private void migrateCourseAgent(
CourseAgent caSrc,
ExpeditedAdverseEventReport aeReportDest,
DomainObjectImportOutcome<ExpeditedAdverseEventReport> outcome) {
Study study = aeReportDest.getStudy();
StudyAgent studyAgent = caSrc.getStudyAgent();
if (studyAgent == null
|| ((studyAgent.getAgent() == null
|| StringUtils.isEmpty(studyAgent.getAgent().getNscNumber()))
&& StringUtils.isEmpty(studyAgent.getOtherAgent()))) {
outcome.addWarning("ER-CA-1", "Study Agent is missing in the source");
return;
}
StudyAgent realStudyAgent =
studyAgent.getAgent() == null
? study.findStudyAgentByNscOrName(studyAgent.getOtherAgent())
: study.findStudyAgentByNscOrName(studyAgent.getAgent().getNscNumber());
if (realStudyAgent == null) {
outcome.addWarning("ER-CA-2", "Given Agent is no longer associated to the study");
return;
}
CourseAgent caDest = new CourseAgent();
aeReportDest.getTreatmentInformation().addCourseAgent(caDest);
// set the study agent
caDest.setStudyAgent(realStudyAgent);
caDest.setDose(caSrc.getDose());
caDest.setAdministrationDelay(caSrc.getAdministrationDelay());
caDest.setAdministrationDelayAmount(caSrc.getAdministrationDelayAmount());
caDest.setAdministrationDelayUnits(caSrc.getAdministrationDelayUnits());
caDest.setComments(caSrc.getComments());
caDest.setAgentAdjustment(caSrc.getAgentAdjustment());
caDest.setModifiedDose(caSrc.getModifiedDose());
caDest.setLastAdministeredDate(caSrc.getLastAdministeredDate());
caDest.setDurationAndSchedule(caSrc.getDurationAndSchedule());
caDest.setFirstAdministeredDate(caSrc.getFirstAdministeredDate());
caDest.setTotalDoseAdministeredThisCourse(caSrc.getTotalDoseAdministeredThisCourse());
caDest.setFormulation(caSrc.getFormulation());
caDest.setLotNumber(caSrc.getLotNumber());
}
public void testSynchronizeStudyWithAgent() {
{
StudyAgent studyAgent = studyAgentDao.getById(-1);
Study s = studyDao.getById(-2);
System.out.println(s.getExpectedAECtcTerms().size());
service.synchronizeStudyWithAgent(studyAgent, AgentSpecificTerm.EXPTECTED_AE_ADDED);
studyDao.save(studyAgent.getStudy());
}
interruptSession();
{
Study s = studyDao.getById(-2);
assertEquals(3, s.getExpectedAECtcTerms().size());
assertEquals(1, s.getExpectedAEMeddraLowLevelTerms().size());
assertEquals(
2, s.getTreatmentAssignments().get(0).getTreatmentAssignmentStudyInterventions().size());
assertEquals(
2, s.getTreatmentAssignments().get(1).getTreatmentAssignmentStudyInterventions().size());
assertEquals(
2, s.getTreatmentAssignments().get(0).getAbstractStudyInterventionExpectedAEs().size());
assertEquals(
2, s.getTreatmentAssignments().get(1).getAbstractStudyInterventionExpectedAEs().size());
assertExpectednessSingleTAAE(
s.getTreatmentAssignments()
.get(0)
.getExistingTerm(agentSpecificTermDao.getById(-1).getTerm()));
}
interruptSession();
{
StudyAgent studyAgent = studyAgentDao.getById(-2);
service.synchronizeStudyWithAgent(studyAgent, AgentSpecificTerm.EXPTECTED_AE_ADDED);
studyDao.save(studyAgent.getStudy());
}
interruptSession();
{
Study s = studyDao.getById(-2);
assertEquals(6, s.getExpectedAECtcTerms().size());
assertEquals(1, s.getExpectedAEMeddraLowLevelTerms().size());
assertEquals(
2, s.getTreatmentAssignments().get(0).getTreatmentAssignmentStudyInterventions().size());
assertEquals(
2, s.getTreatmentAssignments().get(1).getTreatmentAssignmentStudyInterventions().size());
assertEquals(
4, s.getTreatmentAssignments().get(0).getAbstractStudyInterventionExpectedAEs().size());
assertEquals(
4, s.getTreatmentAssignments().get(1).getAbstractStudyInterventionExpectedAEs().size());
assertExpectednessMultipleTAAE(
s.getTreatmentAssignments()
.get(0)
.getExistingTerm(agentSpecificTermDao.getById(-1).getTerm()));
StudyAgent studyAgent = studyAgentDao.getById(-2);
service.synchronizeStudyWithAgent(studyAgent, AgentSpecificTerm.EXPTECTED_AE_ADDED);
studyDao.save(studyAgent.getStudy());
}
interruptSession();
{
Study s = studyDao.getById(-2);
assertEquals(6, s.getExpectedAECtcTerms().size());
