug("found disc notes: " + discNotes.getNumExistingFieldNotes().toString()); session.setAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME, discNotes); if (section.getSection().hasSCDItem()) { section = SCDItemDisplayInfo.generateSCDDisplayInfo(section, this.getServletPage(request).equals(Page.INITIAL_DATA_ENTRY) || this.getServletPage(request).equals(Page.ADMIN_EDIT_SERVLET) && !this.isAdminForcedReasonForChange(request)); } int keyId = ecb.getId(); session.removeAttribute(DoubleDataEntryServlet.COUNT_VALIDATE + keyId); setUpPanel(section); if (newUploadedFiles.size() > 0) { if (this.unloadFiles(newUploadedFiles)) { } else { String missed = ""; Iterator iter = newUploadedFiles.keySet().iterator(); while (iter.hasNext()) { missed += " " + newUploadedFiles.get(iter.next()); } addPageMessage(respage.getString("uploaded_files_not_deleted_or_not_exist") + ": " + missed, request); } } logMe("Entering Checks !submitted entered end forwarding page " + System.currentTimeMillis()); logMe("Time Took for this block" + (System.currentTimeMillis() - t)); forwardPage(getJSPPage(), request, response); return; } else { logMe("Entering Checks !submitted not entered " + System.currentTimeMillis()); // // VALIDATION / LOADING DATA // // If validation is required for this round, we will go through // each item and add an appropriate validation to the Validator // // Otherwise, we will just load the data into the DisplayItemBean // so that we can write to the database later. // // Validation is required if two conditions are met: // 1. The user clicked a "Save" button, not a "Confirm" button // 2. In this type of data entry servlet, when the user clicks // a Save button, the inputs are validated // boolean validate = fp.getBoolean(INPUT_CHECK_INPUTS) && validateInputOnFirstRound(); // did the user click a "Save" button? // is validation required in this type of servlet when the user // clicks // "Save"? // We can conclude that the user is trying to save data; therefore, // set a request // attribute indicating that default values for items shouldn't be // displayed // in the application UI that will subsequently be displayed // TODO: find a better, less random place for this // session.setAttribute(HAS_DATA_FLAG, true); // section.setCheckInputs(fp.getBoolean(INPUT_CHECK_INPUTS)); errors = new HashMap(); // ArrayList items = section.getItems(); discNotes = (FormDiscrepancyNotes) session .getAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME); if (discNotes == null) { discNotes = new FormDiscrepancyNotes(); } // populateNotesWithDBNoteCounts(discNotes, section); // all items- inlcude items in item groups and other single items List<DisplayItemWithGroupBean> allItems = section.getDisplayItemGroups(); String attachedFilePath = Utils.getAttachedFilePath(currentStudy); DiscrepancyValidator v = new DiscrepancyValidator(request, discNotes); RuleValidator ruleValidator = new RuleValidator(request); LOGGER.debug("SZE 1 :: " + allItems.size()); logMe("Looping inside !submitted " + System.currentTimeMillis()); for (int i = 0; i < allItems.size(); i++) { LOGGER.trace("===itering through items: " + i); DisplayItemWithGroupBean diwg = allItems.get(i); if (diwg.isInGroup()) { // for the items in groups DisplayItemGroupBean dgb = diwg.getItemGroup(); List<DisplayItemGroupBean> dbGroups = diwg.getDbItemGroups(); //dbGroups = diwg.getItemGroups(); List<DisplayItemGroupBean> formGroups = new ArrayList<DisplayItemGroupBean>(); LOGGER.debug("got db item group size " + dbGroups.size()); if (validate) { // int manualGroups = getManualRows(dbGroups2); // logger.debug("+++ found manual rows from db group 2: " + manualGroups); LOGGER.debug("===IF VALIDATE NOT A SINGLE ITEM: got to this part in the validation loop: " + dgb.getGroupMetaBean().getName()); // TODO next marker tbh 112007 // formGroups = validateDisplayItemGroupBean(v, // dgb,dbGroups, formGroups, // ruleValidator,groupOrdinalPLusItemOid); formGroups = validateDisplayItemGroupBean(v, dgb, dbGroups, formGroups, request, response); LOGGER.debug("form group size after validation " + formGroups.size()); } else { LOGGER.debug("+++ELSE NOT A SINGLE ITEM: got to this part in the validation loop: " + dgb.getGroupMetaBean().getName()); formGroups = loadFormValueForItemGroup(dgb, dbGroups, formGroups, eventDefinitionCRFId, request); LOGGER.debug("form group size without validation " + formGroups.size()); } diwg.setItemGroup(dgb); diwg.setItemGroups(formGroups); allItems.set(i, diwg); } else {// other single items DisplayItemBean dib = diwg.getSingleItem(); // dib = (DisplayItemBean) allItems.get(i); if (validate) { // generate input name here? // DisplayItemGroupBean dgb = diwg.getItemGroup(); String itemName = getInputName(dib); // no Item group for single item, so just use blank // string as parameter for inputName dib = validateDisplayItemBean(v, dib, "", request);// this // should be // used, // otherwise, // DDE not // working-jxu LOGGER.debug("&&& found name: " + itemName); LOGGER.debug("input VALIDATE " + itemName + ": " + fp.getString(itemName)); // dib.loadFormValue(fp.getString(itemName)); LOGGER.debug("input " + itemName + " has a response set of " + dib.getMetadata().getResponseSet().getOptions().size() + " options"); } else { String itemName = getInputName(dib); LOGGER.debug("input NONVALIDATE " + itemName + ": " + fp.getString(itemName)); // dib.loadFormValue(itemName); dib = loadFormValue(dib, request); // String itemName = getInputName(dib); // dib = loadFormValue(itemName); } ArrayList children = dib.getChildren(); for (int j = 0; j < children.size(); j++) { DisplayItemBean child = (DisplayItemBean) children.get(j); // DisplayItemGroupBean dgb = diwg.getItemGroup(); String itemName = getInputName(child); child.loadFormValue(fp.getString(itemName)); if (validate) { // child = validateDisplayItemBean(v, child, // itemName, ruleValidator, groupOrdinalPLusItemOid, // false); child = validateDisplayItemBean(v, child, itemName, request); // was null changed value 092007 tbh } else { // child.loadFormValue(itemName); child = loadFormValue(child, request); } LOGGER.debug("Checking child value for " + itemName + ": " + child.getData().getValue()); children.set(j, child); } dib.setChildren(children); diwg.setSingleItem(runDynamicsItemCheck(dib, null, request)); // logger.trace("just set single item on line 447: // "+dib.getData().getValue()); // items.set(i, dib); LOGGER.debug(" I : " + i); allItems.set(i, diwg); } } logMe("Loop ended " + System.currentTimeMillis()); //JN: This is the list that contains all the scd-shown items. List<ItemBean> itemBeansWithSCDShown = new ArrayList<ItemBean>(); if (validate && section.getSection().hasSCDItem()) { logMe(" Validate and Loop " + System.currentTimeMillis()); for (int i = 0; i < allItems.size(); ++i) { DisplayItemBean dib = allItems.get(i).getSingleItem(); ItemFormMetadataBean ifmb = dib.getMetadata(); if (ifmb.getParentId() == 0) { if (dib.getScdData().getScdSetsForControl().size() > 0) { //for control item //dib has to loadFormValue first. Here loadFormValue has been done in validateDisplayItemBean(v, dib, "") section.setShowSCDItemIds(SimpleConditionalDisplayService .conditionalDisplayToBeShown(dib, section.getShowSCDItemIds())); } if (dib.getScdData().getScdItemMetadataBean().getScdItemFormMetadataId() > 0) { //for scd item //a control item is always before its scd item dib.setIsSCDtoBeShown( section.getShowSCDItemIds().contains(dib.getMetadata().getItemId())); if (dib.getIsSCDtoBeShown()) itemBeansWithSCDShown.add(dib.getItem()); validateSCDItemBean(v, dib); } ArrayList<DisplayItemBean> children = dib.getChildren(); for (int j = 0; j < children.size(); j++) { DisplayItemBean child = children.get(j); if (child.getScdData().getScdSetsForControl().size() > 0) { //for control item //dib has to loadFormValue first. Here loadFormValue has been done in validateDisplayItemBean(v, dib, "") section.setShowSCDItemIds(SimpleConditionalDisplayService .conditionalDisplayToBeShown(child, section.getShowSCDItemIds())); } if (child.getScdData().getScdItemMetadataBean().getScdItemFormMetadataId() > 0) { //for scd item //a control item is always before its scd item child.setIsSCDtoBeShown( section.getShowSCDItemIds().contains(child.getMetadata().getItemId())); if (child.getIsSCDtoBeShown()) itemBeansWithSCDShown.add(dib.getItem()); validateSCDItemBean(v, child); } } } } logMe(" Validate and Loop end " + System.currentTimeMillis()); } logMe(" Validate and Loop end " + System.currentTimeMillis()); //JN:calling again here, for the items with simple conditional display and rules. List<RuleSetBean> ruleSets = createAndInitializeRuleSet(currentStudy, studyEventDefinition, crfVersionBean, studyEventBean, ecb, true, request, response, itemBeansWithSCDShown); boolean shouldRunRules = getRuleSetService(request).shouldRunRulesForRuleSets(ruleSets, phase2); // this.getItemMetadataService().resetItemCounter(); HashMap<String, ArrayList<String>> groupOrdinalPLusItemOid = null; groupOrdinalPLusItemOid = runRules(allItems, ruleSets, true, shouldRunRules, MessageType.ERROR, phase2, ecb, request); logMe("allItems Loop begin " + System.currentTimeMillis()); for (int i = 0; i < allItems.size(); i++) { DisplayItemWithGroupBean diwg = allItems.get(i); if (diwg.isInGroup()) { // for the items in groups DisplayItemGroupBean dgb = diwg.getItemGroup(); List<DisplayItemGroupBean> dbGroups = diwg.getDbItemGroups(); //dbGroups = diwg.getItemGroups(); // tbh 01/2010 change the group list? List<DisplayItemGroupBean> formGroups = new ArrayList<DisplayItemGroupBean>(); // List<DisplayItemGroupBean> dbGroups2 = loadFormValueForItemGroup(dgb, dbGroups, formGroups, eventDefinitionCRFId); // jxu- this part need to be refined, why need to validate // items again? if (validate) { // int manualGroups = getManualRows(dbGroups2); // logger.debug("+++ found manual rows for db group2: " + manualGroups); formGroups = validateDisplayItemGroupBean(v, dgb, dbGroups, formGroups, ruleValidator, groupOrdinalPLusItemOid, request, response); // formGroups = validateDisplayItemGroupBean(v, dgb, // dbGroups, formGroups); LOGGER.debug("*** form group size after validation " + formGroups.size()); } diwg.setItemGroup(dgb); diwg.setItemGroups(formGroups); allItems.set(i, diwg); } else {// other single items DisplayItemBean dib = diwg.getSingleItem(); // dib = (DisplayItemBean) allItems.get(i); if (validate) { String itemName = getInputName(dib); dib = validateDisplayItemBean(v, dib, "", ruleValidator, groupOrdinalPLusItemOid, false, null, request);// // / dib = validateDisplayItemBean(v, dib, "");// this } ArrayList children = dib.getChildren(); for (int j = 0; j < children.size(); j++) { DisplayItemBean child = (DisplayItemBean) children.get(j); // DisplayItemGroupBean dgb = diwg.getItemGroup(); String itemName = getInputName(child); child.loadFormValue(fp.getString(itemName)); if (validate) { child = validateDisplayItemBean(v, child, "", ruleValidator, groupOrdinalPLusItemOid, false, null, request); // child = validateDisplayItemBean(v, child, // itemName); } children.set(j, child); LOGGER.debug(" J (children): " + j); } dib.setChildren(children); diwg.setSingleItem(runDynamicsItemCheck(dib, null, request)); LOGGER.debug(" I : " + i); allItems.set(i, diwg); } } logMe("allItems Loop end " + System.currentTimeMillis()); // YW, 2-1-2008 << // A map from item name to item bean object. HashMap<String, ItemBean> scoreItems = new HashMap<String, ItemBean>(); HashMap<String, String> scoreItemdata = new HashMap<String, String>(); HashMap<String, ItemDataBean> oldItemdata = prepareSectionItemdataObject(sb.getId(), request); // hold all item names of changed ItemBean in current section TreeSet<String> changedItems = new TreeSet<String>(); // holds complete disply item beans for checking against 'request // for change' restriction ArrayList<DisplayItemBean> changedItemsList = new ArrayList<DisplayItemBean>(); // key is repeating item name, value is its display item group bean HashMap<String, DisplayItemGroupBean> changedItemsMap = new HashMap<String, DisplayItemGroupBean>(); // key is itemid, value is set of itemdata-ordinal HashMap<Integer, TreeSet<Integer>> itemOrdinals = prepareItemdataOrdinals(request); // prepare item data for scoring updateDataOrdinals(allItems); section.setDisplayItemGroups(allItems); scoreItems = prepareScoreItems(request); scoreItemdata = prepareScoreItemdata(request); logMe("allItems 2 Loop begin " + System.currentTimeMillis()); for (int i = 0; i < allItems.size(); i++) { DisplayItemWithGroupBean diwb = allItems.get(i); if (diwb.isInGroup()) { List<DisplayItemGroupBean> dbGroups = diwb.getDbItemGroups(); for (int j = 0; j < dbGroups.size(); j++) { DisplayItemGroupBean displayGroup = dbGroups.get(j); List<DisplayItemBean> items = displayGroup.getItems(); if ("remove".equalsIgnoreCase(displayGroup.getEditFlag())) { for (DisplayItemBean displayItem : items) { int itemId = displayItem.getItem().getId(); int ordinal = displayItem.getData().getOrdinal(); if (itemOrdinals.containsKey(itemId)) { itemOrdinals.get(itemId).remove(ordinal); } if (scoreItemdata.containsKey(itemId + "_" + ordinal)) { scoreItemdata.remove(itemId + "_" + ordinal); } changedItems.add(displayItem.getItem().getName()); changedItemsList.add(displayItem); String formName = displayItem.getItem().getName(); // logger.debug("SET: formName:" + formName); if (displayGroup.isAuto()) { formName = getGroupItemInputName(displayGroup, displayGroup.getFormInputOrdinal(), displayItem); LOGGER.debug("GET: changed formName to " + formName); } else { formName = getGroupItemManualInputName(displayGroup, displayGroup.getFormInputOrdinal(), displayItem); LOGGER.debug("GET-MANUAL: changed formName to " + formName); } changedItemsMap.put(formName, displayGroup); LOGGER.debug("adding to changed items map: " + formName); } } } List<DisplayItemGroupBean> dgbs = diwb.getItemGroups(); int groupsize = dgbs.size(); HashMap<Integer, Integer> maxOrdinals = new HashMap<Integer, Integer>(); boolean first = true; for (int j = 0; j < dgbs.size(); j++) { DisplayItemGroupBean displayGroup = dgbs.get(j); List<DisplayItemBean> items = displayGroup.getItems(); boolean isAdd = "add".equalsIgnoreCase(displayGroup.getEditFlag()) ? true : false; for (DisplayItemBean displayItem : items) { ItemBean ib = displayItem.getItem(); String itemName = ib.getName(); int itemId = ib.getId(); if (first) { maxOrdinals.put(itemId, iddao.getMaxOrdinalForGroup(ecb, sb, displayGroup.getItemGroupBean())); } ItemDataBean idb = displayItem.getData(); String value = idb.getValue(); scoreItems.put(itemName, ib); int ordinal = displayItem.getData().getOrdinal(); if (isAdd && scoreItemdata.containsKey(itemId + "_" + ordinal)) { int formMax = 1; if (maxOrdinals.containsKey(itemId)) { formMax = maxOrdinals.get(itemId); } int dbMax = iddao.getMaxOrdinalForGroup(ecb, sb, displayGroup.getItemGroupBean()); ordinal = ordinal >= dbMax ? formMax + 1 : ordinal; maxOrdinals.put(itemId, ordinal); displayItem.getData().setOrdinal(ordinal); scoreItemdata.put(itemId + "_" + ordinal, value); } else { scoreItemdata.put(itemId + "_" + ordinal, value); } if (itemOrdinals.containsKey(itemId)) { itemOrdinals.get(itemId).add(ordinal); } else { TreeSet<Integer> ordinalSet = new TreeSet<Integer>(); ordinalSet.add(ordinal); itemOrdinals.put(itemId, ordinalSet); } if (isChanged(displayItem, oldItemdata, attachedFilePath)) { changedItems.add(itemName); changedItemsList.add(displayItem); String formName = displayItem.getItem().getName(); // logger.debug("SET: formName:" + formName); if (displayGroup.isAuto()) { formName = getGroupItemInputName(displayGroup, displayGroup.getFormInputOrdinal(), displayItem); LOGGER.debug("RESET: formName group-item-input:" + formName); } else { formName = getGroupItemManualInputName(displayGroup, displayGroup.getFormInputOrdinal(), displayItem); LOGGER.debug("RESET: formName group-item-input-manual:" + formName); } changedItemsMap.put(formName, displayGroup); LOGGER.debug("adding to changed items map: " + formName); } } first = false; } } else { DisplayItemBean dib = diwb.getSingleItem(); ItemBean ib = dib.getItem(); ItemDataBean idb = dib.getData(); int itemId = ib.getId(); String itemName = ib.getName(); String value = idb.getValue(); scoreItems.put(itemName, ib); // for items which are not in any group, their ordinal is // set as 1 TreeSet<Integer> ordinalset = new TreeSet<Integer>(); ordinalset.add(1); itemOrdinals.put(itemId, ordinalset); scoreItemdata.put(itemId + "_" + 1, value); if (isChanged(idb, oldItemdata, dib, attachedFilePath)) { changedItems.add(itemName); changedItemsList.add(dib); // changedItemsMap.put(dib.getItem().getName(), new // DisplayItemGroupBean()); } ArrayList children = dib.getChildren(); for (int j = 0; j < children.size(); j++) { DisplayItemBean child = (DisplayItemBean) children.get(j); ItemBean cib = child.getItem(); scoreItems.put(cib.getName(), cib); TreeSet<Integer> cordinalset = new TreeSet<Integer>(); cordinalset.add(1); itemOrdinals.put(itemId, cordinalset); scoreItemdata.put(cib.getId() + "_" + 1, child.getData().getValue()); if (isChanged(child.getData(), oldItemdata, child, attachedFilePath)) { changedItems.add(itemName); changedItemsList.add(child); // changedItemsMap.put(itemName, new // DisplayItemGroupBean()); } } } } logMe("allItems 2 Loop end " + System.currentTimeMillis()); // do calculation for 'calculation' and 'group-calculation' type // items // and write the result in DisplayItemBean's ItemDateBean - data ScoreItemValidator sv = new ScoreItemValidator(request, discNotes); // *** doing calc here, load it where? *** SessionManager sm = (SessionManager) request.getSession().getAttribute("sm"); ScoreCalculator sc = new ScoreCalculator(sm, ecb, ub); logMe("allItems 3 Loop begin " + System.currentTimeMillis()); for (int i = 0; i < allItems.size(); i++) { DisplayItemWithGroupBean diwb = allItems.get(i); if (diwb.isInGroup()) { List<DisplayItemGroupBean> dgbs = diwb.getItemGroups(); for (int j = 0; j < dgbs.size(); j++) { DisplayItemGroupBean displayGroup = dgbs.get(j); List<DisplayItemBean> items = displayGroup.getItems(); for (DisplayItemBean displayItem : items) { ItemFormMetadataBean ifmb = displayItem.getMetadata(); int responseTypeId = ifmb.getResponseSet().getResponseTypeId(); if (responseTypeId == 8 || responseTypeId == 9) { StringBuffer err = new StringBuffer(); ResponseOptionBean robBean = (ResponseOptionBean) ifmb.getResponseSet().getOptions() .get(0); String value = ""; String inputName = ""; // note that we have to use // getFormInputOrdinal() here, tbh 06/2009 if (displayGroup.isAuto()) { inputName = getGroupItemInputName(displayGroup, displayGroup.getFormInputOrdinal(), displayItem); LOGGER.debug("returning input name: " + inputName); } else { inputName = getGroupItemManualInputName(displayGroup, displayGroup.getFormInputOrdinal(), displayItem); LOGGER.debug("returning input name: " + inputName); } if (robBean.getValue().startsWith("func: getexternalvalue") || robBean.getValue().startsWith("func: getExternalValue")) { value = fp.getString(inputName); LOGGER.debug("*** just set " + fp.getString(inputName) + " for line 815 " + displayItem.getItem().getName() + " with input name " + inputName); } else { value = sc.doCalculation(displayItem, scoreItems, scoreItemdata, itemOrdinals, err, displayItem.getData().getOrdinal()); } displayItem.loadFormValue(value); if (isChanged(displayItem, oldItemdata, attachedFilePath)) { changedItems.add(displayItem.getItem().getName()); changedItemsList.add(displayItem); } request.setAttribute(inputName, value); if (validate) { displayItem = validateCalcTypeDisplayItemBean(sv, displayItem, inputName, request); if (err.length() > 0) { Validation validation = new Validation(Validator.CALCULATION_FAILED); validation.setErrorMessage(err.toString()); sv.addValidation(inputName, validation); } } } } } } else { DisplayItemBean dib = diwb.getSingleItem(); ItemFormMetadataBean ifmb = dib.getMetadata(); int responseTypeId = ifmb.getResponseSet().getResponseTypeId(); if (responseTypeId == 8 || responseTypeId == 9) { StringBuffer err = new StringBuffer(); ResponseOptionBean robBean = (ResponseOptionBean) ifmb.getResponseSet().getOptions().get(0); String value = ""; if (robBean.getValue().startsWith("func: getexternalvalue") || robBean.getValue().startsWith("func: getExternalValue")) { String itemName = getInputName(dib); value = fp.getString(itemName); LOGGER.debug("just set " + fp.getString(itemName) + " for " + dib.getItem().getName()); LOGGER.debug("found in fp: " + fp.getString(dib.getItem().getName())); // logger.debug("scoreitemdata: " + // scoreItemdata.toString()); } else { value = sc.doCalculation(dib, scoreItems, scoreItemdata, itemOrdinals, err, 1); } dib.loadFormValue(value); if (isChanged(dib.getData(), oldItemdata, dib, attachedFilePath)) { changedItems.add(dib.getItem().getName()); changedItemsList.add(dib); // changedItemsMap.put(dib.getItem().getName(), new // DisplayItemGroupBean()); } String inputName = getInputName(dib); request.setAttribute(inputName, value); if (validate) { dib = validateCalcTypeDisplayItemBean(sv, dib, "", request); if (err.length() > 0) { Validation validation = new Validation(Validator.CALCULATION_FAILED); validation.setErrorMessage(err.toString()); sv.addValidation(inputName, validation); } } } ArrayList children = dib.getChildren(); for (int j = 0; j < children.size(); j++) { DisplayItemBean child = (DisplayItemBean) children.get(j); ItemFormMetadataBean cifmb = child.getMetadata(); int resTypeId = cifmb.getResponseSet().getResponseTypeId(); if (resTypeId == 8 || resTypeId == 9) { StringBuffer cerr = new StringBuffer(); child.getDbData().setValue(child.getData().getValue()); ResponseOptionBean crobBean = (ResponseOptionBean) cifmb.getResponseSet().getOptions() .get(0); String cvalue = ""; if (crobBean.getValue().startsWith("func: getexternalvalue") || crobBean.getValue().startsWith("func: getExternalValue")) { String itemName = getInputName(child); cvalue = fp.getString(itemName); LOGGER.debug( "just set " + fp.getString(itemName) + " for " + child.getItem().getName()); } else { cvalue = sc.doCalculation(child, scoreItems, scoreItemdata, itemOrdinals, cerr, 1); } child.loadFormValue(cvalue); if (isChanged(child.getData(), oldItemdata, child, attachedFilePath)) { changedItems.add(child.getItem().getName()); changedItemsList.add(child); // changedItemsMap.put(child.getItem().getName(), // new DisplayItemGroupBean()); } String cinputName = getInputName(child); request.setAttribute(cinputName, cvalue); if (validate) { child = validateCalcTypeDisplayItemBean(sv, child, "", request); if (cerr.length() > 0) { Validation cvalidation = new Validation(Validator.CALCULATION_FAILED); cvalidation.setErrorMessage(cerr.toString()); sv.addValidation(cinputName, cvalidation); } } } children.set(j, child); } } } logMe("allItems 3 Loop end " + System.currentTimeMillis()); // YW >> // we have to do this since we loaded all the form values into the // display // item beans above // section.setItems(items); // setting this AFTER we populate notes - will that make a difference? section.setDisplayItemGroups(allItems); // logger.debug("+++ try to populate notes"); section = populateNotesWithDBNoteCounts(discNotes, section, request); populateInstantOnChange(request.getSession(), ecb, section); // logger.debug("+++ try to populate notes, got count of field notes: " + discNotes.getFieldNotes().toString()); if (currentStudy.getStudyParameterConfig().getInterviewerNameRequired().equals("yes")) { v.addValidation(INPUT_INTERVIEWER, Validator.NO_BLANKS); } if (currentStudy.getStudyParameterConfig().getInterviewDateRequired().equals("yes")) { v.addValidation(INPUT_INTERVIEW_DATE, Validator.NO_BLANKS); } if (!StringUtil.isBlank(fp.getString(INPUT_INTERVIEW_DATE))) { v.addValidation(INPUT_INTERVIEW_DATE, Validator.IS_A_DATE); v.alwaysExecuteLastValidation(INPUT_INTERVIEW_DATE); } if (section.getSection().hasSCDItem()) { section = SCDItemDisplayInfo.generateSCDDisplayInfo(section, this.getServletPage(request).equals(Page.INITIAL_DATA_ENTRY) || this.getServletPage(request).equals(Page.ADMIN_EDIT_SERVLET) && !this.isAdminForcedReasonForChange(request)); } // logger.debug("about