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Similar blocks of code found in 5 locations. Consider refactoring.
Open

            reaction.participants.append(metabolites['amp'][
                transcription_compartment.id].species_coefficients.get_or_create(
                coefficient=pre_rna_count['A']-ntp_count['A']))
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 4 other locations - About 2 hrs to fix
wc_model_gen/eukaryote/transcription.py on lines 526..528
wc_model_gen/eukaryote/transcription.py on lines 532..534
wc_model_gen/eukaryote/transcription.py on lines 535..537
wc_model_gen/eukaryote/transcription.py on lines 538..540

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 53.

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

                eval_rate_law = reaction.rate_laws[0].expression._parsed_expression.eval({
                    wc_lang.Species: init_species_counts,
                    wc_lang.Compartment: {
                        transcription_compartment.id: transcription_compartment.init_volume.mean * \
                            transcription_compartment.init_density.value},
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 2 other locations - About 2 hrs to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 1528..1532
wc_model_gen/eukaryote/translation_translocation.py on lines 1559..1563

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 53.

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

                cyto_deg_rate = cyto_deg_reaction.rate_laws[0].expression._parsed_expression.eval({
                    wc_lang.Species: cyto_species_counts,
                    wc_lang.Compartment: {
                        cytosol.id: cytosol.init_volume.mean * \
                            cytosol.init_density.value}
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 2 other locations - About 2 hrs to fix
wc_model_gen/eukaryote/transcription.py on lines 1258..1262
wc_model_gen/eukaryote/translation_translocation.py on lines 1559..1563

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 53.

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 init_factors:
            if not any(j in i for i in init_factors.keys() for j in ['pol1_', 'pol2_', 'pol3_', 'polm_']):
                raise ValueError(
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 2 other locations - About 2 hrs to fix
wc_model_gen/eukaryote/transcription.py on lines 105..107
wc_model_gen/eukaryote/transcription.py on lines 112..114

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 51.

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_termination_factors:
            if not any(j in i for i in elongation_termination_factors.keys() for j in ['pol1_', 'pol2_', 'pol3_', 'polm_']):
                raise ValueError(
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 2 other locations - About 2 hrs to fix
wc_model_gen/eukaryote/transcription.py on lines 98..100
wc_model_gen/eukaryote/transcription.py on lines 112..114

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 51.

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:
            if not any(j in i for i in elongation_negative_factors.keys() for j in ['pol1_', 'pol2_', 'pol3_', 'polm_']):
                raise ValueError(
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 2 other locations - About 2 hrs to fix
wc_model_gen/eukaryote/transcription.py on lines 98..100
wc_model_gen/eukaryote/transcription.py on lines 105..107

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 51.

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 cl, dictionary in objects.items():
                dictionary.update(aa_functions[translation_compartment.id][
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 1 other location - About 1 hr to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 964..965

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 48.

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 cl, dictionary in objects.items():
                                dictionary.update(aa_functions[translation_compartment.id][
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 1 other location - About 1 hr to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 825..826

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 48.

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

            model_k_m = model.parameters.get_or_create(id='K_m_{}_{}'.format(reaction.id, species.species_type.id),
                                                type=wc_ontology['WC:K_m'],
                                                units=unit_registry.parse_units('M'))
Severity: Major
Found in wc_model_gen/utils.py and 1 other location - About 1 hr to fix
wc_model_gen/utils.py on lines 455..457

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 46.

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

            model_k_m = model.parameters.get_or_create(id='K_m_{}_{}'.format(reaction.id, species.species_type.id),
                                                type=wc_ontology['WC:K_m'],
                                                units=unit_registry.parse_units('M'))
Severity: Major
Found in wc_model_gen/utils.py and 1 other location - About 1 hr to fix
wc_model_gen/utils.py on lines 363..365

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 46.

