private ProtocolAction findProtocolActionForSubmission(
org.kuali.kra.irb.actions.submit.ProtocolSubmissionLite protocolSubmission,
Protocol protocol) {
List<ProtocolActionBase> protocolActions = protocol.getProtocolActions();
for (ProtocolActionBase protocolAction : protocolActions) {
if (protocolAction.getSubmissionNumber() != null
&& protocolAction
.getSubmissionNumber()
.equals(protocolSubmission.getSubmissionNumber())) {
return (ProtocolAction) protocolAction;
}
}
return null;
}
@Override
public void iacucLiftHold(ProtocolBase protocol, ProtocolGenericActionBean actionBean)
throws Exception {
// find the last lift notification protocol action.
ProtocolActionBase selectedPa = null;
for (ProtocolActionBase pa : protocol.getProtocolActions()) {
if (StringUtils.equalsIgnoreCase(pa.getProtocolActionTypeCode(), IacucProtocolActionType.HOLD)
&& (selectedPa == null || pa.getSequenceNumber() > selectedPa.getSequenceNumber())) {
selectedPa = pa;
}
}
performGenericAction(
protocol,
actionBean,
IacucProtocolActionType.LIFT_HOLD,
selectedPa.getPrevProtocolStatusCode());
}
protected void buildAndAttachProtocolCorrespondence(
ProtocolBase protocol, byte[] data, String correspTypeCode) {
ProtocolCorrespondence protocolCorrespondence = getNewProtocolCorrespondenceHook();
protocolCorrespondence.setProtocol(protocol);
protocolCorrespondence.setProtocolId(protocol.getProtocolId());
protocolCorrespondence.setProtocolNumber(protocol.getProtocolNumber());
protocolCorrespondence.setSequenceNumber(protocol.getSequenceNumber());
protocolCorrespondence.setProtoCorrespTypeCode(correspTypeCode);
ProtocolActionBase lastAction = protocol.getLastProtocolAction();
protocolCorrespondence.setProtocolAction(lastAction);
protocolCorrespondence.setActionIdFk(lastAction.getProtocolActionId());
protocolCorrespondence.setCorrespondence(data);
protocolCorrespondence.setActionId(lastAction.getActionId());
// What is Final flag used for? ANSWER: the final flag is used by the IRB admin to denote
// correspondences
// that are ready to be sent/published to the PI etc.
protocolCorrespondence.setFinalFlag(false);
protocolCorrespondence.setCreateUser(GlobalVariables.getUserSession().getPrincipalName());
protocolCorrespondence.setCreateTimestamp(dateTimeService.getCurrentTimestamp());
if (lastAction.getProtocolCorrespondences() == null) {
List<ProtocolCorrespondence> correspondences = new ArrayList<ProtocolCorrespondence>();
correspondences.add(protocolCorrespondence);
lastAction.setProtocolCorrespondences(correspondences);
protocol.refreshReferenceObject("protocolSubmissions");
} else {
lastAction.getProtocolCorrespondences().add(protocolCorrespondence);
}
getBusinessObjectService().save(protocolCorrespondence);
getBusinessObjectService().save(protocol);
}
public Schedule getSchedule(CommitteeSchedule committeeSchedule) {
Schedule schedule = Schedule.Factory.newInstance();
setScheduleMasterData(committeeSchedule, schedule.addNewScheduleMasterData());
PreviousSchedule prevSchedule = schedule.addNewPreviousSchedule();
setPreviousSchedule(committeeSchedule, prevSchedule.addNewScheduleMasterData());
NextSchedule nextScheduleType = schedule.addNewNextSchedule();
setNextSchedule(committeeSchedule, nextScheduleType.addNewScheduleMasterData());
getIrbPrintXmlUtilService().setMinutes(committeeSchedule, schedule);
setAttendance(committeeSchedule, schedule);
committeeSchedule.refreshReferenceObject("protocolSubmissions");