assertEquals(1, s.getExpectedAEMeddraLowLevelTerms().size());
assertEquals(
2, s.getTreatmentAssignments().get(0).getTreatmentAssignmentStudyInterventions().size());
assertEquals(
2, s.getTreatmentAssignments().get(1).getTreatmentAssignmentStudyInterventions().size());
assertEquals(
4, s.getTreatmentAssignments().get(0).getAbstractStudyInterventionExpectedAEs().size());
assertEquals(
4, s.getTreatmentAssignments().get(1).getAbstractStudyInterventionExpectedAEs().size());
assertExpectednessMultipleTAAE(
s.getTreatmentAssignments()
.get(0)
.getExistingTerm(agentSpecificTermDao.getById(-1).getTerm()));
}
interruptSession();
{
Study s = studyDao.getById(-2);
s.getExpectedAECtcTerms().size();
s.getExpectedAEMeddraLowLevelTerms().size();
for (TreatmentAssignment ta : s.getTreatmentAssignments()) {
ta.getTreatmentAssignmentStudyInterventions().size();
for (AbstractStudyInterventionExpectedAE as :
ta.getAbstractStudyInterventionExpectedAEs()) {
as.getTreatmentAssignmentAgents().size();
}
}
for (StudyAgent sa : s.getStudyAgents()) {
if (sa.getAgent() != null) {
sa.getAgent().getAgentSpecificTerms().size();
sa.getTreatmentAssignmentAgents().size();
}
}
}
interruptSession();
{
Study s = studyDao.getById(-2);
StudyAgent studyAgent = s.getStudyAgents().get(0);
studyAgent.retire();
service.synchronizeStudyWithAgent(studyAgent, AgentSpecificTerm.EXPTECTED_AE_DELETED);
studyAgent.removeTreatmentAssignmentAgents();
studyDao.save(studyAgent.getStudy());
interruptSession();
s = studyDao.getById(-2);
for (ExpectedAECtcTerm ex_ae : s.getExpectedAECtcTerms()) {
System.out.println(ex_ae.getCtcTerm().getCtepTerm());
}
assertEquals(4, s.getExpectedAECtcTerms().size());
assertEquals(1, s.getExpectedAEMeddraLowLevelTerms().size());
assertEquals(
1, s.getTreatmentAssignments().get(0).getTreatmentAssignmentStudyInterventions().size());
assertEquals(
1, s.getTreatmentAssignments().get(1).getTreatmentAssignmentStudyInterventions().size());
assertEquals(
2, s.getTreatmentAssignments().get(0).getAbstractStudyInterventionExpectedAEs().size());
assertEquals(
2, s.getTreatmentAssignments().get(1).getAbstractStudyInterventionExpectedAEs().size());
assertExpectednessSingleTAAE(
s.getTreatmentAssignments()
.get(0)
.getExistingTerm(agentSpecificTermDao.getById(-1).getTerm()));
}
}
public void testSynchronizeStudyWithAgentTerm() {
StudyAgent studyAgent = studyAgentDao.getById(-1);
AgentSpecificTerm ast = agentSpecificTermDao.getById(-1);
service.synchronizeStudyWithAgentTerm(studyAgent, ast, AgentSpecificTerm.EXPTECTED_AE_ADDED);
ast = agentSpecificTermDao.getById(-2);
service.synchronizeStudyWithAgentTerm(studyAgent, ast, AgentSpecificTerm.EXPTECTED_AE_ADDED);
studyDao.save(studyAgent.getStudy());
interruptSession();
Study s = studyDao.getById(-2);
assertEquals(3, s.getExpectedAECtcTerms().size());
assertEquals(1, s.getExpectedAEMeddraLowLevelTerms().size());
assertEquals(
2, s.getTreatmentAssignments().get(0).getTreatmentAssignmentStudyInterventions().size());
assertEquals(
2, s.getTreatmentAssignments().get(1).getTreatmentAssignmentStudyInterventions().size());
assertEquals(
2, s.getTreatmentAssignments().get(0).getAbstractStudyInterventionExpectedAEs().size());
assertEquals(
2, s.getTreatmentAssignments().get(1).getAbstractStudyInterventionExpectedAEs().size());
assertExpectednessSingleTAAE(
s.getTreatmentAssignments()
.get(0)
.getExistingTerm(agentSpecificTermDao.getById(-1).getTerm()));
interruptSession();
studyAgent = studyAgentDao.getById(-2);
ast = agentSpecificTermDao.getById(-3);
service.synchronizeStudyWithAgentTerm(studyAgent, ast, AgentSpecificTerm.EXPTECTED_AE_ADDED);
ast = agentSpecificTermDao.getById(-4);
service.synchronizeStudyWithAgentTerm(studyAgent, ast, AgentSpecificTerm.EXPTECTED_AE_ADDED);
ast = agentSpecificTermDao.getById(-5);
service.synchronizeStudyWithAgentTerm(studyAgent, ast, AgentSpecificTerm.EXPTECTED_AE_ADDED);
studyDao.save(studyAgent.getStudy());
interruptSession();
s = studyDao.getById(-2);
assertEquals(6, s.getExpectedAECtcTerms().size());
assertEquals(1, s.getExpectedAEMeddraLowLevelTerms().size());
assertEquals(
2, s.getTreatmentAssignments().get(0).getTreatmentAssignmentStudyInterventions().size());
assertEquals(
2, s.getTreatmentAssignments().get(1).getTreatmentAssignmentStudyInterventions().size());
assertEquals(
4, s.getTreatmentAssignments().get(0).getAbstractStudyInterventionExpectedAEs().size());
assertEquals(
4, s.getTreatmentAssignments().get(1).getAbstractStudyInterventionExpectedAEs().size());
assertExpectednessMultipleTAAE(
s.getTreatmentAssignments()
.get(0)
.getExistingTerm(agentSpecificTermDao.getById(-1).getTerm()));
studyAgent = studyAgentDao.getById(-2);
ast = agentSpecificTermDao.getById(-3);
service.synchronizeStudyWithAgentTerm(studyAgent, ast, AgentSpecificTerm.EXPTECTED_AE_ADDED);
studyDao.save(studyAgent.getStudy());
interruptSession();
s = studyDao.getById(-2);
assertEquals(6, s.getExpectedAECtcTerms().size());
assertEquals(1, s.getExpectedAEMeddraLowLevelTerms().size());
assertEquals(
2, s.getTreatmentAssignments().get(0).getTreatmentAssignmentStudyInterventions().size());
assertEquals(
2, s.getTreatmentAssignments().get(1).getTreatmentAssignmentStudyInterventions().size());
assertEquals(
4, s.getTreatmentAssignments().get(0).getAbstractStudyInterventionExpectedAEs().size());
assertEquals(
4, s.getTreatmentAssignments().get(1).getAbstractStudyInterventionExpectedAEs().size());
assertExpectednessMultipleTAAE(
s.getTreatmentAssignments()
.get(0)
.getExistingTerm(agentSpecificTermDao.getById(-1).getTerm()));
studyAgent = studyAgentDao.getById(-2);
ast = agentSpecificTermDao.getById(-3);
ast.setGrade1Frequency(20.00);
ast.setGrade2Frequency(10.00);
ast.setGrade3Frequency(4.34);
ast.setGrade4Frequency(6.23);
ast.setGrade5Frequency(44.00);
ast.setExpectednessFrequency(60.00);
ast.setExpected(false);
service.synchronizeStudyWithAgentTerm(studyAgent, ast, AgentSpecificTerm.EXPTECTED_AE_UPDATED);
studyDao.save(studyAgent.getStudy());
interruptSession();
s = studyDao.getById(-2);
assertEquals(6, s.getExpectedAECtcTerms().size());
assertEquals(1, s.getExpectedAEMeddraLowLevelTerms().size());
assertEquals(
2, s.getTreatmentAssignments().get(0).getTreatmentAssignmentStudyInterventions().size());
assertEquals(
2, s.getTreatmentAssignments().get(1).getTreatmentAssignmentStudyInterventions().size());
assertEquals(
4, s.getTreatmentAssignments().get(0).getAbstractStudyInterventionExpectedAEs().size());
assertEquals(
4, s.getTreatmentAssignments().get(1).getAbstractStudyInterventionExpectedAEs().size());
assertExpectednessUpdatedTAAE(
s.getTreatmentAssignments()
.get(0)
.getExistingTerm(agentSpecificTermDao.getById(-1).getTerm()));
studyAgent = studyAgentDao.getById(-2);
assertTrue(studyAgent.equals(studyAgent.getStudy().getStudyAgents().get(0)));
ast = agentSpecificTermDao.getById(-3);
service.synchronizeStudyWithAgentTerm(studyAgent, ast, AgentSpecificTerm.EXPTECTED_AE_DELETED);
ast = agentSpecificTermDao.getById(-4);
service.synchronizeStudyWithAgentTerm(studyAgent, ast, AgentSpecificTerm.EXPTECTED_AE_DELETED);
ast = agentSpecificTermDao.getById(-5);
service.synchronizeStudyWithAgentTerm(studyAgent, ast, AgentSpecificTerm.EXPTECTED_AE_DELETED);
studyDao.save(studyAgent.getStudy());
interruptSession();
s = studyDao.getById(-2);
assertEquals(4, s.getExpectedAECtcTerms().size());
assertEquals(1, s.getExpectedAEMeddraLowLevelTerms().size());
assertEquals(
2, s.getTreatmentAssignments().get(0).getTreatmentAssignmentStudyInterventions().size());
assertEquals(
2, s.getTreatmentAssignments().get(1).getTreatmentAssignmentStudyInterventions().size());
assertEquals(
2, s.getTreatmentAssignments().get(0).getAbstractStudyInterventionExpectedAEs().size());
assertEquals(
2, s.getTreatmentAssignments().get(1).getAbstractStudyInterventionExpectedAEs().size());
assertExpectednessSingleTAAE(
s.getTreatmentAssignments()
.get(0)
.getExistingTerm(agentSpecificTermDao.getById(-1).getTerm()));
}