Error generating serial number

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Error generating serial number

James Blackshaw
Hi,
I got this error message while trying to load in mass spectrometry data.
I can't find a reference to the error on the website, could you tell me
what it means please?

Thanks,
James


BUILD FAILED
/home/jab250/intermine_mass_copy/imbuild/integrate.xml:54: The following
error occurred while executing this line:
/home/jab250/intermine_mass_copy/imbuild/source.xml:201: Exception while
reading from: /data/datasets/mitominer/ms_xml/yeast_test.xml
     at
org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:170)
     at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
     at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
     at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
     at java.lang.reflect.Method.invoke(Method.java:616)
     at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
     at org.apache.tools.ant.Task.perform(Task.java:348)
     at org.apache.tools.ant.Target.execute(Target.java:390)
     at org.apache.tools.ant.Target.performTasks(Target.java:411)
     at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1360)
     at
org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
     at org.apache.tools.ant.Project.executeTargets(Project.java:1212)
     at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:441)
     at org.intermine.task.Integrate.performAction(Integrate.java:223)
     at org.intermine.task.Integrate.performAction(Integrate.java:135)
     at org.intermine.task.Integrate.execute(Integrate.java:127)
     at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
     at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
     at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
     at java.lang.reflect.Method.invoke(Method.java:616)
     at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
     at org.apache.tools.ant.Task.perform(Task.java:348)
     at org.apache.tools.ant.Target.execute(Target.java:390)
     at org.apache.tools.ant.Target.performTasks(Target.java:411)
     at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1360)
     at org.apache.tools.ant.Project.executeTarget(Project.java:1329)
     at
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
     at org.apache.tools.ant.Project.executeTargets(Project.java:1212)
     at org.apache.tools.ant.Main.runBuild(Main.java:801)
     at org.apache.tools.ant.Main.startAnt(Main.java:218)
     at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
     at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
Caused by: org.intermine.InterMineException: Problem with store method
     at
org.intermine.dataloader.XmlDataLoader.processXml(XmlDataLoader.java:110)
     at
org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:160)
     ... 31 more
Caused by: org.intermine.objectstore.ObjectStoreException: Error
generating serial number
     at
org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.getSerial(ObjectStoreInterMineImpl.java:2251)
     at
org.intermine.dataloader.IntegrationWriterAbstractImpl.getSerial(IntegrationWriterAbstractImpl.java:566)
     at
org.intermine.dataloader.IntegrationWriterDataTrackingImpl.shortcut(IntegrationWriterDataTrackingImpl.java:540)
     at
org.intermine.dataloader.IntegrationWriterDataTrackingImpl.store(IntegrationWriterDataTrackingImpl.java:263)
     at
org.intermine.dataloader.IntegrationWriterAbstractImpl.store(IntegrationWriterAbstractImpl.java:171)
     at
org.intermine.dataloader.XmlDataLoader.processXml(XmlDataLoader.java:80)
     ... 32 more
Caused by: org.postgresql.util.PSQLException: ERROR: current transaction
is aborted, commands ignored until end of transaction block
     at
org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2079)
     at
org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1812)
     at
org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:257)
     at
org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:500)
     at
org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:374)
     at
org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2Statement.java:254)
     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
     at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
     at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
     at java.lang.reflect.Method.invoke(Method.java:616)
     at
org.postgresql.ds.jdbc23.AbstractJdbc23PooledConnection$StatementHandler.invoke(AbstractJdbc23PooledConnection.java:455)
     at $Proxy7.executeQuery(Unknown Source)
     at
org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.getSerialWithConnection(ObjectStoreInterMineImpl.java:2267)
     at
org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl.getSerialWithConnection(ObjectStoreWriterInterMineImpl.java:1723)
     at
org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.getSerial(ObjectStoreInterMineImpl.java:2246)
     ... 37 more

Total time: 35 seconds


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Re: Error generating serial number

Richard Smith
Hi James,
This looks like the same problem as before - the connection being used
has an aborted transaction and can't run any further statements.  I
don't know what the problem is.

1. Can you try restarting postgres and running the build again, then we
know that the error occurs consistently during the build.
2. Could you send the whole integrate/intermine.log from the build (best
if you ant clean or delete the log before starting).
3. What version of postgres are you using?

