This function is a wrapper for the chado_cleanup_orphaned_nodes function. It breaks up the work of chado_cleanup_orphaned_nodes into smaller pieces that are more managable for servers that may have low php memory settings.

Parameters

$table: The name of the table that corresonds to the node type we want to clean up.

$nentries: Optional. The number of entries to parse at one time (ie: the batch size). Set to zero if no limit is needed.

$linking_table: Optional. The name of the linking table that maps Drupal nodes to Chado records. This is only required if the linking table name is not of the form: chado_[table] where [table] is the value provided to the $table argument.

$node_type: Optional. The name of the node type for the records. This is only required if the node type is not of the form: chado_[table] where [table] is the value provided to the $table.

$job_id: Optional. This should be the job id from the Tripal jobs system. Typically, only the Tripal jobs system will use the argument.

Related topics

File

tripal_core/api/tripal_core.chado_nodes.api.inc, line 1005

API to handle much of the common functionality implemented when creating a drupal node type.

Code

function chado_cleanup_orphaned_nodes($table, $nentries = 25000, $linking_table = NULL, $node_type = NULL, $job_id = NULL) {
  // The max number of records either as nodes or linked records.
  $count = 0;
  // Will hold the number of nodes of this type.
  $ncount = 0;
  // Will hold the number of linked records.
  $clcount = 0;

  if (!$node_type) {
    $node_type = 'chado_' . $table;
  }
  if (!$linking_table) {
    $linking_table = 'chado_' . $table;
  }
  // Find the number nodes of type chado_$table and find the number of entries
  // in chado_$table; keep the larger of the two numbers.
  $dsql = "SELECT COUNT(*) FROM {node} WHERE type = :node_type";
  $ndat = db_query($dsql, array(':node_type' => $node_type));
  $temp = $ndat->fetchObject();
  $ncount = $temp->count;
  $clsql = "SELECT COUNT(*) FROM {" . $linking_table . "}";
  $cdat = db_query($clsql);
  $clcount = $cdat->fetchObject();
  if ($ncount < $clcount) {
    $count = $clcount;
  }
  else {
    $count = $ncount;
  }

  $transaction = db_transaction();
  print "\nNOTE: This operation is performed using a database transaction. \n" .
    "If it fails or is terminated prematurely then the entire set of \n" .
    "changes is rolled back and will not be found in the database\n\n";
  try {
    $m = ceil($count / $nentries);
    for ($i = 0; $i < $m; $i++) {
      $offset = ($nentries * $i);
      chado_cleanup_orphaned_nodes_part($table, $job_id, $nentries, $offset, $linking_table, $node_type);
    }
  }
  catch (Exception $e) {
    $transaction->rollback();
    print "\n"; // make sure we start errors on new line
    watchdog_exception('trp-fsync', $e);
    print "FAILED: Rolling back database changes...\n";
  }
  return '';
}