[InterMine Dev] uniprot and go-annotation failing?
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.
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:
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
"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,
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