 From the previous log it looks as though postgres may be aborting the
transaction when index creation fails, in our setup this doesn't cause
it to abort.

Cheers,
Richard.



On 08/03/2011 13:27, James Blackshaw wrote:

> Hi,
> I got this error message while trying to load in mass spectrometry data.
> I can't find a reference to the error on the website, could you tell me
> what it means please?
>
> Thanks,
> James
>
>
> BUILD FAILED
> /home/jab250/intermine_mass_copy/imbuild/integrate.xml:54: The following
> error occurred while executing this line:
> /home/jab250/intermine_mass_copy/imbuild/source.xml:201: Exception while
> reading from: /data/datasets/mitominer/ms_xml/yeast_test.xml
> at
> org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:170)
>
> at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
> at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>
> at java.lang.reflect.Method.invoke(Method.java:616)
> at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> at org.apache.tools.ant.Task.perform(Task.java:348)
> at org.apache.tools.ant.Target.execute(Target.java:390)
> at org.apache.tools.ant.Target.performTasks(Target.java:411)
> at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1360)
> at
> org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
>
> at org.apache.tools.ant.Project.executeTargets(Project.java:1212)
> at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:441)
> at org.intermine.task.Integrate.performAction(Integrate.java:223)
> at org.intermine.task.Integrate.performAction(Integrate.java:135)
> at org.intermine.task.Integrate.execute(Integrate.java:127)
> at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
> at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>
> at java.lang.reflect.Method.invoke(Method.java:616)
> at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> at org.apache.tools.ant.Task.perform(Task.java:348)
> at org.apache.tools.ant.Target.execute(Target.java:390)
> at org.apache.tools.ant.Target.performTasks(Target.java:411)
> at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1360)
> at org.apache.tools.ant.Project.executeTarget(Project.java:1329)
> at
> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
>
> at org.apache.tools.ant.Project.executeTargets(Project.java:1212)
> at org.apache.tools.ant.Main.runBuild(Main.java:801)
> at org.apache.tools.ant.Main.startAnt(Main.java:218)
> at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
> at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
> Caused by: org.intermine.InterMineException: Problem with store method
> at
> org.intermine.dataloader.XmlDataLoader.processXml(XmlDataLoader.java:110)
> at
> org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:160)
>
> ... 31 more
> Caused by: org.intermine.objectstore.ObjectStoreException: Error
> generating serial number
> at
> org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.getSerial(ObjectStoreInterMineImpl.java:2251)
>
> at
> org.intermine.dataloader.IntegrationWriterAbstractImpl.getSerial(IntegrationWriterAbstractImpl.java:566)
>
> at
> org.intermine.dataloader.IntegrationWriterDataTrackingImpl.shortcut(IntegrationWriterDataTrackingImpl.java:540)
>
> at
> org.intermine.dataloader.IntegrationWriterDataTrackingImpl.store(IntegrationWriterDataTrackingImpl.java:263)
>
> at
> org.intermine.dataloader.IntegrationWriterAbstractImpl.store(IntegrationWriterAbstractImpl.java:171)
>
> at org.intermine.dataloader.XmlDataLoader.processXml(XmlDataLoader.java:80)
> ... 32 more
> Caused by: org.postgresql.util.PSQLException: ERROR: current transaction
> is aborted, commands ignored until end of transaction block
> at
> org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2079)
>
> at
> org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1812)
>
> at
> org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:257)
>
> at
> org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:500)
>
> at
> org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:374)
>
> at
> org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2Statement.java:254)
>
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
>
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>
> at java.lang.reflect.Method.invoke(Method.java:616)
> at
> org.postgresql.ds.jdbc23.AbstractJdbc23PooledConnection$StatementHandler.invoke(AbstractJdbc23PooledConnection.java:455)
>
> at $Proxy7.executeQuery(Unknown Source)
> at
> org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.getSerialWithConnection(ObjectStoreInterMineImpl.java:2267)
>
> at
> org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl.getSerialWithConnection(ObjectStoreWriterInterMineImpl.java:1723)
>
> at
> org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.getSerial(ObjectStoreInterMineImpl.java:2246)
>
> ... 37 more
>
> Total time: 35 seconds
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>


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