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Showing 174 of 174 total issues

Function prepareUpgradeTables has a Cognitive Complexity of 124 (exceeds 7 allowed). Consider refactoring.
Open

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

    // Column-specific upgrade procedures. First level keys are table names,
Severity: Minor
Found in tripal_chado/src/Task/ChadoUpgrader.php - About 2 days 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 buildChadoRecords has a Cognitive Complexity of 107 (exceeds 7 allowed). Consider refactoring.
Open

  protected function buildChadoRecords($values, bool $is_store) {
    $logger = \Drupal::service('tripal.logger');
    $chado = $this->getChadoConnection();
    $schema = $chado->schema();
    $records = [];
Severity: Minor
Found in tripal_chado/src/Plugin/TripalStorage/ChadoStorage.php - About 2 days 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 parseGFF3Line has a Cognitive Complexity of 81 (exceeds 7 allowed). Consider refactoring.
Open

  private function parseGFF3Line($line) {

    // get the columns
    $cols = explode("\t", $line);
    if (sizeof($cols) != 9) {
Severity: Minor
Found in tripal_chado/src/Plugin/TripalImporter/GFF3Importer.php - About 1 day 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 setPropValues has a Cognitive Complexity of 73 (exceeds 7 allowed). Consider refactoring.
Open

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

    $replace = [];
Severity: Minor
Found in tripal_chado/src/Plugin/TripalStorage/ChadoStorage.php - About 1 day 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 parseTableDdlToDrupal has a Cognitive Complexity of 67 (exceeds 7 allowed). Consider refactoring.
Open

  public function parseTableDdlToDrupal(string $table_ddl) :array {
    $tripaldbx = \Drupal::service('tripal.dbx');
    $table_structure = $tripaldbx->parseTableDdl($table_ddl);
    // Start with the name of the table.
    $table_def = [];
Severity: Minor
Found in tripal/src/TripalDBX/TripalDbx.php - About 1 day 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 validateTypes has a Cognitive Complexity of 52 (exceeds 7 allowed). Consider refactoring.
Open

  public function validateTypes($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 7 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

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

    uasort($instances, function ($a, $b) {
      $order = 0;
      // Sort by test/reservation status first.
      if ($a['is_test'] || $a['is_reserved']) {
        if ($b['is_test'] || $b['is_reserved']) {
Severity: Major
Found in tripal_chado/src/Form/ChadoManagerForm.php and 1 other location - About 7 hrs to fix
tripal_chado/src/Form/ChadoInstallForm.php on lines 50..89

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 238.

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

    uasort($instances, function ($a, $b) {
      $order = 0;
      // Sort by test/reservation status first.
      if ($a['is_test'] || $a['is_reserved']) {
        if ($b['is_test'] || $b['is_reserved']) {
Severity: Major
Found in tripal_chado/src/Form/ChadoInstallForm.php and 1 other location - About 7 hrs to fix
tripal_chado/src/Form/ChadoManagerForm.php on lines 144..183

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 238.

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 cleanUnusedSharedLocks has a Cognitive Complexity of 50 (exceeds 7 allowed). Consider refactoring.
Open

  public function cleanUnusedSharedLocks() {
    // Acquire a state modification lock.
    if ($this->modLocker->acquire(static::STATE_KEY_SHARED)) {
      // Get shared lock status.
      $shared_locks = $this->state->get(static::STATE_KEY_SHARED, []);
Severity: Minor
Found in tripal_biodb/src/Lock/PersistentDatabaseSharedLockBackend.php - About 7 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 setFieldDefDefaults has a Cognitive Complexity of 44 (exceeds 7 allowed). Consider refactoring.
Open

  public function setFieldDefDefaults(array $field_def = []) : array {
    $new_defs = [];

