[Soaplab-users] SoaplabException: Cannot create a DB connection

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Hi,

I recently had a scan through my catalina.out file in my tomcat logs  
and noticed a huge number of "Cannot create a DB connection"  
exceptions. I have attached a typical stack trace below.

Is this normal? or is there something wrong with my Soaplab  
installation?

The reason I ask is because I have a number of Taverna workflows  
which use soaplab services. Quite frequently these workflows will  
fail to complete normally. At first I suspected there may be a bug in  
the Taverna/Freefluo software but when I saw the number of these  
stack traces in my catalina log I began to suspect that perhaps I had  
failed tos et up Soaplab correctly.

Any advice would be greatly appreciated.

Thanks, Tim

PS: When I set up Soaplab I chose not to set up a mysql database to  
store data.

org.embl.ebi.SoaplabShare.SoaplabException: Cannot create a DB  
connection (in setJob/applab).
         at  
org.embl.ebi.SoaplabServer.applab.PersistenceAppLabImpl.setJob 
(PersistenceAppLabImpl.java:117)
         at  
org.embl.ebi.SoaplabServer.applab.JobAppLab.connectToAppLab 
(JobAppLab.java:212)
         at org.embl.ebi.SoaplabServer.applab.JobAppLab.<init> 
(JobAppLab.java:115)
         at  
org.embl.ebi.SoaplabServer.applab.JobManagerAppLab.createJob 
(JobManagerAppLab.java:65)
         at  
org.embl.ebi.SoaplabServer.applab.AnalysisWSAppLabImpl.createAndRun 
(AnalysisWSAppLabImpl.java:594)
         at  
org.embl.ebi.SoaplabServer.applab.AnalysisWSAppLabImpl.createAndRun 
(AnalysisWSAppLabImpl.java:591)
         at sun.reflect.GeneratedMethodAccessor73.invoke(Unknown Source)
         at sun.reflect.DelegatingMethodAccessorImpl.invoke 
(DelegatingMethodAccessorImpl.java:25)
         at java.lang.reflect.Method.invoke(Method.java:585)
         at org.apache.axis.providers.java.RPCProvider.invokeMethod 
(RPCProvider.java:388)
         at org.apache.axis.providers.java.RPCProvider.processMessage 
(RPCProvider.java:283)
         at org.apache.axis.providers.java.JavaProvider.invoke 
(JavaProvider.java:323)
         at org.apache.axis.strategies.InvocationStrategy.visit 
(InvocationStrategy.java:32)
         at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118)
         at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83)
         at org.apache.axis.handlers.soap.SOAPService.invoke 
(SOAPService.java:453)
         at org.apache.axis.server.AxisServer.invoke(AxisServer.java: 
281)
         at org.apache.axis.transport.http.AxisServlet.doPost 
(AxisServlet.java:699)
         at javax.servlet.http.HttpServlet.service(HttpServlet.java:709)
         at org.apache.axis.transport.http.AxisServletBase.service 
(AxisServletBase.java:327)
         at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
         at  
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter 
(ApplicationFilterChain.java:252)
         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:856)
         at org.apache.coyote.http11.Http11Protocol 
$Http11ConnectionHandler.processConnection(Http11Protocol.java:744)
         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(Thread.java:613)

