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Tripal 3 error: bundle type does not use correct storage cvterm #11

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bradfordcondon opened this issue Jan 18, 2018 · 1 comment
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@bradfordcondon
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bradfordcondon commented Jan 18, 2018

Major bug: The default bundle storage cvterm is set wrong.

CVterm set by the node when creating interpro analysis:

  chado_insert_property($record, array('type_name' =>'Analysis Type', 'cv_name' => 'analysis_property', 'value' => 'interpro_analysis'));

The Cvterm used by the default bundle created by this module actually looks for the cvterm interpro results instead of Analysis Type:


CHADO TABLE : analysis
type_column: type_id
association table: analysisprop
cvterm table id : 3456
property value: interpro_analysis
rupal=# select * from chado.cvterm where cvterm_id = '3456';
 cvterm_id | cv_id |       name       |           definition           | dbxref_id | is_obsolete | is_relationshiptype
-----------+-------+------------------+--------------------------------+-----------+-------------+---------------------
      3456 |     2 | InterPro results | Results for InterPro analysis. |      4067 |           0 |                   0
(1 row)
@spficklin spficklin added the bug label Jan 19, 2018
@bradfordcondon
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bradfordcondon commented Jan 18, 2019

heres the interpro bundle

screen shot 2019-01-18 at 1 48 49 pm

So, the current bundle is set where the analysisprop "local:interpro_results" = interpro_analysis.

This is actually in line with, say, blast, where the analysisprop format:1333 (blast results) = blast_analysis.

Assuming that old types set via analysis_property:Analysis Type = 'interpro_analysis' are migrated somewhere, we're OK. im not 100% positive they are though- i dont see it in the install.

I can see the reason for swapping this, since we want the bundle mapepd to a cvterm, not a flat "value" in the prop table. So we get rid of the generic "Analysis Type" prop type, since that prevents us from having multiple bundles using that term with different values. It does make sense, we just need to make sure we migrated tripal 2 analyses that used different terms properly.

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