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

Pengcheng Yang yangpc at biols.ac.cn
Tue Jul 28 01:01:49 BST 2015


Hi,

I guess this problem was caused by the more than one XML data loading 
with the same keys. In the two xml files, I have both used "add_item" 
function to add gene item with primaryidentifier, but with different 
reference id in the two data sets. When loading these XML files, there 
will be two entries in the Gene table with the same primaryidentifier, 
which is the key for Gene table. Will this be a problem?

So, the question is when loading XML data, how InterMine dealing with 
the items which has stored in the database with the same primaryidentifier?

Any suggestions will be very helpful and be appreciated.

Best,
Pengcheng Yang

On 2015/7/24 16:53, Pengcheng Yang wrote:
> 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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