Question

[Paulo Nuin]

Hi everyone

Can someone explain how do I get an error like this:


Caused by: org.intermine.metadata.MetaDataException: Exception while merging /mnt/data2/intermine/bio/sources/wormbase-acedb/wormbase-acedb_additions.xml into /mnt/data2/intermine/wormmine/dbmodel/build/model/genomic_model.xml
        at org.intermine.modelproduction.ModelFileMerger.mergeModelFromFiles(ModelFileMerger.java:66)
        at org.intermine.task.ModelMergerTask.execute(ModelMergerTask.java:80)
        ... 21 more
Caused by: org.intermine.modelproduction.ModelMergerException: There were problems merging the model: [Reverse reference names do not match: allele and alleles (org.intermine.model.bio.Gene: <collection name="alleles" referenced-type="Allele" reverse-reference="gene"/>, org.intermine.model.bio.Allele: <collection name="gene" referenced-type="Gene" reverse-reference="allele"/>)]


Both classes are below, and alleles collection is not set anywhere, only allele (without s). If I change gene to genes, things work fine.

Thanks

Paulo


        <class name="Gene" is-interface="true">
                <attribute name="operon" type="java.lang.String"/>
                <attribute name="biotype" type="java.lang.String"/>
                <reference name="referenceAllele" referenced-type="Allele" />
                <collection name="strains" referenced-type="Strain" reverse-reference="genes"/>
                <collection name="expressionPatterns" referenced-type="ExpressionPattern" reverse-reference="gene"/>
                <collection name="expressionClusters" referenced-type="ExpressionCluster" reverse-reference="genes"/>
                <collection name="regulatesExprCluster" referenced-type="ExpressionCluster" reverse-reference="regulatedByGene"/>
`            <collection name="affectedByAlleles" referenced-type="Allele" reverse-reference="affectsGenes" />
                <collection name="RNAiResult" referenced-type="RNAi" reverse-reference="inhibitsGene"/>
                <collection name="geneClass"  referenced-type="GeneClass" reverse-reference="genes"/>
                <collection name="formerGeneClass"  referenced-type="GeneClass" reverse-reference="formerGenes"/> -->
                <collection name="allele" referenced-type="Allele" reverse-reference="gene" />
        </class>


        <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="status" type="java.lang.String" />
          <attribute name="NemaGENETAGConsortiumAllele" 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="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="status" type="java.lang.String" />
          <attribute name="NemaGENETAGConsortiumAllele" 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="gene" referenced-type="Gene" reverse-reference="allele" />
        </class>

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[Sam Hokin-3]

I've had that happen a couple of times. One is when you've got your own installed code with a previous model version, but with the
same version number. That means clearing out ./gradle and ./m2 and doing a clean build. Another is if they've done a tweak in the
core model that stomps on your model. Finally there is always the version thing, which gets me all the time. I just had a conflict
because I had 3.1.1 in my gradle.properties but I'm on 3.1.2 now; so changing to 3.1.+ fixed that particular one.

I've also had this "ghost model entity" thing happen and I never figured it out, it just went away after a combination of the above.
You should be able to find it in your own mine or the core by doing a grep -R alleles, but that won't tell you where it came from or
how to fix it. Another thing I've done is completely delete the mine (I keep it stored on GitHub) and pull it from GitHub again and
start over. I don't store any of the build stuff on GitHub.

But rest assured others have hit this conundrum.

On 2/21/19 1:27 PM, Paulo Nuin wrote:

> Hi everyone
>
> Can someone explain how do I get an error like this:
>
>
> Caused by: org.intermine.metadata.MetaDataException: Exception while merging
> /mnt/data2/intermine/bio/sources/wormbase-acedb/wormbase-acedb_additions.xml into
> /mnt/data2/intermine/wormmine/dbmodel/build/model/genomic_model.xml at
> org.intermine.modelproduction.ModelFileMerger.mergeModelFromFiles(ModelFileMerger.java:66) at
> org.intermine.task.ModelMergerTask.execute(ModelMergerTask.java:80) ... 21 more Caused by:
> org.intermine.modelproduction.ModelMergerException: There were problems merging the model: [Reverse reference names do not match:
> allele and alleles (org.intermine.model.bio.Gene: <collection name="alleles" referenced-type="Allele" reverse-reference="gene"/>,
> org.intermine.model.bio.Allele: <collection name="gene" referenced-type="Gene" reverse-reference="allele"/>)]
>
>
> Both classes are below, and alleles collection is not set anywhere, only allele (without s). If I change gene to genes, things
> work fine.
>
> Thanks
>
> Paulo

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[Paulo Nuin]

Hi Sam

Thanks, quite helpful. I tried most things you mentioned, removed completely the contents of .gradle and .m2, new checkout, and still run into problems (I am using 2.+ still). If I set the collection to 

gene and allele or genes and alleles I get a wrong reference error

If I have

genes and allele or gene and alleles everything works fine, but I end with duplicate entries in the model (Allele and Alleles in the attached screen cap). 

