Interesting problem

classic Classic list List threaded Threaded
13 messages Options
Reply | Threaded
Open this post in threaded view
|

Interesting problem

Paulo Nuin
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






\

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Interesting problem

Daniela Butano-2

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






\

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Interesting problem

Paulo Nuin
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 --&gt; Alleles " comment="">
WormMine/support/templates/original_su_templates:<template name="gene_to_alleles_old" title="Gene --&gt; Alleles old" comment="">
WormMine/support/templates/staff_templates:<template name="gene_alleles" title="Gene --&gt; Alleles " comment="">
WormMine/support/templates/old/templates_superuser.txt:<template name="gene_to_alleles" title="Gene --&gt; Alleles" comment="">
WormMine/support/templates/old/templates.txt: <template name="gene_to_alleles" title="Gene --&gt; 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 <[hidden email]> 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
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev


_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Interesting problem

Daniela Butano-2

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 --&gt; Alleles " comment="">
WormMine/support/templates/original_su_templates:<template name="gene_to_alleles_old" title="Gene --&gt; Alleles old" comment="">
WormMine/support/templates/staff_templates:<template name="gene_alleles" title="Gene --&gt; Alleles " comment="">
WormMine/support/templates/old/templates_superuser.txt:<template name="gene_to_alleles" title="Gene --&gt; Alleles" comment="">
WormMine/support/templates/old/templates.txt: <template name="gene_to_alleles" title="Gene --&gt; 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 <[hidden email]> 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
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev


_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Interesting problem

Paulo Nuin
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 <[hidden email]> 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 --&gt; Alleles " comment="">
WormMine/support/templates/original_su_templates:<template name="gene_to_alleles_old" title="Gene --&gt; Alleles old" comment="">
WormMine/support/templates/staff_templates:<template name="gene_alleles" title="Gene --&gt; Alleles " comment="">
WormMine/support/templates/old/templates_superuser.txt:<template name="gene_to_alleles" title="Gene --&gt; Alleles" comment="">
WormMine/support/templates/old/templates.txt: <template name="gene_to_alleles" title="Gene --&gt; 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 <[hidden email]> 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
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev



_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Interesting problem

sergio contrino-2
hi paulo,
from what i understand you seem to be defining twice (and with different
names) the allele/gene relationship, i suppose one comes from
wormbase-acedb_additions.xml
can you try to 'unify' the relationship (i suppose you need to change it
in one place to the more accurate one (1 to 1 or 1 to many rel).
if still problematic,can you point to a repo on github so we can have a
look?
thanks and have a nice weekend
sergio


On 31/01/2020 15:52, Paulo Nuin wrote:

> 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 <[hidden email]
>> <mailto:[hidden email]>> 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 --&gt; Alleles " comment="">
>>> WormMine/support/templates/original_su_templates:<template
>>> name="gene_to_alleles_old" title="Gene --&gt; Alleles old" comment="">
>>> WormMine/support/templates/staff_templates:<template
>>> name="gene_alleles" title="Gene --&gt; Alleles " comment="">
>>> WormMine/support/templates/old/templates_superuser.txt:<template
>>> name="gene_to_alleles" title="Gene --&gt; Alleles" comment="">
>>> WormMine/support/templates/old/templates.txt: <template
>>> name="gene_to_alleles" title="Gene --&gt; 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 <[hidden email]
>>>> <mailto:[hidden email]>> 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
>>>>> [hidden email]
>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>> _______________________________________________
>>>> dev mailing list
>>>> [hidden email] <mailto:[hidden email]>
>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
>

--
sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org
_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Interesting problem

Paulo Nuin
Hi Sergio

In fact we are defining once in our wormbase-acedb (I couldn’t find any other place where this is being defined, grep below) and we are having a double entry in the model with Allele and Alleles present. I found in the built model (genetic_model.xml) the same reverse reference set as a alleles instead the one I defined as allele.

We had problems defining the reverse references with plural as we ended up not having the relationship correctly set.

Our latest code is on


Our bio sources code hasn’t changed in while

Cheers

Paulo





im-dev1 :: ip-10-0-1-237 :: data2/4.0/wormmine-bio-sources ‹im-271*› % grep -r "reverse-reference=\"allele" *
wormbase-acedb/src/main/resources/wormbase-acedb_additions.xml:   <collection name="genes" referenced-type="Gene" reverse-reference="allele" />
wormbase-acedb/build/resources/main/wormbase-acedb_additions.xml:         <collection name="genes" referenced-type="Gene" reverse-reference="allele" />
wormbase-acedb/build/resources/main/genomic_model.xml:  <collection name="genes" referenced-type="Gene" reverse-reference="allele"/>
wormbase-acedb/misc/wormbase-acedb_additionsORIGINAL:     <collection name="genes" referenced-type="Gene" reverse-reference="allele" />
wormbase-acedb/misc/wormbase-acedb_additions1.85.xml:     <collection name="genes" referenced-type="Gene" reverse-reference="allele" />
wormbase-acedb/misc/wormbase-acedb_additionsWS271:        <collection name="genes" referenced-type="Gene" reverse-reference="allele" />


On Jan 31, 2020, at 10:13 AM, sergio contrino <[hidden email]> wrote:

hi paulo,
from what i understand you seem to be defining twice (and with different names) the allele/gene relationship, i suppose one comes from
wormbase-acedb_additions.xml
can you try to 'unify' the relationship (i suppose you need to change it in one place to the more accurate one (1 to 1 or 1 to many rel).
if still problematic,can you point to a repo on github so we can have a look?
thanks and have a nice weekend
sergio


On 31/01/2020 15:52, Paulo Nuin wrote:
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 <[hidden email] <[hidden email]>> 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 --&gt; Alleles " comment="">
WormMine/support/templates/original_su_templates:<template name="gene_to_alleles_old" title="Gene --&gt; Alleles old" comment="">
WormMine/support/templates/staff_templates:<template name="gene_alleles" title="Gene --&gt; Alleles " comment="">
WormMine/support/templates/old/templates_superuser.txt:<template name="gene_to_alleles" title="Gene --&gt; Alleles" comment="">
WormMine/support/templates/old/templates.txt: <template name="gene_to_alleles" title="Gene --&gt; 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 <[hidden email] <[hidden email]>> 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
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
_______________________________________________
dev mailing list
[hidden email] <[hidden email]>
https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev

-- 
sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org
_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev


_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Interesting problem

Paulo Nuin
Hi

Just to add more information on this, (I think I had this error before, and it’s the reason I changed the reference class from alleles to allele), if I change in the model I get this when trying to build the DB

        at org.gradle.internal.operations.DelegatingBuildOperationExecutor.run(DelegatingBuildOperationExecutor.java:31)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:120)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:99)
        ... 31 more
Caused by: java.lang.reflect.InvocationTargetException
        at org.intermine.plugin.ant.MergeSourceModelsTask.execute(MergeSourceModelsTask.java:131)
        ... 44 more
Caused by: Failed to parse model from input files
        at org.intermine.task.ModelMergerTask.execute(ModelMergerTask.java:85)
        ... 45 more
Caused by: org.intermine.metadata.MetaDataException: Exception while merging wormbase-acedb_additions.xml into /mnt/data2/4.0/WormMine/dbmodel/build/resources/main/genomic_model.xml
        at org.intermine.modelproduction.ModelFileMerger.mergeModelFromFiles(ModelFileMerger.java:70)
        at org.intermine.task.ModelMergerTask.execute(ModelMergerTask.java:80)
        ... 45 more
Caused by: org.intermine.modelproduction.ModelMergerException: mismatch between reverse reference field name: org.intermine.model.bio.Gene.alleles<-genes != org.intermine.model.bio.Gene.alleles<-gene
        at org.intermine.modelproduction.ModelMerger.mergeCollections(ModelMerger.java:366)
        at org.intermine.modelproduction.ModelMerger.mergeClass(ModelMerger.java:258)
        at org.intermine.modelproduction.ModelMerger.mergeModel(ModelMerger.java:76)
        at org.intermine.modelproduction.ModelFileMerger.processFile(ModelFileMerger.java:104)
        at org.intermine.modelproduction.ModelFileMerger.mergeModelFromFiles(ModelFileMerger.java:68)
        ... 46 more

And I am pretty sure I changed the classes and references accordingly.

Cheers

Paulo




On Feb 2, 2020, at 2:29 PM, Paulo Nuin <[hidden email]> wrote:

Hi Sergio

In fact we are defining once in our wormbase-acedb (I couldn’t find any other place where this is being defined, grep below) and we are having a double entry in the model with Allele and Alleles present. I found in the built model (genetic_model.xml) the same reverse reference set as a alleles instead the one I defined as allele.

We had problems defining the reverse references with plural as we ended up not having the relationship correctly set.

Our latest code is on


Our bio sources code hasn’t changed in while

Cheers

Paulo





im-dev1 :: ip-10-0-1-237 :: data2/4.0/wormmine-bio-sources ‹im-271*› % grep -r "reverse-reference=\"allele" *
wormbase-acedb/src/main/resources/wormbase-acedb_additions.xml:   <collection name="genes" referenced-type="Gene" reverse-reference="allele" />
wormbase-acedb/build/resources/main/wormbase-acedb_additions.xml:         <collection name="genes" referenced-type="Gene" reverse-reference="allele" />
wormbase-acedb/build/resources/main/genomic_model.xml:  <collection name="genes" referenced-type="Gene" reverse-reference="allele"/>
wormbase-acedb/misc/wormbase-acedb_additionsORIGINAL:     <collection name="genes" referenced-type="Gene" reverse-reference="allele" />
wormbase-acedb/misc/wormbase-acedb_additions1.85.xml:     <collection name="genes" referenced-type="Gene" reverse-reference="allele" />
wormbase-acedb/misc/wormbase-acedb_additionsWS271:        <collection name="genes" referenced-type="Gene" reverse-reference="allele" />


On Jan 31, 2020, at 10:13 AM, sergio contrino <[hidden email]> wrote:

hi paulo,
from what i understand you seem to be defining twice (and with different names) the allele/gene relationship, i suppose one comes from
wormbase-acedb_additions.xml
can you try to 'unify' the relationship (i suppose you need to change it in one place to the more accurate one (1 to 1 or 1 to many rel).
if still problematic,can you point to a repo on github so we can have a look?
thanks and have a nice weekend
sergio


On 31/01/2020 15:52, Paulo Nuin wrote:
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 <[hidden email] <[hidden email]>> 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 --&gt; Alleles " comment="">
WormMine/support/templates/original_su_templates:<template name="gene_to_alleles_old" title="Gene --&gt; Alleles old" comment="">
WormMine/support/templates/staff_templates:<template name="gene_alleles" title="Gene --&gt; Alleles " comment="">
WormMine/support/templates/old/templates_superuser.txt:<template name="gene_to_alleles" title="Gene --&gt; Alleles" comment="">
WormMine/support/templates/old/templates.txt: <template name="gene_to_alleles" title="Gene --&gt; 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 <[hidden email] <[hidden email]>> 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
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
_______________________________________________
dev mailing list
[hidden email] <[hidden email]>
https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev

-- 
sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org
_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev



_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Interesting problem

Paulo Nuin
Hi Sergio

Any news on this?