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

                no_of_binding_sites = model.parameters.get_or_create(
                    id='total_mitochondrial_genome_binding',
                    type=None,
                    value=self._mitochondrial_max_binding_sites,
                    units=unit_registry.parse_units('molecule'),
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 1 other location - About 1 hr to fix
wc_model_gen/eukaryote/transcription.py on lines 863..869

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 46.

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

                no_of_binding_sites = model.parameters.get_or_create(
                    id='total_nuclear_genome_binding',
                    type=None,
                    value=self._nuclear_max_binding_sites,
                    units=unit_registry.parse_units('molecule'),
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 1 other location - About 1 hr to fix
wc_model_gen/eukaryote/transcription.py on lines 873..879

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 46.

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['gtp'][
                transcription_compartment.id].species_coefficients.get_or_create(
                coefficient=-pre_rna_count['G']))
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 3 other locations - About 1 hr to fix
wc_model_gen/eukaryote/transcription.py on lines 498..500
wc_model_gen/eukaryote/transcription.py on lines 501..503
wc_model_gen/eukaryote/transcription.py on lines 507..509

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 45.

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['ctp'][
                transcription_compartment.id].species_coefficients.get_or_create(
                coefficient=-pre_rna_count['C']))
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 3 other locations - About 1 hr to fix
wc_model_gen/eukaryote/transcription.py on lines 498..500
wc_model_gen/eukaryote/transcription.py on lines 504..506
wc_model_gen/eukaryote/transcription.py on lines 507..509

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 45.

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

            init_reaction = model.reactions.create(
                submodel=self.submodel, id='translation_initiation_' + mrna_kb.id,
                name='translation initiation of ' + mrna_kb.name,
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 3 other locations - About 1 hr to fix
wc_model_gen/eukaryote/transcription.py on lines 419..421
wc_model_gen/eukaryote/transcription.py on lines 457..459
wc_model_gen/eukaryote/translation_translocation.py on lines 395..397

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 45.

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['atp'][
                transcription_compartment.id].species_coefficients.get_or_create(
                coefficient=-pre_rna_count['A']))
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 3 other locations - About 1 hr to fix
wc_model_gen/eukaryote/transcription.py on lines 501..503
wc_model_gen/eukaryote/transcription.py on lines 504..506
wc_model_gen/eukaryote/transcription.py on lines 507..509

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 45.

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

            init_reaction = model.reactions.create(
                submodel=self.submodel, id='transcription_initiation_' + rna_kb.id,
                name='transcription initiation of ' + rna_kb.name,
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 3 other locations - About 1 hr to fix
wc_model_gen/eukaryote/transcription.py on lines 457..459
wc_model_gen/eukaryote/translation_translocation.py on lines 341..343
wc_model_gen/eukaryote/translation_translocation.py on lines 395..397

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 45.

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['utp'][
                transcription_compartment.id].species_coefficients.get_or_create(
                coefficient=-pre_rna_count['U']))
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 3 other locations - About 1 hr to fix
wc_model_gen/eukaryote/transcription.py on lines 498..500
wc_model_gen/eukaryote/transcription.py on lines 501..503
wc_model_gen/eukaryote/transcription.py on lines 504..506

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 45.

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 = model.reactions.get_or_create(
                submodel=self.submodel, id='transcription_elongation_' + rna_kb.id,
                name='transcription elongation of ' + rna_kb.name,
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 3 other locations - About 1 hr to fix
wc_model_gen/eukaryote/transcription.py on lines 419..421
wc_model_gen/eukaryote/translation_translocation.py on lines 341..343
wc_model_gen/eukaryote/translation_translocation.py on lines 395..397

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 45.

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

            el_reaction = model.reactions.get_or_create(
                submodel=self.submodel, id='translation_elongation_' + mrna_kb.id,
                name='translation elongation of ' + mrna_kb.name,
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 3 other locations - About 1 hr to fix
wc_model_gen/eukaryote/transcription.py on lines 419..421
wc_model_gen/eukaryote/transcription.py on lines 457..459
wc_model_gen/eukaryote/translation_translocation.py on lines 341..343

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 45.

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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