List<org.kuali.kra.irb.actions.submit.ProtocolSubmissionLite> submissions =
committeeSchedule.getLatestProtocolSubmissions();
for (org.kuali.kra.irb.actions.submit.ProtocolSubmissionLite protocolSubmission : submissions) {
ProtocolSubmission protocolSubmissionType = schedule.addNewProtocolSubmission();
SubmissionDetails protocolSubmissionDetail = protocolSubmissionType.addNewSubmissionDetails();
ProtocolSummary protocolSummary = protocolSubmissionType.addNewProtocolSummary();
ProtocolMasterData protocolMaster = protocolSummary.addNewProtocolMasterData();
String followUpAction = null;
String actionTypeCode = null;
Protocol protocol =
getBusinessObjectService()
.findByPrimaryKey(
Protocol.class,
Collections.singletonMap("protocolId", protocolSubmission.getProtocolId()));
List<ProtocolActionBase> protocolActions = protocol.getProtocolActions();
for (ProtocolActionBase protocolAction : protocolActions) {
actionTypeCode = protocolAction.getProtocolActionTypeCode();
if (actionTypeCode.equals(EXPEDIT_ACTION_TYPE_CODE)
|| actionTypeCode.equals(EXEMPT_ACTION_TYPE_CODE)) {
if (protocolAction.getFollowupActionCode() != null
&& protocolAction.getFollowupActionCode().equals(FOLLOW_UP_ACTION_CODE)) {
followUpAction = protocolAction.getFollowupActionCode();
}
break;
}
}
protocolMaster.setProtocolNumber(protocol.getProtocolNumber());
protocolMaster.setSequenceNumber(
new BigInteger(String.valueOf(protocol.getSequenceNumber())));
protocolMaster.setProtocolTitle(protocol.getTitle());
protocolMaster.setProtocolStatusCode(
new BigInteger(String.valueOf(protocol.getProtocolStatusCode())));
protocolMaster.setProtocolStatusDesc(protocol.getProtocolStatus().getDescription());
protocolMaster.setProtocolTypeCode(
new BigInteger(String.valueOf(protocol.getProtocolTypeCode())));
protocolMaster.setProtocolTypeDesc(protocol.getProtocolType().getDescription());
if (protocol.getDescription() != null) {
protocolMaster.setProtocolDescription(protocol.getDescription());
}
if (protocol.getApprovalDate() != null) {
protocolMaster.setApprovalDate(
getDateTimeService().getCalendar(protocol.getApprovalDate()));
}
if (protocol.getExpirationDate() != null) {
protocolMaster.setExpirationDate(
getDateTimeService().getCalendar(protocol.getExpirationDate()));
}
if (protocol.getFdaApplicationNumber() != null) {
protocolMaster.setFdaApplicationNumber(protocol.getFdaApplicationNumber());
}
if (protocol.getReferenceNumber1() != null) {
protocolMaster.setRefNumber1(protocol.getReferenceNumber1());
}
if (protocol.getReferenceNumber2() != null) {
protocolMaster.setRefNumber2(protocol.getReferenceNumber2());
}
protocolSubmissionDetail.setProtocolNumber(protocolSubmission.getProtocolNumber());
if (protocolSubmission.getProtocolSubmissionType() != null) {
protocolSubmissionDetail.setSubmissionTypeDesc(
protocolSubmission.getProtocolSubmissionType().getDescription());
}
if (protocolSubmission.getProtocolReviewTypeCode() != null) {
protocolSubmissionDetail.setProtocolReviewTypeCode(
new BigInteger(protocolSubmission.getProtocolReviewTypeCode()));
}
if (protocolSubmission.getProtocolReviewType() != null) {
protocolSubmissionDetail.setProtocolReviewTypeDesc(
protocolSubmission.getProtocolReviewType().getDescription());
}
if (protocolSubmission.getSubmissionTypeCode() != null) {
protocolSubmissionDetail.setSubmissionTypeCode(
new BigInteger(String.valueOf(protocolSubmission.getSubmissionTypeCode())));
}
if (protocolSubmission.getProtocolSubmissionType() != null) {
