[InterMine Dev] Disease Ontology Annotation Parser Error

Vallejos, Andrew avallejos at mcw.edu
Tue Mar 29 20:33:32 BST 2011


Alright,

I'm not sure what I did wrong yesterday.  But I reverted all my changes
and started from scratch, and now everything seems to be working
correctly.

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
dev at intermine.org
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev



More information about the dev mailing list