JIRA Some gadgets broken after upgrade to 7.1.1

Matt Gillan

I have just upgraded our sandbox install from JIRA 6.3.15 to JIRA 7.1.1, and am experiencing problem very similar to this issue: https://answers.atlassian.com/questions/24649645

I have pinpointed the issue to SSL, the issue appears and disappears when switching between the two security modes for JIRA 7.1.1 outlined below:

• Tested JIRA 6.3.15 using HTTP only - Gadgets function correctly
• Tested JIRA 6.3.15 using HTTP and HTTPS (redirect HTTP to HTTPs), set port to 8090 and using our own keystore - Gadgets function correctly
• Tested JIRA 7.1.1 using HTTP only - Gadgets function correctly
• Tested JIRA 7.1.1 using HTTP and HTTPS (redirect HTTP to HTTPs), set port to 8090 and using our own keystore - Gadgets are broken

 

All installed add-ons are up to date.

 

Here's what I'm seeing:

Some gadgets have the correct titles, other don't.

Here's the list of "broken" gadgets:

• __MSG_gadget.activity.stream.title__

• __MSG_gadget.filter.results.title__

• __MSG_gadget.watched.title__

Gadgets.jpg

My focus was on the Activity Stream gadget:

• My existing Activity Stream gadget displays most information, the status information at the bottom of each entry (xx minutes age, Comment, Watch) is missing.
• Trying to add it to my dashboard leaves it hanging on the loading bar.  

Gadget2.jpg

• I can select some options while it is in this state, and choosing configure or reload opens a very broken window:Gadget3.jpg

 

Looking at the Catalina logs

• On startup of JIRA:

  09-Mar-2016 15:12:37.374 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version: Apache Tomcat/8.0.17
  09-Mar-2016 15:12:37.374 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Jan 9 2015 15:58:59 UTC
  09-Mar-2016 15:12:37.375 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server number: 8.0.17.0
  09-Mar-2016 15:12:37.375 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Linux
  09-Mar-2016 15:12:37.375 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 3.2.0-4-amd64
  09-Mar-2016 15:12:37.375 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
  09-Mar-2016 15:12:37.375 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JAVA_HOME: /opt/atlassian/jira/jre
  09-Mar-2016 15:12:37.375 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 1.8.0_51-b16
  09-Mar-2016 15:12:37.375 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Oracle Corporation
  09-Mar-2016 15:12:37.375 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: /opt/atlassian/jira
  09-Mar-2016 15:12:37.376 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: /opt/atlassian/jira
  09-Mar-2016 15:12:37.376 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/opt/atlassian/jira/conf/logging.properties
  09-Mar-2016 15:12:37.376 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
  09-Mar-2016 15:12:37.376 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xms384m
  09-Mar-2016 15:12:37.376 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xmx768m
  09-Mar-2016 15:12:37.376 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.awt.headless=true
  09-Mar-2016 15:12:37.377 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Datlassian.standalone=JIRA
  09-Mar-2016 15:12:37.377 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true
  09-Mar-2016 15:12:37.380 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dmail.mime.decodeparameters=true
  09-Mar-2016 15:12:37.381 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.dom4j.factory=com.atlassian.core.xml.InterningDocumentFactory
  09-Mar-2016 15:12:37.381 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Datlassian.mail.senddisabled=true
  09-Mar-2016 15:12:37.381 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Datlassian.mail.fetchdisabled=true
  09-Mar-2016 15:12:37.382 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Datlassian.mail.popdisabled=true
  09-Mar-2016 15:12:37.382 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCDateStamps
  09-Mar-2016 15:12:37.382 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:-OmitStackTraceInFastThrow
  09-Mar-2016 15:12:37.382 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.endorsed.dirs=/opt/atlassian/jira/endorsed
  09-Mar-2016 15:12:37.382 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/opt/atlassian/jira
  09-Mar-2016 15:12:37.382 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/opt/atlassian/jira
  09-Mar-2016 15:12:37.382 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/opt/atlassian/jira/temp
  09-Mar-2016 15:12:37.383 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
  09-Mar-2016 15:12:38.695 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
  09-Mar-2016 15:12:38.856 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
  09-Mar-2016 15:12:38.858 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-bio-8090"]
  09-Mar-2016 15:12:40.204 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 4580 ms
  09-Mar-2016 15:12:40.335 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service Catalina
  09-Mar-2016 15:12:40.335 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet Engine: Apache Tomcat/8.0.17
  09-Mar-2016 15:13:06.644 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-8080"]
  09-Mar-2016 15:13:06.666 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-bio-8090"]
  09-Mar-2016 15:13:06.675 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 26466 ms

  09-Mar-2016 15:12:37.336 WARNING [main] org.apache.catalina.startup.SetAllPropertiesRule.begin [SetAllPropertiesRule]{Server/Service/Connector} Setting property 'maxSpareThreads' to '75' did not find a matching property.
  
  

• On JIRA Stop:
  09-Mar-2016 15:31:18.873 INFO [main] org.apache.catalina.core.StandardServer.await A valid shutdown command was received via the shutdown port. Stopping the Server instance.
  09-Mar-2016 15:31:18.873 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-nio-8080"]
  09-Mar-2016 15:31:18.925 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-bio-8090"]
  09-Mar-2016 15:31:18.975 INFO [main] org.apache.catalina.core.StandardService.stopInternal Stopping service Catalina
  09-Mar-2016 15:31:33.057 WARNING [localhost-startStop-2] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [ROOT] appears to have started a thread named [Abandoned connection cleanup thread] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
  java.lang.Object.wait(Native Method)
  java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:143)
  com.mysql.jdbc.AbandonedConnectionCleanupThread.run(AbandonedConnectionCleanupThread.java:43)
  09-Mar-2016 15:31:33.058 WARNING [localhost-startStop-2] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [ROOT] appears to have started a thread named [JonasBatch] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
  java.lang.Object.wait(Native Method)
  java.lang.Object.wait(Object.java:502)
  org.objectweb.jonas_timer.TimerManager.batch(TimerManager.java:193)
  org.objectweb.jonas_timer.Batch.run(TimerManager.java:65)
  09-Mar-2016 15:31:33.058 WARNING [localhost-startStop-2] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [ROOT] appears to have started a thread named [JonasClock] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
  java.lang.Thread.sleep(Native Method)
  org.objectweb.jonas_timer.TimerManager.clock(TimerManager.java:142)
  org.objectweb.jonas_timer.Clock.run(TimerManager.java:46)
  09-Mar-2016 15:31:33.069 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-8080"]
  09-Mar-2016 15:31:33.157 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-bio-8090"]
  09-Mar-2016 15:31:33.157 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["http-nio-8080"]
  09-Mar-2016 15:31:33.161 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["http-bio-8090"]

 

Gadget2.jpg

Gadget3.jpg

Gadgets.jpg

Matt Gillan

I solved my problem by adding the following to /opt/atlassian/jira/bin/catalina.sh

JAVA_OPTS="$JAVA_OPTS -Djavax.net.ssl.trustStore=$CATALINA_HOME/certificates/truststore.ks -Djavax.net.ssl.trustStorePassword=truststorePassword -server"