Sign upLogin

tripal/t4d8

View on GitHub
Star
tripal_chado/src/Plugin/TripalImporter/OBOImporter.php

Summary

Maintainability
F
4 days
Test Coverage
F
49%

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 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 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 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 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 oboEbiLookup has a Cognitive Complexity of 21 (exceeds 7 allowed). Consider refactoring.
Open

  private function oboEbiLookup($accession, $type_of_search, $found_iri = NULL, $found_ontology = NULL) {
    // Grab just the ontology from the $accession.
    $parts = explode(':', $accession);
    $ontology = strtolower($parts[0]);
    $ontology = preg_replace('/\s+/', '', $ontology);
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 cacheRelationships has a Cognitive Complexity of 15 (exceeds 7 allowed). Consider refactoring.
Open

  private function cacheRelationships() {

    // Now that we have all of the terms parsed and loaded into the cache,
    // lets run through them one more time cache any terms in relationships
    // as well.
Severity: Minor
Found in tripal_chado/src/Plugin/TripalImporter/OBOImporter.php - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function 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 fixTermMismatch has a Cognitive Complexity of 10 (exceeds 7 allowed). Consider refactoring.
Open

  private function fixTermMismatch($stanza, $dbxref, $cv, $name) {
    $chado = $this->getChadoConnection();

    $name = $stanza['name'][0];
Severity: Minor
Found in tripal_chado/src/Plugin/TripalImporter/OBOImporter.php - About 45 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 loadOBO_v1_2_id has a Cognitive Complexity of 10 (exceeds 7 allowed). Consider refactoring.
Open

  private function loadOBO_v1_2_id($obo) {

    // Convert the module name to the real path if present
    $matches = [];
    if (preg_match("/\{(.*?)\}/", $obo->path, $matches)) {
Severity: Minor
Found in tripal_chado/src/Plugin/TripalImporter/OBOImporter.php - About 45 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

There are no issues that match your filters.

Category
Status