PEPPER-294 made sure all uploaded kits get the same ddpParticipantId …

…(all legacy or all pepper)
broadinstitute · May 30, 2024 · 622f913 · 622f913
1 parent b34f9dd
commit 622f913
Show file tree

Hide file tree

Showing 3 changed files with 41 additions and 7 deletions.
diff --git a/pepper-apis/dsm-core/src/main/java/org/broadinstitute/dsm/db/KitRequestShipping.java b/pepper-apis/dsm-core/src/main/java/org/broadinstitute/dsm/db/KitRequestShipping.java
@@ -1858,6 +1858,27 @@ public static String getCollaboratorSampleId(int kitTypeId, String participantCo
         }
     }
 
+    public static String getParticipantIdFromLegacyKit(DDPInstance ddpInstance, String shortId, String collaboratorParticipantId) {
+        Profile profile = new ElasticSearchService().getParticipantProfileByShortID(shortId, ddpInstance.getParticipantIndexES());
+        if (profile == null) {
+            throw new DsmInternalError("Could not find profile for shortId " + shortId);
+        }
+        if (StringUtils.isBlank(profile.getLegacyAltPid())) {
+            return null;
+        }
+        if (isLegacyCollaboratorParticipantId(collaboratorParticipantId, profile.getLegacyShortId())) {
+            List<KitRequestShipping> legacyKits = kitRequestDao.getKitRequestsForCollaboratorParticipantId(collaboratorParticipantId);
+            if (!legacyKits.isEmpty()) {
+                return legacyKits.get(0).getDdpParticipantId();
+            }
+        }
+        return null;
+    }
+
+    private static boolean isLegacyCollaboratorParticipantId(String collaboratorParticipantId, String legacyShortId) {
+        return StringUtils.isNotBlank(collaboratorParticipantId) && collaboratorParticipantId.contains("_" + legacyShortId);
+    }
+
     public Boolean getError() {
         if (Objects.isNull(error)) {
             return false;

diff --git a/pepper-apis/dsm-core/src/main/java/org/broadinstitute/dsm/route/KitUploadRoute.java b/pepper-apis/dsm-core/src/main/java/org/broadinstitute/dsm/route/KitUploadRoute.java
@@ -234,9 +234,9 @@ private void uploadKit(@NonNull DDPInstance ddpInstance, @NonNull KitType kitTyp
                 String participantLegacyAltPid = "";
                 String collaboratorParticipantId = "";
                 //if kit has ddpParticipantId use that (RGP!) and
-                //For any studies that do not have participants the search will fail and error so
+                //For any studies that do not have participants the search will fail and error, so
                 //we check if ddpInstance.getParticipantIndexES() != null
-                if (StringUtils.isNotBlank((ddpInstance.getParticipantIndexES())) && StringUtils.isBlank(kit.getParticipantId())) {
+                if (ddpInstance.hasEsIndex() && StringUtils.isBlank(kit.getParticipantId())) {
                     ElasticSearchParticipantDto participantByShortId =
                             elasticSearch.getParticipantById(ddpInstance.getParticipantIndexES(), kit.getShortId());
                     participantGuid = participantByShortId.getProfile().map(Profile::getGuid).orElse("");
@@ -292,7 +292,7 @@ private void uploadKit(@NonNull DDPInstance ddpInstance, @NonNull KitType kitTyp
                         orderKits.add(kit);
                     }
                 } else {
-                    //all cmi ddps are currently using this!
+                    //all cmi studies are currently using this!
                     handleNormalKit(conn, ddpInstance, kitType, kit, kitRequestSettings, easyPostUtil, userIdRequest, kitTypeName,
                             collaboratorParticipantId, errorMessage, uploadAnyway, duplicateKitList, orderKits, specialKitList, behavior,
                             externalOrderNumber, uploadReason, carrier);
@@ -403,8 +403,15 @@ private void addKitRequest(Connection conn, String kitTypeName, KitRequestSettin
 
             //If there is a participant change the participantID to the ID of the existing
             //participant
-            if (StringUtils.isNotBlank((ddpInstance.getParticipantIndexES()))) {
-                participantID = kit.getParticipantId().trim();
+            if (ddpInstance.hasEsIndex()) {
+                //check if there are previous kits with the legacy participant id
+                String participantIdOfLegacyKit = KitRequestShipping.getParticipantIdFromLegacyKit(ddpInstance, participantID,
+                        collaboratorParticipantId);
+                if (participantIdOfLegacyKit != null) {
+                    participantID = participantIdOfLegacyKit;
+                } else {
+                    participantID = kit.getParticipantId().trim();
+                }
             }
 
             KitRequestShipping.writeRequest(ddpInstance.getDdpInstanceId(), shippingId, kitTypeId, participantID,

diff --git a/pepper-apis/dsm-core/src/test/java/org/broadinstitute/dsm/kits/KitRequestShippingTest.java b/pepper-apis/dsm-core/src/test/java/org/broadinstitute/dsm/kits/KitRequestShippingTest.java
@@ -34,6 +34,7 @@ public class KitRequestShippingTest extends DbAndElasticBaseTest {
     private static DDPInstance ddpInstance;
     private static DDPInstanceDao ddpInstanceDao = new DDPInstanceDao();
     private static String legacyParticipantGuid = "DDP_PT_ID_1";
+    private static String legacyAltpid;
     private static ParticipantDto legacyParticipant;
     private static String notLegacyParticipantGuid = "DDP_PT_ID_2";
     private static ParticipantDto notLegacyParticipant;
@@ -56,6 +57,7 @@ public static void doFirst() {
         legacyParticipant = legacyParticipantPair.getLeft();
         participants.add(legacyParticipant);
         legacyParticipantGuid = legacyParticipant.getRequiredDdpParticipantId();
+        legacyAltpid = legacyParticipantPair.getRight();
 
         Profile profile = new Profile();
         profile.setHruid(notLegacyParticipantShortId);
@@ -134,9 +136,9 @@ public void testLegacyKitUpload() {
             Assert.assertEquals(collaboratorParticipantId, nextCollaboratorParticipantId);
             Assert.assertEquals(collaboratorSampleId, nextCollaboratorSampleId);
 
-            //now check when legacy participant has a kit with legacy id
+            //now check when legacy participant has a kit with legacy id and legacy altpid
             KitRequestShipping kitRequestShipping =  KitRequestShipping.builder()
-                    .withDdpParticipantId(legacyParticipant.getRequiredDdpParticipantId())
+                    .withDdpParticipantId(legacyAltpid)
                     .withBspCollaboratorParticipantId(legacyCollaboratorParticipantId)
                     .withBspCollaboratorSampleId(legacyCollaboratorSampleId)
                     .withKitTypeName("SALIVA")
@@ -153,6 +155,10 @@ public void testLegacyKitUpload() {
 
             Assert.assertEquals(legacyCollaboratorParticipantId, nextCollaboratorParticipantId);
             Assert.assertEquals(expectedNextCollaboratorSampleId, nextCollaboratorSampleId);
+
+            //test what the participant id will be for this
+            String kitParticipantId = KitRequestShipping.getParticipantIdFromLegacyKit(ddpInstance, shortId, nextCollaboratorParticipantId);
+            Assert.assertEquals(legacyAltpid, kitParticipantId);
             return null;
         });
     }