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obj_tables/bio/seq.py

Summary

Maintainability
F
5 days
Test Coverage
A
100%

File seq.py has 442 lines of code (exceeds 250 allowed). Consider refactoring.
Open

""" Biological attributes

:Author: Jonathan Karr <karr@mssm.edu>
:Date: 2017-05-10
:Copyright: 2017, Karr Lab
Severity: Minor
Found in obj_tables/bio/seq.py - About 6 hrs to fix

    Function validate has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
    Open

        def validate(self, obj, value):
        """ Determine if :obj:`value` is a valid value

        Args:
            obj (:obj:`Model`): class being validated
    Severity: Minor
    Found in obj_tables/bio/seq.py - About 1 hr 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 __init__ has 8 arguments (exceeds 4 allowed). Consider refactoring.
    Open

        def __init__(self, min_length=0, max_length=float('inf'), default=None, none_value=None, verbose_name='', description='',
    Severity: Major
    Found in obj_tables/bio/seq.py - About 1 hr to fix

      Function __init__ has 8 arguments (exceeds 4 allowed). Consider refactoring.
      Open

          def __init__(self, min_length=0, max_length=float('inf'), default=None, none_value=None, verbose_name='', description='',
      Severity: Major
      Found in obj_tables/bio/seq.py - About 1 hr to fix

        Function __init__ has 8 arguments (exceeds 4 allowed). Consider refactoring.
        Open

            def __init__(self, min_length=0, max_length=float('inf'), default=None, none_value=None, verbose_name='', description='',
        Severity: Major
        Found in obj_tables/bio/seq.py - About 1 hr to fix

          Function __init__ has 8 arguments (exceeds 4 allowed). Consider refactoring.
          Open

              def __init__(self, min_length=0, max_length=float('inf'), default=None, none_value=None, verbose_name='', description='',
          Severity: Major
          Found in obj_tables/bio/seq.py - About 1 hr to fix

            Function __init__ has 6 arguments (exceeds 4 allowed). Consider refactoring.
            Open

                def __init__(self, default=None, none_value=None, verbose_name='', description='',
            Severity: Minor
            Found in obj_tables/bio/seq.py - About 45 mins to fix

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

                  def deserialize(self, value):
        """ Deserialize value

        Args:
            value (:obj:`str`): semantically equivalent representation
              Severity: Minor
              Found in obj_tables/bio/seq.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 __init__ has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
              Open

                  def __init__(self, min_length=0, max_length=float('inf'), default=None, none_value=None, verbose_name='', description='',
                 primary=False, unique=False):
        """
        Args:
            min_length (:obj:`int`, optional): minimum length
              Severity: Minor
              Found in obj_tables/bio/seq.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

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

              class ProteinSeqAttribute(SeqAttribute):
    """ Bio.Seq.Seq attribute with Bio.Alphabet.ProteinAlphabet
    """

    def __init__(self, min_length=0, max_length=float('inf'), default=None, none_value=None, verbose_name='', description='',
              Severity: Major
              Found in obj_tables/bio/seq.py and 2 other locations - About 5 hrs to fix
              obj_tables/bio/seq.py on lines 355..376
              obj_tables/bio/seq.py on lines 403..424

              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 87.

              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

              class RnaSeqAttribute(SeqAttribute):
    """ Bio.Seq.Seq attribute with Bio.Alphabet.RNAAlphabet
    """

    def __init__(self, min_length=0, max_length=float('inf'), default=None, none_value=None, verbose_name='', description='',
              Severity: Major
              Found in obj_tables/bio/seq.py and 2 other locations - About 5 hrs to fix
              obj_tables/bio/seq.py on lines 355..376
              obj_tables/bio/seq.py on lines 379..400

              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 87.

              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

              class DnaSeqAttribute(SeqAttribute):
    """ Bio.Seq.Seq attribute with Bio.Alphabet.DNAAlphabet
    """

    def __init__(self, min_length=0, max_length=float('inf'), default=None, none_value=None, verbose_name='', description='',
              Severity: Major
              Found in obj_tables/bio/seq.py and 2 other locations - About 5 hrs to fix
              obj_tables/bio/seq.py on lines 379..400
              obj_tables/bio/seq.py on lines 403..424

              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 87.

