chado_linker_fields.install

<?php
/**
 * @file
 *
 * Installation of the chado_linker_fields module
 */


/**
 * Implements hook_requirements().
 */
function chado_linker_fields_requirements($phase) {
  $requirements = [];
  $minimum_version = '7.x-3.10';
  if ($phase == 'install') {
    if (!module_exists('tripal')) {
      $requirements['chado_linker_fields-tripal'] = [
        'title' => "chado_linker_fields",
        'value' => "ERROR: You must have Tripal $minimum_version or later installed to use this module.",
        'severity' => REQUIREMENT_ERROR,
      ];
    }
    // Requires tripal version >= '7.x-3.10'. '4.x' will also return -1 and trigger incorrect version
    else {
      $tripal_info = system_get_info('module', 'tripal');
      $tripal_version = $tripal_info['version'];
      $status = version_compare($tripal_version, $minimum_version);
      if ( $status < 0 ) {
        $requirements['chado_linker_fields-tripal'] = [
          'title' => "chado_linker_fields",
          'value' => "ERROR: Tripal version $tripal_version is below the required version $minimum_version to use this module.",
          'severity' => REQUIREMENT_ERROR,
        ];
      }
    }

    // Make sure chado is installed.
    if (!$GLOBALS["chado_is_installed"]) {
      $requirements['chado_linker_fields-chado'] = [
        'title' => "chado_linker_fields",
        'value' => "ERROR: Chado is not installed. Version 1.3 must be installed before this module can be enabled",
        'severity' => REQUIREMENT_ERROR,
      ];
    }
    // Requires chado version 1.3
    else {
      $chado_version = chado_get_version();
      if ($chado_version < '1.3') {
        $requirements['chado_linker_fields-chado'] = [
          'title' => "chado_linker_fields",
          'value' => "ERROR: Chado version is $chado_version, this module requires version 1.3",
          'severity' => REQUIREMENT_ERROR,
        ];
      }
    }
  }
  return $requirements;
}

/**
 * Implements hook_install().
 *
 * Performs actions when the module is first installed.
 *
 * @ingroup chado_linker_fields
 */
function chado_linker_fields_install() {

  // Add cv terms used by this module's fields that are not in core Tripal.
  chado_linker_fields_add_cv_terms();

  // Initialize field configuration variables.
  variable_set('chado_linker_field_max_delta', 200);
  variable_set('chado_linker_field_max_height', 200);
}

/**
 * Implements hook_uninstall().
 *
 * Performs actions when the module is uninstalled.
 *
 * @ingroup chado_linker_fields
 */
function chado_linker_fields_uninstall() {

  // Uninstall should remove the fields from this module from
  // any content types currently using them.
  remove_chado_linker_fields();

  // Remove configuration variables specific to this module.
  variable_del('chado_linker_field_max_delta');
  variable_del('chado_linker_field_max_height');

  // CV terms defined by this module are not removed on uninstall.
}

/**
 * Add CV terms used by this module
 */
function chado_linker_fields_add_cv_terms() {

  // For chado_linker__analysis field.
  chado_insert_cvterm([
    'id' => 'NCIT:C25391',
    'name' => 'Analysis',
    'cv_name' => 'ncit',
    'definition' => 'Examination and interpretation; the process of identifying an issue to be understood and'
                  . ' addressed, modelling the issue, investigating the model results, interpreting the results,'
                  . ' and possibly making a recommendation. The concept also refers to the examination and study'
                  . ' of a whole in terms of the parts composing it.',
  ]);

  // For chado_linker__assay field.
  chado_insert_cvterm([
    'id' => 'NCIT:C60819',
    'name' => 'Assay',
    'cv_name' => 'ncit',
    'definition' => 'A qualitative or quantitative analysis performed to determine the amount of a particular'
                  . ' constituent in a sample or the biological or pharmacological properties of a drug.',
  ]);

  // For chado_linker__biomaterial field.
  chado_insert_cvterm([
    'id' => 'NCIT:C43376',
    'name' => 'Biologically-Derived Material',
    'cv_name' => 'ncit',
    'definition' => 'Natural substances derived from living organisms such as cells, tissues, proteins, and DNA.',
  ]);

  // For chado_linker__feature field.
  chado_insert_cvterm([
    'id' => 'NCIT:C73619',
    'name' => 'Feature',
    'cv_name' => 'ncit',
    'definition' => 'A prominent or identifiable aspect, region, or site of interest',
  ]);

  // For chado_linker__organism field.
  chado_insert_cvterm([
    'id' => 'NCIT:C14250',
    'name' => 'Organism',
    'cv_name' => 'ncit',
    'definition' => 'A living entity.',
  ]);

  // For chado_linker__stock field.
  chado_insert_cvterm([
    'id' => 'NCIT:C48288',
    'name' => 'Stock',
    'cv_name' => 'ncit',
    'definition' => 'The merchandise that a shop has on hand.',
  ]);

  // For chado_linker__study field.
  chado_insert_cvterm([
    'id' => 'NCIT:C63536',
    'name' => 'Study',
    'cv_name' => 'ncit',
    'definition' => 'A detailed examination, analysis, or critical inspection of a subject designed'
                  . ' to discover facts about it.',
  ]);

  // For summary when too many records to display.
  chado_insert_cvterm([
    'id' => 'NCIT:C25463',
    'name' => 'Count',
    'cv_name' => 'ncit',
    'definition' => 'Determining the number or amount of something.',
  ]);

}

/**
 * Remove fields defined by this module from all content types.
 */
function remove_chado_linker_fields() {

  // Fields defined by this module
  $field_ids = [
    'NCIT:C25391' => 'analysis',
    'NCIT:C60819' => 'assay',
    'NCIT:C43376' => 'biomaterial',
    'NCIT:C73619' => 'feature',
    'data:C73619' => 'featuremap',
    'NCIT:C14250' => 'organism',
    'NCIT:C47885' => 'project',
    'NCIT:C48288' => 'stock',
    'NCIT:C63536' => 'study',
  ];

  // Find and delete any instances of these fields
  $instances = field_info_instances('TripalEntity');
  $n_deleted = 0;
  foreach ($instances as $entity_type => $entity_info) {
    foreach ($entity_info as $field_name => $field_info) {
      $settings = $field_info['settings'];
      $id = $settings['term_vocabulary'] . ':' . $settings['term_accession'];
      if (isset($field_ids[$id])) {
        // Delete the field $field_name from $entity_type
        field_delete_field($field_name);
        $n_deleted++;
      }
    }
  }
  if ($n_deleted) {
    field_purge_batch($n_deleted);
  }
}