Error integrating XML files

[James Blackshaw]

Hi,
Ive been loading in data to Mitominer, and most of the old files are
failing to integrate, giving the same exception, but no line number of
where the error occurred in the file. It's clearly something in the xml,
but I can't see what. Could you offer any ideas on where to look for the
problem?
Regards,
James

BUILD FAILED
/home/jab250/intermine_rebuild/imbuild/integrate.xml:54: The following
error occurred while executing this line:
/home/jab250/intermine_rebuild/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 java.lang.Class.isAssignableFrom(Native Method)
     at
org.intermine.xml.full.FullParser.populateObject(FullParser.java:205)
     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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[James Blackshaw]

Hello,
Tracked this down to the fact that my *_keys.properties files were uing
the old formatting of [item]=[key], not [item].[key]=[field with the key
in it]. It's sorted now.
-James

On 26/11/2010 16:36, James Blackshaw wrote:

> Hi,
> Ive been loading in data to Mitominer, and most of the old files are
> failing to integrate, giving the same exception, but no line number of
> where the error occurred in the file. It's clearly something in the
> xml, but I can't see what. Could you offer any ideas on where to look
> for the problem?
> Regards,
> James
>
> BUILD FAILED
> /home/jab250/intermine_rebuild/imbuild/integrate.xml:54: The following
> error occurred while executing this line:
> /home/jab250/intermine_rebuild/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 java.lang.Class.isAssignableFrom(Native Method)
>     at
> org.intermine.xml.full.FullParser.populateObject(FullParser.java:205)
>     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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[Richard Smith]

Hi James,
Good to hear you got this working.  I don't think the keys would have
been the problem - they shouldn't be read until after the XML has
successfully been parsed.  So maybe something else you did fixed it.

The original error looks like there was an Item in the XML without
a classname (or implementations) field set.

Let us know if the problem comes back.

Cheers,
Richard.



On 29/11/2010 17:11, James Blackshaw wrote:

> Hello,
> Tracked this down to the fact that my *_keys.properties files were uing
> the old formatting of [item]=[key], not [item].[key]=[field with the key
> in it]. It's sorted now.
> -James
>
> On 26/11/2010 16:36, James Blackshaw wrote:
>> Hi,
>> Ive been loading in data to Mitominer, and most of the old files are
>> failing to integrate, giving the same exception, but no line number of
>> where the error occurred in the file. It's clearly something in the
>> xml, but I can't see what. Could you offer any ideas on where to look
>> for the problem?
>> Regards,
>> James
>>
>> BUILD FAILED
>> /home/jab250/intermine_rebuild/imbuild/integrate.xml:54: The following
>> error occurred while executing this line:
>> /home/jab250/intermine_rebuild/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 java.lang.Class.isAssignableFrom(Native Method)
>> at org.intermine.xml.full.FullParser.populateObject(FullParser.java:205)
>> 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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