              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 8 locations. Consider refactoring.
              Open

                  def validate_unique(self, objects, values):
        """ Determine if the attribute values are unique

        Args:
            objects (:obj:`list` of :obj:`Model`): list of :obj:`Model` objects
              Severity: Major
              Found in obj_tables/bio/seq.py and 7 other locations - About 2 hrs to fix
              obj_tables/bio/seq.py on lines 113..127
              obj_tables/chem/core.py on lines 102..116
              obj_tables/chem/core.py on lines 466..480
              obj_tables/chem/core.py on lines 976..990
              obj_tables/math/numeric.py on lines 135..149
              obj_tables/math/numeric.py on lines 309..323
              obj_tables/math/symbolic.py on lines 93..107

              Duplicated Code

              Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

              Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

              When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

              Tuning

              This issue has a mass of 52.

              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 8 locations. Consider refactoring.
              Open

                  def validate_unique(self, objects, values):
        """ Determine if the attribute values are unique

        Args:
            objects (:obj:`list` of :obj:`Model`): list of :obj:`Model` objects
              Severity: Major
              Found in obj_tables/bio/seq.py and 7 other locations - About 2 hrs to fix
              obj_tables/bio/seq.py on lines 275..289
              obj_tables/chem/core.py on lines 102..116
              obj_tables/chem/core.py on lines 466..480
              obj_tables/chem/core.py on lines 976..990
              obj_tables/math/numeric.py on lines 135..149
              obj_tables/math/numeric.py on lines 309..323
              obj_tables/math/symbolic.py on lines 93..107

              Duplicated Code

              Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

              Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

              When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

              Tuning

              This issue has a mass of 52.

              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

                      if self.primary and (not value or len(value) == 0):
            errors.append('{} value for primary attribute cannot be empty'.format(
                self.__class__.__name__))
              Severity: Major
              Found in obj_tables/bio/seq.py and 1 other location - About 1 hr to fix
              obj_tables/chem/core.py on lines 94..96

              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 49.

              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 self.primary and value is None:
            errors.append('{} value for primary attribute cannot be empty'.format(
                self.__class__.__name__))
              Severity: Minor
              Found in obj_tables/bio/seq.py and 1 other location - About 50 mins to fix
              obj_tables/chem/core.py on lines 458..460

              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 36.

              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

                      if default is not None and not isinstance(default, Bio.SeqFeature.FeatureLocation):
            raise ValueError('`default` must be a `Bio.SeqFeature.FeatureLocation` or `None`')
              Severity: Major
              Found in obj_tables/bio/seq.py and 3 other locations - About 45 mins to fix
              obj_tables/bio/seq.py on lines 197..198
              obj_tables/sci/uncertainty.py on lines 41..42
              obj_tables/sci/uncertainty.py on lines 43..44

              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 4 locations. Consider refactoring.
              Open

                      if default is not None and not isinstance(default, Bio.Seq.Seq):
            raise ValueError('`default` must be a `Bio.Seq.Seq` or `None`')
              Severity: Major
              Found in obj_tables/bio/seq.py and 3 other locations - About 45 mins to fix
              obj_tables/bio/seq.py on lines 46..47
              obj_tables/sci/uncertainty.py on lines 41..42
              obj_tables/sci/uncertainty.py on lines 43..44

              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

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

                      if not isinstance(max_length, (int, float)) or max_length < min_length:
            raise ValueError('`max_length` must be an integer greater than or equal to `min_length`')
              Severity: Minor
              Found in obj_tables/bio/seq.py and 1 other location - About 40 mins to fix
              obj_tables/math/numeric.py on lines 46..47

              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

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

                      if not isinstance(min_length, (int, float)) or min_length < 0:
            raise ValueError('`min_length` must be a non-negative integer')
              Severity: Minor
              Found in obj_tables/bio/seq.py and 1 other location - About 40 mins to fix
              obj_tables/math/numeric.py on lines 44..45

              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

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

                          return {
                'seq': str(value),
                'alphabet': {
                    'type': value.alphabet.__class__.__name__,
                    'letters': value.alphabet.letters,
              Severity: Minor
              Found in obj_tables/bio/seq.py and 1 other location - About 35 mins to fix
              obj_tables/bio/seq.py on lines 304..309

              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 33.

              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

                              return json.dumps({
                    'seq': str(value),
                    'alphabet': {
                        'type': value.alphabet.__class__.__name__,
                        'letters': value.alphabet.letters,
              Severity: Minor
              Found in obj_tables/bio/seq.py and 1 other location - About 35 mins to fix
              obj_tables/bio/seq.py on lines 327..332

              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 33.

              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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