designed model disappeared from the Model browser

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designed model disappeared from the Model browser

Pengcheng Yang
Hi Miners,

I have defined the data model and loaded the data successfully. But
after releasing the webapp, I don't found the data model from the Model
browser. However, I can found the content when querying the database
after loading the data with "select * from sometable;". Also, the
content of the data could not be displayed on the website, although I
have configured the displayers in the file
"webapp/resources/webapp/WEB-INF/webconfig-model.xml".  To debug this
problem I have tried to: 1) rebuild the database and reloading the data
again initially (didn't work). 2) reload the data that not displayed
again from the dump point (didn't work).

Could someone tell me how to debug this problem next?

Thank you and best,

Pengcheng Yang

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Re: designed model disappeared from the Model browser

sergio contrino-2
hi Penchcheng,
do you mean that you cannot see data from the yourmine/tree.do page
(browse data model from the query builder tag)?
your new tables do not appear in the query builder?
could you maybe send some screen-shots?
thanks!
sergio

On 31/05/18 04:25, Pengcheng Yang wrote:

> Hi Miners,
>
> I have defined the data model and loaded the data successfully. But
> after releasing the webapp, I don't found the data model from the Model
> browser. However, I can found the content when querying the database
> after loading the data with "select * from sometable;". Also, the
> content of the data could not be displayed on the website, although I
> have configured the displayers in the file
> "webapp/resources/webapp/WEB-INF/webconfig-model.xml".  To debug this
> problem I have tried to: 1) rebuild the database and reloading the data
> again initially (didn't work). 2) reload the data that not displayed
> again from the dump point (didn't work).
>
> Could someone tell me how to debug this problem next?
>
> Thank you and best,
>
> Pengcheng Yang
>
> _______________________________________________
> 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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Re: designed model disappeared from the Model browser

Pengcheng Yang

Hi sergio,

Thank you for your reply.

I have checked mymine/tree.do. The data model displayed in the tree.do page was as expected. However, for some specific data, the model browser papge (displayed from page: mymine/query.do) didn't display as expected. For example, OrthologueDisease as example [1, 2], whose collection "monarchDiseaseTerms" was not displayed. And further, in the report page for "Gene", the orthologueDiseases collection also not be displayed. Maybe I have falsely configured somewhere. I am still debug this problem.

[1] data model

  <class name="Gene" extends="SequenceFeature" is-interface="true">
    <attribute name="description" type="java.lang.String"/>
    <attribute name="briefDescription" type="java.lang.String"/>
    <reference name="upstreamIntergenicRegion" referenced-type="IntergenicRegion"/>
    <reference name="downstreamIntergenicRegion" referenced-type="IntergenicRegion"/>
    <collection name="UTRs" referenced-type="UTR" reverse-reference="gene"/>
    <collection name="exons" referenced-type="Exon" reverse-reference="gene"/>
    <collection name="CDSs" referenced-type="CDS" reverse-reference="gene"/>
    <collection name="flankingRegions" referenced-type="GeneFlankingRegion" reverse-reference="gene"/>
    <collection name="introns" referenced-type="Intron" reverse-reference="genes"/>
    <collection name="regulatoryRegions" referenced-type="RegulatoryRegion" reverse-reference="gene"/>
    <collection name="transcripts" referenced-type="Transcript" reverse-reference="gene"/>
    <collection name="proteins" referenced-type="Protein" reverse-reference="genes"/>
    <collection name="pathways" referenced-type="Pathway" reverse-reference="genes"/>
    <collection name="geneSets" referenced-type="GeneSet" reverse-reference="genes"/>
    <collection name="rnaSeqResults" referenced-type="RNASeqResult" reverse-reference="gene"/>
    <collection name="probeSets" referenced-type="ProbeSet" reverse-reference="genes"/>
    <collection name="homologues" referenced-type="Homologue" reverse-reference="gene"/>
    <collection name="mRNAExpressionResults" referenced-type="MRNAExpressionResult" reverse-reference="gene"/>
    <collection name="rnaiResults" referenced-type="RNAiResult" reverse-reference="gene"/>
    <collection name="miRNAtargets" referenced-type="MiRNATarget" reverse-reference="mirnagene"/>
    <collection name="clones" referenced-type="CDNAClone" reverse-reference="gene"/>
    <collection name="microArrayResults" referenced-type="MicroArrayResult" reverse-reference="genes"/>
    <collection name="orthologueGroups" referenced-type="OrthologueGroup" reverse-reference="genes"/>
    <collection name="phenotypes" referenced-type="Phenotype" reverse-reference="genes"/>
    <collection name="functionOfAssociatedGenes" referenced-type="FunctionOfAssociatedGene" reverse-reference="gene"/>
    <collection name="anatomyExpressions" referenced-type="AnatomyExpression" reverse-reference="gene"/>
    <collection name="goAnnotation" referenced-type="GOAnnotation"/>
    <collection name="monarchDiseaseAnnotations" referenced-type="MonarchDiseaseAnnotation"/>
    <collection name="monarchPhenotypeAnnotations" referenced-type="MonarchPhenotypeAnnotation"/>
    <collection name="orthologueDiseases" referenced-type="OrthologueDisease"/>
    <collection name="orthologuePhenotypes" referenced-type="OrthologuePhenotype"/>
  <class>

  <class name="OrthologueDisease" extends="Homologue" is-interface="true">
    <collection name="monarchDiseaseTerms" referenced-type="MonarchDiseaseTerm"/>
  </class>
  <class name="OrthologuePhenotype" extends="Homologue" is-interface="true">
    <collection name="monarchPhenotypeTerms" referenced-type="MonarchPhenotypeTerm"/>
  </class>

  <class name="MonarchDiseaseTerm" extends="OntologyTerm" is-interface="true"> </class>
  <class name="MonarchPhenotypeTerm" extends="OntologyTerm" is-interface="true"> </class>

[2] Model browser for OrthologueDisease data model.

Best,

Pengcheng Yang


On 2018-6-1 17:39, sergio contrino wrote:
hi Penchcheng,
do you mean that you cannot see data from the yourmine/tree.do page (browse data model from the query builder tag)?
your new tables do not appear in the query builder?
could you maybe send some screen-shots?
thanks!
sergio

On 31/05/18 04:25, Pengcheng Yang wrote:
Hi Miners,

I have defined the data model and loaded the data successfully. But after releasing the webapp, I don't found the data model from the Model browser. However, I can found the content when querying the database after loading the data with "select * from sometable;". Also, the content of the data could not be displayed on the website, although I have configured the displayers in the file "webapp/resources/webapp/WEB-INF/webconfig-model.xml".  To debug this problem I have tried to: 1) rebuild the database and reloading the data again initially (didn't work). 2) reload the data that not displayed again from the dump point (didn't work).

Could someone tell me how to debug this problem next?

Thank you and best,

Pengcheng Yang

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



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Re: designed model disappeared from the Model browser

Julie Sullivan-2
Hi Pengcheng!

In the query builder, directly below the "model browser" panel you have
in your screenshot, there is a checkbox. Can you check it?

[ ] Show empty fields

I am guessing that will cause the `monarchDiseaseTerms` to appear, as
that collection might be empty.

Try it?

On 06/02/2018 03:01 AM, Pengcheng Yang wrote:

> Hi sergio,
>
> Thank you for your reply.
>
> I have checked mymine/tree.do. The data model displayed in the tree.do
> page was as expected. However, for some specific data, the model browser
> papge (displayed from page: mymine/query.do) didn't display as expected.
> For example, OrthologueDisease as example [1, 2], whose collection
> "monarchDiseaseTerms" was not displayed. And further, in the report page
> for "Gene", the orthologueDiseases collection also not be displayed.
> Maybe I have falsely configured somewhere. I am still debug this problem.
>
> [1] data model
>
>    <class name="Gene" extends="SequenceFeature" is-interface="true">
>      <attribute name="description" type="java.lang.String"/>
>      <attribute name="briefDescription" type="java.lang.String"/>
>      <reference name="upstreamIntergenicRegion"
> referenced-type="IntergenicRegion"/>
>      <reference name="downstreamIntergenicRegion"
> referenced-type="IntergenicRegion"/>
>      <collection name="UTRs" referenced-type="UTR"
> reverse-reference="gene"/>
>      <collection name="exons" referenced-type="Exon"
> reverse-reference="gene"/>
>      <collection name="CDSs" referenced-type="CDS"
> reverse-reference="gene"/>
>      <collection name="flankingRegions"
> referenced-type="GeneFlankingRegion" reverse-reference="gene"/>
>      <collection name="introns" referenced-type="Intron"
> reverse-reference="genes"/>
>      <collection name="regulatoryRegions"
> referenced-type="RegulatoryRegion" reverse-reference="gene"/>
>      <collection name="transcripts" referenced-type="Transcript"
> reverse-reference="gene"/>
>      <collection name="proteins" referenced-type="Protein"
> reverse-reference="genes"/>
>      <collection name="pathways" referenced-type="Pathway"
> reverse-reference="genes"/>
>      <collection name="geneSets" referenced-type="GeneSet"
> reverse-reference="genes"/>
>      <collection name="rnaSeqResults" referenced-type="RNASeqResult"
> reverse-reference="gene"/>
>      <collection name="probeSets" referenced-type="ProbeSet"
> reverse-reference="genes"/>
>      <collection name="homologues" referenced-type="Homologue"
> reverse-reference="gene"/>
>      <collection name="mRNAExpressionResults"
> referenced-type="MRNAExpressionResult" reverse-reference="gene"/>
>      <collection name="rnaiResults" referenced-type="RNAiResult"
> reverse-reference="gene"/>
>      <collection name="miRNAtargets" referenced-type="MiRNATarget"
> reverse-reference="mirnagene"/>
>      <collection name="clones" referenced-type="CDNAClone"
> reverse-reference="gene"/>
>      <collection name="microArrayResults"
> referenced-type="MicroArrayResult" reverse-reference="genes"/>
>      <collection name="orthologueGroups"
> referenced-type="OrthologueGroup" reverse-reference="genes"/>
>      <collection name="phenotypes" referenced-type="Phenotype"
> reverse-reference="genes"/>
>      <collection name="functionOfAssociatedGenes"
> referenced-type="FunctionOfAssociatedGene" reverse-reference="gene"/>
>      <collection name="anatomyExpressions"
> referenced-type="AnatomyExpression" reverse-reference="gene"/>
>      <collection name="goAnnotation" referenced-type="GOAnnotation"/>
>      <collection name="monarchDiseaseAnnotations"
> referenced-type="MonarchDiseaseAnnotation"/>
>      <collection name="monarchPhenotypeAnnotations"
> referenced-type="MonarchPhenotypeAnnotation"/>
>      <collection name="orthologueDiseases"
> referenced-type="OrthologueDisease"/>
>      <collection name="orthologuePhenotypes"
> referenced-type="OrthologuePhenotype"/>
>    <class>
>
>    <class name="OrthologueDisease" extends="Homologue" is-interface="true">
>      <collection name="monarchDiseaseTerms"
> referenced-type="MonarchDiseaseTerm"/>
>    </class>
>    <class name="OrthologuePhenotype" extends="Homologue"
> is-interface="true">
>      <collection name="monarchPhenotypeTerms"
> referenced-type="MonarchPhenotypeTerm"/>
>    </class>
>
>    <class name="MonarchDiseaseTerm" extends="OntologyTerm"
> is-interface="true"> </class>
>    <class name="MonarchPhenotypeTerm" extends="OntologyTerm"
> is-interface="true"> </class>
>
> [2] Model browser for OrthologueDisease data model.
>
> Best,
>
> Pengcheng Yang
>
>
> On 2018-6-1 17:39, sergio contrino wrote:
>> hi Penchcheng,
>> do you mean that you cannot see data from the yourmine/tree.do page
>> (browse data model from the query builder tag)?
>> your new tables do not appear in the query builder?
>> could you maybe send some screen-shots?
>> thanks!
>> sergio
>>
>> On 31/05/18 04:25, Pengcheng Yang wrote:
>>> Hi Miners,
>>>
>>> I have defined the data model and loaded the data successfully. But
>>> after releasing the webapp, I don't found the data model from the
>>> Model browser. However, I can found the content when querying the
>>> database after loading the data with "select * from sometable;".
>>> Also, the content of the data could not be displayed on the website,
>>> although I have configured the displayers in the file
>>> "webapp/resources/webapp/WEB-INF/webconfig-model.xml".  To debug this
>>> problem I have tried to: 1) rebuild the database and reloading the
>>> data again initially (didn't work). 2) reload the data that not
>>> displayed again from the dump point (didn't work).
>>>
>>> Could someone tell me how to debug this problem next?
>>>
>>> Thank you and best,
>>>
>>> Pengcheng Yang
>>>
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> https://lists.intermine.org/mailman/listinfo/dev
>>
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
>
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