/**
* Performs calculation. <br>
* Notice: both parameter 'itemdata' and parameter 'errs' might be updated in this method.
*
* @param displayItems
* @param items
* @param itemdata
* @param errs
* @return
* @author ywang (Jan. 2008)
*/
public String doCalculation(
DisplayItemBean displayItem,
HashMap<String, ItemBean> items,
HashMap<String, String> itemdata,
HashMap<Integer, TreeSet<Integer>> itemOrdinals,
StringBuffer errs,
int ordinal) {
if (itemdata == null) {
logger.error("In DataEntryServlet doCalculation(), itemdata map is empty!");
errs.append("Calculation cannot be started because needed items are empty" + "; ");
return "";
}
String value = "";
NumberFormat nf = NumberFormat.getInstance();
Parser parser = new Parser(items, itemdata);
ItemBean ib = displayItem.getItem();
ItemFormMetadataBean ifm = displayItem.getMetadata();
ResponseOptionBean rob = (ResponseOptionBean) ifm.getResponseSet().getOptions().get(0);
ArrayList<ScoreToken> parsedExp = new ArrayList<ScoreToken>();
int type = ifm.getResponseSet().getResponseTypeId();
if (type == 8) {
parsedExp = parser.assignVariables(parser.parseScoreTokens(rob.getValue()), ordinal);
} else if (type == 9) {
// YW, 1-16-2008, for group-calculation type. Current restrictions:
// 1. only calculate sum(), avg(), min(), max(), median(), stdev()
// 2. formula arguments only contain item beans
// 3. only one item bean per argument
parsedExp = parser.assignVariables(parser.parseScoreTokens(rob.getValue()), itemOrdinals);
}
if (parser.getErrors().length() > 0) {
errs.append(parser.getErrors());
} else {
try {
value = ScoreUtil.eval(parsedExp);
} catch (ScoreException se) {
logger.error(se.getMessage());
}
ItemDataType idt = ib.getDataType();
if (value == null || value.length() == 0) {
value = "";
String exp = rob.getValue();
exp = exp.replace("##", ",");
errs.append("Result is empty in" + " " + exp + "; ");
// errors.append(resexception.getString("result_is_empty_in") +
// " " + exp + "; ");
} else {
value = this.getMathContextValue(value, ifm, idt, errs);
}
// idb.setStatus(Status.UNAVAILABLE);
itemdata.put(ib.getId() + "_" + ordinal, value);
}
return value;
}
protected String getMathContextValue(
String value, ItemFormMetadataBean ifm, ItemDataType idt, StringBuffer errorMessage) {
ResponseOptionBean rob = (ResponseOptionBean) ifm.getResponseSet().getOptions().get(0);
String widthDecimal = ifm.getWidthDecimal();
int width = Validator.parseWidth(widthDecimal);
int decimal = Validator.parseDecimal(widthDecimal);
NumberFormat nf = NumberFormat.getInstance();
if (idt.equals(ItemDataType.INTEGER)) {
try {
Double d = nf.parse(value).doubleValue();
int p = 0;
if (width > 0) {
p = d >= 0 ? width : width - 1;
} else {
p = BigDecimal.valueOf(d).precision();
}
MathContext mc = new MathContext(p, RoundingMode.valueOf(BigDecimal.ROUND_HALF_UP));
value = (new BigDecimal(d, mc)).setScale(0, BigDecimal.ROUND_HALF_UP).toPlainString();
} catch (ParseException e) {
logger.error("Number was expected in " + rob.getValue() + " : " + value);
String exp = rob.getValue();
exp = exp.replace("##", ",");
errorMessage.append("Number was expected in" + " " + exp + " : " + value + "; ");
// errors.append(resexception.getString("number_expected_in")
// + " " + exp + ": " + value + "; ");
value = "";
}
} else if (idt.equals(ItemDataType.REAL)) {
try {
Double d = nf.parse(value).doubleValue();
// there should be no width specify for calculation item
int p = BigDecimal.valueOf(d).precision();
// set default scale as 4
int scale = decimal > 0 ? decimal : DEFAULT_DECIMAL;
MathContext mc = new MathContext(p, RoundingMode.valueOf(BigDecimal.ROUND_HALF_UP));
value = (new BigDecimal(d, mc)).setScale(scale, BigDecimal.ROUND_HALF_UP).toPlainString();
} catch (Exception ee) {
String exp = rob.getValue();
exp = exp.replace("##", ",");
logger.error("Number was expected in " + exp + " : " + value);
