[InterMine Dev] Integration troubles with SQL

James Blackshaw jab250 at mrc-mbu.cam.ac.uk
Tue Mar 1 13:16:59 GMT 2011


Hi,
when I'm trying to load the custom sorces for Mitominer, I keep getting 
an error with the SQL commands used to do part of it. I'm not sure what 
the problem is as I've been testing integration on a reduced data set 
ant the primary keys should all be loaded in.

-James


Error is:

/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/cellularLocation_xml/test2/go.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: java.lang.RuntimeException: ObjectStore error has occurred in 
size()
     at 
org.intermine.objectstore.query.ResultsBatches.size(ResultsBatches.java:236)
     at org.intermine.objectstore.query.Results.size(Results.java:286)
     at 
org.intermine.dataloader.IntegrationWriterDataTrackingImpl.store(IntegrationWriterDataTrackingImpl.java:260)
     at 
org.intermine.dataloader.IntegrationWriterAbstractImpl.store(IntegrationWriterAbstractImpl.java:171)
     at 
org.intermine.dataloader.XmlDataLoader.processXml(XmlDataLoader.java:80)
     at 
org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:160)
     ... 31 more
Caused by: org.intermine.objectstore.ObjectStoreException: Problem 
running SQL statement "SELECT a1_.id AS a1_id FROM Protein AS a1_ WHERE 
a1_.primaryAccession = 'A0AQH0' ORDER BY a1_.id LIMIT 1000" while 
executing query "SELECT a1_ FROM org.intermine.model.bio.Protein AS a1_ 
WHERE (a1_.primaryAccession = 'A0AQH0')"
     at 
org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.executeWithConnection(ObjectStoreInterMineImpl.java:1262)
     at 
org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.executeWithConnection(ObjectStoreInterMineImpl.java:1059)
     at 
org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl.execute(ObjectStoreWriterInterMineImpl.java:1625)
     at 
org.intermine.objectstore.query.ResultsBatches.fetchBatchFromObjectStore(ResultsBatches.java:192)
     at 
org.intermine.objectstore.query.PrefetchManager.doRequest(PrefetchManager.java:240)
     at 
org.intermine.objectstore.query.PrefetchManager.doRequest(PrefetchManager.java:145)
     at 
org.intermine.objectstore.query.ResultsBatches.getBatch(ResultsBatches.java:164)
     at 
org.intermine.objectstore.query.ResultsBatches.size(ResultsBatches.java:234)
     ... 36 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.executeWithConnection(ObjectStoreInterMineImpl.java:1158)
     ... 43 more




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