From 7bdc21e150f4f86f10f100f2100528550180c026 Mon Sep 17 00:00:00 2001
From: hms243 <hms243@cornell.edu>
Date: Fri, 7 Oct 2022 14:38:32 -0400
Subject: [PATCH 1/3] [BI-1632] - Unknown Pedigree not displaying for
 BrAPI-server programs

---
 .../brapi/v2/dao/BrAPIGermplasmDAO.java       | 21 ++++++++++---------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIGermplasmDAO.java b/src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIGermplasmDAO.java
index a76180658..5d56bcbdb 100644
--- a/src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIGermplasmDAO.java
+++ b/src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIGermplasmDAO.java
@@ -162,7 +162,6 @@ private Map<String,BrAPIGermplasm> processGermplasmForDisplay(List<BrAPIGermplas
 
         // Update pedigree string
         for (BrAPIGermplasm germplasm: programGermplasm) {
-            if (germplasm.getPedigree() != null) {
                 JsonObject additionalInfo = germplasm.getAdditionalInfo();
                 if(additionalInfo == null) {
                     additionalInfo = new JsonObject();
@@ -172,7 +171,10 @@ private Map<String,BrAPIGermplasm> processGermplasmForDisplay(List<BrAPIGermplas
                 String newPedigreeString = "";
                 String namePedigreeString = "";
                 String uuidPedigreeString = "";
-                List<String> parents = Arrays.asList(germplasm.getPedigree().split("/"));
+                List<String> parents = Arrays.asList("","");
+                if (germplasm.getPedigree() != null) {
+                    parents = Arrays.asList(germplasm.getPedigree().split("/"));
+                }
                 if (parents.size() >= 1) {
                     if (programGermplasmByFullName.containsKey(parents.get(0))) {
                         String femaleParentAccessionNumber = programGermplasmByFullName.get(parents.get(0)).getAccessionNumber();
@@ -195,19 +197,18 @@ private Map<String,BrAPIGermplasm> processGermplasmForDisplay(List<BrAPIGermplas
                         additionalInfo.addProperty(BrAPIAdditionalInfoFields.GERMPLASM_MALE_PARENT_GID, maleParentAccessionNumber);
                     }
                 }
-                //Add Unknown germplasm for display
-                if (germplasm.getAdditionalInfo().has("femaleParentUnknown") && germplasm.getAdditionalInfo().get("femaleParentUnknown").getAsBoolean()) {
-                    namePedigreeString = "Unknown";
-                }
-                if (germplasm.getAdditionalInfo().has("maleParentUnknown") && germplasm.getAdditionalInfo().get("maleParentUnknown").getAsBoolean()) {
-                    namePedigreeString += "/Unknown";
-                }
+                    //Add Unknown germplasm for display
+                    if (additionalInfo.has("femaleParentUnknown") && additionalInfo.get("femaleParentUnknown").getAsBoolean()) {
+                        namePedigreeString = "Unknown";
+                    }
+                    if (additionalInfo.has("maleParentUnknown") && additionalInfo.get("maleParentUnknown").getAsBoolean()) {
+                        namePedigreeString += "/Unknown";
+                    }
                 //For use in individual germplasm display
                 additionalInfo.addProperty(BrAPIAdditionalInfoFields.GERMPLASM_PEDIGREE_BY_NAME, namePedigreeString);
                 additionalInfo.addProperty(BrAPIAdditionalInfoFields.GERMPLASM_PEDIGREE_BY_UUID, uuidPedigreeString);
 
                 germplasm.setPedigree(newPedigreeString);
-            }
 
             BrAPIExternalReference extRef = germplasm.getExternalReferences().stream().filter(reference -> referenceSource.equals(reference.getReferenceSource())).findFirst().orElseThrow(() -> new IllegalStateException("No BI external reference found"));
             String germplasmId = extRef.getReferenceID();

