updates to java 21 bytecode

.circleci/config.yml

@@ -2,7 +2,7 @@ version: 2.1
 parameters:
   java-tag:
     type: string
-    default: "21.0.5"
+    default: "21.0.9"
   run_against_develop_core:
     type: boolean
     default: false
@@ -179,7 +179,8 @@ jobs:
           # plugin, it has its own JVM. The two of these must add up to a bit less than 4GB.
           JAVA_TOOL_OPTIONS: -Xmx512m
     steps: # a collection of executable commands
-      - checkout # check out source code to working directory
+      - checkout:
+          method: full
       - restore_cache:
           # Read about caching dependencies: https://circleci.com/docs/2.0/caching/
           keys:

.github/workflows/mvnw.yml

@@ -4,10 +4,10 @@ on: [push]
 
 jobs:
   build:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     strategy:
       matrix:
-        java: [ '17.0.4+8', '21.0.5+11.0.LTS' ]
+        java: [ '21.0.5+11.0.LTS' ]
 
     steps:
       - name: install git secrets

dockstore-cli-integration-testing/generated/src/main/resources/pom.xml

@@ -36,7 +36,7 @@
     <dependency>
       <groupId>io.dockstore</groupId>
       <artifactId>dockstore-integration-testing</artifactId>
-      <version>1.19.0-alpha.1</version>
+      <version>1.20.0-alpha.0</version>
       <classifier>tests</classifier>
       <scope>compile</scope>
       <exclusions>
@@ -49,7 +49,7 @@
     <dependency>
       <groupId>io.dockstore</groupId>
       <artifactId>dockstore-common</artifactId>
-      <version>1.19.0-alpha.1</version>
+      <version>1.20.0-alpha.0</version>
       <scope>compile</scope>
       <exclusions>
         <exclusion>
@@ -61,7 +61,7 @@
     <dependency>
       <groupId>io.dockstore</groupId>
       <artifactId>dockstore-webservice</artifactId>
-      <version>1.19.0-alpha.1</version>
+      <version>1.20.0-alpha.0</version>
       <scope>compile</scope>
       <exclusions>
         <exclusion>
@@ -73,13 +73,13 @@
     <dependency>
       <groupId>io.dockstore</groupId>
       <artifactId>openapi-java-client</artifactId>
-      <version>1.19.0-alpha.1</version>
+      <version>1.20.0-alpha.0</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <groupId>io.dropwizard</groupId>
       <artifactId>dropwizard-jdbi3</artifactId>
-      <version>5.0.0</version>
+      <version>5.0.1</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
@@ -97,21 +97,21 @@
     <dependency>
       <groupId>ch.qos.logback</groupId>
       <artifactId>logback-classic</artifactId>
-      <version>1.5.19</version>
+      <version>1.5.26</version>
       <scope>runtime</scope>
       <optional>true</optional>
     </dependency>
     <dependency>
       <groupId>ch.qos.logback</groupId>
       <artifactId>logback-core</artifactId>
-      <version>1.5.19</version>
+      <version>1.5.26</version>
       <scope>runtime</scope>
       <optional>true</optional>
     </dependency>
     <dependency>
       <groupId>com.fasterxml.jackson.dataformat</groupId>
       <artifactId>jackson-dataformat-cbor</artifactId>
-      <version>2.20.0</version>
+      <version>2.21.0</version>
       <scope>compile</scope>
     </dependency>
   </dependencies>

dockstore-cli-reports/generated/src/main/resources/pom.xml

@@ -30,13 +30,13 @@
     <dependency>
       <groupId>io.dockstore</groupId>
       <artifactId>dockstore-webservice</artifactId>
-      <version>1.19.0-alpha.1</version>
+      <version>1.20.0-alpha.0</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <groupId>io.dockstore</groupId>
       <artifactId>dockstore-common</artifactId>
-      <version>1.19.0-alpha.1</version>
+      <version>1.20.0-alpha.0</version>
       <scope>compile</scope>
       <exclusions>
         <exclusion>

dockstore-client/generated/src/main/resources/pom.xml

@@ -66,7 +66,7 @@
     <dependency>
       <groupId>io.dockstore</groupId>
       <artifactId>dockstore-common</artifactId>
-      <version>1.19.0-alpha.1</version>
+      <version>1.20.0-alpha.0</version>
       <scope>compile</scope>
       <exclusions>
         <exclusion>
@@ -82,7 +82,7 @@
     <dependency>
       <groupId>io.dockstore</groupId>
       <artifactId>openapi-java-client</artifactId>
-      <version>1.19.0-alpha.1</version>
+      <version>1.20.0-alpha.0</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
@@ -106,7 +106,7 @@
     <dependency>
       <groupId>org.apache.commons</groupId>
       <artifactId>commons-lang3</artifactId>
-      <version>3.18.0</version>
+      <version>3.20.0</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
@@ -118,7 +118,7 @@
     <dependency>
       <groupId>com.google.guava</groupId>
       <artifactId>guava</artifactId>
-      <version>33.4.8-jre</version>
+      <version>33.5.0-jre</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
@@ -142,25 +142,25 @@
     <dependency>
       <groupId>org.apache.commons</groupId>
       <artifactId>commons-text</artifactId>
-      <version>1.14.0</version>
+      <version>1.15.0</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <groupId>com.fasterxml.jackson.core</groupId>
       <artifactId>jackson-databind</artifactId>
-      <version>2.20.0</version>
+      <version>2.21.0</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <groupId>com.fasterxml.jackson.jaxrs</groupId>
       <artifactId>jackson-jaxrs-base</artifactId>
-      <version>2.20.0</version>
+      <version>2.21.0</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <groupId>com.fasterxml.jackson.core</groupId>
       <artifactId>jackson-core</artifactId>
-      <version>2.20.0</version>
+      <version>2.21.0</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
@@ -228,7 +228,7 @@
     <dependency>
       <groupId>ch.qos.logback</groupId>
       <artifactId>logback-classic</artifactId>
-      <version>1.5.19</version>
+      <version>1.5.26</version>
       <scope>compile</scope>
       <optional>true</optional>
     </dependency>
@@ -301,7 +301,7 @@
     <dependency>
       <groupId>org.apache.httpcomponents.client5</groupId>
       <artifactId>httpclient5</artifactId>
-      <version>5.5</version>
+      <version>5.5.2</version>
       <scope>compile</scope>
     </dependency>
     <dependency>

