tripal/tripal_stock/tripal_stock.install

<?php
/**
 * Install the tripal stock module including it's content type
 * @file
 */

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

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

}

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

/**
 * Implementation of hook_install().
 *
 * @ingroup tripal_stock
 */
function tripal_stock_install() {
  // add some controlled vocabularies
  tripal_stock_add_cvs();

  tripal_stock_add_cvterms();

  // set the default vocabularies
  tripal_set_default_cv('stock', 'type_id', 'stock_type');
  tripal_set_default_cv('stockprop', 'type_id', 'stock_property');
  tripal_set_default_cv('stock_relationship', 'type_id', 'stock_relationship');

  // add the materialized view
  tripal_stock_add_organism_count_mview();
}

/**
 * Implementation of hook_uninstall().
 *
 * @ingroup tripal_stock
 */
function tripal_stock_uninstall() {

}

/**
 * Implementation of hook_schema().
 *
 * @ingroup tripal_stock
 */
function tripal_stock_schema() {
  $schema['chado_stock'] = array(
    'fields' => array(
      'vid' => array(
        'type' => 'int',
        'unsigned' => TRUE,
        'not null' => TRUE,
      ),
      'nid' => array(
        'type' => 'int',
        'unsigned' => TRUE,
        'not null' => TRUE,
      ),
      'stock_id' => array(
        'type' => 'int',
        'unsigned' => TRUE,
        'not null' => TRUE,
      ),
    ),
    'indexes' => array(
      'stock_id' => array('stock_id'),
       'nid' => array('nid'),
    ),
    'unique' => array(
      'stock_id' => array('stock_id'),
    ),
    'primary key' => array('vid'),
  );

  return $schema;
}

/**
 * Creates a materialized view that stores the type & number of stocks per organism
 *
 * @ingroup tripal_stock
 */
function tripal_stock_add_organism_count_mview() {
  $view_name = 'organism_stock_count';
  $comment = 'Stores the type and number of stocks per organism';

  $schema = array(
    'description' => $comment,
    'table' => $view_name,
    'fields' => array(
      'organism_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'genus' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => TRUE,
      ),
      'species' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => TRUE,
      ),
      'common_name' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => FALSE,
      ),
      'num_stocks' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'cvterm_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'stock_type' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => TRUE,
      ),
    ),
    'indexes' => array(
      'organism_stock_count_idx1' => array('organism_id'),
      'organism_stock_count_idx2' => array('cvterm_id'),
      'organism_stock_count_idx3' => array('stock_type'),
    ),
  );

  $sql = "
    SELECT
        O.organism_id, O.genus, O.species, O.common_name,
        count(S.stock_id) as num_stocks,
        CVT.cvterm_id, CVT.name as stock_type
     FROM organism O
        INNER JOIN stock S  ON O.Organism_id = S.organism_id
        INNER JOIN cvterm CVT ON S.type_id     = CVT.cvterm_id
     GROUP BY
        O.Organism_id, O.genus, O.species, O.common_name, CVT.cvterm_id, CVT.name
  ";

  tripal_add_mview($view_name, 'tripal_stock', $schema, $sql, $comment);
}

/**
 * Add cvs related to publications
 *
 * @ingroup tripal_pub
 */
function tripal_stock_add_cvs() {

  // Add cv for relationship types
  tripal_insert_cv(
    'stock_relationship',
    'Contains types of relationships between stocks.'
  );
  tripal_insert_cv(
    'stock_property',
    'Contains properties for stocks.'
  );
  tripal_insert_cv(
    'stock_type',
    'Contains a list of types for stocks.'
  );
}

/**
 * Add cvterms related to publications
 *
 * @ingroup tripal_pub
 */
function tripal_stock_add_cvterms() {

}

/**
 * This is the required update for tripal_stock when upgrading from Drupal core API 6.x.
 *
 */
function tripal_stock_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 stock_relationshp CV
  try {
    $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'stock_relationship'")->fetchField();
    if (!$cv_id) {
      // add the vocabulary
      $cv_id = db_insert('chado.cv')
        ->fields(array(
          'name' => 'stock_relationship',
          'definition' => 'Contains types of relationships between stocks.'
        ))
        ->execute();
    }
    // for backwards compatibility, get the previously set stock relationship CV, otherwise
    // use the new stock_relationship CV we just added
    $default_stockrel_cv = variable_get('chado_stock_relationship_cv', $cv_id);
    $cdi = db_select('tripal_cv_defaults', 't')
      ->fields('t', array('cv_default_id'))
      ->condition('table_name', 'stock_relationship')
      ->condition('field_name', 'type_id')
      ->execute()
      ->fetchField();
    if (!$cdi) {
      db_insert('tripal_cv_defaults')
        ->fields(array(
          'table_name' => 'stock_relationship',
          'field_name' => 'type_id',
          'cv_id' => $default_stockrel_cv
        ))
        ->execute();
    }
  }
  catch (\PDOException $e) {
    $error = $e->getMessage();
    throw new DrupalUpdateException('Failed to add stock_relationship vocabulary: '. $error);
  }

  // add the stock_property CV
  try {
    $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'stock_property'")->fetchField();
    if (!$cv_id) {
      // add the vocabulary
      $cv_id = db_insert('chado.cv')
        ->fields(array(
          'name' => 'stock_property',
          'definition' => 'Contains properties for stocks.'
        ))
        ->execute();
    }
    // for backwards compatibility, get the previously set stock property CV, otherwise
    // use the new stock_property CV we just added
    $default_stockprop_cv = variable_get('chado_stock_prop_types_cv', $cv_id);
    $cdi = db_select('tripal_cv_defaults', 't')
      ->fields('t', array('cv_default_id'))
      ->condition('table_name', 'stockprop')
      ->condition('field_name', 'type_id')
      ->execute()
      ->fetchField();
    if (!$cdi) {
      db_insert('tripal_cv_defaults')
        ->fields(array(
        'table_name' => 'stockprop',
        'field_name' => 'type_id',
        'cv_id' => $default_stockprop_cv
        ))
        ->execute();
    }
  }
  catch (\PDOException $e) {
    $error = $e->getMessage();
    throw new DrupalUpdateException('Failed to add stock_property vocabulary: '. $error);
  }


  // add the stock_type CV
  try {
    $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'stock_type'")->fetchField();
    if (!$cv_id) {
      // add the vocabulary
      $cv_id = db_insert('chado.cv')
      ->fields(array(
        'name' => 'stock_type',
        'definition' => 'Contains a list of types for stocks.'
      ))
      ->execute();
    }
    // for backwards compatibility, get the previously set stock types CV, otherwise
    // use the new stock_type CV we just added
    $default_stocktype_cv = variable_get('chado_stock_types_cv', $cv_id);
    $cdi = db_select('tripal_cv_defaults', 't')
      ->fields('t', array('cv_default_id'))
      ->condition('table_name', 'stock')
      ->condition('field_name', 'type_id')
      ->execute()
      ->fetchField();
    if (!$cdi) {
      db_insert('tripal_cv_defaults')
        ->fields(array(
        'table_name' => 'stock',
        'field_name' => 'type_id',
        'cv_id' => $default_stocktype_cv
        ))
        ->execute();
    }
  }
  catch (\PDOException $e) {
    $error = $e->getMessage();
    throw new DrupalUpdateException('Failed to add stock_type vocabulary: '. $error);
  }

}

/**
 * Add materialized views
 */
function tripal_stock_update_7201() {
  // 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 materialized view
  tripal_stock_add_organism_count_mview();

}

/**
 * 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_stock_update_dependencies() {

  $dependencies = array();

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

  return $dependencies;
}