Error loading data

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Error loading data

James Blackshaw
Hi,

Having got my sources defined, I've started loading in data, but
Intermine's crashing during integration, with the error below. I can't
see a problem in the XML, as I've been using both my newly generated one
and the one used in the previous version of MitoMiner. I've attached
both. Any idea where to start looking for the bug? the exception's not
very informative to my limited knowledge of Java.

-James

-set-xml-tgt-file-includes:
Skipped because property 'src.data.dir.includes' set.

-set-xml-tgt-file:
Skipped because property 'src.data.file' set.

-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/kegg_pathway_xml/kegg_pathway.xml
      [null] Exiting
/home/jab250/intermine_rebuild/bio/sources/kegg_pathway_xml/build.xml.

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/kegg_pathway_xml/kegg_pathway.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.ClassNotFoundException:
org.intermine.model.bio.http://mitominer.services:8080/malariamine
     at java.lang.Class.forName0(Native Method)
     at java.lang.Class.forName(Class.java:186)
     at
org.intermine.util.DynamicUtil.convertToClasses(DynamicUtil.java:222)
     at
org.intermine.util.DynamicUtil.instantiateObject(DynamicUtil.java:312)
     at org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:99)
     at org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:77)
     at org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:62)
     ... 33 more



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kegg_pathway.xml (1M) Download Attachment
kegg_pathway.xml.old.xml (1M) Download Attachment
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Re: Error loading data

Richard Smith
Hi James,
Somehow the url the webapp will be deployed to is in the implements
field of the items:

  <item id="0_1" class="KEGG_pathways"
implements="http://mitominer.services:8080/malariamine">

This should be blank.  Are you using a new checkout of InterMine?

If you're still having problems please send the perl code you're
using to generate the items.

Cheers,
Richard.




James Blackshaw wrote:

> Hi,
>
> Having got my sources defined, I've started loading in data, but
> Intermine's crashing during integration, with the error below. I can't
> see a problem in the XML, as I've been using both my newly generated one
> and the one used in the previous version of MitoMiner. I've attached
> both. Any idea where to start looking for the bug? the exception's not
> very informative to my limited knowledge of Java.
>
> -James
>
> -set-xml-tgt-file-includes:
> Skipped because property 'src.data.dir.includes' set.
>
> -set-xml-tgt-file:
> Skipped because property 'src.data.file' set.
>
> -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/kegg_pathway_xml/kegg_pathway.xml
>      [null] Exiting
> /home/jab250/intermine_rebuild/bio/sources/kegg_pathway_xml/build.xml.
>
> 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/kegg_pathway_xml/kegg_pathway.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.ClassNotFoundException:
> org.intermine.model.bio.http://mitominer.services:8080/malariamine
>     at java.lang.Class.forName0(Native Method)
>     at java.lang.Class.forName(Class.java:186)
>     at
> org.intermine.util.DynamicUtil.convertToClasses(DynamicUtil.java:222)
>     at
> org.intermine.util.DynamicUtil.instantiateObject(DynamicUtil.java:312)
>     at org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:99)
>     at org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:77)
>     at org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:62)
>     ... 33 more
>
>
> ------------------------------------------------------------------------
>
> This body part will be downloaded on demand.


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