dockstore-file-plugin-parent/generated/src/main/resources/pom.xml

@@ -36,7 +36,7 @@
     <dependency>
       <groupId>org.apache.commons</groupId>
       <artifactId>commons-lang3</artifactId>
-      <version>3.18.0</version>
+      <version>3.20.0</version>
       <scope>compile</scope>
     </dependency>
   </dependencies>

openapi-java-wes-client/generated/src/main/resources/pom.xml

@@ -60,19 +60,19 @@
     <dependency>
       <groupId>com.fasterxml.jackson.core</groupId>
       <artifactId>jackson-core</artifactId>
-      <version>2.20.0</version>
+      <version>2.21.0</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <groupId>com.fasterxml.jackson.core</groupId>
       <artifactId>jackson-annotations</artifactId>
-      <version>2.20</version>
+      <version>2.21</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <groupId>com.fasterxml.jackson.core</groupId>
       <artifactId>jackson-databind</artifactId>
-      <version>2.20.0</version>
+      <version>2.21.0</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
@@ -90,7 +90,7 @@
     <dependency>
       <groupId>com.fasterxml.jackson.datatype</groupId>
       <artifactId>jackson-datatype-jsr310</artifactId>
-      <version>2.20.0</version>
+      <version>2.21.0</version>
       <scope>compile</scope>
     </dependency>
   </dependencies>

pom.xml

@@ -38,7 +38,7 @@
 
         <github.url>scm:git:git@github.com:dockstore/dockstore-cli.git</github.url>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <dockstore-core.version>1.19.0-alpha.1</dockstore-core.version>
+        <dockstore-core.version>1.20.0-alpha.0</dockstore-core.version>
         <maven-failsafe.version>2.22.2</maven-failsafe.version>
         <maven-surefire.version>2.22.2</maven-surefire.version>
         <skipTests>false</skipTests>
@@ -226,7 +226,7 @@
                     <artifactId>maven-compiler-plugin</artifactId>
                     <version>3.10.1</version>
                     <configuration>
-                        <release>17</release>
+                        <release>21</release>
                         <showDeprecation>true</showDeprecation>
                     </configuration>
                 </plugin>
@@ -269,7 +269,7 @@
                 <plugin>
                     <groupId>org.apache.maven.plugins</groupId>
                     <artifactId>maven-dependency-plugin</artifactId>
-                    <version>3.3.0</version>
+                    <version>3.6.1</version>
                 </plugin>
                 <plugin>
                     <groupId>org.apache.maven.plugins</groupId>
@@ -529,7 +529,7 @@
                                     <version>3.8.1</version>
                                 </requireMavenVersion>
                                 <requireJavaVersion>
-                                    <version>[17.0,22.0)</version>
+                                    <version>[21.0,22.0)</version>
                                 </requireJavaVersion>
                                 <banDuplicatePomDependencyVersions />
                                 <bannedDependencies>
@@ -599,7 +599,7 @@
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>
                 <configuration>
-                    <release>17</release>
+                    <release>21</release>
                 </configuration>
             </plugin>
             <plugin>
@@ -681,9 +681,9 @@
             <plugin>
                 <groupId>net.revelc.code</groupId>
                 <artifactId>impsort-maven-plugin</artifactId>
-                <version>1.8.0</version>
+                <version>1.12.0</version>
                 <configuration>
-                    <compliance>17</compliance>
+                    <compliance>21</compliance>
                 </configuration>
                 <executions>
                     <execution>
@@ -752,7 +752,7 @@
                     <plugin>
                         <groupId>org.sonarsource.scanner.maven</groupId>
                         <artifactId>sonar-maven-plugin</artifactId>
-                        <version>3.9.1.2184</version>
+                        <version>5.5.0.6356</version>
                     </plugin>
                 </plugins>
             </build>

support/generated/src/main/resources/pom.xml

@@ -69,10 +69,16 @@
       <version>2.31.56</version>
       <scope>compile</scope>
     </dependency>
+    <dependency>
+      <groupId>software.amazon.awssdk</groupId>
+      <artifactId>aws-core</artifactId>
+      <version>2.31.56</version>
+      <scope>compile</scope>
+    </dependency>
     <dependency>
       <groupId>com.google.guava</groupId>
       <artifactId>guava</artifactId>
-      <version>33.4.8-jre</version>
+      <version>33.5.0-jre</version>
       <scope>compile</scope>
     </dependency>
     <dependency>

support/pom.xml

@@ -157,6 +157,11 @@
             <artifactId>rds</artifactId>
             <scope>compile</scope>
         </dependency>
+        <dependency>
+            <groupId>software.amazon.awssdk</groupId>
+            <artifactId>aws-core</artifactId>
+        </dependency>
+
         <!-- uncomment if describing waf
         <dependency>
             <groupId>software.amazon.awssdk</groupId>