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KarrLab/wc_kb

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wc_kb/io.py

Summary

Maintainability
F
4 days
Test Coverage
A
99%

Function run has a Cognitive Complexity of 51 (exceeds 5 allowed). Consider refactoring.
Open

    def run(self, core_path,
            seq_path='', rewrite_seq_path=True, taxon='prokaryote',
            models=None, ignore_missing_models=None, ignore_extra_models=None, ignore_sheet_order=None,
            include_all_attributes=False, ignore_missing_attributes=None, ignore_extra_attributes=None, ignore_attribute_order=None,
            group_objects_by_model=True, validate=True, read_metadata=False):
Severity: Minor
Found in wc_kb/io.py - 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

File io.py has 367 lines of code (exceeds 250 allowed). Consider refactoring.
Open

""" Reading and writing knowledge bases to/from files.

Supported file types:

* Comma separated values (.csv)
Severity: Minor
Found in wc_kb/io.py - About 4 hrs to fix

    Function run has a Cognitive Complexity of 22 (exceeds 5 allowed). Consider refactoring.
    Open

        def run(self, core_path, knowledge_base,
            seq_path=None, rewrite_seq_path=True, taxon='prokaryote',
            models=None, get_related=True, include_all_attributes=False, validate=True,
            title=None, description=None, keywords=None, version=None, language=None, creator=None,
            write_schema=False, write_toc=True,
    Severity: Minor
    Found in wc_kb/io.py - 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 validate_implicit_relationships has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.
    Open

        def validate_implicit_relationships(cls):
        """ Check that relationships to :obj:`core.KnowledgeBase` and :obj:`core.Cell` do not need to be explicitly written to
        workbooks because they can be inferred by :obj:`Reader.run`

        Raises:
    Severity: Minor
    Found in wc_kb/io.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 run has 21 arguments (exceeds 4 allowed). Consider refactoring.
    Open

        def run(self, core_path, knowledge_base,
    Severity: Major
    Found in wc_kb/io.py - About 2 hrs to fix

      Function run has 15 arguments (exceeds 4 allowed). Consider refactoring.
      Open

          def run(self, core_path,
      Severity: Major
      Found in wc_kb/io.py - About 1 hr to fix

        Function validate_implicit_relationships_are_set has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
        Open

            def validate_implicit_relationships_are_set(self, knowledge_base):
        """ Check that there is only 1 :obj:`KnowledgeBase` and <= 1 :obj:`Cell` and that each relationship
        to :obj:`KnowledgeBase` and :obj:`Cell` is set. This is necessary to enable the :obj:`KnowledgeBase` and
        :obj:`Cell` relationships to be implicit in the Excel output and added by :obj:`Reader.run`
        Severity: Minor
        Found in wc_kb/io.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 create_template has 8 arguments (exceeds 4 allowed). Consider refactoring.
        Open

        def create_template(core_path, seq_path, taxon='prokaryote', write_schema=False, write_toc=True,
        Severity: Major
        Found in wc_kb/io.py - About 1 hr to fix

          Function convert has 7 arguments (exceeds 4 allowed). Consider refactoring.
          Open

          def convert(source_core, source_seq, dest_core, dest_seq, taxon='prokaryote', rewrite_seq_path=True, protected=True):
          Severity: Major
          Found in wc_kb/io.py - About 50 mins to fix

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

            EUKARYOTE_MODELS = (
    core.KnowledgeBase,
    core.Cell,
    core.Compartment,
    core.DnaSpeciesType,
            Severity: Major
            Found in wc_kb/io.py and 1 other location - About 3 hrs to fix
            wc_kb/io.py on lines 29..49

            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 66.

            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

            PROKARYOTE_MODELS = (
    core.KnowledgeBase,
    core.Cell,
    core.Compartment,
    core.DnaSpeciesType,
            Severity: Major
            Found in wc_kb/io.py and 1 other location - About 3 hrs to fix
            wc_kb/io.py on lines 51..71

            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 66.

            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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