[InterMine Dev] NullPointer error while loading from source

Richard Smith richard at flymine.org
Thu Mar 3 11:56:00 GMT 2011


Hi James,
Either the class name or, more likely, the value of an attribute is
null/empty.  I can make the error message better, what version of
InterMine are you using?  It doesn't look like 0.96 as the line numbers
don't match up.

Cheers,
Richard.


On 01/03/2011 17:50, James Blackshaw wrote:
> Hi,
> I've been loading data froma few sources and getting the error below. I
> can see it's a problem while trying to load in the source XML file, but
> nothing in it gives an indication of what might be wrong. This
> integration's run under verbose so I'm a bit surprised by the rather
> general error. Any idea what it could be?
>
> -James
>
>
> -retrieve-tgt-from-xml-file:
> Property "ignore.duplicates" has not been set
> Property "src.data.dir" has not been set
> [integrate] Processing file /data/datasets/mitominer/gfp_xml/gfp.xml
> [null] Exiting
> /home/jab250/intermine_mass_copy/bio/sources/gfp_xml/build.xml.
>
> BUILD FAILED
> /home/jab250/intermine_mass_copy/imbuild/integrate.xml:54: The following
> error occurred while executing this line:
> /home/jab250/intermine_mass_copy/imbuild/source.xml:201: Exception while
> reading from: /data/datasets/mitominer/gfp_xml/gfp.xml
> at
> org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:170)
>
> at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
> at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>
> at java.lang.reflect.Method.invoke(Method.java:616)
> at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> at org.apache.tools.ant.Task.perform(Task.java:348)
> at org.apache.tools.ant.Target.execute(Target.java:390)
> at org.apache.tools.ant.Target.performTasks(Target.java:411)
> at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1360)
> at
> org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
>
> at org.apache.tools.ant.Project.executeTargets(Project.java:1212)
> at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:441)
> 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:291)
> at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>
> at java.lang.reflect.Method.invoke(Method.java:616)
> at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> at org.apache.tools.ant.Task.perform(Task.java:348)
> at org.apache.tools.ant.Target.execute(Target.java:390)
> at org.apache.tools.ant.Target.performTasks(Target.java:411)
> at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1360)
> at org.apache.tools.ant.Project.executeTarget(Project.java:1329)
> at
> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
>
> at org.apache.tools.ant.Project.executeTargets(Project.java:1212)
> at org.apache.tools.ant.Main.runBuild(Main.java:801)
> at org.apache.tools.ant.Main.startAnt(Main.java:218)
> at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
> at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
> Caused by: org.intermine.InterMineException: Error during unmarshalling
> at org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:64)
> at org.intermine.dataloader.XmlDataLoader.processXml(XmlDataLoader.java:68)
> at
> org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:160)
>
> ... 31 more
> Caused by: java.lang.NullPointerException
> at org.intermine.util.TypeUtil.stringToObject(TypeUtil.java:518)
> at org.intermine.xml.full.FullParser.populateObject(FullParser.java:177)
> at org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:134)
> at org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:77)
> at org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:62)
> ... 33 more
>
> Total time: 47 seconds
>
>
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