[InterMine Dev] Interesting problem

Daniela Butano daniela at intermine.org
Thu Jan 30 10:28:55 GMT 2020


Hi Paulo,

when you change a class definition, you should see those changes in the 
model and then in the db (if you rebuild the db)

When you did your changes, did you first run ./gradlew clean ? (This 
should delete the build directory and force gradle to regenerate the model)

I have noticed that the wormine you sent me last November (via dropbox)  
has Allele with primaryIdentifier.

Daniela

On 29/01/2020 22:47, Paulo Nuin wrote:
> HI Daniela
>
> We still have some legacy code that still doesn’t use the core 
> entities, which reminds me I need to update a couple of others and 
> strains.
>
> I gripped my whole code and I couldn’t find anything with Alleles, 
> results are below. Only templates have Alleles in them
>
>
> I also grepped my XPATH files and I am not loading anything with the 
> term, with the exception of TEXT entries in the middle of XML. There’s 
> no class or item called Alleles.
>
> I also tried extending the Allele class with BioEntity but nothing 
> changed in the model.
>
> Any ideas?
>
> Cheers
>
> Paulo
>
>
>
>
>
>
>
>
>
>
>
> grep -r -w Alleles *
> intermine-scripts/bio/DataDownloader/lib/DataDownloader/Source/FlyBaseAlleles.pm: 
>    TITLE => 'FlyBase Alleles',
> intermine-scripts/bio/DataDownloader/lib/DataDownloader/Source/FlyBaseAlleles.pm: 
>    DESCRIPTION => 'Alleles from FlyBase',
> Binary file intermine-scripts/reports/data/templates matches
> WormMine/webapp/build/explodedWebApp/model/mouseAllelesDisplayer.jsp: 
>      <h3>Mouse Alleles </h3>
> WormMine/webapp/build/explodedWebApp/js/widgets/mouse-phenotype-dendrogram.js: 
>        'title': "Alleles phenotype terms for " + this.config.symbol
> Binary file 
> WormMine/webapp/build/explodedWebApp/WEB-INF/classes/org/intermine/bio/web/displayer/MetabolicGeneSummaryDisplayer.class 
> matches
> WormMine/support/acedb-dev/acedb/models.wrm:                Alleles 
> ?Variation
> WormMine/support/templates/original_su_templates:<template 
> name="gene_alleles" title="Gene --> Alleles " comment="">
> WormMine/support/templates/original_su_templates:<template 
> name="gene_to_alleles_old" title="Gene --> Alleles old" comment="">
> WormMine/support/templates/staff_templates:<template 
> name="gene_alleles" title="Gene --> Alleles " comment="">
> WormMine/support/templates/old/templates_superuser.txt:<template 
> name="gene_to_alleles" title="Gene --> Alleles" comment="">
> WormMine/support/templates/old/templates.txt: <template 
> name="gene_to_alleles" title="Gene --> Alleles" comment=""><query 
> name="gene_to_alleles" model="genomic" view="Gene.alleles.method 
> Gene.alleles.symbol Gene.alleles.primaryIdentifier" 
> longDescription="List *all* experimentally obtained alleles for a 
> given gene omitting polymorphisms and high-throughput alleles -- TWH" 
> sortOrder="Gene.alleles.method asc" constraintLogic="A and 
> B"><constraint path="Gene.symbol" code="A" editable="true" op="=" 
> value="unc-26"/><constraint path="Gene.alleles.method" code="B" 
> editable="true" op="ONE 
> OF"><value>Allele</value><value>Deletion_allele</value><value>Deletion_an_insertion_allele</value><value>Deletion_and_insertion_allele</value><value>Deletion_with_insertion</value><value>Deltion_allele</value><value>Insertion_allele</value><value>Substitution_allele</value><value>Transposon_insertion</value></constraint></query></template>
>
>
>> On Jan 29, 2020, at 4:14 AM, Daniela Butano <daniela at intermine.org 
>> <mailto:daniela at intermine.org>> wrote:
>>
>> Hi Paulo,
>>
>> I noticed that the Allele class doesn't extend BioEntity.....is it 
>> intentional?
>>
>> It might be possible that wormine loads other bio-sources which 
>> contain in their addionals.xml files a different definition of Allele 
>> (which extend BioEntity)?
>>
>> Daniela
>>
>> On 29/01/2020 03:37, Paulo Nuin wrote:
>>> Hi everyone
>>>
>>> We are stuck with a really interesting problem, that came back 2 or 
>>> 3 releases ago. We have a class in WormMine, Allele, that is getting 
>>> duplicated and showing up in the singular Allele and plural Allele, 
