G1.57 Upgrade use of chado_insert_cvterm() to use the Tripal 4 terms service.

[laceysanderson]

Branch

g1.57-useT4TermsService

Groups

Group 1 - Content Types | Ontology | Fields

Describe

Currently the TripalCultivatePhenotypesTermsService uses chado_insert_cvterm() to insert the terms needed by the module. However, this function is deprecated in Tripal 4 and VERY slow.

Design

My plan is to take the information on default terms in trpcultivate_phenotypes.settings.yml and format them to match the Tripal Default Terms for Content Types.

Then I can update the current loadTerms() method to use the Tripal Core ChadoTermsInit service.

[reynoldtan]

At 4.x, this is an outstanding issue. loadTerms() uses chado_insert_cvterm() to handle terms.

TripalCultivate-Phenotypes/trpcultivate_phenotypes/src/Service/TripalCultivatePhenotypesTermsService.php

Line 135 in b762537

$cvterm = chado_insert_cvterm($config_prop, [], $schema);

[laceysanderson]

The ChadoBuddies have now been implemented in TripalCore which act as a direct replacement for chado_insert_cvterm()! The code for how to handle inserting a cvterm is shown in this example in the docs: https://tripaldoc.readthedocs.io/en/latest/dev_guide/biodata/buddies/buddy_values.html#chado-buddy-example-2

$buddy_service = \Drupal::service('tripal_chado.chado_buddy');
$cvterm_instance = $buddy_service->createInstance('chado_cvterm_buddy', []);

// Create the cvterm and dbxref records in chado, unless they already exist.
$values = [
  'db.name' => 'local',
  'cv.name' => 'local',
  'dbxref.accession' => 'X000002',
  'cvterm.name' => 'Example 2',
  'cvterm.definition' => 'A fake ontology term for example #2',
];
$chado_cvterm_record = $cvterm_instance->upsertCvterm($values, []);
// if for any reason insert failed, an exception is thrown, so
// you should catch exceptions as shown in example #3
$cvterm_id = $chado_cvterm_record->getValue('cvterm.cvterm_id');
print "Created or found cvterm with id=$cvterm_id\n";