ZFIN-9301: Upgrade jenkins war and plugins (#1256)

* Add java.awt "--add-opens" config

Upgrade plugins:

Upgraded commons-lang3 v3.x Jenkins API Plugin (commons-lang3-api) from 3.13.0-62.v7d18e55f51e2 to 3.17.0-84.vb_b_938040b_078
Upgraded commons-text API Plugin (commons-text-api) from 1.11.0-95.v22a_d30ee5d36 to 1.12.0-129.v99a_50df237f7
Upgraded Ionicons API (ionicons-api) from 56.v1b_1c8c49374e to 74.v93d5eb_813d5f
Upgraded Jackson 2 API Plugin (jackson2-api) from 2.15.2-350.v0c2f3f8fc595 to 2.17.0-379.v02de8ec9f64c
Upgraded Jakarta Mail API (jakarta-mail-api) from 2.0.1-3 to 2.1.3-1
Upgraded Pipeline: API (workflow-api) from 1283.v99c10937efcb_ to 1336.vee415d95c521
Upgraded Pipeline: Step API (workflow-step-api) from 639.v6eca_cd8c04a_a_ to 678.v3ee58b_469476
Upgraded asm-api and json-api plugins
Upgraded antisamy-markup-formatter from 155.v795fb_8702324 to 162.v0e6ec0fcfcf6
Upgraded apache-httpcomponents-client-4-api from 4.5.13-138.v4e7d9a_7b_a_e61 to 4.5.14-208.v438351942757
Upgraded bouncycastle-api from 2.27 to 2.30.1.78.1-248.ve27176eb_46cb_
Upgraded javax-activation-api from 1.2.0-6 to 1.2.0-7
Upgraded javax-mail-api from 1.6.2-8 to 1.6.2-10
Upgraded jaxb from 2.3.8-1 to 2.3.9-1
Upgraded jdk-tool from 63.v62d2fd4b_4793 to 80.v8a_dee33ed6f0
Upgraded plugin-util-api from 4.1.0 to 5.1.0
Upgraded snakeyaml-api from 2.2-111.vc6598e30cc65 to 2.3-123.v13484c65210a_
Upgraded sshd from 3.275.v9e17c10f2571 to 3.330.vc866a_8389b_58

Minor version update for jenkins (2.479.1 to 2.479.2)

Author: rtaylorzfin

buildfiles/jenkins.xml

@@ -445,7 +445,7 @@
             <arg value="${jenkins}/jenkins.war"/>
         </exec>
         <symlink link="${jenkins}/jenkins.war" action="single" overwrite="true" failonerror="fail"
-                 resource="${jenkins}/jenkins-2.479.1.war"/>
+                 resource="${jenkins}/jenkins-2.479.2.war"/>
     </target>
 
     <target name="start-jenkins" depends="create-jenkins-symlink" description="Start up Jenkins ">

docker/jenkins/Dockerfile

@@ -96,6 +96,15 @@ RUN cat /tmp/bash_profile >> /home/gradle/.profile
 
 #CMD ["/usr/bin/tcsh"]
 #CMD ["/bin/bash","-l"]
-CMD ["/bin/bash","-l","-c", \
- "/opt/java/openjdk/bin/java --add-opens java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.lang.reflect=ALL-UNNAMED -Dinstance=docker -jar /opt/zfin/source_roots/zfin.org/server_apps/jenkins/jenkins-2.479.1.war --httpPort=9499 --sessionTimeout=604800 --sessionEviction=604800 --prefix=/jobs"]
- #"/usr/lib/jvm/java-11-openjdk-amd64/bin/java -Dinstance=docker -jar /opt/zfin/source_roots/zfin.org/server_apps/jenkins/jenkins-2.249.2.war --httpPort=9499 --sessionTimeout=604800 --sessionEviction=604800 --prefix=/jobs"]
+CMD ["/bin/bash", "-l", "-c", \
+  "/opt/java/openjdk/bin/java", \
+  "--add-opens", "java.base/java.lang=ALL-UNNAMED", \
+  "--add-opens", "java.base/java.lang.reflect=ALL-UNNAMED", \
+  "--add-opens", "java.desktop/java.awt=ALL-UNNAMED", \
+  "-Dinstance=docker", \
+  "-jar", "/opt/zfin/source_roots/zfin.org/server_apps/jenkins/jenkins-2.479.2.war", \
+  "--httpPort=9499", \
+  "--sessionTimeout=604800", \
+  "--sessionEviction=604800", \
+  "--prefix=/jobs" \
+]

server_apps/jenkins/jenkins-2.479.1.war server_apps/jenkins/jenkins-2.479.2.warserver_apps/jenkins/jenkins-2.479.1.war renamed to server_apps/jenkins/jenkins-2.479.2.war

@@ -16,7 +16,7 @@ echo JAVA_HOME $JAVA_HOME
 
 start_jenkins() {
 echo 'Starting Jenkins...'
-    nohup $JAVA_HOME/bin/java --add-opens java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.lang.reflect=ALL-UNNAMED -Dinstance=$INSTANCE -jar $SOURCEROOT/server_apps/jenkins/jenkins.war  --httpPort=$JENKINS_PORT --sessionTimeout=604800 --sessionEviction=604800 --prefix=/jobs  > $JENKINS_HOME/logs/jenkins.log 2>&1 & echo $! > $JENKINS_HOME/jenkins.pid
+    nohup $JAVA_HOME/bin/java --add-opens java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.lang.reflect=ALL-UNNAMED --add-opens java.desktop/java.awt=ALL-UNNAMED -Dinstance=$INSTANCE -jar $SOURCEROOT/server_apps/jenkins/jenkins.war  --httpPort=$JENKINS_PORT --sessionTimeout=604800 --sessionEviction=604800 --prefix=/jobs  > $JENKINS_HOME/logs/jenkins.log 2>&1 & echo $! > $JENKINS_HOME/jenkins.pid
     echo pid: $(cat $PID_FILE)
 #	start-stop-daemon --start --quiet --background --make-pidfile --pidfile $PIDFILE --chuid $RUN_AS --exec $COMMAND
 }