>>> with mostly identical items on the output. I grepped my whole code 
>>> and I don’t see anywhere the class/word Alleles showing up (we have 
>>> affectedByAlleles).
>>>
>>> An example of the result is attached (3 screen caps).
>>>
>>> The class Allele is below.
>>>
>>>
>>>         <class name="Allele" is-interface="true">
>>>           <attribute name="naturalVariant" type="java.lang.String" />
>>>           <attribute name="method" type="java.lang.String" />
>>>           <attribute name="type" type="java.lang.String" />
>>>           <attribute name="publicName" type="java.lang.String" />
>>>           <attribute name="otherName" type="java.lang.String" />
>>>           <attribute name="KOAllele" type="java.lang.String" />
>>>           <attribute name="NBPAllele" type="java.lang.String" />
>>>           <attribute name="nemaAllele" type="java.lang.String" />
>>>           <attribute name="amber_UAG" type="java.lang.String" />
>>>           <attribute name="ochre_UAA" type="java.lang.String" />
>>>           <attribute name="opal_UGA" type="java.lang.String" />
>>>           <attribute name="donorSpliceSite" type="java.lang.String" />
>>>           <attribute name="acceptorSpliceSite" 
>>> type="java.lang.String" />
>>>           <attribute name="productionMethod" type="java.lang.String" />
>>> <!--      <attribute name="sequenceDetails" type="java.lang.String" 
>>> /> -->
>>>           <attribute name="status" type="java.lang.String" />
>>> <!--      <attribute name="affects" type="java.lang.String" /> -->
>>>           <attribute name="NemaGENETAGConsortiumAllele" 
>>> type="java.lang.String" />
>>> <!--      <attribute name="missense" type="java.lang.String" /> -->
>>>           <attribute name="detectionMethod" type="java.lang.String" />
>>>           <attribute name="positiveClone" type="java.lang.String" />
>>>           <attribute name="typeOfMutation" type="java.lang.String" />
>>>           <attribute name="sequenceStatus" type="java.lang.String" />
>>>           <attribute name="KOConsortiumAllele" 
>>> type="java.lang.String" />
>>>           <attribute name="missenseChange" type="java.lang.String" />
>>>           <attribute name="mutagen" type="java.lang.String" />
>>>           <attribute name="natureOfVariation" type="java.lang.String" />
>>>           <attribute name="interpolatedMapPosition" 
>>> type="java.lang.String" />
>>>           <attribute name="species" type="java.lang.String" />
>>>           <attribute name="rearrangement" type="java.lang.String" />
>>>           <attribute name="linkedTo" type="java.lang.String" />
>>>           <collection name="phenotype" referenced-type="Phenotype" 
>>> reverse-reference="phenotypeAllele" />
>>>           <collection name="phenotypeNotObserved" 
>>> referenced-type="Phenotype" 
>>> reverse-reference="phenotypeAlleleNotObserved" />
>>>           <collection name="affectsGenes" referenced-type="Gene" 
>>> reverse-reference="affectedByAlleles" />
>>>           <collection name="affectsCDSs" referenced-type="CDS" 
>>> reverse-reference="affectedByAlleles" />
>>>           <collection name="affectsTranscripts" 
>>> referenced-type="Transcript" reverse-reference="affectedByAlleles" />
>>>           <!--<collection name="strains" referenced-type="Strain" 
>>> reverse-reference="variations" /> -->
>>>           <collection name="fromLabs" referenced-type="Laboratory" 
>>> reverse-reference="variations" />
>>>           <collection name="geneClass" referenced-type="GeneClass" 
>>> reverse-reference="variations" />
>>>           <collection name="genes" referenced-type="Gene" 
>>> reverse-reference="allele" />
>>>         </class>
>>>
>>>
>>> I am at loss here. We have tried most things in our tool belt to 
>>> define why this is happening to no success. Any help appreciated.
>>>
>>> Thanks
>>>
>>> Paulo
>>>
>>>
>>>
>>>
>>>
>>>
>>> <Screenshot 2020-01-28 20.32.45.png>\<Screenshot 2020-01-28 
>>> 19.42.02.png><Screenshot 2020-01-28 19.42.08.png>
>>>
>>> _______________________________________________
>>> dev mailing list
>>> dev at lists.intermine.org
>>> https://lists.intermine.org/mailman/listinfo/dev
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