[InterMine Dev] NullPointer error while loading from source

James Blackshaw jab250 at mrc-mbu.cam.ac.uk
Tue Mar 1 17:50:03 GMT 2011


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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