@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;
}
/*
* this returns a list of submission numbers for a protocol.
*/
private List<Integer> getAvailableSubmissionNumbers() {
List<Integer> submissionNumbers = new ArrayList<Integer>();
for (ProtocolSubmissionBase submission : getProtocol().getProtocolSubmissions()) {
submissionNumbers.add(submission.getSubmissionNumber());
}
return submissionNumbers;
}
@Override
public ProtocolOnlineReviewDocumentBase createAndRouteProtocolOnlineReviewDocument(
ProtocolSubmissionBase protocolSubmission,
ProtocolReviewer protocolReviewer,
String documentDescription,
String documentExplanation,
String documentOrganizationDocumentNumber,
String documentRouteAnnotation,
boolean initialApproval,
Date dateRequested,
Date dateDue,
String principalId) {
ProtocolOnlineReviewDocumentBase document = null;
try {
if (LOG.isDebugEnabled()) {
String protocolNumber = protocolSubmission.getProtocolNumber();
Integer submissionNumber = protocolSubmission.getSubmissionNumber();
LOG.debug(
String.format(
"Assigning online reviewer [%s] to protocol [%s].",
protocolReviewer, protocolNumber));
LOG.debug(
String.format(
"Current submission for protocol %s is %s.", protocolNumber, submissionNumber));
}
document =
createProtocolOnlineReviewDocument(
protocolSubmission,
protocolReviewer,
documentDescription,
documentExplanation,
documentOrganizationDocumentNumber,
dateRequested,
dateDue,
principalId);
documentService.routeDocument(
document,
"Review Requested by PI during protocol submission.",
new ArrayList<AdHocRouteRecipient>());
if (initialApproval) {
documentService.approveDocument(document, "", new ArrayList<AdHocRouteRecipient>());
}
} catch (WorkflowException e) {
String errorString =
String.format(
"WorkflowException creating new ProtocolOnlineReviewDocumentBase for reviewer %s, protocol %s",
protocolReviewer.getPersonId(), protocolSubmission.getProtocolNumber());
LOG.error(errorString, e);
throw new RuntimeException(errorString, e);
}
return document;
}
/*
* create the view link url for protocolsubmission
*/
protected AnchorHtmlData getViewLink(ProtocolSubmissionBase protocolSubmission) {
AnchorHtmlData viewHtmlData =
super.getViewLink(protocolSubmission.getProtocol().getProtocolDocument());
String submissionIdParam = "&submissionId=" + protocolSubmission.getSubmissionId();
String href = viewHtmlData.getHref();
href = href.replace(DOC_TYPE_NAME_PARAM, submissionIdParam + DOC_TYPE_NAME_PARAM);
viewHtmlData.setHref(href);
return viewHtmlData;
}
public ProtocolOnlineReviewDocumentBase createProtocolOnlineReviewDocument(
ProtocolSubmissionBase protocolSubmission,
ProtocolReviewer protocolReviewer,
String documentDescription,
String documentExplanation,
String documentOrganizationDocumentNumber,
Date dateRequested,
Date dateDue,
String principalId)
throws WorkflowException {
IacucProtocolOnlineReviewDocument protocolReviewDocument;
Person person = personService.getPerson(principalId);
WorkflowDocument workflowDocument =
workflowDocumentService.createWorkflowDocument(
IACUC_PROTOCOL_ONLINE_REVIEW_DOCUMENT_TYPE, person);
DocumentHeader docHeader = new DocumentHeader();
docHeader.setWorkflowDocument(workflowDocument);
docHeader.setDocumentNumber(workflowDocument.getDocumentId().toString());
protocolReviewDocument = new IacucProtocolOnlineReviewDocument();
protocolReviewDocument.setDocumentNumber(docHeader.getDocumentNumber());
protocolReviewDocument.setDocumentHeader(docHeader);
protocolReviewDocument.getProtocolOnlineReview().setProtocol(protocolSubmission.getProtocol());
protocolReviewDocument
.getProtocolOnlineReview()
.setProtocolId(protocolSubmission.getProtocolId());
protocolReviewDocument.getProtocolOnlineReview().setProtocolSubmission(protocolSubmission);
protocolReviewDocument
.getProtocolOnlineReview()
.setSubmissionIdFk(protocolSubmission.getSubmissionId());
protocolReviewDocument
