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Function validateForm has a Cognitive Complexity of 14 (exceeds 7 allowed). Consider refactoring.
Open

  public function validateForm(array &$form, FormStateInterface $form_state) {

    // Convert the validation code into the D8/9 equivalent
    $form_values = $form_state->getValues();
    $plugin_id = $form_values['importer_plugin_id'];
Severity: Minor
Found in tripal/src/Form/TripalImporterForm.php - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function queryTableInformation has a Cognitive Complexity of 14 (exceeds 7 allowed). Consider refactoring.
Open

  public function queryTableInformation($table) {

    // Generate a key to reference this table's information on.
    $key = $this->connection
      ->prefixTables('{' . $table . '}');
Severity: Minor
Found in tripal/src/TripalDBX/TripalDbxSchema.php - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function tripal_file_upload has a Cognitive Complexity of 14 (exceeds 7 allowed). Consider refactoring.
Open

function tripal_file_upload($type, $filename, $action = NULL, $chunk = 0) {
  $user = \Drupal::currentUser();
  $uid = $user->id();

  $module = \Drupal::request()->get('module', '');
Severity: Minor
Found in tripal/src/api/tripal.upload.api.php - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function schema has a Cognitive Complexity of 14 (exceeds 7 allowed). Consider refactoring.
Open

  public static function schema(FieldStorageDefinitionInterface $field_definition) {
    $schema = [];
    foreach (get_called_class()::tripalTypes($field_definition) as $type) {
      if ($type instanceof IntStoragePropertyType) {
        $column = [
Severity: Minor
Found in tripal/src/TripalField/TripalFieldItemBase.php - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function createTableSql has a Cognitive Complexity of 14 (exceeds 7 allowed). Consider refactoring.
Open

   function createTableSql($name, $table) {
    $sql_fields = [];
    foreach ($table['fields'] as $field_name => $field) {
      $sql_fields[] = $this
        ->createFieldSql($field_name, $this
Severity: Minor
Found in tripal_chado/src/api/ChadoSchema.php - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function getTableSchema has a Cognitive Complexity of 13 (exceeds 7 allowed). Consider refactoring.
Open

  public function getTableSchema($table) {

    $schema = $this->getSchemaDetails();

    $table_arr =  FALSE;
Severity: Minor
Found in tripal_chado/src/api/ChadoSchema.php - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function getTables has a Cognitive Complexity of 13 (exceeds 7 allowed). Consider refactoring.
Open

  public function getTables(
    array $include = []
  ) :array {
    static $type_to_name = [
      'r' => 'table',
Severity: Minor
Found in tripal/src/TripalDBX/TripalDbxSchema.php - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function insertFeatureSeqs has a Cognitive Complexity of 13 (exceeds 7 allowed). Consider refactoring.
Open

  private function insertFeatureSeqs() {

    $num_residues = count(array_keys($this->residue_index));

    $this->setItemsHandled(0);
Severity: Minor
Found in tripal_chado/src/Plugin/TripalImporter/GFF3Importer.php - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function __construct has a Cognitive Complexity of 13 (exceeds 7 allowed). Consider refactoring.
Open

  public function __construct(
    string $schema_name = '',
    $database = 'default',
    ?\Drupal\tripal\Services\TripalLogger $logger = NULL
  ) {
Severity: Minor
Found in tripal/src/TripalDBX/TripalDbxConnection.php - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function tripalJobsView has a Cognitive Complexity of 13 (exceeds 7 allowed). Consider refactoring.
Open

  public function tripalJobsView($id) {

    // Set the breadcrumb.
    $breadcrumb = new Breadcrumb();
    $breadcrumb->addLink(Link::fromTextAndUrl('Home',
Severity: Minor
Found in tripal/src/Controller/TripalJobController.php - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function createContentType has a Cognitive Complexity of 13 (exceeds 7 allowed). Consider refactoring.
Open

  private function createContentType($details) {

    $entityType = NULL;
    $bundle = '';
Severity: Minor
Found in tripal_chado/src/Task/ChadoPreparer.php - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function run has a Cognitive Complexity of 12 (exceeds 7 allowed). Consider refactoring.
Open

  public function run() {

    $this->start_time = time();
    $this->progress_start_time = time();
Severity: Minor
Found in tripal/src/Services/TripalJob.php - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function findLandmarks has a Cognitive Complexity of 12 (exceeds 7 allowed). Consider refactoring.
Open

  private function findLandmarks() {
    $chado = $this->getChadoConnection();
    $batch_size = 1000;
    $num_landmarks = count(array_keys($this->landmarks));
    $num_batches = (int) ($num_landmarks / $batch_size) + 1;
Severity: Minor
Found in tripal_chado/src/Plugin/TripalImporter/GFF3Importer.php - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function formSubmit has a Cognitive Complexity of 12 (exceeds 7 allowed). Consider refactoring.
Open

  public function formSubmit($form, &$form_state) {
    $public = \Drupal::database();

    $obo_id = $form_state->getValue('obo_id');
    $obo_name = trim($form_state->getValue('obo_name'));
Severity: Minor
Found in tripal_chado/src/Plugin/TripalImporter/OBOImporter.php - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function insertLandmarks has a Cognitive Complexity of 12 (exceeds 7 allowed). Consider refactoring.
Open

  private function insertLandmarks() {
    foreach ($this->landmarks as $uniquename => $feature_id) {
      // If the landmark does not have an entry in the GFF lines, try to
      // find or add it.
      if ($feature_id === FALSE) {
Severity: Minor
Found in tripal_chado/src/Plugin/TripalImporter/GFF3Importer.php - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function insertFeatureDerivesFrom has a Cognitive Complexity of 12 (exceeds 7 allowed). Consider refactoring.
Open

  private function insertFeatureDerivesFrom() {
    $chado = $this->getChadoConnection();
    $batch_size = 100;
    $num_features = count(array_keys($this->features));
    $num_batches = (int) ($num_features / $batch_size) + 1;
Severity: Minor
Found in tripal_chado/src/Plugin/TripalImporter/GFF3Importer.php - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function initId has a Cognitive Complexity of 12 (exceeds 7 allowed). Consider refactoring.
Open

  protected function initId() :void {
    $raw_id =
      static::TASK_NAME
      . '-'
      . $this->connection->getConnectionOptions()['database']
Severity: Minor
Found in tripal_biodb/src/Task/BioTaskBase.php - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function insertFeatureAnalysis has a Cognitive Complexity of 12 (exceeds 7 allowed). Consider refactoring.
Open

  private function insertFeatureAnalysis() {
    $chado = $this->getChadoConnection();
    $batch_size = 1000;
    $num_features = count(array_keys($this->features));
    $num_batches = (int) ($num_features / $batch_size) + 1;
Severity: Minor
Found in tripal_chado/src/Plugin/TripalImporter/GFF3Importer.php - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function submitForm has a Cognitive Complexity of 12 (exceeds 7 allowed). Consider refactoring.
Open

  public function submitForm(array &$form, FormStateInterface $form_state) {
    $user = \Drupal::currentUser();

    //$run_args = $form_state['values'];
    $form_values = $form_state->getValues();
Severity: Minor
Found in tripal/src/Form/TripalImporterForm.php - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function setupReferenceSchema has a Cognitive Complexity of 11 (exceeds 7 allowed). Consider refactoring.
Open

  protected function setupReferenceSchema() {

    $ref_schema = $this->inputSchemas[0];
    $version = $this->parameters['version'];
Severity: Minor
Found in tripal_chado/src/Task/ChadoUpgrader.php - About 55 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

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