Function postLoad has a Cognitive Complexity of 21 (exceeds 7 allowed). Consider refactoring.

Open

  public static function postLoad(EntityStorageInterface $storage, array &$entities) {
    parent::postLoad($storage, $entities);

    // Build the storage operations that will be done and entity references
    $storageOps = [];

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Function parseGFF3 has a Cognitive Complexity of 21 (exceeds 7 allowed). Consider refactoring.

Open

  private function parseGFF3() {
    $filesize = filesize($this->gff_file);
    $this->setTotalItems($filesize);

    // Holds a unique list of cvterms for later lookup.

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Function tripal_launch_job has a Cognitive Complexity of 21 (exceeds 7 allowed). Consider refactoring.

Open

function tripal_launch_job($do_parallel = 0, $job_id = NULL, $max_jobs = -1, $single = 0) {

  $messenger = \Drupal::messenger();

  // First check if any jobs are currently running if they are, don't continue,

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Function buildForm has a Cognitive Complexity of 21 (exceeds 7 allowed). Consider refactoring.

Open

  public function buildForm(array $form, FormStateInterface $form_state, $mview_id = null) {

    $chado = \Drupal::service('tripal_chado.database');

    if (!$mview_id) {

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Function oboEbiLookup has a Cognitive Complexity of 21 (exceeds 7 allowed). Consider refactoring.

Open

  private function oboEbiLookup($accession, $type_of_search, $found_iri = NULL, $found_ontology = NULL) {
    // Grab just the ontology from the $accession.
    $parts = explode(':', $accession);
    $ontology = strtolower($parts[0]);
    $ontology = preg_replace('/\s+/', '', $ontology);

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Function insertFeatureParents has a Cognitive Complexity of 20 (exceeds 7 allowed). Consider refactoring.

Open

  private function insertFeatureParents(){
    $chado = $this->getChadoConnection();
    $batch_size = 100;
    $num_parents = count(array_keys($this->parent_lookup));
    $num_batches = (int) ($num_parents / $batch_size) + 1;

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Consider simplifying this complex logical expression.

Open

        if ($tablename == 'cvterm_dbxref' || $tablename == 'cvterm_relationship' ||
          $tablename == 'cvtermpath' || $tablename == 'cvtermprop' || $tablename == 'chadoprop' ||
          $tablename == 'cvtermsynonym' || preg_match('/_relationship$/', $tablename) ||
          preg_match('/_cvterm$/', $tablename) ||
          // Ignore prop tables

Consider simplifying this complex logical expression.

Open

        if ($tablename == 'cvterm_dbxref' || $tablename == 'cvterm_relationship' ||
          $tablename == 'cvtermpath' || $tablename == 'cvtermprop' || $tablename == 'chadoprop' ||
          $tablename == 'cvtermsynonym' || preg_match('/_relationship$/', $tablename) ||
          preg_match('/_cvterm$/', $tablename) ||
          // Ignore prop tables

Function findMissingProteins has a Cognitive Complexity of 19 (exceeds 7 allowed). Consider refactoring.

Open

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

    // Don't do anything if the user wants to skip creation of non listed

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Function run has a Cognitive Complexity of 19 (exceeds 7 allowed). Consider refactoring.

Open

  public function run() {
    $chado = $this->getChadoConnection();

    $arguments = $this->arguments['run_args'];
    $this->gff_file = $this->arguments['files'][0]['file_path'];

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Function prepareFeature has a Cognitive Complexity of 19 (exceeds 7 allowed). Consider refactoring.

Open

  private function prepareFeature($gff_feature, &$feature_cvterms, &$featureprop_cvterms) {

    // Add the landmark if it doesn't exist in the landmark list.
    if (!array_key_exists($gff_feature['landmark'], $this->landmarks)) {
      $this->landmarks[$gff_feature['landmark']] = FALSE;

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Function getTerm has a Cognitive Complexity of 19 (exceeds 7 allowed). Consider refactoring.

Open

  public function getTerm($accession, $options = []) {

    if (!$this->is_valid) {
      return NULL;
    }

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Function getTableDef has a Cognitive Complexity of 19 (exceeds 7 allowed). Consider refactoring.

Open

  public function getTableDef(string $table, array $parameters) :array {
    static $table_structures = [];

    $source = $parameters['source'] ?? 'file';
    $format = strtolower($parameters['format'] ?? '');

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Function fieldSettingsForm has a Cognitive Complexity of 19 (exceeds 7 allowed). Consider refactoring.

Open

  public function fieldSettingsForm(array $form, FormStateInterface $form_state) {
    $elements = [];

    $is_open = FALSE;
    $term = NULL;

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Function validateParameters has a Cognitive Complexity of 19 (exceeds 7 allowed). Consider refactoring.

Open

  public function validateParameters() :void {
    try {
      // Select a default version if needed.
      if (empty($this->parameters['version'])) {
        $this->parameters['version'] = static::DEFAULT_CHADO_VERSION;

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Function prepareUpgradeTypes has a Cognitive Complexity of 19 (exceeds 7 allowed). Consider refactoring.

Open

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

    // Get database types.

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Function buildMainForm has a Cognitive Complexity of 19 (exceeds 7 allowed). Consider refactoring.

Open

  public function buildMainForm(array $form, FormStateInterface $form_state) {

    $tripal_dbx = \Drupal::service('tripal.dbx');
    $chado = new ChadoConnection();

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Function validateForm has a Cognitive Complexity of 19 (exceeds 7 allowed). Consider refactoring.

Open

  public function validateForm(array &$form, FormStateInterface $form_state) {
    if ($form_state->isSubmitted()) {
      $mail_pi = $form_state->getValue('principal_investigator_email');
      $mail_sa = $form_state->getValue('tripal_reg_site_admin_email');
      if ($form_state->getValue('disable_tripal_reporting') != TRUE) {

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Function prepareUpgradeSequences has a Cognitive Complexity of 19 (exceeds 7 allowed). Consider refactoring.

Open

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

    // Get sequences.

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Function findVersion has a Cognitive Complexity of 18 (exceeds 7 allowed). Consider refactoring.

Open

  public function findVersion(
    ?string $schema_name = NULL,
    bool $exact_version = FALSE
  ) :string {
    // By default, we don't know the version.

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