From 88845976f42ccfe3d77fe9757c5b38e5e362bfd1 Mon Sep 17 00:00:00 2001
From: "Sampath K. Settipalli" <sampath@broadinstitute.org>
Date: Tue, 27 Aug 2024 11:21:27 -0500
Subject: [PATCH] PEPPER-1364 . Additional PHI Manifest changes

---
 .../phimanifest/PhiManifestService.java       | 20 ++++++++++++++-----
 1 file changed, 15 insertions(+), 5 deletions(-)

diff --git a/pepper-apis/dsm-core/src/main/java/org/broadinstitute/dsm/service/phimanifest/PhiManifestService.java b/pepper-apis/dsm-core/src/main/java/org/broadinstitute/dsm/service/phimanifest/PhiManifestService.java
index 57feb2fe85..bb5b0a5af2 100644
--- a/pepper-apis/dsm-core/src/main/java/org/broadinstitute/dsm/service/phimanifest/PhiManifestService.java
+++ b/pepper-apis/dsm-core/src/main/java/org/broadinstitute/dsm/service/phimanifest/PhiManifestService.java
@@ -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";
@@ -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();
@@ -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();
@@ -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)) {
+            //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);
 
         if (hasCompletedPediatricConsentAddendum) {
-            if (age >= 7) {
+            if (age >= 7 || participantStatus.equalsIgnoreCase(CONSENT_SUSPENDED)) {
                 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);