.getProtocolOnlineReview()
.setProtocolOnlineReviewStatusCode(IacucProtocolOnlineReviewStatus.SAVED_STATUS_CD);
protocolReviewDocument
.getProtocolOnlineReview()
.setDateRequested(
dateRequested == null ? new Date((new java.util.Date()).getTime()) : dateRequested);
protocolReviewDocument.getProtocolOnlineReview().setDateDue(dateDue);
protocolReviewDocument
.getProtocolOnlineReview()
.setProtocolReviewerId(protocolReviewer.getProtocolReviewerId());
protocolReviewDocument.getProtocolOnlineReview().setProtocolReviewer(protocolReviewer);
docHeader.setDocumentDescription(documentDescription);
docHeader.setOrganizationDocumentNumber(documentOrganizationDocumentNumber);
docHeader.setExplanation(documentExplanation);
documentService.saveDocument(protocolReviewDocument);
return protocolReviewDocument;
}
/**
* Creates a new ProtocolReviewDocument.
*
* <p>Handles creating the workflow document, and the underlying ProtocolReview BO linking the
* protocol, submission, and reviewer.
*
* @param protocolSubmission The protocol submission
* @param protocolReviewerBean The bean that holds
* @param documentDescription the description for the created document
* @param documentExplanation the explanation for the created document
* @param documentOrganizationNumber the organizationNumber for the created document
* @param principalId The principalId to use when creating the workflow document. Usually this
* should be the principal of the user creating the review.
* @return
* @throws WorkflowException
*/
protected ProtocolOnlineReviewDocumentBase createProtocolOnlineReviewDocument(
ProtocolSubmissionBase protocolSubmission,
ProtocolReviewer protocolReviewer,
String documentDescription,
String documentExplanation,
String documentOrganizationDocumentNumber,
Date dateRequested,
Date dateDue,
String principalId)
throws WorkflowException {
ProtocolOnlineReviewDocumentBase protocolReviewDocument;
Person person = personService.getPerson(principalId);
WorkflowDocument workflowDocument =
workflowDocumentService.createWorkflowDocument(getProtocolOLRDocumentTypeHook(), person);
DocumentHeader docHeader = new DocumentHeader();
docHeader.setWorkflowDocument(workflowDocument);
docHeader.setDocumentNumber(workflowDocument.getDocumentId().toString());
protocolReviewDocument = getNewProtocolOnlineReviewDocumentInstanceHook();
protocolReviewDocument.setDocumentNumber(docHeader.getDocumentNumber());
protocolReviewDocument.setDocumentHeader(docHeader);
protocolReviewDocument.getProtocolOnlineReview().setProtocol(protocolSubmission.getProtocol());
protocolReviewDocument
.getProtocolOnlineReview()
.setProtocolId(protocolSubmission.getProtocolId());
protocolReviewDocument.getProtocolOnlineReview().setProtocolSubmission(protocolSubmission);
protocolReviewDocument
.getProtocolOnlineReview()
.setSubmissionIdFk(protocolSubmission.getSubmissionId());
protocolReviewDocument
.getProtocolOnlineReview()
.setProtocolOnlineReviewStatusCode(getProtocolOLRSavedStatusCodeHook());
protocolReviewDocument
.getProtocolOnlineReview()
.setDateRequested(
dateRequested == null ? new Date((new java.util.Date()).getTime()) : dateRequested);
protocolReviewDocument.getProtocolOnlineReview().setDateDue(dateDue);
protocolReviewDocument
.getProtocolOnlineReview()
.setProtocolReviewerId(protocolReviewer.getProtocolReviewerId());
protocolReviewDocument.getProtocolOnlineReview().setProtocolReviewer(protocolReviewer);
docHeader.setDocumentDescription(documentDescription);
docHeader.setOrganizationDocumentNumber(documentOrganizationDocumentNumber);
docHeader.setExplanation(documentExplanation);
documentService.saveDocument(protocolReviewDocument);
return protocolReviewDocument;
}
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;
}
@Override
public void cancelOnlineReviews(ProtocolSubmissionBase submission, String annotation) {
// get the online reviews, loop through them and finalize them if necessary.