errorMessage.append("Number was expected in" + " " + exp + " : " + value + "; ");
// errors.append(resexception.getString("number_expected_in")
// + " " + exp + ": " + value + "; ");
value = "";
}
}
return value;
}
/**
* 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
protected DisplayItemBean validateDisplayItemBean(
DiscrepancyValidator v, DisplayItemBean dib, String inputName) {
org.akaza.openclinica.bean.core.ResponseType rt =
dib.getMetadata().getResponseSet().getResponseType();
boolean isSingleItem = false;
if (StringUtil.isBlank(inputName)) { // for single items
inputName = getInputName(dib);
isSingleItem = true;
}
// we only give warning to user if data entered in DDE is different from
// IDE when the first
// time user hits 'save'
int keyId = ecb.getId();
Integer validationCount = (Integer) session.getAttribute(COUNT_VALIDATE + keyId);
ItemDataBean valueToCompare = dib.getData();
if (!isSingleItem) {
valueToCompare = dib.getDbData();
}
boolean showOriginalItem =
getItemMetadataService()
.isShown(dib.getItem().getId(), ecb, valueToCompare); // was dib.getData()
boolean showItem = dib.getMetadata().isShowItem();
boolean showDuplicateItem =
getItemMetadataService()
.hasPassedDDE(
dib.getMetadata(),
ecb,
valueToCompare); // .isShown(dib.getItem().getId(), ecb, dib.getDbData());// where
// is the set db data?
logger.debug(
"*** show original item has value "
+ dib.getData().getValue()
+ " and show item has value "
+ valueToCompare.getValue());
logger.debug(
"--- show original: "
+ showOriginalItem
+ " show duplicate: "
+ showDuplicateItem
+ " and just show item: "
+ showItem);
logger.debug("VALIDATION COUNT " + validationCount);
if (showOriginalItem && showDuplicateItem || showItem) {
// it should either be shown already, OR shown in the database?
// logger.debug("=== we passed, adding validation here");
Integer indValidationCount =
(Integer) session.getAttribute(COUNT_VALIDATE + keyId + dib.getMetadata().getId());
if (rt.equals(org.akaza.openclinica.bean.core.ResponseType.TEXT)
|| rt.equals(org.akaza.openclinica.bean.core.ResponseType.TEXTAREA)
|| rt.equals(org.akaza.openclinica.bean.core.ResponseType.FILE)) {
dib = validateDisplayItemBeanText(v, dib, inputName);
// necessary?
// if (indValidationCount == null || validationCount == null || validationCount.intValue()
// == 0) {
logger.debug("=== we passed, adding validation here TEXT " + valueToCompare.getId());
v.addValidation(
inputName, Validator.MATCHES_INITIAL_DATA_ENTRY_VALUE, valueToCompare, false);
v.setErrorMessage(
respage.getString("value_you_specified")
+ " "
+ valueToCompare.getValue()
+ " "
+ respage.getString("from_initial_data_entry"));
// session.setAttribute(COUNT_VALIDATE + keyId + dib.getMetadata().getId(), new Integer(1));
// }
} else if (rt.equals(org.akaza.openclinica.bean.core.ResponseType.RADIO)
|| rt.equals(org.akaza.openclinica.bean.core.ResponseType.SELECT)) {
dib = validateDisplayItemBeanSingleCV(v, dib, inputName);
// ItemFormMetadataBean ifmdb = dib.getMetadata();
// ResponseSetBean rsBean = ifmdb.getResponseSet();
// logger.info("### found a response set count of "+inputName+"
// "+rsBean.getOptions().size());
// TODO sees it at this end tbh 1878
// if (indValidationCount == null || validationCount == null || validationCount.intValue()
// == 0) {
logger.debug("=== we passed, adding validation here RADIO " + valueToCompare.getId());
v.addValidation(
inputName, Validator.MATCHES_INITIAL_DATA_ENTRY_VALUE, valueToCompare, false);
String errorValue = valueToCompare.getValue();
java.util.ArrayList options = dib.getMetadata().getResponseSet().getOptions();
for (int u = 0; u < options.size(); u++) {
ResponseOptionBean rob = (ResponseOptionBean) options.get(u);
if (rob.getValue().equals(errorValue)) {
errorValue = rob.getText();
}
}
v.setErrorMessage(
respage.getString("value_you_specified")
+ " "
