Dear LabKey team,
We've tried to upgrade LabKey from a 16.2 installation to 16, but we get this message in the labkey log files and labkey doesn't boot properly:
ERROR ModuleLoader 2016-12-15 13:16:14,635
localhost-startStop-1 : Failure occurred during ModuleLoader init.
java.lang.AbstractMethodError: Method
org/labkey/illumina/IlluminaModule.getSchemaNames()Ljava/util/Collection;
is abstract
at org.labkey.illumina.IlluminaModule.getSchemaNames(IlluminaModule.java)
at
org.labkey.api.module.ModuleLoader.getModuleDataSourceNames(ModuleLoader.java:1622)
at
org.labkey.api.module.ModuleLoader.getAllModuleDataSourceNames(ModuleLoader.java:1613)
at org.labkey.api.data.DbScope.initializeScopes(DbScope.java:1008)
at
org.labkey.api.module.ModuleLoader.initializeDataSources(ModuleLoader.java:917)
at org.labkey.api.module.ModuleLoader.doInit(ModuleLoader.java:330)
at org.labkey.api.module.ModuleLoader.init(ModuleLoader.java:240)
at
org.apache.catalina.core.ApplicationFilterConfig.initFilter(ApplicationFilterConfig.java:279)
at
org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:260)
at
org.apache.catalina.core.ApplicationFilterConfig.<init>(ApplicationFilterConfig.java:105)
at
org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:4908)
at
org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5602)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147)
at
org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
at
org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:677)
at
org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1962)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
Do you have any hints about what could be the cause?
Thanks a lot,
Eva |
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| Jon (LabKey DevOps) responded: |
2016-12-20 20:10 |
Hi Eva,
According to the error, it looks like the Illumina module is being listed and we don't package that anymore in our newer distributions.
Can you remove that module and any other old modules from your /modules directory and restart Tomcat? That should allow the upgrade to continue.
Regards,
Jon |
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| eva pujadas responded: |
2016-12-23 02:54 |
Hi Jon,
You were right, we removed the Illumina module and now the upgrade was successful. Thanks for that.
But now, when starting Tomcat, we get two NullPointerException reported in the "labkey.log" file:
ERROR ExceptionUtil 2016-12-23 11:01:01,306 SearchService:runner : Exception detected and logged to mothership
java.lang.NullPointerException
at org.labkey.issue.model.IssueManager.getIssue(IssueManager.java:230)
at org.labkey.issue.model.IssueManager.indexIssues(IssueManager.java:1413)
at org.labkey.issue.model.IssueManager$IndexGroup.run(IssueManager.java:1394)
at org.labkey.search.model.AbstractSearchService.lambda$new$3(AbstractSearchService.java:843)
at org.labkey.search.model.AbstractSearchService$$Lambda$65/834210982.run(Unknown Source)
at java.lang.Thread.run(Thread.java:745)
ERROR AbstractSearchService 2016-12-23 11:01:01,308 SearchService:runner : Error running org.labkey.issue.model.IssueManager$IndexGroup@1a3703c
java.lang.NullPointerException
at org.labkey.issue.model.IssueManager.getIssue(IssueManager.java:230)
at org.labkey.issue.model.IssueManager.indexIssues(IssueManager.java:1413)
at org.labkey.issue.model.IssueManager$IndexGroup.run(IssueManager.java:1394)
at org.labkey.search.model.AbstractSearchService.lambda$new$3(AbstractSearchService.java:843)
at org.labkey.search.model.AbstractSearchService$$Lambda$65/834210982.run(Unknown Source)
at java.lang.Thread.run(Thread.java:745)
Could that also be related to old modules? Otherwise, what could that be?
Thank you very much for your support.
Regards,
Eva |
| |
| Jon (LabKey DevOps) responded: |
2016-12-23 09:51 |
Hi Eva,
So with regard to those errors, does LabKey start up and is it accessible and usable?
If it is accessible, are you able to access the Issue Tracker successfully?
Regards,
Jon |
| |
| eva pujadas responded: |
2017-01-10 07:33 |
Hi Jon,
After checking the existing issues, I discovered that a couple of them would bring a "500: Unexpected server error" when trying to view them. Since that was happening in our development instance, I thought that the database entries for those issues somehow got corrupted and I deleted those issues directly from the DB (since it is not possible to delete issues from the UI).
After that, LabKey started without errors, so I'm closing this thread.
Thanks a lot for your help,
Eva |
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