[InterMine Dev] Snp fails due to name change

Richard Smith richard at flymine.org
Thu Aug 6 16:53:51 BST 2009


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
> 
>  
> 
> 
> 
> ------------------------------------------------------------------------
> 
> This body part will be downloaded on demand.




More information about the dev mailing list