[InterMine Dev] Snp fails due to name change

Vallejos, Andrew avallejos at mcw.edu
Thu Aug 6 17:52:08 BST 2009


Changing the name to SNP causes an error as well.

BUILD FAILED
/usr/local/intermine/dev/imbuild/objectstore.xml:147: exception while
invoking execute on org.intermine.task.ModelMergerTask
	at
org.intermine.task.MergeSourceModelsTask.execute(MergeSourceModelsTask.j
ava:162)
	at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
	at sun.reflect.GeneratedMethodAccessor2.invoke(Unknown Source)
	at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:585)
	at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
05)
	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:1329)
	at org.apache.tools.ant.Project.executeTarget(Project.java:1298)
	at
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
or.java:41)
	at
org.apache.tools.ant.Project.executeTargets(Project.java:1181)
	at org.apache.tools.ant.Main.runBuild(Main.java:698)
	at org.apache.tools.ant.Main.startAnt(Main.java:199)
	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.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:585)
	at
org.intermine.task.MergeSourceModelsTask.execute(MergeSourceModelsTask.j
ava:160)
	... 16 more
Caused by: Exception while merging
/usr/local/intermine/dev/bio/core/shortcuts.xml into
/usr/local/intermine/dev/ratmine/dbmodel/build/model/genomic_model.xml
	at
org.intermine.task.ModelMergerTask.processFile(ModelMergerTask.java:115)
	at
org.intermine.task.ModelMergerTask.execute(ModelMergerTask.java:93)
	... 21 more
Caused by: org.intermine.modelproduction.ModelMergerException: replacing
the "org.intermine.model.bio.LocatedSequenceFeature.chromosome"
reference with org.intermine.model.bio.SNP.chromosome failed because the
reverse references differ
	at
org.intermine.modelproduction.ModelMerger.removeRedundancy(ModelMerger.j
ava:158)
	at
org.intermine.modelproduction.ModelMerger.mergeModel(ModelMerger.java:91
)
	at
org.intermine.task.ModelMergerTask.processFile(ModelMergerTask.java:112)
	... 22 more
--- Nested Exception ---
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:585)
	at
org.intermine.task.MergeSourceModelsTask.execute(MergeSourceModelsTask.j
ava:160)
	at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
	at sun.reflect.GeneratedMethodAccessor2.invoke(Unknown Source)
	at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:585)
	at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
05)
	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:1329)
	at org.apache.tools.ant.Project.executeTarget(Project.java:1298)
	at
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
or.java:41)
	at
org.apache.tools.ant.Project.executeTargets(Project.java:1181)
	at org.apache.tools.ant.Main.runBuild(Main.java:698)
	at org.apache.tools.ant.Main.startAnt(Main.java:199)
	at org.apache.tools.ant.launch.Launcher.run(Launcher.java:257)
	at org.apache.tools.ant.launch.Launcher.main(Launcher.java:104)
Caused by: Exception while merging
/usr/local/intermine/dev/bio/core/shortcuts.xml into
/usr/local/intermine/dev/ratmine/dbmodel/build/model/genomic_model.xml
	at
org.intermine.task.ModelMergerTask.processFile(ModelMergerTask.java:115)
	at
org.intermine.task.ModelMergerTask.execute(ModelMergerTask.java:93)
	... 21 more
Caused by: org.intermine.modelproduction.ModelMergerException: replacing
the "org.intermine.model.bio.LocatedSequenceFeature.chromosome"
reference with org.intermine.model.bio.SNP.chromosome failed because the
reverse references differ
	at
org.intermine.modelproduction.ModelMerger.removeRedundancy(ModelMerger.j
ava:158)
	at
org.intermine.modelproduction.ModelMerger.mergeModel(ModelMerger.java:91
)
	at
org.intermine.task.ModelMergerTask.processFile(ModelMergerTask.java:112)
	... 22 more

Total time: 6 seconds

-----Original Message-----
From: Richard Smith [mailto:richard at flymine.org] 
Sent: Thursday, August 06, 2009 10:54 AM
To: Vallejos, Andrew
Cc: dev at intermine.org
Subject: Re: [InterMine Dev] Snp fails due to name change

It looks like you have changed the snp_additions.xml and run build-db.

This seems to be failing because there is already a class 'SNP' in the
data model, you have added one called 'Snp'.  This is fine at the Java
level where names are case sensitive but is failing when it tries to
generate the case-insensitive database table names.

