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

Open

  private function insertSynonyms() {
    $chado = $this->getChadoConnection();
    $batch_size = 1000;
    $num_synonyms = count(array_keys($this->synonym_lookup));
    $num_batches = (int) ($num_synonyms / $batch_size) + 1;

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

Open

  public function onFieldableEntityTypeCreate(EntityTypeInterface $entity_type, array $field_storage_definitions) {
    parent::onFieldableEntityTypeCreate($entity_type,$field_storage_definitions);

    // This is where we create the types each field describes in the
    // associated TripalStorage instance.

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

Open

  public function isInvalidSchemaName(
    string $schema_name,
    bool $ignore_reservation = FALSE,
    bool $reload_config = FALSE
  ) :string {

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

Open

  public function onEntityTypeDelete(EntityTypeInterface $entity_type) {

    // build remove storage operations
    $storageOps = [];
    foreach ($this->fieldStorageDefinitions() as $storageDefinition) {

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

Open

  public function addBundleField(string $bundle, array $field_def) : bool {
    $logger = \Drupal::service('tripal.logger');

    if (!$this->validateFieldDef($field_def)) {
      return False;

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

Open

  public function setSchemaName(string $schema_name) :void {
    // Does schema change?
    if (!empty($this->schemaName) && ($schema_name == $this->schemaName)) {
      return;
    }

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