Function saveTerm has a Cognitive Complexity of 10 (exceeds 7 allowed). Consider refactoring.

Open

  public function saveTerm($term, $options = []) {

    // Don't save terms that aren't valid
    if (!$term->isValid()) {
      $this->messageLogger->error(t('ChadoIdSpace::saveTerm(). The term, "@term" is not valid and cannot be saved. It must include a name, accession, IdSpace and vocabulary.',

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Function prepSynonms has a Cognitive Complexity of 10 (exceeds 7 allowed). Consider refactoring.

Open

  private function prepSynonms() {
    // make sure we have a 'synonym_type' vocabulary
    $select = ['name' => 'synonym_type'];
    $results = chado_select_record('cv', ['*'], $select);

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Function performTask has a Cognitive Complexity of 10 (exceeds 7 allowed). Consider refactoring.

Open

  public function performTask() :bool {
    // Task return status.
    $task_success = FALSE;

    // Validate parameters.

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Function prepareCommentUpgrade has a Cognitive Complexity of 10 (exceeds 7 allowed). Consider refactoring.

Open

  protected function prepareCommentUpgrade() {
    $chado_schema = $this->outputSchemas[0];
    $ref_schema = $this->inputSchemas[0];

    $this->upgradeQueries['#comments'] = [];

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Function findTables has a Cognitive Complexity of 9 (exceeds 7 allowed). Consider refactoring.

Open

  public function findTables($table_expression) {

    if ($table_expression === NULL) {
      return [];
    }

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Function addTypes has a Cognitive Complexity of 9 (exceeds 7 allowed). Consider refactoring.

Open

  public function addTypes($types) {
    $logger = \Drupal::service('tripal.logger');

    // Index the types by their entity type, field type and key.
    foreach ($types as $index => $type) {

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Function checkSequenceExists has a Cognitive Complexity of 9 (exceeds 7 allowed). Consider refactoring.

Open

  public function checkSequenceExists($table, $column, $sequence_name = NULL) {

    if ($sequence_name === NULL) {

      // Ensure they gave us a table.

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Function submitForm has a Cognitive Complexity of 9 (exceeds 7 allowed). Consider refactoring.

Open

  public function submitForm(array &$form, FormStateInterface $form_state) {
    $values = $form_state->getValues();
    $action = $values['action'];
    $mview_id = $values['mview_id'];
    $chado_schema = $values['chado_schema'];

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Function tripalClear has a Cognitive Complexity of 9 (exceeds 7 allowed). Consider refactoring.

Open

  public function tripalClear($field_item, $field_name, $prop_types, $prop_values, $entity) {
    $delta = $field_item->getName();

    foreach ($prop_values as $prop_value) {
      $prop_key = $prop_value->getKey();

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Function associateChildren has a Cognitive Complexity of 9 (exceeds 7 allowed). Consider refactoring.

Open

  private function associateChildren() {
    $this->setItemsHandled(0);
    $this->setTotalItems(count(array_keys($this->features)));

    // Iterate through parent-child relationships and set the ranks.

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Function executeSqlQueries has a Cognitive Complexity of 9 (exceeds 7 allowed). Consider refactoring.

Open

  public function executeSqlQueries(
    string $sql_queries,
    $search_path_mode = FALSE,
    ?string $schema_name = NULL
  ) :bool {

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Function prepDBs has a Cognitive Complexity of 9 (exceeds 7 allowed). Consider refactoring.

Open

  private function prepDBs() {

    // Get the list of database records that are needed by this GFF file. If
    // they do not exist then add them.
    foreach (array_keys($this->db_lookup) as $dbname) {

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Function formElement has a Cognitive Complexity of 9 (exceeds 7 allowed). Consider refactoring.

Open

  public function formElement(FieldItemListInterface $items, $delta, array $element, array &$form, FormStateInterface $form_state) {
    $chado = \Drupal::service('tripal_chado.database');

    // Get the field settings.
    $field_definition = $items[$delta]->getFieldDefinition();

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Function log2Message has a Cognitive Complexity of 9 (exceeds 7 allowed). Consider refactoring.

Open

  protected function log2Message($level, $message, $context = []) {

    if (in_array($level, ['info', 'notice'])) {
      $status = \Drupal\Core\Messenger\MessengerInterface::TYPE_STATUS;
    }

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Function submitForm has a Cognitive Complexity of 9 (exceeds 7 allowed). Consider refactoring.

Open

  public function submitForm(array &$form, FormStateInterface $form_state) {
    $values = $form_state->getValues();
    $action = $values['action'];
    $table_id = $values['table_id'];
    $chado_schema = $values['chado_schema'];

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Function validateParameters has a Cognitive Complexity of 9 (exceeds 7 allowed). Consider refactoring.

Open

  public function validateParameters() :void {
    try {
      // Check input.
      if (empty($this->parameters['input_schemas'])
          || (1 != count($this->parameters['input_schemas']))

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Avoid too many return statements within this method.

Open

      return tripal_file_upload_merge($filename, $type, $user_dir);

Avoid too many return statements within this method.

Open

      return tripal_file_upload_verify($filename, $chunk, $user_dir);

Avoid too many return statements within this method.

Open

      return FALSE;

Function tripalDashboard has a Cognitive Complexity of 8 (exceeds 7 allowed). Consider refactoring.

Open

  public function tripalDashboard() {
    $output = '';
    $block_manager = \Drupal::service('plugin.manager.block');
    // You can hard code configuration or you load from settings.
    $config = [];

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