[InterMine Dev] bioseg error message

Richard Smith richard at flymine.org
Tue Nov 24 19:49:58 GMT 2009


Hi Kalpana,
That isn't actually an error - just some bad logging.  We changed the
model XML file format some time ago so that collections no longer have
an 'ordered' attribute.  It looks like we didn't update all of our
model XML files.

There isn't actually anything wrong as the attribute is being ignored.
We'll fix it so it doesn't log a lot of errors in future.

Cheers,
Richard.


Kalpana Karra wrote:
>  # in malariamine/dbmodel
> when I run 
>>  ant clean build-db
> 
> I see the following lines of ERROR..
> 
> Some version mismatch somewhere?? What do I need to check?
> 
> Thanks!
> -Kalpana
> 
> 
>>grep 'ERROR' intermine.log
> 
> 2009-11-24 11:20:26 ERROR 
> org.intermine.modelproduction.xml.InterMineModelParser     - Deprecated 
> "ordered" attribute on collection org.intermine.model.bio.Exon.transcripts
> 2009-11-24 11:20:26 ERROR 
> org.intermine.modelproduction.xml.InterMineModelParser     - Deprecated 
> "ordered" attribute on collection org.intermine.model.bio.Gene.UTRs
> 2009-11-24 11:20:26 ERROR 
> org.intermine.modelproduction.xml.InterMineModelParser     - Deprecated 
> "ordered" attribute on collection org.intermine.model.bio.Gene.CDSs
> 2009-11-24 11:20:26 ERROR 
> org.intermine.modelproduction.xml.InterMineModelParser     - Deprecated 
> "ordered" attribute on collection org.intermine.model.bio.Gene.publications
> 2009-11-24 11:20:26 ERROR 
> org.intermine.modelproduction.xml.InterMineModelParser     - Deprecated 
> "ordered" attribute on collection org.intermine.model.bio.Intron.transcripts
> 2009-11-24 11:20:27 ERROR 
> org.intermine.modelproduction.xml.InterMineModelParser     - Deprecated 
> "ordered" attribute on collection org.intermine.model.bio.Transcript.introns
> 2009-11-24 11:20:27 ERROR 
> org.intermine.modelproduction.xml.InterMineModelParser     - Deprecated 
> "ordered" attribute on collection org.intermine.model.bio.Transcript.exons
> 2009-11-24 11:20:27 ERROR 
> org.intermine.modelproduction.xml.InterMineModelParser     - Deprecated 
> "ordered" attribute on collection org.intermine.model.bio.Protein.CDSs
> 2009-11-24 11:20:27 ERROR 
> org.intermine.modelproduction.xml.InterMineModelParser     - Deprecated 
> "ordered" attribute on collection 
> org.intermine.model.bio.Protein.transcripts
> 2009-11-24 11:20:27 ERROR 
> org.intermine.modelproduction.xml.InterMineModelParser     - Deprecated 
> "ordered" attribute on collection 
> org.intermine.model.bio.InsertionSite.genes
> 2009-11-24 11:20:27 ERROR 
> org.intermine.modelproduction.xml.InterMineModelParser     - Deprecated 
> "ordered" attribute on collection org.intermine.model.bio.MRNA.UTRs
> 2009-11-24 11:20:27 ERROR 
> org.intermine.modelproduction.xml.InterMineModelParser     - Deprecated 
> "ordered" attribute on collection 
> org.intermine.model.bio.SequenceVariant.genes
> 2009-11-24 11:20:27 ERROR 
> org.intermine.modelproduction.xml.InterMineModelParser     - Deprecated 
> "ordered" attribute on collection 
> org.intermine.model.bio.Chromosome.features
> 2009-11-24 11:20:27 ERROR 
> org.intermine.modelproduction.xml.InterMineModelParser     - Deprecated 
> "ordered" attribute on collection 
> org.intermine.model.bio.Chromosome.transcripts
> 2009-11-24 11:20:27 ERROR 
> org.intermine.modelproduction.xml.InterMineModelParser     - Deprecated 
> "ordered" attribute on collection org.intermine.model.bio.Chromosome.exons
> 2009-11-24 11:20:27 ERROR 
> org.intermine.modelproduction.xml.InterMineModelParser     - Deprecated 
> "ordered" attribute on collection org.intermine.model.bio.Chromosome.genes
> 2009-11-24 11:20:27 ERROR 
> org.intermine.modelproduction.xml.InterMineModelParser     - Deprecated 
> "ordered" attribute on collection 
> org.intermine.model.bio.Chromosome.chromosomeBands
> 2009-11-24 11:20:27 ERROR 
> org.intermine.modelproduction.xml.InterMineModelParser     - Deprecated 
> "ordered" attribute on collection 
> org.intermine.model.bio.Chromosome.chromosomalStructuralElements
> 2009-11-24 11:20:27 ERROR 
> org.intermine.modelproduction.xml.InterMineModelParser     - Deprecated 
> "ordered" attribute on collection 
> org.intermine.model.bio.Chromosome.crossGenomeMatches
> 2009-11-24 11:20:27 ERROR 
> org.intermine.modelproduction.xml.InterMineModelParser     - Deprecated 
> "ordered" attribute on collection org.intermine.model.bio.Gene.exons
> 2009-11-24 11:20:27 ERROR 
> org.intermine.modelproduction.xml.InterMineModelParser     - Deprecated 
> "ordered" attribute on collection 
> org.intermine.model.bio.LocatedSequenceFeature.overlappingFeatures
> 2009-11-24 11:20:27 ERROR 
> org.intermine.modelproduction.xml.InterMineModelParser     - Deprecated 
> "ordered" attribute on collection 
> org.intermine.model.bio.Scaffold.crossGenomeMatches
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> dev mailing list
> dev at mail.intermine.org
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev




More information about the dev mailing list