[InterMine Dev] Interesting problem

Paulo Nuin paulo.nuin at gmail.com
Fri Jan 31 15:52:36 GMT 2020


Hi Daniela

My build process always include on a clean, even when there’s no model changes.

I found more evidence of the error. Our “main” model comes from the wormbase-acedb_additions.xml where we have the Allele and Gene class linked. I am assuming the model when build, classes from this file end up on build/resources/main/genomic_model.xm.

Grepping the dbmodel folder, I get the results below, where the reference of the gene/allele connection gets modified from allele to alleles (output below). Would that be due the fact we are not extending the BioEntity class? I did add to the wormbase-acedb_additions.xml file but I don’t see any difference (at leas on the allele/alleles issue below).

Thanks

Paulo





im-dev1 :: ip-10-0-1-237 :: 4.0/WormMine/dbmodel ‹im-275*› % grep -r -w alleles *
build/so_additions.xml: <reference name="gene" referenced-type="Gene" reverse-reference="alleles"/>
build/so_additions.xml: <collection name="alleles" referenced-type="Allele" reverse-reference="gene"/>
build/gen/org/intermine/model/bio/Gene.java:    public void setAlleles(final java.util.Set<org.intermine.model.bio.Allele> alleles);
build/gen/org/intermine/model/bio/GeneShadow.java:    // Col: org.intermine.model.bio.Gene.alleles
build/gen/org/intermine/model/bio/GeneShadow.java:    protected java.util.Set<org.intermine.model.bio.Allele> alleles = new java.util.HashSet<org.intermine.model.bio.Allele>();
build/gen/org/intermine/model/bio/GeneShadow.java:    public java.util.Set<org.intermine.model.bio.Allele> getAlleles() { return alleles; }
build/gen/org/intermine/model/bio/GeneShadow.java:    public void setAlleles(final java.util.Set<org.intermine.model.bio.Allele> alleles) { this.alleles = alleles; }
build/gen/org/intermine/model/bio/GeneShadow.java:    public void addAlleles(final org.intermine.model.bio.Allele arg) { alleles.add(arg); }
build/gen/org/intermine/model/bio/GeneShadow.java:        if ("alleles".equals(fieldName)) {
build/gen/org/intermine/model/bio/GeneShadow.java:            return alleles;
build/gen/org/intermine/model/bio/GeneShadow.java:        if ("alleles".equals(fieldName)) {
build/gen/org/intermine/model/bio/GeneShadow.java:            return alleles;
build/gen/org/intermine/model/bio/GeneShadow.java:        } else if ("alleles".equals(fieldName)) {
build/gen/org/intermine/model/bio/GeneShadow.java:            alleles = (java.util.Set) value;
build/gen/org/intermine/model/bio/GeneShadow.java:        if ("alleles".equals(fieldName)) {
build/gen/org/intermine/model/bio/GeneShadow.java:        alleles = new ProxyCollection<org.intermine.model.bio.Allele>(os, this, "alleles", org.intermine.model.bio.Allele.class);
build/gen/org/intermine/model/bio/GeneShadow.java:        } else if ("alleles".equals(fieldName)) {
build/gen/org/intermine/model/bio/GeneShadow.java:            alleles.add((org.intermine.model.bio.Allele) element);
build/gen/org/intermine/model/bio/GeneShadow.java:        if ("alleles".equals(fieldName)) {
build/resources/main/genomic_model.xml: <reference name="gene" referenced-type="Gene" reverse-reference="alleles"/>
build/resources/main/genomic_model.xml: <collection name="alleles" referenced-type="Allele" reverse-reference="gene"/>
Binary file build/classes/java/main/org/intermine/model/bio/GeneShadow.class matches

> On Jan 30, 2020, at 3:28 AM, Daniela Butano <daniela at intermine.org> wrote:
> 
> 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>
>>>> 
>>>> 
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