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Similar blocks of code found in 4 locations. Consider refactoring.
Open

                for species in trans_reaction.rate_laws[0].expression.species:
                    trans_species_counts[species.id] = species.distribution_init_concentration.mean
                    model_Km = model.parameters.get_one(
                            id='K_m_{}_{}'.format(trans_reaction.id, species.species_type.id))
                    if model_Km:
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 3 other locations - About 1 day to fix
wc_model_gen/eukaryote/transcription.py on lines 1232..1245
wc_model_gen/eukaryote/translation_translocation.py on lines 1194..1207
wc_model_gen/eukaryote/translation_translocation.py on lines 1237..1250

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 171.

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

Function gen_reactions has a Cognitive Complexity of 74 (exceeds 5 allowed). Consider refactoring.
Open

    def gen_reactions(self):
        """ Generate reactions associated with submodel """
        model = self.model
        cell = self.knowledge_base.cell
Severity: Minor
Found in wc_model_gen/eukaryote/translation_translocation.py - About 1 day 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

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

                    if model.parameters.get(id='K_m_{}_{}'.format(reaction.id, species.species_type.id)):
                        model_Km = model.parameters.get_one(
                            id='K_m_{}_{}'.format(reaction.id, species.species_type.id))
                        if species.distribution_init_concentration.mean:
                            model_Km.value = beta * species.distribution_init_concentration.mean \
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 1 other location - About 1 day to fix
wc_model_gen/eukaryote/rna_degradation.py on lines 235..246

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 159.

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 2 locations. Consider refactoring.
Open

                if model.parameters.get(id='K_m_{}_{}'.format(reaction.id, species.species_type.id)):
                    model_Km = model.parameters.get_one(
                        id='K_m_{}_{}'.format(reaction.id, species.species_type.id))
                    if species.distribution_init_concentration.mean:
                        model_Km.value = beta * species.distribution_init_concentration.mean \
Severity: Major
Found in wc_model_gen/eukaryote/rna_degradation.py and 1 other location - About 1 day to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 1542..1553

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 159.

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 'Kr_' in param.id:
                    repressor_species = model.species.get_one(
                        id='{}[{}]'.format(param.id.split('_')[-1], transcription_compartment.id))
                    init_reg_species_count[repressor_species.id] = \
                        repressor_species.distribution_init_concentration.mean
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 1 other location - About 1 day to fix
wc_model_gen/eukaryote/transcription.py on lines 1141..1154

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 154.

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

                elif 'Ka_' in param.id:
                    activator_species = model.species.get_one(
                        id='{}[{}]'.format(param.id.split('_')[-1], transcription_compartment.id))
                    init_reg_species_count[activator_species.id] = \
                        activator_species.distribution_init_concentration.mean
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 1 other location - About 1 day to fix
wc_model_gen/eukaryote/transcription.py on lines 1126..1139

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 154.

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

Function gen_reactions has a Cognitive Complexity of 65 (exceeds 5 allowed). Consider refactoring.
Open

    def gen_reactions(self):
        """ Generate reactions associated with submodel """
        model = self.model
        cell = self.knowledge_base.cell
        nucleus = model.compartments.get_one(id='n')
Severity: Minor
Found in wc_model_gen/eukaryote/transcription.py - About 1 day 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

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

    for reactant in reactants:            
        obj_reaction = conv_opt.Variable(name=reactant + '_test_reaction', 
                                type=conv_opt.VariableType.continuous,
                                lower_bound=0.0)
        obj_reactants[reactant] = obj_reaction
Severity: Major
Found in wc_model_gen/utils.py and 1 other location - About 1 day to fix
wc_model_gen/utils.py on lines 135..146

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 147.

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

    for product in products:            
        obj_reaction = conv_opt.Variable(name=product + '_test_reaction', 
                            type=conv_opt.VariableType.continuous,
                            lower_bound=0.0)
        obj_products[product] = obj_reaction
Severity: Major
Found in wc_model_gen/utils.py and 1 other location - About 1 day to fix
wc_model_gen/utils.py on lines 120..131

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 147.

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

Function calibrate_submodel has a Cognitive Complexity of 63 (exceeds 5 allowed). Consider refactoring.
Open

    def calibrate_submodel(self):
        """ Calibrate the submodel using data in the KB """
        
        model = self.model        
        cell = self.knowledge_base.cell
Severity: Minor
Found in wc_model_gen/eukaryote/transcription.py - About 1 day 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

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

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

        id = options.get('id', 'eukaryote')
Severity: Major
Found in wc_model_gen/eukaryote/core.py and 1 other location - About 1 day to fix
wc_model_gen/prokaryote/core.py on lines 30..44

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 144.

