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tripal/tripal

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tripal_chado/src/Plugin/TripalImporter/TaxonomyImporter.php

Summary

Maintainability
C
1 day
Test Coverage
F
56%

Function importRecord has a Cognitive Complexity of 59 (exceeds 25 allowed). Consider refactoring.
Open

  private function importRecord($taxid, $root_taxon = NULL, $organism = NULL) {
    $adds_organism = $organism ? FALSE : TRUE;

    // Get the "rank" cvterm. It requires that the TAXRANK vocabulary is loaded.
    $rank_cvterm = chado_get_cvterm([
Severity: Minor
Found in tripal_chado/src/Plugin/TripalImporter/TaxonomyImporter.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 updateExisting has a Cognitive Complexity of 49 (exceeds 25 allowed). Consider refactoring.
Open

  private function updateExisting($root_taxon = NULL) {

    $total = count($this->all_orgs);
    $omitted_organisms = [];
    $api_key = \Drupal::state()->get('tripal_ncbi_api_key', NULL);
Severity: Minor
Found in tripal_chado/src/Plugin/TripalImporter/TaxonomyImporter.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 rebuildTree has a Cognitive Complexity of 31 (exceeds 25 allowed). Consider refactoring.
Open

  private function rebuildTree($root_taxon = NULL) {
    $chado = $this->getChadoConnection();
    $lineage_nodes[] = [];

    // Get the "rank" cvterm. It requires that the TAXRANK vocabulary is loaded.
Severity: Minor
Found in tripal_chado/src/Plugin/TripalImporter/TaxonomyImporter.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

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