tripal/tripal_feature/tripal_feature.install

<?php

/************************************************************************
*  Implementation of hook_install();
*/
function tripal_feature_install(){
   // create the module's data directory
   tripal_create_moddir('tripal_feature');

   // create the tables that correlate drupal nodes with chado 
   // features, organisms, etc....
   drupal_install_schema('tripal_feature');
  
   // add the materialized view
   tripal_feature_add_organism_count_mview();

   // Register this module as having an analysis type
   tripal_analysis_register_child('tripal_feature');

}
/*******************************************************************************
*  Update for Drupal 6.x, Tripal 0.2b, Feature Module 0.2
*  This update adjusts the materialized view by adding a 'cvterm_id' column
*/

function tripal_feature_update_6000(){
   // recreate the materialized view
   tripal_feature_add_organism_count_mview();
   $ret = array(
      '#finished' => 1,
   );
   
   return $ret;
}
/*******************************************************************************

*/
function tripal_feature_update_6300(){
   // add the relationship aggregator table to the database
   $schema = tripal_feature_get_schemas('tripal_feature_relagg');
   $ret = array();
   db_create_table($ret, 'tripal_feature_relagg', $schema['tripal_feature_relagg']);

   // Register this module as having an analysis type
   tripal_analysis_register_child('tripal_feature');
   
   return $ret;
}
/*******************************************************************************

*/
function tripal_feature_add_organism_count_mview(){
   $view_name = 'organism_feature_count';

   // Drop the MView table if it exists
   $mview_id = tripal_mviews_get_mview_id($view_name);
   if($mview_id){
      tripal_mviews_action("delete",$mview_id);
   }

   // Create the MView
   tripal_add_mview(
      // view name
      $view_name,
      // tripal module name
      'tripal_feature',
      // table name
      $view_name,
      // table schema definition
      'organism_id integer, genus character varying(255), '.
      '  species character varying(255), '.
      '  common_name character varying(255), '.
      '  num_features integer, cvterm_id integer, '.
      '  feature_type character varying(255)',
      // columns for indexing
      'organism_id,cvterm_id,feature_type',
      // SQL statement to populate the view
      'SELECT O.organism_id, O.genus, O.species, O.common_name, 
          count(F.feature_id) as num_features, 
          CVT.cvterm_id, CVT.name as feature_type 
       FROM {Organism} O 
          INNER JOIN Feature F           ON O.Organism_id = F.organism_id 
          INNER JOIN Cvterm CVT          ON F.type_id = CVT.cvterm_id 
       GROUP BY O.Organism_id, O.genus, O.species, O.common_name,
          CVT.cvterm_id, CVT.name',
      // special index
      ''
   );

   // add a job to the job queue so this view gets updated automatically next
   // time the job facility is run
   $mview_id = tripal_mviews_get_mview_id($view_name);
   if($mview_id){
      tripal_mviews_action('update',$mview_id);
   }
}
/************************************************************************
* Implementation of hook_schema().
*/
function tripal_feature_schema() {
   $schema = tripal_feature_get_schemas();
   return $schema;
}
/************************************************************************
* Implementation of hook_uninstall()
*/
function tripal_feature_uninstall(){

   // Drop the MView table if it exists
   $mview_id = tripal_mviews_get_mview_id('organism_feature_count');
   if($mview_id){
      tripal_mviews_action("delete",$mview_id);
   }

   drupal_uninstall_schema('tripal_feature');

   // Get the list of nodes to remove
   $sql_feature_id = "SELECT nid, vid ".
                 "FROM {node} ".
                 "WHERE type='chado_feature'";
   $result = db_query($sql_feature_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.
*/
function tripal_feature_get_schemas ($table = NULL){  
  $schema = array();


  if(!$table or strcmp($table,'chado_feature')==0){
     $schema['chado_feature'] = array(
         'fields' => array(
            'vid' => array('type' => 'int', 'unsigned' => TRUE, 'not null' => TRUE, 'default' => 0),
            'nid' => array('type' => 'int', 'unsigned' => TRUE, 'not null' => TRUE, 'default' => 0),
            'feature_id' => array('type' => 'int', 'not null' => TRUE, 'default' => 0),
            'sync_date' => array ('type' => 'int', 'not null' => FALSE, 'description' => 'UNIX integer sync date/time'),
         ),
         'indexes' => array(
            'feature_id' => array('feature_id')
          ),
         'unique keys' => array(
            'nid_vid' => array('nid','vid'),
            'vid' => array('vid')
         ),
         'primary key' => array('nid'),
     );
  }
  if(!$table or strcmp($table,'tripal_feature_relagg')==0){
     $schema['tripal_feature_relagg'] = array(
        'fields' => array(
           'type_id' => array('type' => 'int', 'unsigned' => TRUE, 'not null' => TRUE, 'default' => 0),
           'rel_type_id' => array('type' => 'int', 'unsigned' => TRUE, 'not null' => TRUE, 'default' => 0),
        ),
        'indexes' => array(
           'type_id' => array('type_id')
        ),
     );
  }

  return $schema;
}

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