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

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

        id = options.get('id', 'rand_wc_model')
Severity: Major
Found in wc_model_gen/prokaryote/core.py and 1 other location - About 1 day to fix
wc_model_gen/eukaryote/core.py on lines 44..58

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 144.

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

File utils.py has 567 lines of code (exceeds 250 allowed). Consider refactoring.
Open

""" Utility methods for generating submodels

:Author: Yin Hoon Chew <yinhoon.chew@mssm.edu>
:Date: 2019-01-23
:Copyright: 2019, Karr Lab
Severity: Major
Found in wc_model_gen/utils.py - About 1 day to fix

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

        def calc_rna_copy_num(self):
        """ Calculates the # of RNA molecules at t=0 """

        volume = self.knowledge_base.cell.parameters.get_one(id='mean_volume').value
        cytosol_kb = self.knowledge_base.cell.compartments.get_one(id='c')
    Severity: Major
    Found in wc_model_gen/prokaryote/metabolism.py and 1 other location - About 1 day to fix
    wc_model_gen/prokaryote/metabolism.py on lines 405..420

    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 141.

    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

        def calc_prot_copy_num(self):
        """ Calculates the # of RNA molecules at t=0 """
        # TODO: check if conc is in CN already

        volume = self.knowledge_base.cell.parameters.get_one(id='mean_volume').value
    Severity: Major
    Found in wc_model_gen/prokaryote/metabolism.py and 1 other location - About 1 day to fix
    wc_model_gen/prokaryote/metabolism.py on lines 389..403

    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 141.

    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

    Function gen_rate_laws has a Cognitive Complexity of 60 (exceeds 5 allowed). Consider refactoring.
    Open

        def gen_rate_laws(self):
        """ Generate rate laws for the reactions in the submodel """

        model = self.model        
        cell = self.knowledge_base.cell
    Severity: Minor
    Found in wc_model_gen/eukaryote/transcription.py - About 1 day 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

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

                if rna_kb.id in gvar.transcript_ntp_usage:
                ntp_count = gvar.transcript_ntp_usage[rna_kb.id]
            else:
                if rna_kb.id in rna_input_seq:
                    seq = rna_input_seq[rna_kb.id]
    Severity: Major
    Found in wc_model_gen/eukaryote/transcription.py and 1 other location - About 1 day to fix
    wc_model_gen/eukaryote/rna_degradation.py on lines 97..109

    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 137.

    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 2 locations. Consider refactoring.
    Open

                if rna_kb.id in gvar.transcript_ntp_usage:
                ntp_count = gvar.transcript_ntp_usage[rna_kb.id]
            else:
                if rna_kb.id in rna_input_seq:
                    seq = rna_input_seq[rna_kb.id]
    Severity: Major
    Found in wc_model_gen/eukaryote/rna_degradation.py and 1 other location - About 1 day to fix
    wc_model_gen/eukaryote/transcription.py on lines 475..487

    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 137.

    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 3 locations. Consider refactoring.
    Open

                for factor in elongation_termination_factors[rna_elongation_termination_factors[rna_kb.id]]:
                factor_details = elongation_termination_factor_functions[
                    rna_elongation_termination_factors[rna_kb.id]][','.join(factor)]
                expression_terms.append(factor_details['function'].id)
                for cl, dictionary in objects.items():
    Severity: Major
    Found in wc_model_gen/eukaryote/transcription.py and 2 other locations - About 1 day to fix
    wc_model_gen/eukaryote/transcription.py on lines 973..978
    wc_model_gen/eukaryote/transcription.py on lines 1028..1035

    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 135.

    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 3 locations. Consider refactoring.
    Open

                if elongation_negative_factors.get(rna_elongation_negative_factors[rna_kb.id]):
                for factor in elongation_negative_factors[rna_elongation_negative_factors[rna_kb.id]]:
                    factor_details = elongation_negative_factor_functions[
                        rna_elongation_negative_factors[rna_kb.id]][','.join(factor)]
                    expression_terms.append(factor_details['function'].id)
    Severity: Major
    Found in wc_model_gen/eukaryote/transcription.py and 2 other locations - About 1 day to fix
    wc_model_gen/eukaryote/transcription.py on lines 973..978
    wc_model_gen/eukaryote/transcription.py on lines 1020..1026

    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 135.

    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

    Severity
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