Sign upLogin

tripal/t4d8

View on GitHub
Star

Showing 174 of 174 total issues

Function buildMainForm has a Cognitive Complexity of 19 (exceeds 7 allowed). Consider refactoring.
Open

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

    $tripal_dbx = \Drupal::service('tripal.dbx');
    $chado = new ChadoConnection();
Severity: Minor
Found in tripal_chado/src/Form/ChadoManagerForm.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 validateForm has a Cognitive Complexity of 19 (exceeds 7 allowed). Consider refactoring.
Open

  public function validateForm(array &$form, FormStateInterface $form_state) {
    if ($form_state->isSubmitted()) {
      $mail_pi = $form_state->getValue('principal_investigator_email');
      $mail_sa = $form_state->getValue('tripal_reg_site_admin_email');
      if ($form_state->getValue('disable_tripal_reporting') != TRUE) {
Severity: Minor
Found in tripal/src/Form/Register.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 prepareUpgradeSequences has a Cognitive Complexity of 19 (exceeds 7 allowed). Consider refactoring.
Open

  protected function prepareUpgradeSequences() {
    $chado_schema = $this->outputSchemas[0];
    $ref_schema = $this->inputSchemas[0];

    // Get sequences.
Severity: Minor
Found in tripal_chado/src/Task/ChadoUpgrader.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 findVersion has a Cognitive Complexity of 18 (exceeds 7 allowed). Consider refactoring.
Open

  public function findVersion(
    ?string $schema_name = NULL,
    bool $exact_version = FALSE
  ) :string {
    // By default, we don't know the version.
Severity: Minor
Found in tripal_chado/src/Database/ChadoConnection.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 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

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

  public function storageSettingsForm(array &$form, FormStateInterface $form_state, $has_data) {
    $elements = [];
    $elements['max_length'] = [
      '#type' => 'number',
      '#title' => t('Maximum length'),
Severity: Major
Found in tripal/src/Plugin/Field/FieldType/TripalStringTypeItem.php and 1 other location - About 1 hr to fix
tripal_chado/src/Plugin/Field/FieldType/ChadoStringTypeItem.php on lines 48..60

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 117.

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

  public function storageSettingsForm(array &$form, FormStateInterface $form_state, $has_data) {
    $elements = [];
    $elements['max_length'] = [
      '#type' => 'number',
      '#title' => t('Maximum length'),
Severity: Major
Found in tripal_chado/src/Plugin/Field/FieldType/ChadoStringTypeItem.php and 1 other location - About 1 hr to fix
tripal/src/Plugin/Field/FieldType/TripalStringTypeItem.php on lines 47..59

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 117.

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 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

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

  public function getConstraints() {
    $constraints = parent::getConstraints();
    if ($max_length = $this->getSetting('max_length')) {
      $constraint_manager = \Drupal::typedDataManager()->getValidationConstraintManager();
      $constraints[] = $constraint_manager->create('ComplexData', [
Severity: Major
Found in tripal/src/Plugin/Field/FieldType/TripalStringTypeItem.php and 1 other location - About 1 hr to fix
tripal_chado/src/Plugin/Field/FieldType/ChadoStringTypeItem.php on lines 75..94

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 115.

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

  public function getConstraints() {
    $constraints = parent::getConstraints();
    if ($max_length = $this->getSetting('max_length')) {
      $constraint_manager = \Drupal::typedDataManager()->getValidationConstraintManager();
      $constraints[] = $constraint_manager->create('ComplexData', [
Severity: Major
Found in tripal_chado/src/Plugin/Field/FieldType/ChadoStringTypeItem.php and 1 other location - About 1 hr to fix
tripal/src/Plugin/Field/FieldType/TripalStringTypeItem.php on lines 74..93

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 115.

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

    if ($user->hasPermission('administer tripal')) {
      $jobs_url = Link::fromTextAndUrl('jobs page', Url::fromUri('internal:/admin/tripal/tripal_jobs'))->toString();
      $messenger->addStatus(t("Check the @jobs_url for status.", ['@jobs_url' => $jobs_url]));
      $messenger->addStatus(t("You can execute the job queue manually on the ".
          "command line using the following Drush command: " .
Severity: Major
Found in tripal/src/api/tripal.jobs.api.php and 1 other location - About 1 hr to fix
tripal/src/api/tripal.jobs.api.php on lines 113..124

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 115.

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

      if ($user->hasPermission('administer tripal')) {
        $jobs_url = Link::fromTextAndUrl('jobs page', Url::fromUri('internal:/admin/tripal/tripal_jobs'))->toString();
        $messenger->addStatus(t("Check the @jobs_url for status.", ['@jobs_url' => $jobs_url]));
        $messenger->addStatus(t("You can execute the job queue manually on the ".
          "command line using the following Drush command: " .
Severity: Major
Found in tripal/src/api/tripal.jobs.api.php and 1 other location - About 1 hr to fix
tripal/src/api/tripal.jobs.api.php on lines 284..295

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 115.

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

    foreach ($field_storage_definitions as $storageDefinition) {
      $field = \Drupal::service("plugin.manager.field.field_type").getInstance($storageDefinition->getType());
      if ($field instanceof TripalFieldItemInterface) {
        // Each field can define it's value as a single-depth array of
        // key => value pairs where the key is a name for that data (e.g. accession )
Severity: Major
Found in tripal/src/Entity/TripalEntityStorageSchema.php and 1 other location - About 1 hr to fix
tripal/src/Entity/TripalEntityStorageSchema.php on lines 64..76

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 113.

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

    foreach ($this->fieldStorageDefinitions() as $storageDefinition) {
      $field = \Drupal::service("plugin.manager.field.field_type").getInstance($storageDefinition->getType());
      if ($field instanceof TripalFieldItemInterface) {
        $types = $field->tripalTypes();
        $tsid = $field->tripalStorageId();
Severity: Major
Found in tripal/src/Entity/TripalEntityStorageSchema.php and 1 other location - About 1 hr to fix
tripal/src/Entity/TripalEntityStorageSchema.php on lines 20..46

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 113.

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

Severity
Category
Status
Source
Language