Merge pull request #32 from Breeding-Insight/release/0.9.1

Merging release/0.9.1 into brapi-server-v2

Author: mlm483

src/main/java/org/brapi/test/BrAPITestServer/auth/BrapiTestServerJWTAuthFilter.java

@@ -158,7 +158,7 @@ private AuthDetails validateOAuthToken(String token) throws GeneralSecurityExcep
 			RSAPublicKey pubKey = getPublicKey(oidcDiscoveryUrl);
 
 			Algorithm algorithm = Algorithm.RSA256(pubKey, null);
-			JWTVerifier verifier = JWT.require(algorithm).withIssuer("https://auth.brapi.org/auth/realms/brapi")
+			JWTVerifier verifier = JWT.require(algorithm).withIssuer("https://auth.brapi.org/realms/brapi")
 					.build();
 			DecodedJWT jwt = verifier.verify(token);
 

src/main/java/org/brapi/test/BrAPITestServer/service/germ/PedigreeService.java

@@ -339,8 +339,14 @@ private List<PedigreeNodeEntity> filterGenerations(PedigreeSearchRequest request
 			progenyDepth = Integer.MAX_VALUE;
 		}
 
-		Set<PedigreeNodeEntity> baseNodesSet = new HashSet<>(baseNodes);
-		Set<PedigreeNodeEntity> pedigreeTree = new HashSet<>(baseNodes);
+		// TODO: Should the pedigree node records written to the db be different? Converting to a hashset keeps
+		// an entry for records with null germplasm which is not desired in output. Filtering out here for now.
+		List<PedigreeNodeEntity> filteredBaseNodes = baseNodes.stream()
+				.filter(node -> node.getGermplasm() != null)
+				.collect(Collectors.toList());
+
+		Set<PedigreeNodeEntity> baseNodesSet = new HashSet<>(filteredBaseNodes);
+		Set<PedigreeNodeEntity> pedigreeTree = new HashSet<>(filteredBaseNodes);
 
 		getGenerationsRecursively(baseNodesSet, pedigreeDepth, true, pedigreeTree);
 		getGenerationsRecursively(baseNodesSet, progenyDepth, false, pedigreeTree);