tripal/tripal_library/tripal_library.install

<?php
/**
 * @file
 * @todo Add file header description
 */

/**
 * Implementation of hook_install().
 *
 * @ingroup tripal_library
 */
function tripal_library_install() {
  // create the module's data directory
  tripal_create_moddir('tripal_library');

  // create the tables that correlate drupal nodes with chado
  // features, librarys, etc....
  drupal_install_schema('tripal_library');

  // Insert cvterm 'library_description' into cvterm table of chado
  // database. This CV term is used to keep track of the library
  // description in the libraryprop table.
  tripal_cv_add_cvterm(array('name' => 'library_description', 'def' => 'Description of a library'), 'tripal', 0, 1, 'tripal');

  // Add CVTerms for the library types
  tripal_cv_add_cvterm(array('name' => 'cdna_library', 'def' => 'cDNA Library'), 'tripal', 0, 1, 'tripal');
  tripal_cv_add_cvterm(array('name' => 'bac_library', 'def' => 'BAC Library'), 'tripal', 0, 1, 'tripal');
  tripal_cv_add_cvterm(array('name' => 'fosmid_library', 'def' => 'FOSMID Library'), 'tripal', 0, 1, 'tripal');
  tripal_cv_add_cvterm(array('name' => 'cosmid_library', 'def' => 'COSMID Library'), 'tripal', 0, 1, 'tripal');
  tripal_cv_add_cvterm(array('name' => 'yac_library', 'def' => 'YAC Library'), 'tripal', 0, 1, 'tripal');

  // Add the materialized view needed to count the features for the library
  // Drop the MView table if it exists
  $previous_db = tripal_db_set_active('chado');
  if (db_table_exists('library_feature_count')) {
    $sql = "DROP TABLE library_feature_count";
    db_query($sql);
  }
  tripal_db_set_active($previous_db);
  // Create the MView
  tripal_add_mview('library_feature_count', 'tripal_library',
    'library_feature_count',
    'library_id integer, name character varying(255), '.
  '  num_features integer, feature_type character varying(255)',
   'library_id',
   'SELECT '.
    '   L.library_id, '.
    '   L.name, '.
    '    count(F.feature_id) as num_features, '.
    '    CVT.name as feature_type '.
    'FROM {Library} L '.
    '    INNER JOIN Library_Feature LF  ON LF.library_id = L.library_id '.
    '    INNER JOIN Feature F           ON LF.feature_id = F.feature_id '.
    '    INNER JOIN Cvterm CVT          ON F.type_id = CVT.cvterm_id '.
    'GROUP BY L.library_id, L.name, CVT.name',
   ''
  );

}

/**
 * Implementation of hook_schema().
 *
 * @ingroup tripal_library
 */
function tripal_library_schema() {
  $schema = tripal_library_get_schemas();
  return $schema;
}

/**
 * Implementation of hook_uninstall().
 *
 * @ingroup tripal_library
 */
function tripal_library_uninstall() {
  drupal_uninstall_schema('tripal_library');

  // remove the materialized view
  $sql = "SELECT * FROM {tripal_mviews} ".
        "WHERE name = 'library_feature_count'";

  if (db_table_exists('tripal_mviews')) {
    $mview = db_fetch_object(db_query($sql));
    if ($mview) {
      tripal_mviews_action('delete', $mview->mview_id);
    }
  }

  // Get the list of nodes to remove
  $sql_lib_id = "SELECT nid, vid ".
               "FROM {node} ".
               "WHERE type='chado_library'";
  $result = db_query($sql_lib_id);
  while ($node = db_fetch_object($result)) {
    node_delete($node->nid);
  }
}

/**
 * This function simply defines all tables needed for the module to work
 * correctly.  By putting the table definitions in a separate function we
 * can easily provide the entire list for hook_install or individual
 * tables for an update.
 *
 * @ingroup tripal_library
 */
function tripal_library_get_schemas() {
  $schema = array();
  $schema['chado_library'] = 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
      ),
    'library_id' => array(
      'type' => 'int',
      'not null' => TRUE,
      'default' => 0
      )
      ),
    'indexes' => array(
      'library_id' => array('library_id')
      ),
    'unique keys' => array(
      'nid_vid' => array('nid', 'vid'),
      'vid' => array('vid')
      ),
    'primary key' => array('nid'),
  );
  return $schema;
}

/**
 * Implementation of hook_requirements(). Make sure 'Tripal Core' is enabled
 * before installation
 *
 * @ingroup tripal_library
 */
function tripal_library_requirements($phase) {
  $requirements = array();
  if ($phase == 'install') {
    if (!function_exists('tripal_create_moddir')) {
      $requirements ['tripal_library'] = array(
        'title' => "tripal_library",
        'value' => "error. Some required modules are just being installed. Please try again.",
        'severity' => REQUIREMENT_ERROR,
        );
    }
  }
  return $requirements;
}