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

    for reactant in reactants:
        obj_reaction = obj_reactants[reactant]
        conv_model.objective_terms = [conv_opt.LinearTerm(obj_reaction, 1.),]
        result = conv_model.solve()
        if result.value == 0.0:
Severity: Major
Found in wc_model_gen/utils.py and 1 other location - About 3 hrs to fix
wc_model_gen/utils.py on lines 176..181

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 63.

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

                            objects[wc_lang.Function][aa_functions[translation_compartment.id][
                                aa_met]['function'].id] = aa_functions[translation_compartment.id][
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 1 other location - About 2 hrs to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 822..823

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 61.

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

            objects[wc_lang.Function][aa_functions[translation_compartment.id][
                start_aa_met]['function'].id] = aa_functions[translation_compartment.id][
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 1 other location - About 2 hrs to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 961..962

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 61.

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 test_producibles:
        reactants = test_producibles
    else:    
        reactants = []
        for reaction in submodel.dfba_obj.expression.reactions:
Severity: Major
Found in wc_model_gen/utils.py and 1 other location - About 2 hrs to fix
wc_model_gen/utils.py on lines 86..93

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 60.

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 test_recyclables:
        products = test_recyclables
    else:    
        products = []
        for reaction in submodel.dfba_obj.expression.reactions:
Severity: Major
Found in wc_model_gen/utils.py and 1 other location - About 2 hrs to fix
wc_model_gen/utils.py on lines 77..84

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 60.

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_rxn = model.reactions.create(
                                submodel=self.submodel,
                                id='{}_dissociation_in_{}_degrade_{}'.format(
                                    compl.id, compl_compartment.id, compl_subunit.species_type.id),
                                name='Dissociation of {} in {} and degradation of {}'.format(
Severity: Major
Found in wc_model_gen/eukaryote/complexation.py and 1 other location - About 2 hrs to fix
wc_model_gen/eukaryote/complexation.py on lines 239..244

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 58.

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_rxn = model.reactions.create(
                                submodel=self.submodel,
                                id='{}_dissociation_in_{}_degrade_{}'.format(
                                    compl.id, compl_compartment.id, compl_subunit.species_type.id),
                                name='Dissociation of {} in {} and degradation of {}'.format(
Severity: Major
Found in wc_model_gen/eukaryote/complexation.py and 1 other location - About 2 hrs to fix
wc_model_gen/eukaryote/complexation.py on lines 154..159

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 58.

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

                if protein_kb.transcript.gene.id in selenoproteome:
                    processed_seq = raw_seq[:-1] if raw_seq.endswith('*') else raw_seq
                    protein_seq = ''.join(i if i!='*' else 'U' for i in processed_seq)
Severity: Major
Found in wc_model_gen/eukaryote/protein_degradation.py and 2 other locations - About 2 hrs to fix
wc_model_gen/eukaryote/complexation.py on lines 191..193
wc_model_gen/eukaryote/translation_translocation.py on lines 292..294

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 55.

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 not numpy.isnan(median_init_kcat): 
            for model_kcat in undetermined_init_kcat:
                model_kcat.value = median_init_kcat
                model_kcat.comments = 'Set to the median value because it could not be determined from data'
        else:
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 2 other locations - About 2 hrs to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 1344..1351
wc_model_gen/eukaryote/translation_translocation.py on lines 1354..1361

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 55.

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

                if mrna_kb.gene.id in selenoproteome:
                    processed_seq = raw_seq[:-1] if raw_seq.endswith('*') else raw_seq
                    protein_seq = ''.join(i if i!='*' else 'U' for i in processed_seq)
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 2 other locations - About 2 hrs to fix
wc_model_gen/eukaryote/complexation.py on lines 191..193
wc_model_gen/eukaryote/protein_degradation.py on lines 99..101

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 55.

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 tf_model and tf.direction == wc_kb.eukaryote.RegulatoryDirection.activation:                        
                        F_act, species_act, param_act, func_act = utils.simple_activator(
                            model, reaction_id, tf_model)
                        F_regs.append(F_act)
                        reg_species.update(species_act)
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 1 other location - About 2 hrs to fix
wc_model_gen/eukaryote/transcription.py on lines 909..915

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 55.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

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

                    elif tf_model and tf.direction == wc_kb.eukaryote.RegulatoryDirection.repression:
                        F_rep, species_rep, param_rep, func_rep = utils.simple_repressor(
                            model, reaction_id, tf_model) 
                        F_regs.append(F_rep)
                        reg_species.update(species_rep)
Severity: Major
Found in wc_model_gen/eukaryote/transcription.py and 1 other location - About 2 hrs to fix
wc_model_gen/eukaryote/transcription.py on lines 901..907

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 55.

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

                                        if subunit.species_type.transcript.gene.id in selenoproteome:
                                            processed_seq = raw_seq[:-1] if raw_seq.endswith('*') else raw_seq
                                            protein_seq = ''.join(i if i!='*' else 'U' for i in processed_seq)
Severity: Major
Found in wc_model_gen/eukaryote/complexation.py and 2 other locations - About 2 hrs to fix
wc_model_gen/eukaryote/protein_degradation.py on lines 99..101
wc_model_gen/eukaryote/translation_translocation.py on lines 292..294

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 55.

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 not numpy.isnan(median_transloc_kcat):
            for model_kcat in undetermined_transloc_kcat:
                model_kcat.value = median_transloc_kcat
                model_kcat.comments = 'Set to the median value because it could not be determined from data'
        else:
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 2 other locations - About 2 hrs to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 1334..1341
wc_model_gen/eukaryote/translation_translocation.py on lines 1344..1351

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 55.

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 not numpy.isnan(median_el_kcat):
            for model_kcat in undetermined_el_kcat:
                model_kcat.value = median_el_kcat
                model_kcat.comments = 'Set to the median value because it could not be determined from data'
        else:
Severity: Major
Found in wc_model_gen/eukaryote/translation_translocation.py and 2 other locations - About 2 hrs to fix
wc_model_gen/eukaryote/translation_translocation.py on lines 1334..1341
wc_model_gen/eukaryote/translation_translocation.py on lines 1354..1361

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 55.

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

            reaction.participants.append(metabolites['ppi'][
                transcription_compartment.id].species_coefficients.get_or_create(
                coefficient=pre_rna_count['len']-pre_rna_count['N']))
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 529..531
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 5 locations. Consider refactoring.
Open

            reaction.participants.append(metabolites['cmp'][
                transcription_compartment.id].species_coefficients.get_or_create(
                coefficient=pre_rna_count['C']-ntp_count['C']))
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 529..531
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: mito_species_counts,
                        wc_lang.Compartment: {
                            mitochondria.id: mitochondria.init_volume.mean * \
                                mitochondria.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 1528..1532

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 5 locations. Consider refactoring.
Open

            reaction.participants.append(metabolites['gmp'][
                transcription_compartment.id].species_coefficients.get_or_create(
                coefficient=pre_rna_count['G']-ntp_count['G']))
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 529..531
wc_model_gen/eukaryote/transcription.py on lines 532..534
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 5 locations. Consider refactoring.
Open

            reaction.participants.append(metabolites['ump'][
                transcription_compartment.id].species_coefficients.get_or_create(
                coefficient=pre_rna_count['U']-ntp_count['U']))
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 529..531
wc_model_gen/eukaryote/transcription.py on lines 532..534
wc_model_gen/eukaryote/transcription.py on lines 535..537

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

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