protected boolean writeToDB(
      ItemBean ib,
      ItemFormMetadataBean ifm,
      ItemDataBean idb,
      String exp,
      String value,
      StringBuffer err) {
    ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
    NumberFormat nf = NumberFormat.getInstance();

    if (idb == null) {
      idb = new ItemDataBean();
    }

    ItemDataType idt = ib.getDataType();
    if (value == null || value.length() == 0) {
      if (idb.isActive() && !"".equals(idb.getValue())) {
        idb.setValue("<erased>");
      } else {
        idb.setValue("");
      }
      err.append("Result is empty in" + " " + exp + "; ");
    } else {
      idb.setValue(this.getMathContextValue(value, ifm, idt, err));
    }

    idb.setStatus(Status.UNAVAILABLE);
    // idb.setNeedsRecalc(false);
    if (!idb.isActive()) {
      // will this need to change for double data entry?
      idb.setCreatedDate(new Date());
      idb.setOwner(ub);
      idb.setItemId(ib.getId());
      idb.setEventCRFId(ecb.getId());

      idb = (ItemDataBean) iddao.create(idb);
    } else {
      idb = (ItemDataBean) iddao.update(idb);
    }

    return idb.isActive();
  }
  public void processRequest() throws Exception {

    StudyDAO sdao = new StudyDAO(sm.getDataSource());
    FormProcessor fp = new FormProcessor(request);
    int studyId = fp.getInt("id");

    StudyBean study = (StudyBean) sdao.findByPK(studyId);
    // find all sites
    ArrayList sites = (ArrayList) sdao.findAllByParent(studyId);

    // find all user and roles in the study, include ones in sites
    UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
    ArrayList userRoles = udao.findAllByStudyId(studyId);

    // find all subjects in the study, include ones in sites
    StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
    ArrayList subjects = ssdao.findAllByStudy(study);

    // find all events in the study, include ones in sites
    StudyEventDefinitionDAO sefdao = new StudyEventDefinitionDAO(sm.getDataSource());
    ArrayList definitions = sefdao.findAllByStudy(study);

    String action = request.getParameter("action");
    if (studyId == 0) {
      addPageMessage("Please choose a study to restore.");
      forwardPage(Page.STUDY_LIST_SERVLET);
    } else {
      if ("confirm".equalsIgnoreCase(action)) {
        request.setAttribute("studyToRestore", study);

        request.setAttribute("sitesToRestore", sites);

        request.setAttribute("userRolesToRestore", userRoles);

        request.setAttribute("subjectsToRestore", subjects);

        request.setAttribute("definitionsToRRestore", definitions);
        forwardPage(Page.RESTORE_STUDY);
      } else {
        logger.info("submit to restore the study");
        // change all statuses to unavailable
        StudyDAO studao = new StudyDAO(sm.getDataSource());
        study.setStatus(Status.AVAILABLE);
        study.setUpdater(ub);
        study.setUpdatedDate(new Date());
        studao.update(study);

        // remove all sites
        for (int i = 0; i < sites.size(); i++) {
          StudyBean site = (StudyBean) sites.get(i);
          site.setStatus(Status.AVAILABLE);
          site.setUpdater(ub);
          site.setUpdatedDate(new Date());
          sdao.update(site);
        }

        // remove all users and roles
        for (int i = 0; i < userRoles.size(); i++) {
          StudyUserRoleBean role = (StudyUserRoleBean) userRoles.get(i);
          role.setStatus(Status.AVAILABLE);
          role.setUpdater(ub);
          role.setUpdatedDate(new Date());
          udao.updateStudyUserRole(role, role.getUserName());
        }

        // remove all subjects
        for (int i = 0; i < subjects.size(); i++) {
          StudySubjectBean subject = (StudySubjectBean) subjects.get(i);
          subject.setStatus(Status.AVAILABLE);
          subject.setUpdater(ub);
          subject.setUpdatedDate(new Date());
          ssdao.update(subject);
        }

        // remove all study_group
        StudyGroupDAO sgdao = new StudyGroupDAO(sm.getDataSource());
        SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource());
        ArrayList groups = sgdao.findAllByStudy(study);
        for (int i = 0; i < groups.size(); i++) {
          StudyGroupBean group = (StudyGroupBean) groups.get(i);
          group.setStatus(Status.AVAILABLE);
          group.setUpdater(ub);
          group.setUpdatedDate(new Date());
          sgdao.update(group);
          // all subject_group_map
          ArrayList subjectGroupMaps = sgmdao.findAllByStudyGroupId(group.getId());
          for (int j = 0; j < subjectGroupMaps.size(); j++) {
            SubjectGroupMapBean sgMap = (SubjectGroupMapBean) subjectGroupMaps.get(j);
            sgMap.setStatus(Status.AVAILABLE);
            sgMap.setUpdater(ub);
            sgMap.setUpdatedDate(new Date());
            sgmdao.update(sgMap);
          }
        }

