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File

tripal_feature/tripal_feature.module, line 1420

@todo Add file header description

Code

function tripal_feature_load_organism_feature_counts($organism) {

  // don't show the browser if the settings in the admin page is turned off
  // instead return the array indicating the status of the browser
  $show_counts = variable_get('tripal_feature_summary_setting', 'show_feature_summary');
  if (strcmp($show_counts, 'show_feature_summary') != 0) {
    return array('enabled' => FALSE);
  }


  $args = array();
  $names = array();
  $order = array();

  // build the where clause for the SQL statement if we have a custom term list
  // we'll also keep track of the names the admin provided (if any) and the
  // order that the terms should appear.
  $is_custom = 0;
  $temp = rtrim(variable_get('tripal_feature_summary_report_mapping', ''));
  $where = '';
  if ($temp) {
    $is_custom = 1;
    $temp = explode("\n", $temp);
    foreach ($temp as $key => $value) {
      // separate the key value pairs
      $temp2 = explode("=", $value);
      $feature_type = rtrim($temp2[0]);
      $args[] = $feature_type;
      $order[] = $feature_type;
      // if a new name is provided then use that otherwise just
      // use the feature type
      if (count($temp2) == 2) {
        $names[] = rtrim($temp2[1]);
      }
      else {
        $names[] = $feature_type;
      }
      $where .= "OFC.feature_type = '%s' OR \n";
    }
    if ($where) {
      $where = drupal_substr($where, 0, -5); # remove OR from the end
      $where = "($where) AND";
    }
  }

  // get the feature counts.  This is dependent on a materialized view
  // installed with the organism module
  $sql = "
    SELECT OFC.num_features,OFC.feature_type,CVT.definition
    FROM {organism_feature_count} OFC
      INNER JOIN {cvterm} CVT on OFC.cvterm_id = CVT.cvterm_id
    WHERE $where organism_id = %d
    ORDER BY num_features desc
  ";
  $args[] = $organism->organism_id;
  $org_features = chado_query($sql, $args);

  // iterate through the types
  $types = array();
  while ($type = db_fetch_object($org_features)) {
    $types[$type->feature_type] = $type;
    // if we don't have an order this means we didn't go through the loop
    // above to set the names, so do that now
    if (!$is_custom) {
      $names[] = $type->feature_type;
      $order[] = $type->feature_type;
    }
  }

  # now reorder the types
  $ordered_types = array();
  foreach ($order as $type) {
    $ordered_types[] = $types[$type];
  }
  return array('types' => $ordered_types, 'names' => $names, 'enabled' => TRUE);
}