Thanks

Paulo



On Feb 3, 2020, at 10:18 AM, Paulo Nuin <[hidden email]> wrote:

Hi

Just to add more information on this, (I think I had this error before, and it’s the reason I changed the reference class from alleles to allele), if I change in the model I get this when trying to build the DB

        at org.gradle.internal.operations.DelegatingBuildOperationExecutor.run(DelegatingBuildOperationExecutor.java:31)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:120)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:99)
        ... 31 more
Caused by: java.lang.reflect.InvocationTargetException
        at org.intermine.plugin.ant.MergeSourceModelsTask.execute(MergeSourceModelsTask.java:131)
        ... 44 more
Caused by: Failed to parse model from input files
        at org.intermine.task.ModelMergerTask.execute(ModelMergerTask.java:85)
        ... 45 more
Caused by: org.intermine.metadata.MetaDataException: Exception while merging wormbase-acedb_additions.xml into /mnt/data2/4.0/WormMine/dbmodel/build/resources/main/genomic_model.xml
        at org.intermine.modelproduction.ModelFileMerger.mergeModelFromFiles(ModelFileMerger.java:70)
        at org.intermine.task.ModelMergerTask.execute(ModelMergerTask.java:80)
        ... 45 more
Caused by: org.intermine.modelproduction.ModelMergerException: mismatch between reverse reference field name: org.intermine.model.bio.Gene.alleles<-genes != org.intermine.model.bio.Gene.alleles<-gene
        at org.intermine.modelproduction.ModelMerger.mergeCollections(ModelMerger.java:366)
        at org.intermine.modelproduction.ModelMerger.mergeClass(ModelMerger.java:258)
        at org.intermine.modelproduction.ModelMerger.mergeModel(ModelMerger.java:76)
        at org.intermine.modelproduction.ModelFileMerger.processFile(ModelFileMerger.java:104)
        at org.intermine.modelproduction.ModelFileMerger.mergeModelFromFiles(ModelFileMerger.java:68)
        ... 46 more

And I am pretty sure I changed the classes and references accordingly.

Cheers

Paulo




On Feb 2, 2020, at 2:29 PM, Paulo Nuin <[hidden email]> wrote:

Hi Sergio

In fact we are defining once in our wormbase-acedb (I couldn’t find any other place where this is being defined, grep below) and we are having a double entry in the model with Allele and Alleles present. I found in the built model (genetic_model.xml) the same reverse reference set as a alleles instead the one I defined as allele.

We had problems defining the reverse references with plural as we ended up not having the relationship correctly set.

Our latest code is on


Our bio sources code hasn’t changed in while

Cheers

Paulo





im-dev1 :: ip-10-0-1-237 :: data2/4.0/wormmine-bio-sources ‹im-271*› % grep -r "reverse-reference=\"allele" *
wormbase-acedb/src/main/resources/wormbase-acedb_additions.xml:   <collection name="genes" referenced-type="Gene" reverse-reference="allele" />
wormbase-acedb/build/resources/main/wormbase-acedb_additions.xml:         <collection name="genes" referenced-type="Gene" reverse-reference="allele" />
wormbase-acedb/build/resources/main/genomic_model.xml:  <collection name="genes" referenced-type="Gene" reverse-reference="allele"/>
wormbase-acedb/misc/wormbase-acedb_additionsORIGINAL:     <collection name="genes" referenced-type="Gene" reverse-reference="allele" />
wormbase-acedb/misc/wormbase-acedb_additions1.85.xml:     <collection name="genes" referenced-type="Gene" reverse-reference="allele" />
wormbase-acedb/misc/wormbase-acedb_additionsWS271:        <collection name="genes" referenced-type="Gene" reverse-reference="allele" />


On Jan 31, 2020, at 10:13 AM, sergio contrino <[hidden email]> wrote:

hi paulo,
from what i understand you seem to be defining twice (and with different names) the allele/gene relationship, i suppose one comes from
wormbase-acedb_additions.xml
can you try to 'unify' the relationship (i suppose you need to change it in one place to the more accurate one (1 to 1 or 1 to many rel).
if still problematic,can you point to a repo on github so we can have a look?
thanks and have a nice weekend
sergio


On 31/01/2020 15:52, Paulo Nuin wrote:
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 <[hidden email] <[hidden email]>> 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 --&gt; Alleles " comment="">
WormMine/support/templates/original_su_templates:<template name="gene_to_alleles_old" title="Gene --&gt; Alleles old" comment="">
WormMine/support/templates/staff_templates:<template name="gene_alleles" title="Gene --&gt; Alleles " comment="">
WormMine/support/templates/old/templates_superuser.txt:<template name="gene_to_alleles" title="Gene --&gt; Alleles" comment="">
WormMine/support/templates/old/templates.txt: <template name="gene_to_alleles" title="Gene --&gt; 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 <[hidden email] <[hidden email]>> 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
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
_______________________________________________
dev mailing list
[hidden email] <[hidden email]>
https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev

-- 
sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org
_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev




_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Interesting problem

sergio contrino-2
hi paulo,
sorry, i did not realised you were still having problems.
i'll check your checkout (probably tomorrow) and let you know.
thanks
sergio

On 07/02/2020 21:46, Paulo Nuin wrote:

> Hi Sergio
>
> Any news on this?
>
> Thanks
>
> Paulo
>
>
>
>> On Feb 3, 2020, at 10:18 AM, Paulo Nuin <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>> Hi
>>
>> Just to add more information on this, (I think I had this error
>> before, and it’s the reason I changed the reference class from alleles
>> to allele), if I change in the model I get this when trying to build
>> the DB
>>
>>         at
>> org.gradle.internal.operations.DelegatingBuildOperationExecutor.run(DelegatingBuildOperationExecutor.java:31)
>>         at
>> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:120)
>>         at
>> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:99)
>>         ... 31 more
>> Caused by: java.lang.reflect.InvocationTargetException
>>         at
>> org.intermine.plugin.ant.MergeSourceModelsTask.execute(MergeSourceModelsTask.java:131)
>>         ... 44 more
>> Caused by: Failed to parse model from input files
>>         at
>> org.intermine.task.ModelMergerTask.execute(ModelMergerTask.java:85)
>>         ... 45 more
>> Caused by: org.intermine.metadata.MetaDataException: Exception while
>> merging wormbase-acedb_additions.xml into
>> /mnt/data2/4.0/WormMine/dbmodel/build/resources/main/genomic_model.xml
>>         at
>> org.intermine.modelproduction.ModelFileMerger.mergeModelFromFiles(ModelFileMerger.java:70)
>>         at
>> org.intermine.task.ModelMergerTask.execute(ModelMergerTask.java:80)
>>         ... 45 more
>> Caused by: org.intermine.modelproduction.ModelMergerException:
>> mismatch between reverse reference field name:
>> org.intermine.model.bio.Gene.alleles<-genes !=
>> org.intermine.model.bio.Gene.alleles<-gene
>>         at
>> org.intermine.modelproduction.ModelMerger.mergeCollections(ModelMerger.java:366)
>>         at
>> org.intermine.modelproduction.ModelMerger.mergeClass(ModelMerger.java:258)
>>         at
>> org.intermine.modelproduction.ModelMerger.mergeModel(ModelMerger.java:76)
>>         at
>> org.intermine.modelproduction.ModelFileMerger.processFile(ModelFileMerger.java:104)
>>         at
>> org.intermine.modelproduction.ModelFileMerger.mergeModelFromFiles(ModelFileMerger.java:68)
>>         ... 46 more
>>
>> And I am pretty sure I changed the classes and references accordingly.
>>
>> Cheers
>>
>> Paulo
>>
>>
>>
>>
>>> On Feb 2, 2020, at 2:29 PM, Paulo Nuin <[hidden email]
>>> <mailto:[hidden email]>> wrote:
>>>
>>> Hi Sergio
>>>
>>> In fact we are defining once in our wormbase-acedb (I couldn’t find
>>> any other place where this is being defined, grep below) and we are
>>> having a double entry in the model with Allele and Alleles present. I
>>> found in the built model (genetic_model.xml) the same reverse
>>> reference set as a alleles instead the one I defined as allele.
>>>
>>> We had problems defining the reverse references with plural as we
>>> ended up not having the relationship correctly set.
>>>
>>> Our latest code is on
>>>
>>> https://github.com/WormBase/WormMine/tree/im-275
>>> https://github.com/WormBase/wormmine-bio-sources.git
>>>
>>> Our bio sources code hasn’t changed in while
>>>
>>> Cheers
>>>
>>> Paulo
>>>
>>>
>>>
>>>
>>>
>>> im-dev1 :: ip-10-0-1-237 :: data2/4.0/wormmine-bio-sources ‹im-271*›
>>> % grep -r "reverse-reference=\"allele" *
>>> wormbase-acedb/src/main/resources/wormbase-acedb_additions.xml:  
>>> <collection name="genes" referenced-type="Gene"
>>> reverse-reference="allele" />
>>> wormbase-acedb/build/resources/main/wormbase-acedb_additions.xml:    
>>>     <collection name="genes" referenced-type="Gene"
>>> reverse-reference="allele" />
>>> wormbase-acedb/build/resources/main/genomic_model.xml:  <collection
>>> name="genes" referenced-type="Gene" reverse-reference="allele"/>
>>> wormbase-acedb/misc/wormbase-acedb_additionsORIGINAL:     <collection
>>> name="genes" referenced-type="Gene" reverse-reference="allele" />
>>> wormbase-acedb/misc/wormbase-acedb_additions1.85.xml:     <collection
>>> name="genes" referenced-type="Gene" reverse-reference="allele" />
>>> wormbase-acedb/misc/wormbase-acedb_additionsWS271:        <collection
>>> name="genes" referenced-type="Gene" reverse-reference="allele" />
>>>
>>>
>>>> On Jan 31, 2020, at 10:13 AM, sergio contrino
>>>> <[hidden email] <mailto:[hidden email]>> wrote:
>>>>
>>>> hi paulo,
>>>> from what i understand you seem to be defining twice (and with
>>>> different names) the allele/gene relationship, i suppose one comes from
>>>> wormbase-acedb_additions.xml
>>>> can you try to 'unify' the relationship (i suppose you need to
>>>> change it in one place to the more accurate one (1 to 1 or 1 to many
>>>> rel).
>>>> if still problematic,can you point to a repo on github so we can
>>>> have a look?
>>>> thanks and have a nice weekend
>>>> sergio
>>>>
>>>>
>>>> On 31/01/2020 15:52, Paulo Nuin wrote:
>>>>> 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 <[hidden email]
>>>>>> <mailto:[hidden email]><mailto:[hidden email]>> 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 --&gt; Alleles " comment="">
>>>>>>> WormMine/support/templates/original_su_templates:<template
>>>>>>> name="gene_to_alleles_old" title="Gene --&gt; Alleles old"
>>>>>>> comment="">
>>>>>>> WormMine/support/templates/staff_templates:<template
>>>>>>> name="gene_alleles" title="Gene --&gt; Alleles " comment="">
>>>>>>> WormMine/support/templates/old/templates_superuser.txt:<template
>>>>>>> name="gene_to_alleles" title="Gene --&gt; Alleles" comment="">
>>>>>>> WormMine/support/templates/old/templates.txt: <template
>>>>>>> name="gene_to_alleles" title="Gene --&gt; 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
>>>>>>>> <[hidden email]
>>>>>>>> <mailto:[hidden email]><mailto:[hidden email]>> 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
>>>>>>>>> [hidden email] <mailto:[hidden email]>
>>>>>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>>>>> _______________________________________________
>>>>>>>> dev mailing list
>>>>>>>> [hidden email]
>>>>>>>> <mailto:[hidden email]><mailto:[hidden email]>
>>>>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>>>>
>>>>> _______________________________________________
>>>>> dev mailing list
>>>>> [hidden email] <mailto:[hidden email]>
>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>
>>>> --
>>>> sergio contrino                  InterMine, University of Cambridge
>>>> https://sergiocontrino.github.io 
>>>> <https://sergiocontrino.github.io/>http://www.intermine.org 
>>>> <http://www.intermine.org/>
>>>> _______________________________________________
>>>> dev mailing list
>>>> [hidden email] <mailto:[hidden email]>
>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>
>>
>

--
sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org
_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Interesting problem

Paulo Nuin
Hi

Yes, we are still seeing Allele/Alleles in the model and on the web interface. If I use the plural I get the error.