to validate: " + v.getKeySet()); errors = v.validate(); // tbh >> if (this.isAdminForcedReasonForChange(request) && this.isAdministrativeEditing() && errors.isEmpty()) { // "You have changed data after this CRF was marked complete. " // + // "You must provide a Reason For Change discrepancy note for this item before you can save this updated information." String error = respage.getString("reason_for_change_error"); // "Please enter a reason for change discrepancy note before saving." // ; int nonforcedChanges = 0; // change everything here from changed items list to changed // items map if (changedItemsList.size() > 0) { LOGGER.debug("found admin force reason for change: changed items " + changedItems.toString() + " and changed items list: " + changedItemsList.toString() + " changed items map: " + changedItemsMap.toString()); logMe("DisplayItemBean Loop begin " + System.currentTimeMillis()); for (DisplayItemBean displayItem : changedItemsList) { String formName = getInputName(displayItem); ItemDataBean idb = displayItem.getData(); ItemBean item_bean = displayItem.getItem(); ItemFormMetadataBean ifmb = displayItem.getMetadata(); LOGGER.debug("-- found group label " + ifmb.getGroupLabel()); if (!ifmb.getGroupLabel().equalsIgnoreCase("Ungrouped") && !ifmb.getGroupLabel().equalsIgnoreCase("")) { // << tbh 11/2009 sometimes the group label is blank instead of ungrouped??? Iterator iter = changedItemsMap.entrySet().iterator(); while (iter.hasNext()) { Map.Entry<String, DisplayItemGroupBean> pairs = (Map.Entry) iter.next(); String formName2 = pairs.getKey(); DisplayItemGroupBean dgb = pairs.getValue(); // logger.debug("found auto: " + // dgb.isAuto()); String testFormName = ""; if (dgb.isAuto()) { // testFormName = getGroupItemInputName(dgb, dgb.getFormInputOrdinal(), getManualRows(dgbs), displayItem); testFormName = getGroupItemInputName(dgb, dgb.getFormInputOrdinal(), displayItem); } else { testFormName = getGroupItemManualInputName(dgb, dgb.getFormInputOrdinal(), displayItem); } LOGGER.debug("found test form name: " + testFormName); // if our test is the same with both the display // item and the display group ... // logger.debug("comparing " + // testFormName + " and " + formName2); int existingNotes = dndao.findNumExistingNotesForItem(idb.getId()); if (testFormName.equals(formName2)) { formName = formName2; this.setReasonForChangeError(ecb, item_bean, idb, formName, error, request); changedItemsMap.remove(formName2); LOGGER.debug("form name changed: " + formName); break; // .., send it as the form name } // ... otherwise, don't touch it // how to tell vs. manual and just plain input? } } else { this.setReasonForChangeError(ecb, item_bean, idb, formName, error, request); LOGGER.debug("form name added: " + formName); } } logMe("DisplayItemBean Loop end " + System.currentTimeMillis()); } if (nonforcedChanges > 0) { // do smething here? } } LOGGER.debug("errors here: " + errors.toString()); // << logMe("error check Loop begin " + System.currentTimeMillis()); if (errors.isEmpty() && shouldRunRules) { LOGGER.debug("Errors was empty"); if (session.getAttribute("rulesErrors") != null) { // rules have already generated errors, Let's compare old // error list with new // error list, if lists not same show errors. HashMap h = ruleValidator.validate(); Set<String> a = (Set<String>) session.getAttribute("rulesErrors"); Set<String> ba = h.keySet(); Boolean showErrors = false; for (Object key : ba) { if (!a.contains(key)) { showErrors = true; } } if (showErrors) { errors = h; if (errors.size() > 0) { session.setAttribute("shouldRunValidation", "1"); session.setAttribute("rulesErrors", errors.keySet()); } else { session.setAttribute("shouldRunValidation", null); session.setAttribute("rulesErrors", null); } } else { session.setAttribute("shouldRunValidation", null); session.setAttribute("rulesErrors", null); } } else if (session.getAttribute("shouldRunValidation") != null && session.getAttribute("shouldRunValidation").toString().equals("1")) { session.setAttribute("shouldRunValidation", null); session.setAttribute("rulesErrors", null); } else { errors = ruleValidator.validate(); if (errors.size() > 0) { session.setAttribute("shouldRunValidation", "1"); session.setAttribute("rulesErrors", errors.keySet()); } } } if (!errors.isEmpty()) { LOGGER.debug("threw an error with data entry..."); // copying below three lines, tbh 03/2010 String[] textFields = { INPUT_INTERVIEWER, INPUT_INTERVIEW_DATE }; fp.setCurrentStringValuesAsPreset(textFields); setPresetValues(fp.getPresetValues(), request); // YW, 2-4-2008 << logMe("!errors if Loop begin " + System.currentTimeMillis()); HashMap<String, ArrayList<String>> siErrors = sv.validate(); if (siErrors != null && !siErrors.isEmpty()) { Iterator iter = siErrors.keySet().iterator(); while (iter.hasNext()) { String fieldName = iter.next().toString(); errors.put(fieldName, siErrors.get(fieldName)); } } // we should 'shift' the names here, tbh 02/2010 // need: total number of rows, manual rows, all row names // plus: error names Iterator iter2 = errors.keySet().iterator(); while (iter2.hasNext()) { String fieldName = iter2.next().toString(); LOGGER.debug("found error " + fieldName); } // for (int i = 0; i < allItems.size(); i++) { // DisplayItemWithGroupBean diwb = allItems.get(i); // // if (diwb.isInGroup()) { // List<DisplayItemGroupBean> dgbs = diwb.getItemGroups(); // logger.debug("found manual rows " + getManualRows(dgbs) + " and total rows " + dgbs.size() + " from ordinal " + diwb.getOrdinal()); // } // } errors = reshuffleErrorGroupNamesKK(errors, allItems, request); reshuffleReasonForChangeHashAndDiscrepancyNotes(allItems, request, ecb); // reset manual rows, so that we can catch errors correctly // but it needs to be set per block of repeating items? what if there are two or more? /* int manualRows = 0; // getManualRows(formGroups); for (int i = 0; i < allItems.size(); i++) { DisplayItemWithGroupBean diwb = allItems.get(i); if (diwb.isInGroup()) { List<DisplayItemGroupBean> dgbs = diwb.getItemGroups(); manualRows = getManualRows(dgbs); } } */ //request.setAttribute("manualRows", new Integer(manualRows)); Iterator iter3 = errors.keySet().iterator(); while (iter3.hasNext()) { String fieldName = iter3.next().toString(); LOGGER.debug("found error after shuffle " + fieldName); } //Mantis Issue: 8116. Parsist the markComplete chebox on error request.setAttribute("markComplete", fp.getString(INPUT_MARK_COMPLETE)); // << tbh, 02/2010 // YW >> // copied request.setAttribute(BEAN_DISPLAY, section); request.setAttribute(BEAN_ANNOTATIONS, fp.getString(INPUT_ANNOTATIONS)); setInputMessages(errors, request); addPageMessage(respage.getString("errors_in_submission_see_below"), request); request.setAttribute("hasError", "true"); // addPageMessage("To override these errors and keep the data as // you // entered it, click one of the \"Confirm\" buttons. "); // if (section.isCheckInputs()) { // addPageMessage("Please notice that you must enter data for // the // <b>required</b> entries."); // } // we do not save any DNs if we get here, so we have to set it back into session... session.setAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME, discNotes); // << tbh 01/2010 setUpPanel(section); forwardPage(getJSPPage(), request, response); } else { //reshuffleReasonForChangeHashAndDiscrepancyNotes( allItems, request, ecb); LOGGER.debug("Do we hit this in save ?????"); logMe("Do we hit this in save ???? " + System.currentTimeMillis()); boolean success = true; boolean temp = true; // save interviewer name and date into DB ecb.setInterviewerName(fp.getString(INPUT_INTERVIEWER)); if (!StringUtil.isBlank(fp.getString(INPUT_INTERVIEW_DATE))) { ecb.setDateInterviewed(fp.getDate(INPUT_INTERVIEW_DATE)); } else { ecb.setDateInterviewed(null); } if (ecdao == null) { ecdao = new EventCRFDAO(getDataSource()); } // set validator id for DDE DataEntryStage stage = ecb.getStage(); if (stage.equals(DataEntryStage.INITIAL_DATA_ENTRY_COMPLETE) || stage.equals(DataEntryStage.DOUBLE_DATA_ENTRY)) { ecb.setValidatorId(ub.getId()); } /* * if(studyEventBean.getSubjectEventStatus().equals(SubjectEventStatus .SIGNED)){ if(edcBean.isDoubleEntry()){ * ecb.setStage(DataEntryStage.DOUBLE_DATA_ENTRY_COMPLETE); }else{ ecb.setStage(DataEntryStage.INITIAL_DATA_ENTRY_COMPLETE); } } */ // for Administrative editing if (studyEventBean.getSubjectEventStatus().equals(SubjectEventStatus.SIGNED) && changedItemsList.size() > 0) { studyEventBean.setSubjectEventStatus(SubjectEventStatus.COMPLETED); studyEventBean.setUpdater(ub); studyEventBean.setUpdatedDate(new Date()); seDao.update(studyEventBean); } // If the Study Subject's Satus is signed and we save a section // , change status to available LOGGER.debug("Status of Study Subject {}", ssb.getStatus().getName()); if (ssb.getStatus() == Status.SIGNED && changedItemsList.size() > 0) { LOGGER.debug("Status of Study Subject is Signed we are updating"); StudySubjectDAO studySubjectDao = new StudySubjectDAO(getDataSource()); ssb.setStatus(Status.AVAILABLE); ssb.setUpdater(ub); ssb.setUpdatedDate(new Date()); studySubjectDao.update(ssb); } if (ecb.isSdvStatus() && changedItemsList.size() > 0) { LOGGER.debug("Status of Study Subject is SDV we are updating"); StudySubjectDAO studySubjectDao = new StudySubjectDAO(getDataSource()); ssb.setStatus(Status.AVAILABLE); ssb.setUpdater(ub); ssb.setUpdatedDate(new Date()); studySubjectDao.update(ssb); ecb.setSdvStatus(false); ecb.setSdvUpdateId(ub.getId()); } ecb = (EventCRFBean) ecdao.update(ecb); // save discrepancy notes into DB FormDiscrepancyNotes fdn = (FormDiscrepancyNotes) session .getAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME); dndao = new DiscrepancyNoteDAO(getDataSource()); AddNewSubjectServlet.saveFieldNotes(INPUT_INTERVIEWER, fdn, dndao, ecb.getId(), "EventCRF", currentStudy); AddNewSubjectServlet.saveFieldNotes(INPUT_INTERVIEW_DATE, fdn, dndao, ecb.getId(), "EventCRF", currentStudy); // items = section.getItems(); allItems = section.getDisplayItemGroups(); int nextOrdinal = 0; LOGGER.debug("all items before saving into DB" + allItems.size()); this.output(allItems); //TODO:Seems longer here, check this logMe("DisplayItemWithGroupBean allitems4 " + System.currentTimeMillis()); for (int i = 0; i < allItems.size(); i++) { DisplayItemWithGroupBean diwb = allItems.get(i); // we don't write success = success && writeToDB here // since the short-circuit mechanism may prevent Java // from executing writeToDB. if (diwb.isInGroup()) { List<DisplayItemGroupBean> dgbs = diwb.getItemGroups(); // using the above gets us the correct number of manual groups, tbh 01/2010 List<DisplayItemGroupBean> dbGroups = diwb.getDbItemGroups(); LOGGER.debug("item group size: " + dgbs.size()); LOGGER.debug("item db-group size: " + dbGroups.size()); for (int j = 0; j < dgbs.size(); j++) { DisplayItemGroupBean displayGroup = dgbs.get(j); List<DisplayItemBean> items = displayGroup.getItems(); // this ordinal will only useful to create a new // item data // update an item data won't touch its ordinal // int nextOrdinal = iddao.getMaxOrdinalForGroup(ecb, sb, displayGroup.getItemGroupBean()) + 1; // Determine if any items in this group have data. If so we need to undelete and previously deleted items. boolean undelete = false; for (DisplayItemBean displayItem : items) { String currItemVal = displayItem.getData().getValue(); if (currItemVal != null && !currItemVal.equals("")) { undelete = true; break; } } for (DisplayItemBean displayItem : items) { String fileName = this.addAttachedFilePath(displayItem, attachedFilePath); boolean writeDN = true; displayItem.setEditFlag(displayGroup.getEditFlag()); LOGGER.debug("group item value: " + displayItem.getData().getValue()); // if ("add".equalsIgnoreCase(displayItem.getEditFlag()) && fileName.length() > 0 && !newUploadedFiles.containsKey(fileName)) { // displayItem.getData().setValue(""); // } //15350, this particular logic, takes into consideration that a DN is created properly as long as the item data record exists and it fails to get created when it doesnt. //so, we are expanding the logic from writeToDb method to avoid creating duplicate records. writeDN = writeDN(displayItem); //pulling from dataset instead of database and correcting the flawed logic of using the database ordinals as max ordinal... nextOrdinal = displayItem.getData().getOrdinal(); temp = writeToDB(displayItem, iddao, nextOrdinal, request); LOGGER.debug("just executed writeToDB - 1"); LOGGER.debug("next ordinal: " + nextOrdinal); // Undelete item if any item in the repeating group has data. if (undelete && displayItem.getDbData() != null && displayItem.getDbData().isDeleted()) { iddao.undelete(displayItem.getDbData().getId(), ub.getId()); } if (temp && newUploadedFiles.containsKey(fileName)) { newUploadedFiles.remove(fileName); } // maybe put ordinal in the place of j? maybe subtract max rows from next ordinal if j is gt // next ordinal? String inputName = getGroupItemInputName(displayGroup, j, displayItem); // String inputName2 = getGroupItemManualInputName(displayGroup, j, displayItem); if (!displayGroup.isAuto()) { LOGGER.trace("not auto"); inputName = this.getGroupItemManualInputName(displayGroup, j, displayItem); } //htaycher last DN is not stored for new rows // if (j == dgbs.size() - 1) { // // LAST ONE // logger.trace("last one"); // int ordinal = j - this.getManualRows(dgbs); // logger.debug("+++ found manual rows from line 1326: " + ordinal); // inputName = getGroupItemInputName(displayGroup, ordinal, displayItem); // } // logger.trace("&&& we get previous looking at input name: " + inputName + " " + inputName2); LOGGER.trace("&&& we get previous looking at input name: " + inputName); // input name 2 removed from below inputName = displayItem.getFieldName(); if (writeDN) { AddNewSubjectServlet.saveFieldNotes(inputName, fdn, dndao, displayItem.getData().getId(), "itemData", currentStudy, ecb.getId()); } success = success && temp; } } for (int j = 0; j < dbGroups.size(); j++) { DisplayItemGroupBean displayGroup = dbGroups.get(j); //JN: Since remove button is gone, the following code can be commented out, however it needs to be tested? Can be tackled when handling discrepancy note w/repeating groups issues. if ("remove".equalsIgnoreCase(displayGroup.getEditFlag())) { List<DisplayItemBean> items = displayGroup.getItems(); for (DisplayItemBean displayItem : items) { String fileName = this.addAttachedFilePath(displayItem, attachedFilePath); displayItem.setEditFlag(displayGroup.getEditFlag()); LOGGER.debug("group item value: " + displayItem.getData().getValue()); // if ("add".equalsIgnoreCase(displayItem.getEditFlag()) && fileName.length() > 0 && !newUploadedFiles.containsKey(fileName)) { // displayItem.getData().setValue(""); // } temp = writeToDB(displayItem, iddao, 0, request); LOGGER.debug("just executed writeToDB - 2"); if (temp && newUploadedFiles.containsKey(fileName)) { newUploadedFiles.remove(fileName); } // just use 0 here since update doesn't // touch ordinal success = success && temp; } } } } else { DisplayItemBean dib = diwb.getSingleItem(); // TODO work on this line // this.addAttachedFilePath(dib, attachedFilePath); String fileName = addAttachedFilePath(dib, attachedFilePath); boolean writeDN = writeDN(dib); temp = writeToDB(dib, iddao, 1, request); LOGGER.debug("just executed writeToDB - 3"); if (temp && (newUploadedFiles.containsKey(dib.getItem().getId() + "") || newUploadedFiles.containsKey(fileName))) { // so newUploadedFiles will contain only failed file // items; newUploadedFiles.remove(dib.getItem().getId() + ""); newUploadedFiles.remove(fileName); } String inputName = getInputName(dib); LOGGER.trace("3 - found input name: " + inputName); if (writeDN) AddNewSubjectServlet.saveFieldNotes(inputName, fdn, dndao, dib.getData().getId(), "itemData", currentStudy, ecb.getId()); success = success && temp; ArrayList childItems = dib.getChildren(); for (int j = 0; j < childItems.size(); j++) { DisplayItemBean child = (DisplayItemBean) childItems.get(j); this.addAttachedFilePath(child, attachedFilePath); writeDN = writeDN(child); temp = writeToDB(child, iddao, 1, request); LOGGER.debug("just executed writeToDB - 4"); if (temp && newUploadedFiles.containsKey(child.getItem().getId() + "")) { // so newUploadedFiles will contain only failed // file items; newUploadedFiles.remove(child.getItem().getId() + ""); } inputName = getInputName(child); if (writeDN) AddNewSubjectServlet.saveFieldNotes(inputName, fdn, dndao, child.getData().getId(), "itemData", currentStudy, ecb.getId()); success = success && temp; } } } logMe("DisplayItemWithGroupBean allitems4 end " + System.currentTimeMillis()); LOGGER.debug("running rules: " + phase2.name()); List<Integer> prevShownDynItemDataIds = shouldRunRules ? this.getItemMetadataService().getDynamicsItemFormMetadataDao() .findShowItemDataIdsInSection(section.getSection().getId(), ecb.getCRFVersionId(), ecb.getId()) : new ArrayList<Integer>(); logMe("DisplayItemWithGroupBean dryrun start" + System.currentTimeMillis()); HashMap<String, ArrayList<String>> rulesPostDryRun = runRules(allItems, ruleSets, false, shouldRunRules, MessageType.WARNING, phase2, ecb, request); HashMap<String, ArrayList<String>> errorsPostDryRun = new HashMap<String, ArrayList<String>>(); // additional step needed, run rules and see if any items are 'shown' AFTER saving data logMe("DisplayItemWithGroupBean dryrun end" + System.currentTimeMillis()); boolean inSameSection = false; logMe("DisplayItemWithGroupBean allitems4 " + System.currentTimeMillis()); if (!rulesPostDryRun.isEmpty()) { // in same section? // iterate through the OIDs and see if any of them belong to this section Iterator iter3 = rulesPostDryRun.keySet().iterator(); while (iter3.hasNext()) { String fieldName = iter3.next().toString(); LOGGER.debug("found oid after post dry run " + fieldName); // set up a listing of OIDs in the section // BUT: Oids can have the group name in them. int ordinal = -1; String newFieldName = fieldName; String[] fieldNames = fieldName.split("\\."); if (fieldNames.length == 2) { newFieldName = fieldNames[1]; // check items in item groups here? if (fieldNames[0].contains("[")) { int p1 = fieldNames[0].indexOf("["); int p2 = fieldNames[0].indexOf("]"); try { ordinal = Integer.valueOf(fieldNames[0].substring(p1 + 1, p2)); } catch (NumberFormatException e) { ordinal = -1; } fieldNames[0] = fieldNames[0].substring(0, p1); } } List<DisplayItemWithGroupBean> displayGroupsWithItems = section.getDisplayItemGroups(); //ArrayList<DisplayItemBean> displayItems = section.getItems(); for (int i = 0; i < displayGroupsWithItems.size(); i++) { DisplayItemWithGroupBean itemWithGroup = displayGroupsWithItems.get(i); if (itemWithGroup.isInGroup()) { LOGGER.debug("found group: " + fieldNames[0]); // do something there List<DisplayItemGroupBean> digbs = itemWithGroup.getItemGroups(); LOGGER.debug("digbs size: " + digbs.size()); for (int j = 0; j < digbs.size(); j++) { DisplayItemGroupBean displayGroup = digbs.get(j); if (displayGroup.getItemGroupBean().getOid().equals(fieldNames[0]) && displayGroup.getOrdinal() == ordinal - 1) { List<DisplayItemBean> items = displayGroup.getItems(); for (int k = 0; k < items.size(); k++) { DisplayItemBean dib = items.get(k); if (dib.getItem().getOid().equals(newFieldName)) { //inSameSection = true; if (!dib.getMetadata().isShowItem()) { LOGGER.debug("found item in group " + this.getGroupItemInputName(displayGroup, j, dib) + " vs. " + fieldName + " and is show item: " + dib.getMetadata().isShowItem()); dib.getMetadata().setShowItem(true); } if (prevShownDynItemDataIds == null || !prevShownDynItemDataIds .contains(dib.getData().getId())) { inSameSection = true; errorsPostDryRun.put( this.getGroupItemInputName(displayGroup, j, dib), rulesPostDryRun.get(fieldName)); } } items.set(k, dib); } displayGroup.setItems(items); digbs.set(j, displayGroup); } } itemWithGroup.setItemGroups(digbs); } else { DisplayItemBean displayItemBean = itemWithGroup.getSingleItem(); ItemBean itemBean = displayItemBean.getItem(); if (newFieldName.equals(itemBean.getOid())) { //System.out.println("is show item for " + displayItemBean.getItem().getId() + ": " + displayItemBean.getMetadata().isShowItem()); //System.out.println("check run dynamics item check " + runDynamicsItemCheck(displayItemBean).getMetadata().isShowItem()); if (!displayItemBean.getMetadata().isShowItem()) { // double check there? LOGGER.debug("found item " + this.getInputName(displayItemBean) + " vs. " + fieldName + " and is show item: " + displayItemBean.getMetadata().isShowItem()); // if is repeating, use the other input name? no displayItemBean.getMetadata().setShowItem(true); if (prevShownDynItemDataIds == null || !prevShownDynItemDataIds .contains(displayItemBean.getData().getId())) { inSameSection = true; errorsPostDryRun.put(this.getInputName(displayItemBean), rulesPostDryRun.get(fieldName)); } } } itemWithGroup.setSingleItem(displayItemBean); } displayGroupsWithItems.set(i, itemWithGroup); } logMe("DisplayItemWithGroupBean allitems4 end,begin" + System.currentTimeMillis()); // check groups //List<DisplayItemGroupBean> itemGroups = new ArrayList<DisplayItemGroupBean>(); //itemGroups = section.getDisplayFormGroups(); // But in jsp: section.displayItemGroups.itemGroup.groupMetaBean.showGroup List<DisplayItemWithGroupBean> itemGroups = section.getDisplayItemGroups(); // List<DisplayItemGroupBean> newItemGroups = new ArrayList<DisplayItemGroupBean>(); for (DisplayItemWithGroupBean itemGroup : itemGroups) { DisplayItemGroupBean displayGroup = itemGroup.getItemGroup(); if (newFieldName.equals(displayGroup.getItemGroupBean().getOid())) { if (!displayGroup.getGroupMetaBean().isShowGroup()) { inSameSection = true; LOGGER.debug("found itemgroup " + displayGroup.getItemGroupBean().getOid() + " vs. " + fieldName + " and is show item: " + displayGroup.getGroupMetaBean().isShowGroup()); // hmmm how to set highlighting for a group? errorsPostDryRun.put(displayGroup.getItemGroupBean().getOid(), rulesPostDryRun.get(fieldName)); displayGroup.getGroupMetaBean().setShowGroup(true); // add necessary rows to the display group here???? // we have to set the items in the itemGroup for the displayGroup loadItemsWithGroupRows(itemGroup, sb, edcb, ecb, request); } } // newItemGroups.add(displayGroup); } logMe("DisplayItemWithGroupBean allitems4 end,end" + System.currentTimeMillis()); // trying to reset the display form groups here, tbh // section.setItems(displayItems); section.setDisplayItemGroups(displayGroupsWithItems); populateInstantOnChange(request.getSession(), ecb, section); // section.setDisplayFormGroups(newDisplayBean.getDisplayFormGroups()); } // this.getItemMetadataService().updateGroupDynamicsInSection(displayItemWithGroups, section.getSection().getId(), ecb); toc = TableOfContentsServlet.getDisplayBeanWithShownSections(getDataSource(), (DisplayTableOfContentsBean) request.getAttribute(TOC_DISPLAY), (DynamicsMetadataService) SpringServletAccess.getApplicationContext(getServletContext()) .getBean("dynamicsMetadataService")); request.setAttribute(TOC_DISPLAY, toc); sectionIdsInToc = TableOfContentsServlet.sectionIdsInToc(toc); sIndex = TableOfContentsServlet.sectionIndexInToc(section.getSection(), toc, sectionIdsInToc); previousSec = this.prevSection(section.getSection(), ecb, toc, sIndex); nextSec = this.nextSection(section.getSection(), ecb, toc, sIndex); section.setFirstSection(!previousSec.isActive()); section.setLastSection(!nextSec.isActive()); // // we need the following for repeating groups, tbh // >> tbh 06/2010 // List<DisplayItemWithGroupBean> displayItemWithGroups2 = createItemWithGroups(section, hasGroup, eventDefinitionCRFId); // section.setDisplayItemGroups(displayItemWithGroups2); // if so, stay at this section LOGGER.debug(" in same section: " + inSameSection); if (inSameSection) { // copy of one line from early on around line 400, forcing a re-show of the items // section = getDisplayBean(hasGroup, true);// include all items, tbh // below a copy of three lines from the if errors = true line, tbh 