[InterMine Dev] uniprot and go-annotation failing?

Julie Sullivan julie at flymine.org
Thu Aug 27 09:43:37 BST 2009


Here is the interesting bit of that stracktrace:

 > There are multiple priorities configured for
 > org.intermine.model.bio.Gene.primaryIdentifier. Found a match on
 > Gene.primaryIdentifier and BioEntity.primaryIdentifier

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.

I've added a note to the upgrade page:

	http://intermine.org/wiki/UpgradeInterMine

We fixed a bug in the priority system, previously it would ignore the duplicate 
entry.

Sierra Moxon wrote:
> Hi Julie-
> 
> I upgrade to 0.91 and moved my intermine instance to a new machine.  Now 
> uniprot and go-annotation are failing with this error (see below).  Did 
> I forget to copy over a particular file, or is there something I forgot 
> to change in 0.91?
> 
> I see the bug reported in the doc about having to define shared keys in 
> the parent class (example is gene.length in the LocatedSequenceFeature 
> vs Gene definition), but I don't remember having to set anything really 
> for uniprot or go-annotation for them to work?
> 
> Thanks,
> Sierra
> 
> 
> Caused by: java.lang.RuntimeException: Exception while loading object 
> Organism [abbreviation="null", genus="null", id="180087", name="null", 
> shortName="null", species="null", taxonId="7955"]
>     at 
> org.intermine.dataloader.IntegrationWriterDataTrackingImpl.store(IntegrationWriterDataTrackingImpl.java:574) 
> 
>     at 
> org.intermine.dataloader.IntegrationWriterAbstractImpl.store(IntegrationWriterAbstractImpl.java:167) 
> 
>     at 
> org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLoader.java:146) 
> 
>     ... 33 more
> Caused by: java.lang.IllegalArgumentException: There are multiple 
> priorities configured for 
> org.intermine.model.bio.Gene.primaryIdentifier. Found a match on 
> Gene.primaryIdentifier and BioEntity.primaryIdentifier
>     at 
> org.intermine.dataloader.PriorityConfig.getPriorities(PriorityConfig.java:108) 
> 
>     at 
> org.intermine.dataloader.PriorityConfig.<init>(PriorityConfig.java:60)
>     at 
> org.intermine.dataloader.IntegrationWriterDataTrackingImpl.store(IntegrationWriterDataTrackingImpl.java:393) 
> 
>     ... 35 more
> 
> 



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