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wc_model_gen/eukaryote/rna_degradation.py

Summary

Maintainability
F
4 days
Test Coverage
A
98%

Function calibrate_submodel has a Cognitive Complexity of 22 (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/rna_degradation.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 gen_reactions has a Cognitive Complexity of 14 (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/rna_degradation.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 gen_rate_laws has a Cognitive Complexity of 7 (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
        nucleus = model.compartments.get_one(id='n')
Severity: Minor
Found in wc_model_gen/eukaryote/rna_degradation.py - About 35 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

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

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 met in metabolic_participants:
            met_species_type = model.species_types.get_one(id=met)
            metabolites[met] = {
                'c': met_species_type.species.get_or_create(compartment=cytoplasm, model=model),
                'm': met_species_type.species.get_or_create(compartment=mitochondrion, model=model)
Severity: Major
Found in wc_model_gen/eukaryote/rna_degradation.py and 2 other locations - About 3 hrs to fix
wc_model_gen/eukaryote/complexation.py on lines 103..107
wc_model_gen/eukaryote/transcription.py on lines 175..179

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 64.

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

            reaction.participants.append(metabolites['gmp'][
                degradation_compartment.id].species_coefficients.get_or_create(coefficient=ntp_count['G']))
Severity: Major
Found in wc_model_gen/eukaryote/rna_degradation.py and 3 other locations - About 1 hr to fix
wc_model_gen/eukaryote/rna_degradation.py on lines 125..126
wc_model_gen/eukaryote/rna_degradation.py on lines 127..128
wc_model_gen/eukaryote/rna_degradation.py on lines 131..132

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 41.

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

            reaction.participants.append(metabolites['ump'][
                degradation_compartment.id].species_coefficients.get_or_create(coefficient=ntp_count['U']))
Severity: Major
Found in wc_model_gen/eukaryote/rna_degradation.py and 3 other locations - About 1 hr to fix
wc_model_gen/eukaryote/rna_degradation.py on lines 125..126
wc_model_gen/eukaryote/rna_degradation.py on lines 127..128
wc_model_gen/eukaryote/rna_degradation.py on lines 129..130

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 41.

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

            reaction.participants.append(metabolites['amp'][
                degradation_compartment.id].species_coefficients.get_or_create(coefficient=ntp_count['A']))
Severity: Major
Found in wc_model_gen/eukaryote/rna_degradation.py and 3 other locations - About 1 hr to fix
wc_model_gen/eukaryote/rna_degradation.py on lines 127..128
wc_model_gen/eukaryote/rna_degradation.py on lines 129..130
wc_model_gen/eukaryote/rna_degradation.py on lines 131..132

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 41.

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

            reaction.participants.append(metabolites['cmp'][
                degradation_compartment.id].species_coefficients.get_or_create(coefficient=ntp_count['C']))
Severity: Major
Found in wc_model_gen/eukaryote/rna_degradation.py and 3 other locations - About 1 hr to fix
wc_model_gen/eukaryote/rna_degradation.py on lines 125..126
wc_model_gen/eukaryote/rna_degradation.py on lines 129..130
wc_model_gen/eukaryote/rna_degradation.py on lines 131..132

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 41.

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 3 locations. Consider refactoring.
Open

        Avogadro = self.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/eukaryote/rna_degradation.py and 2 other locations - About 50 mins to fix
wc_model_gen/eukaryote/protein_degradation.py on lines 243..247
wc_model_gen/eukaryote/translation_translocation.py on lines 1124..1128

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 36.

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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