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Showing 174 of 174 total issues

Function findFeatures has a Cognitive Complexity of 36 (exceeds 7 allowed). Consider refactoring.
Open

  private function findFeatures() {
    $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 5 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 insertValues has a Cognitive Complexity of 35 (exceeds 7 allowed). Consider refactoring.
Open

  public function insertValues(&$values) : bool {
    $chado = $this->getChadoConnection();
    $logger = \Drupal::service('tripal.logger');
    $schema = $chado->schema();
Severity: Minor
Found in tripal_chado/src/Plugin/TripalStorage/ChadoStorage.php - About 4 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 tripal_file_upload_merge has a Cognitive Complexity of 34 (exceeds 7 allowed). Consider refactoring.
Open

function tripal_file_upload_merge($filename, $type, $user_dir) {
  $uid = \Drupal::currentUser()->id();
  $db = \Drupal::database();

  $module = $_GET['module'];
Severity: Minor
Found in tripal/src/api/tripal.upload.api.php - About 4 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 updateValues has a Cognitive Complexity of 34 (exceeds 7 allowed). Consider refactoring.
Open

  public function updateValues(&$values) : bool {
    $chado = $this->getChadoConnection();
    $logger = \Drupal::service('tripal.logger');

    $build = $this->buildChadoRecords($values, TRUE);
Severity: Minor
Found in tripal_chado/src/Plugin/TripalStorage/ChadoStorage.php - About 4 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 processUpgradeQueries has a Cognitive Complexity of 34 (exceeds 7 allowed). Consider refactoring.
Open

  protected function processUpgradeQueries() {

    // Setup DB object upgrade priority according to Chado version.
    $priorities = [];
    switch ($this->parameters['version']) {
Severity: Minor
Found in tripal_chado/src/Task/ChadoUpgrader.php - About 4 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 tripal_report_error has a Cognitive Complexity of 29 (exceeds 7 allowed). Consider refactoring.
Open

function tripal_report_error($type, $severity, $message, $variables = [], $options = []) {

  $logger = \Drupal::service('tripal.logger');
  $logger->warning("DEPRECATED: the '@function' function will be removed from the API in " .
      "a future release. Please use the TripalLogger service for logging.",
Severity: Minor
Found in tripal/src/api/tripal.deprecated.api.php - About 3 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 create has a Cognitive Complexity of 28 (exceeds 7 allowed). Consider refactoring.
Open

  public function create($details) {

    // Set some defaults
    if (!array_key_exists('prority', $details)) {
      $details['priority'] = 10;
Severity: Minor
Found in tripal/src/Services/TripalJob.php - About 3 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 setRecordIds has a Cognitive Complexity of 27 (exceeds 7 allowed). Consider refactoring.
Open

  protected function setRecordIds(&$values, $records) {
    $chado = $this->getChadoConnection();
    $schema = $chado->schema();

    // Iterate through the value objects.
Severity: Minor
Found in tripal_chado/src/Plugin/TripalStorage/ChadoStorage.php - About 3 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 findSynonyms has a Cognitive Complexity of 26 (exceeds 7 allowed). Consider refactoring.
Open

  private function findSynonyms() {
    $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 3 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 installTerms has a Cognitive Complexity of 25 (exceeds 7 allowed). Consider refactoring.
Open

  public function installTerms() {
    $config_factory = \Drupal::service('config.factory');
    $config = $config_factory->get('tripal.tripal_content_terms.chado_content_terms');
    $vocabs = $config->get('vocabularies');
    foreach ($vocabs as $vocab_info) {
Severity: Minor
Found in tripal_chado/src/Services/ChadoTermsInit.php - About 3 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 replaceTokens has a Cognitive Complexity of 24 (exceeds 7 allowed). Consider refactoring.
Open

  public function replaceTokens($string, $cache = []) {

    // Pull any items out of the cache.
    if (isset($cache['bundle'])) {
      $bundle_entity = $cache['bundle'];
Severity: Minor
Found in tripal/src/Entity/TripalEntity.php - About 3 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 getDefaultTitleFormat has a Cognitive Complexity of 24 (exceeds 7 allowed). Consider refactoring.
Open

  public function getDefaultTitleFormat() {

    // Retrieve all available tokens.
    $tokens = $this->getTokens([
      'include id' => FALSE,
Severity: Minor
Found in tripal/src/Entity/TripalEntityType.php - About 3 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 addMissingProteins has a Cognitive Complexity of 24 (exceeds 7 allowed). Consider refactoring.
Open

  private function addMissingProteins() {
    $this->setItemsHandled(0);
    $this->setTotalItems(count(array_keys($this->proteins)));

    // Second, iterate through the protein list and for any parents that
Severity: Minor
Found in tripal_chado/src/Plugin/TripalImporter/GFF3Importer.php - About 3 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 saveTermAttributes has a Cognitive Complexity of 24 (exceeds 7 allowed). Consider refactoring.
Open

  protected function saveTermAttributes(TripalTerm $term, object $cvterm, array $options) : bool {

    $update_parent = False;
    if (array_key_exists('updateParent', $options)) {
      $update_parent = $options['updateParent'];
Severity: Minor
Found in tripal_chado/src/Plugin/TripalIdSpace/ChadoIdSpace.php - About 3 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 formValidate has a Cognitive Complexity of 24 (exceeds 7 allowed). Consider refactoring.
Open

  public function formValidate($form, &$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 3 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 getMainTables has a Cognitive Complexity of 23 (exceeds 7 allowed). Consider refactoring.
Open

  public function getMainTables() {

    // Initialize the base tables with those tables that are missing a type.
    // Ideally they should have a type, but that's for a future version of Chado.
    $base_tables = [
Severity: Minor
Found in tripal_chado/src/Database/ChadoSchema.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 saveTerm has a Cognitive Complexity of 23 (exceeds 7 allowed). Consider refactoring.
Open

  private function saveTerm($stanza, $is_relationship = FALSE) {
    $chado = $this->getChadoConnection();

    // Get the term ID.
    $id = $stanza['id'][0];
Severity: Minor
Found in tripal_chado/src/Plugin/TripalImporter/OBOImporter.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 tripal_tripal_cron_notification has a Cognitive Complexity of 23 (exceeds 7 allowed). Consider refactoring.
Open

function tripal_tripal_cron_notification() {
  $num_created = 0;

  // Get all bundle names to cycle through.
  $all_bundles = db_select('tripal_bundle', 'tb')
Severity: Minor
Found in tripal/src/api/tripal.entities.api.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 setDefaults has a Cognitive Complexity of 23 (exceeds 7 allowed). Consider refactoring.
Open

  private function setDefaults($header) {
    $short_name = '';
    $namespace = '';
    $idspaces = [];
Severity: Minor
Found in tripal_chado/src/Plugin/TripalImporter/OBOImporter.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 getBaseTables has a Cognitive Complexity of 23 (exceeds 7 allowed). Consider refactoring.
Open

  function getBaseTables() {

    // Initialize the base tables with those tables that are missing a type.
    // Ideally they should have a type, but that's for a future version of Chado.
    $base_tables = [
Severity: Minor
Found in tripal_chado/src/api/ChadoSchema.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

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