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PEPPER-1364 . Additional PHI Manifest changes #2931

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Aug 27, 2024
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PEPPER-1364 . Additional PHI Manifest changes #2931

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20 changes: 15 additions & 5 deletions ...dsm-core/src/main/java/org/broadinstitute/dsm/service/phimanifest/PhiManifestService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,8 @@ public class PhiManifestService {
public static final String SOMATIC_CONSENT_TUMOR_PEDIATRIC_QUESTION_STABLE_ID = "SOMATIC_CONSENT_TUMOR_PEDIATRIC";
public static final String SOMATIC_ASSENT_ADDENDUM_QUESTION_STABLE_ID = "SOMATIC_ASSENT_ADDENDUM";

public static final String CONSENT_SUSPENDED = "CONSENT_SUSPENDED";
public static final String CONSENT_ACTIVITY_CODE = "CONSENT";
public static final String CONSENT_ADDENDUM_ACTIVITY_ACTIVITY_CODE = "CONSENT_ADDENDUM";
public static final String LMS_QUESTION_SOMATIC_CONSENT_ADDENDUM_TUMOR_STABLE_ID = "SOMATIC_CONSENT_ADDENDUM_TUMOR";
public static final String OS2_QUESTION_SOMATIC_CONSENT_ADDENDUM_TUMOR_STABLE_ID = "SOMATIC_CONSENT_TUMOR";
Expand Down Expand Up @@ -73,7 +75,7 @@ public PhiManifestReportRoute.PhiManifestResponse generateReport(String ddpParti
* Creates a PhiManifest from the information in participant and in a clinical order
*/
public static PhiManifest generateDataForReport(@NonNull ElasticSearchParticipantDto participant, @NonNull List<MercuryOrderDto> orders,
@NonNull DDPInstanceDto ddpInstanceDto) {
@NonNull DDPInstanceDto ddpInstanceDto) {
//This method assumes that each order has at most 1 Tumor and at most 1 Normal sample, which is a correct assumption based on
// clinical ordering criteria currently in place
PhiManifest phiManifest = new PhiManifest();
Expand Down Expand Up @@ -166,7 +168,7 @@ private static String convertBooleanToYesNo(boolean b) {
*/
public static String convertBooleanActivityAnswerToString(Optional<Object> answer) {
if (answer.isPresent() && answer.get() instanceof Boolean) {
return convertBooleanToYesNo((Boolean)answer.get());
return convertBooleanToYesNo((Boolean) answer.get());
} else {
if (answer.isPresent()) {
return answer.get().toString();
Expand Down Expand Up @@ -209,15 +211,23 @@ private boolean hasParticipantConsentedToSharedLearning(ElasticSearchParticipant
}
String dateOfBirth = participant.getDsm().get().getDateOfBirth();
String dateOfMajority = (String) participant.getDsm().get().getDateOfMajority();
if (StringUtils.isBlank(dateOfMajority) || DateTimeUtil.isAdult(dateOfMajority)) {
return (Boolean)getAdultParticipantConsentedToTumorAnswer(participant, ddpInstanceDto.getStudyGuid())
String participantStatus = participant.getStatus().orElse("");
if (StringUtils.isBlank(dateOfMajority) || participant.hasCompletedActivity(CONSENT_ACTIVITY_CODE)) {
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@ssettipalli ssettipalli Aug 27, 2024 •
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explicitly checking for SELF CONSENT will make sure aged-up and self enrolled fall into this category

//self adult enrollment
return (Boolean) getAdultParticipantConsentedToTumorAnswer(participant, ddpInstanceDto.getStudyGuid())
.orElse(false);
} else {
//pediatric or aged-up in lost to followup
return isPediatricValidForPHI(participant, dateOfBirth, participantStatus);
}
}

private static boolean isPediatricValidForPHI(ElasticSearchParticipantDto participant, String dateOfBirth, String participantStatus) {
int age = DateTimeUtil.calculateAgeInYears(dateOfBirth);
boolean hasCompletedPediatricConsentAddendum = participant.hasCompletedActivity(CONSENT_ADDENDUM_PEDIATRICS_ACTIVITY_CODE);
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Might be an edge case in existing code base ... if child was enrolled when < 7 and after few years current age will be > 7.. and the child might not have this question: SOMATIC_ASSENT_ADDENDUM_QUESTION_STABLE_ID answered ! (Need to test this scenario later & might need to fix it) .


if (hasCompletedPediatricConsentAddendum) {
if (age >= 7) {
if (age >= 7 || participantStatus.equalsIgnoreCase(CONSENT_SUSPENDED)) {
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agedup participants should fall into this >7 age for sure any way but explicitly checking for CONSENT_SUSPENDED will help just incase DOB isn't in ES DSM document.
Doesnt hurt to include in OR , hence added

return participant.checkAnswerToActivity(CONSENT_ADDENDUM_PEDIATRICS_ACTIVITY_CODE,
SOMATIC_CONSENT_TUMOR_PEDIATRIC_QUESTION_STABLE_ID, true) && participant.checkAnswerToActivity(
CONSENT_ADDENDUM_PEDIATRICS_ACTIVITY_CODE, SOMATIC_ASSENT_ADDENDUM_QUESTION_STABLE_ID, true);
Expand Down
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