Integration troubles with SQL

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Integration troubles with SQL

James Blackshaw
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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Re: Integration troubles with SQL

Richard Smith
Hi James,
I haven't seen this problem before but the root cause is an aborted
transaction:

Caused by: org.postgresql.util.PSQLException: ERROR: current transaction
is aborted, commands ignored until end of transaction block

Which has happened before the query it is logging has been executed.
Does this happen right at the start of the data load or some way in?
Are there any recent log messages to say e.g. 'Dataloaded x objects'?

It may be that there was a pre-existing dodgy connection.  You could
try restarting postgres and running again.

Cheers,
Richard.



On 01/03/2011 13:16, James Blackshaw wrote:

> 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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>


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