Sign upLogin

KarrLab/wc_kb

View on GitHub
Star
wc_kb/eukaryote.py

Summary

Maintainability
F
2 wks
Test Coverage
A
96%

File eukaryote.py has 565 lines of code (exceeds 250 allowed). Consider refactoring.
Open

""" Schema to represent a knowledge base to build models of eukaryotes

:Author: Yin Hoon Chew <yinhoon.chew@mssm.edu>
:Date: 2018-09-10
:Copyright: 2018, Karr Lab
Severity: Major
Found in wc_kb/eukaryote.py - About 1 day to fix

    Function deserialize has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.
    Open

        def deserialize(cls, value, objects):
        """ Deserialize value
        Args:
            value (:obj:`str`): String representation
            objects (:obj:`dict`): dictionary of objects, grouped by model
    Severity: Minor
    Found in wc_kb/eukaryote.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 deserialize has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
    Open

        def deserialize(self, value, objects, decoded=None):
        """ Deserialize value
        Args:
            value (:obj:`str`): String representation
            objects (:obj:`dict`): dictionary of objects, grouped by model
    Severity: Minor
    Found in wc_kb/eukaryote.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 get_empirical_formula has 32 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

        def get_empirical_formula(self, table=1, cds=True, seq_input=None):
        """ Get the empirical formula

        Args:
            table (:obj:`int`, optional): NCBI identifier for translation table
    Severity: Minor
    Found in wc_kb/eukaryote.py - About 1 hr to fix

      Function deserialize has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
      Open

          def deserialize(self, value, objects, decoded=None):
        """ Deserialize value
        Args:
            value (:obj:`str`): String representation
            objects (:obj:`dict`): dictionary of objects, grouped by model
      Severity: Minor
      Found in wc_kb/eukaryote.py - About 45 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 get_seq_and_start_codon has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
      Open

          def get_seq_and_start_codon(self, table=1, cds=True):
        """ Get the 5' to 3' amino acid sequence and the start codon

        Args:
            table (:obj:`int`, optional): NCBI identifier for translation table
      Severity: Minor
      Found in wc_kb/eukaryote.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

              formula.H = 7 * n_a + 14 * n_r + 8 * n_n + 7 * n_d + 7 * n_c + \
            10 * n_q + 9 * n_e + 5 * n_g + 9 * n_h + 13 * n_i + \
            13 * n_l + 14 * n_k + 11 * n_m + 11 * n_f + 9 * n_p + \
            7 * n_s + 9 * n_t + 12 * n_w + 11 * n_y + 11 * n_v + \
            7 * n_u - 2 * (l - 1)
      Severity: Major
      Found in wc_kb/eukaryote.py and 1 other location - About 2 days to fix
      wc_kb/prokaryote.py on lines 215..219

      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 271.

      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

              formula.O = 2 * n_a + 2 * n_r + 3 * n_n + 4 * n_d + 2 * n_c + \
            3 * n_q + 4 * n_e + 2 * n_g + 2 * n_h + 2 * n_i + \
            2 * n_l + 2 * n_k + 2 * n_m + 2 * n_f + 2 * n_p + \
            3 * n_s + 3 * n_t + 2 * n_w + 3 * n_y + 2 * n_v + \
            2 * n_u - (l - 1)
      Severity: Major
      Found in wc_kb/eukaryote.py and 1 other location - About 2 days to fix
      wc_kb/prokaryote.py on lines 227..231

      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 265.

      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

              formula.C = 3 * n_a + 6 * n_r + 4 * n_n + 4 * n_d + 3 * n_c + \
            5 * n_q + 5 * n_e + 2 * n_g + 6 * n_h + 6 * n_i + \
            6 * n_l + 6 * n_k + 5 * n_m + 9 * n_f + 5 * n_p + \
            3 * n_s + 4 * n_t + 11 * n_w + 9 * n_y + 5 * n_v + \
            3 * n_u
      Severity: Major
      Found in wc_kb/eukaryote.py and 3 other locations - About 2 days to fix
      wc_kb/eukaryote.py on lines 668..672
      wc_kb/prokaryote.py on lines 209..213
      wc_kb/prokaryote.py on lines 221..225

      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 253.

      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

              formula.N = 1 * n_a + 4 * n_r + 2 * n_n + 1 * n_d + 1 * n_c + \
            2 * n_q + 1 * n_e + 1 * n_g + 3 * n_h + 1 * n_i + \
            1 * n_l + 2 * n_k + 1 * n_m + 1 * n_f + 1 * n_p + \
            1 * n_s + 1 * n_t + 2 * n_w + 1 * n_y + 1 * n_v + \
            1 * n_u
      Severity: Major
      Found in wc_kb/eukaryote.py and 3 other locations - About 2 days to fix
      wc_kb/eukaryote.py on lines 656..660
      wc_kb/prokaryote.py on lines 209..213
      wc_kb/prokaryote.py on lines 221..225

      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 253.

      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

              formula.H = 12 * n_a + 12 * n_c + 12 * n_g + 11 * n_u - (l - 1)
      Severity: Major
      Found in wc_kb/eukaryote.py and 3 other locations - About 2 hrs to fix
      wc_kb/eukaryote.py on lines 472..472
      wc_kb/prokaryote.py on lines 85..85
      wc_kb/prokaryote.py on lines 87..87

      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 4 locations. Consider refactoring.
      Open

              formula.O = 7 * n_a + 8 * n_c + 8 * n_g + 9 * n_u - (l - 1)
      Severity: Major
      Found in wc_kb/eukaryote.py and 3 other locations - About 2 hrs to fix
      wc_kb/eukaryote.py on lines 470..470
      wc_kb/prokaryote.py on lines 85..85
      wc_kb/prokaryote.py on lines 87..87

      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 3 locations. Consider refactoring.
      Open

              adjusted_exons = [(i.start - ordered_exons[0].start, i.end - ordered_exons[0].start + 1) \
      Severity: Major
      Found in wc_kb/eukaryote.py and 2 other locations - About 2 hrs to fix
      wc_kb/eukaryote.py on lines 556..556
      wc_kb/eukaryote.py on lines 586..586

      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 54.

      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

              adjusted_cds = [(i.start - ordered_cds[0].start, i.end - ordered_cds[0].start + 1) \
      Severity: Major
      Found in wc_kb/eukaryote.py and 2 other locations - About 2 hrs to fix
      wc_kb/eukaryote.py on lines 430..430
      wc_kb/eukaryote.py on lines 556..556

      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 54.

      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

              adjusted_cds = [(i.start - ordered_cds[0].start, i.end - ordered_cds[0].start + 1) \
      Severity: Major
      Found in wc_kb/eukaryote.py and 2 other locations - About 2 hrs to fix
      wc_kb/eukaryote.py on lines 430..430
      wc_kb/eukaryote.py on lines 586..586

      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 54.

      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

              formula.N = 5 * n_a + 3 * n_c + 5 * n_g + 2 * n_u
      Severity: Major
      Found in wc_kb/eukaryote.py and 3 other locations - About 1 hr to fix
      wc_kb/eukaryote.py on lines 469..469
      wc_kb/prokaryote.py on lines 84..84
      wc_kb/prokaryote.py on lines 86..86

      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 4 locations. Consider refactoring.
      Open

              formula.C = 10 * n_a + 9 * n_c + 10 * n_g + 9 * n_u
      Severity: Major
      Found in wc_kb/eukaryote.py and 3 other locations - About 1 hr to fix
      wc_kb/eukaryote.py on lines 471..471
      wc_kb/prokaryote.py on lines 84..84
      wc_kb/prokaryote.py on lines 86..86

      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

          def serialize(self, coordinates, encoded=None):
        """ Serialize related object
        Args:
            coordinates (:obj:`list` of :obj:`Model`): a list of instances of GenericLocus Python representation
            encoded (:obj:`dict`, optional): dictionary of objects that have already been encoded
      Severity: Major
      Found in wc_kb/eukaryote.py and 1 other location - About 1 hr to fix
      wc_kb/eukaryote.py on lines 130..141

      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 45.

