G4.14 (G0.03.2) Service for managing CV and Cvterm configuration values

[reynoldtan]

This service is the upgraded version of Analyzed Phenotypes Ontology API with a focus on the new D10 functionality.

Service Name: TripalCultivatePhenotypesGenusOntologyService
Found: trpcultivate_phenotypes/src/Service/TripalCultivatePhenotypesOntologyService.php

Associated Config:

Schema:

Genus:
-trait // Trait Vocabulary
-method // Method Vocabulary
-unit // Unit Vocabulary
-database // Database id
-crop_ontology // Crop Ontology Vocabulary

allownew // True or False, Allow new traits to be added during upload

Access to configuration values will be based on the genus.

Methods

/**
 * Fetch all genus from chado.organism in the host site and construct a genus ontology
 * configuration values described above. Each genus will contain a configuration value 
 * for trait+unit+method, database and crop ontology.
 *
 * @return array
 *    Associative array where each element is keyed by genus and configuration values array
 *    as the value.
 */
public function defineGenusOntology()

/**
 * Register a configuration entry and set each genus ontology configuration values to
 * a default value of 0 (not set).
 *
 * @return boolean
 *   True all genus ontology configuration created and set a default value, False on error.
 */
public function loadGenusOntology()

/**
 * Get genus ontology configuration values.
 *
 * @param string $genus
 *    Genus
 *
 * @return array
 *    Associated configuration values trait, unit, method, database and crop ontology.
 */

public function getGenusOntologyConfigValue($genus)

/**
 * Prepare genus text to be used as variable name by removing any formatting and converting spaces to underscore.
 *
 * @param string $genus
 *   Genus
 *
 * @return string
 *    Lowercase version and all spaces replaced by underscore.
 */

public function formatGenus($genus)