Head-scratching.

Cheers

Paulo

On Feb 21, 2019, at 1:38 PM, Sam Hokin <[hidden email]> wrote:

I've had that happen a couple of times. One is when you've got your own installed code with a previous model version, but with the same version number. That means clearing out ./gradle and ./m2 and doing a clean build. Another is if they've done a tweak in the core model that stomps on your model. Finally there is always the version thing, which gets me all the time. I just had a conflict because I had 3.1.1 in my gradle.properties but I'm on 3.1.2 now; so changing to 3.1.+ fixed that particular one.

I've also had this "ghost model entity" thing happen and I never figured it out, it just went away after a combination of the above.
You should be able to find it in your own mine or the core by doing a grep -R alleles, but that won't tell you where it came from or
how to fix it. Another thing I've done is completely delete the mine (I keep it stored on GitHub) and pull it from GitHub again and start over. I don't store any of the build stuff on GitHub.

But rest assured others have hit this conundrum.

On 2/21/19 1:27 PM, Paulo Nuin wrote:

Hi everyone
Can someone explain how do I get an error like this:
Caused by: org.intermine.metadata.MetaDataException: Exception while merging
/mnt/data2/intermine/bio/sources/wormbase-acedb/wormbase-acedb_additions.xml into
/mnt/data2/intermine/wormmine/dbmodel/build/model/genomic_model.xml at
org.intermine.modelproduction.ModelFileMerger.mergeModelFromFiles(ModelFileMerger.java:66) at
org.intermine.task.ModelMergerTask.execute(ModelMergerTask.java:80) ... 21 more Caused by:
org.intermine.modelproduction.ModelMergerException: There were problems merging the model: [Reverse reference names do not match:
allele and alleles (org.intermine.model.bio.Gene: <collection name="alleles" referenced-type="Allele" reverse-reference="gene"/>,
org.intermine.model.bio.Allele: <collection name="gene" referenced-type="Gene" reverse-reference="allele"/>)]
Both classes are below, and alleles collection is not set anywhere, only allele (without s). If I change gene to genes, things
work fine.
Thanks
Paulo

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[Sam Hokin-3]

Hrm, I'm thinking the "allele" collection must be a misspelling buried in your mine's model, I only see "alleles" collections in the
core model, at least in 3.+:

[shokin@shokin-mines bio]$ grep -R "collection name=\"alleles\""
sources/chado-db/src/main/resources/chado-db-stock_additions.xml:    <collection name="alleles" referenced-type="Allele"
reverse-reference="stocks"/>
sources/chado-db/src/main/resources/chado-db_additions.xml:    <collection name="alleles" referenced-type="Allele"
reverse-reference="gene"/>
sources/chado-db/src/main/resources/flybase-chado-db_additions.xml:    <collection name="alleles" referenced-type="Allele"
reverse-reference="mutagens"/>
[shokin@shokin-mines bio]$ grep -R "collection name=\"allele\""
[shokin@shokin-mines bio]$

I think I'd do $ grep -R "collection name=\"allele\"" about everywhere I can think of.

On 2/21/19 2:48 PM, Paulo Nuin wrote:

> Hi Sam
>
> Thanks, quite helpful. I tried most things you mentioned, removed completely the contents of .gradle and .m2, new checkout, and
> still run into problems (I am using 2.+ still). If I set the collection to
>
> gene and allele or genes and alleles I get a wrong reference error
> If I have
>
> genes and allele or gene and alleles everything works fine, but I end with duplicate entries in the model (Allele and Alleles in the
> attached screen cap).
>
> Head-scratching.
>
> Cheers
> Paulo

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[Paulo Nuin]

Hi

I don’t find allele (with or without collection) anywhere in my code, even the one that compiled to 1.8. The strange things is that if gene and allele are singular or plural the building merge doesn’t work, but if only one is plural and the other singular it works fine.

If I also change the name allele to something else it also works fine. I am betting there’s some collision between names somewhere in the core code. Also strange is the duplicate class in the model.

