tripal/tripal_feature/tripal_feature.install

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

/**
 * Implementation of hook_install().
 *
 * @ingroup tripal_feature
 */
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();

}
/**
 *  Update for Drupal 6.x, Tripal 0.2b, Feature Module 0.2
 *  This update adjusts the materialized view by adding a 'cvterm_id' column
 *
 * @ingroup tripal_feature
 */
function tripal_feature_update_6000() {
  // recreate the materialized view
  tripal_feature_add_organism_count_mview();
  $ret = array(
    '#finished' => 1,
  );

  return $ret;
}

/**
 *
 * @ingroup tripal_feature
 */
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']);

  return $ret;
}
/**
 *
 * @ingroup tripal_feature
 */
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().
 *
 * @ingroup tripal_feature
 */
function tripal_feature_schema() {
  $schema = tripal_feature_get_schemas();
  return $schema;
}
/**
 * Implementation of hook_uninstall().
 *
 * @ingroup tripal_feature
 */
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.
 *
 * @ingroup tripal_feature
 */
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
 *
 * @ingroup tripal_feature
 */
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;
}