The easy solution is to change Snp to SNP in the additions file.  We
should really be catching this error earlier than at the database
schema creation.

Cheers,
Richard.



Vallejos, Andrew wrote:
> I tried changing the same from EnsemblSNP to Snp and now building the
> database fails with the following error.  I have looked everywhere I
can
> think of, and I cannot figure out where this is failing.
> 
>  
> 
> -Andrew
> 
>  
> 
> BUILD FAILED
> 
> /usr/local/intermine/dev/imbuild/objectstore.xml:51: The following
error
> occurred while executing this line:
> 
> /usr/local/intermine/dev/imbuild/task.xml:188:
> java.lang.NoClassDefFoundError: org/intermine/model/bio/SNP (wrong
name:
> org/intermine/model/bio/Snp)
> 
>             at
>
org.apache.tools.ant.ProjectHelper.addLocationToBuildException(ProjectHe
> lper.java:541)
> 
>             at
>
org.apache.tools.ant.taskdefs.MacroInstance.execute(MacroInstance.java:3
> 94)
> 
>             at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
> 
>             at sun.reflect.GeneratedMethodAccessor2.invoke(Unknown
> Source)
> 
>             at
>
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
> Impl.java:25)
> 
>             at java.lang.reflect.Method.invoke(Method.java:585)
> 
>             at
>
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
> 05)
> 
>             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:1329)
> 
>             at
> org.apache.tools.ant.Project.executeTarget(Project.java:1298)
> 
>             at
>
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
> or.java:41)
> 
>             at
> org.apache.tools.ant.Project.executeTargets(Project.java:1181)
> 
>             at org.apache.tools.ant.Main.runBuild(Main.java:698)
> 
>             at org.apache.tools.ant.Main.startAnt(Main.java:199)
> 
>             at
> org.apache.tools.ant.launch.Launcher.run(Launcher.java:257)
> 
>             at
> org.apache.tools.ant.launch.Launcher.main(Launcher.java:104)
> 
> Caused by: /usr/local/intermine/dev/imbuild/task.xml:188:
> java.lang.NoClassDefFoundError: org/intermine/model/bio/SNP (wrong
name:
> org/intermine/model/bio/Snp)
> 
>             at
>
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
> 15)
> 
>             at org.apache.tools.ant.Task.perform(Task.java:348)
> 
>             at
> org.apache.tools.ant.taskdefs.Sequential.execute(Sequential.java:62)
> 
>             at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
> 
>             at sun.reflect.GeneratedMethodAccessor2.invoke(Unknown
> Source)
> 
>             at
>
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
> Impl.java:25)
> 
>             at java.lang.reflect.Method.invoke(Method.java:585)
> 
>             at
>
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
> 05)
> 
>             at org.apache.tools.ant.Task.perform(Task.java:348)
> 
>             at
>
org.apache.tools.ant.taskdefs.MacroInstance.execute(MacroInstance.java:3
> 91)
> 
>             ... 16 more
> 
> Caused by: java.lang.NoClassDefFoundError: org/intermine/model/bio/SNP
> (wrong name: org/intermine/model/bio/Snp)
> 
>             at java.lang.ClassLoader.defineClass1(Native Method)
> 
>             at java.lang.ClassLoader.defineClass(ClassLoader.java:675)
> 
>             at
>
org.apache.tools.ant.AntClassLoader.defineClassFromData(AntClassLoader.j
> ava:1130)
> 
>             at
>
org.apache.tools.ant.AntClassLoader.getClassFromStream(AntClassLoader.ja
> va:1307)
> 
>             at
>
org.apache.tools.ant.AntClassLoader.findClassInComponents(AntClassLoader
> .java:1371)
> 
>             at
>
org.apache.tools.ant.AntClassLoader.findClass(AntClassLoader.java:1324)
> 
>             at
>
org.apache.tools.ant.AntClassLoader.loadClass(AntClassLoader.java:1072)
> 
>             at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
> 
>             at
> java.lang.ClassLoader.loadClassInternal(ClassLoader.java:374)
> 
>             at java.lang.Class.forName0(Native Method)
> 
>             at java.lang.Class.forName(Class.java:164)
> 
>             at
>
org.intermine.metadata.ClassDescriptor.getType(ClassDescriptor.java:145)
> 
>             at
>
org.intermine.objectstore.intermine.TorqueModelOutput.generate(TorqueMod
> elOutput.java:196)
> 
>             at
>
org.intermine.objectstore.intermine.TorqueModelOutput.generate(TorqueMod
> elOutput.java:121)
> 
>             at
>
