/**
* @see org.kuali.kra.irb.auth.ProtocolAuthorizer#isAuthorized(java.lang.String,
* org.kuali.kra.irb.auth.ProtocolTask)
*/
public boolean isAuthorized(String username, ProtocolTask task) {
Protocol protocol = task.getProtocol();
return kraWorkflowService.isInWorkflow(protocol.getProtocolDocument())
&& isPendingOrSubmittedToCommittee(protocol)
&& isInSchedule(protocol)
&& hasPermission(username, protocol, PermissionConstants.PERFORM_IRB_ACTIONS_ON_PROTO);
}
public ProtocolDocument getDeferredVersionedDocument(Protocol protocol) throws Exception {
getDocumentService()
.cancelDocument(
protocol.getProtocolDocument(),
"Protocol document cancelled - protocol has been deferred.");
getProtocolOnlineReviewService()
.cancelOnlineReviews(
protocol.getProtocolSubmission(),
"Protocol Review cancelled - protocol has been deferred.");
ProtocolDocument newDocument = (ProtocolDocument) getVersionedDocument(protocol);
setReferencesForProtocolCorrespondence(newDocument);
ProtocolAction assignToAgendaProtocolAction =
(ProtocolAction)
getProtocolAssignToAgendaService()
.getAssignedToAgendaProtocolAction((Protocol) newDocument.getProtocol());
if (assignToAgendaProtocolAction != null) {
newDocument.getProtocol().getProtocolActions().remove(assignToAgendaProtocolAction);
getBusinessObjectService().delete(assignToAgendaProtocolAction);
}
newDocument.getProtocol().refreshReferenceObject("protocolStatus");
getDocumentService().saveDocument(newDocument);
return newDocument;
}
@Test
public void testAddProtocolParticipant() {
ProtocolParticipant protocolParticipant = new ProtocolParticipant();
protocolParticipant.setParticipantTypeCode("4");
final ProtocolParticipantServiceImpl protocolParticipantService =
new ProtocolParticipantServiceImpl();
protocolParticipantService.addProtocolParticipant(protocol, protocolParticipant);
int participantSize = protocol.getProtocolParticipants().size();
assertTrue("participant size is " + participantSize, participantSize == 4);
String participantCode1 = protocol.getProtocolParticipant(0).getParticipantTypeCode();
assertTrue(
"participant type code of participant 1 is " + participantCode1,
"1".equals(participantCode1));
String participantCode2 = protocol.getProtocolParticipant(1).getParticipantTypeCode();
assertTrue(
"participant type code of participant 2 is " + participantCode2,
"2".equals(participantCode2));
String participantCode3 = protocol.getProtocolParticipant(2).getParticipantTypeCode();
assertTrue(
"participant type code of participant 3 is " + participantCode3,
"3".equals(participantCode3));
String participantCode4 = protocol.getProtocolParticipant(3).getParticipantTypeCode();
assertTrue(
"participant type code of participant 4 is " + participantCode4,
"4".equals(participantCode4));
}
@Before
public void setUp() {
ProtocolParticipant protocolParticipant1 = new ProtocolParticipant();
protocolParticipant1.setParticipantTypeCode("1");
protocolParticipant1.setParticipantCount(15);
ProtocolParticipant protocolParticipant2 = new ProtocolParticipant();
protocolParticipant2.setParticipantTypeCode("2");
protocolParticipant2.setParticipantCount(25);
ProtocolParticipant protocolParticipant3 = new ProtocolParticipant();
protocolParticipant3.setParticipantTypeCode("3");
protocolParticipant3.setParticipantCount(35);
protocol =
new Protocol() {
@Override
public void refreshReferenceObject(String referenceObjectName) {}
};
protocol.setProtocolParticipants(new ArrayList<ProtocolParticipant>());
protocol.getProtocolParticipants().add(protocolParticipant1);
protocol.getProtocolParticipants().add(protocolParticipant2);
protocol.getProtocolParticipants().add(protocolParticipant3);
}
/**
* @throws WorkflowException
* @see
* org.kuali.kra.irb.actions.notifycommittee.ProtocolNotifyCommitteeService#submitCommitteeNotification(org.kuali.kra.irb.Protocol,
* org.kuali.kra.irb.actions.notifycommittee.ProtocolNotifyCommitteeBean)
