[InterMine Dev] Error generating serial number

James Blackshaw jab250 at mrc-mbu.cam.ac.uk
Tue Mar 8 13:27:24 GMT 2011


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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