Cheers

Paulo



> On Feb 10, 2020, at 8:20 AM, sergio contrino <[hidden email]> wrote:
>
> hi paulo,
> sorry, i did not realised you were still having problems.
> i'll check your checkout (probably tomorrow) and let you know.
> thanks
> sergio
>
> On 07/02/2020 21:46, Paulo Nuin wrote:
>> Hi Sergio
>> Any news on this?
>> Thanks
>> Paulo
>>> On Feb 3, 2020, at 10:18 AM, Paulo Nuin <[hidden email] <mailto:[hidden email]>> wrote:
>>>
>>> Hi
>>>
>>> Just to add more information on this, (I think I had this error before, and it’s the reason I changed the reference class from alleles to allele), if I change in the model I get this when trying to build the DB
>>>
>>>         at org.gradle.internal.operations.DelegatingBuildOperationExecutor.run(DelegatingBuildOperationExecutor.java:31)
>>>         at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:120)
>>>         at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:99)
>>>         ... 31 more
>>> Caused by: java.lang.reflect.InvocationTargetException
>>>         at org.intermine.plugin.ant.MergeSourceModelsTask.execute(MergeSourceModelsTask.java:131)
>>>         ... 44 more
>>> Caused by: Failed to parse model from input files
>>>         at org.intermine.task.ModelMergerTask.execute(ModelMergerTask.java:85)
>>>         ... 45 more
>>> Caused by: org.intermine.metadata.MetaDataException: Exception while merging wormbase-acedb_additions.xml into /mnt/data2/4.0/WormMine/dbmodel/build/resources/main/genomic_model.xml
>>>         at org.intermine.modelproduction.ModelFileMerger.mergeModelFromFiles(ModelFileMerger.java:70)
>>>         at org.intermine.task.ModelMergerTask.execute(ModelMergerTask.java:80)
>>>         ... 45 more
>>> Caused by: org.intermine.modelproduction.ModelMergerException: mismatch between reverse reference field name: org.intermine.model.bio.Gene.alleles<-genes != org.intermine.model.bio.Gene.alleles<-gene
>>>         at org.intermine.modelproduction.ModelMerger.mergeCollections(ModelMerger.java:366)
>>>         at org.intermine.modelproduction.ModelMerger.mergeClass(ModelMerger.java:258)
>>>         at org.intermine.modelproduction.ModelMerger.mergeModel(ModelMerger.java:76)
>>>         at org.intermine.modelproduction.ModelFileMerger.processFile(ModelFileMerger.java:104)
>>>         at org.intermine.modelproduction.ModelFileMerger.mergeModelFromFiles(ModelFileMerger.java:68)
>>>         ... 46 more
>>>
>>> And I am pretty sure I changed the classes and references accordingly.
>>>
>>> Cheers
>>>
>>> Paulo
>>>
>>>
>>>
>>>
>>>> On Feb 2, 2020, at 2:29 PM, Paulo Nuin <[hidden email] <mailto:[hidden email]>> wrote:
>>>>
>>>> Hi Sergio
>>>>
>>>> In fact we are defining once in our wormbase-acedb (I couldn’t find any other place where this is being defined, grep below) and we are having a double entry in the model with Allele and Alleles present. I found in the built model (genetic_model.xml) the same reverse reference set as a alleles instead the one I defined as allele.
>>>>
>>>> We had problems defining the reverse references with plural as we ended up not having the relationship correctly set.
>>>>
>>>> Our latest code is on
>>>>
>>>> https://github.com/WormBase/WormMine/tree/im-275
>>>> https://github.com/WormBase/wormmine-bio-sources.git
>>>>
>>>> Our bio sources code hasn’t changed in while
>>>>
>>>> Cheers
>>>>
>>>> Paulo
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> im-dev1 :: ip-10-0-1-237 :: data2/4.0/wormmine-bio-sources ‹im-271*› % grep -r "reverse-reference=\"allele" *
>>>> wormbase-acedb/src/main/resources/wormbase-acedb_additions.xml:   <collection name="genes" referenced-type="Gene" reverse-reference="allele" />
>>>> wormbase-acedb/build/resources/main/wormbase-acedb_additions.xml:         <collection name="genes" referenced-type="Gene" reverse-reference="allele" />
>>>> wormbase-acedb/build/resources/main/genomic_model.xml:  <collection name="genes" referenced-type="Gene" reverse-reference="allele"/>
>>>> wormbase-acedb/misc/wormbase-acedb_additionsORIGINAL:     <collection name="genes" referenced-type="Gene" reverse-reference="allele" />
>>>> wormbase-acedb/misc/wormbase-acedb_additions1.85.xml:     <collection name="genes" referenced-type="Gene" reverse-reference="allele" />
>>>> wormbase-acedb/misc/wormbase-acedb_additionsWS271:        <collection name="genes" referenced-type="Gene" reverse-reference="allele" />
>>>>
>>>>
>>>>> On Jan 31, 2020, at 10:13 AM, sergio contrino <[hidden email] <mailto:[hidden email]>> wrote:
>>>>>
>>>>> hi paulo,
>>>>> from what i understand you seem to be defining twice (and with different names) the allele/gene relationship, i suppose one comes from
>>>>> wormbase-acedb_additions.xml
>>>>> can you try to 'unify' the relationship (i suppose you need to change it in one place to the more accurate one (1 to 1 or 1 to many rel).
>>>>> if still problematic,can you point to a repo on github so we can have a look?
>>>>> thanks and have a nice weekend
>>>>> sergio
>>>>>
>>>>>
>>>>> On 31/01/2020 15:52, Paulo Nuin wrote:
>>>>>> 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 <[hidden email] <mailto:[hidden email]><mailto:[hidden email]>> 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 --&gt; Alleles " comment="">
>>>>>>>> WormMine/support/templates/original_su_templates:<template name="gene_to_alleles_old" title="Gene --&gt; Alleles old" comment="">
>>>>>>>> WormMine/support/templates/staff_templates:<template name="gene_alleles" title="Gene --&gt; Alleles " comment="">
>>>>>>>> WormMine/support/templates/old/templates_superuser.txt:<template name="gene_to_alleles" title="Gene --&gt; Alleles" comment="">
>>>>>>>> WormMine/support/templates/old/templates.txt: <template name="gene_to_alleles" title="Gene --&gt; 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 <[hidden email] <mailto:[hidden email]><mailto:[hidden email]>> 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
>>>>>>>>>> [hidden email] <mailto:[hidden email]>
>>>>>>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>>>>>> _______________________________________________
>>>>>>>>> dev mailing list
>>>>>>>>> [hidden email] <mailto:[hidden email]><mailto:[hidden email]>
>>>>>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>>>>>
>>>>>> _______________________________________________
>>>>>> dev mailing list
>>>>>> [hidden email] <mailto:[hidden email]>
>>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>>
>>>>> --
>>>>> sergio contrino                  InterMine, University of Cambridge
>>>>> https://sergiocontrino.github.io <https://sergiocontrino.github.io/>http://www.intermine.org <http://www.intermine.org/>
>>>>> _______________________________________________
>>>>> dev mailing list
>>>>> [hidden email] <mailto:[hidden email]>
>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>
>>>
>
> --
> sergio contrino                  InterMine, University of Cambridge
> https://sergiocontrino.github.io           http://www.intermine.org

