_state

Parameters

unknown $form:

Overrides TripalField::instanceSettingsFormValidate

File

tripal_chado/includes/TripalFields/sbo__relationship/sbo__relationship.inc, line 688

Class

sbo__relationship

Code

public function instanceSettingsFormValidate($form, &$form_state) {
  // Get relationships settings
  $settings = $form_state['values']['instance']['settings']['relationships'];
  $form_state['values']['instance']['settings']['relationships']['relationship_types'] = trim($settings['relationship_types']);

  // Make sure only one option is selected
  $option1test = $settings['option1_vocabs'];
  $option1 = isset($settings['option1_vocabs']) && array_pop($option1test);
  $option2 = (isset($settings['option2_vocab']) && $settings['option2_vocab']) || $settings['option2_parent'];
  $option3 = isset($settings['relationship_types']) && trim($settings['relationship_types']);
  if ($option1 && ($option2 || $option3) == 1 || 
    $option2 && ($option1 || $option3) == 1 || 
    $option3 && ($option1 || $option2) == 1) {
    form_set_error("instance][settings][relationships", t("Only one option is allowed to limit the relationship types."));
    return;
  }

  // For option3, make sure the supplied types are valid cvterms
  if ($option3) {
    $rel_types = explode(PHP_EOL, $settings['relationship_types']);
    foreach ($rel_types as $type) {
      $type = trim($type);
      // Ignore empty lines
      if ($type == '') {
        continue;
      }
      // Find the matching cvterm
      $sql = "SELECT cvterm_id FROM {cvterm} WHERE name = :name";
      $results = chado_query($sql, array(':name' => $type));
      $terms = array();
      while ($obj = $results->fetchObject()) {
        $terms[] = $obj;
      }
      // Don't save the form  if a term can not be found or it matches more than one cvterm
      $cv = '';
      if (count($terms) == 0) {
        // If a term can not be found, maybe the type contains '|', parse it as 'vocabulary|cvterm'
        if (strpos($type, '|')) {
          $tmp = explode('|', $type, 2);
          $type = trim($tmp[1]);
          $cv = chado_get_cv(array('name' => trim($tmp[0])));
          if ($cv) {
            $sql = "SELECT cvterm_id FROM {cvterm} WHERE name = :name AND cv_id = :cv_id";
            $results = chado_query($sql, array(':name' => $type, ':cv_id' => $cv->cv_id));
            while ($obj = $results->fetchObject()) {
              $terms[] = $obj;
            }
          }
          else {
            $cv = $tmp[0];
          }
        }
        if (count($terms) != 1) {
          $message = "The term '@type' can not be found.";
          $token = array('@type' => $type);
          if ($cv) {
            $message = "The term '@type' can not be found within the vocabulary '@vocab'.";
            $token['@vocab'] = $cv;
          }
          form_set_error("instance][settings][relationships][relationship_types", 
          t($message, $token));
        }
      }
      else if (count($terms) > 1) {
        // If a type matches more than one term, parse it as 'vocabulary|cvterm' and try again
        if (strpos($type, '|')) {
          $tmp = explode('|', $type, 2);
          $type = trim($tmp[1]);
          $cv = chado_get_cv(array('name' => trim($tmp[0])));
          if ($cv) {
            $sql = "SELECT cvterm_id FROM {cvterm} WHERE name = :name AND cv_id = :cv_id";
            $results = chado_query($sql, array(':name' => $type, ':cv_id' => $cv->cv_id));
            while ($obj = $results->fetchObject()) {
              $terms[] = $obj;
            }
          }
        }
        if (count($terms) != 1) {
          form_set_error("instance][settings][relationships][relationship_types", 
          t("The term '@type' matches more than one term. Please specify its vocabulary in the format of 'vocabulary|@type'.", array('@type' => $type)));
        }
      }
    }
  }

  // For option2: Make sure the parent term is a valid cvterm
  if ($option2) {
    $cv_id = $settings['option2_vocab'];
    $supertype = $settings['option2_parent'];
    $term = chado_get_cvterm(array(
      'name' => trim($supertype),
      'cv_id' => $cv_id,
    ));
    // Tripal cv autocomplete also allow cvterm synonyms, if the parent term doesn't match
    // a cvterm, try cvtermsynonym
    if (!$term) {
      $synonym = chado_get_cvterm(
      array(
        'synonym' => array(
          'name' => trim($supertype),
        )
      )
      );
      if ($synonym && $synonym->cv_id->cv_id == $cv_id) {
        $term = $synonym;
      }
    }
    if (!isset($term->cvterm_id)) {
      form_set_error("instance][settings][relationships][option2_parent", 
      t("The term '@type' is not a valid term for the vocabulary selected.", array('@type' => $supertype)));
    }
  }
}