*/
public void submitCommitteeNotification(
Protocol protocol, ProtocolNotifyCommitteeBean notifyCommitteeBean) throws WorkflowException {
// we do not create a new submission here unlike in notify IRB
ProtocolAction protocolAction =
new ProtocolAction(protocol, null, ProtocolActionType.NOTIFIED_COMMITTEE);
protocolAction.setComments(notifyCommitteeBean.getComment());
protocolAction.setActionDate(new Timestamp(notifyCommitteeBean.getActionDate().getTime()));
protocol.getProtocolActions().add(protocolAction);
protocolActionService.updateProtocolStatus(protocolAction, protocol);
documentService.saveDocument(protocol.getProtocolDocument());
}
/**
* {@inheritDoc}
*
* @see
* org.kuali.kra.common.specialreview.service.SpecialReviewService#getViewSpecialReviewProtocolRouteHeaderId(java.lang.String)
*/
public Long getViewSpecialReviewProtocolRouteHeaderId(String protocolNumber) throws Exception {
Long routeHeaderId = 0L;
if (StringUtils.isNotBlank(protocolNumber)) {
Protocol protocol = getProtocolFinderDao().findCurrentProtocolByNumber(protocolNumber);
if (protocol != null) {
Document document =
getDocumentService()
.getByDocumentHeaderId(protocol.getProtocolDocument().getDocumentNumber());
routeHeaderId = document.getDocumentHeader().getWorkflowDocument().getRouteHeaderId();
}
}
return routeHeaderId;
}
@Test
public void testGetProtocolVersion() throws Exception {
Protocol protocol = (Protocol) protocolVersionService.getProtocolVersion(PROTOCOL_NUMBER, 1);
assertNull(protocol);
ProtocolDocument protocolDocument1 = ProtocolFactory.createProtocolDocument(PROTOCOL_NUMBER);
ProtocolDocument protocolDocument2 =
(ProtocolDocument) protocolVersionService.versionProtocolDocument(protocolDocument1);
ProtocolDocument protocolDocument3 =
(ProtocolDocument) protocolVersionService.versionProtocolDocument(protocolDocument2);
protocol = (Protocol) protocolVersionService.getProtocolVersion(PROTOCOL_NUMBER, 2);
assertNotNull(protocol);
assertEquals(new Integer(2), protocol.getSequenceNumber());
}
/**
* @see
* org.kuali.kra.irb.protocol.location.ProtocolLocationService#addDefaultProtocolLocation(org.kuali.kra.irb.Protocol)
*/
public void addDefaultProtocolLocation(Protocol protocol) {
if (protocol.getProtocolLocations().size() == 0) {
ProtocolLocation protocolLocation = new ProtocolLocation();
protocolLocation.setProtocolNumber(PROTOCOL_NUMBER);
protocolLocation.setSequenceNumber(SEQUENCE_NUMBER);
Organization organization = getOrganization(Constants.DEFAULT_PROTOCOL_ORGANIZATION_ID);
protocolLocation.setOrganization(organization);
protocolLocation.setOrganizationId(organization.getOrganizationId());
protocolLocation.setRolodexId(organization.getContactAddressId());
protocolLocation.setProtocolOrganizationTypeCode(
Constants.DEFAULT_PROTOCOL_ORGANIZATION_TYPE_CODE);
protocolLocation.refreshReferenceObject(REFERENCE_PROTOCOL_ORGANIZATION_TYPE);
protocolLocation.refreshReferenceObject(REFERENCE_ROLODEX);
protocol.getProtocolLocations().add(protocolLocation);
}
}
protected void setReferencesForProtocolCorrespondence(ProtocolDocument newDocument) {
Protocol newProtocol = newDocument.getProtocol();
newProtocol
.getProtocolActions()
.forEach(
protocolAction -> {
protocolAction.setSequenceNumber(newProtocol.getSequenceNumber());
protocolAction
.getProtocolCorrespondences()
.forEach(
protocolCorrespondence -> {
protocolCorrespondence.setProtocolId(newProtocol.getProtocolId());
protocolCorrespondence.setSequenceNumber(newProtocol.getSequenceNumber());
});
});
}
public void populateProposalPerson_Investigator(
Protocol protocol, ProposalDevelopmentDocument proposalDocument) {
ProposalPerson proposalPerson = new ProposalPerson();
proposalPerson.setPersonId(protocol.getPrincipalInvestigatorId());
PersonEditableService personEditableService =
KraServiceLocator.getService(PersonEditableService.class);