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Interesting problem

Paulo Nuin
Hi

Any news on this? I either would like to know if there’s an error on our end or how we can solved this. We also see this on BlueGenes.

Thanks

Paulo



> On Feb 10, 2020, at 8:26 AM, Paulo Nuin <[hidden email]> wrote:
>
> Hi
>
> Yes, we are still seeing Allele/Alleles in the model and on the web interface. If I use the plural I get the error.
>
> Cheers
>
> Paulo
>
>
>
>> On Feb 10, 2020, at 8:20 AM, sergio contrino <[hidden email]> wrote:
>>
>> hi paulo,
>> sorry, i did not realised you were still having problems.
>> i'll check your checkout (probably tomorrow) and let you know.
>> thanks
>> sergio
>>
>> On 07/02/2020 21:46, Paulo Nuin wrote:
>>> Hi Sergio
>>> Any news on this?
>>> Thanks
>>> Paulo
>>>> On Feb 3, 2020, at 10:18 AM, Paulo Nuin <[hidden email] <mailto:[hidden email]>> wrote:
>>>>
>>>> Hi
>>>>
>>>> Just to add more information on this, (I think I had this error before, and it’s the reason I changed the reference class from alleles to allele), if I change in the model I get this when trying to build the DB
>>>>
>>>>        at org.gradle.internal.operations.DelegatingBuildOperationExecutor.run(DelegatingBuildOperationExecutor.java:31)
>>>>        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:120)
>>>>        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:99)
>>>>        ... 31 more
>>>> Caused by: java.lang.reflect.InvocationTargetException
>>>>        at org.intermine.plugin.ant.MergeSourceModelsTask.execute(MergeSourceModelsTask.java:131)
>>>>        ... 44 more
>>>> Caused by: Failed to parse model from input files
>>>>        at org.intermine.task.ModelMergerTask.execute(ModelMergerTask.java:85)
>>>>        ... 45 more
>>>> Caused by: org.intermine.metadata.MetaDataException: Exception while merging wormbase-acedb_additions.xml into /mnt/data2/4.0/WormMine/dbmodel/build/resources/main/genomic_model.xml
>>>>        at org.intermine.modelproduction.ModelFileMerger.mergeModelFromFiles(ModelFileMerger.java:70)
>>>>        at org.intermine.task.ModelMergerTask.execute(ModelMergerTask.java:80)
>>>>        ... 45 more
>>>> Caused by: org.intermine.modelproduction.ModelMergerException: mismatch between reverse reference field name: org.intermine.model.bio.Gene.alleles<-genes != org.intermine.model.bio.Gene.alleles<-gene
>>>>        at org.intermine.modelproduction.ModelMerger.mergeCollections(ModelMerger.java:366)
>>>>        at org.intermine.modelproduction.ModelMerger.mergeClass(ModelMerger.java:258)
>>>>        at org.intermine.modelproduction.ModelMerger.mergeModel(ModelMerger.java:76)
>>>>        at org.intermine.modelproduction.ModelFileMerger.processFile(ModelFileMerger.java:104)
>>>>        at org.intermine.modelproduction.ModelFileMerger.mergeModelFromFiles(ModelFileMerger.java:68)
>>>>        ... 46 more
>>>>
>>>> And I am pretty sure I changed the classes and references accordingly.
>>>>
>>>> Cheers
>>>>
>>>> Paulo
>>>>
>>>>
>>>>
>>>>
>>>>> On Feb 2, 2020, at 2:29 PM, Paulo Nuin <[hidden email] <mailto:[hidden email]>> wrote:
>>>>>
>>>>> Hi Sergio
>>>>>
>>>>> In fact we are defining once in our wormbase-acedb (I couldn’t find any other place where this is being defined, grep below) and we are having a double entry in the model with Allele and Alleles present. I found in the built model (genetic_model.xml) the same reverse reference set as a alleles instead the one I defined as allele.
>>>>>
>>>>> We had problems defining the reverse references with plural as we ended up not having the relationship correctly set.
>>>>>
>>>>> Our latest code is on
>>>>>
>>>>> https://github.com/WormBase/WormMine/tree/im-275
>>>>> https://github.com/WormBase/wormmine-bio-sources.git
>>>>>
>>>>> Our bio sources code hasn’t changed in while
>>>>>
>>>>> Cheers
>>>>>
>>>>> Paulo
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> im-dev1 :: ip-10-0-1-237 :: data2/4.0/wormmine-bio-sources ‹im-271*› % grep -r "reverse-reference=\"allele" *
>>>>> wormbase-acedb/src/main/resources/wormbase-acedb_additions.xml:   <collection name="genes" referenced-type="Gene" reverse-reference="allele" />
>>>>> wormbase-acedb/build/resources/main/wormbase-acedb_additions.xml:         <collection name="genes" referenced-type="Gene" reverse-reference="allele" />
>>>>> wormbase-acedb/build/resources/main/genomic_model.xml:  <collection name="genes" referenced-type="Gene" reverse-reference="allele"/>
>>>>> wormbase-acedb/misc/wormbase-acedb_additionsORIGINAL:     <collection name="genes" referenced-type="Gene" reverse-reference="allele" />
>>>>> wormbase-acedb/misc/wormbase-acedb_additions1.85.xml:     <collection name="genes" referenced-type="Gene" reverse-reference="allele" />
>>>>> wormbase-acedb/misc/wormbase-acedb_additionsWS271:        <collection name="genes" referenced-type="Gene" reverse-reference="allele" />
>>>>>
>>>>>
>>>>>> On Jan 31, 2020, at 10:13 AM, sergio contrino <[hidden email] <mailto:[hidden email]>> wrote:
>>>>>>
>>>>>> hi paulo,
>>>>>> from what i understand you seem to be defining twice (and with different names) the allele/gene relationship, i suppose one comes from
>>>>>> wormbase-acedb_additions.xml
>>>>>> can you try to 'unify' the relationship (i suppose you need to change it in one place to the more accurate one (1 to 1 or 1 to many rel).
>>>>>> if still problematic,can you point to a repo on github so we can have a look?
>>>>>> thanks and have a nice weekend
>>>>>> sergio
>>>>>>
>>>>>>
>>>>>> On 31/01/2020 15:52, Paulo Nuin wrote:
>>>>>>> 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 <[hidden email] <mailto:[hidden email]><mailto:[hidden email]>> 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 --&gt; Alleles " comment="">
>>>>>>>>> WormMine/support/templates/original_su_templates:<template name="gene_to_alleles_old" title="Gene --&gt; Alleles old" comment="">
>>>>>>>>> WormMine/support/templates/staff_templates:<template name="gene_alleles" title="Gene --&gt; Alleles " comment="">
>>>>>>>>> WormMine/support/templates/old/templates_superuser.txt:<template name="gene_to_alleles" title="Gene --&gt; Alleles" comment="">
>>>>>>>>> WormMine/support/templates/old/templates.txt: <template name="gene_to_alleles" title="Gene --&gt; 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 <[hidden email] <mailto:[hidden email]><mailto:[hidden email]>> 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
>>>>>>>>>>> [hidden email] <mailto:[hidden email]>
>>>>>>>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>>>>>>> _______________________________________________
>>>>>>>>>> dev mailing list
>>>>>>>>>> [hidden email] <mailto:[hidden email]><mailto:[hidden email]>
>>>>>>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> dev mailing list
>>>>>>> [hidden email] <mailto:[hidden email]>
>>>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>>>
>>>>>> --
>>>>>> sergio contrino                  InterMine, University of Cambridge
>>>>>> https://sergiocontrino.github.io <https://sergiocontrino.github.io/>http://www.intermine.org <http://www.intermine.org/>
>>>>>> _______________________________________________
>>>>>> dev mailing list
>>>>>> [hidden email] <mailto:[hidden email]>
>>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>>
>>>>
>>
>> --
>> sergio contrino                  InterMine, University of Cambridge
>> https://sergiocontrino.github.io           http://www.intermine.org
>