    $new_defs['name'] = 'tripal_entity.change.me';
    if (array_key_exists('name', $field_def) and !empty($field_def['name'])) {
Severity: Minor
Found in tripal/src/Services/TripalFieldsManager.php - About 6 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 addBaseTableSVFields has a Cognitive Complexity of 44 (exceeds 7 allowed). Consider refactoring.
Open

  private function addBaseTableSVFields(TripalEntityType $entityType, string $chado_table) {

    // We need the idSpace manager object.
    $idSpace_manager = \Drupal::service('tripal.collection_plugin_manager.idspace');
Severity: Minor
Found in tripal_chado/src/Task/ChadoPreparer.php - About 6 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 preSave has a Cognitive Complexity of 43 (exceeds 7 allowed). Consider refactoring.
Open

  public function preSave(EntityStorageInterface $storage) {
    parent::preSave($storage);

    // Create a values array appropriate for `loadValues()`
    list($values, $tripal_storages) = TripalEntity::getValuesArray($this);
Severity: Minor
Found in tripal/src/Entity/TripalEntity.php - About 6 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 __construct has a Cognitive Complexity of 43 (exceeds 7 allowed). Consider refactoring.
Open

  public function __construct(array $details = NULL) {

    // Instantiate the TripalLogger.
    $this->messageLogger = \Drupal::service('tripal.logger');
Severity: Minor
Found in tripal/src/TripalVocabTerms/TripalTerm.php - About 6 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 parse has a Cognitive Complexity of 41 (exceeds 7 allowed). Consider refactoring.
Open

  private function parse($obo_file, &$header) {
    // Set to 1 if we are in the top header lines of the file.
    $in_header = TRUE;
    // Holds the full stanza for the term.
    $stanza = [];
Severity: Minor
Found in tripal_chado/src/Plugin/TripalImporter/OBOImporter.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 validateUnique has a Cognitive Complexity of 40 (exceeds 7 allowed). Consider refactoring.
Open

  private function validateUnique($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 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 findEBITerm has a Cognitive Complexity of 40 (exceeds 7 allowed). Consider refactoring.
Open

  private function findEBITerm($id) {

    // Warn the user if we're looking up terms in EBI as this will slow the
    // loader if there are many lookups.
    if ($this->ebi_warned == FALSE) {
Severity: Minor
Found in tripal_chado/src/Plugin/TripalImporter/OBOImporter.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 processTerm has a Cognitive Complexity of 39 (exceeds 7 allowed). Consider refactoring.
Open

  private function processTerm($stanza, $is_relationship = 0) {

    $chado = $this->getChadoConnection();

    //
Severity: Minor
Found in tripal_chado/src/Plugin/TripalImporter/OBOImporter.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 cacheTermStanza has a Cognitive Complexity of 38 (exceeds 7 allowed). Consider refactoring.
Open

  private function cacheTermStanza($stanza, $type) {

    // Make sure we have defaults.
    if (!$this->default_namespace) {
      throw new \Exception('Cannot cache terms without a default CV.' . print_r($stanza, TRUE));
Severity: Minor
Found in tripal_chado/src/Plugin/TripalImporter/OBOImporter.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 parseTableDdl has a Cognitive Complexity of 38 (exceeds 7 allowed). Consider refactoring.
Open

  public function parseTableDdl(string $table_ddl) :array {
    $table_definition = [
      'columns' => [],
      'constraints' => [],
      'indexes' => [],
Severity: Minor
Found in tripal/src/TripalDBX/TripalDbx.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 onFieldableEntityTypeUpdate has a Cognitive Complexity of 37 (exceeds 7 allowed). Consider refactoring.
Open

  public function onFieldableEntityTypeUpdate(EntityTypeInterface $entity_type, EntityTypeInterface $original, array $field_storage_definitions, array $original_field_storage_definitions, array &$sandbox = NULL) {
    parent::onFieldableEntityTypeUpdate($entity_type,$original,$field_storage_definitions,$original_field_storage_definitions,$sandbox);

    // build associate array of old fields
    $oldTypes = [];
Severity: Minor
Found in tripal/src/Entity/TripalEntityStorageSchema.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

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