diff --git a/bom-internal/pom.xml b/bom-internal/pom.xml
index ce8d42270d..a808423877 100644
--- a/bom-internal/pom.xml
+++ b/bom-internal/pom.xml
@@ -65,7 +65,7 @@ POM as their parent.
         <swagger-ui.version>3.25.0</swagger-ui.version>
         <httpcomponents.version>4.5.13</httpcomponents.version>
         <httpcore.version>4.4.14</httpcore.version>
-        <jetty-servlet.version>9.4.37.v20210219</jetty-servlet.version>
+        <jetty-servlet.version>9.4.38.v20210224</jetty-servlet.version>
         <netty.version>4.1.60.Final</netty.version>
         <scala.version>2.12.13</scala.version>
         <cromwell.version>57</cromwell.version>
@@ -623,13 +623,13 @@ POM as their parent.
             <dependency>
                 <groupId>net.bytebuddy</groupId>
                 <artifactId>byte-buddy-agent</artifactId>
-                <version>1.10.10</version>
+                <version>1.10.17</version>
                 <scope>test</scope>
             </dependency>
             <dependency>
                 <groupId>net.bytebuddy</groupId>
                 <artifactId>byte-buddy</artifactId>
-                <version>1.10.10</version>
+                <version>1.10.17</version>
                 <scope>test</scope>
             </dependency>
             <dependency>
@@ -894,6 +894,22 @@ POM as their parent.
                 <artifactId>jaxb-impl</artifactId>
                 <version>2.2.8</version>
             </dependency>
+            <dependency>
+                <groupId>org.glassfish.jaxb</groupId>
+                <artifactId>jaxb-runtime</artifactId>
+                <version>2.3.3</version>
+            </dependency>
+            <dependency>
+                <groupId>org.glassfish.jaxb</groupId>
+                <artifactId>jaxb-runtime</artifactId>
+                <version>2.3.3</version>
+            </dependency>
+            <dependency>
+                <groupId>javax.xml.bind</groupId>
+                <artifactId>jaxb-api</artifactId>
+                <version>2.3.1</version>
+            </dependency>
+
             <!-- CVE-2018-1000180 -->
             <dependency>
                 <groupId>org.bouncycastle</groupId>
@@ -1034,11 +1050,6 @@ POM as their parent.
                 <artifactId>metrics-healthchecks</artifactId>
                 <version>${dropwizard-annotations.version}</version>
             </dependency>
-            <dependency>
-                <groupId>org.hibernate</groupId>
-                <artifactId>hibernate-core</artifactId>
-                <version>5.2.8.Final</version>
-            </dependency>
             <dependency>
                 <groupId>io.dropwizard</groupId>
                 <artifactId>dropwizard-db</artifactId>
diff --git a/dockstore-integration-testing/src/test/java/io/dockstore/client/cli/ExtendedTRSIT.java b/dockstore-integration-testing/src/test/java/io/dockstore/client/cli/ExtendedTRSIT.java
index deebfc9e14..f95c96560a 100644
--- a/dockstore-integration-testing/src/test/java/io/dockstore/client/cli/ExtendedTRSIT.java
+++ b/dockstore-integration-testing/src/test/java/io/dockstore/client/cli/ExtendedTRSIT.java
@@ -28,7 +28,6 @@
 import io.swagger.client.ApiClient;
 import io.swagger.client.ApiException;
 import io.swagger.client.api.ContainersApi;
-import io.swagger.client.api.ContainertagsApi;
 import io.swagger.client.api.ExtendedGa4GhApi;
 import io.swagger.client.api.Ga4GhApi;
 import io.swagger.client.api.WorkflowsApi;
@@ -192,8 +191,6 @@ private void testVerificationWithGivenClient(ApiClient registeringUser, ApiClien
     public void testVerificationOnSourceFileLevelForTools() {
         final ApiClient webClient = getWebClient(USER_2_USERNAME, testingPostgres);
         ContainersApi toolApi = new ContainersApi(webClient);
-        ContainertagsApi containertagsApi = new ContainertagsApi(webClient);
-        Ga4GhApi ga4GhApi = new Ga4GhApi(webClient);
         DockstoreTool tool = new DockstoreTool();
         tool.setDefaultCwlPath("/cwls/cgpmap-bamOut.cwl");
         tool.setGitUrl("git@github.com:DockstoreTestUser2/dockstore-cgpmap.git");
diff --git a/dockstore-webservice/pom.xml b/dockstore-webservice/pom.xml
index aef965676e..fcaf0ccc08 100644
--- a/dockstore-webservice/pom.xml
+++ b/dockstore-webservice/pom.xml
@@ -488,29 +488,11 @@
         <dependency>
             <groupId>io.swagger.core.v3</groupId>
             <artifactId>swagger-annotations</artifactId>
-            <!-- note: this brings in a version of jaxb-api that breaks
-            liquibase https://liquibase.jira.com/browse/CORE-3262
-            -->
-            <exclusions>
-                <exclusion>
-                    <groupId>javax.xml.bind</groupId>
-                    <artifactId>jaxb-api</artifactId>
-                </exclusion>
-            </exclusions>
         </dependency>
         <!-- https://mvnrepository.com/artifact/io.swagger.core.v3/swagger-jaxrs2 -->
         <dependency>
             <groupId>io.swagger.core.v3</groupId>
             <artifactId>swagger-jaxrs2</artifactId>
-            <!-- note: this brings in a version of jaxb-api that breaks
-            liquibase https://liquibase.jira.com/browse/CORE-3262
-            -->
-            <exclusions>
-                <exclusion>
-                    <groupId>javax.xml.bind</groupId>
-                    <artifactId>jaxb-api</artifactId>
-                </exclusion>
-            </exclusions>
         </dependency>
         <!-- https://mvnrepository.com/artifact/io.swagger.core.v3/swagger-jaxrs2-servlet-initializer -->
         <dependency>
@@ -930,9 +912,14 @@
         <dependency>
             <groupId>org.glassfish.jaxb</groupId>
             <artifactId>jaxb-runtime</artifactId>
-            <version>2.3.3</version>
             <scope>runtime</scope>
         </dependency>
+        <dependency>
+            <groupId>javax.xml.bind</groupId>
+            <artifactId>jaxb-api</artifactId>
+            <scope>runtime</scope>
+        </dependency>
+
         <dependency>
             <groupId>javax.persistence</groupId>
             <artifactId>javax.persistence-api</artifactId>
@@ -949,15 +936,6 @@
         <dependency>
             <groupId>io.swagger.core.v3</groupId>
             <artifactId>swagger-integration</artifactId>
-            <!-- note: this brings in a version of jaxb-api that breaks
-           liquibase https://liquibase.jira.com/browse/CORE-3262
-           -->
-            <exclusions>
-                <exclusion>
-                    <groupId>javax.xml.bind</groupId>
-                    <artifactId>jaxb-api</artifactId>
-                </exclusion>
-            </exclusions>
         </dependency>
         <dependency>
             <groupId>org.pf4j</groupId>