personEditableService.populateContactFieldsFromPersonId(proposalPerson);
proposalPerson.setProposalPersonRoleId(Constants.PRINCIPAL_INVESTIGATOR_ROLE);
proposalPerson.setDevelopmentProposal(proposalDocument.getDevelopmentProposal());
proposalPerson.setProposalNumber(proposalDocument.getDevelopmentProposal().getProposalNumber());
proposalPerson.setProposalPersonNumber(new Integer(1));
proposalPerson.setOptInUnitStatus("Y");
proposalPerson.setOptInCertificationStatus("Y");
proposalDocument.getDevelopmentProposal().getProposalPersons().add(proposalPerson);
KeyPersonnelService keyPersonnelService =
(KeyPersonnelServiceImpl) KraServiceLocator.getService(KeyPersonnelService.class);
keyPersonnelService.populateProposalPerson(proposalPerson, proposalDocument);
keyPersonnelService.assignLeadUnit(
proposalPerson, proposalDocument.getDevelopmentProposal().getOwnedByUnitNumber());
}
/**
* {@inheritDoc}
*
* @see
* org.kuali.kra.common.specialreview.service.SpecialReviewService#deleteProtocolFundingSourceForSpecialReview(java.lang.String,
* java.lang.String, java.lang.String)
*/
public void deleteProtocolFundingSourceForSpecialReview(
String protocolNumber, String fundingSourceNumber, String fundingSourceTypeCode) {
Protocol protocol = getProtocolFinderDao().findCurrentProtocolByNumber(protocolNumber);
if (protocol != null) {
List<ProtocolFundingSource> deletedProtocolFundingSources =
new ArrayList<ProtocolFundingSource>();
for (ProtocolFundingSource protocolFundingSource : protocol.getProtocolFundingSources()) {
if (StringUtils.equals(protocolFundingSource.getFundingSourceNumber(), fundingSourceNumber)
&& StringUtils.equals(
protocolFundingSource.getFundingSourceTypeCode(), fundingSourceTypeCode)) {
deletedProtocolFundingSources.add(protocolFundingSource);
}
}
getBusinessObjectService().delete(deletedProtocolFundingSources);
}
}
protected void populateProposalSpecialReview(
Protocol protocol, ProposalDevelopmentDocument proposalDocument) {
if (protocol != null) {
Integer specialReviewNumber =
proposalDocument.getDocumentNextValue(Constants.SPECIAL_REVIEW_NUMBER);
ProposalSpecialReview specialReview = new ProposalSpecialReview();
specialReview.setSpecialReviewNumber(specialReviewNumber);
specialReview.setSpecialReviewTypeCode(SpecialReviewType.HUMAN_SUBJECTS);
specialReview.setApprovalTypeCode(SpecialReviewApprovalType.PENDING);
specialReview.setProtocolNumber(protocol.getProtocolNumber());
specialReview.setDevelopmentProposal(proposalDocument.getDevelopmentProposal());
specialReview.setProtocolStatus(protocol.getProtocolStatus().getDescription());
specialReview.setComments(ComplianceConstants.NEW_SPECIAL_REVIEW_COMMENT);
proposalDocument.getDevelopmentProposal().getPropSpecialReviews().add(specialReview);
}
}
protected void populateRequiredFields(
Protocol protocol, ProposalDevelopmentDocument proposalDocument) throws Exception {
DevelopmentProposal developmentProposal = proposalDocument.getDevelopmentProposal();
developmentProposal.setTitle(protocol.getTitle());
developmentProposal.setOwnedByUnit(protocol.getLeadUnit().getUnit());
developmentProposal.setOwnedByUnitNumber(protocol.getLeadUnitNumber());
developmentProposal.setRequestedStartDateInitial(new Date(System.currentTimeMillis()));
ParameterService parameterService = KraServiceLocator.getService(ParameterService.class);
String projectEndDateParameter =
parameterService.getParameterValueAsString(
ProtocolDocument.class,
ProtocolProposalDevelopmentDocumentService.PROJECT_END_DATE_NUMBER_OF_YEARS);
int numberOfYears = Integer.parseInt(projectEndDateParameter);
Calendar calendar = Calendar.getInstance();
calendar.add(Calendar.YEAR, numberOfYears);
calendar.add(Calendar.DATE, -1);
Date projectEndDate = new Date(calendar.getTimeInMillis());
developmentProposal.setRequestedEndDateInitial(projectEndDate);
String activityTypeCode =
ProposalDevelopmentUtils.getProposalDevelopmentDocumentParameter(
ProposalDevelopmentUtils.ACTIVITY_TYPE_CODE_RESEARCH_PARM);
String proposalTypeCode =
ProposalDevelopmentUtils.getProposalDevelopmentDocumentParameter(
ProposalDevelopmentUtils.PROPOSAL_TYPE_CODE_NEW_PARM);
developmentProposal.setActivityTypeCode(activityTypeCode);
developmentProposal.setProposalTypeCode(proposalTypeCode);
// find sponsor from funding source
List<ProtocolFundingSourceBase> protocolFundingSources = protocol.getProtocolFundingSources();
ProtocolFundingSource sponsorProtocolFundingSource = null;
for (ProtocolFundingSourceBase protocolFundingSource : protocolFundingSources) {
if (protocolFundingSource.isSponsorFunding()) {
sponsorProtocolFundingSource = (ProtocolFundingSource) protocolFundingSource;
break;
}
}
if (sponsorProtocolFundingSource != null) {
developmentProposal.setSponsorCode(sponsorProtocolFundingSource.getFundingSourceNumber());
}
}
/** Verfy that the protocol has the given protocol action. */
@SuppressWarnings("unchecked")
private void verifyProtocolAction(Protocol protocol, String actionTypeCode) {
List<ProtocolAction> actions = (List) protocol.getProtocolActions();
for (ProtocolAction action : actions) {
if (StringUtils.equals(actionTypeCode, action.getProtocolActionTypeCode())) {
return;
}
}
assertTrue(actionTypeCode + " not found", false);
}
/**
* @see
* org.kuali.kra.irb.protocol.location.ProtocolLocationService#addProtocolLocation(org.kuali.kra.irb.Protocol,
* org.kuali.kra.irb.protocol.location.ProtocolLocation)
*/
public void addProtocolLocation(Protocol protocol, ProtocolLocation protocolLocation) {
// TODO Framework problem of 2 saves
protocolLocation.setProtocolNumber(PROTOCOL_NUMBER);
protocolLocation.setSequenceNumber(SEQUENCE_NUMBER);
protocolLocation.refreshReferenceObject(REFERENCE_PROTOCOL_ORGANIZATION_TYPE);
protocolLocation.refreshReferenceObject(REFERENCE_ORGANIZATION);
protocolLocation.setRolodexId(protocolLocation.getOrganization().getContactAddressId());
protocolLocation.refreshReferenceObject(REFERENCE_ROLODEX);
protocol.getProtocolLocations().add(protocolLocation);
}
/**
* Find the submission. It is the submission that is either currently pending or already submitted
* to a committee.
*
* @param protocol
* @return
*/
private ProtocolSubmission findSubmission(Protocol protocol) {
for (ProtocolSubmission submission : protocol.getProtocolSubmissions()) {
if (StringUtils.equals(submission.getSubmissionStatusCode(), ProtocolSubmissionStatus.PENDING)
|| StringUtils.equals(
submission.getSubmissionStatusCode(),
ProtocolSubmissionStatus.SUBMITTED_TO_COMMITTEE)) {
return submission;
}
}
return null;
}
/**
* {@inheritDoc}
*
* @see
* org.kuali.kra.common.specialreview.service.SpecialReviewService#isLinkedToProtocolFundingSource(java.lang.String,
* java.lang.String, java.lang.String)
*/
public boolean isLinkedToProtocolFundingSource(
String protocolNumber, String fundingSourceNumber, String fundingSourceTypeCode) {
boolean isLinkedToProtocolFundingSource = false;
if (StringUtils.isNotBlank(protocolNumber)) {
Protocol protocol = getProtocolFinderDao().findCurrentProtocolByNumber(protocolNumber);
if (protocol != null) {
for (ProtocolFundingSource protocolFundingSource : protocol.getProtocolFundingSources()) {
if (StringUtils.equals(
protocolFundingSource.getFundingSourceNumber(), fundingSourceNumber)
&& StringUtils.equals(
protocolFundingSource.getFundingSourceTypeCode(), fundingSourceTypeCode)) {
isLinkedToProtocolFundingSource = true;
break;
}
}
}
}
return isLinkedToProtocolFundingSource;
}
@Test
public void testProcessApproveCommitteeDecision() throws Exception {
Protocol protocol = getProtocolAssignedToAgenda();
CommitteeDecision committeeDecision =
getMockCommitteeDecisionBean(CommitteeDecisionMotionType.APPROVE);
service.processCommitteeDecision(protocol, committeeDecision);
ProtocolAction lastAction = protocol.getLastProtocolAction();
assertNotNull(lastAction);
assertEquals(
ProtocolActionType.RECORD_COMMITTEE_DECISION, lastAction.getProtocolActionTypeCode());
ProtocolSubmission submission = protocol.getProtocolSubmission();
assertNotNull(submission);
assertEquals(
CommitteeDecisionMotionType.APPROVE, submission.getCommitteeDecisionMotionTypeCode());
assertEquals(YES_COUNT, submission.getYesVoteCount());
assertEquals(NO_COUNT, submission.getNoVoteCount());
assertEquals(ABSTAIN_COUNT, submission.getAbstainerCount());
assertEquals(RECUSED_COUNT, submission.getRecusedCount());
assertEquals(VOTING_COMMENTS, submission.getVotingComments());
}
protected void populateDocumentOverview(
Protocol protocol, ProposalDevelopmentDocument proposalDocument) {
ProtocolDocument protocolDocument = (ProtocolDocument) protocol.getProtocolDocument();
DocumentHeader proposalDocumentHeader = proposalDocument.getDocumentHeader();
DocumentHeader protocolDocumentHeader = protocolDocument.getDocumentHeader();
proposalDocumentHeader.setDocumentDescription(
"PD - " + protocolDocumentHeader.getDocumentDescription());
proposalDocumentHeader.setExplanation(
"Document created from Protocol - " + protocolDocument.getDocumentNumber());
proposalDocumentHeader.setOrganizationDocumentNumber(
protocolDocumentHeader.getOrganizationDocumentNumber());
}
/**
* {@inheritDoc}
*
* @see
* org.kuali.kra.common.specialreview.service.SpecialReviewService#addProtocolFundingSourceForSpecialReview(java.lang.String,
* java.lang.String, java.lang.String, java.lang.String, java.lang.String)
*/
public void addProtocolFundingSourceForSpecialReview(
String protocolNumber,
String fundingSourceNumber,
String fundingSourceTypeCode,
String fundingSourceName,
String fundingSourceTitle) {
Protocol protocol = getProtocolFinderDao().findCurrentProtocolByNumber(protocolNumber);
if (protocol != null
&& StringUtils.isNotBlank(fundingSourceNumber)
&& NumberUtils.isNumber(fundingSourceTypeCode)) {
ProtocolFundingSource protocolFundingSource = new ProtocolFundingSource();
protocolFundingSource.setProtocolNumber(protocolNumber);
protocolFundingSource.setFundingSourceNumber(fundingSourceNumber);
protocolFundingSource.setFundingSourceTypeCode(fundingSourceTypeCode);
protocolFundingSource.setFundingSourceName(fundingSourceName);
protocolFundingSource.setFundingSourceTitle(fundingSourceTitle);
protocol.getProtocolFundingSources().add(protocolFundingSource);
getBusinessObjectService().save(protocol);
}
}
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 close(Protocol protocol, ProtocolGenericActionBean actionBean) throws Exception {
if (ProtocolActionType.REQUEST_TO_CLOSE.equals(
protocol.getLastProtocolAction().getProtocolActionType().getProtocolActionTypeCode())) {
// if previous action is request to close then the new status is closed by investigator
performGenericAction(
protocol,
actionBean,
ProtocolActionType.CLOSED_ADMINISTRATIVELY_CLOSED,
ProtocolStatus.CLOSED_BY_INVESTIGATOR);
} else {
// else closed administratively
performGenericAction(
protocol,
actionBean,
ProtocolActionType.CLOSED_ADMINISTRATIVELY_CLOSED,
ProtocolStatus.CLOSED_ADMINISTRATIVELY);
}
}
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());
}
/**
* @see
* org.kuali.kra.irb.protocol.location.ProtocolLocationService#clearProtocolLocation(org.kuali.kra.irb.Protocol,
* int)
*/
public void clearProtocolLocationAddress(Protocol protocol, int lineNumber) {
protocol.getProtocolLocations().get(lineNumber).setRolodexId(new Integer(0));
protocol.getProtocolLocations().get(lineNumber).setRolodex(new Rolodex());
}
private boolean isStatusValid(Protocol protocol) {
String submissionStatusCode =
protocol.getProtocolSubmission().getSubmissionStatus().getProtocolSubmissionStatusCode();
return StringUtils.isNotBlank(submissionStatusCode)
&& (ProtocolSubmissionStatus.SUBMITTED_TO_COMMITTEE.equals(submissionStatusCode));
}
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;
}