for (ProtocolOnlineReviewBase review : submission.getProtocolOnlineReviews()) {
cancelOnlineReviewDocument(review.getProtocolOnlineReviewDocument(), submission, annotation);
}
}
protected boolean isRequestForSuspension(
ProtocolSubmissionBase submission, String submissionType) {
if (submission != null && submissionType.equals(submission.getSubmissionTypeCode())) {
return true;
}
return false;
}
protected void removeOnlineReviewDocument(
ProtocolOnlineReviewDocumentBase protocolOnlineReviewDocument,
ProtocolSubmissionBase submission,
String annotation) {
if (protocolOnlineReviewDocument != null) {
if (LOG.isDebugEnabled()) {
LOG.debug(
String.format(
"Found protocolOnlineReviewDocument %s, removing it.",
protocolOnlineReviewDocument.getDocumentNumber()));
}
cancelOnlineReviewDocument(protocolOnlineReviewDocument, submission, annotation);
protocolOnlineReviewDocument
.getProtocolOnlineReview()
.setProtocolOnlineReviewStatusCode(
ProtocolOnlineReviewStatus.REMOVED_CANCELLED_STATUS_CD);
List<CommitteeScheduleMinuteBase> reviewComments =
protocolOnlineReviewDocument.getProtocolOnlineReview().getCommitteeScheduleMinutes();
List<CommitteeScheduleMinuteBase> deletedReviewComments =
new ArrayList<CommitteeScheduleMinuteBase>();
getReviewerCommentsService().deleteAllReviewComments(reviewComments, deletedReviewComments);
getReviewerCommentsService().saveReviewComments(reviewComments, deletedReviewComments);
submission
.getProtocolReviewers()
.remove(protocolOnlineReviewDocument.getProtocolOnlineReview().getProtocolReviewer());
getBusinessObjectService().save(protocolOnlineReviewDocument.getProtocolOnlineReview());
}
}
@Override
public List<ProtocolOnlineReviewBase> getProtocolReviews(Long submissionId) {
List<ProtocolOnlineReviewBase> reviews = new ArrayList<ProtocolOnlineReviewBase>();
ProtocolSubmissionBase submission =
getBusinessObjectService()
.findBySinglePrimaryKey(getProtocolSubmissionBOClassHook(), submissionId);
if (submission != null) {
for (ProtocolOnlineReviewBase review : submission.getProtocolOnlineReviews()) {
if (review.isActive()) {
reviews.add(review);
}
}
}
return reviews;
}
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 finalizeOnlineReviews(ProtocolSubmissionBase submission, String annotation) {
// get the online reviews, loop through them and finalize them if necessary.
