[InterMine Dev] Disease Ontology Annotation Parser Error

Vallejos, Andrew avallejos at mcw.edu
Mon Mar 28 19:51:47 BST 2011


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

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