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

            reg_species[self._allowable_queue_len[rna_kb.id][0].id] = self._allowable_queue_len[rna_kb.id][0]
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 1 other location - About 1 hr to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 1192..1192

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 2 locations. Consider refactoring.
Open

            init_species_counts[self._allowable_queue_len[mrna_kb.id][0].id] = self._allowable_queue_len[mrna_kb.id][1]
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 1 other location - About 1 hr to fix
wc_model_gen/eukaryote/transcription.py on lines 990..990

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 2 locations. Consider refactoring.
Open

                        'function': model.functions.create(     
                            id='aminoacid_function_{}_{}'.format(aa_id, compartment.id),               
                            name='response function for amino acid {} in {}'.format(aa_id, compartment.name),
                            expression=aa_expression,
                            units=unit_registry.parse_units(''),
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 643..648

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 44.

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

                    trna_factor_function = model.functions.create(     
                        id='trna_function_{}_{}'.format(anticodons, compartment.id),               
                        name='tRNA response function for anticodon(s) {} in {}'.format(
                            anticodons, compartment.name),
                        expression=trna_expression,
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 676..680

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 44.

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

        mrna_kbs = [i for i in cell.species_types.get(__type=wc_kb.eukaryote.TranscriptSpeciesType) \
            if i.type==wc_kb.eukaryote.TranscriptType.mRna]
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 2 other locations - About 1 hr to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 251..252
wc_model_gen/eukaryote/translation_translocation.py on lines 770..771

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 43.

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

            polr_bound_non_specific_species_type = model.species_types.get_or_create(
                id='{}_bound_non_specific_site'.format(polr_complex.id),
                name='{}-bound non-specific site'.format(polr_complex.id),
                type=onto['WC:pseudo_species'],
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 372..375
wc_model_gen/eukaryote/transcription.py on lines 559..562
wc_model_gen/eukaryote/translation_translocation.py on lines 318..321

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 43.

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

                coefficient=-(pre_rna_count['len']-pre_rna_count['N']+len_add_rna
                    -ntp_count['len']+1)))
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 541..544

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 43.

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

                    ribo_binding_site_st = model.species_types.get_or_create(
                        id='{}_ribosome_binding_site'.format(rna.id),
                        name='ribosome binding site of {}'.format(rna.name),
                        type=onto['WC:pseudo_species'],
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 283..286
wc_model_gen/eukaryote/transcription.py on lines 372..375
wc_model_gen/eukaryote/translation_translocation.py on lines 318..321

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 43.

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

        ref_polr_width = wc_lang.Reference(
            model=model,
            title='Structure and mechanism of the RNA Polymerase II transcription machinery',
            author='Steven Hahn',        
            year=2004,
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 208..213

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 43.

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

            polr_binding_site_st = model.species_types.get_or_create(
                id='{}_binding_site'.format(gene.id),
                name='binding site of {}'.format(gene.name),
                type=onto['WC:pseudo_species'],
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 283..286
wc_model_gen/eukaryote/transcription.py on lines 559..562
wc_model_gen/eukaryote/translation_translocation.py on lines 318..321

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 43.

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

            reaction.participants.append(metabolites['h'][
                transcription_compartment.id].species_coefficients.get_or_create(
                coefficient=pre_rna_count['len']-pre_rna_count['N']+len_add_rna
                    -ntp_count['len']+1))
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 512..513

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 43.

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

        ref_ribo_width = wc_lang.Reference(
            model=model,
            title='Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling',
            author='Nicholas T Ingolia, Sina Ghaemmaghami, John R. S. Newman, Jonathan S. Weissman',        
            year=2009,
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 182..187

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 43.

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

        mrna_kbs = [i for i in cell.species_types.get(__type=wc_kb.eukaryote.TranscriptSpeciesType) \
            if i.type==wc_kb.eukaryote.TranscriptType.mRna]
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 2 other locations - About 1 hr to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 770..771
wc_model_gen/eukaryote/translation_translocation.py on lines 1132..1133

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 43.

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

        mrna_kbs = [i for i in cell.species_types.get(__type=wc_kb.eukaryote.TranscriptSpeciesType) \
            if i.type==wc_kb.eukaryote.TranscriptType.mRna]
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 2 other locations - About 1 hr to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 251..252
wc_model_gen/eukaryote/translation_translocation.py on lines 1132..1133

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 43.

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

            ribo_bound_species_type = model.species_types.get_or_create(
                id='ribo_bound_{}'.format(mrna_kb.id),
                name='Ribosome bound {}'.format(mrna_kb.name),
                type=wc_ontology['WC:pseudo_species'],
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 283..286
wc_model_gen/eukaryote/transcription.py on lines 372..375
wc_model_gen/eukaryote/transcription.py on lines 559..562

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 43.

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

                trans_reaction.participants.append(model.species_types.get_one(id='pi').species.get_one(
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 2 other locations - About 1 hr to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 522..522
wc_model_gen/eukaryote/translation_translocation.py on lines 532..532

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 3 locations. Consider refactoring.
Open

                trans_reaction.participants.append(model.species_types.get_one(id='h2o').species.get_one(
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 2 other locations - About 1 hr to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 530..530
wc_model_gen/eukaryote/translation_translocation.py on lines 532..532

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

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

            k_cat_elongation = model.parameters.create(
                id='k_cat_{}'.format(elongation_reaction.id),
                type=wc_ontology['WC:k_cat'],
                units=unit_registry.parse_units('molecule^-1 s^-1'),
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 4 other locations - About 1 hr to fix
wc_model_gen/eukaryote/complexation.py on lines 325..327
wc_model_gen/eukaryote/transcription.py on lines 1050..1053
wc_model_gen/eukaryote/translation_translocation.py on lines 1056..1059
wc_model_gen/prokaryote/metabolism.py on lines 165..167

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

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