        // remove all event definitions and event
        EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
        StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
        for (int i = 0; i < definitions.size(); i++) {
          StudyEventDefinitionBean definition = (StudyEventDefinitionBean) definitions.get(i);
          definition.setStatus(Status.AVAILABLE);
          definition.setUpdater(ub);
          definition.setUpdatedDate(new Date());
          sefdao.update(definition);
          ArrayList edcs = (ArrayList) edcdao.findAllByDefinition(definition.getId());
          for (int j = 0; j < edcs.size(); j++) {
            EventDefinitionCRFBean edc = (EventDefinitionCRFBean) edcs.get(j);
            edc.setStatus(Status.AVAILABLE);
            edc.setUpdater(ub);
            edc.setUpdatedDate(new Date());
            edcdao.update(edc);
          }

          ArrayList events = (ArrayList) sedao.findAllByDefinition(definition.getId());
          EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());

          for (int j = 0; j < events.size(); j++) {
            StudyEventBean event = (StudyEventBean) events.get(j);
            event.setStatus(Status.AVAILABLE);
            event.setUpdater(ub);
            event.setUpdatedDate(new Date());
            sedao.update(event);

            ArrayList eventCRFs = ecdao.findAllByStudyEvent(event);

            ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
            for (int k = 0; k < eventCRFs.size(); k++) {
              EventCRFBean eventCRF = (EventCRFBean) eventCRFs.get(k);
              eventCRF.setStatus(Status.AVAILABLE);
              eventCRF.setUpdater(ub);
              eventCRF.setUpdatedDate(new Date());
              ecdao.update(eventCRF);

              ArrayList itemDatas = iddao.findAllByEventCRFId(eventCRF.getId());
              for (int a = 0; a < itemDatas.size(); a++) {
                ItemDataBean item = (ItemDataBean) itemDatas.get(a);
                item.setStatus(Status.AVAILABLE);
                item.setUpdater(ub);
                item.setUpdatedDate(new Date());
                iddao.update(item);
              }
            }
          }
        } // for definitions

        DatasetDAO datadao = new DatasetDAO(sm.getDataSource());
        ArrayList dataset = datadao.findAllByStudyId(study.getId());
        for (int i = 0; i < dataset.size(); i++) {
          DatasetBean data = (DatasetBean) dataset.get(i);
          data.setStatus(Status.AVAILABLE);
          data.setUpdater(ub);
          data.setUpdatedDate(new Date());
          datadao.update(data);
        }

        addPageMessage("This study has been restored successfully.");
        forwardPage(Page.STUDY_LIST_SERVLET);
      }
    }
  }
  @Override
  public void processRequest() throws Exception {
    FormProcessor fp = new FormProcessor(request);
    int studySubId = fp.getInt(STUDY_SUB_ID, true);
    int eventCRFId = fp.getInt(EVENT_CRF_ID);

    String action = request.getParameter("action");

    StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
    StudySubjectDAO subdao = new StudySubjectDAO(sm.getDataSource());
    EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
    StudyDAO sdao = new StudyDAO(sm.getDataSource());

    if (eventCRFId == 0) {
      addPageMessage(respage.getString("please_choose_an_event_CRF_to_delete"));
      request.setAttribute("id", new Integer(studySubId).toString());
      forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
    } else {
      EventCRFBean eventCRF = (EventCRFBean) ecdao.findByPK(eventCRFId);

      StudySubjectBean studySub = (StudySubjectBean) subdao.findByPK(studySubId);
      request.setAttribute("studySub", studySub);

      // construct info needed on view event crf page
      CRFDAO cdao = new CRFDAO(sm.getDataSource());
      CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());

      int crfVersionId = eventCRF.getCRFVersionId();
      CRFBean cb = cdao.findByVersionId(crfVersionId);
      eventCRF.setCrf(cb);

      CRFVersionBean cvb = (CRFVersionBean) cvdao.findByPK(crfVersionId);
      eventCRF.setCrfVersion(cvb);

      // then get the definition so we can call
      // DisplayEventCRFBean.setFlags
      int studyEventId = eventCRF.getStudyEventId();

      StudyEventBean event = (StudyEventBean) sedao.findByPK(studyEventId);

      int studyEventDefinitionId = sedao.getDefinitionIdFromStudyEventId(studyEventId);
      StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
      StudyEventDefinitionBean sed =
          (StudyEventDefinitionBean) seddao.findByPK(studyEventDefinitionId);
      event.setStudyEventDefinition(sed);
      request.setAttribute("event", event);

      EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());

      StudyBean study = (StudyBean) sdao.findByPK(studySub.getStudyId());
      EventDefinitionCRFBean edc =
          edcdao.findByStudyEventDefinitionIdAndCRFId(study, studyEventDefinitionId, cb.getId());

      DisplayEventCRFBean dec = new DisplayEventCRFBean();
      dec.setEventCRF(eventCRF);
      dec.setFlags(eventCRF, ub, currentRole, edc.isDoubleEntry());

      // find all item data
      ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
      dnDao = new DiscrepancyNoteDAO(sm.getDataSource());
      ArrayList<ItemDataBean> itemData = iddao.findAllByEventCRFId(eventCRF.getId());
      request.setAttribute("items", itemData);

      if ("confirm".equalsIgnoreCase(action)) {

        request.setAttribute("displayEventCRF", dec);

        forwardPage(Page.DELETE_EVENT_CRF);
      } else {
        logger.info("submit to delete the event CRF from event");

