[InterMine Dev] New Error Message

Vallejos, Andrew avallejos at mcw.edu
Tue Mar 15 13:43:40 GMT 2011


Thanks,

I figured it out last night, I had goAnnotations instead of
goAnnotation, notice the extra 's'.

-Andrew

-----Original Message-----
From: julie at flymine.org [mailto:julie at flymine.org] 
Sent: Monday, March 14, 2011 6:11 PM
To: Vallejos, Andrew
Cc: dev at intermine.org
Subject: Re: [InterMine Dev] New Error Message

Hi Andrew,

It looks like one of your objects is referring to an object that doesn't
exist in the database.

What has changed in the new build?  You released ratmine with InterMine
0.96 code.  Did you run a build with these same annotation files?

If you send me your annotation files, I'll track down the bug.

Cheers,
Julie

> I'm trying to do an abbreviated build on DevRatMine and also configure
> the new search function.
>
>
>
> I got the following error message from Go Annoations source that I
have
> never seen before.
>
>
>
> Given a ProxyReference, but id not in ID Map.
>
>
>
>
>
> Here is the full stack:
>
> starting command: ant -v -Dsource=go-annotation
>
>
>
>
>
> BUILD FAILED
>
> /home/intermine/build/intermine_current/imbuild/integrate.xml:54: The
> following error occurred while executing this line:
>
> /home/intermine/build/intermine_current/imbuild/source.xml:330:
> java.lang.RuntimeException: Exception while dataloading - to allow
> multiple errors, set the property "dataLoader.allowMultipleErrors" to
> true
>
> Problem while loading item identifier 8_74144 because
>
> Given a ProxyReference, but id not in ID Map. Source object ID: 86835
>
>         at
>
org.apache.tools.ant.ProjectHelper.addLocationToBuildException(ProjectHe
> lper.java:508)
>
>         at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:418)
>
>         at
> org.intermine.task.Integrate.performAction(Integrate.java:223)
>
>         at
> org.intermine.task.Integrate.performAction(Integrate.java:136)
>
>         at org.intermine.task.Integrate.execute(Integrate.java:127)
>
>         at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
>
>         at sun.reflect.GeneratedMethodAccessor1.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:357)
>
>         at org.apache.tools.ant.Target.performTasks(Target.java:385)
>
>         at
> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1337)
>
>         at
org.apache.tools.ant.Project.executeTarget(Project.java:1306)
>
>         at
>
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
> or.java:41)
>
>         at
> org.apache.tools.ant.Project.executeTargets(Project.java:1189)
>
>         at org.apache.tools.ant.Main.runBuild(Main.java:758)
>
>         at org.apache.tools.ant.Main.startAnt(Main.java:217)
>
>         at org.apache.tools.ant.launch.Launcher.run(Launcher.java:257)
>
>         at
org.apache.tools.ant.launch.Launcher.main(Launcher.java:104)
>
> Caused by:
> /home/intermine/build/intermine_current/imbuild/source.xml:330:
> java.lang.RuntimeException: Exception while dataloading - to allow
> multiple errors, set the property "dataLoader.allowMultipleErrors" to
> true
>
> Problem while loading item identifier 8_74144 because
>
> Given a ProxyReference, but id not in ID Map. Source object ID: 86835
>
>         at
>
org.intermine.dataloader.ObjectStoreDataLoaderTask.execute(ObjectStoreDa
> taLoaderTask.java:133)
>
>         at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
>
>         at sun.reflect.GeneratedMethodAccessor91.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:357)
>
>         at org.apache.tools.ant.Target.performTasks(Target.java:385)
>
>         at
> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1337)
>
>         at
>
org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleChe
> ckExecutor.java:38)
>
>         at
> org.apache.tools.ant.Project.executeTargets(Project.java:1189)
>
>         at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:416)
>
>         ... 19 more
>
> Caused by: java.lang.RuntimeException: Exception while dataloading -
to
> allow multiple errors, set the property
"dataLoader.allowMultipleErrors"
> to true
>
> Problem while loading item identifier 8_74144 because
>
> Given a ProxyReference, but id not in ID Map. Source object ID: 86835
>
>         at
>
org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLo
> ader.java:164)
>
>         at
