tripal/tripal_library/tripal_library.install

<?php

/**
*  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;
}