Cheers
Paulo

> On Feb 21, 2019, at 3:22 PM, Sam Hokin <[hidden email]> wrote:
>
> Hrm, I'm thinking the "allele" collection must be a misspelling buried in your mine's model, I only see "alleles" collections in the core model, at least in 3.+:
>
> [shokin@shokin-mines bio]$ grep -R "collection name=\"alleles\""
> sources/chado-db/src/main/resources/chado-db-stock_additions.xml:    <collection name="alleles" referenced-type="Allele" reverse-reference="stocks"/>
> sources/chado-db/src/main/resources/chado-db_additions.xml:    <collection name="alleles" referenced-type="Allele" reverse-reference="gene"/>
> sources/chado-db/src/main/resources/flybase-chado-db_additions.xml:    <collection name="alleles" referenced-type="Allele" reverse-reference="mutagens"/>
> [shokin@shokin-mines bio]$ grep -R "collection name=\"allele\""
> [shokin@shokin-mines bio]$
>
> I think I'd do $ grep -R "collection name=\"allele\"" about everywhere I can think of.
>
> On 2/21/19 2:48 PM, Paulo Nuin wrote:
>> Hi Sam
>> Thanks, quite helpful. I tried most things you mentioned, removed completely the contents of .gradle and .m2, new checkout, and still run into problems (I am using 2.+ still). If I set the collection to
>> gene and allele or genes and alleles I get a wrong reference error
>> If I have
>> genes and allele or gene and alleles everything works fine, but I end with duplicate entries in the model (Allele and Alleles in the attached screen cap).
>> Head-scratching.
>> Cheers
>> Paulo

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[Paulo Nuin]

Hi again

I set the collections as

<collection name="alleles" referenced-type="Allele" reverse-reference="genes" />

And

<collection name="genes" referenced-type="Gene" reverse-reference="alleles" />

Cleaned everything, including .gradle and re-run the builddb step and got this error

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

And if I

grep -R alleles

dbmodel/build/so_additions.xml: <reference name="gene" referenced-type="Gene" reverse-reference="alleles"/>
dbmodel/build/so_additions.xml: <collection name="alleles" referenced-type="Allele" reverse-reference="gene”/>


The genes collection becomes gene.

No idea what is happening.

Cheers
Paulo

> On Feb 21, 2019, at 4:28 PM, Paulo Nuin <[hidden email]> wrote:
>
> Hi
>
> I don’t find allele (with or without collection) anywhere in my code, even the one that compiled to 1.8. The strange things is that if gene and allele are singular or plural the building merge doesn’t work, but if only one is plural and the other singular it works fine.
>
> If I also change the name allele to something else it also works fine. I am betting there’s some collision between names somewhere in the core code. Also strange is the duplicate class in the model.
>
> Cheers
> Paulo
>
>
>
>
>> On Feb 21, 2019, at 3:22 PM, Sam Hokin <[hidden email]> wrote:
>>
>> Hrm, I'm thinking the "allele" collection must be a misspelling buried in your mine's model, I only see "alleles" collections in the core model, at least in 3.+:
>>
>> [shokin@shokin-mines bio]$ grep -R "collection name=\"alleles\""
>> sources/chado-db/src/main/resources/chado-db-stock_additions.xml:    <collection name="alleles" referenced-type="Allele" reverse-reference="stocks"/>
>> sources/chado-db/src/main/resources/chado-db_additions.xml:    <collection name="alleles" referenced-type="Allele" reverse-reference="gene"/>
>> sources/chado-db/src/main/resources/flybase-chado-db_additions.xml:    <collection name="alleles" referenced-type="Allele" reverse-reference="mutagens"/>
>> [shokin@shokin-mines bio]$ grep -R "collection name=\"allele\""
>> [shokin@shokin-mines bio]$
>>
>> I think I'd do $ grep -R "collection name=\"allele\"" about everywhere I can think of.
>>
>> On 2/21/19 2:48 PM, Paulo Nuin wrote:
>>> Hi Sam
>>> Thanks, quite helpful. I tried most things you mentioned, removed completely the contents of .gradle and .m2, new checkout, and still run into problems (I am using 2.+ still). If I set the collection to
>>> gene and allele or genes and alleles I get a wrong reference error
>>> If I have
>>> genes and allele or gene and alleles everything works fine, but I end with duplicate entries in the model (Allele and Alleles in the attached screen cap).
>>> Head-scratching.
>>> Cheers
>>> Paulo
>

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[Sam Hokin-3]

Are you using chado? Because there is a _reference_ to "allele" in Gene in that source.

[shokin@shokin-mines bio]$ grep -R "reference name=\"gene\"" | grep allele
sources/chado-db/src/main/resources/chado-db_additions.xml:    <reference name="gene" referenced-type="Gene"
reverse-reference="alleles"/>

And that's what you're dealing with: a Gene.allele _reference_ conflicting with your Gene.alleles _collection_.

