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datanator/data_source/modomics.py

Summary

Maintainability
F
1 wk
Test Coverage
F
0%

Function _run_rrna has a Cognitive Complexity of 31 (exceeds 5 allowed). Consider refactoring.
Open

    def _run_rrna(self, session, modomics_short_code_to_monomer, monomer_codes, out_filename):
        response = session.get(self.ENDPOINT, params={
            'RNA_type': 'rRNA',
            'RNA_subtype': 'all',
            'organism': 'all species',
Severity: Minor
Found in datanator/data_source/modomics.py - About 4 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function _run_trna has a Cognitive Complexity of 28 (exceeds 5 allowed). Consider refactoring.
Open

    def _run_trna(self, session, modomics_short_code_to_monomer, monomer_codes, out_filename):
        response = session.get(self.ENDPOINT, params={
            'RNA_type': 'tRNA',
            'RNA_subtype': 'all',
            'organism': 'all species',
Severity: Minor
Found in datanator/data_source/modomics.py - About 4 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function run has 42 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    def run(self):
        # create dict of MODOMICS single character monomer codes
        modomics_short_code_to_monomer = {}
        for monomer in bpforms.rna_alphabet.monomers.values():
            for identifier in monomer.identifiers:
Severity: Minor
Found in datanator/data_source/modomics.py - About 1 hr to fix

    Avoid deeply nested control flow statements.
    Open

                            if monomer is None:
                            unsupported_codes.add(code)
                            monomer = bpforms.Monomer(id=code)
                        else:
                            monomer_codes[code] = monomer
    Severity: Major
    Found in datanator/data_source/modomics.py - About 45 mins to fix

      Avoid deeply nested control flow statements.
      Open

                              if monomer is None:
                            unsupported_codes.add(code)
                            monomer = bpforms.Monomer(id=code)
                        else:
                            monomer_codes[code] = monomer
      Severity: Major
      Found in datanator/data_source/modomics.py - About 45 mins to fix

        Function run has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
        Open

            def run(self):
        # create dict of MODOMICS single character monomer codes
        modomics_short_code_to_monomer = {}
        for monomer in bpforms.rna_alphabet.monomers.values():
            for identifier in monomer.identifiers:
        Severity: Minor
        Found in datanator/data_source/modomics.py - About 25 mins to fix

        Cognitive Complexity

        Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

        A method's cognitive complexity is based on a few simple rules:

        • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
        • Code is considered more complex for each "break in the linear flow of the code"
        • Code is considered more complex when "flow breaking structures are nested"

        Further reading

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

                    for child in cells[5].children:
                if child.name is None or child.name == 'span':
                    if child.name is None:
                        text = str(child)
                    else:
        Severity: Major
        Found in datanator/data_source/modomics.py and 1 other location - About 2 days to fix
        datanator/data_source/modomics.py on lines 170..195

        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 273.

        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

                    for child in cells[5].children:
                if child.name is None or child.name == 'span':
                    if child.name is None:
                        text = str(child)
                    else:
        Severity: Major
        Found in datanator/data_source/modomics.py and 1 other location - About 2 days to fix
        datanator/data_source/modomics.py on lines 109..134

        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 273.

        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

                results_dict['Number of modified C'] = canonical_seq.count('C') - rna_form.seq.count(bpforms.rna_alphabet.monomers.C)
        Severity: Major
        Found in datanator/data_source/modomics.py and 3 other locations - About 55 mins to fix
        datanator/data_source/modomics.py on lines 221..221
        datanator/data_source/modomics.py on lines 223..223
        datanator/data_source/modomics.py on lines 224..224

        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 37.

        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

                results_dict['Number of modified G'] = canonical_seq.count('G') - rna_form.seq.count(bpforms.rna_alphabet.monomers.G)
        Severity: Major
        Found in datanator/data_source/modomics.py and 3 other locations - About 55 mins to fix
        datanator/data_source/modomics.py on lines 221..221
        datanator/data_source/modomics.py on lines 222..222
        datanator/data_source/modomics.py on lines 224..224

        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 37.

        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

                results_dict['Number of modified U'] = canonical_seq.count('U') - rna_form.seq.count(bpforms.rna_alphabet.monomers.U)
        Severity: Major
        Found in datanator/data_source/modomics.py and 3 other locations - About 55 mins to fix
        datanator/data_source/modomics.py on lines 221..221
        datanator/data_source/modomics.py on lines 222..222
        datanator/data_source/modomics.py on lines 223..223

        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 37.

        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

                results_dict['Number of modified A'] = canonical_seq.count('A') - rna_form.seq.count(bpforms.rna_alphabet.monomers.A)
        Severity: Major
        Found in datanator/data_source/modomics.py and 3 other locations - About 55 mins to fix
        datanator/data_source/modomics.py on lines 222..222
        datanator/data_source/modomics.py on lines 223..223
        datanator/data_source/modomics.py on lines 224..224

        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 37.

        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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