        // OC-6303  Deleting Event CRF resets Show / Hide logic
        // delete records from DynamicItemForm and DynamicItemGroup
        getDynamicsItemFormMetadataDao().delete(eventCRFId);
        getDynamicsItemGroupMetadataDao().delete(eventCRFId);

        eventCRF.setOldStatus(eventCRF.getStatus());
        eventCRF.setStatus(Status.RESET);
        eventCRF.setUpdater(ub);
        ecdao.update(eventCRF);

        for (ItemDataBean itemdata : itemData) {
          // OC-6343 Rule behaviour must be reset if an Event CRF is deleted
          // delete the records from ruleActionRunLogDao
          getRuleActionRunLogDao().delete(itemdata.getId());

          // OC-6344 Notes & Discrepancies must be set to "closed" when event CRF is deleted
          // parentDiscrepancyNoteList is the list of the parent DNs records only
          ArrayList<DiscrepancyNoteBean> parentDiscrepancyNoteList =
              getDnDao().findParentNotesOnlyByItemData(itemdata.getId());
          for (DiscrepancyNoteBean parentDiscrepancyNote : parentDiscrepancyNoteList) {
            if (parentDiscrepancyNote.getResolutionStatusId()
                != 4) { // if the DN's resolution status is not set to Closed
              String description = resword.getString("dn_auto-closed_description");
              String detailedNotes = resword.getString("dn_auto_closed_detailed_notes");
              // create new DN record , new DN Map record , also update the parent record
              createDiscrepancyNoteBean(
                  description, detailedNotes, itemdata.getId(), study, ub, parentDiscrepancyNote);
            }
          }
          iddao = new ItemDataDAO(sm.getDataSource());
          ifmdao = new ItemFormMetadataDAO(sm.getDataSource());
          ItemDataBean idBean = (ItemDataBean) iddao.findByPK(itemdata.getId());

          ItemFormMetadataBean ifmBean =
              ifmdao.findByItemIdAndCRFVersionId(idBean.getItemId(), crfVersionId);

          // Updating Dn_item_data_map actovated column into false for the existing DNs
          ArrayList<DiscrepancyNoteBean> dnBeans =
              getDnDao().findExistingNotesForItemData(itemdata.getId());
          if (dnBeans.size() != 0) {
            DiscrepancyNoteBean dnBean = new DiscrepancyNoteBean();
            dnBean.setEntityId(itemdata.getId());
            dnBean.setActivated(false);
            getDnDao().updateDnMapActivation(dnBean);
          }

          // Default Values are not addressed

          itemdata.setValue("");
          itemdata.setOldStatus(itemdata.getStatus());
          itemdata.setOwner(ub);
          itemdata.setStatus(Status.AVAILABLE);
          itemdata.setUpdater(ub);
          iddao.updateUser(itemdata);
          iddao.update(itemdata);
        }
        // OC-6291 event_crf status change

        eventCRF.setOldStatus(eventCRF.getStatus());
        eventCRF.setStatus(Status.AVAILABLE);
        eventCRF.setUpdater(ub);
        ecdao.update(eventCRF);

        if (event.getSubjectEventStatus().isCompleted()
            || event.getSubjectEventStatus().isSigned()) {
          event.setSubjectEventStatus(SubjectEventStatus.DATA_ENTRY_STARTED);
          event.setUpdater(ub);
          sedao = new StudyEventDAO(sm.getDataSource());
          sedao.update(event);
        }

        String emailBody =
            respage.getString("the_event_CRF")
                + cb.getName()
                + respage.getString("has_been_deleted_from_the_event")
                + event.getStudyEventDefinition().getName()
                + ". "
                + respage.getString("has_been_deleted_from_the_event_cont");

        addPageMessage(emailBody);
        // sendEmail(emailBody);
        request.setAttribute("id", new Integer(studySubId).toString());
        forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
      }
    }
  }
  /**
   * Re-do calculations if funcs include changed item(s) and funcs are not included in the current
   * section. If calculation can not sucessfully redo, old value will be erased and "<erased>" will
   * be saved in database. <br>
   * The parameter 'itemdata' might be overwritten.
   *
   * @param itemGroupSizes
   * @param items
   * @param itemdata
   * @param oldItemdata
   * @param updatedData
   * @param sectionId
   * @return ArrayList<String> which records left_item_text of items who failed to be updated into
   *     database.
   */
  public ArrayList<String> redoCalculations(
      HashMap<String, ItemBean> items,
      HashMap<String, String> itemdata,
      TreeSet<String> changedItems,
      HashMap<Integer, TreeSet<Integer>> itemOrdinals,
      int sectionId) {
    ArrayList<String> updateFailedItems = new ArrayList<String>();
    if (itemdata == null) {
      logger.error("In ScoreCalculator redoCalculations(), itemdata is empty!");
      errors.add("In ScoreCalculator redoCalculations(), 'itemdata' map is empty!");
      return updateFailedItems;
    }
    if (changedItems == null) {
      logger.error("In ScoreCalculator redoCalculations(), 'changeItems' set is empty!");
      errors.add("In ScoreCalculator redoCalculations(), 'changeItems' set is empty!");
      return updateFailedItems;
    }
    ItemFormMetadataDAO ifmdao = new ItemFormMetadataDAO(sm.getDataSource());
    ItemDAO idao = new ItemDAO(sm.getDataSource());
    ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());