+ errorValue
+ " "
+ respage.getString("from_initial_data_entry"));
// session.setAttribute(COUNT_VALIDATE + keyId + dib.getMetadata().getId(), new Integer(1));
// }
} else if (rt.equals(org.akaza.openclinica.bean.core.ResponseType.CHECKBOX)
|| rt.equals(org.akaza.openclinica.bean.core.ResponseType.SELECTMULTI)) {
dib = validateDisplayItemBeanMultipleCV(v, dib, inputName);
// if (indValidationCount == null || validationCount == null || validationCount.intValue()
// == 0) {
logger.debug("=== we passed, adding validation here CHECKBOX " + valueToCompare.getId());
v.addValidation(
inputName, Validator.MATCHES_INITIAL_DATA_ENTRY_VALUE, valueToCompare, true);
// repeated from above, tbh 112007
String errorValue = valueToCompare.getValue();
String errorTexts = "";
java.util.ArrayList options = dib.getMetadata().getResponseSet().getOptions();
for (int u = 0; u < options.size(); u++) {
ResponseOptionBean rob = (ResponseOptionBean) options.get(u);
if (errorValue.contains(rob.getValue())) {
errorTexts = errorTexts + rob.getText();
if (u < options.size() - 1) {
// the values for multi-select are seperated by
// comma
errorTexts = errorTexts + ", ";
}
}
}
v.setErrorMessage(
respage.getString("value_you_specified")
+ " "
+ errorTexts
+ " "
+ respage.getString("from_initial_data_entry"));
// session.setAttribute(COUNT_VALIDATE + keyId + dib.getMetadata().getId(), new Integer(1));
// }
}
}
// only load form value when an item is not in a group,
// if in group, the value is already loaded
// see formGroups = loadFormValueForItemGroup(digb,digbs,formGroups);
if (isSingleItem) {
dib = loadFormValue(dib);
}
return dib;
}
@Override
protected DisplayItemBean validateDisplayItemBean(
DiscrepancyValidator v, DisplayItemBean dib, String inputName, HttpServletRequest request) {
org.akaza.openclinica.bean.core.ResponseType rt =
dib.getMetadata().getResponseSet().getResponseType();
HttpSession session = request.getSession();
EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF);
boolean isSingleItem = false;
if (StringUtil.isBlank(inputName)) { // for single items
inputName = getInputName(dib);
isSingleItem = true;
}
// we only give warning to user if data entered in DDE is different from
// IDE when the first
// time user hits 'save'
int keyId = ecb.getId();
Integer validationCount = (Integer) session.getAttribute(COUNT_VALIDATE + keyId);
// @pgawade 12-Aug-2011 issue 10601:
// 1. Moved the call to loadFormValue method setting values
// from form here. It was at the end
// of this method before that is after validations and so an extra
// validation for checking value entered
// against the data type was getting implemented for non-repeating group
// items.
// 2. Copying the form data into new object for non repeating items to
// pass to validation
// for matching IDE and DDE values. Id same reference is used, the way
// code here was written, it affetcs
// the value used in validation of data entered in DDE against the
// related data type
ItemDataBean valueToCompareTmp = dib.getData();
ItemDataBean valueToCompare = copyItemDataBean(valueToCompareTmp);
if (!isSingleItem) {
valueToCompare = dib.getDbData();
}
// only load form value when an item is not in a group,
// if in group, the value is already loaded
// see formGroups = loadFormValueForItemGroup(digb,digbs,formGroups);
if (isSingleItem) {
dib = loadFormValue(dib, request);
}
boolean showOriginalItem =
getItemMetadataService()
.isShown(dib.getItem().getId(), ecb, valueToCompare); // was dib.getData()
boolean showItem = dib.getMetadata().isShowItem();
if (!showItem && dib.getScdData().getScdItemMetadataBean().getScdItemFormMetadataId() > 0) {
showItem = true;
}
boolean showDuplicateItem =
getItemMetadataService()
.hasPassedDDE(
dib.getMetadata(),
ecb,
valueToCompare); // .isShown(dib.getItem().getId(), ecb, dib.getDbData());// where
// is the set db data?
