[InterMine Dev] Disease Ontology Annotation Parser Error

julie at flymine.org julie at flymine.org
Thu Mar 31 23:48:07 BST 2011


I agree, there's no reason to make the code GO-specific.  I'll put this
change in the next InterMine release.

> I hate to suggest a core model change...but RatMine's pathway, gene,
> disease, and mammalian phenotype annotations use the same evidence code
> lexicon.  So wouldn't it be better to have an Evidence Code class,
> rather than a GO Evidence Code class?
>
> -Andrew
>
> -----Original Message-----
> From: dev-bounces at intermine.org [mailto:dev-bounces at intermine.org] On
> Behalf Of Richard Smith
> Sent: Tuesday, March 29, 2011 10:48 AM
> To: dev at intermine.org
> Subject: Re: [InterMine Dev] Disease Ontology Annotation Parser Error
>
> I think it can't find the configuration file.  Is it in
> bio/sources/sourcename/resources?  And readable?
>
> For the GO source the file name is defined in the PROP_FILE constant in
> the GoConverter class.
>
> Richard.
>
>
>
> On 28/03/2011 19:51, Vallejos, Andrew wrote:
>> I'm updating RatMine's annotation parsers to be in line with the
> changes
>> made in 0.94.1, and I keep receiving the following error stack.  It
>> looks as if there is a Null pointer exception when the parser attempts
>> to read the configuration file.  Any ideas why?  I cleaned out all but
>> 10116 from my config file.
>>
>>
>>
>> -Andrew
>>
>>
>>
>> /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:145:
>> java.lang.reflect.InvocationTargetException
>>
>>          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:135)
>>
>>          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:145:
>> java.lang.reflect.InvocationTargetException
>>
>>          at
>>
> org.intermine.task.FileConverterTask.execute(FileConverterTask.java:130)
>>
>>          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.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.reflect.InvocationTargetException
>>
>>          at
> sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
>> Method)
>>
>>          at
>>
> sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorA
>> ccessorImpl.java:39)
>>
>>          at
>>
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingCons
>> tructorAccessorImpl.java:27)
>>
>>          at
>> java.lang.reflect.Constructor.newInstance(Constructor.java:513)
>>
>>          at
>>
> org.intermine.task.FileConverterTask.execute(FileConverterTask.java:99)
>>
>>          ... 31 more
>>
>> Caused by: java.lang.NullPointerException
>>
>>          at
> java.util.Properties$LineReader.readLine(Properties.java:418)
>>
>>          at java.util.Properties.load0(Properties.java:337)
>>
>>          at java.util.Properties.load(Properties.java:325)
>>
>>          at
>>
> org.intermine.bio.dataconversion.DoConverter.readConfig(DoConverter.java
>> :100)
>>
>>          at
>>
> org.intermine.bio.dataconversion.DoConverter.<init>(DoConverter.java:93)
>>
>>         ... 36 more
>>
>> --- Nested Exception ---
>>
>> /home/intermine/build/intermine_current/imbuild/source.xml:145:
>> java.lang.reflect.InvocationTargetException
>>
>>          at
>>
> org.intermine.task.FileConverterTask.execute(FileConverterTask.java:130)
>>
>>          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.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:135)
>>
>>          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.reflect.InvocationTargetException
>>
>>          at
> sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
>> Method)
>>
>>          at
>>
> sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorA
>> ccessorImpl.java:39)
>>
>>          at
>>
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingCons
>> tructorAccessorImpl.java:27)
>>
>>          at
>> java.lang.reflect.Constructor.newInstance(Constructor.java:513)
>>
>>          at
>>
> org.intermine.task.FileConverterTask.execute(FileConverterTask.java:99)
>>
>>          ... 31 more
>>
>> Caused by: java.lang.NullPointerException
>>
>>          at
> java.util.Properties$LineReader.readLine(Properties.java:418)
>>
>>          at java.util.Properties.load0(Properties.java:337)
>>
>>          at java.util.Properties.load(Properties.java:325)
>>
>>          at
>>
> org.intermine.bio.dataconversion.DoConverter.readConfig(DoConverter.java
>> :100)
>>
>>          at
>>
> org.intermine.bio.dataconversion.DoConverter.<init>(DoConverter.java:93)
>>
>>          ... 36 more
>>
>> --- Nested Exception ---
>>
>> java.lang.reflect.InvocationTargetException
>>
>>          at
> sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
>> Method)
>>
>>          at
>>
> sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorA
>> ccessorImpl.java:39)
>>
>>          at
>>
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingCons
>> tructorAccessorImpl.java:27)
>>
>>          at
>> java.lang.reflect.Constructor.newInstance(Constructor.java:513)
>>
>>          at
>>
> org.intermine.task.FileConverterTask.execute(FileConverterTask.java:99)
>>
>>          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.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:135)
>>
>>          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.NullPointerException
>>
>>          at
> java.util.Properties$LineReader.readLine(Properties.java:418)
>>
>>          at java.util.Properties.load0(Properties.java:337)
>>
>>          at java.util.Properties.load(Properties.java:325)
>>
>>          at
>>
> org.intermine.bio.dataconversion.DoConverter.readConfig(DoConverter.java
>> :100)
>>
>>          at
>>
> org.intermine.bio.dataconversion.DoConverter.<init>(DoConverter.java:93)
>>
>>          ... 36 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
>
>
> _______________________________________________
> dev mailing list
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> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
> _______________________________________________
> dev mailing list
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>
>





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