for (ProtocolOnlineReviewBase review : submission.getProtocolOnlineReviews()) {
//
// review.addActionPerformed("Finalize:"+review.getProtocolOnlineReviewDocument().getDocumentHeader().getWorkflowDocument().getStatus().getCode()+":"+review.getProtocolOnlineReviewStatusCode());
finalizeOnlineReviewDocument(
review.getProtocolOnlineReviewDocument(), submission, annotation);
}
}
private void performGenericAction(
Protocol protocol, ProtocolGenericActionBean actionBean, String protocolActionType)
throws Exception {
ProtocolAction protocolAction =
(ProtocolAction) createProtocolActionAndAttach(protocol, actionBean, protocolActionType);
if (protocol.getNotifyIrbSubmissionId() == null) {
getProtocolActionService().updateProtocolStatus(protocolAction, protocol);
} else {
for (ProtocolSubmissionBase submission : protocol.getProtocolSubmissions()) {
if (submission.getSubmissionId().equals(protocol.getNotifyIrbSubmissionId())) {
submission.setSubmissionStatusCode(ProtocolSubmissionStatus.IRB_ACKNOWLEDGEMENT);
}
}
}
protocol.refreshReferenceObject("protocolStatus");
protocol.refreshReferenceObject("protocolSubmission");
getDocumentService().saveDocument(protocol.getProtocolDocument());
}
@Override
public ProtocolOnlineReviewDocumentBase getProtocolOnlineReviewDocument(
String personId, boolean nonEmployeeFlag, ProtocolSubmissionBase protocolSubmission) {
ProtocolOnlineReviewDocumentBase protocolOnlineReviewDocument = null;
if (protocolSubmission != null) {
for (ProtocolOnlineReviewBase protocolOnlineReview :
protocolSubmission.getProtocolOnlineReviews()) {
if (protocolOnlineReview
.getProtocolReviewer()
.isPersonIdProtocolReviewer(personId, nonEmployeeFlag)
&& protocolOnlineReview.isActive()) {
try {
protocolOnlineReviewDocument =
(ProtocolOnlineReviewDocumentBase)
getDocumentService()
.getByDocumentHeaderId(
protocolOnlineReview
.getProtocolOnlineReviewDocument()
.getDocumentNumber());
} catch (WorkflowException e) {
if (LOG.isDebugEnabled()) {
String errorMessage =
String.format(
"WorkflowException encountered while looking up document number %s for ProtocolOnlineReviewDocumentBase associated with (submissionId=%s,personId=%s,nonEmployeeFlag=%s",
protocolOnlineReview.getProtocolOnlineReviewDocument().getDocumentNumber(),
protocolSubmission.getSubmissionId(),
personId,
nonEmployeeFlag);
LOG.error(errorMessage, e);
throw new RuntimeException(errorMessage, e);
}
}
}
}
}
return protocolOnlineReviewDocument;
}
@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;
}
@Override
public ProtocolReviewer createProtocolReviewer(
String principalId,
boolean nonEmployeeFlag,
String reviewerTypeCode,
ProtocolSubmissionBase protocolSubmission) {
ProtocolReviewer reviewer = createNewProtocolReviewerInstanceHook();
reviewer.setProtocolIdFk(protocolSubmission.getProtocolId());
reviewer.setSubmissionIdFk(protocolSubmission.getSubmissionId());
reviewer.setProtocolNumber(protocolSubmission.getProtocolNumber());
reviewer.setSequenceNumber(protocolSubmission.getSequenceNumber());
reviewer.setSubmissionNumber(protocolSubmission.getSubmissionNumber());
if (!nonEmployeeFlag) {
reviewer.setPersonId(principalId);
} else {
reviewer.setRolodexId(Integer.parseInt(principalId));
}
reviewer.setNonEmployeeFlag(nonEmployeeFlag);
reviewer.setReviewerTypeCode(reviewerTypeCode);
businessObjectService.save(reviewer);
return reviewer;
}
@Override
public boolean isProtocolReviewer(
String personId, boolean nonEmployeeFlag, ProtocolSubmissionBase protocolSubmission) {
boolean isReviewer = false;
if (protocolSubmission != null) {
for (ProtocolOnlineReviewBase review : protocolSubmission.getProtocolOnlineReviews()) {
if (review.getProtocolReviewer().isPersonIdProtocolReviewer(personId, nonEmployeeFlag)
&& review.isActive()) {
isReviewer = true;
break;
}
}
}
return isReviewer;
}
@Override
public void moveOnlineReviews(
ProtocolSubmissionBase submission, ProtocolSubmissionBase newSubmission) {
newSubmission.setProtocolOnlineReviews(new ArrayList<ProtocolOnlineReviewBase>());
for (ProtocolOnlineReviewBase review : submission.getProtocolOnlineReviews()) {
review.setProtocol(newSubmission.getProtocol());
review.setProtocolId(newSubmission.getProtocol().getProtocolId());
review.setSubmissionIdFk(newSubmission.getSubmissionId());
if (CollectionUtils.isNotEmpty(review.getCommitteeScheduleMinutes())) {
for (CommitteeScheduleMinuteBase comment : review.getCommitteeScheduleMinutes()) {
comment.setProtocolIdFk(review.getProtocolId());
comment.setScheduleIdFk(newSubmission.getScheduleIdFk());
}
}
newSubmission.getProtocolOnlineReviews().add(review);
}
}
@Override
public ProtocolReviewer getProtocolReviewer(
String personId, boolean nonEmployeeFlag, ProtocolSubmissionBase protocolSubmission) {
ProtocolReviewer protocolReviewer = null;
if (protocolSubmission != null) {
for (ProtocolOnlineReviewBase protocolOnlineReview :
protocolSubmission.getProtocolOnlineReviews()) {
if (protocolOnlineReview
.getProtocolReviewer()
.isPersonIdProtocolReviewer(personId, nonEmployeeFlag)
&& protocolOnlineReview.isActive()) {
protocolReviewer = protocolOnlineReview.getProtocolReviewer();
break;
}
}
}
return protocolReviewer;
}
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;
}
/**
* Is the protocol's submission in a pending or submitted to committee status?