>
org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLo
> ader.java:60)
>
>         at
>
org.intermine.dataloader.ObjectStoreDataLoaderTask.execute(ObjectStoreDa
> taLoaderTask.java:128)
>
>         ... 31 more
>
> Caused by: java.lang.IllegalArgumentException: Given a ProxyReference,
> but id not in ID Map. Source object ID: 86835
>
>         at
>
org.intermine.dataloader.IntegrationWriterAbstractImpl.getEquivalentObje
> cts(IntegrationWriterAbstractImpl.java:146)
>
>         at
>
org.intermine.dataloader.IntegrationWriterDataTrackingImpl.store(Integra
> tionWriterDataTrackingImpl.java:257)
>
>         at
>
org.intermine.dataloader.IntegrationWriterAbstractImpl.copyField(Integra
> tionWriterAbstractImpl.java:343)
>
>         at
>
org.intermine.dataloader.IntegrationWriterDataTrackingImpl.shortcut(Inte
> grationWriterDataTrackingImpl.java:571)
>
>         at
>
org.intermine.dataloader.IntegrationWriterDataTrackingImpl.store(Integra
> tionWriterDataTrackingImpl.java:263)
>
>         at
>
org.intermine.dataloader.IntegrationWriterAbstractImpl.store(Integration
> WriterAbstractImpl.java:171)
>
>         at
>
org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLo
> ader.java:146)
>
>         ... 33 more
>
> --- Nested Exception ---
>
> /home/intermine/build/intermine_current/imbuild/source.xml:330:
> java.lang.RuntimeException: Exception while dataloading - to allow
> multiple errors, set the property "dataLoader.allowMultipleErrors" to
> true
>
> Problem while loading item identifier 8_74144 because
>
> Given a ProxyReference, but id not in ID Map. Source object ID: 86835
>
>         at
>
org.intermine.dataloader.ObjectStoreDataLoaderTask.execute(ObjectStoreDa
> taLoaderTask.java:133)
>
>         at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
>
>         at sun.reflect.GeneratedMethodAccessor91.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:357)
>
>         at org.apache.tools.ant.Target.performTasks(Target.java:385)
>
>         at
> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1337)
>
>         at
>
org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleChe
> ckExecutor.java:38)
>
>         at
> org.apache.tools.ant.Project.executeTargets(Project.java:1189)
>
>         at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:416)
>
>         at
> org.intermine.task.Integrate.performAction(Integrate.java:223)
>
>         at
> org.intermine.task.Integrate.performAction(Integrate.java:136)
>
>         at org.intermine.task.Integrate.execute(Integrate.java:127)
>
>         at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
>
>         at sun.reflect.GeneratedMethodAccessor1.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:357)
>
>         at org.apache.tools.ant.Target.performTasks(Target.java:385)
>
>         at
> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1337)
>
>         at
org.apache.tools.ant.Project.executeTarget(Project.java:1306)
>
>         at
>
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
> or.java:41)
>
>         at
> org.apache.tools.ant.Project.executeTargets(Project.java:1189)
>
>         at org.apache.tools.ant.Main.runBuild(Main.java:758)
>
>         at org.apache.tools.ant.Main.startAnt(Main.java:217)
>
>         at org.apache.tools.ant.launch.Launcher.run(Launcher.java:257)
>
>         at
org.apache.tools.ant.launch.Launcher.main(Launcher.java:104)
>
> Caused by: java.lang.RuntimeException: Exception while dataloading -
to
> allow multiple errors, set the property
"dataLoader.allowMultipleErrors"
> to true
>
> Problem while loading item identifier 8_74144 because
>
> Given a ProxyReference, but id not in ID Map. Source object ID: 86835
>
>         at
>
org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLo
> ader.java:164)
>
>         at
>
org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLo
> ader.java:60)
>
>         at
>
org.intermine.dataloader.ObjectStoreDataLoaderTask.execute(ObjectStoreDa
> taLoaderTask.java:128)
>
>         ... 31 more
>
> Caused by: java.lang.IllegalArgumentException: Given a ProxyReference,
> but id not in ID Map. Source object ID: 86835
>
>         at
>
org.intermine.dataloader.IntegrationWriterAbstractImpl.getEquivalentObje
> cts(IntegrationWriterAbstractImpl.java:146)
>
>         at
>
org.intermine.dataloader.IntegrationWriterDataTrackingImpl.store(Integra
