public void migrate(
ExpeditedAdverseEventReport aeReportSrc,
ExpeditedAdverseEventReport aeReportDest,
DomainObjectImportOutcome<ExpeditedAdverseEventReport> outcome) {
List<SAEReportPriorTherapy> srcSAEReportPriorTherapys =
aeReportSrc.getSaeReportPriorTherapies();
if (srcSAEReportPriorTherapys == null || srcSAEReportPriorTherapys.isEmpty()) {
outcome.addWarning("WR-SPT-1", "Input doesn't contain any SAEReportPriorTherapy Values.");
return;
}
// Copy the SAEReportPriorTherapys Information from Source to Destination.
for (SAEReportPriorTherapy spt : srcSAEReportPriorTherapys) {
PriorTherapy pt = findPriorTherapy(spt.getPriorTherapy(), outcome);
if (outcome.hasErrors()) {
return;
}
validateSAEREportPriorTherapyDates(spt, outcome);
SAEReportPriorTherapy destSAEReportPriorTherapy = new SAEReportPriorTherapy();
destSAEReportPriorTherapy.setPriorTherapy(pt);
destSAEReportPriorTherapy.setReport(aeReportDest);
copyProperties(spt, destSAEReportPriorTherapy);
for (PriorTherapyAgent pta : spt.getPriorTherapyAgents()) {
PriorTherapyAgent priorTherapyAgent =
migratePriorTherapyAgent(pta, destSAEReportPriorTherapy);
destSAEReportPriorTherapy.addPriorTherapyAgent(priorTherapyAgent);
}
aeReportDest.addSaeReportPriorTherapies(destSAEReportPriorTherapy);
}
}
/** find the Prior Therapy from List. */
private PriorTherapy findPriorTherapy(
PriorTherapy pt, DomainObjectImportOutcome<ExpeditedAdverseEventReport> outcome) {
List<PriorTherapy> resultLst = priorTherapyDao.searchByExampleIgnoreCase(pt, false);
if (resultLst == null || resultLst.isEmpty()) {
outcome.addError("ER-SPT-1", "Matching prior therapy is not found for " + pt.getText());
return null;
}
if (resultLst.size() > 1) {
outcome.addError("ER-SPT-2", "Multiple matching prior therapies found for " + pt.getText());
return null;
}
return resultLst.get(0);
}
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());
}
/**
* Validate SAEREportPriorTherapy Dates.
*
* @param saeReportPriorTherapy
* @param outcome
*/
private void validateSAEREportPriorTherapyDates(
SAEReportPriorTherapy saeReportPriorTherapy,
DomainObjectImportOutcome<ExpeditedAdverseEventReport> outcome) {
if (saeReportPriorTherapy.getStartDate() != null
&& saeReportPriorTherapy.getEndDate() != null) {
if (saeReportPriorTherapy
.getStartDate()
.toDate()
.after(saeReportPriorTherapy.getEndDate().toDate())) {
outcome.addError(
"PAT_PTY1_ERR", "Report PriorTherapy 'end date' cannot be before 'start date'' ");
}
}
}
public void migrate(
ExpeditedAdverseEventReport aeReportSrc,
ExpeditedAdverseEventReport aeReportDest,
DomainObjectImportOutcome<ExpeditedAdverseEventReport> outcome) {
TreatmentInformation src = aeReportSrc.getTreatmentInformation();
TreatmentInformation dest = aeReportDest.getTreatmentInformation();
// Setting the Course Information from the reporting period.
CourseDate adverseEventCourseDate = new CourseDate();
adverseEventCourseDate.setDate(dest.getReport().getReportingPeriod().getStartDate());
adverseEventCourseDate.setNumber(dest.getReport().getReportingPeriod().getCycleNumber());
dest.setAdverseEventCourse(adverseEventCourseDate);
if (aeReportDest.getAssignment().getStartDateOfFirstCourse() != null) {
dest.setFirstCourseDate(aeReportDest.getAssignment().getStartDateOfFirstCourse());
}
dest.setTotalCourses(aeReportDest.getAssignment().getMaxCycleNumber());
dest.setTreatmentAssignmentDescription(src.getTreatmentAssignmentDescription());
dest.setInvestigationalAgentAdministered(src.getInvestigationalAgentAdministered());
AdverseEventReportingPeriod reportingPeriod = aeReportDest.getReportingPeriod();
if (src.getTreatmentAssignment() != null
&& !StringUtils.isEmpty(src.getTreatmentAssignment().getCode())) {
// find the tac from study
TreatmentAssignment treatmentAssignment =
reportingPeriod
.getStudy()
.findActiveTreatmentAssignment(src.getTreatmentAssignment().getCode());
if (treatmentAssignment == null) {
outcome.addError(
"WS_SAE_002",
"Treatment assignment is no longer active " + src.getTreatmentAssignment().getCode(),
src.getTreatmentAssignment().getCode());
return;
}
dest.setTreatmentAssignment(treatmentAssignment);
dest.setTreatmentDescription(reportingPeriod.getTreatmentAssignmentDescription());
} else {
// default it to what it is there in reporting period
dest.setTreatmentAssignment(reportingPeriod.getTreatmentAssignment());
dest.setTreatmentDescription(reportingPeriod.getTreatmentAssignmentDescription());
}
// migrate course agents
for (CourseAgent caSrc : src.getCourseAgents()) {
migrateCourseAgent(caSrc, aeReportDest, outcome);
}
}
public void testMigrateWithNoTherapy() {
migrator.migrate(xstreamStudy, dest, outcome);
assertEquals(0, dest.getStudyTherapies().size());
assertTrue("No errors should be there", outcome.getMessages().isEmpty());
}
