[InterMine Dev] Running a script to create an xml file causes an error

Jayaraman, Pushkala pjayaraman at mcw.edu
Wed Mar 13 22:34:46 GMT 2013


Hello,
While we have some time, decided to try and run the script to load the data as well and this is what I found:
The script breaks after a while and this is what it gives out:

tried to set field 'submissions' in class '[implements: Project]' to something other than type: InterMine::Model::Reference

ive tried to set my additions.xml to look like this:

<?xml version="1.0"?>
<!-- This file details any extensions needed to the data model to store data from this source, everything else is automatically generated from the model description so this is all we need to do to add to the model. -->

<classes>
        <class name="Submission" is-interface="true">
                <collection name="dataPoints" referenced-type="DataPoint" reverse-reference="submission"/>
                <attribute name="experimentDate" type="java.util.Date"/>
                <reference name="publication" referenced-type="Publication"/>
                <attribute name="title" type="java.lang.String"/>
        </class>

        <class name="DataPoint" is-interface="true">
                <reference name="submission" referenced-type="Submission" reverse-reference="dataPoints"/>
        </class>

        <class name="eQTL" extends="DataPoint" is-interface="true">
                <attribute name="reaperPValue" type="java.lang.Float"/>
                <reference name="submission" referenced-type="Submission" reverse-reference="dataPoints"/>
                <reference name="sslv" referenced-type="SimpleSequenceLengthVariation"/>
                <reference name="probeSet" referenced-type="ProbeSet"/>
                <collection name="tissueExpressions" referenced-type="Expression"/>
                <reference name="organism" referenced-type="Organism"/>
        </class>

        <class name="Expression" is-interface="true">
                <attribute name="tissue" type="java.lang.String"/>
                <attribute name="foldChange" type="java.lang.Float"/>
                <attribute name="pval" type="java.lang.Float"/>
                <reference name="eqtl" referenced-type="eQTL" reverse-reference="tissueExpressions"/>
        </class>

        <class name="ProbeSet" extends="SequenceCollection" is-interface="true">
                <collection name="eqtls" referenced-type="eQTL" reverse-reference="probeSet"/>
        </class>

        <class name="SimpleSequenceLengthVariation" is-interface="true">
                <collection name="eqtls" referenced-type="eQTL" reverse-reference="sslv"/>
        </class>

        <class name="Project" is-interface="true">
                <attribute name="name" type="java.lang.String"/>
                <reference name="submissions" referenced-type="DataPoint"/>
        </class>

</classes>


Do let me know where I can begin debugging this..
Thanks,
Pushkala Jayaraman
Programmer/Analyst - Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
414-955-2229
http://rgd.mcw.edu

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