public Object getEntityFromHashMap(HashMap hm) { ItemDataBean eb = new ItemDataBean(); this.setEntityAuditInformation(eb, hm); eb.setId(((Integer) hm.get("item_data_id")).intValue()); eb.setEventCRFId(((Integer) hm.get("event_crf_id")).intValue()); eb.setItemId(((Integer) hm.get("item_id")).intValue()); eb.setValue((String) hm.get("value")); eb.setStatus(Status.get(((Integer) hm.get("status_id")).intValue())); return eb; }
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(); }
private ItemDataBean copyItemDataBean(ItemDataBean src) { ItemDataBean result = new ItemDataBean(); result.setEventCRFId(src.getEventCRFId()); result.setItemId(src.getItemId()); result.setValue(src.getValue()); result.setOrdinal(src.getOrdinal()); result.setSelected(src.isSelected()); result.setAuditLog(src.isAuditLog()); result.setCreatedDate(src.getCreatedDate()); result.setUpdatedDate(src.getUpdatedDate()); result.setOwner(src.getOwner()); result.setOwnerId(src.getOwnerId()); result.setUpdater(src.getUpdater()); result.setUpdaterId(src.getUpdaterId()); result.setStatus(src.getStatus()); return result; }
public ArrayList<ItemBean> findAllWithItemDataByCRFVersionId(int crfVersionId, int eventCRFId) { this.unsetTypeExpected(); this.setTypeExpected(1, TypeNames.STRING); // (item)name this.setTypeExpected(2, TypeNames.INT); // ordinal this.setTypeExpected(3, TypeNames.STRING); // oc_oid this.setTypeExpected(4, TypeNames.INT); // item_data_id this.setTypeExpected(5, TypeNames.INT); // item_id this.setTypeExpected(6, TypeNames.STRING); // (item)value ArrayList<ItemBean> answer = new ArrayList<ItemBean>(); HashMap variables = new HashMap(); variables.put(new Integer(1), new Integer(crfVersionId)); variables.put(new Integer(2), new Integer(eventCRFId)); String sql = digester.getQuery("findAllWithItemDataByCRFVersionId"); ArrayList rows = super.select(sql, variables); Iterator it = rows.iterator(); int cur_item_id = 0; ItemBean item_bean = null; ItemDataBean item_data_bean = null; while (it.hasNext()) { HashMap row = (HashMap) it.next(); Integer id = (Integer) row.get("item_id"); if (cur_item_id != id.intValue()) { item_bean = new ItemBean(); answer.add(item_bean); cur_item_id = id.intValue(); item_bean.setId(cur_item_id); item_bean.setName((String) row.get("name")); item_bean.setOid((String) row.get("oc_oid")); } item_data_bean = new ItemDataBean(); item_data_bean.setValue((String) row.get("value")); item_data_bean.setOrdinal(((Integer) row.get("ordinal")).intValue()); item_data_bean.setId(((Integer) row.get("item_data_id")).intValue()); item_data_bean.setItemId(cur_item_id); item_bean.addItemDataElement(item_data_bean); } return answer; }
@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 @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 } }