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New Error Message

Vallejos, Andrew

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(ProjectHelper.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(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: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(DefaultExecutor.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(ObjectStoreDataLoaderTask.java:133)

        at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)

        at sun.reflect.GeneratedMethodAccessor91.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: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(SingleCheckExecutor.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(ObjectStoreDataLoader.java:164)

        at org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLoader.java:60)

        at org.intermine.dataloader.ObjectStoreDataLoaderTask.execute(ObjectStoreDataLoaderTask.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.getEquivalentObjects(IntegrationWriterAbstractImpl.java:146)

        at org.intermine.dataloader.IntegrationWriterDataTrackingImpl.store(IntegrationWriterDataTrackingImpl.java:257)

        at org.intermine.dataloader.IntegrationWriterAbstractImpl.copyField(IntegrationWriterAbstractImpl.java:343)

        at org.intermine.dataloader.IntegrationWriterDataTrackingImpl.shortcut(IntegrationWriterDataTrackingImpl.java:571)

        at org.intermine.dataloader.IntegrationWriterDataTrackingImpl.store(IntegrationWriterDataTrackingImpl.java:263)

        at org.intermine.dataloader.IntegrationWriterAbstractImpl.store(IntegrationWriterAbstractImpl.java:171)

        at org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLoader.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(ObjectStoreDataLoaderTask.java:133)

        at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)

        at sun.reflect.GeneratedMethodAccessor91.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: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(SingleCheckExecutor.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(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: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(DefaultExecutor.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(ObjectStoreDataLoader.java:164)

        at org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLoader.java:60)

        at org.intermine.dataloader.ObjectStoreDataLoaderTask.execute(ObjectStoreDataLoaderTask.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.getEquivalentObjects(IntegrationWriterAbstractImpl.java:146)

        at org.intermine.dataloader.IntegrationWriterDataTrackingImpl.store(IntegrationWriterDataTrackingImpl.java:257)

        at org.intermine.dataloader.IntegrationWriterAbstractImpl.copyField(IntegrationWriterAbstractImpl.java:343)

        at org.intermine.dataloader.IntegrationWriterDataTrackingImpl.shortcut(IntegrationWriterDataTrackingImpl.java:571)

        at org.intermine.dataloader.IntegrationWriterDataTrackingImpl.store(IntegrationWriterDataTrackingImpl.java:263)

        at org.intermine.dataloader.IntegrationWriterAbstractImpl.store(IntegrationWriterAbstractImpl.java:171)

        at org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLoader.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(ObjectStoreDataLoader.java:164)

        at org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLoader.java:60)

        at org.intermine.dataloader.ObjectStoreDataLoaderTask.execute(ObjectStoreDataLoaderTask.java:128)

        at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)

        at sun.reflect.GeneratedMethodAccessor91.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: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(SingleCheckExecutor.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(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: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(DefaultExecutor.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.getEquivalentObjects(IntegrationWriterAbstractImpl.java:146)

        at org.intermine.dataloader.IntegrationWriterDataTrackingImpl.store(IntegrationWriterDataTrackingImpl.java:257)

        at org.intermine.dataloader.IntegrationWriterAbstractImpl.copyField(IntegrationWriterAbstractImpl.java:343)

        at org.intermine.dataloader.IntegrationWriterDataTrackingImpl.shortcut(IntegrationWriterDataTrackingImpl.java:571)

        at org.intermine.dataloader.IntegrationWriterDataTrackingImpl.store(IntegrationWriterDataTrackingImpl.java:263)

        at org.intermine.dataloader.IntegrationWriterAbstractImpl.store(IntegrationWriterAbstractImpl.java:171)

        at org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLoader.java:146)

        ... 33 more

 

======================

Andrew Vallejos

Web Developer II

Biotechnology and Bioengineering Center

Medical College of Wisconsin

414-955-4104

[hidden email]


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Re: New Error Message

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



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Re: New Error Message

Vallejos, Andrew
Thanks,

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

-Andrew

-----Original Message-----
From: [hidden email] [mailto:[hidden email]]
Sent: Monday, March 14, 2011 6:11 PM
To: Vallejos, Andrew
Cc: [hidden email]
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
>
> [hidden email]
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>



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