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File

tripal_feature/tripal_feature.module, line 526

@todo Add file header description

Code

function chado_feature_update($node) {
  if ($node->revision) {
    // there is no way to handle revisions in Chado but leave
    // this here just to make not we've addressed it.
  }

  $residues = preg_replace("/[\n\r\s]/", "", $node->residues);
  $obsolete = 'FALSE';
  if ($node->is_obsolete) {
    $obsolete = 'TRUE';
  }

  // get the feature type id
  $values = array(
    'cv_id' => array(
      'name' => 'sequence'
    ),
    'name' => $node->feature_type
  );
  $type = tripal_core_chado_select('cvterm', array('cvterm_id'), $values);

  $feature_id = chado_get_id_for_node('feature', $node);

  if (sizeof($type) > 0) {
    $match = array(
      'feature_id' => $feature_id,
    );
    $values = array(
      'organism_id' => $node->organism_id,
      'name' => $node->fname,
      'uniquename' => $node->uniquename,
      'residues' => $residues,
      'seqlen' => drupal_strlen($residues),
      'is_obsolete' => $obsolete,
      'type_id' => $type[0]->cvterm_id,
      'md5checksum' => md5($residues)
    );
    $options = array('return_record' => TRUE);
    $status = tripal_core_chado_update('feature', $match, $values, $options);

    // add the genbank synonyms
    chado_feature_add_synonyms($node->synonyms, $feature_id);
  }
  else {
    drupal_set_message(t('Unable to update feature.'), 'warning');
    watchdog('tripal_feature', 
    'Update feature: Unable to update feature where values: %values', 
    array('%values' => print_r($values, TRUE)), 
    WATCHDOG_WARNING
    );
  }


}