[InterMine Dev] Error load XML data: Error during unmarshalling

Pengcheng Yang yangpc at biols.ac.cn
Fri Jul 24 09:53:50 BST 2015


Hi InterMiners,

I want to load the generated xml file, but failed with the following 
error message [1], I have also checked the email archive and found this 
thread, 
http://gmod.827538.n3.nabble.com/Error-integrating-XML-files-td1973714.html, 
which is similar to my error message. But after I setting the keys in 
the sources/type/resources/*_keys.properties file. the error message 
remain.  Part of the XML file looks like this [2]

Many thanks!

Best,
Pengcheng Yang



[1] error message:

BUILD FAILED
/home/pengchy/Soft/05.SystemBiology/intermine/imbuild/integrate.xml:54: 
The following error occurred while executing this line:
/home/pengchy/Soft/05.SystemBiology/intermine/imbuild/source.xml:201: 
Exception while reading from: 
/home/pengchy/Project/LocustMine/locust-expression-xml/Merged_rpkm.xls.xml
         at 
org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:170)
         at 
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:293)
         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
         at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
         at java.lang.reflect.Method.invoke(Method.java:497)
         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:435)
         at org.apache.tools.ant.Target.performTasks(Target.java:456)
         at 
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1405)
         at 
org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
         at org.apache.tools.ant.Project.executeTargets(Project.java:1260)
         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:293)
         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
         at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
         at java.lang.reflect.Method.invoke(Method.java:497)
         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:435)
         at org.apache.tools.ant.Target.performTasks(Target.java:456)
         at 
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1405)
         at org.apache.tools.ant.Project.executeTarget(Project.java:1376)
         at 
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
         at org.apache.tools.ant.Project.executeTargets(Project.java:1260)
         at org.apache.tools.ant.Main.runBuild(Main.java:853)
         at org.apache.tools.ant.Main.startAnt(Main.java:235)
         at org.apache.tools.ant.launch.Launcher.run(Launcher.java:285)
         at org.apache.tools.ant.launch.Launcher.main(Launcher.java:112)
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.IllegalArgumentException: Looking for a reference, 
but found a java.util.Set
         at 
org.intermine.xml.full.FullParser.populateObject(FullParser.java:217)
         at 
org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:136)
         at 
org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:79)
         at org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:62)
         ... 33 more

Total time: 41 seconds



[2] part of the XML file

    <item id="0_2" class="Samples" implements="">
       <attribute name="primaryIdentifier" value="b-C" />
       <attribute name="DevStag" value="4" />
       <reference name="species" ref_id="0_1" />
       <attribute name="Tissue" value="Brain" />
       <attribute name="phase" value="S" />
       <attribute name="year" value="2011" />
    </item>

    <item id="0_144" class="Expression" implements="">
       <reference name="gene" ref_id="0_131" />
       <attribute name="Expr" value="1.42226640578148" />
       <reference name="sample" ref_id="0_93" />
    </item>




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