Configuration for unit and method

[laceysanderson]

Metadata

• Issue #47

• [x] I feel this PR is ready to be merged.
• [x] This PR is dependent upon [PR #/ nothing]

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

When we upgraded the data storage method, we created the need for additional cv's and cvterms in the configuration. Specifically we needed to allow per organism config of method and unit cv and which cvterms should be used for Trait=>Method and Method=>Unit relationships.

Testing?

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

This test requires updating of default variable options. This is usually done in .install but can be done after the fact using the code sample below:

module_load_include('inc','analyzedphenotypes','/api/analyzedphenotypes.ontology.api');
$default_ontology = ap_load_defaultontology();

$sysvars = ap_construct_variablenames();
  foreach($sysvars['terms'] as $v => $var) {
    // Set the variable to default ontology term.
    // base terms: location, replicate, year ...
    $v = trim(str_replace('ap_', '', $v));

    variable_set($var, $default_ontology[$v]);
  }

For Testing,

1. Go to the configuration form and confirm there are now trait/method/unit options per organism
2. In the configuration form, confirm there is a Trait=>Method and Method=>Unit, both with defaults.
3. Try inserting a trait and ensure at the database level that the cvterms are in the correct cv and are connected in cvterm_relationship using the correct type_id.

$info = ap_insert_trait([
  'genus' => 'Tripalus',
  'name' => 'test trait2',
  'description' => 'I though the name was pretty self explanatory',
  'method_title' => 'accurate1',
  'method' => 'A super accurate measurement method for something made up.',
  'unit' => 'Kelvin',
  'type' => 'quant',
]);
dpm($info, 'info');

[reynoldtan]

Tested and confirmed: 👍

A. Trait, Method and Unit vocabulary options in configuration

B. Default values for both Trait=>Method and Method=>Unit.

C. Term relationships Settings for Cicer Genus:

Term: 'genus' => 'Cicer', 'name' => 'Go Trait', 'description' => 'Go Trait Description', 'method_title' => 'go_trait_method_title', 'method' => 'Go trait method of collection', 'unit' => 'seconds', 'type' => 'quant',

Insert result and Relationship: