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File

tripal_feature/includes/gff_loader.inc, line 1737

@todo Add file header description

Code

function tripal_feature_load_gff3_property($feature, $property, $value) {

  // first make sure the cvterm exists.  if not, then add it
  $select = array(
    'name' => $property,
    'cv_id' => array(
      'name' => 'feature_property',
    ),
  );
  $options = array('statement_name' => 'sel_cvterm_name_cvid');
  $result = tripal_core_chado_select('cvterm', array('*'), $select, $options);

  // if we don't have a property like this already, then add it otherwise, just return
  if (count($result) == 0) {
    $term = array(
      'id' => "null:$property",
      'name' => $property,
      'namespace' => 'feature_property',
      'is_obsolete' => 0,
    );
    $cvterm = (object) tripal_cv_add_cvterm($term, 'feature_property', 0, 0);
    if (!$cvterm) {
      watchdog("T_gff3_loader", "Cannot add cvterm, $property", array(), WATCHDOG_WARNING);
      return 0;
    }
  }
  else {
    $cvterm = $result[0];
  }


  // check to see if the property already exists for this feature
  // if it does but the value is unique then increment the rank and add it.
  // if the value is not unique then don't add it.
  $add = 1;
  $rank = 0;
  $select = array(
    'feature_id' => $feature->feature_id,
    'type_id' => $cvterm->cvterm_id,
  );
  $options = array(
    'statement_name' => 'sel_featureprop_featureid_typeid',
    'order_by' => array(
      'rank' => 'ASC',
    ),
  );
  $results = tripal_core_chado_select('featureprop', array('*'), $select, $options);
  foreach ($results as $prop) {
    if (strcmp($prop->value, $value) == 0) {
      $add = NULL; // don't add it, it already exists
    }
    $rank = $prop->rank + 1;
  }

  // add the property if we pass the check above
  if ($add) {
    $values = array(
      'feature_id' => $feature->feature_id,
      'type_id' => $cvterm->cvterm_id,
      'value' => $value,
      'rank' => $rank,
    );
    $options = array('statement_name' => 'ins_featureprop_all');
    $result = tripal_core_chado_insert('featureprop', $values, $options);
    if (!$result) {
      watchdog("T_gff3_loader", "cannot add featureprop, $property", array(), WATCHDOG_WARNING);
    }
  }
}