protocolSubmissionDetail.setSubmissionTypeDesc(
protocolSubmission.getProtocolSubmissionType().getDescription());
}
if (protocolSubmission.getSubmissionNumber() != null) {
protocolSubmissionDetail.setSubmissionNumber(
new BigInteger(String.valueOf(protocolSubmission.getSubmissionNumber())));
}
if (protocolSubmission.getSubmissionStatusCode() != null) {
protocolSubmissionDetail.setSubmissionStatusCode(
new BigInteger(String.valueOf(protocolSubmission.getSubmissionStatusCode())));
}
if (protocolSubmission.getSubmissionStatus() != null) {
protocolSubmissionDetail.setSubmissionStatusDesc(
protocolSubmission.getSubmissionStatus().getDescription());
}
if (protocolSubmission.getSubmissionTypeQualifierCode() != null) {
protocolSubmissionDetail.setSubmissionTypeQualifierCode(
new BigInteger(protocolSubmission.getSubmissionTypeQualifierCode()));
}
if (protocolSubmission.getProtocolSubmissionQualifierType() != null) {
protocolSubmissionDetail.setSubmissionTypeQualifierDesc(
protocolSubmission.getProtocolSubmissionQualifierType().getDescription());
}
if (protocolSubmission.getYesVoteCount() != null) {
protocolSubmissionDetail.setYesVote(
BigInteger.valueOf(protocolSubmission.getYesVoteCount()));
} else {
protocolSubmissionDetail.setYesVote(BigInteger.ZERO);
}
if (protocolSubmission.getNoVoteCount() != null) {
protocolSubmissionDetail.setNoVote(BigInteger.valueOf(protocolSubmission.getNoVoteCount()));
} else {
protocolSubmissionDetail.setNoVote(BigInteger.ZERO);
}
if (protocolSubmission.getAbstainerCount() != null) {
protocolSubmissionDetail.setAbstainerCount(
BigInteger.valueOf(protocolSubmission.getAbstainerCount()));
} else {
protocolSubmissionDetail.setAbstainerCount(BigInteger.ZERO);
}
protocolSubmissionDetail.setVotingComments(protocolSubmission.getVotingComments());
setProtocolSubmissionAction(protocolSubmission, protocol, protocolSubmissionDetail);
if (protocolSubmission.getSubmissionDate() != null) {
protocolSubmissionDetail.setSubmissionDate(
getDateTimeService().getCalendar(protocolSubmission.getSubmissionDate()));
}
setSubmissionCheckListinfo(protocolSubmission, protocolSubmissionDetail);
setProtocolSubmissionReviewers(protocolSubmission, protocolSubmissionDetail);
List<ProtocolPersonBase> protocolPersons = protocol.getProtocolPersons();
for (ProtocolPersonBase protocolPerson : protocolPersons) {
if (protocolPerson
.getProtocolPersonRoleId()
.equals(ProtocolPersonRole.ROLE_PRINCIPAL_INVESTIGATOR)
|| protocolPerson
.getProtocolPersonRoleId()
.equals(ProtocolPersonRole.ROLE_CO_INVESTIGATOR)) {
Investigator investigator = protocolSummary.addNewInvestigator();
getIrbPrintXmlUtilService()
.setPersonRolodexType((ProtocolPerson) protocolPerson, investigator.addNewPerson());
if (protocolPerson
.getProtocolPersonRoleId()
.equals(ProtocolPersonRole.ROLE_PRINCIPAL_INVESTIGATOR)) {
investigator.setPIFlag(true);
}
}
}
List<ProtocolRiskLevel> cvRiskLevels = protocol.getProtocolRiskLevels();
for (ProtocolRiskLevel protocolRiskLevelBean : cvRiskLevels) {
edu.mit.irb.irbnamespace.ProtocolSummaryDocument.ProtocolSummary.RiskLevels riskLevelType =
protocolSummary.addNewRiskLevels();
riskLevelType.setRiskLevelDescription(
protocolRiskLevelBean.getRiskLevel().getDescription());
riskLevelType.setComments(protocolRiskLevelBean.getComments());
}
List<ProtocolFundingSource> vecFundingSource = (List) protocol.getProtocolFundingSources();
int fundingSourceTypeCode;
String fundingSourceName, fundingSourceCode;
