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adding class contig

Sofia Robb
Hello,

I built my own data source of type gff. My reference sequences are not chromosomes, they are contigs. How do I add class contig? 



    <source name="SmedSxl_v31-gff" type="simr-gff">

      <property name="gff3.seqClsName" value="Contig"/>

    </source>

Thanks,
Sofia

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Re: adding class contig

Sergio Contrino
hello sofia,
yes, this seems right to me.
please refer to the docs here
http://intermine.readthedocs.org/en/latest/get-started/tutorial/#loading-genome-data-from-gff3-and-fasta
but i think you did already.
let us know if you have any problem.
thanks
sergio


On 10/09/15 21:41, Sofia Robb wrote:

> Hello,
>
> I built my own data source of type gff. My reference sequences are not
> chromosomes, they are contigs. How do I add class contig?
>
>
>
>      <source name="SmedSxl_v31-gff" type="simr-gff">
>
>        <property name="gff3.seqClsName" value="Contig"/>
>
>      </source>
>
> Thanks,
> Sofia
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

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

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Re: adding class contig

Sofia Robb
Hi Sergio,

I am getting this error about Contig not being in the Model when I run this command:

cd /data/intermine/simrmine/dbmodel/ 
ant clean build-db
cd ../integrate
ant -Dsource=SmedSxl_v31-gff -v

BUILD FAILED
/var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: The following error occurred while executing this line:
/var/lib/pgsql/other_data/intermine/imbuild/source.xml:253: java.lang.IllegalArgumentException: class "org.intermine.model.bio.Contig" is not in the Model

How do I get Contig to be in my model? Here is what I have tried.


#### my project.xml #### 

    <source name="SmedSxl_v31-gff" type="simr-gff">
      <property name="gff3.taxonId" value="79327"/>
      <property name="gff3.seqDataSourceName" value="SmedGD"/>
      <property name="gff3.dataSourceName" value="mk5-SmedSxl-v31"/>
      <property name="gff3.seqClsName" value="Contig"/>
      <property name="gff3.dataSetTitle" value="SmedSxlv31 MK5"/>
      <property name="src.data.dir" location="/home/SGC/smr/data/organisms/planaria/Smed/SmedSxl/genome/v31/split"/>
    </source>

####  my simr-gff_additions.xml #### 

<classes>
<!-- add any <class> elements here -->
   <class name="Contig"  extends="SequenceFeature" is-interface="true"></class>
</classes>




when this didn't work I:

I also added Contig to bio/core/genomic_additions.xml 
  <class name="Contig"  extends="SequenceFeature" is-interface="true"></class>


When I saw that there was no Contig.class in dbmodel/build/classes/org/intermine/model/bio/
I also added contig to dbmodel/resources/so_terms

I have all of the above in place now, and I have done a 'ant clean build-db' after each change.

I think I am missing something.

Thanks,
Sofia




On Fri, Sep 11, 2015 at 3:17 AM, sergio contrino <[hidden email]> wrote:
hello sofia,
yes, this seems right to me.
please refer to the docs here
http://intermine.readthedocs.org/en/latest/get-started/tutorial/#loading-genome-data-from-gff3-and-fasta
but i think you did already.
let us know if you have any problem.
thanks
sergio



On 10/09/15 21:41, Sofia Robb wrote:
Hello,

I built my own data source of type gff. My reference sequences are not
chromosomes, they are contigs. How do I add class contig?



     <source name="SmedSxl_v31-gff" type="simr-gff">

       <property name="gff3.seqClsName" value="Contig"/>

     </source>

Thanks,
Sofia


_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev


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


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Re: adding class contig

Sergio Contrino
hi sofia,
your simr-gff_additions.xml should be enough and you should not need to
add the other 2.
can you try calling your source "simr-gff"?
like

     <source name="simr-gff" type="simr-gff">
       <property name="gff3.taxonId" value="79327"/>
       <property name="gff3.seqDataSourceName" value="SmedGD"/>
       <property name="gff3.dataSourceName" value="mk5-SmedSxl-v31"/>
       <property name="gff3.seqClsName" value="Contig"/>
       <property name="gff3.dataSetTitle" value="SmedSxlv31 MK5"/>
       <property name="src.data.dir"
location="/home/SGC/smr/data/organisms/planaria/Smed/SmedSxl/genome/v31/split"/>
     </source>

thanks
sergio



On 11/09/15 15:54, Sofia Robb wrote:

> Hi Sergio,
>
> I am getting this error about Contig not being in the Model when I run
> this command:
>
> cd /data/intermine/simrmine/dbmodel/
> ant clean build-db
> cd ../integrate
> ant -Dsource=SmedSxl_v31-gff -v
>
> BUILD FAILED
> /var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: The
> following error occurred while executing this line:
> /var/lib/pgsql/other_data/intermine/imbuild/source.xml:253:
> java.lang.IllegalArgumentException: class
> "org.intermine.model.bio.Contig" is not in the Model
>
> How do I get Contig to be in my model? Here is what I have tried.
>
>
> #### my project.xml ####
>
>      <source name="SmedSxl_v31-gff" type="simr-gff">
>        <property name="gff3.taxonId" value="79327"/>
>        <property name="gff3.seqDataSourceName" value="SmedGD"/>
>        <property name="gff3.dataSourceName" value="mk5-SmedSxl-v31"/>
>        <property name="gff3.seqClsName" value="Contig"/>
>        <property name="gff3.dataSetTitle" value="SmedSxlv31 MK5"/>
>        <property name="src.data.dir"
> location="/home/SGC/smr/data/organisms/planaria/Smed/SmedSxl/genome/v31/split"/>
>      </source>
>
> ####  my simr-gff_additions.xml ####
>
> <classes>
> <!-- add any <class> elements here -->
>     <class name="Contig"  extends="SequenceFeature"
> is-interface="true"></class>
> </classes>
>
>
>
>
> when this didn't work I:
>
> I also added Contig to bio/core/genomic_additions.xml
>    <class name="Contig"  extends="SequenceFeature"
> is-interface="true"></class>
>
>
> When I saw that there was no Contig.class in
> dbmodel/build/classes/org/intermine/model/bio/
> I also added contig to dbmodel/resources/so_terms
>
> I have all of the above in place now, and I have done a 'ant clean
> build-db' after each change.
>
> I think I am missing something.
>
> Thanks,
> Sofia
>
>
>
>
> On Fri, Sep 11, 2015 at 3:17 AM, sergio contrino <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     hello sofia,
>     yes, this seems right to me.
>     please refer to the docs here
>     http://intermine.readthedocs.org/en/latest/get-started/tutorial/#loading-genome-data-from-gff3-and-fasta
>     but i think you did already.
>     let us know if you have any problem.
>     thanks
>     sergio
>
>
>
>     On 10/09/15 21:41, Sofia Robb wrote:
>
>         Hello,
>
>         I built my own data source of type gff. My reference sequences
>         are not
>         chromosomes, they are contigs. How do I add class contig?
>
>
>
>               <source name="SmedSxl_v31-gff" type="simr-gff">
>
>                 <property name="gff3.seqClsName" value="Contig"/>
>
>               </source>
>
>         Thanks,
>         Sofia
>
>
>         _______________________________________________
>         dev mailing list
>         [hidden email] <mailto:[hidden email]>
>         http://mail.intermine.org/cgi-bin/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

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Re: adding class contig

Sofia Robb
I changed my project.xml as you suggested but I get the same error. I ran the clean build-db before I ran ant -Dsource=simr-gff -v.

Sofia

On Fri, Sep 11, 2015 at 10:14 AM, sergio contrino <[hidden email]> wrote:
hi sofia,
your simr-gff_additions.xml should be enough and you should not need to add the other 2.
can you try calling your source "simr-gff"?
like

    <source name="simr-gff" type="simr-gff">
      <property name="gff3.taxonId" value="79327"/>
      <property name="gff3.seqDataSourceName" value="SmedGD"/>
      <property name="gff3.dataSourceName" value="mk5-SmedSxl-v31"/>
      <property name="gff3.seqClsName" value="Contig"/>
      <property name="gff3.dataSetTitle" value="SmedSxlv31 MK5"/>
      <property name="src.data.dir" location="/home/SGC/smr/data/organisms/planaria/Smed/SmedSxl/genome/v31/split"/>
    </source>

thanks
sergio




On 11/09/15 15:54, Sofia Robb wrote:
Hi Sergio,

I am getting this error about Contig not being in the Model when I run
this command:

cd /data/intermine/simrmine/dbmodel/
ant clean build-db
cd ../integrate
ant -Dsource=SmedSxl_v31-gff -v

BUILD FAILED
/var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: The
following error occurred while executing this line:
/var/lib/pgsql/other_data/intermine/imbuild/source.xml:253:
java.lang.IllegalArgumentException: class
"org.intermine.model.bio.Contig" is not in the Model

How do I get Contig to be in my model? Here is what I have tried.


#### my project.xml ####

     <source name="SmedSxl_v31-gff" type="simr-gff">
       <property name="gff3.taxonId" value="79327"/>
       <property name="gff3.seqDataSourceName" value="SmedGD"/>
       <property name="gff3.dataSourceName" value="mk5-SmedSxl-v31"/>
       <property name="gff3.seqClsName" value="Contig"/>
       <property name="gff3.dataSetTitle" value="SmedSxlv31 MK5"/>
       <property name="src.data.dir"
location="/home/SGC/smr/data/organisms/planaria/Smed/SmedSxl/genome/v31/split"/>
     </source>

####  my simr-gff_additions.xml ####

<classes>
<!-- add any <class> elements here -->
    <class name="Contig"  extends="SequenceFeature"
is-interface="true"></class>
</classes>




when this didn't work I:

I also added Contig to bio/core/genomic_additions.xml
   <class name="Contig"  extends="SequenceFeature"
is-interface="true"></class>


When I saw that there was no Contig.class in
dbmodel/build/classes/org/intermine/model/bio/
I also added contig to dbmodel/resources/so_terms

I have all of the above in place now, and I have done a 'ant clean
build-db' after each change.

I think I am missing something.

Thanks,
Sofia




On Fri, Sep 11, 2015 at 3:17 AM, sergio contrino <[hidden email]
<mailto:[hidden email]>> wrote:

    hello sofia,
    yes, this seems right to me.
    please refer to the docs here
    http://intermine.readthedocs.org/en/latest/get-started/tutorial/#loading-genome-data-from-gff3-and-fasta
    but i think you did already.
    let us know if you have any problem.
    thanks
    sergio



    On 10/09/15 21:41, Sofia Robb wrote:

        Hello,

        I built my own data source of type gff. My reference sequences
        are not
        chromosomes, they are contigs. How do I add class contig?



              <source name="SmedSxl_v31-gff" type="simr-gff">

                <property name="gff3.seqClsName" value="Contig"/>

              </source>

        Thanks,
        Sofia


        _______________________________________________
        dev mailing list
        [hidden email] <mailto:[hidden email]>
        http://mail.intermine.org/cgi-bin/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


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dev mailing list
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Re: adding class contig

vkrishna
Hi Sofia,

The error you are encountering seems to be because ‘Contig’ is not part of the core (https://github.com/intermine/intermine/blob/master/bio/core/core.xml) InterMine data model or the genomic additions (https://github.com/intermine/intermine/blob/master/bio/core/genomic_additions.xml).

You would have to extend your data model, preferably within the simr-gff_additions.xml (an example additions file: https://github.com/intermine/intermine/blob/beta/bio/sources/fly/drosdel-gff/drosdel-gff_additions.xml).

You can define the ‘Contig’ entity in the data model similar to how the ‘Chromosome’ entity is defined:

Hope this helps!

Thank you.
Vivek

On Sep 11, 2015, at 12:30 PM, Sofia Robb <[hidden email]> wrote:

I changed my project.xml as you suggested but I get the same error. I ran the clean build-db before I ran ant -Dsource=simr-gff -v.

Sofia

On Fri, Sep 11, 2015 at 10:14 AM, sergio contrino <[hidden email]> wrote:
hi sofia,
your simr-gff_additions.xml should be enough and you should not need to add the other 2.
can you try calling your source "simr-gff"?
like

    <source name="simr-gff" type="simr-gff">
      <property name="gff3.taxonId" value="79327"/>
      <property name="gff3.seqDataSourceName" value="SmedGD"/>
      <property name="gff3.dataSourceName" value="mk5-SmedSxl-v31"/>
      <property name="gff3.seqClsName" value="Contig"/>
      <property name="gff3.dataSetTitle" value="SmedSxlv31 MK5"/>
      <property name="src.data.dir" location="/home/SGC/smr/data/organisms/planaria/Smed/SmedSxl/genome/v31/split"/>
    </source>

thanks
sergio




On 11/09/15 15:54, Sofia Robb wrote:
Hi Sergio,

I am getting this error about Contig not being in the Model when I run
this command:

cd /data/intermine/simrmine/dbmodel/
ant clean build-db
cd ../integrate
ant -Dsource=SmedSxl_v31-gff -v

BUILD FAILED
/var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: The
following error occurred while executing this line:
/var/lib/pgsql/other_data/intermine/imbuild/source.xml:253:
java.lang.IllegalArgumentException: class
"org.intermine.model.bio.Contig" is not in the Model

How do I get Contig to be in my model? Here is what I have tried.


#### my project.xml ####

     <source name="SmedSxl_v31-gff" type="simr-gff">
       <property name="gff3.taxonId" value="79327"/>
       <property name="gff3.seqDataSourceName" value="SmedGD"/>
       <property name="gff3.dataSourceName" value="mk5-SmedSxl-v31"/>
       <property name="gff3.seqClsName" value="Contig"/>
       <property name="gff3.dataSetTitle" value="SmedSxlv31 MK5"/>
       <property name="src.data.dir"
location="/home/SGC/smr/data/organisms/planaria/Smed/SmedSxl/genome/v31/split"/>
     </source>

####  my simr-gff_additions.xml ####

<classes>
<!-- add any <class> elements here -->
    <class name="Contig"  extends="SequenceFeature"
is-interface="true"></class>
</classes>




when this didn't work I:

I also added Contig to bio/core/genomic_additions.xml
   <class name="Contig"  extends="SequenceFeature"
is-interface="true"></class>


When I saw that there was no Contig.class in
dbmodel/build/classes/org/intermine/model/bio/
I also added contig to dbmodel/resources/so_terms

I have all of the above in place now, and I have done a 'ant clean
build-db' after each change.

I think I am missing something.

Thanks,
Sofia




On Fri, Sep 11, 2015 at 3:17 AM, sergio contrino <[hidden email]
<mailto:[hidden email]>> wrote:

    hello sofia,
    yes, this seems right to me.
    please refer to the docs here
    http://intermine.readthedocs.org/en/latest/get-started/tutorial/#loading-genome-data-from-gff3-and-fasta
    but i think you did already.
    let us know if you have any problem.
    thanks
    sergio



    On 10/09/15 21:41, Sofia Robb wrote:

        Hello,

        I built my own data source of type gff. My reference sequences
        are not
        chromosomes, they are contigs. How do I add class contig?



              <source name="SmedSxl_v31-gff" type="simr-gff">

                <property name="gff3.seqClsName" value="Contig"/>

              </source>

        Thanks,
        Sofia


        _______________________________________________
        dev mailing list
        [hidden email] <mailto:[hidden email]>
        http://mail.intermine.org/cgi-bin/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]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev


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Re: adding class contig

vkrishna
Also, since ‘Gene’ extends ‘SequenceFeature’, you would also have to extend the model to replace this reference:

Replace this: <reference name="chromosome" referenced-type="Chromosome" />
With this: <reference name=config" referenced-type=Contig" />

Thank you.
Vivek

On Sep 11, 2015, at 12:37 PM, Krishnakumar, Vivek <[hidden email]> wrote:

Hi Sofia,

The error you are encountering seems to be because ‘Contig’ is not part of the core (https://github.com/intermine/intermine/blob/master/bio/core/core.xml) InterMine data model or the genomic additions (https://github.com/intermine/intermine/blob/master/bio/core/genomic_additions.xml).

You would have to extend your data model, preferably within the simr-gff_additions.xml (an example additions file: https://github.com/intermine/intermine/blob/beta/bio/sources/fly/drosdel-gff/drosdel-gff_additions.xml).

You can define the ‘Contig’ entity in the data model similar to how the ‘Chromosome’ entity is defined:

Hope this helps!

Thank you.
Vivek

On Sep 11, 2015, at 12:30 PM, Sofia Robb <[hidden email]> wrote:

I changed my project.xml as you suggested but I get the same error. I ran the clean build-db before I ran ant -Dsource=simr-gff -v.

Sofia

On Fri, Sep 11, 2015 at 10:14 AM, sergio contrino <[hidden email]> wrote:
hi sofia,
your simr-gff_additions.xml should be enough and you should not need to add the other 2.
can you try calling your source "simr-gff"?
like

    <source name="simr-gff" type="simr-gff">
      <property name="gff3.taxonId" value="79327"/>
      <property name="gff3.seqDataSourceName" value="SmedGD"/>
      <property name="gff3.dataSourceName" value="mk5-SmedSxl-v31"/>
      <property name="gff3.seqClsName" value="Contig"/>
      <property name="gff3.dataSetTitle" value="SmedSxlv31 MK5"/>
      <property name="src.data.dir" location="/home/SGC/smr/data/organisms/planaria/Smed/SmedSxl/genome/v31/split"/>
    </source>

thanks
sergio




On 11/09/15 15:54, Sofia Robb wrote:
Hi Sergio,

I am getting this error about Contig not being in the Model when I run
this command:

cd /data/intermine/simrmine/dbmodel/
ant clean build-db
cd ../integrate
ant -Dsource=SmedSxl_v31-gff -v

BUILD FAILED
/var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: The
following error occurred while executing this line:
/var/lib/pgsql/other_data/intermine/imbuild/source.xml:253:
java.lang.IllegalArgumentException: class
"org.intermine.model.bio.Contig" is not in the Model

How do I get Contig to be in my model? Here is what I have tried.


#### my project.xml ####

     <source name="SmedSxl_v31-gff" type="simr-gff">
       <property name="gff3.taxonId" value="79327"/>
       <property name="gff3.seqDataSourceName" value="SmedGD"/>
       <property name="gff3.dataSourceName" value="mk5-SmedSxl-v31"/>
       <property name="gff3.seqClsName" value="Contig"/>
       <property name="gff3.dataSetTitle" value="SmedSxlv31 MK5"/>
       <property name="src.data.dir"
location="/home/SGC/smr/data/organisms/planaria/Smed/SmedSxl/genome/v31/split"/>
     </source>

####  my simr-gff_additions.xml ####

<classes>
<!-- add any <class> elements here -->
    <class name="Contig"  extends="SequenceFeature"
is-interface="true"></class>
</classes>




when this didn't work I:

I also added Contig to bio/core/genomic_additions.xml
   <class name="Contig"  extends="SequenceFeature"
is-interface="true"></class>


When I saw that there was no Contig.class in
dbmodel/build/classes/org/intermine/model/bio/
I also added contig to dbmodel/resources/so_terms

I have all of the above in place now, and I have done a 'ant clean
build-db' after each change.

I think I am missing something.

Thanks,
Sofia




On Fri, Sep 11, 2015 at 3:17 AM, sergio contrino <[hidden email]
<mailto:[hidden email]>> wrote:

    hello sofia,
    yes, this seems right to me.
    please refer to the docs here
    http://intermine.readthedocs.org/en/latest/get-started/tutorial/#loading-genome-data-from-gff3-and-fasta
    but i think you did already.
    let us know if you have any problem.
    thanks
    sergio



    On 10/09/15 21:41, Sofia Robb wrote:

        Hello,

        I built my own data source of type gff. My reference sequences
        are not
        chromosomes, they are contigs. How do I add class contig?



              <source name="SmedSxl_v31-gff" type="simr-gff">

                <property name="gff3.seqClsName" value="Contig"/>

              </source>

        Thanks,
        Sofia


        _______________________________________________
        dev mailing list
        [hidden email] <mailto:[hidden email]>
        http://mail.intermine.org/cgi-bin/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]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

_______________________________________________
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[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev


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Re: adding class contig

vkrishna
Actually, the original reference to a ‘Chromosome’ can be left in (in the core.xml), and a new reference can be added to the ‘Contig’ class (in the simr-gff_additions.xml), like so:
<class name="SequenceFeature" extends="BioEntity" is-interface="true">
<reference name=“contig referenced-type=“Contig"/>
</class>

Thank you.
Vivek

On Sep 11, 2015, at 12:41 PM, Krishnakumar, Vivek <[hidden email]> wrote:

Also, since ‘Gene’ extends ‘SequenceFeature’, you would also have to extend the model to replace this reference:

Replace this: <reference name="chromosome" referenced-type="Chromosome" />
With this: <reference name=config" referenced-type=Contig" />

Thank you.
Vivek

On Sep 11, 2015, at 12:37 PM, Krishnakumar, Vivek <[hidden email]> wrote:

Hi Sofia,

The error you are encountering seems to be because ‘Contig’ is not part of the core (https://github.com/intermine/intermine/blob/master/bio/core/core.xml) InterMine data model or the genomic additions (https://github.com/intermine/intermine/blob/master/bio/core/genomic_additions.xml).

You would have to extend your data model, preferably within the simr-gff_additions.xml (an example additions file: https://github.com/intermine/intermine/blob/beta/bio/sources/fly/drosdel-gff/drosdel-gff_additions.xml).

You can define the ‘Contig’ entity in the data model similar to how the ‘Chromosome’ entity is defined:

Hope this helps!

Thank you.
Vivek

On Sep 11, 2015, at 12:30 PM, Sofia Robb <[hidden email]> wrote:

I changed my project.xml as you suggested but I get the same error. I ran the clean build-db before I ran ant -Dsource=simr-gff -v.

Sofia

On Fri, Sep 11, 2015 at 10:14 AM, sergio contrino <[hidden email]> wrote:
hi sofia,
your simr-gff_additions.xml should be enough and you should not need to add the other 2.
can you try calling your source "simr-gff"?
like

    <source name="simr-gff" type="simr-gff">
      <property name="gff3.taxonId" value="79327"/>
      <property name="gff3.seqDataSourceName" value="SmedGD"/>
      <property name="gff3.dataSourceName" value="mk5-SmedSxl-v31"/>
      <property name="gff3.seqClsName" value="Contig"/>
      <property name="gff3.dataSetTitle" value="SmedSxlv31 MK5"/>
      <property name="src.data.dir" location="/home/SGC/smr/data/organisms/planaria/Smed/SmedSxl/genome/v31/split"/>
    </source>

thanks
sergio




On 11/09/15 15:54, Sofia Robb wrote:
Hi Sergio,

I am getting this error about Contig not being in the Model when I run
this command:

cd /data/intermine/simrmine/dbmodel/
ant clean build-db
cd ../integrate
ant -Dsource=SmedSxl_v31-gff -v

BUILD FAILED
/var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: The
following error occurred while executing this line:
/var/lib/pgsql/other_data/intermine/imbuild/source.xml:253:
java.lang.IllegalArgumentException: class
"org.intermine.model.bio.Contig" is not in the Model

How do I get Contig to be in my model? Here is what I have tried.


#### my project.xml ####

     <source name="SmedSxl_v31-gff" type="simr-gff">
       <property name="gff3.taxonId" value="79327"/>
       <property name="gff3.seqDataSourceName" value="SmedGD"/>
       <property name="gff3.dataSourceName" value="mk5-SmedSxl-v31"/>
       <property name="gff3.seqClsName" value="Contig"/>
       <property name="gff3.dataSetTitle" value="SmedSxlv31 MK5"/>
       <property name="src.data.dir"
location="/home/SGC/smr/data/organisms/planaria/Smed/SmedSxl/genome/v31/split"/>
     </source>

####  my simr-gff_additions.xml ####

<classes>
<!-- add any <class> elements here -->
    <class name="Contig"  extends="SequenceFeature"
is-interface="true"></class>
</classes>




when this didn't work I:

I also added Contig to bio/core/genomic_additions.xml
   <class name="Contig"  extends="SequenceFeature"
is-interface="true"></class>


When I saw that there was no Contig.class in
dbmodel/build/classes/org/intermine/model/bio/
I also added contig to dbmodel/resources/so_terms

I have all of the above in place now, and I have done a 'ant clean
build-db' after each change.

I think I am missing something.

Thanks,
Sofia




On Fri, Sep 11, 2015 at 3:17 AM, sergio contrino <[hidden email]
<mailto:[hidden email]>> wrote:

    hello sofia,
    yes, this seems right to me.
    please refer to the docs here
    http://intermine.readthedocs.org/en/latest/get-started/tutorial/#loading-genome-data-from-gff3-and-fasta
    but i think you did already.
    let us know if you have any problem.
    thanks
    sergio



    On 10/09/15 21:41, Sofia Robb wrote:

        Hello,

        I built my own data source of type gff. My reference sequences
        are not
        chromosomes, they are contigs. How do I add class contig?



              <source name="SmedSxl_v31-gff" type="simr-gff">

                <property name="gff3.seqClsName" value="Contig"/>

              </source>

        Thanks,
        Sofia


        _______________________________________________
        dev mailing list
        [hidden email] <mailto:[hidden email]>
        http://mail.intermine.org/cgi-bin/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]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev


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Re: adding class contig

Sofia Robb
In reply to this post by vkrishna
Hi Vivek

I tried adding the following to my simr-gff_additions.xml.

   <class name="Contig"  extends="SequenceFeature" is-interface="true"></class>


I added the reference line you mentioned to core.xml as you suggested, and ran clean-db an  ant -Dsource=simr-gff -v but u get the same errors.

I then tried adding the reference line to my additions.xml, this also did not work.

Any other ideas???
Thank you very much,
Sofia





On Fri, Sep 11, 2015 at 10:41 AM, Krishnakumar, Vivek <[hidden email]> wrote:
Also, since ‘Gene’ extends ‘SequenceFeature’, you would also have to extend the model to replace this reference:

Replace this: <reference name="chromosome" referenced-type="Chromosome" />
With this: <reference name=config" referenced-type=Contig" />

Thank you.
Vivek

On Sep 11, 2015, at 12:37 PM, Krishnakumar, Vivek <[hidden email]> wrote:

Hi Sofia,

The error you are encountering seems to be because ‘Contig’ is not part of the core (https://github.com/intermine/intermine/blob/master/bio/core/core.xml) InterMine data model or the genomic additions (https://github.com/intermine/intermine/blob/master/bio/core/genomic_additions.xml).

You would have to extend your data model, preferably within the simr-gff_additions.xml (an example additions file: https://github.com/intermine/intermine/blob/beta/bio/sources/fly/drosdel-gff/drosdel-gff_additions.xml).

You can define the ‘Contig’ entity in the data model similar to how the ‘Chromosome’ entity is defined:

Hope this helps!

Thank you.
Vivek

On Sep 11, 2015, at 12:30 PM, Sofia Robb <[hidden email]> wrote:

I changed my project.xml as you suggested but I get the same error. I ran the clean build-db before I ran ant -Dsource=simr-gff -v.

Sofia

On Fri, Sep 11, 2015 at 10:14 AM, sergio contrino <[hidden email]> wrote:
hi sofia,
your simr-gff_additions.xml should be enough and you should not need to add the other 2.
can you try calling your source "simr-gff"?
like

    <source name="simr-gff" type="simr-gff">
      <property name="gff3.taxonId" value="79327"/>
      <property name="gff3.seqDataSourceName" value="SmedGD"/>
      <property name="gff3.dataSourceName" value="mk5-SmedSxl-v31"/>
      <property name="gff3.seqClsName" value="Contig"/>
      <property name="gff3.dataSetTitle" value="SmedSxlv31 MK5"/>
      <property name="src.data.dir" location="/home/SGC/smr/data/organisms/planaria/Smed/SmedSxl/genome/v31/split"/>
    </source>

thanks
sergio




On 11/09/15 15:54, Sofia Robb wrote:
Hi Sergio,

I am getting this error about Contig not being in the Model when I run
this command:

cd /data/intermine/simrmine/dbmodel/
ant clean build-db
cd ../integrate
ant -Dsource=SmedSxl_v31-gff -v

BUILD FAILED
/var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: The
following error occurred while executing this line:
/var/lib/pgsql/other_data/intermine/imbuild/source.xml:253:
java.lang.IllegalArgumentException: class
"org.intermine.model.bio.Contig" is not in the Model

How do I get Contig to be in my model? Here is what I have tried.


#### my project.xml ####

     <source name="SmedSxl_v31-gff" type="simr-gff">
       <property name="gff3.taxonId" value="79327"/>
       <property name="gff3.seqDataSourceName" value="SmedGD"/>
       <property name="gff3.dataSourceName" value="mk5-SmedSxl-v31"/>
       <property name="gff3.seqClsName" value="Contig"/>
       <property name="gff3.dataSetTitle" value="SmedSxlv31 MK5"/>
       <property name="src.data.dir"
location="/home/SGC/smr/data/organisms/planaria/Smed/SmedSxl/genome/v31/split"/>
     </source>

####  my simr-gff_additions.xml ####

<classes>
<!-- add any <class> elements here -->
    <class name="Contig"  extends="SequenceFeature"
is-interface="true"></class>
</classes>




when this didn't work I:

I also added Contig to bio/core/genomic_additions.xml
   <class name="Contig"  extends="SequenceFeature"
is-interface="true"></class>


When I saw that there was no Contig.class in
dbmodel/build/classes/org/intermine/model/bio/
I also added contig to dbmodel/resources/so_terms

I have all of the above in place now, and I have done a 'ant clean
build-db' after each change.

I think I am missing something.

Thanks,
Sofia




On Fri, Sep 11, 2015 at 3:17 AM, sergio contrino <[hidden email]
<mailto:[hidden email]>> wrote:

    hello sofia,
    yes, this seems right to me.
    please refer to the docs here
    http://intermine.readthedocs.org/en/latest/get-started/tutorial/#loading-genome-data-from-gff3-and-fasta
    but i think you did already.
    let us know if you have any problem.
    thanks
    sergio



    On 10/09/15 21:41, Sofia Robb wrote:

        Hello,

        I built my own data source of type gff. My reference sequences
        are not
        chromosomes, they are contigs. How do I add class contig?



              <source name="SmedSxl_v31-gff" type="simr-gff">

                <property name="gff3.seqClsName" value="Contig"/>

              </source>

        Thanks,
        Sofia


        _______________________________________________
        dev mailing list
        [hidden email] <mailto:[hidden email]>
        http://mail.intermine.org/cgi-bin/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]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev



_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
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Re: adding class contig

vkrishna
After the model merging is complete, what do you see within the file: dbmodel/build/model/genomic_model.xml
(The above file should be inside your mine directory).

Does the ‘Contig’ class appear here?

Thank you.
Vivek

On Sep 11, 2015, at 12:52 PM, Sofia Robb <[hidden email]> wrote:

Hi Vivek

I tried adding the following to my simr-gff_additions.xml.

   <class name="Contig"  extends="SequenceFeature" is-interface="true"></class>


I added the reference line you mentioned to core.xml as you suggested, and ran clean-db an  ant -Dsource=simr-gff -v but u get the same errors.

I then tried adding the reference line to my additions.xml, this also did not work.

Any other ideas???
Thank you very much,
Sofia





On Fri, Sep 11, 2015 at 10:41 AM, Krishnakumar, Vivek <[hidden email]> wrote:
Also, since ‘Gene’ extends ‘SequenceFeature’, you would also have to extend the model to replace this reference:

Replace this: <reference name="chromosome" referenced-type="Chromosome" />
With this: <reference name=config" referenced-type=Contig" />

Thank you.
Vivek

On Sep 11, 2015, at 12:37 PM, Krishnakumar, Vivek <[hidden email]> wrote:

Hi Sofia,

The error you are encountering seems to be because ‘Contig’ is not part of the core (https://github.com/intermine/intermine/blob/master/bio/core/core.xml) InterMine data model or the genomic additions (https://github.com/intermine/intermine/blob/master/bio/core/genomic_additions.xml).

You would have to extend your data model, preferably within the simr-gff_additions.xml (an example additions file: https://github.com/intermine/intermine/blob/beta/bio/sources/fly/drosdel-gff/drosdel-gff_additions.xml).

You can define the ‘Contig’ entity in the data model similar to how the ‘Chromosome’ entity is defined:

Hope this helps!

Thank you.
Vivek

On Sep 11, 2015, at 12:30 PM, Sofia Robb <[hidden email]> wrote:

I changed my project.xml as you suggested but I get the same error. I ran the clean build-db before I ran ant -Dsource=simr-gff -v.

Sofia

On Fri, Sep 11, 2015 at 10:14 AM, sergio contrino <[hidden email]> wrote:
hi sofia,
your simr-gff_additions.xml should be enough and you should not need to add the other 2.
can you try calling your source "simr-gff"?
like

    <source name="simr-gff" type="simr-gff">
      <property name="gff3.taxonId" value="79327"/>
      <property name="gff3.seqDataSourceName" value="SmedGD"/>
      <property name="gff3.dataSourceName" value="mk5-SmedSxl-v31"/>
      <property name="gff3.seqClsName" value="Contig"/>
      <property name="gff3.dataSetTitle" value="SmedSxlv31 MK5"/>
      <property name="src.data.dir" location="/home/SGC/smr/data/organisms/planaria/Smed/SmedSxl/genome/v31/split"/>
    </source>

thanks
sergio




On 11/09/15 15:54, Sofia Robb wrote:
Hi Sergio,

I am getting this error about Contig not being in the Model when I run
this command:

cd /data/intermine/simrmine/dbmodel/
ant clean build-db
cd ../integrate
ant -Dsource=SmedSxl_v31-gff -v

BUILD FAILED
/var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: The
following error occurred while executing this line:
/var/lib/pgsql/other_data/intermine/imbuild/source.xml:253:
java.lang.IllegalArgumentException: class
"org.intermine.model.bio.Contig" is not in the Model

How do I get Contig to be in my model? Here is what I have tried.


#### my project.xml ####

     <source name="SmedSxl_v31-gff" type="simr-gff">
       <property name="gff3.taxonId" value="79327"/>
       <property name="gff3.seqDataSourceName" value="SmedGD"/>
       <property name="gff3.dataSourceName" value="mk5-SmedSxl-v31"/>
       <property name="gff3.seqClsName" value="Contig"/>
       <property name="gff3.dataSetTitle" value="SmedSxlv31 MK5"/>
       <property name="src.data.dir"
location="/home/SGC/smr/data/organisms/planaria/Smed/SmedSxl/genome/v31/split"/>
     </source>

####  my simr-gff_additions.xml ####

<classes>
<!-- add any <class> elements here -->
    <class name="Contig"  extends="SequenceFeature"
is-interface="true"></class>
</classes>




when this didn't work I:

I also added Contig to bio/core/genomic_additions.xml
   <class name="Contig"  extends="SequenceFeature"
is-interface="true"></class>


When I saw that there was no Contig.class in
dbmodel/build/classes/org/intermine/model/bio/
I also added contig to dbmodel/resources/so_terms

I have all of the above in place now, and I have done a 'ant clean
build-db' after each change.

I think I am missing something.

Thanks,
Sofia




On Fri, Sep 11, 2015 at 3:17 AM, sergio contrino <[hidden email]
<mailto:[hidden email]>> wrote:

    hello sofia,
    yes, this seems right to me.
    please refer to the docs here
    http://intermine.readthedocs.org/en/latest/get-started/tutorial/#loading-genome-data-from-gff3-and-fasta
    but i think you did already.
    let us know if you have any problem.
    thanks
    sergio



    On 10/09/15 21:41, Sofia Robb wrote:

        Hello,

        I built my own data source of type gff. My reference sequences
        are not
        chromosomes, they are contigs. How do I add class contig?



              <source name="SmedSxl_v31-gff" type="simr-gff">

                <property name="gff3.seqClsName" value="Contig"/>

              </source>

        Thanks,
        Sofia


        _______________________________________________
        dev mailing list
        [hidden email] <mailto:[hidden email]>
        http://mail.intermine.org/cgi-bin/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]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev




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dev mailing list
[hidden email]
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Re: adding class contig

Sofia Robb
no, it is not there. What am I missing? 

I do have a Contig.class in dbmodel/build/classes/org/intermine/model/bio/

On Fri, Sep 11, 2015 at 10:58 AM, Krishnakumar, Vivek <[hidden email]> wrote:
After the model merging is complete, what do you see within the file: dbmodel/build/model/genomic_model.xml
(The above file should be inside your mine directory).

Does the ‘Contig’ class appear here?

Thank you.
Vivek

On Sep 11, 2015, at 12:52 PM, Sofia Robb <[hidden email]> wrote:

Hi Vivek

I tried adding the following to my simr-gff_additions.xml.

   <class name="Contig"  extends="SequenceFeature" is-interface="true"></class>


I added the reference line you mentioned to core.xml as you suggested, and ran clean-db an  ant -Dsource=simr-gff -v but u get the same errors.

I then tried adding the reference line to my additions.xml, this also did not work.

Any other ideas???
Thank you very much,
Sofia





On Fri, Sep 11, 2015 at 10:41 AM, Krishnakumar, Vivek <[hidden email]> wrote:
Also, since ‘Gene’ extends ‘SequenceFeature’, you would also have to extend the model to replace this reference:

Replace this: <reference name="chromosome" referenced-type="Chromosome" />
With this: <reference name=config" referenced-type=Contig" />

Thank you.
Vivek

On Sep 11, 2015, at 12:37 PM, Krishnakumar, Vivek <[hidden email]> wrote:

Hi Sofia,

The error you are encountering seems to be because ‘Contig’ is not part of the core (https://github.com/intermine/intermine/blob/master/bio/core/core.xml) InterMine data model or the genomic additions (https://github.com/intermine/intermine/blob/master/bio/core/genomic_additions.xml).

You would have to extend your data model, preferably within the simr-gff_additions.xml (an example additions file: https://github.com/intermine/intermine/blob/beta/bio/sources/fly/drosdel-gff/drosdel-gff_additions.xml).

You can define the ‘Contig’ entity in the data model similar to how the ‘Chromosome’ entity is defined:

Hope this helps!

Thank you.
Vivek

On Sep 11, 2015, at 12:30 PM, Sofia Robb <[hidden email]> wrote:

I changed my project.xml as you suggested but I get the same error. I ran the clean build-db before I ran ant -Dsource=simr-gff -v.

Sofia

On Fri, Sep 11, 2015 at 10:14 AM, sergio contrino <[hidden email]> wrote:
hi sofia,
your simr-gff_additions.xml should be enough and you should not need to add the other 2.
can you try calling your source "simr-gff"?
like

    <source name="simr-gff" type="simr-gff">
      <property name="gff3.taxonId" value="79327"/>
      <property name="gff3.seqDataSourceName" value="SmedGD"/>
      <property name="gff3.dataSourceName" value="mk5-SmedSxl-v31"/>
      <property name="gff3.seqClsName" value="Contig"/>
      <property name="gff3.dataSetTitle" value="SmedSxlv31 MK5"/>
      <property name="src.data.dir" location="/home/SGC/smr/data/organisms/planaria/Smed/SmedSxl/genome/v31/split"/>
    </source>

thanks
sergio




On 11/09/15 15:54, Sofia Robb wrote:
Hi Sergio,

I am getting this error about Contig not being in the Model when I run
this command:

cd /data/intermine/simrmine/dbmodel/
ant clean build-db
cd ../integrate
ant -Dsource=SmedSxl_v31-gff -v

BUILD FAILED
/var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: The
following error occurred while executing this line:
/var/lib/pgsql/other_data/intermine/imbuild/source.xml:253:
java.lang.IllegalArgumentException: class
"org.intermine.model.bio.Contig" is not in the Model

How do I get Contig to be in my model? Here is what I have tried.


#### my project.xml ####

     <source name="SmedSxl_v31-gff" type="simr-gff">
       <property name="gff3.taxonId" value="79327"/>
       <property name="gff3.seqDataSourceName" value="SmedGD"/>
       <property name="gff3.dataSourceName" value="mk5-SmedSxl-v31"/>
       <property name="gff3.seqClsName" value="Contig"/>
       <property name="gff3.dataSetTitle" value="SmedSxlv31 MK5"/>
       <property name="src.data.dir"
location="/home/SGC/smr/data/organisms/planaria/Smed/SmedSxl/genome/v31/split"/>
     </source>

####  my simr-gff_additions.xml ####

<classes>
<!-- add any <class> elements here -->
    <class name="Contig"  extends="SequenceFeature"
is-interface="true"></class>
</classes>




when this didn't work I:

I also added Contig to bio/core/genomic_additions.xml
   <class name="Contig"  extends="SequenceFeature"
is-interface="true"></class>


When I saw that there was no Contig.class in
dbmodel/build/classes/org/intermine/model/bio/
I also added contig to dbmodel/resources/so_terms

I have all of the above in place now, and I have done a 'ant clean
build-db' after each change.

I think I am missing something.

Thanks,
Sofia




On Fri, Sep 11, 2015 at 3:17 AM, sergio contrino <[hidden email]
<mailto:[hidden email]>> wrote:

    hello sofia,
    yes, this seems right to me.
    please refer to the docs here
    http://intermine.readthedocs.org/en/latest/get-started/tutorial/#loading-genome-data-from-gff3-and-fasta
    but i think you did already.
    let us know if you have any problem.
    thanks
    sergio



    On 10/09/15 21:41, Sofia Robb wrote:

        Hello,

        I built my own data source of type gff. My reference sequences
        are not
        chromosomes, they are contigs. How do I add class contig?



              <source name="SmedSxl_v31-gff" type="simr-gff">

                <property name="gff3.seqClsName" value="Contig"/>

              </source>

        Thanks,
        Sofia


        _______________________________________________
        dev mailing list
        [hidden email] <mailto:[hidden email]>
        http://mail.intermine.org/cgi-bin/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]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

_______________________________________________
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[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev





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Re: adding class contig

vkrishna
Hi Sofia,

I just came to realize that the concept of the ‘Chromosome’ class forms the core of InterMine and its woven into every aspect of the data model and has been adapted by other mines/data-loaders as well.

So, for now you would need to use this class to accommodate your ‘Contigs’.

What you can do however, is at the display level, map the ‘Chromosome’ class to a desired label of your liking, following the instructions in this page: http://intermine.readthedocs.org/en/latest/data-model/data-labels/

The InterMine devs can chime in regarding this, as I personally do not have an example implementation which uses this form of an override.

Hope this helps!

Thank you.
Vivek

On Sep 11, 2015, at 1:03 PM, Sofia Robb <[hidden email]> wrote:

no, it is not there. What am I missing? 

I do have a Contig.class in dbmodel/build/classes/org/intermine/model/bio/

On Fri, Sep 11, 2015 at 10:58 AM, Krishnakumar, Vivek <[hidden email]> wrote:
After the model merging is complete, what do you see within the file: dbmodel/build/model/genomic_model.xml
(The above file should be inside your mine directory).

Does the ‘Contig’ class appear here?

Thank you.
Vivek

On Sep 11, 2015, at 12:52 PM, Sofia Robb <[hidden email]> wrote:

Hi Vivek

I tried adding the following to my simr-gff_additions.xml.

   <class name="Contig"  extends="SequenceFeature" is-interface="true"></class>


I added the reference line you mentioned to core.xml as you suggested, and ran clean-db an  ant -Dsource=simr-gff -v but u get the same errors.

I then tried adding the reference line to my additions.xml, this also did not work.

Any other ideas???
Thank you very much,
Sofia





On Fri, Sep 11, 2015 at 10:41 AM, Krishnakumar, Vivek <[hidden email]> wrote:
Also, since ‘Gene’ extends ‘SequenceFeature’, you would also have to extend the model to replace this reference:

Replace this: <reference name="chromosome" referenced-type="Chromosome" />
With this: <reference name=config" referenced-type=Contig" />

Thank you.
Vivek

On Sep 11, 2015, at 12:37 PM, Krishnakumar, Vivek <[hidden email]> wrote:

Hi Sofia,

The error you are encountering seems to be because ‘Contig’ is not part of the core (https://github.com/intermine/intermine/blob/master/bio/core/core.xml) InterMine data model or the genomic additions (https://github.com/intermine/intermine/blob/master/bio/core/genomic_additions.xml).

You would have to extend your data model, preferably within the simr-gff_additions.xml (an example additions file: https://github.com/intermine/intermine/blob/beta/bio/sources/fly/drosdel-gff/drosdel-gff_additions.xml).

You can define the ‘Contig’ entity in the data model similar to how the ‘Chromosome’ entity is defined:

Hope this helps!

Thank you.
Vivek

On Sep 11, 2015, at 12:30 PM, Sofia Robb <[hidden email]> wrote:

I changed my project.xml as you suggested but I get the same error. I ran the clean build-db before I ran ant -Dsource=simr-gff -v.

Sofia

On Fri, Sep 11, 2015 at 10:14 AM, sergio contrino <[hidden email]> wrote:
hi sofia,
your simr-gff_additions.xml should be enough and you should not need to add the other 2.
can you try calling your source "simr-gff"?
like

    <source name="simr-gff" type="simr-gff">
      <property name="gff3.taxonId" value="79327"/>
      <property name="gff3.seqDataSourceName" value="SmedGD"/>
      <property name="gff3.dataSourceName" value="mk5-SmedSxl-v31"/>
      <property name="gff3.seqClsName" value="Contig"/>
      <property name="gff3.dataSetTitle" value="SmedSxlv31 MK5"/>
      <property name="src.data.dir" location="/home/SGC/smr/data/organisms/planaria/Smed/SmedSxl/genome/v31/split"/>
    </source>

thanks
sergio




On 11/09/15 15:54, Sofia Robb wrote:
Hi Sergio,

I am getting this error about Contig not being in the Model when I run
this command:

cd /data/intermine/simrmine/dbmodel/
ant clean build-db
cd ../integrate
ant -Dsource=SmedSxl_v31-gff -v

BUILD FAILED
/var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: The
following error occurred while executing this line:
/var/lib/pgsql/other_data/intermine/imbuild/source.xml:253:
java.lang.IllegalArgumentException: class
"org.intermine.model.bio.Contig" is not in the Model

How do I get Contig to be in my model? Here is what I have tried.


#### my project.xml ####

     <source name="SmedSxl_v31-gff" type="simr-gff">
       <property name="gff3.taxonId" value="79327"/>
       <property name="gff3.seqDataSourceName" value="SmedGD"/>
       <property name="gff3.dataSourceName" value="mk5-SmedSxl-v31"/>
       <property name="gff3.seqClsName" value="Contig"/>
       <property name="gff3.dataSetTitle" value="SmedSxlv31 MK5"/>
       <property name="src.data.dir"
location="/home/SGC/smr/data/organisms/planaria/Smed/SmedSxl/genome/v31/split"/>
     </source>

####  my simr-gff_additions.xml ####

<classes>
<!-- add any <class> elements here -->
    <class name="Contig"  extends="SequenceFeature"
is-interface="true"></class>
</classes>




when this didn't work I:

I also added Contig to bio/core/genomic_additions.xml
   <class name="Contig"  extends="SequenceFeature"
is-interface="true"></class>


When I saw that there was no Contig.class in
dbmodel/build/classes/org/intermine/model/bio/
I also added contig to dbmodel/resources/so_terms

I have all of the above in place now, and I have done a 'ant clean
build-db' after each change.

I think I am missing something.

Thanks,
Sofia




On Fri, Sep 11, 2015 at 3:17 AM, sergio contrino <[hidden email]
<mailto:[hidden email]>> wrote:

    hello sofia,
    yes, this seems right to me.
    please refer to the docs here
    http://intermine.readthedocs.org/en/latest/get-started/tutorial/#loading-genome-data-from-gff3-and-fasta
    but i think you did already.
    let us know if you have any problem.
    thanks
    sergio



    On 10/09/15 21:41, Sofia Robb wrote:

        Hello,

        I built my own data source of type gff. My reference sequences
        are not
        chromosomes, they are contigs. How do I add class contig?



              <source name="SmedSxl_v31-gff" type="simr-gff">

                <property name="gff3.seqClsName" value="Contig"/>

              </source>

        Thanks,
        Sofia


        _______________________________________________
        dev mailing list
        [hidden email] <mailto:[hidden email]>
        http://mail.intermine.org/cgi-bin/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]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev






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Re: adding class contig

Sofia Robb
Ok. It makes sense now why I couldn't get it to work. Thank you! This probably explains why I was unsuccessful when I was trying to load my data from my chado-db.

Thank you,
Sofia

On Fri, Sep 11, 2015 at 11:27 AM, Krishnakumar, Vivek <[hidden email]> wrote:
Hi Sofia,

I just came to realize that the concept of the ‘Chromosome’ class forms the core of InterMine and its woven into every aspect of the data model and has been adapted by other mines/data-loaders as well.

So, for now you would need to use this class to accommodate your ‘Contigs’.

What you can do however, is at the display level, map the ‘Chromosome’ class to a desired label of your liking, following the instructions in this page: http://intermine.readthedocs.org/en/latest/data-model/data-labels/

The InterMine devs can chime in regarding this, as I personally do not have an example implementation which uses this form of an override.

Hope this helps!

Thank you.
Vivek

On Sep 11, 2015, at 1:03 PM, Sofia Robb <[hidden email]> wrote:

no, it is not there. What am I missing? 

I do have a Contig.class in dbmodel/build/classes/org/intermine/model/bio/

On Fri, Sep 11, 2015 at 10:58 AM, Krishnakumar, Vivek <[hidden email]> wrote:
After the model merging is complete, what do you see within the file: dbmodel/build/model/genomic_model.xml
(The above file should be inside your mine directory).

Does the ‘Contig’ class appear here?

Thank you.
Vivek

On Sep 11, 2015, at 12:52 PM, Sofia Robb <[hidden email]> wrote:

Hi Vivek

I tried adding the following to my simr-gff_additions.xml.

   <class name="Contig"  extends="SequenceFeature" is-interface="true"></class>


I added the reference line you mentioned to core.xml as you suggested, and ran clean-db an  ant -Dsource=simr-gff -v but u get the same errors.

I then tried adding the reference line to my additions.xml, this also did not work.

Any other ideas???
Thank you very much,
Sofia





On Fri, Sep 11, 2015 at 10:41 AM, Krishnakumar, Vivek <[hidden email]> wrote:
Also, since ‘Gene’ extends ‘SequenceFeature’, you would also have to extend the model to replace this reference:

Replace this: <reference name="chromosome" referenced-type="Chromosome" />
With this: <reference name=config" referenced-type=Contig" />

Thank you.
Vivek

On Sep 11, 2015, at 12:37 PM, Krishnakumar, Vivek <[hidden email]> wrote:

Hi Sofia,

The error you are encountering seems to be because ‘Contig’ is not part of the core (https://github.com/intermine/intermine/blob/master/bio/core/core.xml) InterMine data model or the genomic additions (https://github.com/intermine/intermine/blob/master/bio/core/genomic_additions.xml).

You would have to extend your data model, preferably within the simr-gff_additions.xml (an example additions file: https://github.com/intermine/intermine/blob/beta/bio/sources/fly/drosdel-gff/drosdel-gff_additions.xml).

You can define the ‘Contig’ entity in the data model similar to how the ‘Chromosome’ entity is defined:

Hope this helps!

Thank you.
Vivek

On Sep 11, 2015, at 12:30 PM, Sofia Robb <[hidden email]> wrote:

I changed my project.xml as you suggested but I get the same error. I ran the clean build-db before I ran ant -Dsource=simr-gff -v.

Sofia

On Fri, Sep 11, 2015 at 10:14 AM, sergio contrino <[hidden email]> wrote:
hi sofia,
your simr-gff_additions.xml should be enough and you should not need to add the other 2.
can you try calling your source "simr-gff"?
like

    <source name="simr-gff" type="simr-gff">
      <property name="gff3.taxonId" value="79327"/>
      <property name="gff3.seqDataSourceName" value="SmedGD"/>
      <property name="gff3.dataSourceName" value="mk5-SmedSxl-v31"/>
      <property name="gff3.seqClsName" value="Contig"/>
      <property name="gff3.dataSetTitle" value="SmedSxlv31 MK5"/>
      <property name="src.data.dir" location="/home/SGC/smr/data/organisms/planaria/Smed/SmedSxl/genome/v31/split"/>
    </source>

thanks
sergio




On 11/09/15 15:54, Sofia Robb wrote:
Hi Sergio,

I am getting this error about Contig not being in the Model when I run
this command:

cd /data/intermine/simrmine/dbmodel/
ant clean build-db
cd ../integrate
ant -Dsource=SmedSxl_v31-gff -v

BUILD FAILED
/var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: The
following error occurred while executing this line:
/var/lib/pgsql/other_data/intermine/imbuild/source.xml:253:
java.lang.IllegalArgumentException: class
"org.intermine.model.bio.Contig" is not in the Model

How do I get Contig to be in my model? Here is what I have tried.


#### my project.xml ####

     <source name="SmedSxl_v31-gff" type="simr-gff">
       <property name="gff3.taxonId" value="79327"/>
       <property name="gff3.seqDataSourceName" value="SmedGD"/>
       <property name="gff3.dataSourceName" value="mk5-SmedSxl-v31"/>
       <property name="gff3.seqClsName" value="Contig"/>
       <property name="gff3.dataSetTitle" value="SmedSxlv31 MK5"/>
       <property name="src.data.dir"
location="/home/SGC/smr/data/organisms/planaria/Smed/SmedSxl/genome/v31/split"/>
     </source>

####  my simr-gff_additions.xml ####

<classes>
<!-- add any <class> elements here -->
    <class name="Contig"  extends="SequenceFeature"
is-interface="true"></class>
</classes>




when this didn't work I:

I also added Contig to bio/core/genomic_additions.xml
   <class name="Contig"  extends="SequenceFeature"
is-interface="true"></class>


When I saw that there was no Contig.class in
dbmodel/build/classes/org/intermine/model/bio/
I also added contig to dbmodel/resources/so_terms

I have all of the above in place now, and I have done a 'ant clean
build-db' after each change.

I think I am missing something.

Thanks,
Sofia




On Fri, Sep 11, 2015 at 3:17 AM, sergio contrino <[hidden email]
<mailto:[hidden email]>> wrote:

    hello sofia,
    yes, this seems right to me.
    please refer to the docs here
    http://intermine.readthedocs.org/en/latest/get-started/tutorial/#loading-genome-data-from-gff3-and-fasta
    but i think you did already.
    let us know if you have any problem.
    thanks
    sergio



    On 10/09/15 21:41, Sofia Robb wrote:

        Hello,

        I built my own data source of type gff. My reference sequences
        are not
        chromosomes, they are contigs. How do I add class contig?



              <source name="SmedSxl_v31-gff" type="simr-gff">

                <property name="gff3.seqClsName" value="Contig"/>

              </source>

        Thanks,
        Sofia


        _______________________________________________
        dev mailing list
        [hidden email] <mailto:[hidden email]>
        http://mail.intermine.org/cgi-bin/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]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev







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Re: adding class contig

adf_ncgr
In reply to this post by vkrishna
Hi Vivek-
I'm probably not understanding much of the thread, but just curious how you have dealt with the
"scaffolds" for the Medicago truncatula genome; I see cases in medicmine where they appear, e.g.:
http://medicmine.jcvi.org/medicmine/report.do?id=32335145&trail=|32335145
and I'm just guessing that what Sofia wants to accomplish would be something similar?

We'll also face this with several of our other legume genomes, so I thought I'd just try to make sure I
understand the options up front.

thanks for providing us with the benefits of your experience here...

Andrew Farmer


On 9/11/15 11:27 AM, Krishnakumar, Vivek wrote:
Hi Sofia,

I just came to realize that the concept of the ‘Chromosome’ class forms the core of InterMine and its woven into every aspect of the data model and has been adapted by other mines/data-loaders as well.

So, for now you would need to use this class to accommodate your ‘Contigs’.

What you can do however, is at the display level, map the ‘Chromosome’ class to a desired label of your liking, following the instructions in this page: http://intermine.readthedocs.org/en/latest/data-model/data-labels/

The InterMine devs can chime in regarding this, as I personally do not have an example implementation which uses this form of an override.

Hope this helps!

Thank you.
Vivek

On Sep 11, 2015, at 1:03 PM, Sofia Robb <[hidden email]> wrote:

no, it is not there. What am I missing? 

I do have a Contig.class in dbmodel/build/classes/org/intermine/model/bio/

On Fri, Sep 11, 2015 at 10:58 AM, Krishnakumar, Vivek <[hidden email]> wrote:
After the model merging is complete, what do you see within the file: dbmodel/build/model/genomic_model.xml
(The above file should be inside your mine directory).

Does the ‘Contig’ class appear here?

Thank you.
Vivek

On Sep 11, 2015, at 12:52 PM, Sofia Robb <[hidden email]> wrote:

Hi Vivek

I tried adding the following to my simr-gff_additions.xml.

   <class name="Contig"  extends="SequenceFeature" is-interface="true"></class>


I added the reference line you mentioned to core.xml as you suggested, and ran clean-db an  ant -Dsource=simr-gff -v but u get the same errors.

I then tried adding the reference line to my additions.xml, this also did not work.

Any other ideas???
Thank you very much,
Sofia





On Fri, Sep 11, 2015 at 10:41 AM, Krishnakumar, Vivek <[hidden email]> wrote:
Also, since ‘Gene’ extends ‘SequenceFeature’, you would also have to extend the model to replace this reference:

Replace this: <reference name="chromosome" referenced-type="Chromosome" />
With this: <reference name=config" referenced-type=Contig" />

Thank you.
Vivek

On Sep 11, 2015, at 12:37 PM, Krishnakumar, Vivek <[hidden email]> wrote:

Hi Sofia,

The error you are encountering seems to be because ‘Contig’ is not part of the core (https://github.com/intermine/intermine/blob/master/bio/core/core.xml) InterMine data model or the genomic additions (https://github.com/intermine/intermine/blob/master/bio/core/genomic_additions.xml).

You would have to extend your data model, preferably within the simr-gff_additions.xml (an example additions file: https://github.com/intermine/intermine/blob/beta/bio/sources/fly/drosdel-gff/drosdel-gff_additions.xml).

You can define the ‘Contig’ entity in the data model similar to how the ‘Chromosome’ entity is defined:

Hope this helps!

Thank you.
Vivek

On Sep 11, 2015, at 12:30 PM, Sofia Robb <[hidden email]> wrote:

I changed my project.xml as you suggested but I get the same error. I ran the clean build-db before I ran ant -Dsource=simr-gff -v.

Sofia

On Fri, Sep 11, 2015 at 10:14 AM, sergio contrino <[hidden email]> wrote:
hi sofia,
your simr-gff_additions.xml should be enough and you should not need to add the other 2.
can you try calling your source "simr-gff"?
like

    <source name="simr-gff" type="simr-gff">
      <property name="gff3.taxonId" value="79327"/>
      <property name="gff3.seqDataSourceName" value="SmedGD"/>
      <property name="gff3.dataSourceName" value="mk5-SmedSxl-v31"/>
      <property name="gff3.seqClsName" value="Contig"/>
      <property name="gff3.dataSetTitle" value="SmedSxlv31 MK5"/>
      <property name="src.data.dir" location="/home/SGC/smr/data/organisms/planaria/Smed/SmedSxl/genome/v31/split"/>
    </source>

thanks
sergio




On 11/09/15 15:54, Sofia Robb wrote:
Hi Sergio,

I am getting this error about Contig not being in the Model when I run
this command:

cd /data/intermine/simrmine/dbmodel/
ant clean build-db
cd ../integrate
ant -Dsource=SmedSxl_v31-gff -v

BUILD FAILED
/var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: The
following error occurred while executing this line:
/var/lib/pgsql/other_data/intermine/imbuild/source.xml:253:
java.lang.IllegalArgumentException: class
"org.intermine.model.bio.Contig" is not in the Model

How do I get Contig to be in my model? Here is what I have tried.


#### my project.xml ####

     <source name="SmedSxl_v31-gff" type="simr-gff">
       <property name="gff3.taxonId" value="79327"/>
       <property name="gff3.seqDataSourceName" value="SmedGD"/>
       <property name="gff3.dataSourceName" value="mk5-SmedSxl-v31"/>
       <property name="gff3.seqClsName" value="Contig"/>
       <property name="gff3.dataSetTitle" value="SmedSxlv31 MK5"/>
       <property name="src.data.dir"
location="/home/SGC/smr/data/organisms/planaria/Smed/SmedSxl/genome/v31/split"/>
     </source>

####  my simr-gff_additions.xml ####

<classes>
<!-- add any <class> elements here -->
    <class name="Contig"  extends="SequenceFeature"
is-interface="true"></class>
</classes>




when this didn't work I:

I also added Contig to bio/core/genomic_additions.xml
   <class name="Contig"  extends="SequenceFeature"
is-interface="true"></class>


When I saw that there was no Contig.class in
dbmodel/build/classes/org/intermine/model/bio/
I also added contig to dbmodel/resources/so_terms

I have all of the above in place now, and I have done a 'ant clean
build-db' after each change.

I think I am missing something.

Thanks,
Sofia




On Fri, Sep 11, 2015 at 3:17 AM, sergio contrino <[hidden email]
<mailto:[hidden email]>> wrote:

    hello sofia,
    yes, this seems right to me.
    please refer to the docs here
    http://intermine.readthedocs.org/en/latest/get-started/tutorial/#loading-genome-data-from-gff3-and-fasta
    but i think you did already.
    let us know if you have any problem.
    thanks
    sergio



    On 10/09/15 21:41, Sofia Robb wrote:

        Hello,

        I built my own data source of type gff. My reference sequences
        are not
        chromosomes, they are contigs. How do I add class contig?



              <source name="SmedSxl_v31-gff" type="simr-gff">

                <property name="gff3.seqClsName" value="Contig"/>

              </source>

        Thanks,
        Sofia


        _______________________________________________
        dev mailing list
        [hidden email] <mailto:[hidden email]>
        http://mail.intermine.org/cgi-bin/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

_______________________________________________
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-- 
...all concepts in which an entire process is semiotically concentrated
elude definition; only that which has no history is definable.

Friedrich Nietzsche

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Re: adding class contig

vkrishna
Hi Andrew,

In the case of MedicMine, we’ve chosen to stick with the ‘Chromosome' class since we do have 8 assembled chromosomes + unplaced scaffolds.

In such a situation, users need to be aware that when developing a query using the QueryBuilder, the ‘Chromosome’ class is to be chosen irrespective of whether the query involves a chromosome or scaffold entity. I believe there is no way to selectively alter the label for the ‘Chromosome’ class based on different SequenceFeature entities.

Looking through GitHub, I found one example of where FlyMine is using class labels to alter the display:

Labels are not restricted to classes. They can also be applied to fields within a class, like so:

More information about data labels are available here: http://intermine.readthedocs.org/en/latest/data-model/data-labels/

Hope the above information clarifies the issue somewhat.

Thank you.
Vivek

On Sep 11, 2015, at 2:02 PM, Andrew Farmer <[hidden email]> wrote:

Hi Vivek-
I'm probably not understanding much of the thread, but just curious how you have dealt with the
"scaffolds" for the Medicago truncatula genome; I see cases in medicmine where they appear, e.g.:
http://medicmine.jcvi.org/medicmine/report.do?id=32335145&trail=|32335145
and I'm just guessing that what Sofia wants to accomplish would be something similar?

We'll also face this with several of our other legume genomes, so I thought I'd just try to make sure I
understand the options up front.

thanks for providing us with the benefits of your experience here...

Andrew Farmer


On 9/11/15 11:27 AM, Krishnakumar, Vivek wrote:
Hi Sofia,

I just came to realize that the concept of the ‘Chromosome’ class forms the core of InterMine and its woven into every aspect of the data model and has been adapted by other mines/data-loaders as well.

So, for now you would need to use this class to accommodate your ‘Contigs’.

What you can do however, is at the display level, map the ‘Chromosome’ class to a desired label of your liking, following the instructions in this page: http://intermine.readthedocs.org/en/latest/data-model/data-labels/

The InterMine devs can chime in regarding this, as I personally do not have an example implementation which uses this form of an override.

Hope this helps!

Thank you.
Vivek

On Sep 11, 2015, at 1:03 PM, Sofia Robb <[hidden email][hidden email]> wrote:

no, it is not there. What am I missing? 

I do have a Contig.class in dbmodel/build/classes/org/intermine/model/bio/

On Fri, Sep 11, 2015 at 10:58 AM, Krishnakumar, Vivek <[hidden email][hidden email]> wrote:
After the model merging is complete, what do you see within the file: dbmodel/build/model/genomic_model.xml
(The above file should be inside your mine directory).

Does the ‘Contig’ class appear here?

Thank you.
Vivek

On Sep 11, 2015, at 12:52 PM, Sofia Robb <[hidden email][hidden email]> wrote:

Hi Vivek

I tried adding the following to my simr-gff_additions.xml.

   <class name="Contig"  extends="SequenceFeature" is-interface="true"></class>


I added the reference line you mentioned to core.xml as you suggested, and ran clean-db an  ant -Dsource=simr-gff -v but u get the same errors.

I then tried adding the reference line to my additions.xml, this also did not work.

Any other ideas???
Thank you very much,
Sofia





On Fri, Sep 11, 2015 at 10:41 AM, Krishnakumar, Vivek <[hidden email][hidden email]> wrote:
Also, since ‘Gene’ extends ‘SequenceFeature’, you would also have to extend the model to replace this reference:

Replace this: <reference name="chromosome" referenced-type="Chromosome" />
With this: <reference name=config" referenced-type=Contig" />

Thank you.
Vivek

On Sep 11, 2015, at 12:37 PM, Krishnakumar, Vivek <[hidden email][hidden email]> wrote:

Hi Sofia,

The error you are encountering seems to be because ‘Contig’ is not part of the core (https://github.com/intermine/intermine/blob/master/bio/core/core.xml) InterMine data model or the genomic additions (https://github.com/intermine/intermine/blob/master/bio/core/genomic_additions.xml).

You would have to extend your data model, preferably within the simr-gff_additions.xml (an example additions file: https://github.com/intermine/intermine/blob/beta/bio/sources/fly/drosdel-gff/drosdel-gff_additions.xml).

You can define the ‘Contig’ entity in the data model similar to how the ‘Chromosome’ entity is defined:

Hope this helps!

Thank you.
Vivek

On Sep 11, 2015, at 12:30 PM, Sofia Robb <[hidden email][hidden email]> wrote:

I changed my project.xml as you suggested but I get the same error. I ran the clean build-db before I ran ant -Dsource=simr-gff -v.

Sofia

On Fri, Sep 11, 2015 at 10:14 AM, sergio contrino <[hidden email][hidden email]> wrote:
hi sofia,
your simr-gff_additions.xml should be enough and you should not need to add the other 2.
can you try calling your source "simr-gff"?
like

    <source name="simr-gff" type="simr-gff">
      <property name="gff3.taxonId" value="79327"/>
      <property name="gff3.seqDataSourceName" value="SmedGD"/>
      <property name="gff3.dataSourceName" value="mk5-SmedSxl-v31"/>
      <property name="gff3.seqClsName" value="Contig"/>
      <property name="gff3.dataSetTitle" value="SmedSxlv31 MK5"/>
      <property name="src.data.dir" location="/home/SGC/smr/data/organisms/planaria/Smed/SmedSxl/genome/v31/split"/>
    </source>

thanks
sergio




On 11/09/15 15:54, Sofia Robb wrote:
Hi Sergio,

I am getting this error about Contig not being in the Model when I run
this command:

cd /data/intermine/simrmine/dbmodel/
ant clean build-db
cd ../integrate
ant -Dsource=SmedSxl_v31-gff -v

BUILD FAILED
/var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: The
following error occurred while executing this line:
/var/lib/pgsql/other_data/intermine/imbuild/source.xml:253:
java.lang.IllegalArgumentException: class
"org.intermine.model.bio.Contig" is not in the Model

How do I get Contig to be in my model? Here is what I have tried.


#### my project.xml ####

     <source name="SmedSxl_v31-gff" type="simr-gff">
       <property name="gff3.taxonId" value="79327"/>
       <property name="gff3.seqDataSourceName" value="SmedGD"/>
       <property name="gff3.dataSourceName" value="mk5-SmedSxl-v31"/>
       <property name="gff3.seqClsName" value="Contig"/>
       <property name="gff3.dataSetTitle" value="SmedSxlv31 MK5"/>
       <property name="src.data.dir"
location="/home/SGC/smr/data/organisms/planaria/Smed/SmedSxl/genome/v31/split"/>
     </source>

####  my simr-gff_additions.xml ####

<classes>
<!-- add any <class> elements here -->
    <class name="Contig"  extends="SequenceFeature"
is-interface="true"></class>
</classes>




when this didn't work I:

I also added Contig to bio/core/genomic_additions.xml
   <class name="Contig"  extends="SequenceFeature"
is-interface="true"></class>


When I saw that there was no Contig.class in
dbmodel/build/classes/org/intermine/model/bio/
I also added contig to dbmodel/resources/so_terms

I have all of the above in place now, and I have done a 'ant clean
build-db' after each change.

I think I am missing something.

Thanks,
Sofia




On Fri, Sep 11, 2015 at 3:17 AM, sergio contrino <[hidden email][hidden email]
<mailto:[hidden email][hidden email]>> wrote:

    hello sofia,
    yes, this seems right to me.
    please refer to the docs here
    http://intermine.readthedocs.org/en/latest/get-started/tutorial/#loading-genome-data-from-gff3-and-fasta
    but i think you did already.
    let us know if you have any problem.
    thanks
    sergio



    On 10/09/15 21:41, Sofia Robb wrote:

        Hello,

        I built my own data source of type gff. My reference sequences
        are not
        chromosomes, they are contigs. How do I add class contig?



              <source name="SmedSxl_v31-gff" type="simr-gff">

                <property name="gff3.seqClsName" value="Contig"/>

              </source>

        Thanks,
        Sofia


        _______________________________________________
        dev mailing list
        [hidden email][hidden email] <mailto:[hidden email][hidden email]>
        http://mail.intermine.org/cgi-bin/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][hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email][hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev







_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

-- 
...all concepts in which an entire process is semiotically concentrated
elude definition; only that which has no history is definable.

Friedrich Nietzsche


_______________________________________________
dev mailing list
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http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
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|

Re: adding class contig

adf_ncgr
Thanks Vivek-
it definitely helps clarify things a bit. I'm probably still thinking about things more from the
Chado/SequenceOntology perspective, and not exactly clear on how these should be mapped
to the intermine classes. I'll spend some more time looking at the data model and might have
a further question for you next time our project meets.

regards

Andrew


On 9/11/15 1:47 PM, Krishnakumar, Vivek wrote:
Hi Andrew,

In the case of MedicMine, we’ve chosen to stick with the ‘Chromosome' class since we do have 8 assembled chromosomes + unplaced scaffolds.

In such a situation, users need to be aware that when developing a query using the QueryBuilder, the ‘Chromosome’ class is to be chosen irrespective of whether the query involves a chromosome or scaffold entity. I believe there is no way to selectively alter the label for the ‘Chromosome’ class based on different SequenceFeature entities.

Looking through GitHub, I found one example of where FlyMine is using class labels to alter the display:

Labels are not restricted to classes. They can also be applied to fields within a class, like so:

More information about data labels are available here: http://intermine.readthedocs.org/en/latest/data-model/data-labels/

Hope the above information clarifies the issue somewhat.

Thank you.
Vivek

On Sep 11, 2015, at 2:02 PM, Andrew Farmer <[hidden email]> wrote:

Hi Vivek-
I'm probably not understanding much of the thread, but just curious how you have dealt with the
"scaffolds" for the Medicago truncatula genome; I see cases in medicmine where they appear, e.g.:
http://medicmine.jcvi.org/medicmine/report.do?id=32335145&trail=|32335145
and I'm just guessing that what Sofia wants to accomplish would be something similar?

We'll also face this with several of our other legume genomes, so I thought I'd just try to make sure I
understand the options up front.

thanks for providing us with the benefits of your experience here...

Andrew Farmer


On 9/11/15 11:27 AM, Krishnakumar, Vivek wrote:
Hi Sofia,

I just came to realize that the concept of the ‘Chromosome’ class forms the core of InterMine and its woven into every aspect of the data model and has been adapted by other mines/data-loaders as well.

So, for now you would need to use this class to accommodate your ‘Contigs’.

What you can do however, is at the display level, map the ‘Chromosome’ class to a desired label of your liking, following the instructions in this page: http://intermine.readthedocs.org/en/latest/data-model/data-labels/

The InterMine devs can chime in regarding this, as I personally do not have an example implementation which uses this form of an override.

Hope this helps!

Thank you.
Vivek

On Sep 11, 2015, at 1:03 PM, Sofia Robb <[hidden email]> wrote:

no, it is not there. What am I missing? 

I do have a Contig.class in dbmodel/build/classes/org/intermine/model/bio/

On Fri, Sep 11, 2015 at 10:58 AM, Krishnakumar, Vivek <[hidden email]> wrote:
After the model merging is complete, what do you see within the file: dbmodel/build/model/genomic_model.xml
(The above file should be inside your mine directory).

Does the ‘Contig’ class appear here?

Thank you.
Vivek

On Sep 11, 2015, at 12:52 PM, Sofia Robb <[hidden email]> wrote:

Hi Vivek

I tried adding the following to my simr-gff_additions.xml.

   <class name="Contig"  extends="SequenceFeature" is-interface="true"></class>


I added the reference line you mentioned to core.xml as you suggested, and ran clean-db an  ant -Dsource=simr-gff -v but u get the same errors.

I then tried adding the reference line to my additions.xml, this also did not work.

Any other ideas???
Thank you very much,
Sofia





On Fri, Sep 11, 2015 at 10:41 AM, Krishnakumar, Vivek <[hidden email]> wrote:
Also, since ‘Gene’ extends ‘SequenceFeature’, you would also have to extend the model to replace this reference:

Replace this: <reference name="chromosome" referenced-type="Chromosome" />
With this: <reference name=config" referenced-type=Contig" />

Thank you.
Vivek

On Sep 11, 2015, at 12:37 PM, Krishnakumar, Vivek <[hidden email]> wrote:

Hi Sofia,

The error you are encountering seems to be because ‘Contig’ is not part of the core (https://github.com/intermine/intermine/blob/master/bio/core/core.xml) InterMine data model or the genomic additions (https://github.com/intermine/intermine/blob/master/bio/core/genomic_additions.xml).

You would have to extend your data model, preferably within the simr-gff_additions.xml (an example additions file: https://github.com/intermine/intermine/blob/beta/bio/sources/fly/drosdel-gff/drosdel-gff_additions.xml).

You can define the ‘Contig’ entity in the data model similar to how the ‘Chromosome’ entity is defined:

Hope this helps!

Thank you.
Vivek

On Sep 11, 2015, at 12:30 PM, Sofia Robb <[hidden email]> wrote:

I changed my project.xml as you suggested but I get the same error. I ran the clean build-db before I ran ant -Dsource=simr-gff -v.

Sofia

On Fri, Sep 11, 2015 at 10:14 AM, sergio contrino <[hidden email]> wrote:
hi sofia,
your simr-gff_additions.xml should be enough and you should not need to add the other 2.
can you try calling your source "simr-gff"?
like

    <source name="simr-gff" type="simr-gff">
      <property name="gff3.taxonId" value="79327"/>
      <property name="gff3.seqDataSourceName" value="SmedGD"/>
      <property name="gff3.dataSourceName" value="mk5-SmedSxl-v31"/>
      <property name="gff3.seqClsName" value="Contig"/>
      <property name="gff3.dataSetTitle" value="SmedSxlv31 MK5"/>
      <property name="src.data.dir" location="/home/SGC/smr/data/organisms/planaria/Smed/SmedSxl/genome/v31/split"/>
    </source>

thanks
sergio




On 11/09/15 15:54, Sofia Robb wrote:
Hi Sergio,

I am getting this error about Contig not being in the Model when I run
this command:

cd /data/intermine/simrmine/dbmodel/
ant clean build-db
cd ../integrate
ant -Dsource=SmedSxl_v31-gff -v

BUILD FAILED
/var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: The
following error occurred while executing this line:
/var/lib/pgsql/other_data/intermine/imbuild/source.xml:253:
java.lang.IllegalArgumentException: class
"org.intermine.model.bio.Contig" is not in the Model

How do I get Contig to be in my model? Here is what I have tried.


#### my project.xml ####

     <source name="SmedSxl_v31-gff" type="simr-gff">
       <property name="gff3.taxonId" value="79327"/>
       <property name="gff3.seqDataSourceName" value="SmedGD"/>
       <property name="gff3.dataSourceName" value="mk5-SmedSxl-v31"/>
       <property name="gff3.seqClsName" value="Contig"/>
       <property name="gff3.dataSetTitle" value="SmedSxlv31 MK5"/>
       <property name="src.data.dir"
location="/home/SGC/smr/data/organisms/planaria/Smed/SmedSxl/genome/v31/split"/>
     </source>

####  my simr-gff_additions.xml ####

<classes>
<!-- add any <class> elements here -->
    <class name="Contig"  extends="SequenceFeature"
is-interface="true"></class>
</classes>




when this didn't work I:

I also added Contig to bio/core/genomic_additions.xml
   <class name="Contig"  extends="SequenceFeature"
is-interface="true"></class>


When I saw that there was no Contig.class in
dbmodel/build/classes/org/intermine/model/bio/
I also added contig to dbmodel/resources/so_terms

I have all of the above in place now, and I have done a 'ant clean
build-db' after each change.

I think I am missing something.

Thanks,
Sofia




On Fri, Sep 11, 2015 at 3:17 AM, sergio contrino <[hidden email]
<mailto:[hidden email]>> wrote:

    hello sofia,
    yes, this seems right to me.
    please refer to the docs here
    http://intermine.readthedocs.org/en/latest/get-started/tutorial/#loading-genome-data-from-gff3-and-fasta
    but i think you did already.
    let us know if you have any problem.
    thanks
    sergio



    On 10/09/15 21:41, Sofia Robb wrote:

        Hello,

        I built my own data source of type gff. My reference sequences
        are not
        chromosomes, they are contigs. How do I add class contig?



              <source name="SmedSxl_v31-gff" type="simr-gff">

                <property name="gff3.seqClsName" value="Contig"/>

              </source>

        Thanks,
        Sofia


        _______________________________________________
        dev mailing list
        [hidden email] <mailto:[hidden email]>
        http://mail.intermine.org/cgi-bin/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]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev







_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

-- 
...all concepts in which an entire process is semiotically concentrated
elude definition; only that which has no history is definable.

Friedrich Nietzsche


-- 
...all concepts in which an entire process is semiotically concentrated
elude definition; only that which has no history is definable.

Friedrich Nietzsche

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev