NullPointer error while loading from source

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NullPointer error while loading from source

James Blackshaw
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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Re: NullPointer error while loading from source

Richard Smith
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
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>


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Re: NullPointer error while loading from source

Richard Smith
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
>>> [hidden email]
>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>>
>>
>
>


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[hidden email]
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