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obj_tables/sci/onto.py

Summary

Maintainability
D
2 days
Test Coverage
A
100%

Function __init__ has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.
Open

    def __init__(self, ontology, namespace=None, namespace_sep=':', terms=None, none=True,
                 default=None, default_cleaned_value=None, none_value=None,
                 verbose_name='', description='',
                 primary=False, unique=False, unique_case_insensitive=False):
        """
Severity: Minor
Found in obj_tables/sci/onto.py - 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 get_xlsx_validation has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
Open

    def get_xlsx_validation(self, sheet_models=None, doc_metadata_model=None):
        """ Get XLSX validation

        Args:
            sheet_models (:obj:`list` of :obj:`Model`, optional): models encoded as separate sheets
Severity: Minor
Found in obj_tables/sci/onto.py - 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 clean has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
Open

    def clean(self, value):
        """ Convert attribute value into the appropriate type

        Args:
            value (:obj:`object`): value of attribute to clean
Severity: Minor
Found in obj_tables/sci/onto.py - 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 __init__ has 13 arguments (exceeds 4 allowed). Consider refactoring.
Open

    def __init__(self, ontology, namespace=None, namespace_sep=':', terms=None, none=True,
Severity: Major
Found in obj_tables/sci/onto.py - About 1 hr to fix

    Function serialize has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
    Open

        def serialize(self, value):
        """ Serialize ontology instance

        Args:
            value (:obj:`pronto.Term`): Python representation
    Severity: Minor
    Found in obj_tables/sci/onto.py - 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 validate has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
    Open

        def validate(self, obj, value):
        """ Determine if :obj:`value` is a valid value of the attribute

        Args:
            obj (:obj:`Model`): object being validated
    Severity: Minor
    Found in obj_tables/sci/onto.py - 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

    Avoid too many return statements within this function.
    Open

            return None
    Severity: Major
    Found in obj_tables/sci/onto.py - About 30 mins to fix

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

              if default_cleaned_value is not None and \
                (not isinstance(default_cleaned_value, pronto.Term)
                    or default_cleaned_value not in ontology.terms()
                    or (isinstance(terms, list) and default_cleaned_value not in terms)):
            raise ValueError(
      Severity: Major
      Found in obj_tables/sci/onto.py and 1 other location - About 3 hrs to fix
      obj_tables/sci/onto.py on lines 65..69

      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 65.

      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

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

              if default is not None and \
                (not isinstance(default, pronto.Term)
                    or default not in ontology.terms()
                    or (isinstance(terms, list) and default not in terms)):
            raise ValueError(
      Severity: Major
      Found in obj_tables/sci/onto.py and 1 other location - About 3 hrs to fix
      obj_tables/sci/onto.py on lines 71..75

      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 65.

      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

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