reactome data loading error

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reactome data loading error

wang su
Hi,

When I load the reactome data (home sapiens.owl) but there are some errors like

/mnt/Storage/home/wangs/dev/imbuild/integrate.xml:54: The following error occurred while executing this line:
/mnt/Storage/home/wangs/dev/imbuild/source.xml:145: java.lang.IllegalArgumentException: class "org.intermine.model.bio.protein" is not in the Model

I don't know how to correct it ,can you help me?

Thanks!
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Re: reactome data loading error

Julie Sullivan
The model is case sensitive, eg. "Gene" is in the model but "gene" is not.

This is wrong:

        org.intermine.model.bio.protein

It should be:

        org.intermine.model.bio.Protein

I think it's getting the lowercase "protein" from the config file.  For BioPAX
the config file determines which type of object to load and is case sensitive,
can you check that yours looks something like this:

        # bio/sources/biopax/main/resources/biopax_config.properties
        9606.primaryAccession=UniProt
        9606.bioentity=Protein

That should fix your problem, let me know if it doesn't.  I'll update the code
to have more informative error messages and not to be so picky!

Cheers
Julie


On 01/12/11 06:56, wang su wrote:

> Hi,
>
> When I load the reactome data (home sapiens.owl) but there are some errors like
>
> /mnt/Storage/home/wangs/dev/imbuild/integrate.xml:54: The following error occurred while executing this line:
> /mnt/Storage/home/wangs/dev/imbuild/source.xml:145: java.lang.IllegalArgumentException: class "org.intermine.model.bio.protein" is not in the Model
>
> I don't know how to correct it ,can you help me?
>
> Thanks!
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

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