On 2/21/19 4:38 PM, Paulo Nuin wrote:

> Hi again
>
> I set the collections as
>
> <collection name="alleles" referenced-type="Allele" reverse-reference="genes" />
>
> And
>
> <collection name="genes" referenced-type="Gene" reverse-reference="alleles" />
>
> Cleaned everything, including .gradle and re-run the builddb step and got this error
>
> 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
>
> And if I
>
> grep -R alleles
>
> dbmodel/build/so_additions.xml: <reference name="gene" referenced-type="Gene" reverse-reference="alleles"/>
> dbmodel/build/so_additions.xml: <collection name="alleles" referenced-type="Allele" reverse-reference="gene”/>
>
>
> The genes collection becomes gene.
>
> No idea what is happening.
>
> Cheers
> Paulo
>
>
>
>> On Feb 21, 2019, at 4:28 PM, Paulo Nuin <[hidden email]> wrote:
>>
>> Hi
>>
>> I don’t find allele (with or without collection) anywhere in my code, even the one that compiled to 1.8. The strange things is that if gene and allele are singular or plural the building merge doesn’t work, but if only one is plural and the other singular it works fine.
>>
>> If I also change the name allele to something else it also works fine. I am betting there’s some collision between names somewhere in the core code. Also strange is the duplicate class in the model.
>>
>> Cheers
>> Paulo
>>
>>
>>
>>
>>> On Feb 21, 2019, at 3:22 PM, Sam Hokin <[hidden email]> wrote:
>>>
>>> Hrm, I'm thinking the "allele" collection must be a misspelling buried in your mine's model, I only see "alleles" collections in the core model, at least in 3.+:
>>>
>>> [shokin@shokin-mines bio]$ grep -R "collection name=\"alleles\""
>>> sources/chado-db/src/main/resources/chado-db-stock_additions.xml:    <collection name="alleles" referenced-type="Allele" reverse-reference="stocks"/>
>>> sources/chado-db/src/main/resources/chado-db_additions.xml:    <collection name="alleles" referenced-type="Allele" reverse-reference="gene"/>
>>> sources/chado-db/src/main/resources/flybase-chado-db_additions.xml:    <collection name="alleles" referenced-type="Allele" reverse-reference="mutagens"/>
>>> [shokin@shokin-mines bio]$ grep -R "collection name=\"allele\""
>>> [shokin@shokin-mines bio]$
>>>
>>> I think I'd do $ grep -R "collection name=\"allele\"" about everywhere I can think of.
>>>
>>> On 2/21/19 2:48 PM, Paulo Nuin wrote:
>>>> Hi Sam
>>>> Thanks, quite helpful. I tried most things you mentioned, removed completely the contents of .gradle and .m2, new checkout, and still run into problems (I am using 2.+ still). If I set the collection to
>>>> gene and allele or genes and alleles I get a wrong reference error
>>>> If I have
>>>> genes and allele or gene and alleles everything works fine, but I end with duplicate entries in the model (Allele and Alleles in the attached screen cap).
>>>> Head-scratching.
>>>> Cheers
>>>> Paulo
>>
>

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[Sam Hokin-3]

Sorry! Meant to say there is a _reference_ to "gene" in the Allele definition in that source. That Allele.gene _reference_ conflicts
with your Allele.genes _collection_.

On 2/21/19 4:48 PM, Sam Hokin wrote:

