From d3280a3feb595e293cec8744eea502b7ba046be7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Guilhem=20Semp=C3=A9r=C3=A9?= <guilhem.sempere@cirad.fr>
Date: Thu, 4 Jan 2024 10:38:18 +0100
Subject: [PATCH] Minor changes

---
 pom.xml                                                         | 2 +-
 .../java/org/brapi/v2/api/AttributevaluesApiController.java     | 2 +-
 src/main/java/org/brapi/v2/api/CallsetsApiController.java       | 2 +-
 src/main/java/org/brapi/v2/api/GermplasmApiController.java      | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/pom.xml b/pom.xml
index f53d0be..92fc0d0 100644
--- a/pom.xml
+++ b/pom.xml
@@ -57,7 +57,7 @@
         <dependency>
             <groupId>com.github.joschi.jackson</groupId>
             <artifactId>jackson-datatype-threetenbp</artifactId>
-            <version>2.12.5</version>
+            <version>2.13.5</version>
         </dependency>
     <!-- Bean Validation API support -->
 		<dependency>
diff --git a/src/main/java/org/brapi/v2/api/AttributevaluesApiController.java b/src/main/java/org/brapi/v2/api/AttributevaluesApiController.java
index 47c3370..355bc49 100644
--- a/src/main/java/org/brapi/v2/api/AttributevaluesApiController.java
+++ b/src/main/java/org/brapi/v2/api/AttributevaluesApiController.java
@@ -149,7 +149,7 @@ public ResponseEntity<GermplasmAttributeValueListResponse> searchAttributevalues
 	                
 	                Authentication auth = tokenManager.getAuthenticationFromToken(tokenManager.readToken(request));
 	                String sCurrentUser = auth == null || "anonymousUser".equals(auth.getName()) ? "anonymousUser" : auth.getName();
-	                LinkedHashMap<String, Individual> individuals = MgdbDao.getInstance().loadIndividualsWithAllMetadata(programDbId, sCurrentUser, null, germplasmIdsToReturn);
+	                LinkedHashMap<String, Individual> individuals = MgdbDao.getInstance().loadIndividualsWithAllMetadata(programDbId, sCurrentUser, null, germplasmIdsToReturn, null);
 	                
 	                ArrayList<GermplasmAttributeValue> data = new ArrayList<>();
 	                for (String individualId : individuals.keySet()) {
diff --git a/src/main/java/org/brapi/v2/api/CallsetsApiController.java b/src/main/java/org/brapi/v2/api/CallsetsApiController.java
index 0fba6cb..44a0465 100644
--- a/src/main/java/org/brapi/v2/api/CallsetsApiController.java
+++ b/src/main/java/org/brapi/v2/api/CallsetsApiController.java
@@ -232,7 +232,7 @@ public ResponseEntity<CallSetsListResponse> searchCallsetsPost(	@ApiParam(value
                                 indIdToSampleIdMap.put(sample.getIndividual(), sample.getId());
 
                         // attach individual metadata to callsets
-                        Map<String, Individual> indMap = MgdbDao.getInstance().loadIndividualsWithAllMetadata(db, sCurrentUser, null, indIdToSampleIdMap.keySet());
+                        Map<String, Individual> indMap = MgdbDao.getInstance().loadIndividualsWithAllMetadata(db, sCurrentUser, null, indIdToSampleIdMap.keySet(), null);
 
                                 for (int i=0; i<samples.size(); i++) {
                                         GenotypingSample sample = samples.get(i);
diff --git a/src/main/java/org/brapi/v2/api/GermplasmApiController.java b/src/main/java/org/brapi/v2/api/GermplasmApiController.java
index ec4bda1..87bc392 100644
--- a/src/main/java/org/brapi/v2/api/GermplasmApiController.java
+++ b/src/main/java/org/brapi/v2/api/GermplasmApiController.java
@@ -239,7 +239,7 @@ else if (!fGotGermplasmNames && !fGotExtRefs) {
             }
 
             for (String database : dbsToAccountFor) {
-                for (Individual ind : MgdbDao.getInstance().loadIndividualsWithAllMetadata(database, sCurrentUser, !projectsByModuleFromSpecifiedStudies.isEmpty() ? projectsByModuleFromSpecifiedStudies.get(database) : null, !individualsByModuleFromSpecifiedGermplasm.isEmpty() ? individualsByModuleFromSpecifiedGermplasm.get(database) : null).values()) {
+                for (Individual ind : MgdbDao.getInstance().loadIndividualsWithAllMetadata(database, sCurrentUser, !projectsByModuleFromSpecifiedStudies.isEmpty() ? projectsByModuleFromSpecifiedStudies.get(database) : null, !individualsByModuleFromSpecifiedGermplasm.isEmpty() ? individualsByModuleFromSpecifiedGermplasm.get(database) : null, null).values()) {
                 	
                 	List synonyms = (List) ind.getAdditionalInfo().get("synonyms");
             		if (synonyms != null)