      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 serialize(self, directions, encoded=None):
        """ Serialize related object
        Args:
            directions (:obj:`list` of :obj:`Model`): a list of instances of TFdirection Python representation
            encoded (:obj:`dict`, optional): dictionary of objects that have already been encoded
      Severity: Major
      Found in wc_kb/eukaryote.py and 1 other location - About 1 hr to fix
      wc_kb/eukaryote.py on lines 67..78

      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 45.

      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 not re.match(lst_pattern, value, flags=re.I):
            return (None, obj_tables.InvalidAttribute(self, ['Incorrectly formatted list of transcription factor regulation: {}'.format(value)]))
      Severity: Major
      Found in wc_kb/eukaryote.py and 1 other location - About 1 hr to fix
      wc_kb/eukaryote.py on lines 95..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 42.

      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 not re.match(lst_pattern, value, flags=re.I):
            return (None, obj_tables.InvalidAttribute(self, ['Incorrectly formatted list of coordinates: {}'.format(value)]))
      Severity: Major
      Found in wc_kb/eukaryote.py and 1 other location - About 1 hr to fix
      wc_kb/eukaryote.py on lines 160..161

      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 42.

      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

              dna_seq = self.transcript.gene.polymer.get_subseq(
                    start=ordered_cds[0].start, end=ordered_cds[-1].end)
      Severity: Major
      Found in wc_kb/eukaryote.py and 1 other location - About 1 hr to fix
      wc_kb/eukaryote.py on lines 583..584

      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 38.

      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

              dna_seq = self.transcript.gene.polymer.get_subseq(
                    start=ordered_cds[0].start, end=ordered_cds[-1].end)
      Severity: Major
      Found in wc_kb/eukaryote.py and 1 other location - About 1 hr to fix
      wc_kb/eukaryote.py on lines 553..554

      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 38.

      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

              for i in adjusted_cds:
            spliced_dna_seq += dna_seq[i[0]:i[1]]
      Severity: Minor
      Found in wc_kb/eukaryote.py and 2 other locations - About 35 mins to fix
      wc_kb/eukaryote.py on lines 434..435
      wc_kb/eukaryote.py on lines 590..591

      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

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

              for i in adjusted_cds:
            spliced_dna_seq += dna_seq[i[0]:i[1]]
      Severity: Minor
      Found in wc_kb/eukaryote.py and 2 other locations - About 35 mins to fix
      wc_kb/eukaryote.py on lines 434..435
      wc_kb/eukaryote.py on lines 560..561

      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

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

              for exon in adjusted_exons:
            spliced_dna_seq += dna_seq[exon[0]:exon[1]]
      Severity: Minor
      Found in wc_kb/eukaryote.py and 2 other locations - About 35 mins to fix
      wc_kb/eukaryote.py on lines 560..561
      wc_kb/eukaryote.py on lines 590..591

      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

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

          class Meta(obj_tables.Model.Meta):
        verbose_name = 'Transcript'
        verbose_name_plural = 'Transcripts'
        attribute_order = ('id', 'name', 'gene', 'exons', 'type', 'identifiers', 'references', 'comments')
      Severity: Minor
      Found in wc_kb/eukaryote.py and 1 other location - About 30 mins to fix
      wc_kb/eukaryote.py on lines 534..538

      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 32.

      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 Meta(obj_tables.Model.Meta):
        verbose_name = 'Protein'
        verbose_name_plural = 'Proteins'
        attribute_order = ('id', 'name', 'uniprot', 'transcript', 'coding_regions', 
                           'identifiers', 'references', 'comments')
      Severity: Minor
      Found in wc_kb/eukaryote.py and 1 other location - About 30 mins to fix
      wc_kb/eukaryote.py on lines 414..417

      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 32.

      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

      There are no issues that match your filters.

      Category
      Status