From 1110225e3b910068d608f7d69cbcb10110b9861d Mon Sep 17 00:00:00 2001
From: Jason Loux <jloux.brapi@gmail.com>
Date: Mon, 1 Jun 2026 15:48:51 -0400
Subject: [PATCH 1/3] Fix pom jackson depedency issues

---
 pom.xml | 54 ++++++++++++++----------------------------------------
 1 file changed, 14 insertions(+), 40 deletions(-)

diff --git a/pom.xml b/pom.xml
index 962d101a..a1e201c5 100644
--- a/pom.xml
+++ b/pom.xml
@@ -20,6 +20,7 @@
 		<maven.compiler.target>21</maven.compiler.target>
 		<springfox-version>2.10.0</springfox-version>
 		<slf4j-version>2.0.16</slf4j-version>
+		<jackson.version>2.18.1</jackson.version>
 	</properties>
 
 	<dependencies>
@@ -73,28 +74,11 @@
 			<groupId>io.jsonwebtoken</groupId>
 			<artifactId>jjwt</artifactId>
 			<version>0.9.1</version>
-			<exclusions>
-				<exclusion>
-					<groupId>com.fasterxml.jackson.core</groupId>
-					<artifactId>jackson-databind</artifactId>
-				</exclusion>
-			</exclusions>
 		</dependency>
 		<dependency>
 			<groupId>com.google.api-client</groupId>
 			<artifactId>google-api-client</artifactId>
 			<version>1.27.0</version>
-			<exclusions>
-				<exclusion>
-					<groupId>com.fasterxml.jackson.core</groupId>
-					<artifactId>jackson-core</artifactId>
-				</exclusion>
-			</exclusions>
-		</dependency>
-		<dependency>
-			<groupId>com.fasterxml.jackson.core</groupId>
-			<artifactId>jackson-databind</artifactId>
-			<version>[2.9.9.1,)</version>
 		</dependency>
 		<dependency>
 			<groupId>io.springfox</groupId>
@@ -106,11 +90,6 @@
 			<artifactId>springfox-swagger-ui</artifactId>
 			<version>${springfox-version}</version>
 		</dependency>
-		<dependency>
-			<groupId>com.github.joschi.jackson</groupId>
-			<artifactId>jackson-datatype-threetenbp</artifactId>
-			<version>2.8.4</version>
-		</dependency>
 		<dependency>
 			<groupId>jakarta.annotation</groupId>
 			<artifactId>jakarta.annotation-api</artifactId>
@@ -143,6 +122,18 @@
 		</dependency>
 	</dependencies>
 
+	<dependencyManagement>
+		<dependencies>
+			<dependency>
+				<groupId>com.fasterxml.jackson</groupId>
+				<artifactId>jackson-bom</artifactId>
+				<version>${jackson.version}</version>
+				<type>pom</type>
+				<scope>import</scope>
+			</dependency>
+		</dependencies>
+	</dependencyManagement>
+
 	<build>
 		<plugins>
 			<plugin>
@@ -161,7 +152,7 @@
 			<plugin>
 				<groupId>org.springframework.boot</groupId>
 				<artifactId>spring-boot-maven-plugin</artifactId>
-				<version>2.7.5</version>
+				<version>${spring.version}</version>
 				<executions>
 					<execution>
 						<goals>
@@ -173,21 +164,4 @@
 		</plugins>
 	</build>
 
-	<repositories>
-		<repository>
-			<id>spring-releases</id>
-			<url>https://repo.spring.io/libs-release</url>
-		</repository>
-		<repository>
-			<id>spring-milestone</id>
-			<url>https://repo.spring.io/libs-milestone</url>
-		</repository>
-	</repositories>
-	<pluginRepositories>
-		<pluginRepository>
-			<id>spring-releases</id>
-			<url>https://repo.spring.io/libs-release</url>
-		</pluginRepository>
-	</pluginRepositories>
-
 </project>

From 5e05e31ba8c6801fbfdf7f5695d9f39dd2c983c8 Mon Sep 17 00:00:00 2001
From: Jason Loux <jloux.brapi@gmail.com>
Date: Tue, 2 Jun 2026 08:57:52 -0400
Subject: [PATCH 2/3] Changes to pom to support deploy failures

---
 pom.xml | 19 ++++++++++++++++++-
 1 file changed, 18 insertions(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index a1e201c5..e5017b16 100644
--- a/pom.xml
+++ b/pom.xml
@@ -152,7 +152,7 @@
 			<plugin>
 				<groupId>org.springframework.boot</groupId>
 				<artifactId>spring-boot-maven-plugin</artifactId>
-				<version>${spring.version}</version>
+				<version>2.7.5</version>
 				<executions>
 					<execution>
 						<goals>
@@ -164,4 +164,21 @@
 		</plugins>
 	</build>
 
+	<repositories>
+		<repository>
+			<id>spring-releases</id>
+			<url>https://repo.spring.io/libs-release</url>
+		</repository>
+		<repository>
+			<id>spring-milestone</id>
+			<url>https://repo.spring.io/libs-milestone</url>
+		</repository>
+	</repositories>
+	<pluginRepositories>
+		<pluginRepository>
+			<id>spring-releases</id>
+			<url>https://repo.spring.io/libs-release</url>
+		</pluginRepository>
+	</pluginRepositories>
+
 </project>

From a70a96314bb9eab5b3a5f922ed7ff0e25c9fb6b0 Mon Sep 17 00:00:00 2001
From: nickpalladino <np398@cornell.edu>
Date: Thu, 30 Jul 2026 17:09:26 -0400
Subject: [PATCH 3/3] Add external uid migration

---
 .../V005.005__migrate_germplasm_external_uid.sql | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)
 create mode 100644 src/main/resources/db/migration/V005.005__migrate_germplasm_external_uid.sql

diff --git a/src/main/resources/db/migration/V005.005__migrate_germplasm_external_uid.sql b/src/main/resources/db/migration/V005.005__migrate_germplasm_external_uid.sql
new file mode 100644
index 00000000..283f61f4
--- /dev/null
+++ b/src/main/resources/db/migration/V005.005__migrate_germplasm_external_uid.sql
@@ -0,0 +1,16 @@
+-- Update germplasm exref sources to 'External UID' instead of
+-- seed source value for external UIDs.
+
+UPDATE external_reference exref
+SET external_reference_source = 'External UID'
+WHERE exref.external_reference_source IS DISTINCT FROM 'External UID'
+  AND NULLIF(btrim(exref.external_reference_source), '') IS NOT NULL
+  AND EXISTS (
+    SELECT 1
+    FROM germplasm_external_references ger
+      JOIN germplasm g
+        ON g.id = ger.germplasm_entity_id
+    WHERE ger.external_references_id = exref.id
+      AND NULLIF(btrim(g.seed_source), '') IS NOT NULL
+      AND btrim(g.seed_source) = btrim(exref.external_reference_source)
+  );