Duplicate of _fill_cvtermpath4root() stored procedure in Chado.

This function process a "branch" of the ontology. Initially, the "root" starts at the top of the tree. But, as the cvtermpath is populated the "root" becomes terms deeper in the tree.

Parameters

$rootid: The term ID from the cvterm table of Chado (i.e. cvterm.cvterm_id).

$cvid: The controlled vocabulary ID from the cv table of Chado (i.e. cv.cv_id).

Related topics

File

tripal_chado/api/modules/tripal_chado.cv.api.inc, line 430

Provides API functions specificially for managing controlled vocabulary records in Chado.

Code

function _chado_update_cvtermpath_root_loop($rootid, $cvid, &$roots) {
  $ttype = db_query(
  'SELECT cv.cvterm_id 
    FROM cvterm cv
    WHERE cv.name = :isa 
          OR cv.name = :is_a
    '
  , 
  array(':isa' => "isa", ':is_a' => "is_a")
  );

  $result = $ttype->fetchObject();
  $term_id = $rootid . '|' . $rootid . '|' . $cvid . '|' . $result->cvterm_id;
  // If the child_id matches any other id in the array then we've hit a loop.
  foreach ($roots as $element_id) {
    if ($element_id == $term_id) {
      return;
    }
  }
  // Then add that new entry to the $tree_path.
  $roots[] = $term_id;

  // Descends through the branch starting at this "root" term.
  $tree_path =[];
  $matched_rows =[];
  $possible_start_of_loop =[];
  $depth = 0;
  _chado_update_cvtermpath_loop($rootid, $rootid, $cvid, $result->cvterm_id, $depth, 
  0, $tree_path, FALSE, $matched_rows, $possible_start_of_loop, FALSE);

  // Get's the children terms of this "root" term and then recursively calls
  // this function making each child root.
  $cterm = db_query(
  'SELECT *
      FROM cvterm_relationship
      WHERE object_id = :rootid
    ', 
  [':rootid' $rootid]
  );
  while ($cterm_result = $cterm->fetchAssoc()) {
    _chado_update_cvtermpath_root_loop($cterm_result['subject_id'], $cvid, $roots);
  }
}