org.embl.ebi.SoaplabShare.SoaplabException: Cannot create a DB  
connection (in getResult).
         at  
org.embl.ebi.SoaplabServer.PersistenceManagerImpl.getResult 
(PersistenceManagerImpl.java:246)
         at org.embl.ebi.SoaplabServer.applab.JobAppLab.getResults 
(JobAppLab.java:647)
         at  
org.embl.ebi.SoaplabServer.applab.AnalysisWSAppLabImpl.getSomeResults 
(AnalysisWSAppLabImpl.java:769)
         at  
org.embl.ebi.SoaplabServer.applab.AnalysisWSAppLabImpl.getSomeResults 
(AnalysisWSAppLabImpl.java:768)
         at sun.reflect.GeneratedMethodAccessor77.invoke(Unknown Source)
         at sun.reflect.DelegatingMethodAccessorImpl.invoke 
(DelegatingMethodAccessorImpl.java:25)
         at java.lang.reflect.Method.invoke(Method.java:585)
         at org.apache.axis.providers.java.RPCProvider.invokeMethod 
(RPCProvider.java:388)
         at org.apache.axis.providers.java.RPCProvider.processMessage 
(RPCProvider.java:283)
         at org.apache.axis.providers.java.JavaProvider.invoke 
(JavaProvider.java:323)
         at org.apache.axis.strategies.InvocationStrategy.visit 
(InvocationStrategy.java:32)
         at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118)
         at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83)
         at org.apache.axis.handlers.soap.SOAPService.invoke 
(SOAPService.java:453)
         at org.apache.axis.server.AxisServer.invoke(AxisServer.java: 
281)
         at org.apache.axis.transport.http.AxisServlet.doPost 
(AxisServlet.java:699)
         at javax.servlet.http.HttpServlet.service(HttpServlet.java:709)
         at org.apache.axis.transport.http.AxisServletBase.service 
(AxisServletBase.java:327)
         at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
         at  
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter 
(ApplicationFilterChain.java:252)
         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:856)
         at org.apache.coyote.http11.Http11Protocol 
$Http11ConnectionHandler.processConnection(Http11Protocol.java:744)
         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(Thread.java:613)

org.embl.ebi.SoaplabShare.SoaplabException: Cannot create a DB  
connection (in localize).
         at org.embl.ebi.SoaplabServer.PersistenceManagerImpl.localize 
(PersistenceManagerImpl.java:485)
         at  
org.embl.ebi.SoaplabServer.applab.PersistenceAppLabImpl.localize 
(PersistenceAppLabImpl.java:148)
         at org.embl.ebi.SoaplabServer.applab.JobAppLab 
$ResultFetcherThread.run(JobAppLab.java:1003)

org.embl.ebi.SoaplabShare.SoaplabException: Cannot create a DB  
connection (in setResults).
         at  
org.embl.ebi.SoaplabServer.PersistenceManagerImpl.setResults 
(PersistenceManagerImpl.java:345)
         at org.embl.ebi.SoaplabServer.applab.JobAppLab 
$ResultFetcherThread.run(JobAppLab.java:999)

org.embl.ebi.SoaplabShare.SoaplabException: Cannot create a DB  
connection (in removeJob).
         at  
org.embl.ebi.SoaplabServer.PersistenceManagerImpl.removeJob 
(PersistenceManagerImpl.java:136)
         at org.embl.ebi.SoaplabServer.applab.JobAppLab.destroy 
(JobAppLab.java:711)
         at org.embl.ebi.SoaplabServer.JobManager.removeJob 
(JobManager.java:56)
         at  
org.embl.ebi.SoaplabServer.applab.AnalysisWSAppLabImpl.destroy 
(AnalysisWSAppLabImpl.java:790)
         at  
org.embl.ebi.SoaplabServer.applab.AnalysisWSAppLabImpl.destroy 
(AnalysisWSAppLabImpl.java:788)
         at sun.reflect.GeneratedMethodAccessor78.invoke(Unknown Source)
         at sun.reflect.DelegatingMethodAccessorImpl.invoke 
(DelegatingMethodAccessorImpl.java:25)
         at java.lang.reflect.Method.invoke(Method.java:585)
         at org.apache.axis.providers.java.RPCProvider.invokeMethod 
(RPCProvider.java:388)
         at org.apache.axis.providers.java.RPCProvider.processMessage 
(RPCProvider.java:283)
         at org.apache.axis.providers.java.JavaProvider.invoke 
(JavaProvider.java:323)
         at org.apache.axis.strategies.InvocationStrategy.visit 
(InvocationStrategy.java:32)
         at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118)
         at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83)
         at org.apache.axis.handlers.soap.SOAPService.invoke 
(SOAPService.java:453)
         at org.apache.axis.server.AxisServer.invoke(AxisServer.java: 
281)
         at org.apache.axis.transport.http.AxisServlet.doPost 
(AxisServlet.java:699)
         at javax.servlet.http.HttpServlet.service(HttpServlet.java:709)
         at org.apache.axis.transport.http.AxisServletBase.service 
(AxisServletBase.java:327)
         at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
         at  
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter 
(ApplicationFilterChain.java:252)
         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:856)
         at org.apache.coyote.http11.Http11Protocol 
$Http11ConnectionHandler.processConnection(Http11Protocol.java:744)
         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(Thread.java:613)