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datanator/core/data_model.py

Summary

Maintainability
F
4 days
Test Coverage
A
92%

File data_model.py has 490 lines of code (exceeds 250 allowed). Consider refactoring.
Open

"""
:Author: Jonathan Karr <jonrkarr@gmail.com>
:Author: Yosef Roth <yosefdroth@gmail.com>
:Date: 2017-04-10
:Copyright: 2017, Karr Lab
Severity: Minor
Found in datanator/core/data_model.py - About 7 hrs to fix

    Function get_ordered_participants has a Cognitive Complexity of 20 (exceeds 5 allowed). Consider refactoring.
    Open

        def get_ordered_participants(self, collapse_repeated=True):
        """ Get an ordered list of the participants

        Args:
            collapse_repeated (:obj:`bool`): if :obj:`True`, collapse any repeated participants
    Severity: Minor
    Found in datanator/core/data_model.py - About 2 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

    Consider simplifying this complex logical expression.
    Open

                        if other_part.specie.structure == part.specie.structure and \
                            other_part.specie.id == part.specie.id and \
                            ((other_part.compartment is None and part.compartment is None) or
                                other_part.compartment.id == part.compartment.id) and \
                            numpy.sign(other_part.coefficient) == numpy.sign(part.coefficient):
    Severity: Major
    Found in datanator/core/data_model.py - About 40 mins to fix

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

          def stringify(self):
        #TODO: Add the modifier

        participants = self.get_ordered_participants()
        result = ''
      Severity: Minor
      Found in datanator/core/data_model.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

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

      class ProteinComplexSpecie(ProteinSpecie):
    """ Represents a protein interaction

        Attributes:
      Severity: Major
      Found in datanator/core/data_model.py and 1 other location - About 7 hrs to fix
      datanator/core/data_model.py on lines 617..643

      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 114.

      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

      class Reference(obj_tables.core.Model):
    """ Represent a reference for an observation

    Attributes:
        title (:obj:`str`): title
      Severity: Major
      Found in datanator/core/data_model.py and 1 other location - About 7 hrs to fix
      datanator/core/data_model.py on lines 269..285

      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 114.

      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

      class Method(obj_tables.core.Model):
    """ Represents a method used to generate an observation

    Attributes:
        name (:obj:`str`): name
      Severity: Major
      Found in datanator/core/data_model.py and 1 other location - About 3 hrs to fix
      datanator/core/data_model.py on lines 537..551

      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 66.

      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

      class Environment(obj_tables.core.Model):
    """ Represents the environment (temperature, pH, media chemical composition) of an observation

    Attributes:
        temperature (:obj:`float`): temperature in Celcius
      Severity: Major
      Found in datanator/core/data_model.py and 1 other location - About 3 hrs to fix
      datanator/core/data_model.py on lines 554..567

      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 66.

      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

          def get_manual_ec_numbers(self):
        """ Get the manually assigned EC numbers from the list of cross references

        Returns:
            :obj:`list` of :obj:`str`: list of EC manually assigned numbers
      Severity: Major
      Found in datanator/core/data_model.py and 1 other location - About 2 hrs to fix
      datanator/core/data_model.py on lines 454..461

      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 2 locations. Consider refactoring.
      Open

          def get_predicted_ec_numbers(self):
        """ Get the predicted EC numbers from the list of cross references

        Returns:
            :obj:`list` of :obj:`str`: list of predicted EC numbers
      Severity: Major
      Found in datanator/core/data_model.py and 1 other location - About 2 hrs to fix
      datanator/core/data_model.py on lines 445..452

      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

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