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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

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

Similar blocks of code found in 3 locations. Consider refactoring.
Open

            for factor in init_factors[rna_init_factors[rna_kb.id]]:
                factor_details = init_factor_functions[rna_init_factors[rna_kb.id]][','.join(factor)]
                expression_terms.append(factor_details['function'].id)
                for cl, dictionary in objects.items():
                    dictionary.update(factor_details['objects'][cl])
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 1020..1026
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 2 locations. Consider refactoring.
Open

                if trna.species[0].compartment.id == 'm':
                    if codon in trna_grouping['m']: 
                        trna_grouping['m'][codon]['trna'].append(trna.id)
                        trna_grouping['m'][codon]['anticodon'].append(anticodon_prop[0])
                    else:
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 1 other location - About 1 day to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 591..609

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 122.

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_factors:
                factor_details = el_factor_functions[translation_compartment.id][','.join(factor)]
                expression_terms.append(factor_details['function'].id)
                for cl, dictionary in objects.items():
                    dictionary.update(factor_details['objects'][cl])
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 2 other locations - About 7 hrs to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 804..809
wc_model_gen/eukaryote/translation_translocation.py on lines 1041..1046

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 115.

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 initiation_factors:
                factor_details = init_factor_functions[translation_compartment.id][','.join(factor)]
                expression_terms.append(factor_details['function'].id)
                for cl, dictionary in objects.items():
                    dictionary.update(factor_details['objects'][cl])
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 2 other locations - About 7 hrs to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 868..873
wc_model_gen/eukaryote/translation_translocation.py on lines 1041..1046

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 115.

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 chaperones:
                    factor_details = trans_factor_functions[chaperone_compartment.id][','.join(factor)]
                    expression_terms.append(factor_details['function'].id)
                    for cl, dictionary in objects.items():
                        dictionary.update(factor_details['objects'][cl])
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 2 other locations - About 7 hrs to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 804..809
wc_model_gen/eukaryote/translation_translocation.py on lines 868..873

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 115.

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_aa_transfer_rate(self):
        """ Calculates the rate of monophosphate transfer from the extracellular space """

        # Calculate # of new AA molecules needed = # of AA molecules tied up in prots at t=0
        avg_aa_per_prot = self.calc_aa_per_prot()
Severity: Major
Found in wc_model_gen/prokaryote/metabolism.py and 1 other location - About 7 hrs to fix
wc_model_gen/prokaryote/metabolism.py on lines 226..239

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 114.

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_mpp_transfer_rate(self):
        """ Calculates the rate of monophosphate transfer from the extracellular space """

        # Calculate # of new TPP molecules needed = # of TPP molecules tied up in RNAs at T=0
        avg_tpp_per_rna = self.calc_tpp_per_rna()
Severity: Major
Found in wc_model_gen/prokaryote/metabolism.py and 1 other location - About 7 hrs to fix
wc_model_gen/prokaryote/metabolism.py on lines 241..254

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 114.

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 gen_rate_laws(self):
        """ Generate rate laws for the reactions in the submodel """
        model = self.model

        modifier = model.observables.get_one(id='rna_polymerase_obs')
Severity: Major
Found in wc_model_gen/prokaryote/transcription.py and 1 other location - About 6 hrs to fix
wc_model_gen/prokaryote/rna_degradation.py on lines 83..100

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 101.

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

        model = self.model
Severity: Major
Found in wc_model_gen/prokaryote/rna_degradation.py and 1 other location - About 6 hrs to fix
wc_model_gen/prokaryote/transcription.py on lines 83..98

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 101.

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 aa in protein_seq:
                    aa_id = amino_acid_id_conversion[aa]
                    if aa_id not in aa_content:
                        aa_content[aa_id] = 1
                        gvar.protein_aa_usage[mrna_kb.protein.id][aa] = 1
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 1 other location - About 6 hrs to fix
wc_model_gen/eukaryote/complexation.py on lines 197..204

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 100.

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 aa in protein_seq:
                                            aa_id = amino_acid_id_conversion[aa]
                                            if aa_id not in aa_content:
                                                aa_content[aa_id] = 1
                                                gvar.protein_aa_usage[subunit.species_type.id][aa] = 1
Severity: Major
Found in wc_model_gen/eukaryote/complexation.py and 1 other location - About 6 hrs to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 297..304

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 100.

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

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

            for rnap_kb in cell.observables.get_one(id='rna_polymerase_obs').expression.species:
                rnap_species_type_model = model.species_types.get_one(id=rnap_kb.species_type.id)
                rnap_model = rnap_species_type_model.species.get_one(compartment=cytosol)

                reaction.participants.add(rnap_model.species_coefficients.get_or_create(coefficient=-1))
Severity: Major
Found in wc_model_gen/prokaryote/transcription.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/translation.py on lines 140..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 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

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

            for degradosome_kb in cell.observables.get_one(id='degrade_rnase_obs').expression.species:
                degradosome_species_type_model = model.species_types.get_one(id=degradosome_kb.species_type.id)
                degradosome_species_model = degradosome_species_type_model.species.get_one(compartment=cytosol)

                reaction.participants.add(degradosome_species_model.species_coefficients.get_or_create(
Severity: Major
Found in wc_model_gen/prokaryote/rna_degradation.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/transcription.py on lines 76..81
wc_model_gen/prokaryote/translation.py on lines 140..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 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

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

            for degradosome_kb in cell.observables.get_one(id='degrade_protease_obs').expression.species:
                degradosome_species_type_model = model.species_types.get_one(id=degradosome_kb.species_type.id)
                degradosome_species_model = degradosome_species_type_model.species.get_one(compartment=cytosol)

                reaction.participants.add(degradosome_species_model.species_coefficients.get_or_create(
Severity: Major
Found in wc_model_gen/prokaryote/protein_degradation.py and 3 other locations - About 5 hrs to fix
wc_model_gen/prokaryote/rna_degradation.py on lines 74..80
wc_model_gen/prokaryote/transcription.py on lines 76..81
wc_model_gen/prokaryote/translation.py on lines 140..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 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

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