[InterMine Dev] uniprot and go-annotation failing?

Sierra Moxon staylor at cs.uoregon.edu
Thu Aug 27 16:06:42 BST 2009


> Gene is a subclass of BioEntity, and you can't set the priority for 
> primaryIdentifier twice.  Remove the priority entry for 
> "BioEntity.primaryIdentifier" and check for any other duplicate entries, eg. 
> Gene/Protein/BioEntity.name.
>
Thanks Julie,
I don't think I added this in the first place?  Is it possible to remove
the duplication from the file in SVN, or would that break other things?

I commented out the entries for BioEntity in genomic_priorities.properties
and got this error when running uniprot again:

Caused by: java.lang.IllegalArgumentException: Conflicting values for 
field org.intermine.model.bio.GeneShadow.symbol between zfin-identifiers 
(value thrap6) and uniprot-zebrafish (value med30) while comparing: Gene

Here is my priority for genes in zfinmine:
Gene=zfin-identifiers,zfin_genotypes,zfin_expression,go-annotation,uniprot-zebrafish

and I loaded zfin-identifiers before uniprot-zebrafish.

Also, the doc indicates that I should be removing the sub-entity's (I
think) priority: the Gene primary identifier in this case, or is this a
different issue?

"Note - there is currently a 'bug' with the priority system, the priority
needs to be defined for the class in which the field is defined, it cannot
be defined in a class that inherits that field. For example length is
defined in LocatedSequenceFeature and inherited by Gene and Exon, to
configure a priority for Gene lengths it must be set for
LocatedSequenceFeature. It isn't possible to set different priorities for
each subclass. "

Thanks and talk to you soon,
Sierra :)



More information about the dev mailing list