public static DiscrepancyNoteBean createDiscrepancyNote(
      ItemBean itemBean,
      String message,
      EventCRFBean eventCrfBean,
      DisplayItemBean displayItemBean,
      Integer parentId,
      UserAccountBean uab,
      DataSource ds,
      StudyBean study) {
    // DisplayItemBean displayItemBean) {
    DiscrepancyNoteBean note = new DiscrepancyNoteBean();
    StudySubjectDAO ssdao = new StudySubjectDAO(ds);
    note.setDescription(message);
    note.setDetailedNotes("Failed Validation Check");
    note.setOwner(uab);
    note.setCreatedDate(new Date());
    note.setResolutionStatusId(ResolutionStatus.OPEN.getId());
    note.setDiscrepancyNoteTypeId(DiscrepancyNoteType.FAILEDVAL.getId());
    if (parentId != null) {
      note.setParentDnId(parentId);
    }

    note.setField(itemBean.getName());
    note.setStudyId(study.getId());
    note.setEntityName(itemBean.getName());
    note.setEntityType("ItemData");
    note.setEntityValue(displayItemBean.getData().getValue());

    note.setEventName(eventCrfBean.getName());
    note.setEventStart(eventCrfBean.getCreatedDate());
    note.setCrfName(displayItemBean.getEventDefinitionCRF().getCrfName());

    StudySubjectBean ss = (StudySubjectBean) ssdao.findByPK(eventCrfBean.getStudySubjectId());
    note.setSubjectName(ss.getName());

    note.setEntityId(displayItemBean.getData().getId());
    note.setColumn("value");

    DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(ds);
    note = (DiscrepancyNoteBean) dndao.create(note);
    // so that the below method works, need to set the entity above
    // System.out.println("trying to create mapping with " + note.getId() + " " + note.getEntityId()
    // + " " + note.getColumn() + " " + note.getEntityType());
    dndao.createMapping(note);
    // System.out.println("just created mapping");
    return note;
  }
Beispiel #2
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 public EntityBean update(EntityBean eb) {
   ItemBean ib = (ItemBean) eb;
   HashMap variables = new HashMap();
   variables.put(new Integer(1), ib.getName());
   variables.put(new Integer(2), ib.getDescription());
   variables.put(new Integer(3), ib.getUnits());
   variables.put(new Integer(4), new Boolean(ib.isPhiStatus()));
   variables.put(new Integer(5), new Integer(ib.getItemDataTypeId()));
   variables.put(new Integer(6), new Integer(ib.getItemReferenceTypeId()));
   variables.put(new Integer(7), new Integer(ib.getStatus().getId()));
   variables.put(new Integer(8), new Integer(ib.getUpdaterId()));
   variables.put(new Integer(9), new Integer(ib.getId()));
   this.execute(digester.getQuery("update"), variables);
   return eb;
 }
Beispiel #3
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 public EntityBean create(EntityBean eb) {
   ItemBean ib = (ItemBean) eb;
   // per the create sql statement
   HashMap variables = new HashMap();
   variables.put(new Integer(1), ib.getName());
   variables.put(new Integer(2), ib.getDescription());
   variables.put(new Integer(3), ib.getUnits());
   variables.put(new Integer(4), new Boolean(ib.isPhiStatus()));
   variables.put(new Integer(5), new Integer(ib.getItemDataTypeId()));
   variables.put(new Integer(6), new Integer(ib.getItemReferenceTypeId()));
   variables.put(new Integer(7), new Integer(ib.getStatus().getId()));
   variables.put(new Integer(8), new Integer(ib.getOwnerId()));
   // date_created=now() in Postgres
   this.execute(digester.getQuery("create"), variables);
   // set the id here????
   return eb;
 }
  /**
   * 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;
  }
  /**
   * Organize objects in a certain way so that we can show to Users on UI. step1 : Get StudyEvent ,
   * eventCrf , crfVersion from studyEventId.
   *
   * @param crfViewSpecificOrderedObjects
   * @param ruleSet
   * @param rule
   * @return
   */
  private HashMap<RuleBulkExecuteContainer, HashMap<RuleBulkExecuteContainerTwo, Set<String>>>
      populateForCrfBasedRulesView(
          HashMap<RuleBulkExecuteContainer, HashMap<RuleBulkExecuteContainerTwo, Set<String>>>
              crfViewSpecificOrderedObjects,
          RuleSetBean ruleSet,
          RuleBean rule,
          String result,
          StudyBean currentStudy,
          List<RuleActionBean> actions) {

    // step1
    StudyEventBean studyEvent =
        (StudyEventBean)
            getStudyEventDao()
                .findByPK(
                    Integer.valueOf(
                        getExpressionService()
                            .getStudyEventDefenitionOrdninalCurated(
                                ruleSet.getTarget().getValue())));
    EventCRFBean eventCrf =
        (EventCRFBean)
            getEventCrfDao()
                .findAllByStudyEventAndCrfOrCrfVersionOid(
                    studyEvent, getExpressionService().getCrfOid(ruleSet.getTarget().getValue()))
                .get(0);
    CRFVersionBean crfVersion =
        (CRFVersionBean) getCrfVersionDao().findByPK(eventCrf.getCRFVersionId());

    RuleBulkExecuteContainer key =
        new RuleBulkExecuteContainer(crfVersion.getName(), rule, result, actions);
    String key2String =
        getExpressionService()
            .getCustomExpressionUsedToCreateView(
                ruleSet.getTarget().getValue(), studyEvent.getSampleOrdinal());
    String studyEventDefinitionName =
        getExpressionService()
            .getStudyEventDefinitionFromExpression(ruleSet.getTarget().getValue(), currentStudy)
            .getName();
    studyEventDefinitionName += " [" + studyEvent.getSampleOrdinal() + "]";
    // String itemGroupName =
    // getExpressionService().getItemGroupNameAndOrdinal(ruleSet.getTarget().getValue());
    // String itemName =
    // getExpressionService().getItemGroupExpression(ruleSet.getTarget().getValue()).getName();

    String itemGroupName =
        getExpressionService().getItemGroupNameAndOrdinal(ruleSet.getTarget().getValue());
    ItemGroupBean itemGroupBean =
        getExpressionService().getItemGroupExpression(ruleSet.getTarget().getValue());
    ItemBean itemBean =
        getExpressionService().getItemExpression(ruleSet.getTarget().getValue(), itemGroupBean);
    String itemName = itemBean.getName();

    RuleBulkExecuteContainerTwo key2 =
        new RuleBulkExecuteContainerTwo(
            key2String, studyEvent, studyEventDefinitionName, itemGroupName, itemName);
    StudySubjectBean studySubject =
        (StudySubjectBean) getStudySubjectDao().findByPK(studyEvent.getStudySubjectId());

    if (crfViewSpecificOrderedObjects.containsKey(key)) {
      HashMap<RuleBulkExecuteContainerTwo, Set<String>> k = crfViewSpecificOrderedObjects.get(key);
      if (k.containsKey(key2)) {
        k.get(key2).add(String.valueOf(studySubject.getLabel()));
      } else {
        HashSet<String> values = new HashSet<String>();
        values.add(String.valueOf(studySubject.getLabel()));
        k.put(key2, values);
      }
    } else {
      HashMap<RuleBulkExecuteContainerTwo, Set<String>> k =
          new HashMap<RuleBulkExecuteContainerTwo, Set<String>>();
      HashSet<String> values = new HashSet<String>();
      values.add(String.valueOf(studySubject.getLabel()));
      k.put(key2, values);
      crfViewSpecificOrderedObjects.put(key, k);
    }
    return crfViewSpecificOrderedObjects;
  }