From d81a3437f638aea9edaa3143f3a90df91146fe53 Mon Sep 17 00:00:00 2001
From: Luke Sikina <lucas.skina@gmail.com>
Date: Sun, 15 Oct 2023 10:26:08 -0400
Subject: [PATCH] [ALS-5056] QueryRequest sumtype

- Update jackson deps to support serialization of polymorphic types
---
 data/pom.xml                                  | 16 ++++++++++++----
 .../hpds/data/phenotype/ColumnMeta.java       |  4 ++--
 pom.xml                                       | 19 ++++++++++++-------
 service/pom.xml                               | 16 ++++++++++------
 service/src/main/resources/jaxrs-context.xml  |  2 +-
 5 files changed, 37 insertions(+), 20 deletions(-)

diff --git a/data/pom.xml b/data/pom.xml
index 298160fc..f4afa848 100644
--- a/data/pom.xml
+++ b/data/pom.xml
@@ -8,6 +8,10 @@
 		<version>1.0-SNAPSHOT</version>
 	</parent>
 
+	<properties>
+		<jackson.version>2.15.2</jackson.version>
+	</properties>
+
 	<artifactId>data</artifactId>
 
 	<name>data</name>
@@ -26,12 +30,16 @@
 			<artifactId>commons-csv</artifactId>
 		</dependency>
 		<dependency>
-			<groupId>org.codehaus.jackson</groupId>
-			<artifactId>jackson-core-asl</artifactId>
+			<groupId>com.fasterxml.jackson.core</groupId>
+			<artifactId>jackson-core</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>com.fasterxml.jackson.core</groupId>
+			<artifactId>jackson-databind</artifactId>
 		</dependency>
 		<dependency>
-			<groupId>org.codehaus.jackson</groupId>
-			<artifactId>jackson-mapper-asl</artifactId>
+			<groupId>com.fasterxml.jackson.core</groupId>
+			<artifactId>jackson-annotations</artifactId>
 		</dependency>
 		<dependency>
 			<groupId>edu.harvard.hms.dbmi.avillach</groupId>
diff --git a/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/ColumnMeta.java b/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/ColumnMeta.java
index 3831c31c..98d2fa8d 100644
--- a/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/ColumnMeta.java
+++ b/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/ColumnMeta.java
@@ -3,8 +3,8 @@
 import java.io.Serializable;
 import java.util.List;
 
-import org.codehaus.jackson.annotate.JsonIgnore;
-import org.codehaus.jackson.map.annotate.JsonSerialize;
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.databind.annotation.JsonSerialize;
 
 @JsonSerialize(include=JsonSerialize.Inclusion.NON_NULL)
 public class ColumnMeta implements Serializable{
diff --git a/pom.xml b/pom.xml
index 879eeaf9..1c3c964d 100644
--- a/pom.xml
+++ b/pom.xml
@@ -17,7 +17,7 @@
     <module>client-api</module>
   </modules>
   <properties>
-    <jackson.version>1.8.6</jackson.version>
+    <jackson.version>2.15.2</jackson.version>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <dockerfile-maven-version>1.4.10</dockerfile-maven-version>
   </properties>
@@ -245,13 +245,18 @@
         <version>3.2.5</version>
       </dependency>
       <dependency>
-        <groupId>org.codehaus.jackson</groupId>
-        <artifactId>jackson-core-asl</artifactId>
+        <groupId>com.fasterxml.jackson.core</groupId>
+        <artifactId>jackson-core</artifactId>
         <version>${jackson.version}</version>
       </dependency>
       <dependency>
-        <groupId>org.codehaus.jackson</groupId>
-        <artifactId>jackson-mapper-asl</artifactId>
+        <groupId>com.fasterxml.jackson.core</groupId>
+        <artifactId>jackson-databind</artifactId>
+				<version>${jackson.version}</version>
+			</dependency>
+			<dependency>
+				<groupId>com.fasterxml.jackson.core</groupId>
+				<artifactId>jackson-annotations</artifactId>
         <version>${jackson.version}</version>
       </dependency>
       <dependency>
@@ -275,8 +280,8 @@
         <version>1.1.1</version>
       </dependency>
       <dependency>
-        <groupId>org.codehaus.jackson</groupId>
-        <artifactId>jackson-jaxrs</artifactId>
+        <groupId>com.fasterxml.jackson.jaxrs</groupId>
+        <artifactId>jackson-jaxrs-json-provider</artifactId>
         <version>${jackson.version}</version>
       </dependency>
       <dependency>
diff --git a/service/pom.xml b/service/pom.xml
index 734e3a94..267d3092 100644
--- a/service/pom.xml
+++ b/service/pom.xml
@@ -45,12 +45,16 @@
 			<artifactId>guava</artifactId>
 		</dependency>
 		<dependency>
-			<groupId>org.codehaus.jackson</groupId>
-			<artifactId>jackson-core-asl</artifactId>
+			<groupId>com.fasterxml.jackson.core</groupId>
+			<artifactId>jackson-core</artifactId>
 		</dependency>
 		<dependency>
-			<groupId>org.codehaus.jackson</groupId>
-			<artifactId>jackson-mapper-asl</artifactId>
+			<groupId>com.fasterxml.jackson.core</groupId>
+			<artifactId>jackson-databind</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>com.fasterxml.jackson.core</groupId>
+			<artifactId>jackson-annotations</artifactId>
 		</dependency>
 		<dependency>
 			<groupId>javax.xml.bind</groupId>
@@ -69,8 +73,8 @@
 			<artifactId>activation</artifactId>
 		</dependency>
 		<dependency>
-			<groupId>org.codehaus.jackson</groupId>
-			<artifactId>jackson-jaxrs</artifactId>
+			<groupId>com.fasterxml.jackson.jaxrs</groupId>
+			<artifactId>jackson-jaxrs-json-provider</artifactId>
 		</dependency>
 		<dependency>
 			<groupId>org.springframework</groupId>
diff --git a/service/src/main/resources/jaxrs-context.xml b/service/src/main/resources/jaxrs-context.xml
index 08a237bf..006ed56d 100644
--- a/service/src/main/resources/jaxrs-context.xml
+++ b/service/src/main/resources/jaxrs-context.xml
@@ -14,7 +14,7 @@
             <bean class="org.apache.cxf.transport.common.gzip.GZIPOutInterceptor" />
         </jaxrs:outInterceptors>
         <jaxrs:providers>
-            <bean class="org.codehaus.jackson.jaxrs.JacksonJsonProvider" />
+            <bean class="com.fasterxml.jackson.jaxrs.json.JacksonJsonProvider" />
         </jaxrs:providers>
     </jaxrs:server>
 </beans>