[InterMine Dev] NullPointer error while loading from source

Richard Smith richard at flymine.org
Tue Mar 8 17:32:44 GMT 2011


The problem is caused by an Item in the XML that specifies an attribute
name that doesn't exist in the model.

I've checked in a change to the 0.94.1 branch to make the error message
explain the problem.  If you do an svn update you should see the
improved message.

Cheers,
Richard.



On 04/03/2011 10:07, James Blackshaw wrote:
> Hi Richard,
> Thanks, I'm going through the source now. I'm on 0.94.1, don't want to
> upgrade until I have this version's webapp actually working. It's taking
> a while since I'm upgrading from the the database structure from 2008.
> -James
>
> On 03/03/2011 11:56, Richard Smith wrote:
>> 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
>>>
>>>
>>> _______________________________________________
>>> dev mailing list
>>> dev at intermine.org
>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>>
>>
>
>




More information about the dev mailing list