@Override
public boolean hasDerivedRole(
String principalId,
List<String> groupIds,
String namespaceCode,
String roleName,
Map<String, String> qualification) {
validateRequiredAttributesAgainstReceived(qualification);
String protocolNumber = qualification.get(KcKimAttributes.PROTOCOL);
ProtocolBase protocol = getProtocol(protocolNumber);
if (protocol != null && CollectionUtils.isNotEmpty(protocol.getProtocolPersons())) {
for (ProtocolPersonBase person : protocol.getProtocolPersons()) {
// Find protocol person that matches the principal id
if (StringUtils.equals(principalId, person.getPersonId())) {
if (StringUtils.equals(roleName, person.getProtocolPersonRoleId())) {
return true;
}
}
}
}
return false;
}
@Override
public List<CommitteeMembershipBase> getAvailableCommitteeMembersForCurrentSubmission(
ProtocolBase protocol) {
List<CommitteeMembershipBase> results = new ArrayList<CommitteeMembershipBase>();
ProtocolSubmissionBase submission = protocol.getProtocolSubmission();
submission.refreshReferenceObject("protocolOnlineReviews");
if (LOG.isDebugEnabled()) {
LOG.debug(
String.format(
"Fetching available committee members for protocol %s, submission %s",
protocol.getProtocolNumber(), submission.getSubmissionNumber()));
}
List<ProtocolOnlineReviewBase> currentReviews = submission.getProtocolOnlineReviews();
List<CommitteeMembershipBase> committeeMembers =
getCommitteeService()
.getAvailableMembers(submission.getCommitteeId(), submission.getScheduleId());
// TODO: Make this better.
for (CommitteeMembershipBase member : committeeMembers) {
boolean found = false;
for (ProtocolOnlineReviewBase review : currentReviews) {
if (review.getProtocolReviewer().isProtocolReviewerFromCommitteeMembership(member)
&& review.isActive()) {
found = true;
break;
}
}
if (!found && !isProtocolPersonnel(protocol, member)) {
results.add(member);
}
}
return results;
}
/*
* if questionnaire is associated with Amendment/renewal submodulecode.
* if this protocol is normal protocol, then it has to check whether the A/R of this
* questionnaire has merged to this protocol yet.
*/
private boolean isCurrentAorRQn(AnswerHeader answerHeader) {
boolean isCurrentQn = false;
if (getProtocol().isAmendment() || getProtocol().isRenewal()) {
// if this is A/R, then just match sequencenumber and modulesubitemkey
isCurrentQn =
answerHeader.getModuleSubItemKey().equals(getProtocol().getSequenceNumber().toString());
} else {
// if this is a regular protocol, then get this A/R associated this this Qn and see if
// A/R has been merged to this version of protocol
Map keyValues = new HashMap();
keyValues.put("protocolNumber", answerHeader.getModuleItemKey());
ProtocolBase protocol =
((List<ProtocolBase>)
getBusinessObjectService()
.findMatchingOrderBy(
getProtocolBOClassHook(), keyValues, "sequenceNumber", false))
.get(0);
isCurrentQn =
answerHeader.getModuleSubItemKey().equals(protocol.getSequenceNumber().toString())
&& !CollectionUtils.isEmpty(protocol.getProtocolSubmissions())
&& isMergedToProtocol(getProtocol(), protocol);
}
return isCurrentQn;
}
@Override
public void setPrincipalInvestigator(
ProtocolPersonBase newPrincipalInvestigator, ProtocolBase protocol) {
if (protocol != null) {
ProtocolPerson currentPrincipalInvestigator =
(ProtocolPerson) getPrincipalInvestigator(protocol.getProtocolPersons());
if (newPrincipalInvestigator != null) {
newPrincipalInvestigator.setProtocolPersonRoleId(getPrincipalInvestigatorRole());
if (currentPrincipalInvestigator == null) {
protocol.getProtocolPersons().add(newPrincipalInvestigator);
} else if (!isDuplicatePerson(protocol.getProtocolPersons(), newPrincipalInvestigator)) {
protocol.getProtocolPersons().remove(currentPrincipalInvestigator);
protocol.getProtocolPersons().add(newPrincipalInvestigator);
}
// Assign the PI the APPROVER role if PI has a personId (for doc cancel).
