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Showing 174 of 174 total issues

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

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

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