> Are you using chado? Because there is a _reference_ to "allele" in Gene in that source.
>
> [shokin@shokin-mines bio]$ grep -R "reference name=\"gene\"" | grep allele
> sources/chado-db/src/main/resources/chado-db_additions.xml:    <reference name="gene" referenced-type="Gene"
> reverse-reference="alleles"/>
>
> And that's what you're dealing with: a Gene.allele _reference_ conflicting with your Gene.alleles _collection_.
>
> On 2/21/19 4:38 PM, Paulo Nuin wrote:
>> Hi again
>>
>> I set the collections as
>>
>> <collection name="alleles" referenced-type="Allele" reverse-reference="genes" />
>>
>> And
>>
>> <collection name="genes" referenced-type="Gene" reverse-reference="alleles" />
>>
>> Cleaned everything, including .gradle and re-run the builddb step and got this error
>>
>> 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
>>
>> And if I
>>
>> grep -R alleles
>>
>> dbmodel/build/so_additions.xml: <reference name="gene" referenced-type="Gene" reverse-reference="alleles"/>
>> dbmodel/build/so_additions.xml: <collection name="alleles" referenced-type="Allele" reverse-reference="gene”/>
>>
>>
>> The genes collection becomes gene.
>>
>> No idea what is happening.
>>
>> Cheers
>> Paulo
>>
>>
>>
>>> On Feb 21, 2019, at 4:28 PM, Paulo Nuin <[hidden email]> wrote:
>>>
>>> Hi
>>>
>>> I don’t find allele (with or without collection) anywhere in my code, even the one that compiled to 1.8. The strange things is
>>> that if gene and allele are singular or plural the building merge doesn’t work, but if only one is plural and the other singular
>>> it works fine.
>>>
>>> If I also change the name allele to something else it also works fine. I am betting there’s some collision between names
>>> somewhere in the core code. Also strange is the duplicate class in the model.
>>>
>>> Cheers
>>> Paulo
>>>
>>>
>>>
>>>
>>>> On Feb 21, 2019, at 3:22 PM, Sam Hokin <[hidden email]> wrote:
>>>>
>>>> Hrm, I'm thinking the "allele" collection must be a misspelling buried in your mine's model, I only see "alleles" collections in
>>>> the core model, at least in 3.+:
>>>>
>>>> [shokin@shokin-mines bio]$ grep -R "collection name=\"alleles\""
>>>> sources/chado-db/src/main/resources/chado-db-stock_additions.xml:    <collection name="alleles" referenced-type="Allele"
>>>> reverse-reference="stocks"/>
>>>> sources/chado-db/src/main/resources/chado-db_additions.xml:    <collection name="alleles" referenced-type="Allele"
>>>> reverse-reference="gene"/>
>>>> sources/chado-db/src/main/resources/flybase-chado-db_additions.xml:    <collection name="alleles" referenced-type="Allele"
>>>> reverse-reference="mutagens"/>
>>>> [shokin@shokin-mines bio]$ grep -R "collection name=\"allele\""
>>>> [shokin@shokin-mines bio]$
>>>>
>>>> I think I'd do $ grep -R "collection name=\"allele\"" about everywhere I can think of.
>>>>
>>>> On 2/21/19 2:48 PM, Paulo Nuin wrote:
>>>>> Hi Sam
>>>>> Thanks, quite helpful. I tried most things you mentioned, removed completely the contents of .gradle and .m2, new checkout, and
>>>>> still run into problems (I am using 2.+ still). If I set the collection to
>>>>> gene and allele or genes and alleles I get a wrong reference error
>>>>> If I have
>>>>> genes and allele or gene and alleles everything works fine, but I end with duplicate entries in the model (Allele and Alleles
>>>>> in the attached screen cap).
>>>>> Head-scratching.
>>>>> Cheers
>>>>> Paulo
>>>
>>

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[Paulo Nuin]

I am using XMLs from AceDB. I will double check the source and see. From the start I thought it was some conflict due to the fact that it builds OK if I change the name.

Thanks

Paulo

> On Feb 21, 2019, at 4:50 PM, Sam Hokin <[hidden email]> wrote:
>
> Sorry! Meant to say there is a _reference_ to "gene" in the Allele definition in that source. That Allele.gene _reference_ conflicts with your Allele.genes _collection_.
>
> On 2/21/19 4:48 PM, Sam Hokin wrote:
>> Are you using chado? Because there is a _reference_ to "allele" in Gene in that source.
>> [shokin@shokin-mines bio]$ grep -R "reference name=\"gene\"" | grep allele
>> sources/chado-db/src/main/resources/chado-db_additions.xml:    <reference name="gene" referenced-type="Gene" reverse-reference="alleles"/>
>> And that's what you're dealing with: a Gene.allele _reference_ conflicting with your Gene.alleles _collection_.
>> On 2/21/19 4:38 PM, Paulo Nuin wrote:
>>> Hi again
>>>
>>> I set the collections as
>>>
>>> <collection name="alleles" referenced-type="Allele" reverse-reference="genes" />
>>>
>>> And
>>>
>>> <collection name="genes" referenced-type="Gene" reverse-reference="alleles" />
>>>
>>> Cleaned everything, including .gradle and re-run the builddb step and got this error
>>>
>>> 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
>>>
>>> And if I
>>>
>>> grep -R alleles
>>>
>>> dbmodel/build/so_additions.xml: <reference name="gene" referenced-type="Gene" reverse-reference="alleles"/>
>>> dbmodel/build/so_additions.xml: <collection name="alleles" referenced-type="Allele" reverse-reference="gene”/>
>>>
>>>
>>> The genes collection becomes gene.
>>>
>>> No idea what is happening.
>>>
>>> Cheers
>>> Paulo
>>>
>>>
>>>
>>>> On Feb 21, 2019, at 4:28 PM, Paulo Nuin <[hidden email]> wrote:
>>>>
>>>> Hi
>>>>
>>>> I don’t find allele (with or without collection) anywhere in my code, even the one that compiled to 1.8. The strange things is that if gene and allele are singular or plural the building merge doesn’t work, but if only one is plural and the other singular it works fine.
>>>>
>>>> If I also change the name allele to something else it also works fine. I am betting there’s some collision between names somewhere in the core code. Also strange is the duplicate class in the model.
>>>>
>>>> Cheers
>>>> Paulo
>>>>
>>>>
>>>>
>>>>
>>>>> On Feb 21, 2019, at 3:22 PM, Sam Hokin <[hidden email]> wrote:
>>>>>
>>>>> Hrm, I'm thinking the "allele" collection must be a misspelling buried in your mine's model, I only see "alleles" collections in the core model, at least in 3.+:
>>>>>
>>>>> [shokin@shokin-mines bio]$ grep -R "collection name=\"alleles\""
>>>>> sources/chado-db/src/main/resources/chado-db-stock_additions.xml:    <collection name="alleles" referenced-type="Allele" reverse-reference="stocks"/>
>>>>> sources/chado-db/src/main/resources/chado-db_additions.xml:    <collection name="alleles" referenced-type="Allele" reverse-reference="gene"/>
>>>>> sources/chado-db/src/main/resources/flybase-chado-db_additions.xml:    <collection name="alleles" referenced-type="Allele" reverse-reference="mutagens"/>
>>>>> [shokin@shokin-mines bio]$ grep -R "collection name=\"allele\""
>>>>> [shokin@shokin-mines bio]$
>>>>>
>>>>> I think I'd do $ grep -R "collection name=\"allele\"" about everywhere I can think of.
>>>>>
>>>>> On 2/21/19 2:48 PM, Paulo Nuin wrote:
>>>>>> Hi Sam
>>>>>> Thanks, quite helpful. I tried most things you mentioned, removed completely the contents of .gradle and .m2, new checkout, and still run into problems (I am using 2.+ still). If I set the collection to
>>>>>> gene and allele or genes and alleles I get a wrong reference error
>>>>>> If I have
>>>>>> genes and allele or gene and alleles everything works fine, but I end with duplicate entries in the model (Allele and Alleles in the attached screen cap).
>>>>>> Head-scratching.
>>>>>> Cheers
>>>>>> Paulo
>>>>
>>>

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[sergio contrino-2]

hi paul,
i think that sam found the error and you are sorted. please let me know
if this is not correct. i think that in a previous thread we found that
you have these 2 settings that are potentially conflicting with your
latest addition. please  see below in case.
thanks
sergio

./sources/chado-db/chado-db_additions.xml:    <collection name="alleles"
referenced-type="Allele" reverse-reference="gene"/>
./sources/chado-db/chado-db_additions.xml:    <reference name="gene"
referenced-type="Gene" reverse-reference="alleles"/>

wormmine/support/acedb-dev/im/genomic_model.xml:    <collection
name="alleles" referenced-type="Allele" reverse-reference="gene"/>
wormmine/support/acedb-dev/im/genomic_model.xml:    <reference
name="gene" referenced-type="Gene" reverse-reference="alleles"/>


On 22/02/2019 02:13, Paulo Nuin wrote:

> I am using XMLs from AceDB. I will double check the source and see. From the start I thought it was some conflict due to the fact that it builds OK if I change the name.
>
> Thanks
>
> Paulo
>
>
>> On Feb 21, 2019, at 4:50 PM, Sam Hokin <[hidden email]> wrote:
>>
>> Sorry! Meant to say there is a _reference_ to "gene" in the Allele definition in that source. That Allele.gene _reference_ conflicts with your Allele.genes _collection_.
>>
>> On 2/21/19 4:48 PM, Sam Hokin wrote:
>>> Are you using chado? Because there is a _reference_ to "allele" in Gene in that source.
>>> [shokin@shokin-mines bio]$ grep -R "reference name=\"gene\"" | grep allele
>>> sources/chado-db/src/main/resources/chado-db_additions.xml:    <reference name="gene" referenced-type="Gene" reverse-reference="alleles"/>
>>> And that's what you're dealing with: a Gene.allele _reference_ conflicting with your Gene.alleles _collection_.
>>> On 2/21/19 4:38 PM, Paulo Nuin wrote:
>>>> Hi again
>>>>
>>>> I set the collections as
>>>>
>>>> <collection name="alleles" referenced-type="Allele" reverse-reference="genes" />
>>>>
>>>> And
>>>>
>>>> <collection name="genes" referenced-type="Gene" reverse-reference="alleles" />
>>>>
>>>> Cleaned everything, including .gradle and re-run the builddb step and got this error
>>>>
>>>> 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
>>>>
>>>> And if I
>>>>
>>>> grep -R alleles
>>>>
>>>> dbmodel/build/so_additions.xml: <reference name="gene" referenced-type="Gene" reverse-reference="alleles"/>
>>>> dbmodel/build/so_additions.xml: <collection name="alleles" referenced-type="Allele" reverse-reference="gene”/>
>>>>
>>>>
>>>> The genes collection becomes gene.
>>>>
>>>> No idea what is happening.
>>>>
>>>> Cheers
>>>> Paulo
>>>>
>>>>
>>>>
>>>>> On Feb 21, 2019, at 4:28 PM, Paulo Nuin <[hidden email]> wrote:
>>>>>
>>>>> Hi
>>>>>
>>>>> I don’t find allele (with or without collection) anywhere in my code, even the one that compiled to 1.8. The strange things is that if gene and allele are singular or plural the building merge doesn’t work, but if only one is plural and the other singular it works fine.
>>>>>
>>>>> If I also change the name allele to something else it also works fine. I am betting there’s some collision between names somewhere in the core code. Also strange is the duplicate class in the model.
>>>>>
>>>>> Cheers
>>>>> Paulo
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> On Feb 21, 2019, at 3:22 PM, Sam Hokin <[hidden email]> wrote:
>>>>>>
>>>>>> Hrm, I'm thinking the "allele" collection must be a misspelling buried in your mine's model, I only see "alleles" collections in the core model, at least in 3.+:
>>>>>>
>>>>>> [shokin@shokin-mines bio]$ grep -R "collection name=\"alleles\""
>>>>>> sources/chado-db/src/main/resources/chado-db-stock_additions.xml:    <collection name="alleles" referenced-type="Allele" reverse-reference="stocks"/>
>>>>>> sources/chado-db/src/main/resources/chado-db_additions.xml:    <collection name="alleles" referenced-type="Allele" reverse-reference="gene"/>
>>>>>> sources/chado-db/src/main/resources/flybase-chado-db_additions.xml:    <collection name="alleles" referenced-type="Allele" reverse-reference="mutagens"/>
>>>>>> [shokin@shokin-mines bio]$ grep -R "collection name=\"allele\""
>>>>>> [shokin@shokin-mines bio]$
>>>>>>
>>>>>> I think I'd do $ grep -R "collection name=\"allele\"" about everywhere I can think of.
>>>>>>
>>>>>> On 2/21/19 2:48 PM, Paulo Nuin wrote:
>>>>>>> Hi Sam
>>>>>>> Thanks, quite helpful. I tried most things you mentioned, removed completely the contents of .gradle and .m2, new checkout, and still run into problems (I am using 2.+ still). If I set the collection to
>>>>>>> gene and allele or genes and alleles I get a wrong reference error
>>>>>>> If I have
>>>>>>> genes and allele or gene and alleles everything works fine, but I end with duplicate entries in the model (Allele and Alleles in the attached screen cap).
>>>>>>> Head-scratching.
>>>>>>> Cheers
>>>>>>> Paulo
>>>>>
>>>>
>
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> [hidden email]
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>

--
sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org
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[Paulo Nuin]

Hi Sergio

I have sorted the error, but it wasn’t a logic process and I have no conclusion to what is/was wrong. I had problems in the past with the same collection/model setting but this time I my code was correct and double checked in most attempts and, as I said, I have no idea why the current solution works and all the others don’t work.

Sam’s advice was spot on, and now I have more things to try when things go wrong, but checking InterMine’s code I couldn’t find anything that would explain why things behaved the way they did.

Cheers

Paulo

> On Feb 22, 2019, at 9:04 AM, sergio contrino <[hidden email]> wrote:
>
> hi paul,
> i think that sam found the error and you are sorted. please let me know if this is not correct. i think that in a previous thread we found that you have these 2 settings that are potentially conflicting with your latest addition. please  see below in case.
> thanks
> sergio
>
> ./sources/chado-db/chado-db_additions.xml:    <collection name="alleles" referenced-type="Allele" reverse-reference="gene"/>
> ./sources/chado-db/chado-db_additions.xml:    <reference name="gene" referenced-type="Gene" reverse-reference="alleles"/>
>
> wormmine/support/acedb-dev/im/genomic_model.xml:    <collection name="alleles" referenced-type="Allele" reverse-reference="gene"/>
> wormmine/support/acedb-dev/im/genomic_model.xml:    <reference name="gene" referenced-type="Gene" reverse-reference="alleles"/>
>
>
> On 22/02/2019 02:13, Paulo Nuin wrote:
>> I am using XMLs from AceDB. I will double check the source and see. From the start I thought it was some conflict due to the fact that it builds OK if I change the name.
>> Thanks
>> Paulo
>>> On Feb 21, 2019, at 4:50 PM, Sam Hokin <[hidden email]> wrote:
>>>
>>> Sorry! Meant to say there is a _reference_ to "gene" in the Allele definition in that source. That Allele.gene _reference_ conflicts with your Allele.genes _collection_.
>>>
>>> On 2/21/19 4:48 PM, Sam Hokin wrote:
>>>> Are you using chado? Because there is a _reference_ to "allele" in Gene in that source.
>>>> [shokin@shokin-mines bio]$ grep -R "reference name=\"gene\"" | grep allele
>>>> sources/chado-db/src/main/resources/chado-db_additions.xml:    <reference name="gene" referenced-type="Gene" reverse-reference="alleles"/>
>>>> And that's what you're dealing with: a Gene.allele _reference_ conflicting with your Gene.alleles _collection_.
>>>> On 2/21/19 4:38 PM, Paulo Nuin wrote:
>>>>> Hi again
>>>>>
>>>>> I set the collections as
>>>>>
>>>>> <collection name="alleles" referenced-type="Allele" reverse-reference="genes" />
>>>>>
>>>>> And
>>>>>
>>>>> <collection name="genes" referenced-type="Gene" reverse-reference="alleles" />
>>>>>
>>>>> Cleaned everything, including .gradle and re-run the builddb step and got this error
>>>>>
>>>>> 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
>>>>>
>>>>> And if I
>>>>>
>>>>> grep -R alleles
>>>>>
>>>>> dbmodel/build/so_additions.xml: <reference name="gene" referenced-type="Gene" reverse-reference="alleles"/>
>>>>> dbmodel/build/so_additions.xml: <collection name="alleles" referenced-type="Allele" reverse-reference="gene”/>
>>>>>
>>>>>
>>>>> The genes collection becomes gene.
>>>>>
>>>>> No idea what is happening.
>>>>>
>>>>> Cheers
>>>>> Paulo
>>>>>
>>>>>
>>>>>
>>>>>> On Feb 21, 2019, at 4:28 PM, Paulo Nuin <[hidden email]> wrote:
>>>>>>
>>>>>> Hi
>>>>>>
>>>>>> I don’t find allele (with or without collection) anywhere in my code, even the one that compiled to 1.8. The strange things is that if gene and allele are singular or plural the building merge doesn’t work, but if only one is plural and the other singular it works fine.
>>>>>>
>>>>>> If I also change the name allele to something else it also works fine. I am betting there’s some collision between names somewhere in the core code. Also strange is the duplicate class in the model.
>>>>>>
>>>>>> Cheers
>>>>>> Paulo
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>> On Feb 21, 2019, at 3:22 PM, Sam Hokin <[hidden email]> wrote:
>>>>>>>
>>>>>>> Hrm, I'm thinking the "allele" collection must be a misspelling buried in your mine's model, I only see "alleles" collections in the core model, at least in 3.+:
>>>>>>>
>>>>>>> [shokin@shokin-mines bio]$ grep -R "collection name=\"alleles\""
>>>>>>> sources/chado-db/src/main/resources/chado-db-stock_additions.xml:    <collection name="alleles" referenced-type="Allele" reverse-reference="stocks"/>
>>>>>>> sources/chado-db/src/main/resources/chado-db_additions.xml:    <collection name="alleles" referenced-type="Allele" reverse-reference="gene"/>
>>>>>>> sources/chado-db/src/main/resources/flybase-chado-db_additions.xml:    <collection name="alleles" referenced-type="Allele" reverse-reference="mutagens"/>
>>>>>>> [shokin@shokin-mines bio]$ grep -R "collection name=\"allele\""
>>>>>>> [shokin@shokin-mines bio]$
>>>>>>>
>>>>>>> I think I'd do $ grep -R "collection name=\"allele\"" about everywhere I can think of.
>>>>>>>
>>>>>>> On 2/21/19 2:48 PM, Paulo Nuin wrote:
>>>>>>>> Hi Sam
>>>>>>>> Thanks, quite helpful. I tried most things you mentioned, removed completely the contents of .gradle and .m2, new checkout, and still run into problems (I am using 2.+ still). If I set the collection to
>>>>>>>> gene and allele or genes and alleles I get a wrong reference error
>>>>>>>> If I have
>>>>>>>> genes and allele or gene and alleles everything works fine, but I end with duplicate entries in the model (Allele and Alleles in the attached screen cap).
>>>>>>>> Head-scratching.
>>>>>>>> Cheers
>>>>>>>> Paulo
>>>>>>
>>>>>
>> _______________________________________________
>> 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

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