    NumberFormat nf = NumberFormat.getInstance();
    Parser parser = new Parser(items, itemdata);
    try {
      // for calculation type
      List<ItemFormMetadataBean> derivedItemList =
          ifmdao.findAllByCRFVersionIdAndResponseTypeId(
              ecb.getCRFVersionId(), ResponseType.CALCULATION.getId());
      if (derivedItemList.size() > 0) {
        Collections.sort(derivedItemList);
        for (ItemFormMetadataBean ifmb : derivedItemList) {
          if (ifmb.getSectionId() != sectionId) {
            ItemBean ib = (ItemBean) idao.findByPK(ifmb.getItemId());
            ResponseOptionBean rob = (ResponseOptionBean) ifmb.getResponseSet().getOptions().get(0);
            int groupsize = 1;
            if (itemOrdinals.containsKey(ib.getId())) {
              groupsize = itemOrdinals.get(ib.getId()).size();
            }
            String value = "";
            ArrayList<ScoreToken> parsedExp = new ArrayList<ScoreToken>();
            for (int i = 0; i < groupsize; ++i) {
              ItemDataBean idb =
                  iddao.findByItemIdAndEventCRFIdAndOrdinal(ifmb.getItemId(), ecb.getId(), i + 1);
              // is there any changed item
              Parser p = new Parser(items, itemdata);
              parsedExp = parser.parseScoreTokens(rob.getValue());
              if (p.isChanged(changedItems, parsedExp)) {
                StringBuffer err = new StringBuffer();
                parsedExp = parser.assignVariables(parsedExp, i + 1);
                // if parser has error and has been calculated
                // before, set "<erased>"
                if (parser.getErrors().length() > 0) {
                  err.append(parser.getErrors());
                  if (idb.isActive()) {
                    idb.setValue("<erased>");
                    idb.setStatus(Status.UNAVAILABLE);
                    idb = (ItemDataBean) iddao.update(idb);
                    if (!idb.isActive()) {
                      String key =
                          i + 1 > 1
                              ? ifmb.getLeftItemText() + "_" + (i + 1)
                              : ifmb.getLeftItemText();
                      updateFailedItems.add(key);
                    }
                  }
                  parser.setErrors(new StringBuffer());
                }
                // otherwise do calculation
                else {
                  try {
                    value = ScoreUtil.eval(parsedExp);
                  } catch (ScoreException se) {
                    logger.error(se.getMessage());
                  }
                  String exp = rob.getValue();
                  exp = exp.replace("##", ",");
                  if (writeToDB(ib, ifmb, idb, exp, value, err)) {
                    changedItems.add(ib.getName());
                    itemdata.put(ib.getId() + "_" + (i + 1), idb.getValue());
                  } else {
                    String key =
                        i + 1 > 1 ? ifmb.getLeftItemText() + "_" + (i + 1) : ifmb.getLeftItemText();
                    updateFailedItems.add(key);
                  }
                }
                if (err.length() > 0) {
                  String key =
                      i + 1 > 1 ? ifmb.getLeftItemText() + "_" + (i + 1) : ifmb.getLeftItemText();
                  errors.add("Item " + key + " contains calculation errors: " + err.toString());
                }
              }
            }
          }
        }
      }

      List<ItemFormMetadataBean> itemList =
          ifmdao.findAllByCRFVersionIdAndResponseTypeId(
              ecb.getCRFVersionId(), ResponseType.GROUP_CALCULATION.getId());
      if (itemList.size() > 0) {
        Collections.sort(itemList);
        for (ItemFormMetadataBean ifmb : itemList) {
          if (ifmb.getSectionId() != sectionId) {
            ItemBean ib = (ItemBean) idao.findByPK(ifmb.getItemId());
            ResponseOptionBean rob = (ResponseOptionBean) ifmb.getResponseSet().getOptions().get(0);
            String value = "";
            Parser p = new Parser(items, itemdata);
            ArrayList<ScoreToken> parsedExp = parser.parseScoreTokens(rob.getValue());
            if (p.isChanged(changedItems, parsedExp)) {
              StringBuffer err = new StringBuffer();
              parser.setErrors(err);
              parsedExp = parser.assignVariables(parsedExp, itemOrdinals);
              ItemDataBean idb =
                  iddao.findByItemIdAndEventCRFIdAndOrdinal(ifmb.getItemId(), ecb.getId(), 1);
              if (parser.getErrors().length() > 0) {
                err.append(parser.getErrors());
                if (idb.isActive()) {
                  idb.setValue("<erased>");
                  idb.setStatus(Status.UNAVAILABLE);
                  idb = (ItemDataBean) iddao.update(idb);
                  if (!idb.isActive()) {
                    updateFailedItems.add(ifmb.getLeftItemText());
                  }
                }
              } else {
                try {
                  value = ScoreUtil.eval(parsedExp);
                } catch (ScoreException se) {
                  logger.error(se.getMessage());
                }
                String exp = rob.getValue();
                exp = exp.replace("##", ",");
                if (writeToDB(ib, ifmb, idb, exp, value, err)) {
                  changedItems.add(ib.getName());
                  itemdata.put(ib.getId() + "_" + idb.getOrdinal(), idb.getValue());
                } else {
                  updateFailedItems.add(ifmb.getLeftItemText());
                }
              }
              if (err.length() > 0) {
                errors.add(
                    "Item "
                        + ifmb.getLeftItemText()
                        + " contains calculation errors: "
                        + err.toString());
              }
            }
          }
        }
      }
    } catch (OpenClinicaException e) {
      logger.error(e.getMessage());
    }

    return updateFailedItems;
  }
  @Override
  public void processRequest() throws Exception {

    SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
    FormProcessor fp = new FormProcessor(request);
    int subjectId = fp.getInt("id");

    String action = fp.getString("action");
    if (subjectId == 0 || StringUtil.isBlank(action)) {
      addPageMessage(respage.getString("please_choose_a_subject_to_remove"));
      forwardPage(Page.SUBJECT_LIST_SERVLET);
    } else {

      SubjectBean subject = (SubjectBean) sdao.findByPK(subjectId);

      // find all study subjects
      StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
      ArrayList studySubs = ssdao.findAllBySubjectId(subjectId);

      // find study events
      StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
      ArrayList events = sedao.findAllBySubjectId(subjectId);
      if ("confirm".equalsIgnoreCase(action)) {
        request.setAttribute("subjectToRemove", subject);
        request.setAttribute("studySubs", studySubs);
        request.setAttribute("events", events);
        forwardPage(Page.REMOVE_SUBJECT);
      } else {
        logger.info("submit to remove the subject");
        // change all statuses to deleted
        subject.setStatus(Status.DELETED);
        subject.setUpdater(ub);
        subject.setUpdatedDate(new Date());
        sdao.update(subject);

        // remove subject references from study
        for (int i = 0; i < studySubs.size(); i++) {
          StudySubjectBean studySub = (StudySubjectBean) studySubs.get(i);
          if (!studySub.getStatus().equals(Status.DELETED)) {
            studySub.setStatus(Status.AUTO_DELETED);
            studySub.setUpdater(ub);
            studySub.setUpdatedDate(new Date());
            ssdao.update(studySub);
          }
        }

        EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());

        for (int j = 0; j < events.size(); j++) {
          StudyEventBean event = (StudyEventBean) events.get(j);
          if (!event.getStatus().equals(Status.DELETED)) {
            event.setStatus(Status.AUTO_DELETED);
            event.setUpdater(ub);
            event.setUpdatedDate(new Date());
            sedao.update(event);

            ArrayList eventCRFs = ecdao.findAllByStudyEvent(event);

            ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
            for (int k = 0; k < eventCRFs.size(); k++) {
              EventCRFBean eventCRF = (EventCRFBean) eventCRFs.get(k);
              if (!eventCRF.getStatus().equals(Status.DELETED)) {
                eventCRF.setStatus(Status.AUTO_DELETED);
                eventCRF.setUpdater(ub);
                eventCRF.setUpdatedDate(new Date());
                ecdao.update(eventCRF);
                // remove all the item data
                ArrayList itemDatas = iddao.findAllByEventCRFId(eventCRF.getId());
                for (int a = 0; a < itemDatas.size(); a++) {
                  ItemDataBean item = (ItemDataBean) itemDatas.get(a);
                  if (!item.getStatus().equals(Status.DELETED)) {
                    item.setStatus(Status.AUTO_DELETED);
                    item.setUpdater(ub);
                    item.setUpdatedDate(new Date());
                    iddao.update(item);
                  }
                }
              }
            }
          }
        }

        String emailBody =
            respage.getString("the_subject")
                + " "
                + respage.getString("has_been_removed_succesfully");

        addPageMessage(emailBody);
        //                sendEmail(emailBody);

        forwardPage(Page.SUBJECT_LIST_SERVLET);
      }
    }
  }
  @Override
  @SuppressWarnings(value = "unchecked")
  public void processRequest() throws Exception {
    ItemDataDAO itemDataDao = new ItemDataDAO(sm.getDataSource());
    EventCRFDAO eventCrfDao = new EventCRFDAO(sm.getDataSource());
    CrfBusinessLogicHelper crfBusinessLogicHelper = new CrfBusinessLogicHelper(sm.getDataSource());
    String action = request.getParameter("action");

    FormProcessor fp = new FormProcessor(request);

    // checks which module the requests are from
    String module = fp.getString(MODULE);
    request.setAttribute(MODULE, module);

    resetPanel();
    panel.setStudyInfoShown(false);
    panel.setOrderedData(true);

    setToPanel(resword.getString("create_CRF"), respage.getString("br_create_new_CRF_entering"));

    setToPanel(
        resword.getString("create_CRF_version"), respage.getString("br_create_new_CRF_uploading"));
    setToPanel(
        resword.getString("revise_CRF_version"), respage.getString("br_if_you_owner_CRF_version"));
    setToPanel(
        resword.getString("CRF_spreadsheet_template"),
        respage.getString("br_download_blank_CRF_spreadsheet_from"));
    setToPanel(
        resword.getString("example_CRF_br_spreadsheets"),
        respage.getString("br_download_example_CRF_instructions_from"));

