Fix determination of qualitative vs. quantitative

[laceysanderson]

Metadata

• Issue n/a

• [x] I feel this PR is ready to be merged.

Documentation:

• [x] My code follows the code style of this project.
• [ ] My change requires a change to the documentation.
• [ ] I have updated the documentation accordingly.

Description

This PR adds automated testing to ensure the type of method is set properly. It also changes the default type to quantitative.

Dependencies

None

Testing?

• [x] I tested on a generic Tripal Site
• [ ] I tested on a KnowPulse Clone
• [x] This PR includes automated testing

1. Create a project (Admin » Add Tripal Content » Project)
2. Create germplasm for your file

   $species = 'databasica';
   for ($i=1; $i <= 15; $i++) {
   $stock = [
    'name' => 'GERM'.$i,
    'uniquename' => 'ID:'.$i,
    'type_id' => ['name' => 'SNP'],
    'organism_id' => ['species' => $species],
   ];
   $stock = chado_insert_record(
   'stock',
    $stock
   );
   }

3. Configure the module for your organism (Administration » Tripal » Extensions » Analyzed Phenotypes » Configuration) by selecting at least a "Trait Vocabulary" and "Associated DB". Which you choose doesn't matter for testing purposes other then to ensure the trait is added to the vocabulary when loaded. Documentation: https://analyzedphenotypes.readthedocs.io/en/latest/admin_guide/configuration.html
4. Upload a test file (Administration » Tripal » Extensions » Analyzed Phenotypes » Upload Phenotypic Data). Documentation: https://analyzedphenotypes.readthedocs.io/en/latest/user_guide/loading.html
5. Check the type for the methods you uploaded using the following query:

   SELECT value
   FROM chado.cvtermprop
   WHERE 
   cvterm_id IN (SELECT cvterm_id FROM chado.cvterm WHERE name='YOUR UNIT HERE') AND
   type_id IN (SELECT cvterm_id FROM chado.cvterm WHERE name='additionalType');

NOTE: qualitative/quantitative are attached to the unit. In order to be detected as qualitative, a unit must have the word Scale in it; all other traits should be quantitative.

[reynoldtan]

My scale unit was correctly identified as qualitative trait, however, my other traits I set to metris with values 5.3, 2.2, 4.9 and 2.6 were set to qualitative as well. I was expecting it to be quantitative?

here is my data file.

[laceysanderson]

I just double checked and it works perfectly. metris is a common unit I've used in the past so maybe it re-used an existing unit in your case. Could you try again with a unique unit? You can ensure the unit doesn't already exist by using SELECT * FROM chado.cvterm WHERE name='YOUR UNIT HERE'; before you load your test data.

[laceysanderson]

Confirmed it works on Reynold's test site with his data. There was a problem with the clone he was working on originally which is unrelated to this PR. As such I'm merging this simple change.