summarise object store error

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summarise object store error

Vallejos, Andrew

Hi,

 

I am trying to upgrade public ratmine to 0.98.  And I am getting the following object store summary error.  Any clues as to what is going on?

 

BUILD FAILED

/home/intermine/build/ratmine_current/imbuild/postprocess.xml:31: error running PostProcessTask (action: summarise-objectstore)

        at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:148)

        at org.intermine.task.PostProcessTask.execute(PostProcessTask.java:121)

        at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)

        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)

        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

        at java.lang.reflect.Method.invoke(Method.java:597)

        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:1397)

        at org.apache.tools.ant.Project.executeTarget(Project.java:1366)

        at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)

        at org.apache.tools.ant.Project.executeTargets(Project.java:1249)

        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.reflect.InvocationTargetException

        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)

        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

        at java.lang.reflect.Method.invoke(Method.java:597)

        at org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:146)

        ... 17 more

Caused by: Operation was:summarise-objectstore

        at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:293)

        ... 22 more

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:269)

        at org.intermine.objectstore.ObjectStoreSummary.<init>(ObjectStoreSummary.java:144)

        at org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:209)

        ... 22 more

Caused by: org.intermine.objectstore.ObjectStoreException: Problem executing query "SELECT DISTINCT a2_.embargoDate AS a1_ FROM org.intermine.model.bio.Submission AS a2_"

        at org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.executeWithConnection(ObjectStoreInterMineImpl.java:1265)

        at org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.executeWithConnection(ObjectStoreInterMineImpl.java:1059)

        at org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.execute(ObjectStoreInterMineImpl.java:958)

        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)

        ... 25 more

Caused by: java.lang.NullPointerException

        at org.intermine.objectstore.intermine.ResultsConverter.convert(ResultsConverter.java:160)

        at org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.executeWithConnection(ObjectStoreInterMineImpl.java:1164)

        ... 32 more

 

Total time: 8 minutes 6 seconds

Thu Dec 22 00:37:39 CST 2011

 

Thanks,

 

Andrew Vallejos

Web Developer

Biotechnology and Bioengineering Center

Human and Molecular Genomics Center

Medical College of Wisconsin

414-955-4104

[hidden email]

 


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Re: summarise object store error

Julie Sullivan
Andrew

Run "svn update" and try again?  I think we weren't handling empty date fields
correctly.

On 22/12/11 12:57, Vallejos, Andrew wrote:

> Hi,
>
>
>
> I am trying to upgrade public ratmine to 0.98.  And I am getting the
> following object store summary error.  Any clues as to what is going on?
>
>
>
> BUILD FAILED
>
> /home/intermine/build/ratmine_current/imbuild/postprocess.xml:31: error
> running PostProcessTask (action: summarise-objectstore)
>
>          at
> org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.jav
> a:148)
>
>          at
> org.intermine.task.PostProcessTask.execute(PostProcessTask.java:121)
>
>          at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>
>          at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>
>          at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
> Impl.java:25)
>
>          at java.lang.reflect.Method.invoke(Method.java:597)
>
>          at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
> 06)
>
>          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:1397)
>
>          at org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>
>          at
> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
> or.java:41)
>
>          at
> org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>
>          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.reflect.InvocationTargetException
>
>          at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>
>          at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.jav
> a:39)
>
>          at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
> Impl.java:25)
>
>          at java.lang.reflect.Method.invoke(Method.java:597)
>
>          at
> org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.jav
> a:146)
>
>          ... 17 more
>
> Caused by: Operation was:summarise-objectstore
>
>          at
> org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProc
> essOperationsTask.java:293)
>
>          ... 22 more
>
> 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:269)
>
>          at
> org.intermine.objectstore.ObjectStoreSummary.<init>(ObjectStoreSummary.j
> ava:144)
>
>          at
> org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProc
> essOperationsTask.java:209)
>
>          ... 22 more
>
> Caused by: org.intermine.objectstore.ObjectStoreException: Problem
> executing query "SELECT DISTINCT a2_.embargoDate AS a1_ FROM
> org.intermine.model.bio.Submission AS a2_"
>
>          at
> org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.executeWith
> Connection(ObjectStoreInterMineImpl.java:1265)
>
>          at
> org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.executeWith
> Connection(ObjectStoreInterMineImpl.java:1059)
>
>          at
> org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.execute(Obj
> ectStoreInterMineImpl.java:958)
>
>          at
> org.intermine.objectstore.query.ResultsBatches.fetchBatchFromObjectStore
> (ResultsBatches.java:192)
>
>          at
> org.intermine.objectstore.query.PrefetchManager.doRequest(PrefetchManage
> r.java:240)
>
>          at
> org.intermine.objectstore.query.PrefetchManager.doRequest(PrefetchManage
> r.java:145)
>
>          at
> org.intermine.objectstore.query.ResultsBatches.getBatch(ResultsBatches.j
> ava:164)
>
>          at
> org.intermine.objectstore.query.ResultsBatches.size(ResultsBatches.java:
> 234)
>
>          ... 25 more
>
> Caused by: java.lang.NullPointerException
>
>          at
> org.intermine.objectstore.intermine.ResultsConverter.convert(ResultsConv
> erter.java:160)
>
>          at
> org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.executeWith
> Connection(ObjectStoreInterMineImpl.java:1164)
>
>          ... 32 more
>
>
>
> Total time: 8 minutes 6 seconds
>
> Thu Dec 22 00:37:39 CST 2011
>
>
>
> Thanks,
>
>
>
> Andrew Vallejos
>
> Web Developer
>
> Biotechnology and Bioengineering Center
>
> Human and Molecular Genomics Center
>
> Medical College of Wisconsin
>
> 414-955-4104
>
> [hidden email]
>
>
>
>
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
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Re: summarise object store error