03/2010 String[] textFields = { INPUT_INTERVIEWER, INPUT_INTERVIEW_DATE }; fp.setCurrentStringValuesAsPreset(textFields); setPresetValues(fp.getPresetValues(), request); // below essetially a copy except for rulesPostDryRun request.setAttribute(BEAN_DISPLAY, section); request.setAttribute(BEAN_ANNOTATIONS, fp.getString(INPUT_ANNOTATIONS)); setInputMessages(errorsPostDryRun, request); addPageMessage(respage.getString("your_answers_activated_hidden_items"), request); request.setAttribute("hasError", "true"); request.setAttribute("hasShown", "true"); session.setAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME, discNotes); setUpPanel(section); forwardPage(getJSPPage(), request, response); } } if (!inSameSection) {// else if not in same section, progress as usual /* toc = TableOfContentsServlet.getDisplayBeanWithShownSections(getDataSource(), (DisplayTableOfContentsBean) request.getAttribute(TOC_DISPLAY), (DynamicsMetadataService) SpringServletAccess.getApplicationContext(getServletContext()).getBean("dynamicsMetadataService")); request.setAttribute(TOC_DISPLAY, toc); sectionIdsInToc = TableOfContentsServlet.sectionIdsInToc(toc); sIndex = TableOfContentsServlet.sectionIndexInToc(section.getSection(), toc, sectionIdsInToc); previousSec = this.prevSection(section.getSection(), ecb, toc, sIndex); nextSec = this.nextSection(section.getSection(), ecb, toc, sIndex); section.setFirstSection(!previousSec.isActive()); section.setLastSection(!nextSec.isActive()); */ // can we just forward page or do we actually need an ELSE here? // yes, we do. tbh 05/03/2010 ArrayList<String> updateFailedItems = sc.redoCalculations(scoreItems, scoreItemdata, changedItems, itemOrdinals, sb.getId()); success = updateFailedItems.size() > 0 ? false : true; // now check if CRF is marked complete boolean markComplete = fp.getString(INPUT_MARK_COMPLETE).equals(VALUE_YES); boolean markSuccessfully = false; // if the CRF was marked // complete // successfully if (markComplete && section.isLastSection()) { LOGGER.debug("need to mark CRF as complete"); markSuccessfully = markCRFComplete(request); LOGGER.debug("...marked CRF as complete: " + markSuccessfully); if (!markSuccessfully) { request.setAttribute(BEAN_DISPLAY, section); request.setAttribute(BEAN_ANNOTATIONS, fp.getString(INPUT_ANNOTATIONS)); setUpPanel(section); forwardPage(getJSPPage(), request, response); return; } } // now write the event crf bean to the database String annotations = fp.getString(INPUT_ANNOTATIONS); setEventCRFAnnotations(annotations, request); Date now = new Date(); ecb.setUpdatedDate(now); ecb.setUpdater(ub); ecb = (EventCRFBean) ecdao.update(ecb); success = success && ecb.isActive(); StudyEventDAO sedao = new StudyEventDAO(getDataSource()); StudyEventBean seb = (StudyEventBean) sedao.findByPK(ecb.getStudyEventId()); seb.setUpdatedDate(now); seb.setUpdater(ub); seb = (StudyEventBean) sedao.update(seb); success = success && seb.isActive(); request.setAttribute(INPUT_IGNORE_PARAMETERS, Boolean.TRUE); if (newUploadedFiles.size() > 0) { if (this.unloadFiles(newUploadedFiles)) { } else { String missed = ""; Iterator iter = newUploadedFiles.keySet().iterator(); while (iter.hasNext()) { missed += " " + newUploadedFiles.get(iter.next()); } addPageMessage( respage.getString("uploaded_files_not_deleted_or_not_exist") + ": " + missed, request); } } if (!success) { // YW, 3-6-2008 << if (updateFailedItems.size() > 0) { String mess = ""; for (String ss : updateFailedItems) { mess += ss + ", "; } mess = mess.substring(0, mess.length() - 2); addPageMessage(resexception.getString("item_save_failed_because_database_error") + mess, request); } else { // YW>> addPageMessage(resexception.getString("database_error"), request); } request.setAttribute(BEAN_DISPLAY, section); session.removeAttribute(GROUP_HAS_DATA); session.removeAttribute(HAS_DATA_FLAG); session.removeAttribute(DDE_PROGESS); session.removeAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME); LOGGER.debug("try to remove to_create_crf"); session.removeAttribute("to_create_crf"); session.removeAttribute(instantAtt); // forwardPage(Page.SUBMIT_DATA_SERVLET); forwardPage(Page.LIST_STUDY_SUBJECTS_SERVLET, request, response); // >> changed tbh, 06/2009 } else { boolean forwardingSucceeded = false; if (!fp.getString(GO_PREVIOUS).equals("")) { if (previousSec.isActive()) { forwardingSucceeded = true; request.setAttribute(INPUT_EVENT_CRF, ecb); request.setAttribute(INPUT_SECTION, previousSec); int tabNum = 0; if (fp.getString("tab") == null) { tabNum = 1; } else { tabNum = fp.getInt("tab"); } request.setAttribute("tab", new Integer(tabNum - 1).toString()); // forwardPage(getServletPage(request), request, response); getServletContext().getRequestDispatcher(getServletPage(request)).forward(request, response); } } else if (!fp.getString(GO_NEXT).equals("")) { if (nextSec.isActive()) { forwardingSucceeded = true; request.setAttribute(INPUT_EVENT_CRF, ecb); request.setAttribute(INPUT_SECTION, nextSec); int tabNum = 0; if (fp.getString("tab") == null) { tabNum = 1; } else { tabNum = fp.getInt("tab"); } request.setAttribute("tab", new Integer(tabNum + 1).toString()); getServletContext().getRequestDispatcher(getServletPage(request)).forward(request, response); //forwardPage(getServletPage(request), request, response); } } if (!forwardingSucceeded) { // request.setAttribute(TableOfContentsServlet. // INPUT_EVENT_CRF_BEAN, // ecb); if (markSuccessfully) { addPageMessage(respage.getString("data_saved_CRF_marked_complete"), request); session.removeAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME); session.removeAttribute(GROUP_HAS_DATA); session.removeAttribute(HAS_DATA_FLAG); session.removeAttribute(DDE_PROGESS); session.removeAttribute("to_create_crf"); request.setAttribute("eventId", new Integer(ecb.getStudyEventId()).toString()); forwardPage(Page.ENTER_DATA_FOR_STUDY_EVENT_SERVLET, request, response); } else { // use clicked 'save' addPageMessage(respage.getString("data_saved_continue_entering_edit_later"), request); request.setAttribute(INPUT_EVENT_CRF, ecb); request.setAttribute(INPUT_EVENT_CRF_ID, new Integer(ecb.getId()).toString()); // forward to the next section if the previous one // is not the last section if (!section.isLastSection()) { request.setAttribute(INPUT_SECTION, nextSec); request.setAttribute(INPUT_SECTION_ID, new Integer(nextSec.getId()).toString()); session.removeAttribute("mayProcessUploading"); } else if (section.isLastSection()) { //JN ADDED TO avoid return down // already the last section, should go back to // view event page session.removeAttribute(GROUP_HAS_DATA); session.removeAttribute(HAS_DATA_FLAG); session.removeAttribute(DDE_PROGESS); session.removeAttribute("to_create_crf"); session.removeAttribute("mayProcessUploading"); request.setAttribute("eventId", new Integer(ecb.getStudyEventId()).toString()); if (fromViewNotes != null && "1".equals(fromViewNotes)) { String viewNotesPageFileName = (String) session .getAttribute("viewNotesPageFileName"); session.removeAttribute("viewNotesPageFileName"); session.removeAttribute("viewNotesURL"); if (viewNotesPageFileName != null && viewNotesPageFileName.length() > 0) { // forwardPage(Page.setNewPage(viewNotesPageFileName, "View Notes"), request, response); getServletContext().getRequestDispatcher(viewNotesPageFileName) .forward(request, response); } } session.removeAttribute(instantAtt); forwardPage(Page.ENTER_DATA_FOR_STUDY_EVENT_SERVLET, request, response); return; } int tabNum = 0; if (fp.getString("tab") == null) { tabNum = 1; } else { tabNum = fp.getInt("tab"); } if (!section.isLastSection()) { request.setAttribute("tab", new Integer(tabNum + 1).toString()); } // forwardPage(getServletPage(request), request, response); getServletContext().getRequestDispatcher(getServletPage(request)).forward(request, response); } // session.removeAttribute(AddNewSubjectServlet. // FORM_DISCREPANCY_NOTES_NAME); // forwardPage(Page.SUBMIT_DATA_SERVLET); } } } // end of if-block for dynamic rules not in same section, tbh 05/2010 } // end of save } } protected boolean writeDN(DisplayItemBean displayItem) { boolean writeDN = true; if (StringUtils.isBlank(displayItem.getEditFlag())) { if (!displayItem.getData().isActive()) { writeDN = true; } else writeDN = false; } else { if ("add".equalsIgnoreCase(displayItem.getEditFlag())) { writeDN = true; } else if ("edit".equalsIgnoreCase(displayItem.getEditFlag())) { if (displayItem.getData().getId() != 0) { writeDN = false; } else { writeDN = true; } } } return writeDN; } /** * Changed by thickerson 05/2010 * @param idb * @param formName * @param error * @param request TODO */ protected void setReasonForChangeError(EventCRFBean ecb, ItemBean item_bean, ItemDataBean idb, String formName, String error, HttpServletRequest request) { HttpSession session = request.getSession(); /* * Having existing notes is not enough to let it pass through after changing data. There has to be a DiscrepancyNote for the latest changed data */ HashMap<String, Boolean> noteSubmitted = (HashMap<String, Boolean>) session .getAttribute(DataEntryServlet.NOTE_SUBMITTED); //String key_for_rfc = String.valueOf(idb.getId()); String key_for_rfc = String.valueOf(ecb.getId() + "_" + formName); boolean isRFCFiled = false; if (noteSubmitted != null) { if (noteSubmitted.get(key_for_rfc) != null) {//item in database isRFCFiled = true; } } if (!isRFCFiled) { errors.put(formName, error); } else { LOGGER.debug("has a note in db: entered an error here: " + formName + ": " + errors.toString()); } } /** * Get the input beans - the EventCRFBean and the SectionBean. For both beans, look first in the request attributes to see if the bean has been stored * there. If not, look in the parameters for the bean id, and then retrieve the bean from the database. The beans are stored as protected class members. * @param request TODO */ protected void getInputBeans(HttpServletRequest request) throws InsufficientPermissionException { HttpSession session = request.getSession(); StudyBean currentStudy = (StudyBean) session.getAttribute("study"); // BWP >>we should have the correct crfVersionId, in order to acquire // the correct // section IDs FormProcessor fp = new FormProcessor(request); EventCRFDAO ecdao = new EventCRFDAO(getDataSource()); SectionDAO sdao = new SectionDAO(getDataSource()); EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); //JN:Happening when drilling down? if (ecb == null) { int eventCRFId = fp.getInt(INPUT_EVENT_CRF_ID, true); LOGGER.debug("found event crf id: " + eventCRFId); if (eventCRFId > 0) { LOGGER.debug("***NOTE*** that we didnt have to create an event crf because we already have one: " + eventCRFId); // there is an event CRF already, only need to update ecb = (EventCRFBean) ecdao.findByPK(eventCRFId); // ecb.setUpdatedDate(new Date()); // ecb.setUpdater(ub); // ecb = (EventCRFBean) ecdao.update(ecb); // logger.trace("found an event crf id "+eventCRFId); // YW 11-12-2007 << if interviewer or/and interview date // has/have been updated for study/site from "blank" to // "pre-populated" // But at this point, this update only shows on web page and // will not be updated to database. int studyEventId = fp.getInt(INPUT_STUDY_EVENT_ID); request.setAttribute(INPUT_EVENT_CRF, ecb); if (studyEventId > 0) { StudyEventDAO sedao = new StudyEventDAO(getDataSource()); StudyEventBean sEvent = (StudyEventBean) sedao.findByPK(studyEventId); ecb = updateECB(sEvent, request); } request.setAttribute(INPUT_EVENT_CRF, ecb); // YW >> } else { // CRF id <=0, so we need to create a new CRF // use toCreateCRF as a flag to prevent user to submit event CRF // more than once // for example, user reloads the page String toCreateCRF = (String) session.getAttribute("to_create_crf"); if (StringUtil.isBlank(toCreateCRF) || "0".equals(toCreateCRF)) { session.setAttribute("to_create_crf", "1"); } try { // if (ecb.getInterviewerName() != null) { LOGGER.debug("Initial: to create an event CRF."); String toCreateCRF1 = (String) session.getAttribute("to_create_crf"); if (!StringUtil.isBlank(toCreateCRF1) && "1".equals(toCreateCRF1)) { ecb = createEventCRF(request, fp); session.setAttribute("ecb", ecb); request.setAttribute(INPUT_EVENT_CRF, ecb); session.setAttribute("to_create_crf", "0"); } else { ecb = (EventCRFBean) session.getAttribute("ecb"); } // } } catch (InconsistentStateException ie) { ie.printStackTrace(); addPageMessage(ie.getOpenClinicaMessage(), request); throw new InsufficientPermissionException(Page.LIST_STUDY_SUBJECTS_SERVLET, ie.getOpenClinicaMessage(), "1"); } catch (NullPointerException ne) { ne.printStackTrace(); addPageMessage(ne.getMessage(), request); throw new InsufficientPermissionException(Page.LIST_STUDY_SUBJECTS_SERVLET, ne.getMessage(), "1"); } } } // added to allow sections shown on this page DisplayTableOfContentsBean displayBean = new DisplayTableOfContentsBean(); displayBean = TableOfContentsServlet.getDisplayBean(ecb, getDataSource(), currentStudy); // escape apostrophe in event name displayBean.getStudyEventDefinition() .setName(StringEscapeUtils.escapeJavaScript(displayBean.getStudyEventDefinition().getName())); request.setAttribute(TOC_DISPLAY, displayBean); int sectionId = fp.getInt(INPUT_SECTION_ID, true); ArrayList sections; if (sectionId <= 0) { StudyEventDAO studyEventDao = new StudyEventDAO(getDataSource()); int maximumSampleOrdinal = studyEventDao.getMaxSampleOrdinal(displayBean.getStudyEventDefinition(), displayBean.getStudySubject()); request.setAttribute("maximumSampleOrdinal", maximumSampleOrdinal); sections = sdao.findAllByCRFVersionId(ecb.getCRFVersionId()); for (int i = 0; i < sections.size(); i++) { SectionBean sb = (SectionBean) sections.get(i); sectionId = sb.getId();// find the first section of this CRF break; } } SectionBean sb = new SectionBean(); if (sectionId > 0) { // int sectionId = fp.getInt(INPUT_SECTION_ID, true); //synchronized(this) { sb = (SectionBean) sdao.findByPK(sectionId); } } int tabId = fp.getInt("tab", true); if (tabId <= 0) { tabId = 1; } request.setAttribute(INPUT_TAB, new Integer(tabId)); request.setAttribute(SECTION_BEAN, sb); } /** * Tries to check if a seciton has item groups * @param fp TODO * @param ecb TODO * * @return */ protected boolean checkGroups(FormProcessor fp, EventCRFBean ecb) { int sectionId = fp.getInt(INPUT_SECTION_ID, true); SectionDAO sdao = new SectionDAO(getDataSource()); if (sectionId <= 0) { ArrayList sections = sdao.findAllByCRFVersionId(ecb.getCRFVersionId()); for (int i = 0; i < sections.size(); i++) { SectionBean sb = (SectionBean) sections.get(i); sectionId = sb.getId();// find the first section of this CRF break; } } // we will look into db to see if any repeating items for this CRF // section ItemGroupDAO igdao = new ItemGroupDAO(getDataSource()); // find any item group which doesn't equal to 'Ungrouped' ItemGroupBean itemGroup = igdao.findTopOneGroupBySectionId(sectionId); if (itemGroup != null && itemGroup.getId() > 0) { LOGGER.trace("This section has group"); return true; } return false; } /** * Creates a new Event CRF or update the exsiting one, that is, an event CRF can be created but not item data yet, in this case, still consider it is not * started(called uncompleted before) * @param request TODO * @param fp TODO * * @return * @throws Exception */ private EventCRFBean createEventCRF(HttpServletRequest request, FormProcessor fp) throws InconsistentStateException { locale = LocaleResolver.getLocale(request); // < resmessage = // ResourceBundle.getBundle("org.akaza.openclinica.i18n.page_messages", // locale); // < restext = // ResourceBundle.getBundle("org.akaza.openclinica.i18n.notes",locale); // < // resexception=ResourceBundle.getBundle( // "org.akaza.openclinica.i18n.exceptions",locale); UserAccountBean ub = (UserAccountBean) request.getSession().getAttribute(USER_BEAN_NAME); StudyBean currentStudy = (StudyBean) request.getSession().getAttribute("study"); EventCRFBean ecb; EventCRFDAO ecdao = new EventCRFDAO(getDataSource()); int crfVersionId = fp.getInt(INPUT_CRF_VERSION_ID); LOGGER.trace("***FOUND*** crfversionid: " + crfVersionId); int studyEventId = fp.getInt(INPUT_STUDY_EVENT_ID); int eventDefinitionCRFId = fp.getInt(INPUT_EVENT_DEFINITION_CRF_ID); int subjectId = fp.getInt(INPUT_SUBJECT_ID); int eventCRFId = fp.getInt(INPUT_EVENT_CRF_ID); LOGGER.trace("look specifically wrt event crf id: " + eventCRFId); LOGGER.trace("Creating event CRF. Study id: " + currentStudy.getId() + "; CRF Version id: " + crfVersionId + "; Study Event id: " + studyEventId + "; Event Definition CRF id: " + eventDefinitionCRFId + "; Subject: " + subjectId); StudySubjectDAO ssdao = new StudySubjectDAO(getDataSource()); StudySubjectBean ssb = ssdao.findBySubjectIdAndStudy(subjectId, currentStudy); if (ssb.getId() <= 0) { LOGGER.trace("throwing ISE with study subject bean id of " + ssb.getId()); // addPageMessage(resexception.getString( // "begin_data_entry_without_event_but_subject")); throw new InconsistentStateException(Page.LIST_STUDY_SUBJECTS_SERVLET, resexception.getString("begin_data_entry_without_event_but_subject")); } StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(getDataSource()); StudyEventDefinitionBean sedb = seddao.findByEventDefinitionCRFId(eventDefinitionCRFId); // logger.trace("study event definition:" + sedb.getId()); if (sedb.getId() <= 0) { addPageMessage(resexception.getString("begin_data_entry_without_event_but_study"), request); throw new InconsistentStateException(Page.LIST_STUDY_SUBJECTS_SERVLET, resexception.getString("begin_data_entry_without_event_but_study")); } CRFVersionDAO cvdao = new CRFVersionDAO(getDataSource()); EntityBean eb = cvdao.findByPK(crfVersionId); if (eb.getId() <= 0) { //addPageMessage(resexception.getString("begin_data_entry_without_event_but_CRF")); throw new InconsistentStateException(Page.LIST_STUDY_SUBJECTS_SERVLET, resexception.getString("begin_data_entry_without_event_but_CRF")); } StudyEventDAO sedao = new StudyEventDAO(getDataSource()); StudyEventBean sEvent = (StudyEventBean) sedao.findByPK(studyEventId); StudyBean studyWithSED = currentStudy; if (currentStudy.getParentStudyId() > 0) { studyWithSED = new StudyBean(); studyWithSED.setId(currentStudy.getParentStudyId()); } AuditableEntityBean aeb = sedao.findByPKAndStudy(studyEventId, studyWithSED); if (aeb.getId() <= 0) { addPageMessage(resexception.getString("begin_data_entry_without_event_but_especified_event"), request); throw new InconsistentStateException(Page.LIST_STUDY_SUBJECTS_SERVLET, resexception.getString("begin_data_entry_without_event_but_especified_event")); } ecb = new EventCRFBean(); if (eventCRFId == 0) {// no event CRF created yet ArrayList ecList = ecdao.findByEventSubjectVersion(sEvent, ssb, (CRFVersionBean) eb); if (ecList.size() > 0) { ecb = (EventCRFBean) ecList.get(0); } else { ecb.setAnnotations(""); ecb.setCreatedDate(new Date()); ecb.setCRFVersionId(crfVersionId); if (currentStudy.getStudyParameterConfig().getInterviewerNameDefault().equals("blank")) { ecb.setInterviewerName(""); } else { // default will be event's owner name ecb.setInterviewerName(sEvent.getOwner().getName()); } if (!currentStudy.getStudyParameterConfig().getInterviewDateDefault().equals("blank")) { if (sEvent.getDateStarted() != null) { ecb.setDateInterviewed(sEvent.getDateStarted());// default // date } else { // logger.trace("evnet start date is null, so date // interviewed is null"); ecb.setDateInterviewed(null); } } else { ecb.setDateInterviewed(null); // logger.trace("date interviewed is // null,getInterviewDateDefault() is blank"); } // ecb.setOwnerId(ub.getId()); // above depreciated, try without it, tbh ecb.setOwner(ub); ecb.setStatus(Status.AVAILABLE); ecb.setCompletionStatusId(1); ecb.setStudySubjectId(ssb.getId()); ecb.setStudyEventId(studyEventId); ecb.setValidateString(""); ecb.setValidatorAnnotations(""); ecb = (EventCRFBean) ecdao.create(ecb); LOGGER.debug("*********CREATED EVENT CRF"); } } else { // there is an event CRF already, only need to update ecb = (EventCRFBean) ecdao.findByPK(eventCRFId); ecb.setCRFVersionId(crfVersionId); ecb.setUpdatedDate(new Date()); ecb.setUpdater(ub); ecb = updateECB(sEvent, request); ecb = (EventCRFBean) ecdao.update(ecb); } if (ecb.getId() <= 0) { addPageMessage(resexception.getString("new_event_CRF_not_created"), request); throw new InconsistentStateException(Page.LIST_STUDY_SUBJECTS_SERVLET, resexception.getString("new_event_CRF_not_created")); } else { if (sEvent.getSubjectEventStatus().equals(SubjectEventStatus.SIGNED)) { sEvent.setSubjectEventStatus(SubjectEventStatus.COMPLETED); sEvent.setUpdater(ub); sEvent.setUpdatedDate(new Date()); sedao.update(sEvent); } else { sEvent.setSubjectEventStatus(SubjectEventStatus.DATA_ENTRY_STARTED); sEvent.setUpdater(ub); sEvent.setUpdatedDate(new Date()); sedao.update(sEvent); } } return ecb; } /** * Read in form values and write them to a display item bean. Note that this results in the form value being written to both the response set bean and the * item data bean. The ResponseSetBean is used to display preset values on the form in the event of error, and the ItemDataBean is used to send values to * the database. * * @param dib * The DisplayItemBean to write data into. * @param request TODO * @return The DisplayItemBean, with form data loaded. */ protected DisplayItemBean loadFormValue(DisplayItemBean dib, HttpServletRequest request) { String inputName = getInputName(dib); FormProcessor fp = new FormProcessor(request); org.akaza.openclinica.bean.core.ResponseType rt = dib.getMetadata().getResponseSet().getResponseType(); if (rt.equals(org.akaza.openclinica.bean.core.ResponseType.CHECKBOX) || rt.equals(org.akaza.openclinica.bean.core.ResponseType.SELECTMULTI) || rt.equals(org.akaza.openclinica.bean.core.ResponseType.SELECT)) { dib.loadFormValue(fp.getStringArray(inputName)); // YW, 2-4-2008 << calculation result has been written in dib-data } else if (rt.equals(org.akaza.openclinica.bean.core.ResponseType.CALCULATION) || rt.equals(org.akaza.openclinica.bean.core.ResponseType.GROUP_CALCULATION)) { dib.loadFormValue(dib.getData().getValue()); ResponseOptionBean rob = (ResponseOptionBean) dib.getMetadata().getResponseSet().getOptions().get(0); LOGGER.trace("test print of options for coding: " + rob.getValue()); // YW >> } else { LOGGER.trace("test print: " + inputName + ": " + fp.getString(inputName)); dib.loadFormValue(fp.getString(inputName)); } return dib; } /** * This methods will create an array of DisplayItemGroupBean, which contains multiple rows for an item group on the data entry form. * * @param digb * The Item group which has multiple data rows * @param dbGroups * The original array got from DB which contains multiple data rows * @param formGroups * The new array got from front end which contains multiple data rows * @param request TODO * @return new constructed formGroups, compare to dbGroups, some rows are update, some new ones are added and some are removed */ protected List<DisplayItemGroupBean> loadFormValueForItemGroup(DisplayItemGroupBean digb, List<DisplayItemGroupBean> dbGroups, List<DisplayItemGroupBean> formGroups, int eventDefCRFId, HttpServletRequest request) { SectionBean sb = (SectionBean) request.getAttribute(SECTION_BEAN); int repeatMax = digb.getGroupMetaBean().getRepeatMax(); FormProcessor fp = new FormProcessor(request); ItemDAO idao = new ItemDAO(getDataSource()); List<ItemBean> itBeans = idao.findAllItemsByGroupId(digb.getItemGroupBean().getId(), sb.getCRFVersionId()); LOGGER.debug("+++ starting to review groups: " + repeatMax); long timeCheck = System.currentTimeMillis(); EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); // adding this code from below, since we want to pass a null values list // in all cases of getDisplayBeansFromItems(). // For adding null values to display items FormBeanUtil formBeanUtil = new FormBeanUtil(); List<String> nullValuesList = new ArrayList<String>(); // BWP>> Get a List<String> of any null values such as NA or NI // method returns null values as a List<String> nullValuesList = formBeanUtil.getNullValuesByEventCRFDefId(eventDefCRFId, getDataSource()); // >>BWP // logger.trace("+++ starting to review groups 2: " + repeatMax); long two = System.currentTimeMillis() - timeCheck; // logger.trace("time 2: " + two + "ms"); // >>TBH below dual for loops need a breaker to avoid a performance hit int firstLoopBreak = 0; int secondLoopBreak = 0; ItemDataDAO iddao = new ItemDataDAO(getDataSource(), locale); int maxOrdinal = iddao.getMaxOrdinalForGroup(ecb, sb, digb.getItemGroupBean()); repeatMax = (repeatMax < maxOrdinal) ? maxOrdinal : repeatMax; for (int i = 0; i < repeatMax; i++) { DisplayItemGroupBean formGroup = new DisplayItemGroupBean(); formGroup.setItemGroupBean(digb.getItemGroupBean()); formGroup.setGroupMetaBean(runDynamicsCheck(digb.getGroupMetaBean(), request)); ItemGroupBean igb = digb.getItemGroupBean(); // want to do deep copy here, so always get a fresh copy for items, // may use other better way to do, like clone List<DisplayItemBean> dibs = FormBeanUtil.getDisplayBeansFromItems(itBeans, getDataSource(), ecb, sb.getId(), nullValuesList, getServletContext()); // get the values from the manually created rows first- not from the // rep model // second half of the if line is here to protect against looping tbh 01/2010 // split the if loop into two parts, so that we can get what's existing first // and then get newly created rows later, tbh 01/2010 if (fp.getStartsWith(igb.getOid() + "_manual" + i + "input")) { formGroup.setOrdinal(i); formGroup.setFormInputOrdinal(i); formGroup.setAuto(false); formGroup.setInputId(igb.getOid() + "_manual" + i); LOGGER.debug("1: set auto to false for " + igb.getOid() + " " + i); dibs = processInputForGroupItem(fp, dibs, i, digb, false); formGroup.setItems(dibs); formGroups.add(formGroup); } else if (!StringUtil.isBlank(fp.getString(igb.getOid() + "_manual" + i + ".newRow"))) { // || // (fp.getStartsWith(igb.getOid() + "_manual" + i + "input"))) { // the ordinal is the number got from [ ] and submitted by // repetition javascript formGroup.setOrdinal(i); formGroup.setFormInputOrdinal(i); formGroup.setInputId(igb.getOid() + "_manual" + i + ".newRow"); formGroup.setAuto(false); LOGGER.debug("2: set auto to false for " + igb.getOid() + " " + i); dibs = processInputForGroupItem(fp, dibs, i, digb, false); formGroup.setItems(dibs); formGroups.add(formGroup); } else { firstLoopBreak++; } if (firstLoopBreak > 14) { LOGGER.debug("break first loop"); break; } } // end of for (int i = 0; i < repeatMax; i++) // >>TBH remove the above eventually, repeat some work here? LOGGER.trace("+++ starting to review groups 3: " + repeatMax); two = System.currentTimeMillis() - timeCheck; LOGGER.trace("time 3: " + two + "ms"); // >>TBH taking the nullvalues list out of the for loop, since it should // be the same for all display beans // nullValuesList = formBeanUtil.getNullValuesByEventCRFDefId( // eventDefCRFId, // getDataSource()); /* * logger.trace("+++ count for null values list: " + nullValuesList.size()); logger.trace(nullValuesList.toString() + " found with " + eventDefCRFId); */ // had the call to form bean utils here, tbh for (int i = 0; i < repeatMax; i++) { DisplayItemGroupBean formGroup = new DisplayItemGroupBean(); formGroup.setItemGroupBean(digb.getItemGroupBean()); // try { // // set isShown here, tbh 04/2010 // boolean showGroup = getItemMetadataService().isGroupShown(digb.getGroupMetaBean().getId(), ecb); // logger.debug("found show group for group meta bean " + digb.getGroupMetaBean().getId() + ": " + showGroup); // if (showGroup) { // digb.getGroupMetaBean().setShowGroup(showGroup); // // we are only hiding, not showing (for now) tbh // } // // << tbh 04/2010 // } catch (OpenClinicaException oce) { // // do nothing for right now, just store the bean // logger.debug("throws an OCE for " + digb.getGroupMetaBean().getId()); // } formGroup.setGroupMetaBean(runDynamicsCheck(digb.getGroupMetaBean(), request)); ItemGroupBean igb = digb.getItemGroupBean(); // adding this code from below, since we want to pass a null values // list // in all cases of getDisplayBeansFromItems(). // For adding null values to display items // FormBeanUtil formBeanUtil = new FormBeanUtil(); // List<String> nullValuesList = new ArrayList<String>(); // BWP>> Get a List<String> of any null values such as NA or NI // method returns null values as a List<String> // >>BWP // want to do deep copy here, so always get a fresh copy for items, // may use other better way to do, like clone // moved it back down here to fix another bug, tbh 12-3-2007 List<DisplayItemBean> dibs = FormBeanUtil.getDisplayBeansFromItems(itBeans, getDataSource(), ecb, sb.getId(), nullValuesList, getServletContext()); LOGGER.trace("+++count for dibs after deep copy: " + dibs.size()); two = System.currentTimeMillis() - timeCheck; // logger.trace("time 3.dibs: " + two + "ms"); // >>tbh // let's get the values from the rep model, which includes the first // row and any new rows // created by rep model(add button) if (fp.getStartsWith(igb.getOid() + "_" + i + "input")) { formGroup.setInputId(igb.getOid() + "_" + i); if (i == 0) { formGroup.setOrdinal(i);// ordinal that will be saved into // DB } else { formGroup.setFormInputOrdinal(i);// from 0 again, the // ordinal from front // end page, needs to be // reprocessed } formGroup.setAuto(true); LOGGER.debug("1: set auto to TRUE for " + igb.getOid() + " " + i); dibs = processInputForGroupItem(fp, dibs, i, digb, true); LOGGER.trace("+++ group ordinal: " + i + " igb name " + igb.getName()); formGroup.setItems(dibs); formGroups.add(formGroup); } else if (!StringUtil.isBlank(fp.getString(igb.getOid() + "_" + i + ".newRow"))) { // || (fp.getStartsWith(igb.getOid() + "_" + i + "input"))) { // the ordinal is the number got from [ ] and submitted by // repetition javascript formGroup.setInputId(igb.getOid() + "_" + i); if (i == 0) { formGroup.setOrdinal(i);// ordinal that will be saved into // DB } else { formGroup.setFormInputOrdinal(i);// from 0 again, the // ordinal from front // end page, needs to be // reprocessed } // String fieldName = igb.getOid() + "_" + i + this.getInputName(dib); // if (!StringUtil.isBlank(fp.getString(fieldName))) { // if (i != repeatMax) { // formGroup.setAuto(false); // logger.debug("set auto to false for " + igb.getOid() + " " + i); // } else { formGroup.setAuto(true); LOGGER.debug("2: set auto to TRUE for " + igb.getOid() + " " + i); dibs = processInputForGroupItem(fp, dibs, i, digb, true); LOGGER.trace("+++ group ordinal: " + i + " igb name " + igb.getName()); formGroup.setItems(dibs); formGroups.add(formGroup); } else { secondLoopBreak++; } if (secondLoopBreak > 14) { LOGGER.debug("break second loop"); break; } } // end of for (int i = 0; i < repeatMax; i++) LOGGER.debug("first loop: " + firstLoopBreak); LOGGER.debug("second loop: " + secondLoopBreak); LOGGER.trace("+++ starting to review groups 4: " + repeatMax); two = System.currentTimeMillis() - timeCheck; LOGGER.trace("time 4: " + two + "ms"); // checks how many rows are manually created, not added by repetition // model int manualRows = getManualRows(formGroups); // for (int j = 0; j < formGroups.size(); j++) { // DisplayItemGroupBean formItemGroup = formGroups.get(j); // // logger.trace("begin formGroup Ordinal:" + // // formItemGroup.getOrdinal()); // if (formItemGroup.isAuto() == false) { // manualRows = manualRows + 1; // } // } LOGGER.debug(" manual rows " + manualRows + " formGroup size " + formGroups.size()); request.setAttribute("manualRows", new Integer(manualRows)); // reset ordinal for the auto-created rows except for the first row for (int j = 0; j < formGroups.size(); j++) { DisplayItemGroupBean formItemGroup = formGroups.get(j); if (formItemGroup.isAuto() && formItemGroup.getFormInputOrdinal() > 0) { LOGGER.trace("+++ formInputOrdinal() " + formItemGroup.getFormInputOrdinal()); // rows included in the model: first row, last existing row and // new rows // the rows in between are manually added // set the correct ordinal that will be saved into DB // the rows generated by model starts from 0, need to add the // number of manual rows to // get the correct ordinals, otherwise, we will have duplicate // ordinals like two ordinal 0 formItemGroup.setOrdinal(formItemGroup.getFormInputOrdinal() + manualRows); } } LOGGER.trace("+++ starting to review groups 5: " + repeatMax); two = System.currentTimeMillis() - timeCheck; LOGGER.trace("time 5: " + two + "ms"); Collections.sort(formGroups);// sort all the rows by ordinal LOGGER.trace("group row size:" + formGroups.size()); // suppose we have 3 rows of data from db, the orginal order is 0,1,2, // repetition model will submit row number in [ ] like the following: // 0,1,2.. consecutive numbers, means no row removed in between // 0,1,3,4.. the 2rd row is removed, 3 and 4 are new rows int previous = -1; for (int j = 0; j < formGroups.size(); j++) { DisplayItemGroupBean formItemGroup = formGroups.get(j); LOGGER.trace("formGroup Ordinal:" + formItemGroup.getOrdinal()); // logger.debug("=== formGroup Ordinal:" + formItemGroup.getOrdinal()); // the below if loop addresses a specific problem with the repeating model // if we cut a row out of a long list, the repeater returns double ordinals of another row // and a second row gets deleted by mistake. // tbh 08/2009 if (formItemGroup.getOrdinal() == previous) { LOGGER.debug("found a match btw previous and ordinal"); formItemGroup.setEditFlag("edit"); formItemGroup.setOrdinal(previous + 1); // dbGroups.get(j).setEditFlag("edit"); } // << tbh 08/2009 if (formItemGroup.getOrdinal() > dbGroups.size() - 1) { formItemGroup.setEditFlag("add"); } else { for (int i = 0; i < dbGroups.size(); i++) { DisplayItemGroupBean dbItemGroup = dbGroups.get(i); if (formItemGroup.getOrdinal() == i) { // the first row is different, it could be blank on page // just for // display, so need to insert this row, not update if ("initial".equalsIgnoreCase(dbItemGroup.getEditFlag())) { formItemGroup.setEditFlag("add"); } else { dbItemGroup.setEditFlag("edit"); // need to set up item data id in order to update for (DisplayItemBean dib : dbItemGroup.getItems()) { ItemDataBean data = dib.getData(); for (DisplayItemBean formDib : formItemGroup.getItems()) { if (formDib.getItem().getId() == dib.getItem().getId()) { formDib.getData().setId(data.getId()); // this will save the data from IDE // complete, used only for DDE formDib.setDbData(dib.getData()); // tbh removed below line so as not to // log so much, 112007 LOGGER.debug("+++ +++ form dib get data set id " + data.getId()); break; } } } formItemGroup.setEditFlag("edit"); } // else break; } } } // else previous = formItemGroup.getOrdinal(); } LOGGER.trace("+++ === DB group row:" + dbGroups.size()); LOGGER.trace("+++ === DB group contents: " + dbGroups.toString()); // why do we need to remove this one row below? // For the existing rows in dbGroups,if cannot get the edit flag or // initial flag for a row, // it means the row is removed on the front-end, so the back-end servlet // cannot get it.-jxu for (int i = 0; i < dbGroups.size(); i++) { DisplayItemGroupBean dbItemGroup = dbGroups.get(i); LOGGER.trace( "+++ found edit flag of " + dbItemGroup.getEditFlag() + " for #" + dbItemGroup.getOrdinal()); // logger.debug("+++ found edit flag of " + dbItemGroup.getEditFlag() + " for #" + dbItemGroup.getOrdinal() + ": " + i); if (!"edit".equalsIgnoreCase(dbItemGroup.getEditFlag()) && !"initial".equalsIgnoreCase(dbItemGroup.getEditFlag())) { // && !"".equalsIgnoreCase(dbItemGroup.getEditFlag())) { // >> tbh if the group is not shown, we should not touch it 05/2010 if (dbItemGroup.getGroupMetaBean().isShowGroup()) { LOGGER.trace("+++ one row removed, edit flag was " + dbItemGroup.getEditFlag()); LOGGER.debug("+++ one row removed, edit flag was " + dbItemGroup.getEditFlag()); dbItemGroup.setEditFlag("remove"); } // << tbh } } LOGGER.debug("+++ about to return form groups: " + formGroups.toString()); for (int j = 0; j < formGroups.size(); j++) { DisplayItemGroupBean formGroup = formGroups.get(j); formGroup.setIndex(j); } return formGroups; } /** * @return <code>true</code> if processRequest should validate inputs when the user clicks the "Save" button, <code>false</code> otherwise. */ protected abstract boolean validateInputOnFirstRound(); /** * Validate the input from the form corresponding to the provided item. Implementing methods should load data from the form into the bean before validating. * The loadFormValue method should be used for this purpose. * <p/> * validateDisplayItemBeanText, validateDisplayItemBeanSingleCV, and validateDisplayItemBeanMultipleCV are provided to make implementing this method easy. * * @param v * The Validator to add validations to. * @param dib * The DisplayItemBean to validate. * @param request TODO * @return The DisplayItemBean which is validated and has form values loaded into it. */ protected abstract DisplayItemBean validateDisplayItemBean(DiscrepancyValidator v, DisplayItemBean dib, String inputName, HttpServletRequest request); protected void validateSCDItemBean(DiscrepancyValidator v, DisplayItemBean dib) { ItemFormMetadataBean ibMeta = dib.getMetadata(); ItemDataBean idb = dib.getData(); if (StringUtil.isBlank(idb.getValue())) { //if (ibMeta.isRequired() && showSCDItemIds.contains(ibMeta.getId())) { if (ibMeta.isRequired() && dib.getIsSCDtoBeShown()) { v.addValidation(this.getInputName(dib), Validator.IS_REQUIRED); /*if(dib.getIsSCDtoBeShown()) { v.addValidation(this.getInputName(dib), Validator.IS_REQUIRED); } else { validateShownSCDToBeHiddenSingle(v,dib); }*/ } } else { validateShownSCDToBeHiddenSingle(v, dib); } } protected DisplayItemBean validateDisplayItemBean(DiscrepancyValidator v, DisplayItemBean dib, String inputName, RuleValidator rv, HashMap<String, ArrayList<String>> groupOrdinalPLusItemOid, Boolean fireRuleValidation, ArrayList<String> messages, HttpServletRequest request) { return dib; } protected abstract List<DisplayItemGroupBean> validateDisplayItemGroupBean(DiscrepancyValidator v, DisplayItemGroupBean dib, List<DisplayItemGroupBean> digbs, List<DisplayItemGroupBean> formGroups, HttpServletRequest request, HttpServletResponse response); protected List<DisplayItemGroupBean> validateDisplayItemGroupBean(DiscrepancyValidator v, DisplayItemGroupBean dib, List<DisplayItemGroupBean> digbs, List<DisplayItemGroupBean> formGroups, RuleValidator rv, HashMap<String, ArrayList<String>> groupOrdinalPLusItemOid, HttpServletRequest request, HttpServletResponse response) { return digbs; } /* * function written out here to return itemMetadataGroupBeans after they have been checked for show/hide via dynamics. * author: tbh 04/2010 * */ private ItemGroupMetadataBean runDynamicsCheck(ItemGroupMetadataBean metadataBean, HttpServletRequest request) { EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); try { if (!metadataBean.isShowGroup()) { // set isShown here, tbh 04/2010 boolean showGroup = getItemMetadataService().isGroupShown(metadataBean.getId(), ecb); // logger.debug("found show group for group meta bean " + metadataBean.getId() + ": " + // metadataBean.getItemGroupId() + // ": " + ecb.getId() + ": " + showGroup); if (getServletPage(request).equals(Page.DOUBLE_DATA_ENTRY_SERVLET)) { showGroup = getItemMetadataService().hasGroupPassedDDE(metadataBean.getId(), ecb.getId()); } metadataBean.setShowGroup(showGroup); // what about the items which should be shown? // if (getServletPage().equals(Page.ADMIN_EDIT_SERVLET) && metadataBean.isShowGroup()) { // metadataBean.setHighlighted(true); // } // sets highlighting for AE, tbh 05/2010 // unset highlighting for admin editing, tbh 06/2010 } // << tbh 04/2010 } catch (OpenClinicaException oce) { // do nothing for right now, just store the bean LOGGER.debug("throws an OCE for " + metadataBean.getId()); } return metadataBean; } private DisplayItemBean runDynamicsItemCheck(DisplayItemBean dib, Object newParam, HttpServletRequest request) { EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); try { LOGGER.debug("trying run dynamics item check: item id " + dib.getItem().getId() + " item data id " + dib.getData().getId()); if (!dib.getMetadata().isShowItem()) { boolean showItem = getItemMetadataService().isShown(dib.getItem().getId(), ecb, dib.getData()); dib.getMetadata().setShowItem(showItem); // //System.out.println("returning " + showItem); } } catch (NullPointerException npe) { LOGGER.debug("found NPE! item id " + dib.getItem().getId()); } return dib; } /* * Perform validation for calculation and group-calculation type. <br> Pre-condition: passed DisplayItemBean parameter has been loaded with value. @param sv * @param dib @param inputName @return dib @author ywang (Feb.,2008) */ protected DisplayItemBean validateCalcTypeDisplayItemBean(ScoreItemValidator sv, DisplayItemBean dib, String inputName, HttpServletRequest request) { dib = validateDisplayItemBeanText(sv, dib, inputName, request); return dib; } /** * Peform validation on a item which has a TEXT or TEXTAREA response type. If the item has a null value, it's automatically validated. Otherwise, it's * checked against its data type. * * @param v * The Validator to add validations to. * @param dib * The DisplayItemBean to validate. * @param request TODO * @return The DisplayItemBean which is validated. */ protected DisplayItemBean validateDisplayItemBeanText(DiscrepancyValidator v, DisplayItemBean dib, String inputName, HttpServletRequest request) { FormProcessor fp = new FormProcessor(request); EventDefinitionCRFBean edcb = (EventDefinitionCRFBean) request.getAttribute(EVENT_DEF_CRF_BEAN); if (StringUtil.isBlank(inputName)) {// for single items inputName = getInputName(dib); } ItemBean ib = dib.getItem(); ItemFormMetadataBean ibMeta = dib.getMetadata(); ItemDataType idt = ib.getDataType(); ItemDataBean idb = dib.getData(); boolean isNull = false; ArrayList nullValues = edcb.getNullValuesList(); for (int i = 0; i < nullValues.size(); i++) { NullValue nv = (NullValue) nullValues.get(i); if (nv.getName().equals(fp.getString(inputName))) { isNull = true; } } if (!isNull) { if (StringUtil.isBlank(idb.getValue())) { // check required first if (ibMeta.isRequired() && ibMeta.isShowItem()) { v.addValidation(inputName, Validator.IS_REQUIRED); } } else { if (idt.equals(ItemDataType.ST)) { // a string's size could be more than 3999, which is more // than // the db field length v.addValidation(inputName, Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 3999); } else if (idt.equals(ItemDataType.INTEGER)) { v.addValidation(inputName, Validator.IS_AN_INTEGER); v.alwaysExecuteLastValidation(inputName); } else if (idt.equals(ItemDataType.REAL)) { v.addValidation(inputName, Validator.IS_A_NUMBER); v.alwaysExecuteLastValidation(inputName); } else if (idt.equals(ItemDataType.BL)) { // there is no validation here since this data type is // explicitly // allowed to be null // if the string input for this field parses to a non-zero // number, the // value will be true; otherwise, 0 } else if (idt.equals(ItemDataType.BN)) { } else if (idt.equals(ItemDataType.SET)) { // v.addValidation(inputName, Validator.NO_BLANKS_SET); v.addValidation(inputName, Validator.IN_RESPONSE_SET_SINGLE_VALUE, dib.getMetadata().getResponseSet()); } else if (idt.equals(ItemDataType.DATE)) { v.addValidation(inputName, Validator.IS_A_DATE); v.alwaysExecuteLastValidation(inputName); } else if (idt.equals(ItemDataType.PDATE)) { v.addValidation(inputName, Validator.IS_PARTIAL_DATE); v.alwaysExecuteLastValidation(inputName); } if (ibMeta.getWidthDecimal().length() > 0) { ArrayList<String> params = new ArrayList<String>(); params.add(0, idt.getName()); params.add(1, ibMeta.getWidthDecimal()); v.addValidation(inputName, Validator.IS_VALID_WIDTH_DECIMAL, params); v.alwaysExecuteLastValidation(inputName); } // >> tbh 4/30/2010 #4963 removing custom validations firing during AE customValidation(v, dib, inputName); /* * if (!StringUtil.isBlank(customValidationString)) { Validation customValidation = null; if (customValidationString.startsWith("func:")) { try * { customValidation = Validator.processCRFValidationFunction(customValidationString ); } catch (Exception e) { e.printStackTrace(); } } else * if (customValidationString.startsWith("regexp:")) { try { customValidation = Validator.processCRFValidationRegex(customValidationString); } * catch (Exception e) { } } if (customValidation != null) { customValidation .setErrorMessage(dib.getMetadata().getRegexpErrorMsg()); * v.addValidation(inputName, customValidation); } } */ } } return dib; } protected DisplayItemBean validateDisplayItemBeanSingleCV(RuleValidator v, DisplayItemBean dib, String inputName, ArrayList<String> messages) { if (StringUtil.isBlank(inputName)) { inputName = getInputName(dib); } ItemFormMetadataBean ibMeta = dib.getMetadata(); ItemDataBean idb = dib.getData(); if (StringUtil.isBlank(idb.getValue())) { if (ibMeta.isRequired() && ibMeta.isShowItem()) { v.addValidation(inputName, Validator.IS_REQUIRED); } v.addValidation(inputName, Validator.IS_AN_RULE, messages); } else { v.addValidation(inputName, Validator.IS_AN_RULE, messages); } // customValidation(v, dib, inputName); return dib; } /** * Peform validation on a item which has a RADIO or SINGLESELECTresponse type. This function checks that the input isn't blank, and that its value comes * from the controlled vocabulary (ResponseSetBean) in the DisplayItemBean. * * @param v * The Validator to add validations to. * @param dib * The DisplayItemBean to validate. * @return The DisplayItemBean which is validated. */ protected DisplayItemBean validateDisplayItemBeanSingleCV(DiscrepancyValidator v, DisplayItemBean dib, String inputName) { if (StringUtil.isBlank(inputName)) { inputName = getInputName(dib); } ItemFormMetadataBean ibMeta = dib.getMetadata(); ItemDataBean idb = dib.getData(); if (StringUtil.isBlank(idb.getValue())) { if (ibMeta.isRequired() && ibMeta.isShowItem()) { v.addValidation(inputName, Validator.IS_REQUIRED); } } else { v.addValidation(inputName, Validator.IN_RESPONSE_SET_SINGLE_VALUE, dib.getMetadata().getResponseSet()); } customValidation(v, dib, inputName); return dib; } //validate simple-conditional-display item to be changed from shown to hidden protected void validateShownSCDToBeHiddenSingle(DiscrepancyValidator v, DisplayItemBean dib) { ItemFormMetadataBean ifmb = dib.getMetadata(); String value = dib.getData().getValue(); boolean hasDN = dib.getDiscrepancyNotes() != null && dib.getDiscrepancyNotes().size() > 0 ? true : false; if (value != null && value.length() > 0 && !dib.getIsSCDtoBeShown() && !hasDN) { //String message = ifmb.getConditionalDisplay().replaceAll("\\\\,", "##").split(",")[2].trim(); //message = message.replaceAll("##", "\\,"); String message = dib.getScdData().getScdItemMetadataBean().getMessage(); Validation vl = new Validation(Validator.TO_HIDE_CONDITIONAL_DISPLAY); vl.setErrorMessage(message); v.addValidation(getInputName(dib), vl); } } /** * Peform validation on a item which has a RADIO or SINGLESELECT response type. This function checks that the input isn't blank, and that its value comes * from the controlled vocabulary (ResponseSetBean) in the DisplayItemBean. * * @param v * The Validator to add validations to. * @param dib * The DisplayItemBean to validate. * @return The DisplayItemBean which is validated. */ protected DisplayItemBean validateDisplayItemBeanMultipleCV(DiscrepancyValidator v, DisplayItemBean dib, String inputName) { if (StringUtil.isBlank(inputName)) { inputName = getInputName(dib); } ItemFormMetadataBean ibMeta = dib.getMetadata(); ItemDataBean idb = dib.getData(); if (StringUtil.isBlank(idb.getValue())) { if (ibMeta.isRequired() && ibMeta.isShowItem()) { v.addValidation(inputName, Validator.IS_REQUIRED); } } else { v.addValidation(inputName, Validator.IN_RESPONSE_SET, dib.getMetadata().getResponseSet()); } customValidation(v, dib, inputName); return dib; } /** * @param dib * A DisplayItemBean representing an input on the CRF. * @return The name of the input in the HTML form. */ public final String getInputName(DisplayItemBean dib) { ItemBean ib = dib.getItem(); String inputName = "input" + ib.getId(); return inputName; } /** * Creates an input name for an item data entry in an item group * * @param digb * @param dib * @return */ public final String getGroupItemInputName(DisplayItemGroupBean digb, int rowCount, int manualRows, DisplayItemBean dib) { int ordinal = rowCount - manualRows; String inputName = digb.getItemGroupBean().getOid() + "_" + ordinal + getInputName(dib); LOGGER.debug("===returning: " + inputName); return inputName; } public final String getGroupItemInputName(DisplayItemGroupBean digb, int ordinal, DisplayItemBean dib) { String inputName = digb.getItemGroupBean().getOid() + "_" + ordinal + getInputName(dib); LOGGER.debug("+++returning: " + inputName); return inputName; } /** * Writes data from the DisplayItemBean to the database. Note that if the bean contains an inactive ItemDataBean, the ItemDataBean is created; otherwise, * the ItemDataBean is updated. * * @param dib * The DisplayItemBean from which to write data. * @param iddao * The DAO to use to access the database. * @param request TODO * @return <code>true</code> if the query succeeded, <code>false</code> otherwise. */ protected boolean writeToDB(DisplayItemBean dib, ItemDataDAO iddao, int ordinal, HttpServletRequest request) { ItemDataBean idb = dib.getData(); EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); if (dib.getEditFlag() != null && "remove".equalsIgnoreCase(dib.getEditFlag()) && getItemMetadataService().isShown(idb.getItemId(), ecb, idb)) { getItemMetadataService().hideItem(dib.getMetadata(), ecb, idb); } else { if (getServletPage(request).equals(Page.DOUBLE_DATA_ENTRY_SERVLET)) { if (!dib.getMetadata().isShowItem() && !