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Interesting problem

sergio contrino-2
hi paulo,
from what i see from your branch im-275, allele is defined as a so
entity as a class with reference to gene, which has a reverse reference
to a collection of alleles.
if you want something different, i think you have to suppress the
original so definition. to do so, i think you need to remove the allele
entry from the dbmodel/resources/so_terms file
i hope this helps
sergio

On 13/02/2020 13:40, Paulo Nuin wrote:

> Hi
>
> Any news on this? I either would like to know if there’s an error on our end or how we can solved this. We also see this on BlueGenes.
>
> Thanks
>
> Paulo
>
>
>
>> On Feb 10, 2020, at 8:26 AM, Paulo Nuin <[hidden email]> wrote:
>>
>> Hi
>>
>> Yes, we are still seeing Allele/Alleles in the model and on the web interface. If I use the plural I get the error.
>>
>> Cheers
>>
>> Paulo
>>
>>
>>
>>> On Feb 10, 2020, at 8:20 AM, sergio contrino <[hidden email]> wrote:
>>>
>>> hi paulo,
>>> sorry, i did not realised you were still having problems.
>>> i'll check your checkout (probably tomorrow) and let you know.
>>> thanks
>>> sergio
>>>
>>> On 07/02/2020 21:46, Paulo Nuin wrote:
>>>> Hi Sergio
>>>> Any news on this?
>>>> Thanks
>>>> Paulo
>>>>> On Feb 3, 2020, at 10:18 AM, Paulo Nuin <[hidden email] <mailto:[hidden email]>> wrote:
>>>>>
>>>>> Hi
>>>>>
>>>>> Just to add more information on this, (I think I had this error before, and it’s the reason I changed the reference class from alleles to allele), if I change in the model I get this when trying to build the DB
>>>>>
>>>>>         at org.gradle.internal.operations.DelegatingBuildOperationExecutor.run(DelegatingBuildOperationExecutor.java:31)
>>>>>         at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:120)
>>>>>         at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:99)
>>>>>         ... 31 more
>>>>> Caused by: java.lang.reflect.InvocationTargetException
>>>>>         at org.intermine.plugin.ant.MergeSourceModelsTask.execute(MergeSourceModelsTask.java:131)
>>>>>         ... 44 more
>>>>> Caused by: Failed to parse model from input files
>>>>>         at org.intermine.task.ModelMergerTask.execute(ModelMergerTask.java:85)
>>>>>         ... 45 more
>>>>> Caused by: org.intermine.metadata.MetaDataException: Exception while merging wormbase-acedb_additions.xml into /mnt/data2/4.0/WormMine/dbmodel/build/resources/main/genomic_model.xml
>>>>>         at org.intermine.modelproduction.ModelFileMerger.mergeModelFromFiles(ModelFileMerger.java:70)
>>>>>         at org.intermine.task.ModelMergerTask.execute(ModelMergerTask.java:80)
>>>>>         ... 45 more
>>>>> Caused by: org.intermine.modelproduction.ModelMergerException: mismatch between reverse reference field name: org.intermine.model.bio.Gene.alleles<-genes != org.intermine.model.bio.Gene.alleles<-gene
>>>>>         at org.intermine.modelproduction.ModelMerger.mergeCollections(ModelMerger.java:366)
>>>>>         at org.intermine.modelproduction.ModelMerger.mergeClass(ModelMerger.java:258)
>>>>>         at org.intermine.modelproduction.ModelMerger.mergeModel(ModelMerger.java:76)
>>>>>         at org.intermine.modelproduction.ModelFileMerger.processFile(ModelFileMerger.java:104)
>>>>>         at org.intermine.modelproduction.ModelFileMerger.mergeModelFromFiles(ModelFileMerger.java:68)
>>>>>         ... 46 more
>>>>>
>>>>> And I am pretty sure I changed the classes and references accordingly.
>>>>>
>>>>> Cheers
>>>>>
>>>>> Paulo
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> On Feb 2, 2020, at 2:29 PM, Paulo Nuin <[hidden email] <mailto:[hidden email]>> wrote:
>>>>>>
>>>>>> Hi Sergio
>>>>>>
>>>>>> In fact we are defining once in our wormbase-acedb (I couldn’t find any other place where this is being defined, grep below) and we are having a double entry in the model with Allele and Alleles present. I found in the built model (genetic_model.xml) the same reverse reference set as a alleles instead the one I defined as allele.
>>>>>>