*
* @param protocol
* @return
*/
private boolean isAssignedToCommittee(ProtocolBase protocol) {
ProtocolSubmissionBase ps = findSubmission(protocol);
return ps != null
&& ps.getCommitteeSchedule() != null
&& ps.getCommitteeSchedule().getScheduledDate() != null;
}
@Override
public void removeOnlineReviewDocument(
String personId,
boolean nonEmployeeFlag,
ProtocolSubmissionBase submission,
String annotation) {
ProtocolOnlineReviewDocumentBase protocolOnlineReviewDocument =
this.getProtocolOnlineReviewDocument(personId, nonEmployeeFlag, submission);
ProtocolOnlineReviewBase submissionsProtocolOnlineReview = null;
for (ProtocolOnlineReviewBase rev : submission.getProtocolOnlineReviews()) {
if (rev.getProtocolOnlineReviewId()
.equals(
protocolOnlineReviewDocument.getProtocolOnlineReview().getProtocolOnlineReviewId())) {
submissionsProtocolOnlineReview = rev;
break;
}
}
if (submissionsProtocolOnlineReview == null) {
throw new IllegalStateException(
"Could not match OnlineReview document being removed to a protocolOnlineReview in the submission.");
}
if (LOG.isDebugEnabled()) {
LOG.debug(
String.format(
"Processing request to remove online review for (personId=%s,nonEmployeeFlag=%s) from (protocol=%s,submission=%s)",
personId,
nonEmployeeFlag,
submission.getProtocol().getProtocolNumber(),
submission.getSubmissionNumber()));
}
if (protocolOnlineReviewDocument != null) {
if (LOG.isDebugEnabled()) {
LOG.debug(
String.format(
"Found protocolOnlineReviewDocument %s, removing it.",
protocolOnlineReviewDocument.getDocumentNumber()));
}
cancelOnlineReviewDocument(protocolOnlineReviewDocument, submission, annotation);
submissionsProtocolOnlineReview.setProtocolOnlineReviewStatusCode(
getProtocolOLRRemovedCancelledStatusCodeHook());
List<CommitteeScheduleMinuteBase> reviewComments =
protocolOnlineReviewDocument.getProtocolOnlineReview().getCommitteeScheduleMinutes();
List<CommitteeScheduleMinuteBase> deletedReviewComments =
new ArrayList<CommitteeScheduleMinuteBase>();
getReviewerCommentsService().deleteAllReviewComments(reviewComments, deletedReviewComments);
getReviewerCommentsService().saveReviewComments(reviewComments, deletedReviewComments);
getBusinessObjectService().save(submissionsProtocolOnlineReview);
} else {
LOG.warn(
String.format(
"ProtocolBase Online Review document could not be found for (personId=%s,nonEmployeeFlag=%s) from (protocol=%s,submission=%s)",
personId,
nonEmployeeFlag,
submission.getProtocol().getProtocolNumber(),
submission.getSubmissionNumber()));
}
}