    if ("confirm".equalsIgnoreCase(action)) {
      List<DisplayItemBeanWrapper> displayItemBeanWrappers =
          (List<DisplayItemBeanWrapper>) session.getAttribute("importedData");
      logger.info("Size of displayItemBeanWrappers : " + displayItemBeanWrappers.size());
      forwardPage(Page.VERIFY_IMPORT_CRF_DATA);
    }

    if ("save".equalsIgnoreCase(action)) {
      List<DisplayItemBeanWrapper> displayItemBeanWrappers =
          (List<DisplayItemBeanWrapper>) session.getAttribute("importedData");
      // System.out.println("Size of displayItemBeanWrappers : " + displayItemBeanWrappers.size());

      for (DisplayItemBeanWrapper wrapper : displayItemBeanWrappers) {

        int eventCrfBeanId = -1;
        EventCRFBean eventCrfBean = new EventCRFBean();

        // TODO : tom , the wrapper object has all the necessary data -
        // as you see we check the
        // is to see if this data is Savable if it is then we go ahead
        // and save it. if not we discard.
        // So the change needs to happen here , instead of discarding we
        // need to file discrepancy notes
        // and save the data. If you look in the
        // Page.VERIFY_IMPORT_CRF_DATA jsp file you can see how I am
        // pulling the errors. and use that in the same way.

        logger.info("right before we check to make sure it is savable: " + wrapper.isSavable());
        if (wrapper.isSavable()) {
          ArrayList<Integer> eventCrfInts = new ArrayList<Integer>();
          // based on the use case: "If any of the data does not meet
          // validations specified in the CRF
          // Template, a discrepancy note is automatically logged.
          // The DN will have a type of Failed Validation Check, and
          // a message of Failed Validation check."
          // System.out.println("wrapper problems found : " +
          // wrapper.getValidationErrors().toString());
          for (DisplayItemBean displayItemBean : wrapper.getDisplayItemBeans()) {
            eventCrfBeanId = displayItemBean.getData().getEventCRFId();
            eventCrfBean = (EventCRFBean) eventCrfDao.findByPK(eventCrfBeanId);
            logger.info("found value here: " + displayItemBean.getData().getValue());
            logger.info("found status here: " + eventCrfBean.getStatus().getName());
            // System.out.println("found event crf bean name here: "
            // +
            // eventCrfBean.getEventName()+" id "+eventCrfBean.getId
            // ());
            // SO, items can be created in a wrapper which is set to
            // overwrite
            // we get around this by checking the bean first, to
            // make sure it's not null
            ItemDataBean itemDataBean = new ItemDataBean();
            itemDataBean =
                itemDataDao.findByItemIdAndEventCRFIdAndOrdinal(
                    displayItemBean.getItem().getId(),
                    eventCrfBean.getId(),
                    displayItemBean.getData().getOrdinal());
            if (wrapper.isOverwrite() && itemDataBean.getStatus() != null) {
              // ItemDataBean itemDataBean = new ItemDataBean();
              // itemDataBean =
              // itemDataDao.findByItemIdAndEventCRFIdAndOrdinal(
              // displayItemBean.getItem().getId(),
              // eventCrfBean.getId(), displayItemBean
              // .getData().getOrdinal());
              // itemDataBean =
              // itemDataDao.findByEventCRFIdAndItemName(
              // eventCrfBean,
              // displayItemBean.getItem().getName());
              logger.info(
                  "just tried to find item data bean on item name "
                      + displayItemBean.getItem().getName());
              itemDataBean.setUpdatedDate(new Date());
              itemDataBean.setUpdater(ub);
              itemDataBean.setValue(displayItemBean.getData().getValue());
              // set status?
              itemDataDao.update(itemDataBean);
              logger.info("updated: " + itemDataBean.getItemId());
              // need to set pk here in order to create dn
              displayItemBean.getData().setId(itemDataBean.getId());
            } else {
              itemDataDao.create(displayItemBean.getData());
              logger.info(
                  "created: "
                      + displayItemBean.getData().getItemId()
                      + "event CRF ID = "
                      + eventCrfBean.getId()
                      + "CRF VERSION ID ="
                      + eventCrfBean.getCRFVersionId());

