Question about Add a column feature, dropdown lists

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Question about Add a column feature, dropdown lists

Paulo Nuin
Hi everyone

We have a ticket issued for an issue that I couldn’t find a solution. It’s on GitHub https://github.com/WormBase/website/issues/6795

Basically, the Add a column feature on the Manage columns of a result page allows for an empty column (not shown in the Model Browser, unless selected) to be added to the result page, something that seems to be causing some confusion. Is there a way to make these empty columns to be hidden in the Add a column?

Also, we have added a number of FASTA files for some other species loaded in the DB, but not all of them. Is there a way to control which sequences appear in the dropdown list of templates and other queries?

Thanks in advance

Paulo


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Re: Question about Add a column feature, dropdown lists

sergio contrino-2
thank you paul,
i have added a ticket in our repo as well
https://github.com/intermine/imjs/issues/21
i am not sure i understood the second part about the fasta load: could
you send an example?
thanks!
sergio

On 18/12/2018 22:43, Paulo Nuin wrote:

> Hi everyone
>
> We have a ticket issued for an issue that I couldn’t find a solution. It’s on GitHub https://github.com/WormBase/website/issues/6795
>
> Basically, the Add a column feature on the Manage columns of a result page allows for an empty column (not shown in the Model Browser, unless selected) to be added to the result page, something that seems to be causing some confusion. Is there a way to make these empty columns to be hidden in the Add a column?
>
> Also, we have added a number of FASTA files for some other species loaded in the DB, but not all of them. Is there a way to control which sequences appear in the dropdown list of templates and other queries?
>
> Thanks in advance
>
> Paulo
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
>

--
sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org
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Re: Question about Add a column feature, dropdown lists

Paulo Nuin
Hi Sergio

The second part is about FASTA files loading: Let’s say I load 10 different FASTA files for 10 different species, but overall I have 25 species represented on the DB (homology, etc). So 15 species won’t have a FASTA sequence loaded for them, but they will still show in the dropdown box when I go to search the DB. Is there a way to remove/hide species that don’t have sequences in the query?

Cheers
Paulo



> On Dec 19, 2018, at 4:01 AM, sergio contrino <[hidden email]> wrote:
>
> thank you paul,
> i have added a ticket in our repo as well
> https://github.com/intermine/imjs/issues/21
> i am not sure i understood the second part about the fasta load: could you send an example?
> thanks!
> sergio
>
> On 18/12/2018 22:43, Paulo Nuin wrote:
>> Hi everyone
>> We have a ticket issued for an issue that I couldn’t find a solution. It’s on GitHub https://github.com/WormBase/website/issues/6795
>> Basically, the Add a column feature on the Manage columns of a result page allows for an empty column (not shown in the Model Browser, unless selected) to be added to the result page, something that seems to be causing some confusion. Is there a way to make these empty columns to be hidden in the Add a column?
>> Also, we have added a number of FASTA files for some other species loaded in the DB, but not all of them. Is there a way to control which sequences appear in the dropdown list of templates and other queries?
>> Thanks in advance
>> Paulo
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev
>
> --
> sergio contrino                  InterMine, University of Cambridge
> https://sergiocontrino.github.io           http://www.intermine.org

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Re: Question about Add a column feature, dropdown lists

sergio contrino-2
hi paulo,
i think you are talking about the query builder; for it the answer is
no, you cannot hide species (from the dropdown of the organism).
of course you can add another constraint asking only for feature which
have sequence, an example below.
note that the fasta widget on the report page won't appear if there is
no sequence.
please let me know if i misunderstood the question
thanks!
sergio


<query model="genomic" view="Gene.secondaryIdentifier Gene.symbol
Gene.primaryIdentifier Gene.organism.name"
sortOrder="Gene.secondaryIdentifier ASC" >
   <constraint path="Gene.sequence" op="IS NULL" code="B" />
</query>

On 19/12/2018 18:26, Paulo Nuin wrote:

> Hi Sergio
>
> The second part is about FASTA files loading: Let’s say I load 10 different FASTA files for 10 different species, but overall I have 25 species represented on the DB (homology, etc). So 15 species won’t have a FASTA sequence loaded for them, but they will still show in the dropdown box when I go to search the DB. Is there a way to remove/hide species that don’t have sequences in the query?
>
> Cheers
> Paulo
>
>
>
>> On Dec 19, 2018, at 4:01 AM, sergio contrino <[hidden email]> wrote:
>>
>> thank you paul,
>> i have added a ticket in our repo as well
>> https://github.com/intermine/imjs/issues/21
>> i am not sure i understood the second part about the fasta load: could you send an example?
>> thanks!
>> sergio
>>
>> On 18/12/2018 22:43, Paulo Nuin wrote:
>>> Hi everyone
>>> We have a ticket issued for an issue that I couldn’t find a solution. It’s on GitHub https://github.com/WormBase/website/issues/6795
>>> Basically, the Add a column feature on the Manage columns of a result page allows for an empty column (not shown in the Model Browser, unless selected) to be added to the result page, something that seems to be causing some confusion. Is there a way to make these empty columns to be hidden in the Add a column?
>>> Also, we have added a number of FASTA files for some other species loaded in the DB, but not all of them. Is there a way to control which sequences appear in the dropdown list of templates and other queries?
>>> Thanks in advance
>>> Paulo
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> https://lists.intermine.org/mailman/listinfo/dev
>>
>> --
>> sergio contrino                  InterMine, University of Cambridge
>> https://sergiocontrino.github.io           http://www.intermine.org
>

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