[InterMine Dev] error whil loading genes items xml file

Jayaraman, Pushkala pjayaraman at mcw.edu
Mon Aug 12 13:44:56 BST 2013


Hello,
This error is fairly new I don't know a I'm doing wrong here and I need help figuring this out:

Caused by: java.lang.IllegalArgumentException: There are duplicate objects in the source being loaded, multiple items are identical according to the primary key being used. Storing again to id 1019692 object from source Gene [briefDescription="null", chromosome=null, chromosomeLocation=null, description="null", downstreamIntergenicRegion=null, ensemblIdentifier="null", fishBand="null", geneType="pseudo", id="24621", length="null", name="crooked neck pre-mRNA splicing factor-like 1 (Drosophila) pseudogene", ncbiGeneNumber="116481", nomenclatureStatus="APPROVED", organism=1, pharmGKBidentifier="null", primaryIdentifier="RGD:7242712", score="null", scoreType="null", secondaryIdentifier="RGD:7242712", sequence=null, sequenceOntologyTerm=3, soTerm=null, symbol="Crnkl1-ps1", upstreamIntergenicRegion=null]
        at org.intermine.dataloader.IntegrationWriterDataTrackingImpl.store(IntegrationWriterDataTrackingImpl.java:297)
        at org.intermine.dataloader.IntegrationWriterAbstractImpl.store(IntegrationWriterAbstractImpl.java:171)
        at org.intermine.dataloader.XmlDataLoader.processXml(XmlDataLoader.java:80)
        at org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:160)
        ... 31 more

Total time: 22 seconds
Mon Aug 12 07:22:34 CDT 2013

Here is the part of the xml file in question..

<item id="0_24621" class="" implements="Gene">
      <attribute name="symbol" value="Crnkl1-ps1" />
      <reference name="sequenceOntologyTerm" ref_id="0_3" />
      <attribute name="primaryIdentifier" value="RGD:7242712" />
      <attribute name="name" value="crooked neck pre-mRNA splicing factor-like 1 (Drosophila) pseudogene" />
      <collection name="dataSets">
         <reference ref_id="0_2" />
      </collection>
      <attribute name="secondaryIdentifier" value="RGD:7242712" />
      <attribute name="geneType" value="pseudo" />
      <attribute name="ncbiGeneNumber" value="116481" />
      <reference name="organism" ref_id="0_1" />
      <attribute name="nomenclatureStatus" value="APPROVED" />
   </item>
   <item id="0_24622" class="" implements="Synonym">
      <attribute name="value" value="116481" />
      <reference name="subject" ref_id="0_24621" />
   </item>
   <item id="0_24623" class="" implements="Publication">
      <attribute name="pubMedId" value="11804325" />
   </item>
   <item id="0_24624" class="" implements="Publication">
      <attribute name="pubMedId" value="10217146" />
   </item>
   <item id="0_24625" class="" implements="Protein">
      <attribute name="primaryAccession" value="B2GUU9" />
      <reference name="organism" ref_id="0_1" />
   </item>
   <item id="0_24626" class="" implements="Protein">
      <attribute name="primaryAccession" value="Q923I8" />
      <reference name="organism" ref_id="0_1" />
   </item>



Pushkala Jayaraman
Programmer/Analyst - Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
414-955-2229
http://rgd.mcw.edu

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