for (ProtocolFundingSource protocolFundingSourceBean : vecFundingSource) {
protocolFundingSourceBean.refreshNonUpdateableReferences();
edu.mit.irb.irbnamespace.ProtocolSummaryDocument.ProtocolSummary.FundingSource
fundingSource = protocolSummary.addNewFundingSource();
fundingSourceCode = protocolFundingSourceBean.getFundingSourceNumber();
fundingSourceTypeCode =
Integer.valueOf(protocolFundingSourceBean.getFundingSourceTypeCode());
fundingSourceName = getFundingSourceNameForType(fundingSourceTypeCode, fundingSourceCode);
fundingSource.setFundingSourceName(fundingSourceName);
if (protocolFundingSourceBean.getFundingSourceType() != null) {
fundingSource.setTypeOfFundingSource(
protocolFundingSourceBean.getFundingSourceType().getDescription());
}
}
getIrbPrintXmlUtilService()
.setProcotolMinutes(committeeSchedule, protocolSubmission, protocolSubmissionType);
}
setOtherActionItems(committeeSchedule, schedule);
return schedule;
}
private String getQuestionnaireLabel(AnswerHeader answerHeader) {
String label = null;
List<QuestionnaireUsage> usages = answerHeader.getQuestionnaire().getQuestionnaireUsages();
if (CollectionUtils.isNotEmpty(usages) && usages.size() > 1) {
Collections.sort((List<QuestionnaireUsage>) usages);
}
for (QuestionnaireUsage usage : usages) {
if (getCoeusModuleCode().equals(usage.getModuleItemCode())
&& answerHeader.getModuleSubItemCode().equals(usage.getModuleSubItemCode())) {
if ("0".equals(answerHeader.getModuleSubItemCode())) {
label = usage.getQuestionnaireLabel();
} else if (CoeusSubModule.PROTOCOL_SUBMISSION.equals(answerHeader.getModuleSubItemCode())) {
Map keyValues = new HashMap();
keyValues.put("protocolNumber", answerHeader.getModuleItemKey());
keyValues.put("submissionNumber", answerHeader.getModuleSubItemKey());
List<ProtocolSubmissionBase> submissions =
((List<ProtocolSubmissionBase>)
getBusinessObjectService()
.findMatchingOrderBy(
getProtocolSubmissionBOClassHook(), keyValues, "submissionId", false));
if (submissions.isEmpty()) {
// this may happen if it is undo last action
label = usage.getQuestionnaireLabel();
} else {
keyValues.clear();
keyValues.put("protocolId", submissions.get(0).getProtocolId());
keyValues.put("submissionNumber", answerHeader.getModuleSubItemKey());
ProtocolActionBase protocolAction =
((List<ProtocolActionBase>)
getBusinessObjectService()
.findMatching(getProtocolActionBOClassHook(), keyValues))
.get(0);
label =
usage.getQuestionnaireLabel()
+ " - "
+ protocolAction.getProtocolActionType().getDescription()
+ " - "
+ protocolAction.getActionDateString();
}
} else if (CoeusSubModule.AMENDMENT_RENEWAL.equals(answerHeader.getModuleSubItemCode())) {
if (answerHeader.getModuleItemKey().contains("A")) {
label =
usage.getQuestionnaireLabel()
+ " - Amendment "
+ answerHeader.getModuleItemKey().substring(10);
} else {
label =
usage.getQuestionnaireLabel()
+ " - Renewal "
+ answerHeader.getModuleItemKey().substring(10);
}
} else if (CoeusSubModule.AMENDMENT.equals(answerHeader.getModuleSubItemCode())) {
if (answerHeader.getModuleItemKey().contains("A")) {
label =
usage.getQuestionnaireLabel()
+ " - Amendment "
+ answerHeader.getModuleItemKey().substring(10);
}
} else if (CoeusSubModule.RENEWAL.equals(answerHeader.getModuleSubItemCode())) {
if (answerHeader.getModuleItemKey().contains("R")) {
label =
usage.getQuestionnaireLabel()
+ " - Renewal "
+ answerHeader.getModuleItemKey().substring(10);
}
}
}
}
return label;
}