(dib.getScdData().getScdItemMetadataBean().getScdItemFormMetadataId() > 0) && idb.getValue().equals("") && !getItemMetadataService().hasPassedDDE(dib.getMetadata(), ecb, idb)) {//(dib.getItem().getId(), ecb, idb)) {// && !getItemMetadataService().isShown(dib.getItem().getId(), ecb, dib.getData())) { LOGGER.debug("*** not shown - not writing for idb id " + dib.getData().getId() + " and item id " + dib.getItem().getId()); return true; } } else { if (!dib.getMetadata().isShowItem() && idb.getValue().equals("") && !getItemMetadataService().isShown(dib.getItem().getId(), ecb, dib.getData()) && !(dib.getScdData().getScdItemMetadataBean().getScdItemFormMetadataId() > 0)) { LOGGER.debug("*** not shown - not writing for idb id " + dib.getData().getId() + " and item id " + dib.getItem().getId()); return true; } } } return writeToDB(idb, dib, iddao, ordinal, request); } protected boolean writeToDB(ItemDataBean itemData, DisplayItemBean dib, ItemDataDAO iddao, int ordinal, HttpServletRequest request) { ItemDataBean idb = itemData; UserAccountBean ub = (UserAccountBean) request.getSession().getAttribute(USER_BEAN_NAME); StudyBean currentStudy = (StudyBean) request.getSession().getAttribute("study"); EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); idb.setItemId(dib.getItem().getId()); idb.setEventCRFId(ecb.getId()); if (idb.getValue().equals("")) { idb.setStatus(getBlankItemStatus()); } else { idb.setStatus(getNonBlankItemStatus(request)); } if (StringUtils.isBlank(dib.getEditFlag())) { if (!idb.isActive()) { // will this need to change for double data entry? idb.setOrdinal(ordinal); idb.setCreatedDate(new Date()); idb.setOwner(ub); idb = (ItemDataBean) iddao.create(idb); } else { idb.setUpdater(ub); // tbh 5990: should we update the logic here for nonrepeats? // //System.out.println("string util is blank: update an item data " + idb.getId() + " :" + idb.getValue()); LOGGER.debug("update item update_id " + idb.getUpdater().getId()); idb = (ItemDataBean) iddao.updateValue(idb); } } else { // for the items in group, they have editFlag if ("add".equalsIgnoreCase(dib.getEditFlag())) { idb.setOrdinal(ordinal); idb.setCreatedDate(new Date()); idb.setOwner(ub); LOGGER.debug("create a new item data" + idb.getItemId() + idb.getValue()); // idb = (ItemDataBean) iddao.create(idb); // >>tbh 08/2008 idb.setUpdater(ub); // idb = (ItemDataBean) iddao.updateValue(idb); // instead of two hits to the db, we perform an 'upsert' // combining them into one idb = (ItemDataBean) iddao.upsert(idb); // <<tbh } else if ("edit".equalsIgnoreCase(dib.getEditFlag())) { idb.setUpdater(ub); // //System.out.println("update an item data - running update value " + idb.getId() + " :" + idb.getValue()); LOGGER.debug("update item update_id " + idb.getUpdater().getId()); // update tbh #5999, #5998; if an item_data was not included in // an import data, it won't exist; we need to check on item_data_id // to make sure we are running the correct command on the db if (idb.getId() != 0) { idb.setUpdatedDate(new Date()); idb = (ItemDataBean) iddao.updateValue(idb); } else { idb.setCreatedDate(new Date()); idb.setOrdinal(ordinal); idb.setOwner(ub); idb = (ItemDataBean) iddao.upsert(idb); LOGGER.debug("just ran upsert! " + idb.getId()); } } // else if ("remove".equalsIgnoreCase(dib.getEditFlag())) { // LOGGER.debug("REMOVE an item data" + idb.getItemId() + idb.getValue()); // idb.setUpdater(ub); // idb.setStatus(Status.DELETED); // idb = (ItemDataBean) iddao.updateValueForRemoved(idb); // // DiscrepancyNoteDAO dnDao = new DiscrepancyNoteDAO(getDataSource()); // List dnNotesOfRemovedItem = dnDao.findExistingNotesForItemData(idb.getId()); // if (!dnNotesOfRemovedItem.isEmpty()) { // DiscrepancyNoteBean itemParentNote = null; // for (Object obj : dnNotesOfRemovedItem) { // if (((DiscrepancyNoteBean) obj).getParentDnId() == 0) { // itemParentNote = (DiscrepancyNoteBean) obj; // } // } // DiscrepancyNoteBean dnb = new DiscrepancyNoteBean(); // if (itemParentNote != null) { // dnb.setParentDnId(itemParentNote.getId()); // dnb.setDiscrepancyNoteTypeId(itemParentNote.getDiscrepancyNoteTypeId()); // } // dnb.setResolutionStatusId(ResolutionStatus.CLOSED.getId()); // dnb.setStudyId(currentStudy.getId()); // dnb.setAssignedUserId(ub.getId()); // dnb.setOwner(ub); // dnb.setEntityType(DiscrepancyNoteBean.ITEM_DATA); // dnb.setEntityId(idb.getId()); // dnb.setCreatedDate(new Date()); // dnb.setColumn("value"); // dnb.setDescription("The item has been removed, this Discrepancy Note has been Closed."); // dnDao.create(dnb); // dnDao.createMapping(dnb); // itemParentNote.setResolutionStatusId(ResolutionStatus.CLOSED.getId()); // dnDao.update(itemParentNote); // } // } } return idb.isActive(); } protected String addAttachedFilePath(DisplayItemBean dib, String attachedFilePath) { String fileName = ""; ItemDataBean idb = dib.getData(); String itemDataValue = idb.getValue(); String dbValue = dib.getDbData().getValue(); ResponseSetBean rsb = dib.getMetadata().getResponseSet(); org.akaza.openclinica.bean.core.ResponseType rt = rsb.getResponseType(); if (rt.equals(org.akaza.openclinica.bean.core.ResponseType.FILE) && itemDataValue.length() > 0) { File file = new File(itemDataValue); fileName = file.getName(); if (itemDataValue.length() > fileName.length()) { // itemDataValue includes file path idb.setValue(itemDataValue); } else { File f = new File(dbValue); fileName = f.getName(); if (fileName.equals(itemDataValue) && dbValue.length() > itemDataValue.length()) { // since filename is unique by timestamp, re-upload will // append // another timestamp to the same filename idb.setValue(dbValue); } else { idb.setValue(attachedFilePath + itemDataValue); fileName = itemDataValue; } } } return fileName; } /** * Retrieve the status which should be assigned to ItemDataBeans which have blank values for this data entry servlet. */ protected abstract Status getBlankItemStatus(); // unavailable in admin. editing /** * Retrieve the status which should be assigned to ItemDataBeans which have non-blank values for this data entry servlet. * @param request TODO */ protected abstract Status getNonBlankItemStatus(HttpServletRequest request); // unavailable in admin. editing /** * Get the eventCRF's annotations as appropriate for this data entry servlet. * @param request TODO */ protected abstract String getEventCRFAnnotations(HttpServletRequest request); /** * Set the eventCRF's annotations properties as appropriate for this data entry servlet. * @param request TODO */ protected abstract void setEventCRFAnnotations(String annotations, HttpServletRequest request); /** * Retrieve the DisplaySectionBean which will be used to display the Event CRF Section on the JSP, and also is used to controll processRequest. * @param request TODO * @param isSubmitted TODO */ protected DisplaySectionBean getDisplayBean(boolean hasGroup, boolean includeUngroupedItems, HttpServletRequest request, boolean isSubmitted) throws Exception { DisplaySectionBean section = new DisplaySectionBean(); FormProcessor fp = new FormProcessor(request); HttpSession session = request.getSession(); Locale loc = this.locale == null ? LocaleResolver.getLocale(request) : this.locale; StudyBean study = (StudyBean) session.getAttribute("study"); SessionManager sm = (SessionManager) request.getSession().getAttribute("sm"); EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); SectionBean sb = (SectionBean) request.getAttribute(SECTION_BEAN); EventDefinitionCRFBean edcb = (EventDefinitionCRFBean) request.getAttribute(EVENT_DEF_CRF_BEAN); SectionDAO sdao; // Find out whether there are ungrouped items in this section boolean hasUngroupedItems = false; int eventDefinitionCRFId = fp.getInt("eventDefinitionCRFId"); if (eventDefinitionCRFId <= 0) { // TODO: this block of code repeats // many times, need to clean up //synchronized(this) { EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(getDataSource()); EventDefinitionCRFBean edcBean = edcdao.findByStudyEventIdAndCRFVersionId(study, ecb.getStudyEventId(), ecb.getCRFVersionId()); eventDefinitionCRFId = edcBean.getId(); } } LOGGER.trace("eventDefinitionCRFId " + eventDefinitionCRFId); // Use this class to find out whether there are ungrouped items in this // section FormBeanUtil formBeanUtil = new FormBeanUtil(); List<DisplayItemGroupBean> itemGroups = new ArrayList<DisplayItemGroupBean>(); if (hasGroup) { DisplaySectionBean newDisplayBean = new DisplaySectionBean(); if (includeUngroupedItems) { // Null values: this method adds null values to the // displayitembeans newDisplayBean = formBeanUtil.createDisplaySectionBWithFormGroups(sb.getId(), ecb.getCRFVersionId(), getDataSource(), eventDefinitionCRFId, ecb, getServletContext()); } else { newDisplayBean = formBeanUtil.createDisplaySectionWithItemGroups(study, sb.getId(), ecb, ecb.getStudyEventId(), sm, eventDefinitionCRFId, getServletContext()); } itemGroups = newDisplayBean.getDisplayFormGroups(); // setDataForDisplayItemGroups(itemGroups, sb,ecb,sm); LOGGER.trace( "found item group size: " + itemGroups.size() + " and to string: " + itemGroups.toString()); section.setDisplayFormGroups(itemGroups); } // Find out whether any display items are *not* grouped; see issue 1689 hasUngroupedItems = formBeanUtil.sectionHasUngroupedItems(getDataSource(), sb.getId(), itemGroups); sdao = new SectionDAO(getDataSource()); // sb.setHasSCDItem(hasUngroupedItems ? sdao.hasSCDItem(sb.getId()) : false); section.setEventCRF(ecb); if (sb.getParentId() > 0) { SectionBean parent = (SectionBean) sdao.findByPK(sb.getParentId()); sb.setParent(parent); } section.setSection(sb); CRFVersionDAO cvdao = new CRFVersionDAO(getDataSource()); CRFVersionBean cvb = (CRFVersionBean) cvdao.findByPK(ecb.getCRFVersionId()); section.setCrfVersion(cvb); CRFDAO cdao = new CRFDAO(getDataSource()); CRFBean cb = (CRFBean) cdao.findByPK(cvb.getCrfId()); section.setCrf(cb); EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(getDataSource()); // EventDefinitionCRFBean edcb = // edcdao.findByStudyEventIdAndCRFVersionId(study, // ecb.getStudyEventId(), cvb.getId()); section.setEventDefinitionCRF(edcb); // setup DAO's here to avoid creating too many objects ItemDAO idao = new ItemDAO(getDataSource()); ItemFormMetadataDAO ifmdao = new ItemFormMetadataDAO(getDataSource()); ItemDataDAO iddao = new ItemDataDAO(getDataSource(), loc); // Use itemGroups to determine if there are any ungrouped items // get all the parent display item beans not in group logMe("Entering getParentDisplayItems::: Thread is? " + Thread.currentThread()); ArrayList displayItems = getParentDisplayItems(hasGroup, sb, edcb, idao, ifmdao, iddao, hasUngroupedItems, request); logMe("Entering getParentDisplayItems::: Done and Thread is? " + Thread.currentThread()); LOGGER.debug("just ran get parent display, has group " + hasGroup + " has ungrouped " + hasUngroupedItems); // now sort them by ordinal, //JN: Commenting out this logic, its wrong and will give erroneous results. Collections.sort(displayItems); // now get the child DisplayItemBeans for (int i = 0; i < displayItems.size(); i++) { DisplayItemBean dib = (DisplayItemBean) displayItems.get(i); dib.setChildren(getChildrenDisplayItems(dib, edcb, request)); // TODO use the setData command here to make sure we get a value? //On Submition of the Admin Editing form the loadDBValue does not required // if (ecb.getStage() == DataEntryStage.INITIAL_DATA_ENTRY_COMPLETE || ecb.getStage() == DataEntryStage.DOUBLE_DATA_ENTRY_COMPLETE) { if (shouldLoadDBValues(dib) && !isSubmitted) { dib.loadDBValue(); } } else { if (shouldLoadDBValues(dib)) { LOGGER.trace("should load db values is true, set value"); dib.loadDBValue(); LOGGER.trace("just got data loaded: " + dib.getData().getValue()); } } displayItems.set(i, dib); } section.setItems(displayItems); return section; } /** * Retrieve the DisplaySectionBean which will be used to display the Event CRF Section on the JSP, and also is used to controll processRequest. * @param request TODO */ protected ArrayList getAllDisplayBeans(HttpServletRequest request) throws Exception { EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); ArrayList sections = new ArrayList(); HttpSession session = request.getSession(); StudyBean study = (StudyBean) session.getAttribute("study"); SectionDAO sdao = new SectionDAO(getDataSource()); ItemDataDAO iddao = new ItemDataDAO(getDataSource(), locale); // ALL_SECTION_BEANS ArrayList<SectionBean> allSectionBeans = (ArrayList<SectionBean>) request.getAttribute(ALL_SECTION_BEANS); for (int j = 0; j < allSectionBeans.size(); j++) { SectionBean sb = allSectionBeans.get(j); DisplaySectionBean section = new DisplaySectionBean(); section.setEventCRF(ecb); if (sb.getParentId() > 0) { SectionBean parent = (SectionBean) sdao.findByPK(sb.getParentId()); sb.setParent(parent); } section.setSection(sb); CRFVersionDAO cvdao = new CRFVersionDAO(getDataSource()); CRFVersionBean cvb = (CRFVersionBean) cvdao.findByPK(ecb.getCRFVersionId()); section.setCrfVersion(cvb); CRFDAO cdao = new CRFDAO(getDataSource()); CRFBean cb = (CRFBean) cdao.findByPK(cvb.getCrfId()); section.setCrf(cb); EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(getDataSource()); EventDefinitionCRFBean edcb = edcdao.findByStudyEventIdAndCRFVersionId(study, ecb.getStudyEventId(), cvb.getId()); section.setEventDefinitionCRF(edcb); // setup DAO's here to avoid creating too many objects ItemDAO idao = new ItemDAO(getDataSource()); ItemFormMetadataDAO ifmdao = new ItemFormMetadataDAO(getDataSource()); iddao = new ItemDataDAO(getDataSource(), locale); // get all the display item beans ArrayList displayItems = getParentDisplayItems(false, sb, edcb, idao, ifmdao, iddao, false, request); LOGGER.debug("222 just ran get parent display, has group " + " FALSE has ungrouped FALSE"); // now sort them by ordinal Collections.sort(displayItems); // now get the child DisplayItemBeans for (int i = 0; i < displayItems.size(); i++) { DisplayItemBean dib = (DisplayItemBean) displayItems.get(i); dib.setChildren(getChildrenDisplayItems(dib, edcb, request)); if (shouldLoadDBValues(dib)) { LOGGER.trace("should load db values is true, set value"); dib.loadDBValue(); } displayItems.set(i, dib); } section.setItems(displayItems); sections.add(section); } return sections; } /** * For each single item in this section which is a parent, get a DisplayItemBean corresponding to that item. Note that an item is a parent iff its parentId * == 0. * @param sb * The section whose items we are retrieving. * @param hasUngroupedItems * @param request TODO * * @return An array of DisplayItemBean objects, one per parent item in the section. Note that there is no guarantee on the ordering of the objects. * @throws Exception */ private ArrayList getParentDisplayItems(boolean hasGroup, SectionBean sb, EventDefinitionCRFBean edcb, ItemDAO idao, ItemFormMetadataDAO ifmdao, ItemDataDAO iddao, boolean hasUngroupedItems, HttpServletRequest request) throws Exception { ArrayList answer = new ArrayList(); EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); HashMap displayItems = new HashMap(); // ArrayList items = idao.findAllParentsBySectionId(sb.getId()); ArrayList items = new ArrayList(); ArrayList itemsUngrped = new ArrayList(); if (hasGroup) { // issue 1689: this method causes problems with items that have // been defined as grouped, then redefined as ungrouped; thus it // is "checked twice" with hasUngroupedItems. // See: FormBeanUtil.sectionHasUngroupedItems. if (hasUngroupedItems) { // @pgawade 05-Aug-2011 fix for issue 10628 - commented out the // if-else logic based on 'hasGroup' flag. // 'if' part is unchanged but else part is changed to be // executed always because that is to get the non-repeating and // ungrouped item details and was getting skipped in case the // section has repeating group items plus non-repeating group // items itemsUngrped = idao.findAllUngroupedParentsBySectionId(sb.getId(), sb.getCRFVersionId()); } // however, if we have true:true, we exclude all grouped items // items.addAll( // idao.findAllGroupedParentsBySectionId( // sb.getId(), sb.getCRFVersionId())); } // else { LOGGER.trace("no item groups"); // items = idao.findAllParentsBySectionId(sb.getId()); items = idao.findAllNonRepeatingParentsBySectionId(sb.getId()); items.addAll(itemsUngrped); // } LOGGER.debug("items size" + items.size()); for (int i = 0; i < items.size(); i++) { DisplayItemBean dib = new DisplayItemBean(); dib.setEventDefinitionCRF(edcb); ItemBean ib = (ItemBean) items.get(i); dib.setItem(ib); displayItems.put(new Integer(dib.getItem().getId()), dib); } ArrayList data = iddao.findAllBySectionIdAndEventCRFId(sb.getId(), ecb.getId()); for (int i = 0; i < data.size(); i++) { ItemDataBean idb = (ItemDataBean) data.get(i); DisplayItemBean dib = (DisplayItemBean) displayItems.get(new Integer(idb.getItemId())); if (dib != null) { dib.setData(idb); dib.setDbData((ItemDataBean) BeanUtils.cloneBean(idb)); displayItems.put(new Integer(idb.getItemId()), dib); } } ArrayList metadata = ifmdao.findAllBySectionId(sb.getId()); for (int i = 0; i < metadata.size(); i++) { ItemFormMetadataBean ifmb = (ItemFormMetadataBean) metadata.get(i); DisplayItemBean dib = (DisplayItemBean) displayItems.get(new Integer(ifmb.getItemId())); if (dib != null) { // boolean showItem = false; boolean needsHighlighting = !ifmb.isShowItem(); logMe("Entering thread before getting ItemMetadataService:::" + Thread.currentThread()); boolean showItem = getItemMetadataService().isShown(ifmb.getItemId(), ecb, dib.getData()); if (getServletPage(request).equals(Page.DOUBLE_DATA_ENTRY_SERVLET)) { showItem = getItemMetadataService().hasPassedDDE(ifmb, ecb, dib.getData()); } // is the above needed for children items too? boolean passedDDE = getItemMetadataService().hasPassedDDE(ifmb, ecb, dib.getData()); if (showItem) { // we are only showing, not hiding LOGGER.debug("set show item " + ifmb.getItemId() + " idb " + dib.getData().getId() + " show item " + showItem + " passed dde " + passedDDE); // ifmb.setShowItem(showItem); ifmb.setShowItem(true); } else { LOGGER.debug("DID NOT set show item " + ifmb.getItemId() + " idb " + dib.getData().getId() + " show item " + showItem + " passed dde " + passedDDE + " value " + dib.getData().getValue()); } dib.setMetadata(ifmb); displayItems.put(new Integer(ifmb.getItemId()), dib); } } Iterator hmIt = displayItems.keySet().iterator(); while (hmIt.hasNext()) { Integer key = (Integer) hmIt.next(); DisplayItemBean dib = (DisplayItemBean) displayItems.get(key); answer.add(dib); LOGGER.debug( "*** getting with key: " + key + " display item bean with value: " + dib.getData().getValue()); } LOGGER.debug("*** test of the display items: " + displayItems.toString()); return answer; } /** * Get the DisplayItemBean objects corresponding to the items which are children of the specified parent. * * @param parent * The item whose children are to be retrieved. * @param request TODO * @return An array of DisplayItemBean objects corresponding to the items which are children of parent, and are sorted by column number (ascending), then * ordinal (ascending). */ private ArrayList getChildrenDisplayItems(DisplayItemBean parent, EventDefinitionCRFBean edcb, HttpServletRequest request) { ArrayList answer = new ArrayList(); EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); int parentId = parent.getItem().getId(); ItemDAO idao = new ItemDAO(getDataSource()); ArrayList childItemBeans = idao.findAllByParentIdAndCRFVersionId(parentId, ecb.getCRFVersionId()); ItemDataDAO iddao = new ItemDataDAO(getDataSource(), locale); ItemFormMetadataDAO ifmdao = new ItemFormMetadataDAO(getDataSource()); for (int i = 0; i < childItemBeans.size(); i++) { ItemBean child = (ItemBean) childItemBeans.get(i); ItemDataBean data = iddao.findByItemIdAndEventCRFId(child.getId(), ecb.getId()); ItemFormMetadataBean metadata = ifmdao.findByItemIdAndCRFVersionId(child.getId(), ecb.getCRFVersionId()); DisplayItemBean dib = new DisplayItemBean(); dib.setEventDefinitionCRF(edcb); dib.setItem(child); // tbh if (!getServletPage(request).equals(Page.DOUBLE_DATA_ENTRY_SERVLET)) { dib.setData(data); } // <<tbh 07/2009, bug #3883 // ItemDataBean dbData = iddao.findByItemIdAndEventCRFIdAndOrdinal(itemId, eventCRFId, ordinal) dib.setDbData(data); boolean showItem = getItemMetadataService().isShown(metadata.getItemId(), ecb, data); if (getServletPage(request).equals(Page.DOUBLE_DATA_ENTRY_SERVLET)) { showItem = getItemMetadataService().hasPassedDDE(metadata, ecb, data); } //else { // showItem = getItemMetadataService().isShown(metadata.getItemId(), ecb, dib.getDbData()); // } // boolean passedDDE = getItemMetadataService().hasPassedDDE(data); if (showItem) { LOGGER.debug("set show item: " + metadata.getItemId() + " data " + data.getId()); // metadata.setShowItem(showItem); metadata.setShowItem(true); } // logger.debug("did not catch NPE"); dib.setMetadata(metadata); if (shouldLoadDBValues(dib)) { LOGGER.trace("should load db values is true, set value"); dib.loadDBValue(); LOGGER.trace("just loaded the child value: " + dib.getData().getValue()); } answer.add(dib); } // this is a pretty slow and memory intensive way to sort... see if we // can // have the db do this instead Collections.sort(answer); return answer; } /** * gets the available dynamics service */ public DynamicsMetadataService getItemMetadataService() { DynamicsMetadataService itemMetadataService = null; itemMetadataService = itemMetadataService != null ? itemMetadataService : (DynamicsMetadataService) SpringServletAccess.getApplicationContext(getServletContext()) .getBean("dynamicsMetadataService"); return itemMetadataService; } /** * @return The Page object which represents this servlet's JSP. */ protected abstract Page getJSPPage(); /** * @param request TODO * @return The Page object which represents this servlet. */ protected abstract String getServletPage(HttpServletRequest request); protected abstract boolean shouldLoadDBValues(DisplayItemBean dib); protected void setUpPanel(DisplaySectionBean section) { resetPanel(); panel.setStudyInfoShown(false); panel.setOrderedData(true); } /* * change to explicitly re-set the section bean after reviewing the disc note counts, tbh 01/2010 */ protected DisplaySectionBean populateNotesWithDBNoteCounts(FormDiscrepancyNotes discNotes, DisplaySectionBean section, HttpServletRequest request) { DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(getDataSource()); // ArrayList items = section.getItems(); EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); ArrayList<DiscrepancyNoteBean> ecNotes = dndao.findEventCRFDNotesFromEventCRF(ecb); ArrayList<DiscrepancyNoteBean> existingNameNotes = new ArrayList(), nameNotes = new ArrayList(); ArrayList<DiscrepancyNoteBean> existingIntrvDateNotes = new ArrayList(), dateNotes = new ArrayList(); long t = System.currentTimeMillis(); logMe("Method:populateNotesWithDBNoteCounts" + t); int intNew = 0, intRes = 0, intUpdated = 0, intClosed = 0, intNA = 0; int dateNew = 0, dateRes = 0, dateUpdated = 0, dateClosed = 0, dateNA = 0; boolean hasMoreThreads = false; for (int i = 0; i < ecNotes.size(); i++) { DiscrepancyNoteBean dn = ecNotes.get(i); if (INTERVIEWER_NAME.equalsIgnoreCase(dn.getColumn())) { discNotes.setNumExistingFieldNotes(INPUT_INTERVIEWER, 1); request.setAttribute("hasNameNote", "yes"); request.setAttribute(INTERVIEWER_NAME_NOTE, dn); if (dn.getParentDnId() == 0) existingNameNotes.add(dn); } if (DATE_INTERVIEWED.equalsIgnoreCase(dn.getColumn())) { discNotes.setNumExistingFieldNotes(INPUT_INTERVIEW_DATE, 1); request.setAttribute("hasDateNote", "yes"); request.setAttribute(INTERVIEWER_DATE_NOTE, dn); if (dn.getParentDnId() == 0) existingIntrvDateNotes.add(dn); } } logMe("Method:populateNotesWithDBNoteCounts before calling setToolTipEventNotes" + System.currentTimeMillis() + "time took:" + (System.currentTimeMillis() - t)); setToolTipEventNotes(request); request.setAttribute("nameNoteResStatus", getDiscrepancyNoteResolutionStatus(existingNameNotes)); request.setAttribute("IntrvDateNoteResStatus", getDiscrepancyNoteResolutionStatus(existingIntrvDateNotes)); request.setAttribute("existingNameNotes", existingNameNotes); request.setAttribute("existingIntrvDateNotes", existingIntrvDateNotes); List<DisplayItemWithGroupBean> allItems = section.getDisplayItemGroups(); LOGGER.debug("start to populate notes: " + section.getDisplayItemGroups().size()); this.output(allItems); logMe("Looping through allItems time:" + System.currentTimeMillis() + "time took from the begining" + (System.currentTimeMillis() - t)); for (int k = 0; k < allItems.size(); k++) { DisplayItemWithGroupBean itemWithGroup = allItems.get(k); if (itemWithGroup.isInGroup()) { LOGGER.debug("group item DNote..."); List<DisplayItemGroupBean> digbs = itemWithGroup.getItemGroups(); LOGGER.trace("digbs size: " + digbs.size()); for (int i = 0; i < digbs.size(); i++) { DisplayItemGroupBean displayGroup = digbs.get(i); List<DisplayItemBean> items = displayGroup.getItems(); for (int j = 0; j < items.size(); j++) { DisplayItemBean dib = items.get(j); int itemDataId = dib.getData().getId(); int numNotes = dndao.findNumExistingNotesForItem(itemDataId); int numNotes1 = dndao.findNumOfActiveExistingNotesForItemData(itemDataId); int ordinal = this.getManualRows(digbs); String inputName = getGroupItemInputName(displayGroup, displayGroup.getFormInputOrdinal(), dib); if (!displayGroup.isAuto()) { inputName = getGroupItemManualInputName(displayGroup, i, dib); } discNotes.setNumExistingFieldNotes(inputName, numNotes1); ArrayList notes = discNotes.getNotes(inputName); dib.setNumDiscrepancyNotes(numNotes + notes.size());// + notes2.size()); dib.setDiscrepancyNoteStatus(getDiscrepancyNoteResolutionStatus(itemDataId, notes)); dib = setTotals(dib, itemDataId, notes, ecb.getId()); LOGGER.debug("dib note size:" + dib.getNumDiscrepancyNotes() + " " + dib.getData().getId() + " " + inputName); items.set(j, dib); } displayGroup.setItems(items); digbs.set(i, displayGroup); } itemWithGroup.setItemGroups(digbs); } else { LOGGER.trace("single item db note"); DisplayItemBean dib = itemWithGroup.getSingleItem(); try { ResponseOptionBean rob = (ResponseOptionBean) dib.getMetadata().getResponseSet().getOptions() .get(0); LOGGER.trace("test print of options for coding: " + rob.getValue()); } catch (NullPointerException e) { // TODO Auto-generated catch block // e.printStackTrace(); } int itemDataId = dib.getData().getId(); int itemId = dib.getItem().getId(); int numNotes = dndao.findNumExistingNotesForItem(itemDataId); int numNotes1 = dndao.findNumOfActiveExistingNotesForItemData(itemDataId); String inputFieldName = "input" + itemId; discNotes.setNumExistingFieldNotes(inputFieldName, numNotes1); dib.setNumDiscrepancyNotes(numNotes + discNotes.getNotes(inputFieldName).size()); dib.setDiscrepancyNoteStatus( getDiscrepancyNoteResolutionStatus(itemDataId, discNotes.getNotes(inputFieldName))); dib = setTotals(dib, itemDataId, discNotes.getNotes(inputFieldName), ecb.getId()); ArrayList childItems = dib.getChildren(); for (int j = 0; j < childItems.size(); j++) { DisplayItemBean child = (DisplayItemBean) childItems.get(j); int childItemDataId = child.getData().getId(); int childItemId = child.getItem().getId(); int childNumNotes = dndao.findNumExistingNotesForItem(childItemDataId); String childInputFieldName = "input" + childItemId; LOGGER.debug("*** setting " + childInputFieldName); discNotes.setNumExistingFieldNotes(childInputFieldName, childNumNotes); child.setNumDiscrepancyNotes(childNumNotes + discNotes.getNotes(childInputFieldName).size()); child.setDiscrepancyNoteStatus(getDiscrepancyNoteResolutionStatus(childItemDataId, discNotes.getNotes(childInputFieldName))); child = setTotals(child, childItemDataId, discNotes.getNotes(childInputFieldName), ecb.getId()); childItems.set(j, child); } dib.setChildren(childItems); itemWithGroup.setSingleItem(runDynamicsItemCheck(dib, null, request)); } // missing piece of the puzzle - reset the itemgroup into all items? allItems.set(k, itemWithGroup); } section.setDisplayItemGroups(allItems); return section; } private void setToolTipEventNotes(HttpServletRequest request) { long t = System.currentTimeMillis(); logMe("Method:setToolTipEventNotes" + t); DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(getDataSource()); EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); ArrayList<DiscrepancyNoteBean> ecNotes = dndao.findEventCRFDNotesToolTips(ecb); ArrayList<DiscrepancyNoteBean> nameNotes = new ArrayList(); ArrayList<DiscrepancyNoteBean> dateNotes = new ArrayList(); for (int i = 0; i < ecNotes.size(); i++) { DiscrepancyNoteBean dn = ecNotes.get(i); if (INTERVIEWER_NAME.equalsIgnoreCase(dn.getColumn())) { nameNotes.add(dn); } if (DATE_INTERVIEWED.equalsIgnoreCase(dn.getColumn())) { dateNotes.add(dn); } } request.setAttribute("nameNotes", nameNotes); request.setAttribute("intrvDates", dateNotes); logMe("existing Method:setToolTipEventNotes, time took" + (System.currentTimeMillis() - t)); } /** * To set the totals of each resolution status on the DisplayItemBean for each item. * @param dib * @param notes * @param ecbId TODO */ private DisplayItemBean setTotals(DisplayItemBean dib, int itemDataId, ArrayList<DiscrepancyNoteBean> notes, int ecbId) { long t = System.currentTimeMillis(); logMe("Method::::::setTotals" + t); int resolutionStatus; int totNew = 0, totRes = 0, totClosed = 0, totUpdated = 0, totNA = 0; boolean hasOtherThread = false; DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(getDataSource()); ArrayList<DiscrepancyNoteBean> existingNotes = dndao.findExistingNotesForToolTip(itemDataId); dib.setDiscrepancyNotes(existingNotes); for (DiscrepancyNoteBean obj : dib.getDiscrepancyNotes()) { DiscrepancyNoteBean note = obj; if (note.getParentDnId() == 0) { resolutionStatus = note.getResolutionStatusId(); totNew++;//using totNew to show the total parent threads /* if(resolutionStatus==ResolutionStatus.UPDATED.getId())totUpdated++; else if(resolutionStatus==ResolutionStatus.RESOLVED.getId())totRes++;//Resolution proposed count else if(resolutionStatus==ResolutionStatus.CLOSED.getId())totClosed++; else if(resolutionStatus==ResolutionStatus.NOT_APPLICABLE.getId())totNA++;*/// not needed any more } } ArrayList parentNotes = dndao.findExistingNotesForItemData(itemDataId); //Adding this to show the value of only parent threads on discrepancy notes tool tip for (Object obj : parentNotes) { DiscrepancyNoteBean note = (DiscrepancyNoteBean) obj; /*We would only take the resolution status of the parent note of any note thread. If there * are more than one note thread, the thread with the worst resolution status will be taken.*/ if (note.getParentDnId() == 0) { if (hasOtherThread) { totNew++; } hasOtherThread = true; } } logMe("time taken thus far, before audit log check" + (System.currentTimeMillis() - t)); long t1 = System.currentTimeMillis(); AuditDAO adao = new AuditDAO(getDataSource()); ArrayList itemAuditEvents = adao.checkItemAuditEventsExist(dib.getItem().getId(), "item_data", ecbId); if (itemAuditEvents.size() > 0) { AuditBean itemFirstAudit = (AuditBean) itemAuditEvents.get(0); String firstRFC = itemFirstAudit.getReasonForChange(); String oldValue = itemFirstAudit.getOldValue(); if (firstRFC != null && "initial value".equalsIgnoreCase(firstRFC) && (oldValue == null || oldValue.isEmpty())) { dib.getData().setAuditLog(false); } else { dib.getData().setAuditLog(true); } } logMe("time taken thus far, after audit log check" + (System.currentTimeMillis() - t)); logMe("Only for audit check::" + (System.currentTimeMillis() - t1)); dib.setTotNew(totNew);//totNew is used for parent thread count dib.setTotRes(totRes); dib.setTotUpdated(totUpdated); dib.setTotClosed(totClosed); dib.setTotNA(totNA); logMe("returning back..time taken" + (System.currentTimeMillis() - t)); return dib; } /** * The following methods are for 'mark CRF complete' * @param request TODO * * @return */ protected boolean markCRFComplete(HttpServletRequest request) throws Exception { locale = LocaleResolver.getLocale(request); HttpSession session = request.getSession(); UserAccountBean ub = (UserAccountBean) request.getSession().getAttribute(USER_BEAN_NAME); EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); EventDefinitionCRFBean edcb = (EventDefinitionCRFBean) request.getAttribute(EVENT_DEF_CRF_BEAN); EventCRFDAO ecdao = new EventCRFDAO(getDataSource()); ItemDataDAO iddao = new ItemDataDAO(getDataSource(), locale); // < respage = // ResourceBundle.getBundle("org.akaza.openclinica.i18n.page_messages", // locale); // < restext = // ResourceBundle.getBundle("org.akaza.openclinica.i18n.notes",locale); // < // resexception=ResourceBundle.getBundle( // "org.akaza.openclinica.i18n.exceptions",locale); getEventCRFBean(request); getEventDefinitionCRFBean(request); DataEntryStage stage = ecb.getStage(); // request.setAttribute(TableOfContentsServlet.INPUT_EVENT_CRF_BEAN, // ecb); // request.setAttribute(INPUT_EVENT_CRF_ID, new Integer(ecb.getId())); LOGGER.trace("inout_event_crf_id:" + ecb.getId()); if (stage.equals(DataEntryStage.UNCOMPLETED) || stage.equals(DataEntryStage.DOUBLE_DATA_ENTRY_COMPLETE) || stage.equals(DataEntryStage.LOCKED)) { addPageMessage(respage.getString("not_mark_CRF_complete1"), request); return false; } if (stage.equals(DataEntryStage.INITIAL_DATA_ENTRY_COMPLETE) || stage.equals(DataEntryStage.DOUBLE_DATA_ENTRY)) { if (!edcb.isDoubleEntry()) { addPageMessage(respage.getString("not_mark_CRF_complete2"), request); return false; } } /* * if (!isEachSectionReviewedOnce()) { addPageMessage("You may not mark this Event CRF complete, because there are some sections which have not been * reviewed once."); return false; } */ if (isEachRequiredFieldFillout(request) == false) { addPageMessage(respage.getString("not_mark_CRF_complete4"), request); return false; } /* * if (ecb.getInterviewerName().trim().equals("")) { throw new InconsistentStateException(errorPage, "You may not mark this Event CRF complete, because * the interviewer name is blank."); } */ Status newStatus = ecb.getStatus(); boolean ide = true; if (stage.equals(DataEntryStage.INITIAL_DATA_ENTRY) && edcb.isDoubleEntry()) { newStatus = Status.PENDING; ecb.setUpdaterId(ub.getId()); ecb.setUpdater(ub); ecb.setUpdatedDate(new Date()); ecb.setDateCompleted(new Date()); } else if (stage.equals(DataEntryStage.INITIAL_DATA_ENTRY) && !edcb.isDoubleEntry()) { newStatus = Status.UNAVAILABLE; ecb.setUpdaterId(ub.getId()); ecb.setUpdater(ub); ecb.setUpdatedDate(new Date()); ecb.setDateCompleted(new Date()); ecb.setDateValidateCompleted(new Date()); } else if (stage.equals(DataEntryStage.DOUBLE_DATA_ENTRY_COMPLETE) && edcb.isDoubleEntry()) { newStatus = Status.UNAVAILABLE; ecb.setUpdaterId(ub.getId()); ecb.setUpdater(ub); ecb.setUpdatedDate(new Date()); ecb.setDateCompleted(new Date()); ecb.setDateValidateCompleted(new Date()); ide = false; } else if (stage.equals(DataEntryStage.INITIAL_DATA_ENTRY_COMPLETE) || stage.equals(DataEntryStage.DOUBLE_DATA_ENTRY)) { newStatus = Status.UNAVAILABLE; ecb.setDateValidateCompleted(new Date()); ide = false; } // for the non-reviewed sections, no item data in DB yet, need to // create them if (!isEachSectionReviewedOnce(request)) { boolean canSave = saveItemsToMarkComplete(newStatus, request); if (canSave == false) { addPageMessage(respage.getString("not_mark_CRF_complete3"), request); return false; } } ecb.setStatus(newStatus); /* * Marking the data entry as signed if the corresponding EventDefinitionCRF is being enabled for electronic signature. */ if (edcb.isElectronicSignature()) { ecb.setElectronicSignatureStatus(true); } ecb = (EventCRFBean) ecdao.update(ecb); // note the below statement only updates the DATES, not the STATUS ecdao.markComplete(ecb, ide); // update all the items' status to complete iddao.updateStatusByEventCRF(ecb, newStatus); // change status for study event StudyEventDAO sedao = new StudyEventDAO(getDataSource()); StudyEventBean seb = (StudyEventBean) sedao.findByPK(ecb.getStudyEventId()); seb.setUpdatedDate(new Date()); seb.setUpdater(ub); EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(getDataSource()); ArrayList allCRFs = ecdao.findAllByStudyEventAndStatus(seb, Status.UNAVAILABLE); StudyBean study = (StudyBean) session.getAttribute("study"); ArrayList allEDCs = (ArrayList) edcdao.findAllActiveByEventDefinitionId(study, seb.getStudyEventDefinitionId()); CRFVersionDAO crfversionDao = new CRFVersionDAO(getDataSource()); boolean eventCompleted = true; boolean allRequired = true; //JN Adding another flag boolean allCrfsCompleted = false; int allEDCsize = allEDCs.size(); ArrayList nonRequiredCrfIds = new ArrayList(); ArrayList requiredCrfIds = new ArrayList(); if (allCRFs.size() == allEDCs.size()) {// was //JN: all crfs are completed and then set the subject event status as complete seb.setSubjectEventStatus(SubjectEventStatus.COMPLETED); } seb = (StudyEventBean) sedao.update(seb); request.setAttribute(INPUT_EVENT_CRF, ecb); request.setAttribute(EVENT_DEF_CRF_BEAN, edcb); return true; } private void getEventCRFBean(HttpServletRequest request) { EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); FormProcessor fp = new FormProcessor(request); int eventCRFId = fp.getInt(INPUT_EVENT_CRF_ID); EventCRFDAO ecdao = new EventCRFDAO(getDataSource()); ecb = (EventCRFBean) ecdao.findByPK(eventCRFId); } protected boolean isEachRequiredFieldFillout(HttpServletRequest request) { HttpSession session = request.getSession(); EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(getDataSource()); // need to update this method to accomodate dynamics, tbh ItemDataDAO iddao = new ItemDataDAO(getDataSource(), locale); ItemDAO idao = new ItemDAO(getDataSource()); ItemFormMetadataDAO itemFormMetadataDao = new ItemFormMetadataDAO(getDataSource()); int allRequiredNum = idao.findAllRequiredByCRFVersionId(ecb.getCRFVersionId()); int allRequiredFilledOut = iddao.findAllRequiredByEventCRFId(ecb); int allRequiredButHidden = itemFormMetadataDao.findCountAllHiddenByCRFVersionId(ecb.getCRFVersionId()); int allHiddenButShown = itemFormMetadataDao.findCountAllHiddenButShownByEventCRFId(ecb.getId()); // add all hidden items minus all hidden but now shown items to the allRequiredFilledOut variable if (allRequiredNum > allRequiredFilledOut + allRequiredButHidden - allHiddenButShown) { LOGGER.debug("using crf version number: " + ecb.getCRFVersionId()); LOGGER.debug("allRequiredNum > allRequiredFilledOut:" + allRequiredNum + " " + allRequiredFilledOut + " plus " + allRequiredButHidden + " minus " + allHiddenButShown); return false; } // had to change the query below to allow for hidden items here, tbh 04/2010 ArrayList allFilled = iddao.findAllBlankRequiredByEventCRFId(ecb.getId(), ecb.getCRFVersionId()); int numNotes = 0; if (!allFilled.isEmpty()) { LOGGER.trace("allFilled is not empty"); FormDiscrepancyNotes fdn = (FormDiscrepancyNotes) session .getAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME); HashMap idNotes = fdn.getIdNotes(); for (int i = 0; i < allFilled.size(); i++) { ItemDataBean idb = (ItemDataBean) allFilled.get(i); int exsitingNotes = dndao.findNumExistingNotesForItem(idb.getId()); if (exsitingNotes > 0) { LOGGER.trace("has existing note"); numNotes++; } else if (idNotes.containsKey(idb.getId())) { LOGGER.trace("has note in session"); numNotes++; } } LOGGER.trace("numNotes allFilled.size:" + numNotes + " " + allFilled.size()); if (numNotes >= allFilled.size()) { LOGGER.trace("all required are filled out"); return true; } else { LOGGER.debug("numNotes < allFilled.size() " + numNotes + ": " + allFilled.size()); return false; } } return true; } /** * 06/13/2007- jxu Since we don't require users to review each section before mark a CRF as complete, we need to create item data in the database because * items will not be created unless the section which contains the items is reviewed by users * @param request TODO */ private boolean saveItemsToMarkComplete(Status completeStatus, HttpServletRequest request) throws Exception { EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); SectionDAO sdao = new SectionDAO(getDataSource()); ArrayList sections = sdao.findAllByCRFVersionId(ecb.getCRFVersionId()); UserAccountBean ub = (UserAccountBean) request.getSession().getAttribute(USER_BEAN_NAME); ItemDataDAO iddao = new ItemDataDAO(getDataSource(), locale); ItemDAO idao = new ItemDAO(getDataSource()); for (int i = 0; i < sections.size(); i++) { SectionBean sb = (SectionBean) sections.get(i); if (!isCreateItemReqd(sb, request)) { // ArrayList requiredItems = // idao.findAllRequiredBySectionId(sb.getId()); // if (!requiredItems.isEmpty()) { // return false; // } ArrayList items = idao.findAllBySectionId(sb.getId()); for (int j = 0; j < items.size(); j++) { ItemBean item = (ItemBean) items.get(j); ArrayList<ItemDataBean> itemBean = iddao.findAllByEventCRFIdAndItemIdNoStatus(ecb.getId(), item.getId()); ItemDataBean idb = new ItemDataBean(); idb.setItemId(item.getId()); idb.setEventCRFId(ecb.getId()); idb.setCreatedDate(new Date()); idb.setOrdinal(1); idb.setOwner(ub); if (completeStatus != null) {// to avoid null exception idb.setStatus(completeStatus); } else { idb.setStatus(Status.UNAVAILABLE); } idb.setValue(""); boolean save = true; if (itemBean.size() > 0) save = false; /* while(itemBean.iterator().hasNext()) { ItemDataBean temp = itemBean.iterator().next(); if(idb.getEventCRFId()==(temp.getEventCRFId())) { if(idb.getItemId()==(temp.getItemId())){ save = false; } } }*/ if (save) { iddao.create(idb); } } } } return true; } /** * Checks if a section is reviewed at least once by user * updated tbh 03/2011, to fix duplicates issues * @param sb * @param request TODO * @return */ protected boolean isSectionReviewedOnce(SectionBean sb, HttpServletRequest request) { SectionDAO sdao = new SectionDAO(getDataSource()); EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); EventDefinitionCRFBean edcb = (EventDefinitionCRFBean) request.getAttribute(EVENT_DEF_CRF_BEAN); DataEntryStage stage = ecb.getStage(); HashMap numItemsHM = sdao.getNumItemsBySectionId(); HashMap numItemsPendingHM = sdao.getNumItemsPendingBySectionId(ecb); HashMap numItemsCompletedHM = sdao.getNumItemsCompletedBySectionId(ecb); HashMap numItemsBlankHM = sdao.getNumItemsBlankBySectionId(ecb); Integer key = new Integer(sb.getId()); int numItems = TableOfContentsServlet.getIntById(numItemsHM, key); int numItemsPending = TableOfContentsServlet.getIntById(numItemsPendingHM, key); int numItemsCompleted = TableOfContentsServlet.getIntById(numItemsCompletedHM, key); int numItemsBlank = TableOfContentsServlet.getIntById(numItemsBlankHM, key); LOGGER.debug(" for " + key + " num items " + numItems + " num items blank " + numItemsBlank + " num items pending " + numItemsPending + " completed " + numItemsCompleted); if (stage.equals(DataEntryStage.INITIAL_DATA_ENTRY) && edcb.isDoubleEntry()) { if (numItemsPending == 0 && numItems > 0) { LOGGER.debug("returns false on ide loop " + key); return false; } } else { if (numItemsCompleted == 0 && numItems > 0) { LOGGER.debug("returns false on other loop " + key); return false; } } return true; } protected boolean isCreateItemReqd(SectionBean sb, HttpServletRequest request) { SectionDAO sdao = new SectionDAO(getDataSource()); EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); EventDefinitionCRFBean edcb = (EventDefinitionCRFBean) request.getAttribute(EVENT_DEF_CRF_BEAN); DataEntryStage stage = ecb.getStage(); HashMap numItemsHM = sdao.getNumItemsBySectionId(); HashMap numItemsPendingHM = sdao.getNumItemsPendingBySectionId(ecb); HashMap numItemsCompletedHM = sdao.getNumItemsCompletedBySection(ecb); HashMap numItemsBlankHM = sdao.getNumItemsBlankBySectionId(ecb); Integer key = new Integer(sb.getId()); int numItems = TableOfContentsServlet.getIntById(numItemsHM, key); int numItemsPending = TableOfContentsServlet.getIntById(numItemsPendingHM, key); int numItemsCompleted = TableOfContentsServlet.getIntById(numItemsCompletedHM, key); int numItemsBlank = TableOfContentsServlet.getIntById(numItemsBlankHM, key); LOGGER.debug(" for " + key + " num items " + numItems + " num items blank " + numItemsBlank + " num items pending " + numItemsPending + " completed " + numItemsCompleted); if (stage.equals(DataEntryStage.INITIAL_DATA_ENTRY) && edcb.isDoubleEntry()) { if (numItemsPending == 0 && numItems > 0) { // System.out.println("returns false on ide loop " + key); return false; } } else { if (numItemsCompleted < numItems) { return false; } } return true; } /** * Checks if all the sections in an event crf are reviewed once * tbh updated to prevent duplicates, 03/2011 * @param request TODO * * @return */ protected boolean isEachSectionReviewedOnce(HttpServletRequest request) { SectionDAO sdao = new SectionDAO(getDataSource()); EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); DataEntryStage stage = ecb.getStage(); EventDefinitionCRFBean edcb = (EventDefinitionCRFBean) request.getAttribute(EVENT_DEF_CRF_BEAN); // below block changed tbh 04/2011, to remove repeating items generated by mistake ArrayList<SectionBean> sections = sdao.findAllByCRFVersionId(ecb.getCRFVersionId()); /* for (SectionBean section : sections) { boolean toContinue = isSectionReviewedOnce(section, request); if (!toContinue) { return false; } }*/ HashMap numItemsHM = sdao.getNumItemsBySectionId(); HashMap numItemsPendingHM = sdao.getNumItemsPendingBySectionId(ecb); HashMap numItemsCompletedHM = sdao.getNumItemsCompletedBySectionId(ecb); for (int i = 0; i < sections.size(); i++) { SectionBean sb = sections.get(i); Integer key = new Integer(sb.getId()); int numItems = TableOfContentsServlet.getIntById(numItemsHM, key); int numItemsPending = TableOfContentsServlet.getIntById(numItemsPendingHM, key); int numItemsCompleted = TableOfContentsServlet.getIntById(numItemsCompletedHM, key); if (stage.equals(DataEntryStage.INITIAL_DATA_ENTRY) && edcb.isDoubleEntry()) { if (numItemsPending == 0 && numItems > 0) { return false; } } else { if (numItemsCompleted == 0 && numItems > 0) { return false; } else if (numItemsCompleted < numItems) { return false; } } } return true; // if we get this far, all sections are checked and we return a true // return true; } protected void getEventDefinitionCRFBean(HttpServletRequest request) { HttpSession session = request.getSession(); EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); EventDefinitionCRFBean edcb = (EventDefinitionCRFBean) request.getAttribute(EVENT_DEF_CRF_BEAN); { EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(getDataSource()); StudyBean study = (StudyBean) session.getAttribute("study"); edcb = edcdao.findByStudyEventIdAndCRFVersionId(study, ecb.getStudyEventId(), ecb.getCRFVersionId()); } } //@pgawade 30-May-2012 Fix for issue 13963 - added an extra parameter 'isSubmitted' to method createItemWithGroups