org.intermine.objectstore.intermine.TorqueModelOutput.process(TorqueMode
> lOutput.java:82)
> 
>             at
>
org.intermine.objectstore.intermine.TorqueModelOutputTask.execute(Torque
> ModelOutputTask.java:122)
> 
>             at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
> 
>             at sun.reflect.GeneratedMethodAccessor2.invoke(Unknown
> Source)
> 
>             at
>
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
> Impl.java:25)
> 
>             at java.lang.reflect.Method.invoke(Method.java:585)
> 
>             at
>
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
> 05)
> 
>             ... 25 more
> 
> --- Nested Exception ---
> 
> /usr/local/intermine/dev/imbuild/task.xml:188:
> java.lang.NoClassDefFoundError: org/intermine/model/bio/SNP (wrong
name:
> org/intermine/model/bio/Snp)
> 
>             at
>
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
> 15)
> 
>             at org.apache.tools.ant.Task.perform(Task.java:348)
> 
>             at
> org.apache.tools.ant.taskdefs.Sequential.execute(Sequential.java:62)
> 
>             at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
> 
>             at sun.reflect.GeneratedMethodAccessor2.invoke(Unknown
> Source)
> 
>             at
>
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
> Impl.java:25)
> 
>             at java.lang.reflect.Method.invoke(Method.java:585)
> 
>             at
>
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
> 05)
> 
>             at org.apache.tools.ant.Task.perform(Task.java:348)
> 
>             at
>
org.apache.tools.ant.taskdefs.MacroInstance.execute(MacroInstance.java:3
> 91)
> 
>             at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
> 
>             at sun.reflect.GeneratedMethodAccessor2.invoke(Unknown
> Source)
> 
>             at
>
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
> Impl.java:25)
> 
>             at java.lang.reflect.Method.invoke(Method.java:585)
> 
>             at
>
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
> 05)
> 
>             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:1329)
> 
>             at
> org.apache.tools.ant.Project.executeTarget(Project.java:1298)
> 
>             at
>
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
> or.java:41)
> 
>             at
> org.apache.tools.ant.Project.executeTargets(Project.java:1181)
> 
>             at org.apache.tools.ant.Main.runBuild(Main.java:698)
> 
>             at org.apache.tools.ant.Main.startAnt(Main.java:199)
> 
>             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.NoClassDefFoundError: org/intermine/model/bio/SNP
> (wrong name: org/intermine/model/bio/Snp)
> 
>             at java.lang.ClassLoader.defineClass1(Native Method)
> 
>             at java.lang.ClassLoader.defineClass(ClassLoader.java:675)
> 
>             at
>
org.apache.tools.ant.AntClassLoader.defineClassFromData(AntClassLoader.j
> ava:1130)
> 
>             at
>
org.apache.tools.ant.AntClassLoader.getClassFromStream(AntClassLoader.ja
> va:1307)
> 
>             at
>
org.apache.tools.ant.AntClassLoader.findClassInComponents(AntClassLoader
> .java:1371)
> 
>             at
>
org.apache.tools.ant.AntClassLoader.findClass(AntClassLoader.java:1324)
> 
>             at
>
org.apache.tools.ant.AntClassLoader.loadClass(AntClassLoader.java:1072)
> 
>             at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
> 
>             at
> java.lang.ClassLoader.loadClassInternal(ClassLoader.java:374)
> 
>             at java.lang.Class.forName0(Native Method)
> 
>             at java.lang.Class.forName(Class.java:164)
> 
>             at
>
org.intermine.metadata.ClassDescriptor.getType(ClassDescriptor.java:145)
> 
>             at
>
org.intermine.objectstore.intermine.TorqueModelOutput.generate(TorqueMod
> elOutput.java:196)
> 
>             at
>
org.intermine.objectstore.intermine.TorqueModelOutput.generate(TorqueMod
> elOutput.java:121)
> 
>             at
>
org.intermine.objectstore.intermine.TorqueModelOutput.process(TorqueMode
> lOutput.java:82)
> 
>             at
>
org.intermine.objectstore.intermine.TorqueModelOutputTask.execute(Torque
> ModelOutputTask.java:122)
> 
>             at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
> 
>             at sun.reflect.GeneratedMethodAccessor2.invoke(Unknown
> Source)
> 
>             at
>
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
