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

                    component_dict[args[0][0]] = args[0][1]
Severity: Major
Found in bcforms/core.py and 2 other locations - About 45 mins to fix
bcforms/core.py on lines 1610..1610
bcforms/core.py on lines 1614..1614

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 35.

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 'id' in subunit:
                new_subunit['id'] = subunit['id']
            else:
                raise ValueError('`subunit` has no `id`')
Severity: Minor
Found in bcforms/core.py and 1 other location - About 45 mins to fix
bcforms/core.py on lines 1806..1809

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 35.

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

Avoid deeply nested control flow statements.
Open

                        if 'formula' in subunit:
                            try:
                                bc_form.set_subunit_attribute(subunit_id, 'formula', subunit['formula'])
                            except Exception as error:
                                flask_restplus.abort(400, 'Unable to parse formula', errors={'formula': str(error)})
Severity: Major
Found in bcforms/rest.py - About 45 mins to fix

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

                @lark.v_args(inline=True)
            def coefficient(self, *args):
                return ('stoichiometry', int(args[0].value))
    Severity: Major
    Found in bcforms/core.py and 4 other locations - About 40 mins to fix
    bcforms/core.py on lines 1328..1330
    bcforms/core.py on lines 1332..1334
    bcforms/core.py on lines 1742..1744
    bcforms/core.py on lines 1754..1756

    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 34.

    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

                @lark.v_args(inline=True)
            def monomer_position(self, *args):
                return ('monomer_position', int(args[0].value))
    Severity: Major
    Found in bcforms/core.py and 4 other locations - About 40 mins to fix
    bcforms/core.py on lines 1328..1330
    bcforms/core.py on lines 1332..1334
    bcforms/core.py on lines 1618..1620
    bcforms/core.py on lines 1754..1756

    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 34.

    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 attr == 'l_monomer':
                            l_subunit = val[0]
                            l_subunit_idx = val[1]
                            l_monomer = val[2]
    Severity: Minor
    Found in bcforms/core.py and 1 other location - About 40 mins to fix
    bcforms/core.py on lines 1650..1653

    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 34.

    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 attr == 'r_monomer':
                            r_subunit = val[0]
                            r_subunit_idx = val[1]
                            r_monomer = val[2]
    Severity: Minor
    Found in bcforms/core.py and 1 other location - About 40 mins to fix
    bcforms/core.py on lines 1646..1649

    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 34.

    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

            @lark.v_args(inline=True)
        def atom_charge(self, *args):
            return ('atom_charge', int(args[0].value))
    Severity: Major
    Found in bcforms/core.py and 4 other locations - About 40 mins to fix
    bcforms/core.py on lines 1328..1330
    bcforms/core.py on lines 1618..1620
    bcforms/core.py on lines 1742..1744
    bcforms/core.py on lines 1754..1756

    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 34.

    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

            @lark.v_args(inline=True)
        def atom_position(self, *args):
            return ('atom_position', int(args[0].value))
    Severity: Major
    Found in bcforms/core.py and 4 other locations - About 40 mins to fix
    bcforms/core.py on lines 1332..1334
    bcforms/core.py on lines 1618..1620
    bcforms/core.py on lines 1742..1744
    bcforms/core.py on lines 1754..1756

    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 34.

    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

                @lark.v_args(inline=True)
            def atom_position(self, *args):
                return ('atom_position', int(args[0].value))
    Severity: Major
    Found in bcforms/core.py and 4 other locations - About 40 mins to fix
    bcforms/core.py on lines 1328..1330
    bcforms/core.py on lines 1332..1334
    bcforms/core.py on lines 1618..1620
    bcforms/core.py on lines 1742..1744

    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 34.

    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

    Function from_set has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
    Open

        def from_set(self, subunits):
        """ Set the subunits from a list of subunits

        Note: this method does not support crosslinks
    Severity: Minor
    Found in bcforms/core.py - About 35 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

    Avoid too many return statements within this function.
    Open

            return True
    Severity: Major
    Found in bcforms/core.py - About 30 mins to fix

      Avoid too many return statements within this function.
      Open

              return True
      Severity: Major
      Found in bcforms/core.py - About 30 mins to fix

        Avoid too many return statements within this function.
        Open

                    return False
        Severity: Major
        Found in bcforms/core.py - About 30 mins to fix

          Avoid too many return statements within this function.
          Open

                      return False
          Severity: Major
          Found in bcforms/core.py - About 30 mins to fix

            Avoid too many return statements within this function.
            Open

                    return True
            Severity: Major
            Found in bcforms/core.py - About 30 mins to fix

              Avoid too many return statements within this function.
              Open

                              return False
              Severity: Major
              Found in bcforms/core.py - About 30 mins to fix

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

                def get_hydrogen_atom(parent_atom, bonding_hydrogens, i_monomer):
    """ Get a hydrogen atom attached to a parent atom
    Args:
        parent_atom (:obj:`openbabel.OBAtom`): parent atom
        bonding_hydrogens (:obj:`list`): hydrogens that have already been gotten
                Severity: Minor
                Found in bcforms/core.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

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

                    def __str__(self):
        """Generate a string representation

        Returns:
            :obj:`str`: string representation
                Severity: Minor
                Found in bcforms/core.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

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

                    def mol_wt(self, value):
        """ Set the molecular weight of the subunit

        Args:
            value (:obj:`float` or :obj:`int` or :obj:`None`): molecular weight of the subunit
                Severity: Minor
                Found in bcforms/core.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

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