protected List<DisplayItemWithGroupBean> createItemWithGroups(DisplaySectionBean dsb, boolean hasItemGroup, int eventCRFDefId, HttpServletRequest request, boolean isSubmitted) { HttpSession session = request.getSession(); List<DisplayItemWithGroupBean> displayItemWithGroups = new ArrayList<DisplayItemWithGroupBean>(); EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); ItemDAO idao = new ItemDAO(getDataSource()); SectionBean sb = (SectionBean) request.getAttribute(SECTION_BEAN); EventDefinitionCRFBean edcb = (EventDefinitionCRFBean) request.getAttribute(EVENT_DEF_CRF_BEAN); // BWP>> Get a List<String> of any null values such as NA or NI // method returns null values as a List<String> // >>BWP ArrayList items = dsb.getItems(); // For adding null values to display items FormBeanUtil formBeanUtil = new FormBeanUtil(); List<String> nullValuesList = formBeanUtil.getNullValuesByEventCRFDefId(eventCRFDefId, getDataSource()); LOGGER.trace("single items size: " + items.size()); for (int i = 0; i < items.size(); i++) { DisplayItemBean item = (DisplayItemBean) items.get(i); DisplayItemWithGroupBean newOne = new DisplayItemWithGroupBean(); newOne.setSingleItem(runDynamicsItemCheck(item, null, request)); newOne.setOrdinal(item.getMetadata().getOrdinal()); newOne.setInGroup(false); newOne.setPageNumberLabel(item.getMetadata().getPageNumberLabel()); displayItemWithGroups.add(newOne); // logger.trace("just added on line 1979: // "+newOne.getSingleItem().getData().getValue()); } if (hasItemGroup) { ItemDataDAO iddao = new ItemDataDAO(getDataSource(), locale); ArrayList<ItemDataBean> data = iddao.findAllBySectionIdAndEventCRFId(sb.getId(), ecb.getId()); HashMap<String, ItemDataBean> dataMap = (HashMap<String, ItemDataBean>) getAllActive(data); if (data != null && data.size() > 0) { session.setAttribute(HAS_DATA_FLAG, true); } LOGGER.trace("found data: " + data.size()); LOGGER.trace("data.toString: " + data.toString()); for (DisplayItemGroupBean itemGroup : dsb.getDisplayFormGroups()) { LOGGER.debug("found one itemGroup"); DisplayItemWithGroupBean newOne = new DisplayItemWithGroupBean(); // to arrange item groups and other single items, the ordinal of // a item group will be the ordinal of the first item in this // group DisplayItemBean firstItem = itemGroup.getItems().get(0); // so we are either checking the first or the last item, BUT ONLY ONCE newOne.setPageNumberLabel(firstItem.getMetadata().getPageNumberLabel()); newOne.setItemGroup(itemGroup); newOne.setInGroup(true); newOne.setOrdinal(itemGroup.getGroupMetaBean().getOrdinal()); List<ItemBean> itBeans = idao.findAllItemsByGroupIdOrdered(itemGroup.getItemGroupBean().getId(), sb.getCRFVersionId()); List<DisplayItemBean> dibs = new ArrayList(); boolean hasData = false; int checkAllColumns = 0; if (data.size() > 0) hasData = true; //@pgawade 30-May-2012 Fix for issue 13963 - added an extra parameter 'isSubmitted' to method buildMatrixForRepeatingGroups newOne = buildMatrixForRepeatingGroups(newOne, itemGroup, ecb, sb, itBeans, dataMap, nullValuesList, isSubmitted); if (hasData) { //TODO: fix the group_has_data flag on bean not on session session.setAttribute(GROUP_HAS_DATA, Boolean.TRUE); } else { session.setAttribute(GROUP_HAS_DATA, Boolean.FALSE); // no data, still add a blank row for displaying if (nullValuesList != null && nullValuesList.size() > 0) { LOGGER.trace("set with nullValuesList of : " + nullValuesList); } dibs = FormBeanUtil.getDisplayBeansFromItems(itBeans, getDataSource(), ecb, sb.getId(), nullValuesList, getServletContext()); DisplayItemGroupBean digb2 = new DisplayItemGroupBean(); digb2.setItems(dibs); digb2.setEditFlag("initial"); } displayItemWithGroups.add(newOne); } } // if hasItemGroup Collections.sort(displayItemWithGroups); return displayItemWithGroups; } private Map getAllActive(List<ItemDataBean> al) { Map returnMap = new HashMap<String, ItemDataBean>(); for (ItemDataBean itBean : al) { if (itBean != null) returnMap.put(new String(itBean.getItemId() + "," + itBean.getOrdinal()), itBean); } return returnMap; } //@pgawade 30-May-2012 Fix for issue 13963 - added an extra parameter 'isSubmitted' to method buildMatrixForRepeatingGroups protected DisplayItemWithGroupBean buildMatrixForRepeatingGroups(DisplayItemWithGroupBean diwgb, DisplayItemGroupBean itemGroup, EventCRFBean ecb, SectionBean sb, List<ItemBean> itBeans, Map<String, ItemDataBean> dataMap, List<String> nullValuesList, boolean isSubmitted) { int tempOrdinal = 1; ItemDataDAO iddao = new ItemDataDAO(getDataSource(), locale); int maxOrdinal = iddao.getMaxOrdinalForGroup(ecb, sb, itemGroup.getItemGroupBean()); if (maxOrdinal == 0) maxOrdinal = 1;//Incase of no data ItemFormMetadataDAO ifmdao = new ItemFormMetadataDAO<String, ArrayList>(getDataSource()); List<DisplayItemGroupBean> itemGroups = new ArrayList<DisplayItemGroupBean>(); boolean groupHasData = false; for (int i = 1; i <= maxOrdinal; i++) { List<DisplayItemBean> displayItemBeans = new ArrayList<DisplayItemBean>(); DisplayItemGroupBean dig = new DisplayItemGroupBean(); for (ItemBean itBean : itBeans) { DisplayItemBean displayItemBean = new DisplayItemBean(); ItemFormMetadataBean ifm = ifmdao.findByItemIdAndCRFVersionId(itBean.getId(), ecb.getCRFVersionId()); // itBean.setItemMeta(ifm);//TODO:remove this or the one down displayItemBean.setMetadata(ifm); displayItemBean.setMetadata(ifm); displayItemBean.setItem(itBean); ItemDataBean itemData = dataMap.get(itBean.getId() + "," + i); if (itemData != null) { groupHasData = true;//to indicate any item in the group has data; displayItemBean.setIsNewItem(false); } if (itemData == null) { itemData = displayItemBean.getData(); itemData.setValue(""); itemData.setOrdinal(i); } addNullValues(displayItemBean, nullValuesList); displayItemBean.setData(itemData); //@pgawade 30-May-2012 Fix for issue 13963 Call to method "displayItemBean.loadDBValue()" is made conditional to show // the data wherever it is appropriate in the stages of data entry // displayItemBean.loadDBValue(); if (ecb.getStage() == DataEntryStage.INITIAL_DATA_ENTRY_COMPLETE || ecb.getStage() == DataEntryStage.DOUBLE_DATA_ENTRY_COMPLETE) { if (shouldLoadDBValues(displayItemBean) && !isSubmitted) { displayItemBean.loadDBValue(); } } else { if (shouldLoadDBValues(displayItemBean)) { LOGGER.trace("should load db values is true, set value"); displayItemBean.loadDBValue(); LOGGER.trace("just got data loaded: " + displayItemBean.getData().getValue()); } } displayItemBeans.add(displayItemBean); } Collections.sort(displayItemBeans); dig.setItems(displayItemBeans); dig.setHasData(groupHasData); itemGroups.add(dig); } diwgb.setItemGroups(itemGroups); diwgb.setDbItemGroups(itemGroups); return diwgb; } /* * * @param nullValuesList * A List of Strings containing "null values" such as "not * applicable" or NA. */ private void addNullValues(DisplayItemBean displayItemBean, List<String> nullValuesList) { // logger = LoggerFactory.getLogger(getClass().getName()); boolean hasNullValues = nullValuesList != null && !nullValuesList.isEmpty(); if (!hasNullValues) { return; } String tmpVal = ""; String responseName = displayItemBean.getMetadata().getResponseSet().getResponseType().getName(); ; List<ResponseOptionBean> respOptions = displayItemBean.getMetadata().getResponseSet().getOptions(); ResponseOptionBean respBean; if (respOptions != null && ("checkbox".equalsIgnoreCase(responseName) || "radio".equalsIgnoreCase(responseName) || "single-select".equalsIgnoreCase(responseName) || "multi-select".equalsIgnoreCase(responseName))) { for (String val : nullValuesList) { respBean = new ResponseOptionBean(); // BWP>> set text to the extended version, "not // applicable"? tmpVal = DataEntryInputGenerator.NULL_VALUES_LONGVERSION.get(val); if (tmpVal != null && tmpVal.length() > 0) { respBean.setText(tmpVal); } else { respBean.setText(val); } respBean.setValue(val); displayItemBean.getMetadata().getResponseSet().addOption(respBean); //respOptions.add(respBean); } } } protected void loadItemsWithGroupRows(DisplayItemWithGroupBean itemWithGroup, SectionBean sb, EventDefinitionCRFBean edcb, EventCRFBean ecb, HttpServletRequest request) { //this method is a copy of the method: createItemWithGroups , //only modified for load one DisplayItemWithGroupBean. // ItemDAO idao = new ItemDAO(getDataSource()); // For adding null values to display items FormBeanUtil formBeanUtil = new FormBeanUtil(); List<String> nullValuesList = new ArrayList<String>(); // BWP>> Get a List<String> of any null values such as NA or NI // method returns null values as a List<String> nullValuesList = formBeanUtil.getNullValuesByEventCRFDefId(edcb.getId(), getDataSource()); // >>BWP ItemDataDAO iddao = new ItemDataDAO(getDataSource(), locale); ArrayList data = iddao.findAllActiveBySectionIdAndEventCRFId(sb.getId(), ecb.getId()); DisplayItemGroupBean itemGroup = itemWithGroup.getItemGroup(); // to arrange item groups and other single items, the ordinal of // a item group will be the ordinal of the first item in this // group DisplayItemBean firstItem = itemGroup.getItems().get(0); DisplayItemBean checkItem = firstItem; // does not work if there is not any data in the first item of the group // i.e. imports. // does it make a difference if we take a last item? boolean noNeedToSwitch = false; for (int i = 0; i < data.size(); i++) { ItemDataBean idb = (ItemDataBean) data.get(i); if (idb.getItemId() == firstItem.getItem().getId()) { noNeedToSwitch = true; } } if (!noNeedToSwitch) { checkItem = itemGroup.getItems().get(itemGroup.getItems().size() - 1); } // so we are either checking the first or the last item, BUT ONLY ONCE itemWithGroup.setPageNumberLabel(firstItem.getMetadata().getPageNumberLabel()); itemWithGroup.setItemGroup(itemGroup); itemWithGroup.setInGroup(true); itemWithGroup.setOrdinal(itemGroup.getGroupMetaBean().getOrdinal()); List<ItemBean> itBeans = idao.findAllItemsByGroupId(itemGroup.getItemGroupBean().getId(), sb.getCRFVersionId()); boolean hasData = false; int checkAllColumns = 0; // if a group has repetitions, the number of data of // first item should be same as the row number for (int i = 0; i < data.size(); i++) { ItemDataBean idb = (ItemDataBean) data.get(i); LOGGER.debug("check all columns: " + checkAllColumns); if (idb.getItemId() == checkItem.getItem().getId()) { hasData = true; LOGGER.debug("set has data to --TRUE--"); checkAllColumns = 0; // so that we only fire once a row LOGGER.debug("has data set to true"); DisplayItemGroupBean digb = new DisplayItemGroupBean(); // always get a fresh copy for items, may use other // better way to // do deep copy, like clone List<DisplayItemBean> dibs = FormBeanUtil.getDisplayBeansFromItems(itBeans, getDataSource(), ecb, sb.getId(), edcb, 0, getServletContext()); digb.setItems(dibs); LOGGER.trace("set with dibs list of : " + dibs.size()); digb.setGroupMetaBean(runDynamicsCheck(itemGroup.getGroupMetaBean(), request)); digb.setItemGroupBean(itemGroup.getItemGroupBean()); itemWithGroup.getItemGroups().add(digb); itemWithGroup.getDbItemGroups().add(digb); } } List<DisplayItemGroupBean> groupRows = itemWithGroup.getItemGroups(); LOGGER.trace("how many group rows:" + groupRows.size()); LOGGER.trace("how big is the data:" + data.size()); if (hasData) { // iterate through the group rows, set data for each item in // the group for (int i = 0; i < groupRows.size(); i++) { DisplayItemGroupBean displayGroup = groupRows.get(i); for (DisplayItemBean dib : displayGroup.getItems()) { for (int j = 0; j < data.size(); j++) { ItemDataBean idb = (ItemDataBean) data.get(j); if (idb.getItemId() == dib.getItem().getId() && !idb.isSelected()) { idb.setSelected(true); dib.setData(idb); LOGGER.debug("--> set data " + idb.getId() + ": " + idb.getValue()); if (shouldLoadDBValues(dib)) { LOGGER.debug("+++should load db values is true, set value"); dib.loadDBValue(); LOGGER.debug("+++data loaded: " + idb.getName() + ": " + idb.getOrdinal() + " " + idb.getValue()); LOGGER.debug("+++try dib OID: " + dib.getItem().getOid()); } break; } } } } } else { // no data, still add a blank row for displaying DisplayItemGroupBean digb2 = new DisplayItemGroupBean(); List<DisplayItemBean> dibs = FormBeanUtil.getDisplayBeansFromItems(itBeans, getDataSource(), ecb, sb.getId(), nullValuesList, getServletContext()); digb2.setItems(dibs); LOGGER.trace("set with nullValuesList of : " + nullValuesList); digb2.setEditFlag("initial"); digb2.setGroupMetaBean(itemGroup.getGroupMetaBean()); digb2.setItemGroupBean(itemGroup.getItemGroupBean()); itemWithGroup.getItemGroups().add(digb2); itemWithGroup.getDbItemGroups().add(digb2); } } /** * @param fp * @param dibs * @param i * @param digb * @return */ private List<DisplayItemBean> processInputForGroupItem(FormProcessor fp, List<DisplayItemBean> dibs, int i, DisplayItemGroupBean digb, boolean isAuto) { for (int j = 0; j < dibs.size(); j++) { DisplayItemBean displayItem = dibs.get(j); String inputName = ""; org.akaza.openclinica.bean.core.ResponseType rt = displayItem.getMetadata().getResponseSet() .getResponseType(); if (rt.equals(org.akaza.openclinica.bean.core.ResponseType.CHECKBOX) || rt.equals(org.akaza.openclinica.bean.core.ResponseType.SELECTMULTI)) { if (isAuto) { inputName = getGroupItemInputName(digb, i, displayItem); } else { inputName = getGroupItemManualInputName(digb, i, displayItem); } ArrayList valueArray = fp.getStringArray(inputName); displayItem.setFieldName(inputName); displayItem.loadFormValue(valueArray); } else { if (isAuto) { inputName = getGroupItemInputName(digb, i, displayItem); } else { inputName = getGroupItemManualInputName(digb, i, displayItem); } displayItem.setFieldName(inputName); displayItem.loadFormValue(fp.getString(inputName)); // BWP issue 3257 << This seems to be an apt place to check any // single-select options as "selected" // if the data in the displayItem matches the options text; // although this code is very // confusing and murky, ; refactoring of form handling is // necessary here if (rt.equals(org.akaza.openclinica.bean.core.ResponseType.SELECT)) { ensureSelectedOption(displayItem); } // BWP>> } } return dibs; } /** * @param digb * @param ordinal * @param dib * @return */ public final String getGroupItemManualInputName(DisplayItemGroupBean digb, int ordinal, DisplayItemBean dib) { String inputName = digb.getItemGroupBean().getOid() + "_manual" + ordinal + getInputName(dib); LOGGER.debug("+++ returning manual: " + inputName); return inputName; } // YW 11-12-2007 private EventCRFBean updateECB(StudyEventBean sEvent, HttpServletRequest request) { StudyBean currentStudy = (StudyBean) request.getSession().getAttribute("study"); EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); if (!currentStudy.getStudyParameterConfig().getInterviewerNameDefault().equals("blank") && ("".equals(ecb.getInterviewerName()) || ecb.getInterviewerName() == null)) { // default will be event's owner name ecb.setInterviewerName(sEvent.getOwner().getName()); } if (!currentStudy.getStudyParameterConfig().getInterviewDateDefault().equals("blank") && ("".equals(ecb.getDateInterviewed()) || ecb.getDateInterviewed() == null)) { if (sEvent.getDateStarted() != null) { ecb.setDateInterviewed(sEvent.getDateStarted());// default date } else { // logger.trace("evnet start date is null, so date interviewed is // null"); ecb.setDateInterviewed(null); } } return ecb; } protected HashMap<String, ItemBean> prepareScoreItems(HttpServletRequest request) { HashMap<String, ItemBean> scoreItems = new HashMap<String, ItemBean>(); EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); ItemDAO idao = new ItemDAO(getDataSource()); ArrayList<ItemBean> ibs = idao.findAllItemsByVersionId(ecb.getCRFVersionId()); for (ItemBean ib : ibs) { scoreItems.put(ib.getName(), ib); } return scoreItems; } protected HashMap<String, String> prepareScoreItemdata(HttpServletRequest request) { HashMap<String, String> scoreItemdata = new HashMap<String, String>(); EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); SectionDAO sdao = new SectionDAO(getDataSource()); ArrayList<SectionBean> sbs = sdao.findAllByCRFVersionId(ecb.getCRFVersionId()); for (SectionBean section : sbs) { HashMap<String, String> data = prepareSectionItemDataBeans(section.getId(), request); if (data != null && data.size() > 0) { scoreItemdata.putAll(data); } } return scoreItemdata; } protected HashMap<String, String> prepareSectionItemDataBeans(int sectionId, HttpServletRequest request) { EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); HashMap<String, String> scoreItemdata = new HashMap<String, String>(); ItemDataDAO iddao = new ItemDataDAO(getDataSource(), locale); ArrayList<ItemDataBean> idbs = iddao.findAllActiveBySectionIdAndEventCRFId(sectionId, ecb.getId()); for (ItemDataBean idb : idbs) { if (idb.getId() > 0) { int ordinal = idb.getOrdinal(); ordinal = ordinal > 0 ? ordinal : 1; scoreItemdata.put(idb.getItemId() + "_" + ordinal, idb.getValue().length() > 0 ? idb.getValue() : ""); } } return scoreItemdata; } protected HashMap<Integer, TreeSet<Integer>> prepareItemdataOrdinals(HttpServletRequest request) { EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); HashMap<Integer, TreeSet<Integer>> ordinals = new HashMap<Integer, TreeSet<Integer>>(); SectionDAO sdao = new SectionDAO(getDataSource()); ArrayList<SectionBean> sbs = sdao.findAllByCRFVersionId(ecb.getCRFVersionId()); ItemDataDAO iddao = new ItemDataDAO(getDataSource(), locale); for (SectionBean section : sbs) { ArrayList<ItemDataBean> idbs = iddao.findAllActiveBySectionIdAndEventCRFId(section.getId(), ecb.getId()); if (idbs != null && idbs.size() > 0) { for (ItemDataBean idb : idbs) { int itemId = idb.getItemId(); TreeSet<Integer> os = new TreeSet<Integer>(); if (ordinals == null) { os.add(idb.getOrdinal()); ordinals.put(itemId, os); } else if (ordinals.containsKey(itemId)) { os = ordinals.get(itemId); os.add(idb.getOrdinal()); ordinals.put(itemId, os); } else { os.add(idb.getOrdinal()); ordinals.put(itemId, os); } } } } return ordinals; } protected HashMap<Integer, Integer> prepareGroupSizes(HashMap<String, ItemBean> scoreItems, HttpServletRequest request) { HashMap<Integer, Integer> groupSizes = new HashMap<Integer, Integer>(); EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); ItemDataDAO iddao = new ItemDataDAO(getDataSource(), locale); SectionDAO sdao = new SectionDAO(getDataSource()); Iterator iter = scoreItems.keySet().iterator(); while (iter.hasNext()) { int itemId = scoreItems.get(iter.next().toString()).getId(); groupSizes.put(itemId, 1); } ArrayList<SectionBean> sbs = sdao.findAllByCRFVersionId(ecb.getCRFVersionId()); for (SectionBean section : sbs) { ArrayList<ItemDataBean> idbs = iddao.findAllActiveBySectionIdAndEventCRFId(section.getId(), ecb.getId()); for (ItemDataBean idb : idbs) { int itemId = idb.getItemId(); if (groupSizes != null && groupSizes.containsKey(itemId)) { int groupsize = iddao.getGroupSize(itemId, ecb.getId()); groupsize = groupsize > 0 ? groupsize : 1; groupSizes.put(itemId, groupsize); } } } return groupSizes; } protected HashMap<Integer, String> prepareSectionItemdata(int sectionId, HttpServletRequest request) { EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); ItemDataDAO iddao = new ItemDataDAO(getDataSource(), locale); HashMap<Integer, String> itemdata = new HashMap<Integer, String>(); ArrayList<ItemDataBean> idbs = iddao.findAllActiveBySectionIdAndEventCRFId(sectionId, ecb.getId()); for (ItemDataBean idb : idbs) { itemdata.put(idb.getId(), idb.getValue()); } return itemdata; } protected HashMap<String, ItemDataBean> prepareSectionItemdataObject(int sectionId, HttpServletRequest request) { EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF); ItemDataDAO iddao = new ItemDataDAO(getDataSource(), locale); HashMap<String, ItemDataBean> itemdata = new HashMap<String, ItemDataBean>(); ArrayList<ItemDataBean> idbs = iddao.findAllActiveBySectionIdAndEventCRFId(sectionId, ecb.getId()); for (ItemDataBean idb : idbs) { itemdata.put(idb.getItemId() + "," + idb.getOrdinal(), idb); } return itemdata; } protected boolean isChanged(ItemDataBean idb, HashMap<Integer, String> oldItemdata) { String value = idb.getValue(); if (!oldItemdata.containsKey(idb.getId())) return true; else { String oldValue = oldItemdata.get(idb.getId()); if (oldValue != null) { if (value == null) return true; else if (!oldValue.equals(value)) return true; } else if (value.isEmpty()) { return false; } else if (value != null) return true; } return false; } protected boolean isChanged(DisplayItemBean dib, HashMap<String, ItemDataBean> oldItemdata, String attachedFilePath) { ItemDataBean idb = dib.getData(); String value = idb.getValue(); int ordinal = idb.getOrdinal(); // if(value != null && value.length()>0 && dib.getItem().getDataType().getId()==11) { // value = attachedFilePath + value; // } //isChanged should not be run for calc/group-calc type, only for fields that they depend upon org.akaza.openclinica.bean.core.ResponseType rt = dib.getMetadata().getResponseSet().getResponseType(); if (rt.equals(org.akaza.openclinica.bean.core.ResponseType.CALCULATION) || rt.equals(org.akaza.openclinica.bean.core.ResponseType.GROUP_CALCULATION)) { return false; } String tempKey = idb.getItemId() + "," + idb.getOrdinal(); if (!oldItemdata.containsKey(tempKey)) { if (value != null && value.isEmpty())//This is to address the case where the record does not exist due to Import and upon saving the value could be empty string. return false; else { return true; } } else { ItemDataBean existingItemData = oldItemdata.get(tempKey); String oldValue = existingItemData.getValue(); int oldOrdinal = existingItemData.getOrdinal(); if (oldValue != null) { if (value == null) { if (ordinal == oldOrdinal) return true; } else if (dib.getItem().getDataType().getId() == 11) { String theOldValue = oldValue.split("(/|\\\\)")[oldValue.split("(/|\\\\)").length - 1].trim(); return !value.equals(theOldValue); } else if (!oldValue.equals(value) && (ordinal == oldOrdinal)) return true; } else if (value != null && value.isEmpty()) return false; else if (value != null) { return true; } } return false; } protected boolean isChanged(ItemDataBean idb, HashMap<String, ItemDataBean> oldItemdata, DisplayItemBean dib, String attachedFilePath) { //if(dib.getMetadata().isConditionalDisplayItem() && !dib.getIsSCDtoBeShown()) { //return false; //} else { return isChanged(dib, oldItemdata, attachedFilePath); //} } /** * Output, just logs all contents of the allItems list. tbh, 01/2010 * * @param displayItemWithGroups */ protected void output(List<DisplayItemWithGroupBean> displayItemWithGroups) { for (int i = 0; i < displayItemWithGroups.size(); ++i) { DisplayItemWithGroupBean diwb = displayItemWithGroups.get(i); if (diwb.isInGroup()) { List<DisplayItemGroupBean> dbGroups = diwb.getDbItemGroups(); LOGGER.trace("+++++++ DB ITEM GROUPS ++++++++"); for (int j = 0; j < dbGroups.size(); j++) { DisplayItemGroupBean displayGroup = dbGroups.get(j); List<DisplayItemBean> items = displayGroup.getItems(); for (DisplayItemBean displayItem : items) { int itemId = displayItem.getItem().getId(); int ordinal = displayItem.getData().getOrdinal(); if ("initial".equalsIgnoreCase(displayGroup.getEditFlag())) { // nextOrdinals.put(itemId, 1); LOGGER.trace("* found initial: " + itemId + " " + ordinal); } else { LOGGER.trace("** found NOT initial: " + itemId + " " + ordinal); } // editFlags.put(displayItem.getData().getId(), displayGroup.getEditFlag()); } } List<DisplayItemGroupBean> dgbs = diwb.getItemGroups(); LOGGER.trace("+++++++++ ITEM GROUPS ++++++++++"); int nextOrdinal = 0; for (int j = 0; j < dgbs.size(); j++) { DisplayItemGroupBean displayGroup = dgbs.get(j); List<DisplayItemBean> oItems = displayGroup.getItems(); String editFlag = displayGroup.getEditFlag(); for (DisplayItemBean displayItem : oItems) { int itemId = displayItem.getItem().getId(); // nextOrdinal = nextOrdinals.get(itemId); int ordinal = 0; // String editflag = "add".equalsIgnoreCase(editFlag) ? editFlag : editFlags.get(displayItem.getData().getId()); // if (editflag.length() > 0) { // logger.trace("*** found: edit flag for " + itemId + ": " + editflag); LOGGER.trace("*** found edit