[InterMine Dev] ClassShadow.primaryIdentifier snafu

Paulo Nuin paulo.nuin at gmail.com
Thu Oct 8 18:42:38 BST 2020


Hi Sam

Maybe related or not to your error, I have been having problems with a class called SOTerm (which I changes to WBSOTerm at one point), where the builddb process was complaining of a primaryIdentifier not present when my first attribute was called just identifier. I changed to primaryIdentifier and even after many clean installl etc commands, I was still not able to create the class in the model, and when it’s created it goes to the opposite name that I am setting on my additions XML. I wean’t able to locate the root of the problem.

I am doing some more tests soon, and I plan to send to InterMine and the list.

Cheers

Paulo

> On Oct 8, 2020, at 11:33 AM, Sam Hokin <shokin at ncgr.org> wrote:
> 
> I've got a bug in one of my mines that I simply cannot figure out. I have a class, which does not extend any other classes, called QTL, and here's how it's declared in dbmodel/build/resources/main/genomic_model.xml:
> 
> <class name="QTL" is-interface="true" term="http://purl.obolibrary.org/obo/SO:0001645">
>        <attribute name="lod" type="java.lang.Double"/>
>        <attribute name="likelihoodRatio" type="java.lang.Double"/>
>        <attribute name="intervalDescription" type="java.lang.String"/>
>        <attribute name="end" type="java.lang.Double"/>
>        <attribute name="identifier" type="java.lang.String"/>
>        <attribute name="start" type="java.lang.Double"/>
>        <reference name="organism" referenced-type="Organism"/>
>        <reference name="phenotype" referenced-type="Phenotype" reverse-reference="QTLs"/>
>        <reference name="geneticMap" referenced-type="GeneticMap" reverse-reference="QTLs"/>
>        <reference name="linkageGroup" referenced-type="LinkageGroup" reverse-reference="QTLs"/>
>        <collection name="dataSets" referenced-type="DataSet"/>
> </class>
> 
> Note that is has an attribute called "identifier" and no attribute called "primaryIdentifier". This is my practice for classes which don't extend Annotatable/BioEntity/SequenceFeature.
> 
> But whenever I build the mine and look at a QTL report page, it stops after the header and I get the following in the Tomcat localhost log (and no client-side error in the Javascript console):
> 
> 08-Oct-2020 11:27:28.121 SEVERE [ajp-nio-8009-exec-193] org.apache.catalina.core.StandardWrapperValve.invoke Servlet.service() for servlet [action] in context with path [/soymine] threw exception [An exception occurred processing [/layout.jsp] at line [93]
> 
> 90:       <tiles:insert page="/contextHelp.jsp"/>
> 91:
> 92:       <tiles:get name="body"/>
> 93:
> 94: <script type="text/javascript">
> 95: jQuery(document).ready(function() {
> 96:   jQuery("p#contactUsLink").toggle();
> 
> 
> Stacktrace:] with root cause
> 	javax.el.PropertyNotFoundException: Property [primaryIdentifier] not found on type [org.intermine.model.bio.QTLShadow]
> 
> So this is a server-side error, but where on earth is this desired QTLShadow.primaryIdentifier property coming from? It looks like it may be associated with a tile, but a grep of the entire mine tree shows no instance of QTL and primaryIdentifier. This is really mysterious! Thanks in advance for tips!
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