logger.debug(
"*** show original item has value "
+ dib.getData().getValue()
+ " and show item has value "
+ valueToCompare.getValue());
logger.debug(
"--- show original: "
+ showOriginalItem
+ " show duplicate: "
+ showDuplicateItem
+ " and just show item: "
+ showItem);
logger.debug("VALIDATION COUNT " + validationCount);
if (showOriginalItem && showDuplicateItem || showItem) {
if (rt.equals(org.akaza.openclinica.bean.core.ResponseType.TEXT)
|| rt.equals(org.akaza.openclinica.bean.core.ResponseType.TEXTAREA)
|| rt.equals(org.akaza.openclinica.bean.core.ResponseType.FILE)) {
dib = validateDisplayItemBeanText(v, dib, inputName, request);
if (validationCount == null || validationCount.intValue() == 0) {
v.addValidation(
inputName, Validator.MATCHES_INITIAL_DATA_ENTRY_VALUE, valueToCompare, false);
v.setErrorMessage(
respage.getString("value_you_specified")
+ " "
+ valueToCompare.getValue()
+ " "
+ respage.getString("from_initial_data_entry"));
}
} else if (rt.equals(org.akaza.openclinica.bean.core.ResponseType.RADIO)
|| rt.equals(org.akaza.openclinica.bean.core.ResponseType.SELECT)) {
dib = validateDisplayItemBeanSingleCV(v, dib, inputName);
// ItemFormMetadataBean ifmdb = dib.getMetadata();
// ResponseSetBean rsBean = ifmdb.getResponseSet();
// logger.info("### found a response set count of "+inputName+"
// "+rsBean.getOptions().size());
// TODO sees it at this end tbh 1878
if (validationCount == null || validationCount.intValue() == 0) {
v.addValidation(
inputName, Validator.MATCHES_INITIAL_DATA_ENTRY_VALUE, valueToCompare, false);
String errorValue = valueToCompare.getValue();
java.util.ArrayList options = dib.getMetadata().getResponseSet().getOptions();
for (int u = 0; u < options.size(); u++) {
ResponseOptionBean rob = (ResponseOptionBean) options.get(u);
if (rob.getValue().equals(errorValue)) {
errorValue = rob.getText();
}
}
v.setErrorMessage(
respage.getString("value_you_specified")
+ " "
+ errorValue
+ " "
+ respage.getString("from_initial_data_entry"));
}
} else if (rt.equals(org.akaza.openclinica.bean.core.ResponseType.CHECKBOX)
|| rt.equals(org.akaza.openclinica.bean.core.ResponseType.SELECTMULTI)) {
dib = validateDisplayItemBeanMultipleCV(v, dib, inputName);
if (validationCount == null || validationCount.intValue() == 0) {
v.addValidation(
inputName, Validator.MATCHES_INITIAL_DATA_ENTRY_VALUE, valueToCompare, true);
// repeated from above, tbh 112007
String errorValue = valueToCompare.getValue();
String errorTexts = "";
java.util.ArrayList options = dib.getMetadata().getResponseSet().getOptions();
for (int u = 0; u < options.size(); u++) {
ResponseOptionBean rob = (ResponseOptionBean) options.get(u);
if (errorValue.contains(rob.getValue())) {
errorTexts = errorTexts + rob.getText();
if (u < options.size() - 1) {
// the values for multi-select are seperated by
// comma
errorTexts = errorTexts + ", ";
}
}
}
v.setErrorMessage(
respage.getString("value_you_specified")
+ " "
+ errorTexts
+ " "
+ respage.getString("from_initial_data_entry"));
}
}
}
// // only load form value when an item is not in a group,
// // if in group, the value is already loaded
// // see formGroups = loadFormValueForItemGroup(digb,digbs,formGroups);
// if (isSingleItem) {
// dib = loadFormValue(dib, request);
// }
return dib;
}