Flag " + itemId + ": " + editFlag); // } } } } } } protected void updateDataOrdinals(List<DisplayItemWithGroupBean> displayItemWithGroups) { for (int i = 0; i < displayItemWithGroups.size(); ++i) { DisplayItemWithGroupBean diwb = displayItemWithGroups.get(i); HashMap<Integer, String> editFlags = new HashMap<Integer, String>(); HashMap<Integer, Integer> nextOrdinals = new HashMap<Integer, Integer>(); if (diwb.isInGroup()) { List<DisplayItemGroupBean> dbGroups = diwb.getDbItemGroups(); for (int j = 0; j < dbGroups.size(); j++) { DisplayItemGroupBean displayGroup = dbGroups.get(j); List<DisplayItemBean> items = displayGroup.getItems(); for (DisplayItemBean displayItem : items) { int itemId = displayItem.getItem().getId(); int ordinal = displayItem.getData().getOrdinal(); if ("initial".equalsIgnoreCase(displayGroup.getEditFlag())) { nextOrdinals.put(itemId, 1); } else { if (nextOrdinals.containsKey(itemId)) { int max = nextOrdinals.get(itemId); nextOrdinals.put(itemId, ordinal > max ? ordinal + 1 : max); } else { nextOrdinals.put(itemId, ordinal + 1); } } editFlags.put(displayItem.getData().getId(), displayGroup.getEditFlag()); } } List<DisplayItemGroupBean> dgbs = diwb.getItemGroups(); int nextOrdinal = 0; for (int j = 0; j < dgbs.size(); j++) { DisplayItemGroupBean displayGroup = dgbs.get(j); List<DisplayItemBean> oItems = displayGroup.getItems(); String editFlag = displayGroup.getEditFlag(); for (DisplayItemBean displayItem : oItems) { int itemId = displayItem.getItem().getId(); nextOrdinal = nextOrdinals.get(itemId); int ordinal = 0; String editflag = "add".equalsIgnoreCase(editFlag) ? editFlag : editFlags.get(displayItem.getData().getId()); if (editflag.length() > 0) { if ("add".equalsIgnoreCase(editflag)) { ordinal = nextOrdinals.get(itemId); displayItem.getData().setOrdinal(ordinal); nextOrdinals.put(itemId, nextOrdinal + 1); } else if ("edit".equalsIgnoreCase(editflag)) { displayItem.getData().setOrdinal(displayItem.getDbData().getOrdinal()); } } } } } } } /** * Customized validation for item input * * @param v * @param dib * @param inputName */ private void customValidation(DiscrepancyValidator v, DisplayItemBean dib, String inputName) { String customValidationString = dib.getMetadata().getRegexp(); if (!StringUtil.isBlank(customValidationString)) { Validation customValidation = null; if (customValidationString.startsWith("func:")) { try { customValidation = Validator.processCRFValidationFunction(customValidationString); } catch (Exception e) { e.printStackTrace(); } } else if (customValidationString.startsWith("regexp:")) { try { customValidation = Validator.processCRFValidationRegex(customValidationString); } catch (Exception e) { } } if (customValidation != null) { customValidation.setErrorMessage(dib.getMetadata().getRegexpErrorMsg()); v.addValidation(inputName, customValidation); } } // custom validation } private String ifValueIsDate(ItemBean itemBean, String value, boolean dryRun) { String dateFormat = ResourceBundleProvider.getFormatBundle().getString("date_format_string"); String dateRegexp = ResourceBundleProvider.getFormatBundle().getString("date_regexp"); // isValidDateMMddyyyy String theFinalValue = value; if (value != null && itemBean.getDataType() == ItemDataType.DATE && dryRun) { theFinalValue = ExpressionTreeHelper.ifValidDateFormatAsyyyyMMdd(value, dateFormat, dateRegexp); } else { theFinalValue = ExpressionTreeHelper.isValidDateMMddyyyy(value); } return theFinalValue; } /** * This method will populate grouped and variableAndValue HashMaps grouped : Used to correctly populate group ordinals variableAndValue : Holds itemOID , * value (in Form ) pairs passed in to rule processor * * @param allItems */ private Container populateRuleSpecificHashMaps(List<DisplayItemWithGroupBean> allItems, Container c, Boolean dryRun) { for (DisplayItemWithGroupBean displayItemWithGroupBean : allItems) { // Items in Non Repeating group also known as UNGROUPED if (displayItemWithGroupBean.getSingleItem() != null) { if (displayItemWithGroupBean.getSingleItem().getItem().getOid() != null) { c.grouped.put(displayItemWithGroupBean.getSingleItem().getItem().getOid(), 1); c.variableAndValue.put(displayItemWithGroupBean.getSingleItem().getItem().getOid(), ifValueIsDate(displayItemWithGroupBean.getSingleItem().getItem(), displayItemWithGroupBean.getSingleItem().getData().getValue(), dryRun)); LOGGER.debug( "Type : " + displayItemWithGroupBean.getSingleItem().getItem().getItemDataTypeId()); for (Object displayItemBean : displayItemWithGroupBean.getSingleItem().getChildren()) { String oid = ((DisplayItemBean) displayItemBean).getItem().getOid(); String value = ifValueIsDate(((DisplayItemBean) displayItemBean).getItem(), ((DisplayItemBean) displayItemBean).getData().getValue(), dryRun); LOGGER.debug("Type : " + ((DisplayItemBean) displayItemBean).getItem().getItemDataTypeId()); c.grouped.put(oid, 1); c.variableAndValue.put(oid, value); } } LOGGER.debug("Item Name : {} , Item Value : {} , Item Data Ordinal : {} , Item OID : {} ", new Object[] { displayItemWithGroupBean.getSingleItem().getItem().getName(), displayItemWithGroupBean.getSingleItem().getData().getValue(), displayItemWithGroupBean.getSingleItem().getData().getOrdinal(), displayItemWithGroupBean.getSingleItem().getItem().getOid() }); } // Items in repeating groups for (DisplayItemGroupBean itemGroupBean : displayItemWithGroupBean.getItemGroups()) { LOGGER.debug("Item Group Name : {} , Item Group OID : {} , Ordinal : {} ", new Object[] { itemGroupBean.getItemGroupBean().getName(), itemGroupBean.getItemGroupBean().getOid(), itemGroupBean.getIndex() }); for (DisplayItemBean displayItemBean : itemGroupBean.getItems()) { String key1 = itemGroupBean.getItemGroupBean().getOid() + "[" + (itemGroupBean.getIndex() + 1) + "]." + displayItemBean.getItem().getOid(); String key = itemGroupBean.getItemGroupBean().getOid() + "." + displayItemBean.getItem().getOid(); c.variableAndValue.put(key1, ifValueIsDate(displayItemBean.getItem(), displayItemBean.getData().getValue(), dryRun)); if (c.grouped.containsKey(key)) { c.grouped.put(key, c.grouped.get(key) + 1); } else { c.grouped.put(key, 1); } LOGGER.debug("Item Name : {} , Item Value : {} , Item OID : {} ", new Object[] { displayItemBean.getItem().getName(), displayItemBean.getData().getValue(), displayItemBean.getItem().getOid() }); } } } if (LOGGER.isDebugEnabled()) { for (String key : c.grouped.keySet()) { LOGGER.debug("key : {} , value : {}", key, c.grouped.get(key)); } for (String key : c.variableAndValue.keySet()) { LOGGER.debug("key : {} , value : {}", key, c.variableAndValue.get(key)); } } return c; } /** * @deprecated Use {@link #createAndInitializeRuleSet(StudyBean,StudyEventDefinitionBean,CRFVersionBean,StudyEventBean,EventCRFBean,Boolean,HttpServletRequest,HttpServletResponse,List)} instead */ @Deprecated private List<RuleSetBean> createAndInitializeRuleSet(StudyBean currentStudy, StudyEventDefinitionBean studyEventDefinition, CRFVersionBean crfVersionBean, StudyEventBean studyEventBean, EventCRFBean eventCrfBean, Boolean shouldRunRules, HttpServletRequest request, HttpServletResponse response) { return createAndInitializeRuleSet(currentStudy, studyEventDefinition, crfVersionBean, studyEventBean, eventCrfBean, shouldRunRules, request, response, null); } private List<RuleSetBean> createAndInitializeRuleSet(StudyBean currentStudy, StudyEventDefinitionBean studyEventDefinition, CRFVersionBean crfVersionBean, StudyEventBean studyEventBean, EventCRFBean eventCrfBean, Boolean shouldRunRules, HttpServletRequest request, HttpServletResponse response, List<ItemBean> itemBeansWithSCDShown) { if (shouldRunRules) { logMe("Current Thread:::" + Thread.currentThread()); List<RuleSetBean> ruleSets = getRuleSetService(request).getRuleSetsByCrfStudyAndStudyEventDefinition( currentStudy, studyEventDefinition, crfVersionBean); logMe("Current Thread:::" + Thread.currentThread() + "RuleSet Now?" + ruleSets); if (ruleSets != null && ruleSets.size() > 0) { ruleSets = getRuleSetService(request).filterByStatusEqualsAvailable(ruleSets); ruleSets = getRuleSetService(request).filterRuleSetsByStudyEventOrdinal(ruleSets, studyEventBean, crfVersionBean, studyEventDefinition); // place next line here, tbh ruleSets = getRuleSetService(request).filterRuleSetsByHiddenItems(ruleSets, eventCrfBean, crfVersionBean, itemBeansWithSCDShown); } return ruleSets != null && ruleSets.size() > 0 ? ruleSets : new ArrayList<RuleSetBean>(); } else return new ArrayList<RuleSetBean>(); } private HashMap<String, ArrayList<String>> runRules(List<DisplayItemWithGroupBean> allItems, List<RuleSetBean> ruleSets, Boolean dryRun, Boolean shouldRunRules, MessageType mt, Phase phase, EventCRFBean ecb, HttpServletRequest request) { UserAccountBean ub = (UserAccountBean) request.getSession().getAttribute(USER_BEAN_NAME); StudyBean currentStudy = (StudyBean) request.getSession().getAttribute("study"); if (shouldRunRules) { Container c = new Container(); try { c = populateRuleSpecificHashMaps(allItems, c, dryRun); ruleSets = getRuleSetService(request).filterRuleSetsBySectionAndGroupOrdinal(ruleSets, c.grouped); ruleSets = getRuleSetService(request).solidifyGroupOrdinalsUsingFormProperties(ruleSets, c.grouped); // next line here ? } catch (NullPointerException npe) { LOGGER.debug("found NPE " + npe.getMessage()); npe.printStackTrace(); } // above throws NPE? // return getRuleSetService().runRules(ruleSets, dryRun, // currentStudy, c.variableAndValue, ub); LOGGER.debug("running rules ... rule sets size is " + ruleSets.size()); return getRuleSetService(request).runRulesInDataEntry(ruleSets, dryRun, currentStudy, ub, c.variableAndValue, phase, ecb, request).getByMessageType(mt); } else { return new HashMap<String, ArrayList<String>>(); } } protected abstract boolean shouldRunRules(); protected abstract boolean isAdministrativeEditing(); protected abstract boolean isAdminForcedReasonForChange(HttpServletRequest request); private RuleSetServiceInterface getRuleSetService(HttpServletRequest request) { RuleSetServiceInterface ruleSetService = null; ruleSetService = ruleSetService != null ? ruleSetService : (RuleSetServiceInterface) SpringServletAccess.getApplicationContext(getServletContext()) .getBean("ruleSetService"); ruleSetService.setContextPath(getContextPath(request)); ruleSetService.setMailSender((JavaMailSenderImpl) SpringServletAccess .getApplicationContext(getServletContext()).getBean("mailSender")); ruleSetService.setRequestURLMinusServletPath(getRequestURLMinusServletPath(request)); return ruleSetService; } private RuleSetServiceInterface getRuleSetServicePerRequest(HttpServletRequest request) { //TODO:where is the ruleservice initialized? does not have any references. Check it RuleSetServiceInterface ruleSetService = null; ruleSetService = ruleSetService != null ? ruleSetService : (RuleSetServiceInterface) SpringServletAccess.getApplicationContext(getServletContext()) .getBean("ruleSetServicePerRequest"); ruleSetService.setContextPath(getContextPath(request)); ruleSetService.setMailSender((JavaMailSenderImpl) SpringServletAccess .getApplicationContext(getServletContext()).getBean("mailSender")); ruleSetService.setRequestURLMinusServletPath(getRequestURLMinusServletPath(request)); return ruleSetService; } private void ensureSelectedOption(DisplayItemBean displayItemBean) { if (displayItemBean == null || displayItemBean.getData() == null) { return; } ItemDataBean itemDataBean = displayItemBean.getData(); String dataName = itemDataBean.getName(); String dataValue = itemDataBean.getValue(); if ("".equalsIgnoreCase(dataValue)) { return; } List<ResponseOptionBean> responseOptionBeans = new ArrayList<ResponseOptionBean>(); ResponseSetBean responseSetBean = displayItemBean.getMetadata().getResponseSet(); if (responseSetBean == null) { return; } responseOptionBeans = responseSetBean.getOptions(); String tempVal = ""; for (ResponseOptionBean responseOptionBean : responseOptionBeans) { tempVal = responseOptionBean.getValue(); if (tempVal != null && tempVal.equalsIgnoreCase(dataValue)) { responseOptionBean.setSelected(true); } } } protected boolean unloadFiles(HashMap<String, String> newUploadedFiles) { boolean success = true; Iterator iter = newUploadedFiles.keySet().iterator(); while (iter.hasNext()) { String itemId = (String) iter.next(); String filename = newUploadedFiles.get(itemId); File f = new File(filename); if (f.exists()) { if (f.delete()) { newUploadedFiles.remove("filename"); } else { success = false; } } else { newUploadedFiles.remove("filename"); // success = false; } } return success; } class Container { HashMap<String, Integer> grouped; HashMap<String, String> variableAndValue; public Container() { super(); this.grouped = new HashMap<String, Integer>(); this.variableAndValue = new HashMap<String, String>(); } } public int getManualRows(List<DisplayItemGroupBean> formGroups) { int manualRows = 0; for (int j = 0; j < formGroups.size(); j++) { DisplayItemGroupBean formItemGroup = formGroups.get(j); LOGGER.debug("begin formGroup Ordinal:" + formItemGroup.getOrdinal()); if (formItemGroup.isAuto() == false) { manualRows = manualRows + 1; } } LOGGER.debug( "+++ returning manual rows: " + manualRows + " from a form group size of " + formGroups.size()); // logger.debug("+++ returning manual rows: " + manualRows + " from a form group size of " + formGroups.size()); return manualRows; } private HashMap reshuffleErrorGroupNamesKK(HashMap errors, List<DisplayItemWithGroupBean> allItems, HttpServletRequest request) { int manualRows = 0; if (errors == null || errors.size() < 1) { return errors; } for (int i = 0; i < allItems.size(); i++) { DisplayItemWithGroupBean diwb = allItems.get(i); if (diwb.isInGroup()) { List<DisplayItemGroupBean> dgbs = diwb.getItemGroups(); for (int j = 0; j < dgbs.size(); j++) { DisplayItemGroupBean digb = dgbs.get(j); ItemGroupBean igb = digb.getItemGroupBean(); List<DisplayItemBean> dibs = digb.getItems(); if (j == 0) { // first repeat for (DisplayItemBean dib : dibs) { String intendedKey = digb.getInputId() + getInputName(dib); String replacementKey = digb.getItemGroupBean().getOid() + "_" + j + getInputName(dib); if (!replacementKey.equals(intendedKey) && errors.containsKey(intendedKey)) { // String errorMessage = (String)errors.get(intendedKey); errors.put(replacementKey, errors.get(intendedKey)); errors.remove(intendedKey); LOGGER.debug( "removing: " + intendedKey + " and replacing it with " + replacementKey); } } } else { // everything in between manualRows++; for (DisplayItemBean dib : dibs) { String intendedKey = digb.getInputId() + getInputName(dib); String replacementKey = digb.getItemGroupBean().getOid() + "_manual" + j + getInputName(dib); if (!replacementKey.equals(intendedKey) && errors.containsKey(intendedKey)) { // String errorMessage = (String)errors.get(intendedKey); errors.put(replacementKey, errors.get(intendedKey)); errors.remove(intendedKey); LOGGER.debug( "removing: " + intendedKey + " and replacing it with " + replacementKey); } } } } } } request.setAttribute("manualRows", new Integer(manualRows)); return errors; } private void reshuffleReasonForChangeHashAndDiscrepancyNotes(List<DisplayItemWithGroupBean> allItems, HttpServletRequest request, EventCRFBean ecb) { int manualRows = 0; HashMap<String, Boolean> noteSubmitted = (HashMap<String, Boolean>) request.getSession() .getAttribute(DataEntryServlet.NOTE_SUBMITTED); FormDiscrepancyNotes noteTree = (FormDiscrepancyNotes) request.getSession() .getAttribute(CreateDiscrepancyNoteServlet.FLAG_DISCREPANCY_RFC); ArrayList<DiscrepancyNoteBean> fieldNote = null; String intendedKey = null; String replacementKey = null; if ((noteSubmitted == null || noteSubmitted.size() < 1) && (noteTree == null || noteTree.getFieldNotes() == null || noteTree.getFieldNotes().size() < 1)) { return; } for (int i = 0; i < allItems.size(); i++) { DisplayItemWithGroupBean diwb = allItems.get(i); if (diwb.isInGroup()) { List<DisplayItemGroupBean> dgbs = diwb.getItemGroups(); for (int j = 0; j < dgbs.size(); j++) { DisplayItemGroupBean digb = dgbs.get(j); ItemGroupBean igb = digb.getItemGroupBean(); List<DisplayItemBean> dibs = digb.getItems(); if (j == 0) { // first repeat for (DisplayItemBean dib : dibs) { intendedKey = ecb.getId() + "_" + digb.getInputId() + getInputName(dib); replacementKey = ecb.getId() + "_" + digb.getItemGroupBean().getOid() + "_" + j + getInputName(dib); if (!replacementKey.equals(intendedKey)) { if (noteSubmitted.containsKey(intendedKey)) { noteSubmitted.put(replacementKey, Boolean.TRUE); noteSubmitted.remove(intendedKey); } if (noteTree.getNotes(intendedKey) != null) { fieldNote = (ArrayList<DiscrepancyNoteBean>) noteTree.getNotes(intendedKey); if (fieldNote != null && fieldNote.size() > 0) { noteTree.getFieldNotes().put(replacementKey, fieldNote); noteTree.getFieldNotes().remove(intendedKey); } //not changing here because this hash should not be used // noteTree.addIdNote(note.getEntityId(), field); // } } } } else { // everything in between manualRows++; for (DisplayItemBean dib : dibs) { intendedKey = ecb.getId() + "_" + digb.getInputId() + getInputName(dib); replacementKey = ecb.getId() + "_" + digb.getItemGroupBean().getOid() + "_manual" + (j) + getInputName(dib); if (!replacementKey.equals(intendedKey)) { if (noteSubmitted != null && noteSubmitted.containsKey(intendedKey)) { noteSubmitted.put(replacementKey, Boolean.TRUE); noteSubmitted.remove(intendedKey); } if (noteTree != null && noteTree.getNotes(intendedKey) != null) { fieldNote = (ArrayList<DiscrepancyNoteBean>) noteTree.getNotes(intendedKey); if (fieldNote != null && fieldNote.size() > 0) { noteTree.getFieldNotes().put(replacementKey, fieldNote); noteTree.getFieldNotes().remove(intendedKey); } } } } } LOGGER.debug("removing: " + intendedKey + " and replacing it with " + replacementKey); } } } request.getSession().setAttribute(DataEntryServlet.NOTE_SUBMITTED, noteSubmitted); } /*Determining the resolution status that will be shown in color flag for an item.*/ private int getDiscrepancyNoteResolutionStatus(int itemDataId, ArrayList formNotes) { int resolutionStatus = 0; boolean hasOtherThread = false; int parentNotesNum = 0; DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(getDataSource()); ArrayList existingNotes = dndao.findExistingNotesForItemData(itemDataId); for (Object obj : existingNotes) { DiscrepancyNoteBean note = (DiscrepancyNoteBean) obj; /*We would only take the resolution status of the parent note of any note thread. If there * are more than one note thread, the thread with the worst resolution status will be taken.*/ if (note.getParentDnId() == 0) { if (hasOtherThread) { if (resolutionStatus > note.getResolutionStatusId()) { resolutionStatus = note.getResolutionStatusId(); } } else { resolutionStatus = note.getResolutionStatusId(); } hasOtherThread = true; } } if (formNotes == null || formNotes.isEmpty()) { return resolutionStatus; } for (Object obj : formNotes) { DiscrepancyNoteBean note = (DiscrepancyNoteBean) obj; if (note.getParentDnId() == 0) { if (hasOtherThread) { if (resolutionStatus > note.getResolutionStatusId()) { resolutionStatus = note.getResolutionStatusId(); } } else { resolutionStatus = note.getResolutionStatusId(); } hasOtherThread = true; } } return resolutionStatus; } private int getDiscrepancyNoteResolutionStatus(List existingNotes) { int resolutionStatus = 0; boolean hasOtherThread = false; for (Object obj : existingNotes) { DiscrepancyNoteBean note = (DiscrepancyNoteBean) obj; /*We would only take the resolution status of the parent note of any note thread. If there * are more than one note thread, the thread with the worst resolution status will be taken.*/ if (note.getParentDnId() == 0) { if (hasOtherThread) { if (resolutionStatus > note.getResolutionStatusId()) { resolutionStatus = note.getResolutionStatusId(); } } else { resolutionStatus = note.getResolutionStatusId(); } hasOtherThread = true; } } return resolutionStatus; } /* * Update DisplaySectionBean's firstSection & lastSection; */ protected void updateDisplaySectionPlace(DisplaySectionBean displaySectionBean, DisplayTableOfContentsBean toc, HttpServletRequest request) { if (toc != null) { ArrayList<SectionBean> sectionBeans = toc.getSections(); if (sectionBeans != null && sectionBeans.size() > 0) { int sid = displaySectionBean.getSection().getId(); displaySectionBean.setFirstSection(sid == sectionBeans.get(0).getId() ? true : false); displaySectionBean .setLastSection(sid == sectionBeans.get(sectionBeans.size() - 1).getId() ? true : false); } } } protected SectionBean prevSection(SectionBean sb, EventCRFBean ecb, DisplayTableOfContentsBean toc, int sbPos) { SectionBean p = new SectionBean(); ArrayList<SectionBean> sectionBeans = new ArrayList<SectionBean>(); if (toc != null) { sectionBeans = toc.getSections(); if (sbPos > 0) { p = sectionBeans.get(sbPos - 1); } } return p != null && p.getId() > 0 ? p : new SectionBean(); } protected SectionBean nextSection(SectionBean sb, EventCRFBean ecb, DisplayTableOfContentsBean toc, int sbPos) { SectionBean n = new SectionBean(); ArrayList<SectionBean> sectionBeans = new ArrayList<SectionBean>(); if (toc != null) { sectionBeans = toc.getSections(); int size = sectionBeans.size(); if (sbPos >= 0 && size > 1 && sbPos < size - 1) { n = sectionBeans.get(sbPos + 1); } } return n != null && n.getId() > 0 ? n : new SectionBean(); } public void mayAccess(HttpServletRequest request) throws InsufficientPermissionException { FormProcessor fp = new FormProcessor(request); EventCRFDAO edao = new EventCRFDAO(getDataSource()); UserAccountBean ub = (UserAccountBean) request.getSession().getAttribute(USER_BEAN_NAME); int eventCRFId = fp.getInt("ecId", true); if (eventCRFId == 0) { eventCRFId = fp.getInt("eventCRFId", true); } if (eventCRFId > 0) { if (!entityIncluded(eventCRFId, ub.getName(), edao, getDataSource())) { addPageMessage(respage.getString("required_event_CRF_belong"), request); throw new InsufficientPermissionException(Page.MENU_SERVLET, resexception.getString("entity_not_belong_studies"), "1"); } } } protected void populateInstantOnChange(HttpSession session, EventCRFBean ecb, DisplaySectionBean section) { int cvId = ecb.getCRFVersionId(); int sectionId = section.getSection().getId(); InstantOnChangeService ins = (InstantOnChangeService) SpringServletAccess .getApplicationContext(getServletContext()).getBean("instantOnChangeService"); InstantOnChangeFrontStrParcel strsInSec = new InstantOnChangeFrontStrParcel(); HashMap<Integer, InstantOnChangeFrontStrGroup> nonRepOri = null; HashMap<String, Map<Integer, InstantOnChangeFrontStrGroup>> grpOri = null; HashMap<Integer, InstantOnChangeFrontStrParcel> instantOnChangeFrontStrParcels = (HashMap<Integer, InstantOnChangeFrontStrParcel>) session .getAttribute(CV_INSTANT_META + cvId); if (instantOnChangeFrontStrParcels != null && instantOnChangeFrontStrParcels.containsKey(sectionId)) { strsInSec = instantOnChangeFrontStrParcels.get(sectionId); nonRepOri = (HashMap<Integer, InstantOnChangeFrontStrGroup>) strsInSec.getNonRepOrigins(); grpOri = (HashMap<String, Map<Integer, InstantOnChangeFrontStrGroup>>) strsInSec.getRepOrigins(); } else if (instantOnChangeFrontStrParcels == null || instantOnChangeFrontStrParcels.size() == 0) { //if(ins.needRunInstantInSection(sectionId)) { boolean shouldSetAtt = false; instantOnChangeFrontStrParcels = (HashMap<Integer, InstantOnChangeFrontStrParcel>) ins .instantOnChangeFrontStrParcelInCrfVersion(cvId); if (instantOnChangeFrontStrParcels.size() > 0) { session.setAttribute(CV_INSTANT_META + cvId, instantOnChangeFrontStrParcels); if (instantOnChangeFrontStrParcels.containsKey(sectionId)) { strsInSec = instantOnChangeFrontStrParcels.get(sectionId); if (strsInSec != null) { grpOri = (HashMap<String, Map<Integer, InstantOnChangeFrontStrGroup>>) strsInSec .getRepOrigins(); nonRepOri = (HashMap<Integer, InstantOnChangeFrontStrGroup>) strsInSec.getNonRepOrigins(); } } } //} } if (grpOri != null && grpOri.size() > 0) { ins.itemGroupsInstantUpdate(section.getDisplayItemGroups(), grpOri); } if (nonRepOri != null && nonRepOri.size() > 0) { ins.itemsInstantUpdate(section.getDisplayItemGroups(), nonRepOri); } } }