> Impl.java:25)
> 
>             at java.lang.reflect.Method.invoke(Method.java:585)
> 
>             at
>
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
> 05)
> 
>             ... 25 more
> 
> --- Nested Exception ---
> 
> java.lang.NoClassDefFoundError: org/intermine/model/bio/SNP (wrong
name:
> org/intermine/model/bio/Snp)
> 
>             at java.lang.ClassLoader.defineClass1(Native Method)
> 
>             at java.lang.ClassLoader.defineClass(ClassLoader.java:675)
> 
>             at
>
org.apache.tools.ant.AntClassLoader.defineClassFromData(AntClassLoader.j
> ava:1130)
> 
>             at
>
org.apache.tools.ant.AntClassLoader.getClassFromStream(AntClassLoader.ja
> va:1307)
> 
>             at
>
org.apache.tools.ant.AntClassLoader.findClassInComponents(AntClassLoader
> .java:1371)
> 
>             at
>
org.apache.tools.ant.AntClassLoader.findClass(AntClassLoader.java:1324)
> 
>             at
>
org.apache.tools.ant.AntClassLoader.loadClass(AntClassLoader.java:1072)
> 
>             at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
> 
>             at
> java.lang.ClassLoader.loadClassInternal(ClassLoader.java:374)
> 
>             at java.lang.Class.forName0(Native Method)
> 
>             at java.lang.Class.forName(Class.java:164)
> 
>             at
>
org.intermine.metadata.ClassDescriptor.getType(ClassDescriptor.java:145)
> 
>             at
>
org.intermine.objectstore.intermine.TorqueModelOutput.generate(TorqueMod
> elOutput.java:196)
> 
>             at
>
org.intermine.objectstore.intermine.TorqueModelOutput.generate(TorqueMod
> elOutput.java:121)
> 
>             at
>
org.intermine.objectstore.intermine.TorqueModelOutput.process(TorqueMode
> lOutput.java:82)
> 
>             at
>
org.intermine.objectstore.intermine.TorqueModelOutputTask.execute(Torque
> ModelOutputTask.java:122)
> 
>             at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
> 
>             at sun.reflect.GeneratedMethodAccessor2.invoke(Unknown
> Source)
> 
>             at
>
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
> Impl.java:25)
> 
>             at java.lang.reflect.Method.invoke(Method.java:585)
> 
>             at
>
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
> 05)
> 
>             at org.apache.tools.ant.Task.perform(Task.java:348)
> 
>             at
> org.apache.tools.ant.taskdefs.Sequential.execute(Sequential.java:62)
> 
>             at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
> 
>             at sun.reflect.GeneratedMethodAccessor2.invoke(Unknown
> Source)
> 
>             at
>
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
> Impl.java:25)
> 
>             at java.lang.reflect.Method.invoke(Method.java:585)
> 
>             at
>
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
> 05)
> 
>             at org.apache.tools.ant.Task.perform(Task.java:348)
> 
>             at
>
org.apache.tools.ant.taskdefs.MacroInstance.execute(MacroInstance.java:3
> 91)
> 
>             at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
> 
>             at sun.reflect.GeneratedMethodAccessor2.invoke(Unknown
> Source)
> 
>             at
>
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
> Impl.java:25)
> 
>             at java.lang.reflect.Method.invoke(Method.java:585)
> 
>             at
>
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:1
> 05)
> 
>             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:1329)
> 
>             at
> org.apache.tools.ant.Project.executeTarget(Project.java:1298)
> 
>             at
>
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecut
> or.java:41)
> 
>             at
> org.apache.tools.ant.Project.executeTargets(Project.java:1181)
> 
>             at org.apache.tools.ant.Main.runBuild(Main.java:698)
> 
>             at org.apache.tools.ant.Main.startAnt(Main.java:199)
> 
>             at
> org.apache.tools.ant.launch.Launcher.run(Launcher.java:257)
> 
>             at
> org.apache.tools.ant.launch.Launcher.main(Launcher.java:104)
> 
>  
> 
>  
> 
> ======================
> 
> Andrew Vallejos
> 
> Web Developer II
> 
> Biotechnology and Bioengineering Center
> 
> Medical College of Wisconsin
> 
> 414-955-4104
> 
> avallejos at mcw.edu
> 
>  
> 
> 
> 
>
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> 
> This body part will be downloaded on demand.




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