> tionWriterDataTrackingImpl.java:257)
>
>         at
>
org.intermine.dataloader.IntegrationWriterAbstractImpl.copyField(Integra
> tionWriterAbstractImpl.java:343)
>
>         at
>
org.intermine.dataloader.IntegrationWriterDataTrackingImpl.shortcut(Inte
> grationWriterDataTrackingImpl.java:571)
>
>         at
>
org.intermine.dataloader.IntegrationWriterDataTrackingImpl.store(Integra
> tionWriterDataTrackingImpl.java:263)
>
>         at
>
org.intermine.dataloader.IntegrationWriterAbstractImpl.store(Integration
> WriterAbstractImpl.java:171)
>
>         at
>
org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLo
> ader.java:146)
>
>         ... 33 more
>
> --- Nested Exception ---
>
> java.lang.RuntimeException: Exception while dataloading - to allow
> multiple errors, set the property "dataLoader.allowMultipleErrors" to
> true
>
> Problem while loading item identifier 8_74144 because
>
> Given a ProxyReference, but id not in ID Map. Source object ID: 86835
>
>         at
>
org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLo
> ader.java:164)
>
>         at
>
org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLo
> ader.java:60)
>
>         at
>
org.intermine.dataloader.ObjectStoreDataLoaderTask.execute(ObjectStoreDa
> taLoaderTask.java:128)
>
>         at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
>
>         at sun.reflect.GeneratedMethodAccessor91.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:357)
>
>         at org.apache.tools.ant.Target.performTasks(Target.java:385)
>
>         at
> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1337)
>
>         at
>
org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleChe
> ckExecutor.java:38)
>
>         at
> org.apache.tools.ant.Project.executeTargets(Project.java:1189)
>
>         at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:416)
>
>         at
> org.intermine.task.Integrate.performAction(Integrate.java:223)
>
>         at
> org.intermine.task.Integrate.performAction(Integrate.java:136)
>
>         at org.intermine.task.Integrate.execute(Integrate.java:127)
>
>         at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
>
>         at sun.reflect.GeneratedMethodAccessor1.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:357)
>
>         at org.apache.tools.ant.Target.performTasks(Target.java:385)
>
>         at
> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1337)
>
>         at
org.apache.tools.ant.Project.executeTarget(Project.java:1306)
>
>         at
>
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
> or.java:41)
>
>         at
> org.apache.tools.ant.Project.executeTargets(Project.java:1189)
>
>         at org.apache.tools.ant.Main.runBuild(Main.java:758)
>
>         at org.apache.tools.ant.Main.startAnt(Main.java:217)
>
>         at org.apache.tools.ant.launch.Launcher.run(Launcher.java:257)
>
>         at
org.apache.tools.ant.launch.Launcher.main(Launcher.java:104)
>
> Caused by: java.lang.IllegalArgumentException: Given a ProxyReference,
> but id not in ID Map. Source object ID: 86835
>
>         at
>
org.intermine.dataloader.IntegrationWriterAbstractImpl.getEquivalentObje
> cts(IntegrationWriterAbstractImpl.java:146)
>
>         at
>
org.intermine.dataloader.IntegrationWriterDataTrackingImpl.store(Integra
> tionWriterDataTrackingImpl.java:257)
>
>         at
>
org.intermine.dataloader.IntegrationWriterAbstractImpl.copyField(Integra
> tionWriterAbstractImpl.java:343)
>
>         at
>
org.intermine.dataloader.IntegrationWriterDataTrackingImpl.shortcut(Inte
> grationWriterDataTrackingImpl.java:571)
>
>         at
>
org.intermine.dataloader.IntegrationWriterDataTrackingImpl.store(Integra
> tionWriterDataTrackingImpl.java:263)
>
>         at
>
org.intermine.dataloader.IntegrationWriterAbstractImpl.store(Integration
> WriterAbstractImpl.java:171)
>
>         at
>
org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLo
> ader.java:146)
>
>         ... 33 more
>
>
>
> ======================
>
> Andrew Vallejos
>
> Web Developer II
>
> Biotechnology and Bioengineering Center
>
> Medical College of Wisconsin
>
> 414-955-4104
>
> avallejos at mcw.edu
>
> _______________________________________________
> dev mailing list
> dev at intermine.org
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>





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