[InterMine Dev] Interesting problem

Paulo Nuin paulo.nuin at gmail.com
Wed Jan 29 03:37:28 GMT 2020


Hi everyone

We are stuck with a really interesting problem, that came back 2 or 3 releases ago. We have a class in WormMine, Allele, that is getting duplicated and showing up in the singular Allele and plural Allele, with mostly identical items on the output. I grepped my whole code and I don’t see anywhere the class/word Alleles showing up (we have affectedByAlleles). 

An example of the result is attached (3 screen caps). 

The class Allele is below.


        <class name="Allele" is-interface="true">
          <attribute name="naturalVariant" type="java.lang.String" />
          <attribute name="method" type="java.lang.String" />
          <attribute name="type" type="java.lang.String" />
          <attribute name="publicName" type="java.lang.String" />
          <attribute name="otherName" type="java.lang.String" />
          <attribute name="KOAllele" type="java.lang.String" />
          <attribute name="NBPAllele" type="java.lang.String" />
          <attribute name="nemaAllele" type="java.lang.String" />
          <attribute name="amber_UAG" type="java.lang.String" />
          <attribute name="ochre_UAA" type="java.lang.String" />
          <attribute name="opal_UGA" type="java.lang.String" />
          <attribute name="donorSpliceSite" type="java.lang.String" />
          <attribute name="acceptorSpliceSite" type="java.lang.String" />
          <attribute name="productionMethod" type="java.lang.String" />
<!--      <attribute name="sequenceDetails" type="java.lang.String" /> -->
          <attribute name="status" type="java.lang.String" />
<!--      <attribute name="affects" type="java.lang.String" /> -->
          <attribute name="NemaGENETAGConsortiumAllele" type="java.lang.String" />
<!--      <attribute name="missense" type="java.lang.String" /> -->
          <attribute name="detectionMethod" type="java.lang.String" />
          <attribute name="positiveClone" type="java.lang.String" />
          <attribute name="typeOfMutation" type="java.lang.String" />
          <attribute name="sequenceStatus" type="java.lang.String" />
          <attribute name="KOConsortiumAllele" type="java.lang.String" />
          <attribute name="missenseChange" type="java.lang.String" />
          <attribute name="mutagen" type="java.lang.String" />
          <attribute name="natureOfVariation" type="java.lang.String" />
          <attribute name="interpolatedMapPosition" type="java.lang.String" />
          <attribute name="species" type="java.lang.String" />
          <attribute name="rearrangement" type="java.lang.String" />
          <attribute name="linkedTo" type="java.lang.String" />
          <collection name="phenotype" referenced-type="Phenotype" reverse-reference="phenotypeAllele" />
          <collection name="phenotypeNotObserved" referenced-type="Phenotype" reverse-reference="phenotypeAlleleNotObserved" />
          <collection name="affectsGenes" referenced-type="Gene" reverse-reference="affectedByAlleles" />
          <collection name="affectsCDSs" referenced-type="CDS" reverse-reference="affectedByAlleles" />
          <collection name="affectsTranscripts" referenced-type="Transcript" reverse-reference="affectedByAlleles" />
          <!--<collection name="strains" referenced-type="Strain" reverse-reference="variations" /> -->
          <collection name="fromLabs" referenced-type="Laboratory" reverse-reference="variations" />
          <collection name="geneClass" referenced-type="GeneClass" reverse-reference="variations" />
          <collection name="genes" referenced-type="Gene" reverse-reference="allele" />
        </class>


I am at loss here. We have tried most things in our tool belt to define why this is happening to no success. Any help appreciated.

Thanks

Paulo






\
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.intermine.org/pipermail/dev/attachments/20200128/77da1f08/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot 2020-01-28 20.32.45.png
Type: image/png
Size: 91170 bytes
Desc: not available
URL: <http://lists.intermine.org/pipermail/dev/attachments/20200128/77da1f08/attachment-0003.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot 2020-01-28 19.42.02.png
Type: image/png
Size: 149420 bytes
Desc: not available
URL: <http://lists.intermine.org/pipermail/dev/attachments/20200128/77da1f08/attachment-0004.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot 2020-01-28 19.42.08.png
Type: image/png
Size: 156047 bytes
Desc: not available
URL: <http://lists.intermine.org/pipermail/dev/attachments/20200128/77da1f08/attachment-0005.png>


More information about the dev mailing list