From 931a1059aae9a4190ed1def8b6535d2dfda38f07 Mon Sep 17 00:00:00 2001
From: hms243 <hms243@cornell.edu>
Date: Fri, 7 Oct 2022 14:45:00 -0400
Subject: [PATCH 2/3] [BI-1632] - Clean up spacing

---
 .../brapi/v2/dao/BrAPIGermplasmDAO.java            | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIGermplasmDAO.java b/src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIGermplasmDAO.java
index 5d56bcbdb..b8ad848cd 100644
--- a/src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIGermplasmDAO.java
+++ b/src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIGermplasmDAO.java
@@ -197,13 +197,13 @@ private Map<String,BrAPIGermplasm> processGermplasmForDisplay(List<BrAPIGermplas
                         additionalInfo.addProperty(BrAPIAdditionalInfoFields.GERMPLASM_MALE_PARENT_GID, maleParentAccessionNumber);
                     }
                 }
-                    //Add Unknown germplasm for display
-                    if (additionalInfo.has("femaleParentUnknown") && additionalInfo.get("femaleParentUnknown").getAsBoolean()) {
-                        namePedigreeString = "Unknown";
-                    }
-                    if (additionalInfo.has("maleParentUnknown") && additionalInfo.get("maleParentUnknown").getAsBoolean()) {
-                        namePedigreeString += "/Unknown";
-                    }
+                //Add Unknown germplasm for display
+                if (additionalInfo.has("femaleParentUnknown") && additionalInfo.get("femaleParentUnknown").getAsBoolean()) {
+                    namePedigreeString = "Unknown";
+                }
+                if (additionalInfo.has("maleParentUnknown") && additionalInfo.get("maleParentUnknown").getAsBoolean()) {
+                    namePedigreeString += "/Unknown";
+                }
                 //For use in individual germplasm display
                 additionalInfo.addProperty(BrAPIAdditionalInfoFields.GERMPLASM_PEDIGREE_BY_NAME, namePedigreeString);
                 additionalInfo.addProperty(BrAPIAdditionalInfoFields.GERMPLASM_PEDIGREE_BY_UUID, uuidPedigreeString);

From cb4d0eff469f01b003b84972f73414a10912f666 Mon Sep 17 00:00:00 2001
From: hms243 <hms243@cornell.edu>
Date: Fri, 7 Oct 2022 17:09:08 -0400
Subject: [PATCH 3/3] [BI-1632] - Unit test fix

---
 .../org/breedinginsight/brapi/v2/dao/BrAPIGermplasmDAO.java   | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIGermplasmDAO.java b/src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIGermplasmDAO.java
index b8ad848cd..85e021fbd 100644
--- a/src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIGermplasmDAO.java
+++ b/src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIGermplasmDAO.java
@@ -93,8 +93,8 @@ public List<BrAPIGermplasm> getRawGermplasm(UUID programId) throws ApiException
         List<BrAPIGermplasm> cacheList = new ArrayList<>(programGermplasmCache.get(programId).values());
         return cacheList.stream().map(germplasm -> {
             germplasm.setGermplasmName(Utilities.appendProgramKey(germplasm.getDefaultDisplayName(), program.getKey(), germplasm.getAccessionNumber()));
-            if(germplasm.getAdditionalInfo() != null && germplasm.getAdditionalInfo()
-                                                                 .has(BrAPIAdditionalInfoFields.GERMPLASM_RAW_PEDIGREE)) {
+            if(germplasm.getAdditionalInfo() != null && germplasm.getAdditionalInfo().has(BrAPIAdditionalInfoFields.GERMPLASM_RAW_PEDIGREE)
+                    && !(germplasm.getAdditionalInfo().get(BrAPIAdditionalInfoFields.GERMPLASM_RAW_PEDIGREE).isJsonNull())) {
                 germplasm.setPedigree(germplasm.getAdditionalInfo().get(BrAPIAdditionalInfoFields.GERMPLASM_RAW_PEDIGREE).getAsString());
             }