Vallejos, Andrew
Worked.

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On
Behalf Of Julie Sullivan
Sent: Thursday, December 22, 2011 7:26 AM
To: [hidden email]
Subject: Re: [InterMine Dev] summarise object store error

Andrew

Run "svn update" and try again?  I think we weren't handling empty date
fields
correctly.

On 22/12/11 12:57, Vallejos, Andrew wrote:
> Hi,
>
>
>
> I am trying to upgrade public ratmine to 0.98.  And I am getting the
> following object store summary error.  Any clues as to what is going
on?
>
>
>
> BUILD FAILED
>
> /home/intermine/build/ratmine_current/imbuild/postprocess.xml:31:
error
> running PostProcessTask (action: summarise-objectstore)
>
>          at
>
org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.jav
> a:148)
>
>          at
> org.intermine.task.PostProcessTask.execute(PostProcessTask.java:121)
>
>          at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>
>          at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
Source)
>
>          at
>
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
> Impl.java:25)
>
>          at java.lang.reflect.Method.invoke(Method.java:597)
>
>          at
>
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1

> 06)
>
>          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:1397)
>
>          at
org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>
>          at
>
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut

> or.java:41)
>
>          at
> org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>
>          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.reflect.InvocationTargetException
>
>          at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
Method)
>
>          at
>
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.jav
> a:39)
>
>          at
>
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
> Impl.java:25)
>
>          at java.lang.reflect.Method.invoke(Method.java:597)
>
>          at
>
org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.jav
> a:146)
>
>          ... 17 more
>
> Caused by: Operation was:summarise-objectstore
>
>          at
>
org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProc
> essOperationsTask.java:293)
>
>          ... 22 more
>
> 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:269)
>
>          at
>
org.intermine.objectstore.ObjectStoreSummary.<init>(ObjectStoreSummary.j
> ava:144)
>
>          at
>
org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProc

> essOperationsTask.java:209)
>
>          ... 22 more
>
> Caused by: org.intermine.objectstore.ObjectStoreException: Problem
> executing query "SELECT DISTINCT a2_.embargoDate AS a1_ FROM
> org.intermine.model.bio.Submission AS a2_"
>
>          at
>
org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.executeWith
> Connection(ObjectStoreInterMineImpl.java:1265)
>
>          at
>
org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.executeWith
> Connection(ObjectStoreInterMineImpl.java:1059)
>
>          at
>
org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.execute(Obj
> ectStoreInterMineImpl.java:958)
>
>          at
>
org.intermine.objectstore.query.ResultsBatches.fetchBatchFromObjectStore
> (ResultsBatches.java:192)
>
>          at
>
org.intermine.objectstore.query.PrefetchManager.doRequest(PrefetchManage
> r.java:240)
>
>          at
>
org.intermine.objectstore.query.PrefetchManager.doRequest(PrefetchManage
> r.java:145)
>
>          at
>
org.intermine.objectstore.query.ResultsBatches.getBatch(ResultsBatches.j
> ava:164)
>
>          at
>
org.intermine.objectstore.query.ResultsBatches.size(ResultsBatches.java:
> 234)
>
>          ... 25 more
>
> Caused by: java.lang.NullPointerException
>
>          at
>
org.intermine.objectstore.intermine.ResultsConverter.convert(ResultsConv
> erter.java:160)
>
>          at
>
org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.executeWith

> Connection(ObjectStoreInterMineImpl.java:1164)
>
>          ... 32 more
>
>
>
> Total time: 8 minutes 6 seconds
>
> Thu Dec 22 00:37:39 CST 2011
>
>
>
> Thanks,
>
>
>
> Andrew Vallejos
>
> Web Developer
>
> Biotechnology and Bioengineering Center
>
> Human and Molecular Genomics Center
>
> Medical College of Wisconsin
>
> 414-955-4104
>
> [hidden email]
>
>
>
>
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev