Creates a materialized view that stores the type & number of features per organism

Related topics

File

tripal_feature/tripal_feature.install, line 243

Installation of the feature module

Code

function tripal_feature_add_organism_count_mview() {
  $view_name = 'organism_feature_count';
  $comment = 'Stores the type and number of features per organism';

  $schema = array(
    'description' => $comment,
    'table' => $view_name,
    'fields' => array(
      'organism_id' => array(
        'size' => 'big',
        '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_features' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'cvterm_id' => array(
        'size' => 'big',
        'type' => 'int',
        'not null' => TRUE,
      ),
      'feature_type' => array(
        'type' => 'varchar',
        'length' => '255',
        'not null' => TRUE,
      ),
    ),
    'indexes' => array(
      'organism_feature_count_idx1' => array('organism_id'),
      'organism_feature_count_idx2' => array('cvterm_id'),
      'organism_feature_count_idx3' => array('feature_type'),
    ),
  );

  $sql = "
    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
  ";

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