if (newPrincipalInvestigator.getPersonId() != null) {
personEditableService.populateContactFieldsFromPersonId(newPrincipalInvestigator);
KcAuthorizationService kraAuthService =
KcServiceLocator.getService(KcAuthorizationService.class);
kraAuthService.addDocumentLevelRole(
newPrincipalInvestigator.getPersonId(), RoleConstants.PROTOCOL_APPROVER, protocol);
} else {
personEditableService.populateContactFieldsFromRolodexId(newPrincipalInvestigator);
}
}
}
}
@Override
public List<ProtocolOnlineReviewDocumentBase> getProtocolReviewDocumentsForCurrentSubmission(
ProtocolBase protocol) {
List<ProtocolOnlineReviewDocumentBase> onlineReviewDocuments =
new ArrayList<ProtocolOnlineReviewDocumentBase>();
ProtocolSubmissionBase submission = protocol.getProtocolSubmission();
List<ProtocolOnlineReviewBase> reviews =
findProtocolOnlineReviews(protocol.getProtocolId(), submission.getSubmissionId());
for (ProtocolOnlineReviewBase review : reviews) {
if (review.isActive()) {
review.refresh();
try {
onlineReviewDocuments.add(
(ProtocolOnlineReviewDocumentBase)
(documentService.getByDocumentHeaderId(
review.getProtocolOnlineReviewDocument().getDocumentNumber())));
} catch (WorkflowException e) {
throw new RuntimeException(
String.format(
"Could not load ProtocolOnlineReviewBase docuemnt %s due to WorkflowException: %s",
review.getProtocolOnlineReviewDocument().getDocumentNumber(), e.getMessage()),
e);
}
}
}
return onlineReviewDocuments;
}
@Override
public boolean isAuthorized(String username, IacucProtocolTask task) {
ProtocolBase protocol = task.getProtocol();
return !(kraWorkflowService.isInWorkflow(protocol.getProtocolDocument())
&& kraWorkflowService.isCurrentNode(
protocol.getProtocolDocument(), Constants.PROTOCOL_IACUCREVIEW_ROUTE_NODE_NAME)
&& canExecuteAction(protocol, IacucProtocolActionType.ASSIGNED_TO_AGENDA)
&& isAssignedToCommittee(protocol))
&& hasPermission(username, protocol, PermissionConstants.PERFORM_IACUC_ACTIONS_ON_PROTO);
}
protected ProtocolDocument getReturnedVersionedDocument(ProtocolBase protocol) throws Exception {
getDocumentService()
.cancelDocument(
protocol.getProtocolDocument(),
"Protocol document cancelled - protocol has been returned for revisions.");
getProtocolOnlineReviewService()
.finalizeOnlineReviews(
protocol.getProtocolSubmission(),
"Protocol Review finalized - protocol has been returned for revisions.");
return (ProtocolDocument) getVersionedDocument(protocol);
}
@Override
public ModuleQuestionnaireBean getModuleQnBean() {
String baseProtocolNumber = protocol.getProtocolNumber();
baseProtocolNumber = baseProtocolNumber.replaceAll("[A-Z]+", "");
return new ProtocolModuleQuestionnaireBean(
getModuleCode(),
baseProtocolNumber,
CoeusSubModule.PROTOCOL_SUBMISSION,
StringUtils.isNotBlank(submissionNumber) ? submissionNumber : actionTypeCode,
StringUtils.isNotBlank(submissionNumber)
|| protocol.getProtocolNumber().endsWith(SUFFIX_T)
|| readOnlyView);
}
@Override
public List<ProtocolOnlineReviewBase> getProtocolReviews(String protocolNumber) {
ProtocolBase protocol = protocolFinderDao.findCurrentProtocolByNumber(protocolNumber);
List<ProtocolOnlineReviewBase> reviews = null;
if (protocol != null && protocol.getProtocolSubmission() != null) {
reviews = protocol.getProtocolSubmission().getProtocolOnlineReviews();
} else {
reviews = new ArrayList<ProtocolOnlineReviewBase>();
}
return reviews;
}
/**
* This method is to return appropriate watermark with respect to the protocol document status.
*
* @return waterMarkBean
*/
public WatermarkBean getWatermark() {
ProtocolBase protocol = (ProtocolBase) getPersistableBusinessObject();
String protocolStatusCode = protocol.getProtocolStatusCode();
if (protocolStatusCode != null) {
WatermarkBean waterMarkBean = null;
try {
waterMarkBean = getProtocolWatermarkBeanObject(protocolStatusCode);
} catch (Exception e) {
LOG.error("Exception Occured in (ProtocolPrintWatermarkBase) :", e);
}
return waterMarkBean;
}
return null;
}
protected void performDisapprove(ProtocolBase protocol) throws Exception {
if (protocol.getProtocolDocument() != null) {
WorkflowDocument currentWorkflowDocument =
protocol.getProtocolDocument().getDocumentHeader().getWorkflowDocument();
if (currentWorkflowDocument != null) {
currentWorkflowDocument.disapprove(
"Protocol document disapproved after committee decision");
}
}
getProtocolOnlineReviewService()
.cancelOnlineReviews(
protocol.getProtocolSubmission(),
"Protocol Review cancelled - protocol has been disapproved.");
}
private boolean isMergedToProtocol(ProtocolBase protocol, ProtocolBase amendment) {
boolean merged = false;
int submissionNumber =
amendment
.getProtocolSubmissions()
.get(amendment.getProtocolSubmissions().size() - 1)
.getSubmissionNumber();
for (ProtocolSubmissionBase submission : protocol.getProtocolSubmissions()) {
if (submissionNumber == submission.getSubmissionNumber().intValue()) {
merged = true;
break;
}
}
return merged;
}
/** {@inheritDoc} */
@Override
public boolean isAuthorized(String username, IacucProtocolTask task) {
ProtocolBase protocol = task.getProtocol();
return (!canExecuteAction(protocol, IacucProtocolActionType.NOTIFY_IACUC)
|| isAmendmentOrRenewal(protocol)
|| (isRequestForSuspension(
findSubmisionHook(task.getProtocol()),
IacucProtocolSubmissionType.REQUEST_SUSPEND)
&& !isAdmin(
username,
RoleConstants.DEPARTMENT_ROLE_TYPE,
RoleConstants.IACUC_ADMINISTRATOR)))
&& (hasPermission(username, protocol, PermissionConstants.SUBMIT_IACUC_PROTOCOL)
|| hasPermission(username, protocol, PermissionConstants.SUBMIT_ANY_IACUC_PROTOCOL)
|| StringUtils.equals(protocol.getPrincipalInvestigator().getUserName(), username));
}
@Override
protected ProtocolActionBase getNewDisapprovedInRoutingProtocolActionInstanceHook(
ProtocolBase protocol) {
return new IacucProtocolAction(
(IacucProtocol) protocol,
(IacucProtocolSubmission) protocol.getProtocolSubmission(),
IacucProtocolActionType.REJECTED_IN_ROUTING);
}
@Override
public void iacucAcknowledgement(ProtocolBase protocol, ProtocolGenericActionBean actionBean)
throws Exception {
performGenericAction(
protocol,
actionBean,
IacucProtocolActionType.IACUC_ACKNOWLEDGEMENT,
protocol.getProtocolStatusCode());
}
private List<String> getPersonnelIds(ProtocolBase protocol) {
List<String> PersonnelIds = new ArrayList<String>();
for (ProtocolPersonBase person : protocol.getProtocolPersons()) {
if (StringUtils.isNotBlank(person.getPersonId())) {
PersonnelIds.add(person.getPersonId());
} else {
PersonnelIds.add(person.getRolodexId().toString());
}
}
return PersonnelIds;
}
@Override
public List<RoleMembership> getRoleMembersFromDerivedRole(
String namespaceCode, String roleName, Map<String, String> qualification) {
validateRequiredAttributesAgainstReceived(qualification);
List<RoleMembership> members = new ArrayList<RoleMembership>();
String protocolNumber = qualification.get(KcKimAttributes.PROTOCOL);
ProtocolBase protocol = getProtocol(protocolNumber);
if (protocol != null && CollectionUtils.isNotEmpty(protocol.getProtocolPersons())) {
for (ProtocolPersonBase person : protocol.getProtocolPersons()) {
if (StringUtils.equals(person.getProtocolPersonRoleId(), roleName)
&& StringUtils.isNotBlank(person.getPerson().getPersonId())) {
members.add(
RoleMembership.Builder.create(
null, null, person.getPerson().getPersonId(), MemberType.PRINCIPAL, null)
.build());
}
}
}
return members;
}
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);
}
/*
* This is Questionnaire answer is with submodulecode of "0".
* Then if this protocol is A/R, then it has to check whether this is the first version
* A/R merged into.
*/
private boolean isCurrentRegularQn(AnswerHeader answerHeader) {
boolean isCurrentQn = false;
if ((getProtocol().isAmendment() || getProtocol().isRenewal())
&& !answerHeader.getModuleItemKey().equals(getProtocol().getProtocolNumber())) {
Map keyValues = new HashMap();
keyValues.put("protocolNumber", answerHeader.getModuleItemKey());
ProtocolBase prevProtocol = null;
// if this is an A/R protocol, then need to find the original protocol that the A/R first
// merged into.
for (ProtocolBase protocol :
((List<ProtocolBase>)
getBusinessObjectService()
.findMatchingOrderBy(
getProtocolBOClassHook(), keyValues, "sequenceNumber", true))) {
isCurrentQn =
answerHeader.getModuleSubItemKey().equals(protocol.getSequenceNumber().toString())
&& !CollectionUtils.isEmpty(getProtocol().getProtocolSubmissions())
&& isMergedToProtocol(protocol, getProtocol());
if (isCurrentQn) {
if (prevProtocol == null || !isMergedToProtocol(prevProtocol, getProtocol())) {
// this is the protocol this A/R merged into. so, use this questionnaire.
break;
} else {
// prevProtocol is the initial ProtocolBase that this A/R merged into.
isCurrentQn = false;
}
}
prevProtocol = protocol;
}
} else {
// if this is a regular protocol, then check if sequencenumber & modulesubitemkey match
isCurrentQn =
answerHeader.getModuleSubItemKey().equals(getProtocol().getSequenceNumber().toString());
}
return isCurrentQn;
}
@Override
public void suspend(
ProtocolBase protocol,
org.kuali.kra.protocol.actions.genericactions.ProtocolGenericActionBean actionBean)
throws Exception {
if (ProtocolActionType.REQUEST_FOR_SUSPENSION.equals(
protocol.getLastProtocolAction().getProtocolActionType().getProtocolActionTypeCode())) {
// if previous action is request to suspend then the new status is suspend by investigator
performGenericAction(
protocol, actionBean, ProtocolActionType.SUSPENDED, ProtocolStatus.SUSPENDED_BY_PI);
} else {
// else suspend by IRB
performGenericAction(
protocol, actionBean, ProtocolActionType.SUSPENDED, ProtocolStatus.SUSPENDED_BY_IRB);
}
}
protected ProtocolSubmission getSubmission(ProtocolBase protocol) {
// There are 'findCommission' in other classes. Consider to create a utility static method for
// this
// need to loop thru to find the last submission.
// it may have submit/Wd/notify irb/submit, and this will cause problem if don't loop thru.
ProtocolSubmission protocolSubmission = null;
for (ProtocolSubmissionBase submission : protocol.getProtocolSubmissions()) {
if (StringUtils.equals(
submission.getSubmissionStatusCode(), ProtocolSubmissionStatus.IN_AGENDA)
|| StringUtils.equals(
submission.getSubmissionStatusCode(),
ProtocolSubmissionStatus.SUBMITTED_TO_COMMITTEE)) {
protocolSubmission = (ProtocolSubmission) submission;
}
}
return protocolSubmission;
}
@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());
}
@Override
public boolean isProtocolInStateToBeReviewed(ProtocolBase protocol) {
boolean isReviewable = false;
ProtocolSubmission submission =
(ProtocolSubmission) ((Protocol) protocol).getProtocolSubmission();
if (submission != null) {
try {
isReviewable =
StringUtils.isNotEmpty(submission.getScheduleId())
|| ProtocolReviewType.EXPEDITED_REVIEW_TYPE_CODE.equals(
submission.getProtocolReviewTypeCode())
|| (ProtocolReviewType.FYI_TYPE_CODE.equalsIgnoreCase(
submission.getProtocolReviewTypeCode())
&& ProtocolSubmissionType.NOTIFY_IRB.equalsIgnoreCase(
submission.getProtocolSubmissionType().getSubmissionTypeCode()));
isReviewable &=
(StringUtils.equals(
submission.getSubmissionStatusCode(),
ProtocolSubmissionStatus.SUBMITTED_TO_COMMITTEE)
|| StringUtils.equals(
submission.getSubmissionStatusCode(), ProtocolSubmissionStatus.IN_AGENDA));
ProtocolDocument protocolDocument =
(ProtocolDocument)
protocol
.getProtocolDocument(); // (ProtocolDocument)
// documentService.getByDocumentHeaderId(protocol.getProtocolDocument().getDocumentNumber());
isReviewable &=
getKraWorkflowService()
.isCurrentNode(protocolDocument, Constants.PROTOCOL_IRBREVIEW_ROUTE_NODE_NAME);
} catch (Exception e) {
String errorString =
String.format(
"WorkflowException checking route node for creating new ProtocolOnlineReviewDocument "
+ "for protocol %s",
submission.getProtocolNumber());
LOG.error(errorString, e);
throw new RuntimeException(errorString, e);
}
}
return isReviewable;
}
public boolean isProtocolInStateToBeReviewed(ProtocolBase protocol) {
boolean isReviewable = false;
ProtocolSubmissionBase submission =
(IacucProtocolSubmission) ((IacucProtocol) protocol).getProtocolSubmission();
if (submission != null) {
try {
isReviewable =
StringUtils.isNotEmpty(submission.getScheduleId())
|| StringUtils.equals(
submission.getProtocolSubmissionType().getSubmissionTypeCode(),
IacucProtocolSubmissionType.NOTIFY_IACUC);
isReviewable &=
(StringUtils.equals(
submission.getSubmissionStatusCode(),
IacucProtocolSubmissionStatus.SUBMITTED_TO_COMMITTEE)
|| StringUtils.equals(
submission.getSubmissionStatusCode(), IacucProtocolSubmissionStatus.IN_AGENDA));
ProtocolDocumentBase protocolDocument =
(ProtocolDocumentBase)
documentService.getByDocumentHeaderId(
protocol.getProtocolDocument().getDocumentNumber());
isReviewable &=
kraWorkflowService.isCurrentNode(
protocolDocument, Constants.IACUC_PROTOCOL_IACUCREVIEW_ROUTE_NODE_NAME);
} catch (WorkflowException e) {
String errorString =
String.format(
"WorkflowException checking route node for creating new ProtocolOnlineReviewDocumentBase "
+ "for protocol %s",
submission.getProtocolNumber());
LOG.error(errorString, e);
throw new RuntimeException(errorString, e);
}
}
return isReviewable;
}
/**
* Can the user on the current thread execute the given action for the given protocol?
*
* @param protocol
* @param protocolActionTypeCode
* @return true if the action can be executed; otherwise false
*/
protected final boolean canExecuteAction(ProtocolBase protocol, String protocolActionTypeCode) {
return protocol.isActive()
&& !protocol.getProtocolDocument().isViewOnly()
&& protocolActionService.isActionAllowed(protocolActionTypeCode, protocol);
}
/**
* Is the protocol an amendment or renewal protocol? Including continuation here - since
* continuation is similar to renewal
*
* @param protocol the protocol
* @return true if the protocol is an amendment or renewal; otherwise false
*/
protected final boolean isAmendmentOrRenewal(ProtocolBase protocol) {
return protocol.getProtocolNumber() != null
&& (protocol.getProtocolNumber().contains("A")
|| protocol.getProtocolNumber().contains("R")
|| protocol.getProtocolNumber().contains("C"));
}