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Showing 174 of 174 total issues

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

Identical blocks of code found in 2 locations. Consider refactoring.
Open

    $form['table_schema'] = [
      '#type' => 'textarea',
      '#title' => t('Schema Array'),
      '#description' => t('Please enter the ' . Link::fromTextAndUrl('Drupal Schema API', Url::fromUri('https://api.drupal.org/api/drupal/includes!database!schema.inc/group/schemaapi/7', ['attributes' => ['target' => '_blank']]))->toString() . ' compatible array that defines the table.'),
      '#required' => TRUE,
Severity: Major
Found in tripal_chado/src/Form/ChadoMviewForm.php and 1 other location - About 1 hr to fix
tripal_chado/src/Form/ChadoCustomTableForm.php on lines 187..194

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 102.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Identical blocks of code found in 2 locations. Consider refactoring.
Open

    $form['table_schema'] = [
      '#type' => 'textarea',
      '#title' => t('Schema Array'),
      '#description' => t('Please enter the ' . Link::fromTextAndUrl('Drupal Schema API', Url::fromUri('https://api.drupal.org/api/drupal/includes!database!schema.inc/group/schemaapi/7', ['attributes' => ['target' => '_blank']]))->toString() . ' compatible array that defines the table.'),
      '#required' => TRUE,
Severity: Major
Found in tripal_chado/src/Form/ChadoCustomTableForm.php and 1 other location - About 1 hr to fix
tripal_chado/src/Form/ChadoMviewForm.php on lines 219..226

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 102.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

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

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

  private function insertFeatureSynonyms(){
    $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 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

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

  private function insertFeatureCVterms() {
    $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 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

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

  public function create($run_args, $file_details = []) {

    // global $user;
    $user = User::load(\Drupal::currentUser()->id());
Severity: Minor
Found in tripal/src/TripalImporter/TripalImporterBase.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

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

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

    $chado = new ChadoConnection();

    $form['msg-top'] = [
Severity: Minor
Found in tripal_chado/src/Form/ChadoInstallForm.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

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

  private function insertFeatureDbxrefs() {
    $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 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

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

  public function shouldUseTripalDbxSchema() :bool {
    $should = FALSE;

    // Check the class/object who is using Tripal DBX:
    // We do this using the backtrace functionality with the assumption that
Severity: Minor
Found in tripal/src/TripalDBX/TripalDbxConnection.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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