Tripal Chado Organism API is deprecated in favour of the ChadoOrganismBuddy and ChadoOrganismFormElementController

Deprecated in tripal 4.0.0-alpha5
Removed in tripal 4.1.0
Issue #2424
PR #2426

Methods in ChadoOrganismBuddy and ChadoOrganismFormElementController classes replace the majority of the functionality of the existing Chado Organism API methods.

Some of these methods can be provided a ChadyBuddyRecord as a parameter, and may return one or more Organism buddies. To learn more about ChadoBuddies, refer to: Chado Buddies Documentation

Note

The examples below demonstrate static service calls to the ChadoOrganismBuddy and ChadoOrganismFormElementController classes; however, Dependency Injection is preferred when integrating services, as recommended by Drupal best practices. For more details regarding Injecting ChadoBuddy Services, refer to: Injecting the Buddy Service Documentation

chado_get_organism()

Before:

$identifiers = [
    'genus' => 'Tripalus',
    'species' => 'databasica',
];
$organism_object = chado_get_organism($identifiers, []);

After:

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

$conditions = [
    'organism.genus' => 'Tripalus',
    'organism.species' => 'databasica',
];
// Retrieves an array of ChadoOrganismBuddy records. This array will be empty if no records
// matched the input values, and can have one or more records if matches were found.
$organism_buddies = $organism_buddy_instance->getOrganism($conditions, []);

chado_get_organism_scientific_name()

Before:

// Returns a string of the matching organism's scientific name
$organism_name = chado_get_organism_scientific_name($organism_object);

After:

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

$conditions = [
    'organism.common_name' => 'Tripal',
];

// Returns a string of the matching organism's scientific name
$organism_name = $organism_buddy_instance->getOrganismScientificName($conditions);

chado_get_organism_image_url()

This function currently has no replacement in Tripal 4.

chado_get_organism_select_options()

Before:

$organisms = chado_get_organism_select_options();

After:

use Drupal\tripal_chado\Controller\ChadoOrganismFormElementController;

...

$organisms = ChadoOrganismFormElementController::getSelectOptions([]);

chado_get_organism_id_from_scientific_name()

Before:

By Scientific Name:

$scientific_name = 'Tripalus databasica';
// Returns an array of organism IDs that match the specified scientific name.
$organism_ids = chado_get_organism_id_from_scientific_name($scientific_name);

By Common Name:

$common_name = 'Tripal';
// Returns an array of organism IDs that match the specified common name.
$organism_ids = chado_get_organism_id_from_scientific_name($common_name,
  ['check_common_name' => TRUE]);

After:

By Scientific Name:

$scientific_name = 'Tripalus databasica';
// Retrieves an array of ChadoOrganismBuddy records. This array will be empty if no records
// matched the input values, and can have one or more records if matches were found.
$organism_buddies = $organism_buddy_instance->getOrganismFromScientificName($scientific_name);
// Then grab the organism's ID
$organism_id = $organism_buddies[0]->getValue('organism.organism_id');

By Common Name:

$common_name = 'Tripal';
$organism_buddies = $organism_buddy_instance->getOrganismFromScientificName($common_name,
  ['check_common_name' => TRUE]);
// Then grab the organism's ID
$organism_id = $organism_buddies[0]->getValue('organism.organism_id');

chado_abbreviate_infraspecific_rank()

Before:

// Returns the abbreviation of an organism's rank.
$rank_abbreviation = chado_abbreviate_infraspecific_rank($rank);

After:

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

$rank_abbreviation = $organism_buddy_instance->abbreviateInfraspecificRank($rank);

chado_unabbreviate_infraspecific_rank()

Before:

$rank = chado_unabbreviate_infraspecific_rank($rank_abbreviation);

After:

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

$rank = $organism_buddy_instance->unabbreviateInfraspecificRank($rank_abbreviation);

chado_autocomplete_organism()

Before:

$organism_autocomplete = chado_autocomplete_organism($text);

After:

use Drupal\tripal_chado\Controller\ChadoOrganismFormElementController;

...

$organism_autocomplete = new ChadoOrganismFormElementController();
$request = Request::create(
    'chado/organism/autocomplete/10',
    'GET',
    ['q' => $text]
);
$organism_autocomplete->handleAutocomplete($request, 5);