tripal/tripal_organism/tripal_organism.install

<?php
/**
 * @file
 * Functions pertaining to the install/uninstall of this module
 */

/**
 * Implements hook_disable().
 * Disable default views when module is disabled
 *
 * @ingroup tripal_organism
 */
function tripal_organism_disable() {

  // Disable all default views provided by this module
  require_once("tripal_organism.views_default.inc");
  $views = tripal_organism_views_default_views();
  foreach (array_keys($views) as $view_name) {
    tripal_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
  }

}

/**
 * Implementation of hook_install().
 *
 * @ingroup tripal_organism
 */
function tripal_organism_install() {
  // cvs & cvterms
  tripal_organism_add_cvs();
  tripal_organism_add_cvterms();

  // set the default vocabularies
  tripal_set_default_cv('organismprop', 'type_id', 'organism_property');

}

/**
 * Implementation of hook_schema().
 *
 * @ingroup tripal_organism
 */
function tripal_organism_schema() {
 $schema['chado_organism'] = array(
      'fields' => array(
         'vid' => array(
            'type' => 'int',
            'unsigned' => TRUE,
            'not null' => TRUE,
            'default' => 0
          ),
         'nid' => array(
            'type' => 'int',
            'unsigned' => TRUE,
            'not null' => TRUE,
            'default' => 0
          ),
         'organism_id' => array(
            'type' => 'int',
            'not null' => TRUE,
            'default' => 0
          )
      ),
      'indexes' => array(
         'organism_id' => array('organism_id')
      ),
      'unique keys' => array(
         'nid_vid' => array('nid', 'vid'),
         'vid' => array('vid')
      ),
      'primary key' => array('nid'),
  );
  return $schema;
}

/**
 * Implementation of hook_uninstall().
 *
 * @ingroup tripal_organism
 */
function tripal_organism_uninstall() {

}

/**
 * Implementation of hook_requirements().
 *
 * @ingroup tripal_organism
 */
function tripal_organism_requirements($phase) {
  $requirements = array();
  if ($phase == 'install') {
    // make sure chado is installed
    if (!$GLOBALS["chado_is_installed"]) {
      $requirements ['tripal_organism'] = array(
            'title' => "tripal_organism",
            'value' => "ERROR: Chado must be installed before this module can be enabled",
            'severity' => REQUIREMENT_ERROR,
      );
    }
  }
  return $requirements;
}

/**
 * Add cvterms related to organisms
 *
 * @ingroup tripal_organism
 */
function tripal_organism_add_cvs() {
  tripal_insert_cv(
    'organism_property',
    'Contains properties for organisms'
  );
}

/**
 * Add cvterms pertaining to organisms
 *
 * @ingroup tripal_organism
 */
function tripal_organism_add_cvterms() {

}

/**
 * This is the required update for tripal_organism when upgrading from Drupal core API 6.x.
 *
 */
function tripal_organism_update_7200() {

  // Make sure we have the full API loaded this will help during a
  // site upgrade when the tripal_core module is disabled.
  module_load_include('module', 'tripal_core', 'tripal_core');
  tripal_core_import_api();

  // Add the new organism_property vocabulary
  // We cannot use the Tripal API calls in the 7000 update
  // because during upgrade the tripal_core should also be disabled
  try {
    $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'organism_property'")->fetchField();
    if (!$cv_id) {
      $sql = "INSERT INTO chado.cv (name, definition) VALUES (
        'organism_property',
        'Contains properties for organisms.')
      ";
      db_query($sql);
    }
    // If a record already exists then don't change it.
    $cdi = db_select('tripal_cv_defaults', 't')
      ->fields('t', array('cv_default_id'))
      ->condition('table_name', 'organismprop')
      ->condition('field_name', 'type_id')
      ->execute()
      ->fetchField();

    // Add in the default vocabulary.
    if (!$cdi) {
      db_insert('tripal_cv_defaults')
        ->fields(array(
          'table_name' => 'organismprop',
          'field_name' => 'type_id',
          'cv_id' => $cv_id
        ))
        ->execute();
    }
  }
  catch (\PDOException $e) {
    $error = $e->getMessage();
    throw new DrupalUpdateException('Failed to add organism_property vocabulary: '. $error);
  }


  // During the upgrade from D6 to D7 the vocabulary terms assigned to organisms were
  // copied to the field_data_taxonomyextra table rather than to the correct
  // field_data_taxonomy_vocabulary_[vid] table. We'll move them.
  $vid = db_query("SELECT vid FROM {taxonomy_vocabulary} WHERE name = 'Organism'")->fetchField();
  if ($vid) {
    try {
      if (db_table_exists('field_data_taxonomyextra')) {
        // first move from the field_data_taxonomyextra table
        $sql = "
          INSERT INTO {field_data_taxonomy_vocabulary_$vid}
            (entity_type, bundle, deleted, entity_id, revision_id, language, delta, taxonomy_vocabulary_" . $vid. "_tid)
          (SELECT entity_type, bundle, deleted, entity_id, revision_id, language, delta, taxonomyextra_tid
           FROM field_data_taxonomyextra
           WHERE bundle = 'chado_feature')
        ";
        db_query($sql);
        $sql = "DELETE FROM field_data_taxonomyextra WHERE bundle = 'chado_organism'";
        db_query($sql);

        // next move from the field_revision_taxonomyextra table
        $sql = "
          INSERT INTO {field_revision_taxonomy_vocabulary_$vid}
            (entity_type, bundle, deleted, entity_id, revision_id, language, delta, taxonomy_vocabulary_" . $vid. "_tid)
          (SELECT entity_type, bundle, deleted, entity_id, revision_id, language, delta, taxonomyextra_tid
           FROM field_revision_taxonomyextra
           WHERE bundle = 'chado_feature')
        ";
        db_query($sql);
        $sql = "DELETE FROM field_revision_taxonomyextra WHERE bundle = 'chado_organism'";
        db_query($sql);
      }
    }
    catch (\PDOException $e) {
      $error = $e->getMessage();
      throw new DrupalUpdateException('Could not move organism taxonomy terms: '. $error);
    }
  }
}

/**
 * Implementation of hook_update_dependencies().
 *
 * It specifies a list of other modules whose updates must be run prior to
 * this one.  It also ensures the the Tripal API is in scope for site
 * upgrades when tripal_core is disabled.
 */
function tripal_organism_update_dependencies() {

  $dependencies = array();

  // the tripal_cv update 7200 must run prior to update 7200 of this module
  $dependencies['tripal_organism'][7200] = array(
    'tripal_cv' => 7200
  );

  return $dependencies;
}