[InterMine Dev] Error loading BioGRID data

De Pons, Jeffrey jdepons at mcw.edu
Fri Feb 12 16:44:28 GMT 2016


Hello,

I am attempting to load BioGRID data for rat, mouse, and human and am getting an error.  Something is not configured correctly and I'm hoping you can help.

Here is the error

-retrieve-tgt-from-custom-file:
[integrate] Processing file: /data/intermine/git_ratmine/ratmine_src_data_mod/biogrid/BIOGRID-ORGANISM-Homo_sapiens-3.4.133.psi25.xml
[integrate] java.lang.RuntimeException: Entry in configuration file for 9606 not found
[integrate]     at org.intermine.bio.dataconversion.BioGridConverter$BioGridHandler.startElement(BioGridConverter.java:334)
[integrate]     at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source)


My project.xml file is configured as follows

<source name="rat-biogrid" type="biogrid">
                <property name="src.data.dir" location="../../../ratmine_src_data_mod/biogrid"/>
                <property name="src.data.dir.includes" value="*psi25.xml"/>
                <property name="biogrid.organisms" value="10116 10090 9606"/>
</source>
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