RE: Issue #3666, "Sequest pipeline broken," has been updated

LabKey Support Forum (Inactive)
RE: Issue #3666, "Sequest pipeline broken," has been updated wnels2  2007-08-14 05:54
Status: Closed
 
Hi,
I’m trying to resolve the bug #3666 and to patch a new server install. To do this I need to move the newly compiled ms2 module to a labkey server that was installed with the installer. I think I had been able to do this before buy just moving the ms2.jar. Now it appears that ms2.module is the file to be moved but this doesn’t work either. I get the error below. I really do need to patch this system so that it will run fractions with sequest. Is that possible?

Thanks,
Bill

A failure occurred during LabKey Server startup.
java.lang.NoSuchMethodError: org.labkey.api.exp.api.ExperimentService$Interface.registerExperimentRunFilter(Lorg/labkey/api/exp/ExperimentRunFilter;)V
       at org.labkey.ms2.MS2Module.startup(MS2Module.java:139)
       at org.labkey.api.module.ModuleLoader.startup(ModuleLoader.java:912)
       at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:866)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
       at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:82)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
       at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
       at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178)
       at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126)
       at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105)
       at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107)
       at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148)
       at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:869)
       at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:664)
       at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527)
       at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80)
       at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)
       at java.lang.Thread.run(Unknown Source)
 
 
brendanx responded:  2007-08-14 11:47
Bill,

If you are using a 2.1 install, I would suggest sticking with the 2.1 branch. Apply the same fix there to your local copy, and then use the resulting ms2.module. The fix is quite simple (a change of 4 characters on a single line - change getName() to getPath()). Use Subversion to see the exact change made by Josh Eckels to SequestPipelineJob.

--Brendan