Create the taxonomic tree in Chado.

If the tree already exists it will not be recreated.

Return value

Returns the phylotree object.

Throws

Exception

File

tripal_chado/includes/TripalImporter/TaxonomyImporter.inc, line 272

Class

TaxonomyImporter

Code

private function initTree() {
  // Add the taxonomy tree record into the phylotree table. If the tree
  // already exists then don't insert it again.
  $tree_name = $site_name . 'Taxonomy Tree';
  $phylotree = chado_select_record('phylotree', array('*'), array('name' => $tree_name));
  if (count($phylotree) == 0) {
    // Add the taxonomic tree.
    $phylotree = array(
      'name' => $site_name . 'Taxonomy Tree',
      'description' => 'A phylogenetic tree based on taxonomic rank.',
      'leaf_type' => 'taxonomy',
      'tree_file' => '/dev/null',
      'format' => 'taxonomy',
      'no_load' => TRUE,
    );
    $errors = array();
    $warnings = array();
    $success = tripal_insert_phylotree($phylotree, $errors, $warnings);
    if (!$success) {
      throw new Exception("Cannot add the Taxonomy Tree record.");
    }
    $phylotree = (object) $phylotree;
  }
  else {
    $phylotree = $phylotree[0];
  }
  return $phylotree;
}