From fb8b04252dbd944bd68e39841aded1f8d5087a3d Mon Sep 17 00:00:00 2001
From: Nick <53413353+nickpalladino@users.noreply.github.com>
Date: Wed, 9 Oct 2024 16:11:52 -0400
Subject: [PATCH] Add accession number parameter

---
 .../brapi/v2/BrAPIPedigreeController.java     | 15 +++++-----
 .../brapi/v2/dao/BrAPIPedigreeDAO.java        | 30 ++++++++++---------
 2 files changed, 24 insertions(+), 21 deletions(-)

diff --git a/src/main/java/org/breedinginsight/brapi/v2/BrAPIPedigreeController.java b/src/main/java/org/breedinginsight/brapi/v2/BrAPIPedigreeController.java
index 1e6d673fe..1be0bfce2 100644
--- a/src/main/java/org/breedinginsight/brapi/v2/BrAPIPedigreeController.java
+++ b/src/main/java/org/breedinginsight/brapi/v2/BrAPIPedigreeController.java
@@ -95,13 +95,14 @@ public HttpResponse<BrAPIPedigreeListResponse> pedigreeGet(@PathVariable("progra
         try {
             List<BrAPIPedigreeNode> pedigree = pedigreeDAO.getPedigree(
                     program.get(),
-                    Optional.ofNullable(includeParents),
-                    Optional.ofNullable(includeSiblings),
-                    Optional.ofNullable(includeProgeny),
-                    Optional.ofNullable(includeFullTree),
-                    Optional.ofNullable(pedigreeDepth),
-                    Optional.ofNullable(progenyDepth),
-                    Optional.ofNullable(germplasmName));
+                    includeParents,
+                    includeSiblings,
+                    includeProgeny,
+                    includeFullTree,
+                    pedigreeDepth,
+                    progenyDepth,
+                    germplasmName,
+                    accessionNumber);
 
             return HttpResponse.ok(
                     new BrAPIPedigreeListResponse()
diff --git a/src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIPedigreeDAO.java b/src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIPedigreeDAO.java
index a00957f2c..3a164c07d 100644
--- a/src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIPedigreeDAO.java
+++ b/src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIPedigreeDAO.java
@@ -73,13 +73,14 @@ public BrAPIPedigreeDAO(ProgramDAO programDAO, BrAPIDAOUtil brAPIDAOUtil,
      */
     public List<BrAPIPedigreeNode> getPedigree(
             Program program,
-            Optional<Boolean> includeParents,
-            Optional<Boolean> includeSiblings,
-            Optional<Boolean> includeProgeny,
-            Optional<Boolean> includeFullTree,
-            Optional<Integer> pedigreeDepth,
-            Optional<Integer> progenyDepth,
-            Optional<String> germplasmName
+            Boolean includeParents,
+            Boolean includeSiblings,
+            Boolean includeProgeny,
+            Boolean includeFullTree,
+            Integer pedigreeDepth,
+            Integer progenyDepth,
+            String germplasmName,
+            String accessionNumber
     ) throws ApiException {
 
         PedigreeQueryParams pedigreeRequest = new PedigreeQueryParams();
@@ -94,13 +95,14 @@ public List<BrAPIPedigreeNode> getPedigree(
         pedigreeRequest.externalReferenceId(extRefId);
         pedigreeRequest.externalReferenceSource(extRefSrc);
 
-        includeParents.ifPresent(pedigreeRequest::includeParents);
-        includeSiblings.ifPresent(pedigreeRequest::includeSiblings);
-        includeProgeny.ifPresent(pedigreeRequest::includeProgeny);
-        includeFullTree.ifPresent(pedigreeRequest::includeFullTree);
-        pedigreeDepth.ifPresent(pedigreeRequest::pedigreeDepth);
-        progenyDepth.ifPresent(pedigreeRequest::progenyDepth);
-        germplasmName.ifPresent(pedigreeRequest::germplasmName);
+        if (includeParents != null) pedigreeRequest.includeParents(includeParents);
+        if (includeSiblings != null) pedigreeRequest.includeSiblings(includeSiblings);
+        if (includeProgeny != null) pedigreeRequest.includeProgeny(includeProgeny);
+        if (includeFullTree != null) pedigreeRequest.includeFullTree(includeFullTree);
+        if (pedigreeDepth != null) pedigreeRequest.pedigreeDepth(pedigreeDepth);
+        if (progenyDepth != null) pedigreeRequest.progenyDepth(progenyDepth);
+        if (germplasmName != null) pedigreeRequest.germplasmName(germplasmName);
+        if (accessionNumber != null) pedigreeRequest.accessionNumber(accessionNumber);
         // TODO: other parameters
 
         // TODO: write utility to do paging instead of hardcoding