[Soaplab-users] SoaplabException: Cannot create a DB connection
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From: Tim T. <Tim...@ed...> - 2006-01-31 11:35:06
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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)
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