>>>>>> We had problems defining the reverse references with plural as we ended up not having the relationship correctly set.
>>>>>>
>>>>>> Our latest code is on
>>>>>>
>>>>>> https://github.com/WormBase/WormMine/tree/im-275
>>>>>> https://github.com/WormBase/wormmine-bio-sources.git
>>>>>>
>>>>>> Our bio sources code hasn’t changed in while
>>>>>>
>>>>>> Cheers
>>>>>>
>>>>>> Paulo
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> im-dev1 :: ip-10-0-1-237 :: data2/4.0/wormmine-bio-sources ‹im-271*› % grep -r "reverse-reference=\"allele" *
>>>>>> wormbase-acedb/src/main/resources/wormbase-acedb_additions.xml:   <collection name="genes" referenced-type="Gene" reverse-reference="allele" />
>>>>>> wormbase-acedb/build/resources/main/wormbase-acedb_additions.xml:         <collection name="genes" referenced-type="Gene" reverse-reference="allele" />
>>>>>> wormbase-acedb/build/resources/main/genomic_model.xml:  <collection name="genes" referenced-type="Gene" reverse-reference="allele"/>
>>>>>> wormbase-acedb/misc/wormbase-acedb_additionsORIGINAL:     <collection name="genes" referenced-type="Gene" reverse-reference="allele" />
>>>>>> wormbase-acedb/misc/wormbase-acedb_additions1.85.xml:     <collection name="genes" referenced-type="Gene" reverse-reference="allele" />
>>>>>> wormbase-acedb/misc/wormbase-acedb_additionsWS271:        <collection name="genes" referenced-type="Gene" reverse-reference="allele" />
>>>>>>
>>>>>>
>>>>>>> On Jan 31, 2020, at 10:13 AM, sergio contrino <[hidden email] <mailto:[hidden email]>> wrote:
>>>>>>>
>>>>>>> hi paulo,
>>>>>>> from what i understand you seem to be defining twice (and with different names) the allele/gene relationship, i suppose one comes from
>>>>>>> wormbase-acedb_additions.xml
>>>>>>> can you try to 'unify' the relationship (i suppose you need to change it in one place to the more accurate one (1 to 1 or 1 to many rel).
>>>>>>> if still problematic,can you point to a repo on github so we can have a look?
>>>>>>> thanks and have a nice weekend
>>>>>>> sergio
>>>>>>>
>>>>>>>
>>>>>>> On 31/01/2020 15:52, Paulo Nuin wrote:
>>>>>>>> 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 <[hidden email] <mailto:[hidden email]><mailto:[hidden email]>> 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 --&gt; Alleles " comment="">
>>>>>>>>>> WormMine/support/templates/original_su_templates:<template name="gene_to_alleles_old" title="Gene --&gt; Alleles old" comment="">
>>>>>>>>>> WormMine/support/templates/staff_templates:<template name="gene_alleles" title="Gene --&gt; Alleles " comment="">
>>>>>>>>>> WormMine/support/templates/old/templates_superuser.txt:<template name="gene_to_alleles" title="Gene --&gt; Alleles" comment="">
>>>>>>>>>> WormMine/support/templates/old/templates.txt: <template name="gene_to_alleles" title="Gene --&gt; 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 <[hidden email] <mailto:[hidden email]><mailto:[hidden email]>> 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
>>>>>>>>>>>> [hidden email] <mailto:[hidden email]>
>>>>>>>>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> dev mailing list
>>>>>>>>>>> [hidden email] <mailto:[hidden email]><mailto:[hidden email]>
>>>>>>>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> dev mailing list
>>>>>>>> [hidden email] <mailto:[hidden email]>
>>>>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>>>>
>>>>>>> --
>>>>>>> sergio contrino                  InterMine, University of Cambridge
>>>>>>> https://sergiocontrino.github.io <https://sergiocontrino.github.io/>http://www.intermine.org <http://www.intermine.org/>
>>>>>>> _______________________________________________
>>>>>>> dev mailing list
>>>>>>> [hidden email] <mailto:[hidden email]>
>>>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>>>
>>>>>
>>>
>>> --
>>> sergio contrino                  InterMine, University of Cambridge
>>> https://sergiocontrino.github.io           http://www.intermine.org
>>
>

--
sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org
_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev