[Gmod-tripal-devel] Filter blast hits by evalue in a view

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[Gmod-tripal-devel] Filter blast hits by evalue in a view

Michael Dondrup-3
Hi,

I have defined a view to search within blast hits (View blast_results, displaying items of type Chado Blast Hit Data.). The view has currently filters for hit accession,
description, and database. I thought it would be neat to also have filters on max. e-value
and minimum score, so I tried to add filters to the view for:
Chado Blast Hit Data: Hit Best Eval
Hit Best Eval
Chado Blast Hit Data: Hit Best Score
Hit Best Score

However, in the filter configuration, the possible operators displayed for both are those for text fields (Is equal to, Is not equal to
 Contains, Starts with, Ends with) and not the ones for numeric data (Is less than, Is less than or equal to, etc.)
as it would be required. I looked into the DB definition for blast_hit_data and both columns are of type
double precision, so this looks ok. Is there any way to configure such filters?

Thanks a lot in advance

Michael


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Re: [Gmod-tripal-devel] Filter blast hits by evalue in a view

Stephen Ficklin-2
Hi Michael,

I'm CC'ing this question to Tripal mailing list as well.

Because the blast hit data table was added by the Tripal Analysis Blast module, that table has been automatically integrated with Drupal Views for you.  Those fields should have been set with numeric filters, so we will check the code to see why not.  But, I think you can fix this if you go to 'Administer' -> 'Tripal Management' -> 'Views Integration'.  Then click on the link 'List of integrated tables'.  You will then see the list of all Chado and custom tables.  Look for the table 'Chado Blast Hit Data' and click the 'Edit' link.    Here you can change the filters for all of the fields in that table.  Scroll down to the fields 'hit_best_eval' and 'hit_best_score' and change the filter handler from 'chado_views_handler_filter_string' to 'chado_views_handler_filter_numeric'.   Save the configuration and then go back to your View and see if that helps.  (You may have to also clear the cache (drush cc all)).

Stephen


On 10/14/2013 4:43 AM, Michael Dondrup wrote:
Hi,

I have defined a view to search within blast hits (View blast_results, displaying items of type Chado Blast Hit Data.). The view has currently filters for hit accession,
description, and database. I thought it would be neat to also have filters on max. e-value
and minimum score, so I tried to add filters to the view for:
Chado Blast Hit Data: Hit Best Eval
Hit Best Eval
Chado Blast Hit Data: Hit Best Score
Hit Best Score

However, in the filter configuration, the possible operators displayed for both are those for text fields (Is equal to, Is not equal to
 Contains, Starts with, Ends with) and not the ones for numeric data (Is less than, Is less than or equal to, etc.)
as it would be required. I looked into the DB definition for blast_hit_data and both columns are of type
double precision, so this looks ok. Is there any way to configure such filters?

Thanks a lot in advance

Michael



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Re: [Gmod-tripal-devel] Filter blast hits by evalue in a view

Michael Dondrup-3
Hi Stephen,
thank your yes that worked.

I attach the exported view for reference, in case someone wants to make something similar.

Michael

On Oct 14, 2013, at 9:36 PM, Stephen Ficklin wrote:

> Hi Michael,
>
> I'm CC'ing this question to Tripal mailing list as well.
>
> Because the blast hit data table was added by the Tripal Analysis Blast module, that table has been automatically integrated with Drupal Views for you.  Those fields should have been set with numeric filters, so we will check the code to see why not.  But, I think you can fix this if you go to 'Administer' -> 'Tripal Management' -> 'Views Integration'.  Then click on the link 'List of integrated tables'.  You will then see the list of all Chado and custom tables.  Look for the table 'Chado Blast Hit Data' and click the 'Edit' link.    Here you can change the filters for all of the fields in that table.  Scroll down to the fields 'hit_best_eval' and 'hit_best_score' and change the filter handler from 'chado_views_handler_filter_string' to 'chado_views_handler_filter_numeric'.   Save the configuration and then go back to your View and see if that helps.  (You may have to also clear the cache (drush cc all)).
>
> Stephen
>
>
> On 10/14/2013 4:43 AM, Michael Dondrup wrote:
>> Hi,
>>
>> I have defined a view to search within blast hits (View blast_results, displaying items of type Chado Blast Hit Data.). The view has currently filters for hit accession,
>> description, and database. I thought it would be neat to also have filters on max. e-value
>> and minimum score, so I tried to add filters to the view for:
>> Chado Blast Hit Data: Hit Best Eval
>> Hit Best Eval
>> Chado Blast Hit Data: Hit Best Score
>> Hit Best Score
>>
>> However, in the filter configuration, the possible operators displayed for both are those for text fields (Is equal to, Is not equal to
>>  Contains, Starts with, Ends with) and not the ones for numeric data (Is less than, Is less than or equal to, etc.)
>> as it would be required. I looked into the DB definition for blast_hit_data and both columns are of type
>> double precision, so this looks ok. Is there any way to configure such filters?
>>
>> Thanks a lot in advance
>>
>> Michael
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> October Webinars: Code for Performance
>> Free Intel webinars can help you accelerate application performance.
>> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
>> the latest Intel processors and coprocessors. See abstracts and register >
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk
>>
>>
>> _______________________________________________
>> Gmod-tripal-devel mailing list
>>
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>
> ------------------------------------------------------------------------------
> October Webinars: Code for Performance
> Free Intel webinars can help you accelerate application performance.
> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
> the latest Intel processors and coprocessors. See abstracts and register >
> http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk_______________________________________________
> Gmod-tripal-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel



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