@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;
}
/*
* 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;
}
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 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 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()));
}
}