[InterMine Dev] ClassShadow.primaryIdentifier snafu

daniela at intermine.org daniela at intermine.org
Fri Oct 9 12:13:18 BST 2020


Hi Sam,
sorry for the issue.
Initially I was thinking that the issue was related to some work I have 
done to create the Share link button.
BUt after looking at the code it seems that the otherMinesLinks.jsp page 
uses the primaryIdentifer (se here 
https://github.com/intermine/intermine/blob/dev/intermine/webapp/src/main/webapp/otherMinesLink.jsp#L32).

In fact, if you look at the source code of the QTL report page, it seems 
it breaks on friendlyMines section.

I will add a ticket for that.
Not sure why it worked before??!!!

Daniela

> 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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>> dev at lists.intermine.org
>> https://lists.intermine.org/mailman/listinfo/dev
> 
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