              // does this dao function work for repeating
              // events/groups?
              // ItemDataBean itemDataBean =
              // itemDataDao.findByEventCRFIdAndItemName(
              // eventCrfBean,
              // displayItemBean.getItem().getName());
              ItemDataBean itemDataBean2 =
                  itemDataDao.findByItemIdAndEventCRFIdAndOrdinal(
                      displayItemBean.getItem().getId(),
                      eventCrfBean.getId(),
                      displayItemBean.getData().getOrdinal());
              logger.info(
                  "found: id " + itemDataBean2.getId() + " name " + itemDataBean2.getName());
              displayItemBean.getData().setId(itemDataBean2.getId());
            }
            // logger.info("created item data bean:
            // "+displayItemBean.getData().getId());
            // logger.info("created:
            // "+displayItemBean.getData().getName());
            // logger.info("continued:
            // "+displayItemBean.getData().getItemId());
            ItemDAO idao = new ItemDAO(sm.getDataSource());
            ItemBean ibean = (ItemBean) idao.findByPK(displayItemBean.getData().getItemId());
            // logger.info("continued2: getName " +
            // ibean.getName());
            // System.out.println("*** checking for validation errors: " + ibean.getName());
            String itemOid =
                displayItemBean.getItem().getOid()
                    + "_"
                    + wrapper.getStudyEventRepeatKey()
                    + "_"
                    + displayItemBean.getData().getOrdinal()
                    + "_"
                    + wrapper.getStudySubjectOid();
            if (wrapper.getValidationErrors().containsKey(itemOid)) {
              ArrayList messageList = (ArrayList) wrapper.getValidationErrors().get(itemOid);
              // if
              // (wrapper.getValidationErrors().containsKey(ibean
              // .getName())) {
              // ArrayList messageList = (ArrayList)
              // wrapper.getValidationErrors
              // ().get(ibean.getName());
              // could be more then one will have to iterate
              // could it be more than one? tbh 08/2008
              for (int iter = 0; iter < messageList.size(); iter++) {
                String message = (String) messageList.get(iter);
                DiscrepancyNoteBean parentDn =
                    ImportSpringJob.createDiscrepancyNote(
                        ibean,
                        message,
                        eventCrfBean,
                        displayItemBean,
                        null,
                        ub,
                        sm.getDataSource(),
                        currentStudy);
                ImportSpringJob.createDiscrepancyNote(
                    ibean,
                    message,
                    eventCrfBean,
                    displayItemBean,
                    parentDn.getId(),
                    ub,
                    sm.getDataSource(),
                    currentStudy);
                // System.out.println("*** created disc note with message: " + message);
                // displayItemBean);
              }
            }
            // logger.info("created:
            // "+displayItemBean.getDbData().getName());
            if (!eventCrfInts.contains(new Integer(eventCrfBean.getId()))) {
              crfBusinessLogicHelper.markCRFComplete(eventCrfBean, ub);
              // System.out.println("*** just updated event crf bean: " + eventCrfBean.getId());
              eventCrfInts.add(new Integer(eventCrfBean.getId()));
            }
          }
          // end of item datas, tbh
          // crfBusinessLogicHelper.markCRFComplete(eventCrfBean, ub);
          // System .out.println("*** just updated event crf bean: "+
          // eventCrfBean.getId());
          // need to update the study event status as well, tbh
          // crfBusinessLogicHelper.updateStudyEvent(eventCrfBean,
          // ub);
          // above should do it for us, tbh 08/2008
        }
      }

      addPageMessage(respage.getString("data_has_been_successfully_import"));
      // forwardPage(Page.SUBMIT_DATA_SERVLET);
      forwardPage(Page.LIST_STUDY_SUBJECTS_SERVLET);
      // replaced tbh, 06/2009
    }
  }
  @Override
  public void processRequest() throws Exception {

    CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
    FormProcessor fp = new FormProcessor(request);
    int versionId = fp.getInt("id", true);
    String module = fp.getString("module");
    request.setAttribute("module", module);

    String action = fp.getString("action");
    if (versionId == 0) {
      addPageMessage(respage.getString("please_choose_a_CRF_version_to_remove"));
      forwardPage(Page.CRF_LIST_SERVLET);
    } else {
      if (StringUtil.isBlank(action)) {
        addPageMessage(respage.getString("no_action_specified"));
        forwardPage(Page.CRF_LIST_SERVLET);
        return;
      }
      CRFVersionBean version = (CRFVersionBean) cvdao.findByPK(versionId);

      SectionDAO secdao = new SectionDAO(sm.getDataSource());

      EventCRFDAO evdao = new EventCRFDAO(sm.getDataSource());
      // find all event crfs by version id
      ArrayList eventCRFs = evdao.findUndeletedWithStudySubjectsByCRFVersion(versionId);
      if ("confirm".equalsIgnoreCase(action)) {
        request.setAttribute("versionToRemove", version);
        request.setAttribute("eventCRFs", eventCRFs);
        forwardPage(Page.REMOVE_CRF_VERSION);
      } else {
        logger.info("submit to remove the crf version");
        // version
        version.setStatus(Status.DELETED);
        version.setUpdater(ub);
        version.setUpdatedDate(new Date());
        cvdao.update(version);
        // added below tbh 092007, seems that we don't remove the event
        // crfs in the second pass
        for (int ii = 0; ii < eventCRFs.size(); ii++) {
          EventCRFBean ecbean = (EventCRFBean) eventCRFs.get(ii);
          ecbean.setStatus(Status.AUTO_DELETED);
          ecbean.setUpdater(ub);
          ecbean.setUpdatedDate(new Date());
          evdao.update(ecbean);
        }
        // added above tbh 092007, to fix task
        // all sections
        ArrayList sections = secdao.findAllByCRFVersionId(version.getId());
        for (int j = 0; j < sections.size(); j++) {
          SectionBean section = (SectionBean) sections.get(j);
          if (!section.getStatus().equals(Status.DELETED)) {
            section.setStatus(Status.AUTO_DELETED);
            section.setUpdater(ub);
            section.setUpdatedDate(new Date());
            secdao.update(section);
          }
        }

