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Showing 174 of 174 total issues

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

function tripal_create_files_dir($module_name, $path = FALSE) {
  $fs = \Drupal::service('file_system');
  $messenger = \Drupal::messenger();
  $flags = \Drupal\Core\File\FileSystemInterface::CREATE_DIRECTORY | \Drupal\Core\File\FileSystemInterface::MODIFY_PERMISSIONS;
Severity: Minor
Found in tripal/src/api/tripal.files.api.php - About 25 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

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

function tripal_run_importer($import_id, TripalJob $job = NULL) {

  // Initialize the logger.
  $logger = \Drupal::service('tripal.logger');
Severity: Minor
Found in tripal/src/api/tripal.importer.api.php - About 25 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

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

  private function getTypeID($type, $is_prop_type) {
    $chado = $this->getChadoConnection();

    $cv = $this->feature_cv;
    if ($is_prop_type) {
Severity: Minor
Found in tripal_chado/src/Plugin/TripalImporter/GFF3Importer.php - About 25 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

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

  public function addProperty(TripalTerm $term, string $value, int $rank = NULL) : bool {
    $this->loaded_attributes['properties'] = True;

    // Get the max rank for this property.
    $term_id = $term->getTermId();
Severity: Minor
Found in tripal/src/TripalVocabTerms/TripalTerm.php - About 25 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

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

  protected function acquireTaskLocks() :bool {
    $all_locked = FALSE;
    try {
      // Lock task.
      $success = $this->locker->acquire($this->id);
Severity: Minor
Found in tripal_biodb/src/Task/BioTaskBase.php - About 25 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

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

  public function getDrupalSchemaName() :string {

    // We only need to look this up if it hasn't been set yet.
    if (!isset(static::$drupalSchema)) {
Severity: Minor
Found in tripal/src/TripalDBX/TripalDbx.php - About 25 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

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

  private function insertFeatures() {
    $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 25 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

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

  private function insertDbxrefs() {
    $chado = $this->getChadoConnection();
    $batch_size = 1000;
    $num_dbxrefs = count(array_keys($this->dbxref_lookup));
    $num_batches = (int) ($num_dbxrefs / $batch_size) + 1;
Severity: Minor
Found in tripal_chado/src/Plugin/TripalImporter/GFF3Importer.php - About 25 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

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

  private function insertFeatureTargets() {
    $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 25 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

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

  public function preSave(EntityStorageInterface $storage) {
    parent::preSave($storage);

    // Build all storage operations that will be done, saving the tripal
    // fields that will be saved and clearing them from each entity.
Severity: Minor
Found in tripal/src/TripalStorage/TripalEntityBase.php - About 25 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

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

  private function deleteFeatureData() {
    $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 25 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

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

  public function buildForm(array $form, FormStateInterface $form_state) {
    // Get values from state.
    $schema_name = $form_state->getValue('chado_schema');
    $task = $form_state->getValue('task');
Severity: Minor
Found in tripal_chado/src/Form/ChadoManagerForm.php - About 25 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

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

  private function insertFeatureLocs() {
    $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 25 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

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

  public function getProgress() :float {
    $data = $this->state->get(static::STATE_KEY_DATA_PREFIX . $this->id, []);

    if (empty($data)) {
      // No more data available. Assume process ended.
Severity: Minor
Found in tripal_chado/src/Task/ChadoCloner.php - About 25 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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