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

PROKARYOTE_MODELS = (
    core.KnowledgeBase,
    core.Cell,
    core.Compartment,
    core.DnaSpeciesType,
Severity: Major
Found in wc_kb/io.py and 1 other location - About 3 hrs to fix
wc_kb/io.py on lines 51..71

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

        elif self.start > self.end:
            if self.strand == core.PolymerStrand.positive:
                return core.PolymerDirection.reverse
            elif self.strand == core.PolymerStrand.negative:
                return core.PolymerStrand.forward
Severity: Major
Found in wc_kb/prokaryote.py and 1 other location - About 3 hrs to fix
wc_kb/prokaryote.py on lines 126..132

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

        if self.start < self.end:
            if self.strand == core.PolymerStrand.positive:
                return core.PolymerDirection.forward
            elif self.strand == core.PolymerStrand.negative:
                return core.PolymerDirection.reverse
Severity: Major
Found in wc_kb/prokaryote.py and 1 other location - About 3 hrs to fix
wc_kb/prokaryote.py on lines 133..139

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

Function run has a Cognitive Complexity of 22 (exceeds 5 allowed). Consider refactoring.
Open

    def run(self, core_path, knowledge_base,
            seq_path=None, rewrite_seq_path=True, taxon='prokaryote',
            models=None, get_related=True, include_all_attributes=False, validate=True,
            title=None, description=None, keywords=None, version=None, language=None, creator=None,
            write_schema=False, write_toc=True,
Severity: Minor
Found in wc_kb/io.py - About 3 hrs to fix

Cognitive Complexity

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

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

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

Further reading

Function deserialize has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.
Open

    def deserialize(cls, attribute, value, objects):
        """ Deserialize value

        Args:
            attribute (:obj:`Attribute`): attribute
Severity: Minor
Found in wc_kb/core.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

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

Function validate_implicit_relationships has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.
Open

    def validate_implicit_relationships(cls):
        """ Check that relationships to :obj:`core.KnowledgeBase` and :obj:`core.Cell` do not need to be explicitly written to
        workbooks because they can be inferred by :obj:`Reader.run`

        Raises:
Severity: Minor
Found in wc_kb/io.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

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/prokaryote.py and 3 other locations - About 2 hrs to fix
wc_kb/eukaryote.py on lines 470..470
wc_kb/eukaryote.py on lines 472..472
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/prokaryote.py and 3 other locations - About 2 hrs to fix
wc_kb/eukaryote.py on lines 470..470
wc_kb/eukaryote.py on lines 472..472
wc_kb/prokaryote.py on lines 85..85

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

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

def transform(filename, taxon):
    # read
    wb = openpyxl.load_workbook(filename=filename)

    for ws in wb:
Severity: Minor
Found in migrations/migration_2019_10_10.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

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

                for i_col in range(ws.max_column):
                    cell = ws.cell(i_row + 2, i_col + 1)
                    if cell.value and isinstance(cell.value, str):
                        cell.value = '!' + cell.value
Severity: Major
Found in migrations/migration_2019_09_20.py and 1 other location - About 2 hrs to fix
migrations/migration_2019_09_20.py on lines 74..77

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 58.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

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

                for i_col in range(n_head_rows):
                    cell = ws.cell(i_row + 2, i_col + 1)
                    if cell.value and isinstance(cell.value, str):
                        cell.value = '!' + cell.value
Severity: Major
Found in migrations/migration_2019_09_20.py and 1 other location - About 2 hrs to fix
migrations/migration_2019_09_20.py on lines 68..71

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 58.

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 run has 21 arguments (exceeds 4 allowed). Consider refactoring.
Open

    def run(self, core_path, knowledge_base,
Severity: Major
Found in wc_kb/io.py - About 2 hrs to fix

    Function deserialize has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.
    Open

        def deserialize(cls, attribute, value, objects):
        """ Deserialize value

        Args:
            attribute (:obj:`Attribute`): attribute
    Severity: Minor
    Found in wc_kb/core.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

    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

    Function deserialize has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
    Open

        def deserialize(self, value, objects, decoded=None):
        """ Deserialize value

        Args:
            value (:obj:`str`): String representation
    Severity: Minor
    Found in wc_kb/core.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

    File prokaryote.py has 253 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

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

:Author: Balazs Szigeti <balazs.szigeti@mssm.edu>
:Author: Jonathan Karr <jonrkarr@gmail.com>
:Author: Bilal Shaikh  <bilal.shaikh@columbia.edu>
    Severity: Minor
    Found in wc_kb/prokaryote.py - About 2 hrs to fix
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