        // all item data related to event crfs
        ItemDataDAO idao = new ItemDataDAO(sm.getDataSource());
        for (int i = 0; i < eventCRFs.size(); i++) {
          EventCRFBean eventCRF = (EventCRFBean) eventCRFs.get(i);
          if (!eventCRF.getStatus().equals(Status.DELETED)) {
            eventCRF.setStatus(Status.AUTO_DELETED);
            eventCRF.setUpdater(ub);
            eventCRF.setUpdatedDate(new Date());
            evdao.update(eventCRF);

            ArrayList items = idao.findAllByEventCRFId(eventCRF.getId());
            for (int j = 0; j < items.size(); j++) {
              ItemDataBean item = (ItemDataBean) items.get(j);
              if (!item.getStatus().equals(Status.DELETED)) {
                item.setStatus(Status.AUTO_DELETED);
                item.setUpdater(ub);
                item.setUpdatedDate(new Date());
                idao.update(item);
              }
            }
          }
        }

        addPageMessage(
            respage.getString("the_CRF")
                + version.getName()
                + " "
                + respage.getString("has_been_removed_succesfully"));
        forwardPage(Page.CRF_LIST_SERVLET);
      }
    }
  }
  @Override
  public void processRequest() throws Exception {
    String studySubIdString = request.getParameter("id"); // studySubjectId
    String subIdString = request.getParameter("subjectId");
    String studyIdString = request.getParameter("studyId");

    SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
    StudySubjectDAO subdao = new StudySubjectDAO(sm.getDataSource());

    if (StringUtil.isBlank(studySubIdString)
        || StringUtil.isBlank(subIdString)
        || StringUtil.isBlank(studyIdString)) {
      addPageMessage(respage.getString("please_choose_a_study_subject_to_remove"));
      forwardPage(Page.LIST_STUDY_SUBJECT_SERVLET);
    } else {
      int studyId = Integer.valueOf(studyIdString.trim()).intValue();
      int studySubId = Integer.valueOf(studySubIdString.trim()).intValue();
      int subjectId = Integer.valueOf(subIdString.trim()).intValue();

      SubjectBean subject = (SubjectBean) sdao.findByPK(subjectId);

      StudySubjectBean studySub = (StudySubjectBean) subdao.findByPK(studySubId);

      StudyDAO studydao = new StudyDAO(sm.getDataSource());
      StudyBean study = (StudyBean) studydao.findByPK(studyId);

      // find study events
      StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
      ArrayList events = sedao.findAllByStudyAndStudySubjectId(study, studySubId);

      String action = request.getParameter("action");
      if ("confirm".equalsIgnoreCase(action)) {
        if (!studySub.getStatus().equals(Status.AVAILABLE)) {
          addPageMessage(
              respage.getString("this_subject_is_not_available_for_this_study")
                  + " "
                  + respage.getString("please_contact_sysadmin_for_more_information"));
          forwardPage(Page.LIST_STUDY_SUBJECT_SERVLET);
          return;
        }

        request.setAttribute("subject", subject);
        request.setAttribute("study", study);
        request.setAttribute("studySub", studySub);
        request.setAttribute("events", events);

        forwardPage(Page.REMOVE_STUDY_SUBJECT);
      } else {
        logger.info("submit to remove the subject from study");
        // remove subject from study
        studySub.setStatus(Status.DELETED);
        studySub.setUpdater(ub);
        studySub.setUpdatedDate(new Date());
        subdao.update(studySub);

        // remove all study events
        // remove all event crfs
        EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());

        for (int j = 0; j < events.size(); j++) {
          StudyEventBean event = (StudyEventBean) events.get(j);
          if (!event.getStatus().equals(Status.DELETED)) {
            event.setStatus(Status.AUTO_DELETED);
            event.setUpdater(ub);
            event.setUpdatedDate(new Date());
            sedao.update(event);

            ArrayList eventCRFs = ecdao.findAllByStudyEvent(event);

            ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
            for (int k = 0; k < eventCRFs.size(); k++) {
              EventCRFBean eventCRF = (EventCRFBean) eventCRFs.get(k);
              if (!eventCRF.getStatus().equals(Status.DELETED)) {
                eventCRF.setStatus(Status.AUTO_DELETED);
                eventCRF.setUpdater(ub);
                eventCRF.setUpdatedDate(new Date());
                ecdao.update(eventCRF);
                // remove all the item data
                ArrayList itemDatas = iddao.findAllByEventCRFId(eventCRF.getId());
                for (int a = 0; a < itemDatas.size(); a++) {
                  ItemDataBean item = (ItemDataBean) itemDatas.get(a);
                  if (!item.getStatus().equals(Status.DELETED)) {
                    item.setStatus(Status.AUTO_DELETED);
                    item.setUpdater(ub);
                    item.setUpdatedDate(new Date());
                    iddao.update(item);
                  }
                }
              }
            }
          }
        }

        String emailBody =
            respage.getString("the_subject")
                + " "
                + subject.getName()
                + " "
                + respage.getString("has_been_removed_from_the_study")
                + study.getName()
                + ".";

        addPageMessage(emailBody);
        sendEmail(emailBody);
        forwardPage(Page.LIST_STUDY_SUBJECT_SERVLET);
      }
    }
  }