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;
}
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;
}
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;
}