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Showing 160 of 174 total issues

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

  public function validateSize($values, $chado_table, $record_id, $record, &$violations) {
    $chado = $this->getChadoConnection();
    $schema = $chado->schema();
    $table_def = $schema->getTableDef($chado_table, ['format' => 'drupal']);
Severity: Minor
Found in tripal_chado/src/Plugin/TripalStorage/ChadoStorage.php - About 2 hrs 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 validateFKs has a Cognitive Complexity of 18 (exceeds 7 allowed). Consider refactoring.
Open

  private function validateFKs($values, $chado_table, $record_id, $record, &$violations) {
    $chado = $this->getChadoConnection();
    $schema = $chado->schema();
    $table_def = $schema->getTableDef($chado_table, ['format' => 'drupal']);
Severity: Minor
Found in tripal_chado/src/Plugin/TripalStorage/ChadoStorage.php - About 2 hrs 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 17 (exceeds 7 allowed). Consider refactoring.
Open

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

    $chado = \Drupal::service('tripal_chado.database');
    $custom_tables = \Drupal::service('tripal_chado.custom_tables');
Severity: Minor
Found in tripal_chado/src/Form/ChadoCustomTableForm.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 getFeatureNames has a Cognitive Complexity of 17 (exceeds 7 allowed). Consider refactoring.
Open

  private function getFeatureNames($attrs, $type, $landmark_name, $fmin, $fmax) {
    $uniquename = '';
    $name = '';

    if (!array_key_exists('ID', $attrs) and !array_key_exists('Name', $attrs)) {
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 getSchemaDef has a Cognitive Complexity of 17 (exceeds 7 allowed). Consider refactoring.
Open

  public function getSchemaDef(array $parameters) :array {
    static $schema_structure = [];

    $source = $parameters['source'] ?? 'file';
    $format = strtolower($parameters['format'] ?? '');
Severity: Minor
Found in tripal_chado/src/Database/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 getValuesArray has a Cognitive Complexity of 16 (exceeds 7 allowed). Consider refactoring.
Open

  public static function getValuesArray($entity) {
    $values = [];
    $tripal_storages = [];
    $fields = $entity->getFields();
Severity: Minor
Found in tripal/src/Entity/TripalEntity.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 selectChadoRecord has a Cognitive Complexity of 16 (exceeds 7 allowed). Consider refactoring.
Open

  public function selectChadoRecord(&$records, $base_tables, $chado_table, $delta, $record) {
    $chado = $this->getChadoConnection();

    if (!array_key_exists('conditions', $record)) {
      throw new \Exception($this->t('Cannot select record in the Chado "@table" table due to missing conditions. Record: @record',
Severity: Minor
Found in tripal_chado/src/Plugin/TripalStorage/ChadoStorage.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 checkColumnType has a Cognitive Complexity of 16 (exceeds 7 allowed). Consider refactoring.
Open

  public function checkColumnType($table, $column, $expected_type = NULL) {

    // Ensure this column exists before moving forward.
    if (!$this->checkColumnExists($table, $column)) {
      tripal_report_error(
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 storageSettingsForm has a Cognitive Complexity of 15 (exceeds 7 allowed). Consider refactoring.
Open

  public function storageSettingsForm(array &$form, FormStateInterface $form_state, $has_data) {
    $elements = [];
    $settings = $this->getSetting('storage_plugin_settings');

    // turn into selection
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 cacheRelationships has a Cognitive Complexity of 15 (exceeds 7 allowed). Consider refactoring.
Open

  private function cacheRelationships() {

    // Now that we have all of the terms parsed and loaded into the cache,
    // lets run through them one more time cache any terms in relationships
    // as well.
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 prefixTables has a Cognitive Complexity of 15 (exceeds 7 allowed). Consider refactoring.
Open

  public function prefixTables($sql) {

    // Make sure there is no extra "{number:" in the query.
    $matches = [];
    if (preg_match_all('/\{(\d+):/', $sql, $matches)) {
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 validateRequired has a Cognitive Complexity of 15 (exceeds 7 allowed). Consider refactoring.
Open

  private function validateRequired($values, $chado_table, $record_id, $record, &$violations) {
    $chado = $this->getChadoConnection();
    $schema = $chado->schema();
    $table_def = $schema->getTableDef($chado_table, ['format' => 'drupal']);
    $pkey = $table_def['primary key'];
Severity: Minor
Found in tripal_chado/src/Plugin/TripalStorage/ChadoStorage.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 setTableSchema has a Cognitive Complexity of 15 (exceeds 7 allowed). Consider refactoring.
Open

  public function setTableSchema($table_schema, $force = False) {

    $logger = \Drupal::service('tripal.logger');
    if (!$this->table_id) {
      $logger->error('Cannot set the schema for the custom table. Please, first run the init() function.');
Severity: Minor
Found in tripal_chado/src/ChadoCustomTables/ChadoCustomTable.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 insertFeatureProps has a Cognitive Complexity of 15 (exceeds 7 allowed). Consider refactoring.
Open

  private function insertFeatureProps(){
    $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 propertyDefinitions has a Cognitive Complexity of 14 (exceeds 7 allowed). Consider refactoring.
Open

  public static function propertyDefinitions(FieldStorageDefinitionInterface $field_definition) {
    $properties = [];

    foreach (get_called_class()::tripalTypes($field_definition) as $type) {
      if ($type instanceof IntStoragePropertyType) {
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 form has a Cognitive Complexity of 14 (exceeds 7 allowed). Consider refactoring.
Open

  public function form(array $form, FormStateInterface $form_state) {
    $form = parent::form($form, $form_state);

    $chado_tables = $this->entity->getTableNames();
    $chado_table = $form_state->hasValue('chado_table') ? $form_state->getValue('chado_table') : 0;
Severity: Minor
Found in tripal_chado/src/Form/ChadoTermMappingForm.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 validateForm has a Cognitive Complexity of 14 (exceeds 7 allowed). Consider refactoring.
Open

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

    $values = $form_state->getValues();
    $tripal_entity_type = $this->entity;
Severity: Minor
Found in tripal/src/Form/TripalEntityTypeForm.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 setPrefix has a Cognitive Complexity of 14 (exceeds 7 allowed). Consider refactoring.
Open

  protected function setPrefix($prefix) {
    if (is_array($prefix)) {
      $this->prefixes = $prefix + [
        'default' => '',
      ];
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 getAvailableInstances has a Cognitive Complexity of 14 (exceeds 7 allowed). Consider refactoring.
Open

  public function getAvailableInstances() :array {
    $chado_schemas = [];

    // Get test schema prefix. If none set, we use '0' so we can test the prefix
    // and avoid false-positive since no schema name is allowed to start by a
Severity: Minor
Found in tripal_chado/src/Database/ChadoConnection.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 buildForm has a Cognitive Complexity of 14 (exceeds 7 allowed). Consider refactoring.
Open

  public function buildForm(array $form, FormStateInterface $form_state, $plugin_id = NULL) {

    if (!$plugin_id) {
      return $form;
    }
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

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