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wc_model_gen/prokaryote/translation.py

Summary

Maintainability
F
5 days
Test Coverage
A
99%

Function gen_reactions has a Cognitive Complexity of 39 (exceeds 5 allowed). Consider refactoring.
Open

    def gen_reactions(self):
        """ Generate a lumped reaction that covers initiation, elongation and termination for each protein translated """
        model = self.model
        submodel = self.submodel
        cell = self.knowledge_base.cell
Severity: Minor
Found in wc_model_gen/prokaryote/translation.py - 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

Consider simplifying this complex logical expression.
Open

                        if codon == 'ATG':
                            aa = model.species_types.get_one(id='met').species.get_one(compartment=cytosol)
                        elif codon == 'ACT' or codon == 'ACC' or codon == 'ACA' or codon == 'ACG':
                            aa = model.species_types.get_one(id='thr').species.get_one(compartment=cytosol)
                        elif codon == 'ATT' or codon == 'ATC' or codon == 'ATA':
Severity: Critical
Found in wc_model_gen/prokaryote/translation.py - About 2 hrs to fix

    Function calibrate_submodel has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
    Open

        def calibrate_submodel(self):
        """ Calibrate the submodel using data in the KB """
        model = self.model
        beta = self.options.get('beta')
    Severity: Minor
    Found in wc_model_gen/prokaryote/translation.py - About 55 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 deeply nested control flow statements.
    Open

                            if trna_obs not in self._modifiers:
                            self._modifiers.append(trna_obs)
                        trna = trna_obs.expression.species.get_one(compartment=cytosol)
    Severity: Major
    Found in wc_model_gen/prokaryote/translation.py - About 45 mins to fix

      Avoid deeply nested control flow statements.
      Open

                              if codon == 'ATG':
                            aa = model.species_types.get_one(id='met').species.get_one(compartment=cytosol)
                        elif codon == 'ACT' or codon == 'ACC' or codon == 'ACA' or codon == 'ACG':
                            aa = model.species_types.get_one(id='thr').species.get_one(compartment=cytosol)
                        elif codon == 'ATT' or codon == 'ATC' or codon == 'ATA':
      Severity: Major
      Found in wc_model_gen/prokaryote/translation.py - About 45 mins to fix

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

                for protein_kb, reaction in zip(protein_kb, self.submodel.reactions):

            protein_product = model.species_types.get_one(id=protein_kb.id).species.get_one(compartment=cytosol)
            half_life = protein_kb.properties.get_one(property='half_life').get_value()
            mean_concentration = protein_product.distribution_init_concentration.mean
        Severity: Major
        Found in wc_model_gen/prokaryote/translation.py and 1 other location - About 2 days to fix
        wc_model_gen/prokaryote/transcription.py on lines 122..145

        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 298.

        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 4 locations. Consider refactoring.
        Open

                    for ribosome_kb in cell.observables.get_one(id='ribosome_obs').expression.species:
                ribosome_species_type_model = model.species_types.get_one(id=ribosome_kb.species_type.id)
                ribosome_model = ribosome_species_type_model.species.get_one(compartment=cytosol)

                reaction.participants.add(ribosome_model.species_coefficients.get_or_create(coefficient=-1))
        Severity: Major
        Found in wc_model_gen/prokaryote/translation.py and 3 other locations - About 5 hrs to fix
        wc_model_gen/prokaryote/protein_degradation.py on lines 93..99
        wc_model_gen/prokaryote/rna_degradation.py on lines 74..80
        wc_model_gen/prokaryote/transcription.py on lines 76..81

        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 96.

        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 4 locations. Consider refactoring.
        Open

            def clean_and_validate_options(self):
        """ Apply default options and validate options """
        options = self.options

        beta = options.get('beta', 1.)
        Severity: Major
        Found in wc_model_gen/prokaryote/translation.py and 3 other locations - About 1 hr to fix
        wc_model_gen/prokaryote/protein_degradation.py on lines 31..36
        wc_model_gen/prokaryote/rna_degradation.py on lines 30..35
        wc_model_gen/prokaryote/transcription.py on lines 30..35

        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 39.

        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 12 locations. Consider refactoring.
        Open

                Avogadro = model.parameters.get_or_create(
            id='Avogadro',
            type=None,
            value=scipy.constants.Avogadro,
            units=unit_registry.parse_units('molecule mol^-1'))
        Severity: Major
        Found in wc_model_gen/prokaryote/translation.py and 11 other locations - About 40 mins to fix
        wc_model_gen/eukaryote/complexation.py on lines 363..367
        wc_model_gen/eukaryote/transcription.py on lines 1095..1099
        wc_model_gen/eukaryote/translation_translocation.py on lines 1387..1391
        wc_model_gen/prokaryote/protein_degradation.py on lines 131..135
        wc_model_gen/prokaryote/rna_degradation.py on lines 107..111
        wc_model_gen/prokaryote/transcription.py on lines 105..109
        wc_model_gen/utils.py on lines 210..214
        wc_model_gen/utils.py on lines 255..259
        wc_model_gen/utils.py on lines 343..347
        wc_model_gen/utils.py on lines 432..436
        wc_model_gen/utils.py on lines 514..518

        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 34.

        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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