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

class Company(obj_tables.Model):
    name = obj_tables.StringAttribute(primary=True, unique=True, verbose_name='Name')
    url = obj_tables.UrlAttribute(verbose_name='URL')
    address = obj_tables.OneToOneAttribute('Address', related_name='company', verbose_name='Address')
Severity: Major
Found in examples/address_book/schema.py and 1 other location - About 5 hrs to fix
examples/genomics/schema.py on lines 13..26

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 92.

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

class Metabolite(obj_tables.Model):
    id = obj_tables.StringAttribute(primary=True, unique=True)
    name = obj_tables.StringAttribute(none=True, default=None, default_cleaned_value=None)
    formula = obj_tables.chem.ChemicalFormulaAttribute()
Severity: Major
Found in examples/kinetic_metabolic_model/schema.py and 1 other location - About 5 hrs to fix
examples/thermodynamic_metabolic_model/schema.py on lines 38..51

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 88.

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

class Metabolite(obj_tables.Model):
    id = obj_tables.StringAttribute(primary=True, unique=True)
    name = obj_tables.StringAttribute(none=True, default=None, default_cleaned_value=None)
    formula = obj_tables.chem.ChemicalFormulaAttribute()
Severity: Major
Found in examples/thermodynamic_metabolic_model/schema.py and 1 other location - About 5 hrs to fix
examples/kinetic_metabolic_model/schema.py on lines 42..55

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 88.

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 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 3 locations. Consider refactoring.
Open

class SparseMatrix(obj_tables.Model):
    row_i_d = obj_tables.StringAttribute(verbose_name='RowID')
    column_i_d = obj_tables.StringAttribute(verbose_name='ColumnID')
    value = obj_tables.FloatAttribute(verbose_name='Value')
Severity: Major
Found in examples/sbtab/SBtab.py and 2 other locations - About 4 hrs to fix
examples/sbtab/SBtab.py on lines 1016..1029
examples/sbtab/SBtab.py on lines 1100..1113

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 81.

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 Position(obj_tables.Model):
    element = obj_tables.StringAttribute(verbose_name='Element')
    position_x = obj_tables.FloatAttribute(verbose_name='PositionX')
    position_y = obj_tables.FloatAttribute(verbose_name='PositionY')
Severity: Major
Found in examples/sbtab/SBtab.py and 2 other locations - About 4 hrs to fix
examples/sbtab/SBtab.py on lines 1016..1029
examples/sbtab/SBtab.py on lines 1032..1045

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 81.

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 SparseMatrixOrdered(obj_tables.Model):
    row_number = obj_tables.IntegerAttribute(verbose_name='RowNumber')
    column_number = obj_tables.IntegerAttribute(verbose_name='ColumnNumber')
    value = obj_tables.FloatAttribute(verbose_name='Value')
Severity: Major
Found in examples/sbtab/SBtab.py and 2 other locations - About 4 hrs to fix
examples/sbtab/SBtab.py on lines 1032..1045
examples/sbtab/SBtab.py on lines 1100..1113

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 81.

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

class Compartment(obj_tables.Model):
    id = obj_tables.StringAttribute(primary=True, unique=True)
    name = obj_tables.StringAttribute(none=True, default=None, default_cleaned_value=None)

    class Meta(obj_tables.Model.Meta):
Severity: Major
Found in examples/thermodynamic_metabolic_model/schema.py and 1 other location - About 4 hrs to fix
examples/kinetic_metabolic_model/schema.py on lines 28..39

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 76.

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

class Compartment(obj_tables.Model):
    id = obj_tables.StringAttribute(primary=True, unique=True)
    name = obj_tables.StringAttribute(none=True, default=None, default_cleaned_value=None)

    class Meta(obj_tables.Model.Meta):
Severity: Major
Found in examples/kinetic_metabolic_model/schema.py and 1 other location - About 4 hrs to fix
examples/thermodynamic_metabolic_model/schema.py on lines 24..35

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 76.

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 isinstance(ws.cell(2, 1).value, str) and ws.cell(2, 1).value.startswith('!!'):
            ws.cell(2, 1).value = re.sub(r" +id=('((?:[^'\\]|\\.)*)'|\"((?:[^\"\\]|\\.)*)\")", r" class=\1",
                                         ws.cell(2, 1).value)
Severity: Major
Found in migrations/migration_2020_04_27.py and 1 other location - About 3 hrs to fix
migrations/migration_2020_04_27.py on lines 21..23

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 69.

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 isinstance(ws.cell(1, 1).value, str) and ws.cell(1, 1).value.startswith('!!'):
            ws.cell(1, 1).value = re.sub(r" +id=('((?:[^'\\]|\\.)*)'|\"((?:[^\"\\]|\\.)*)\")", r" class=\1",
                                         ws.cell(1, 1).value)
Severity: Major
Found in migrations/migration_2020_04_27.py and 1 other location - About 3 hrs to fix
migrations/migration_2020_04_27.py on lines 25..27

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 69.

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 PbConfig(obj_tables.Model):
    option = obj_tables.StringAttribute(verbose_name='Option')
    value = obj_tables.StringAttribute(verbose_name='Value')

    class Meta(obj_tables.Model.Meta):
Severity: Major
Found in examples/sbtab/SBtab.py and 2 other locations - About 3 hrs to fix
examples/sbtab/SBtab.py on lines 1048..1059
examples/sbtab/SBtab.py on lines 1062..1073

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 67.

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 SparseMatrixColumn(obj_tables.Model):
    column_i_d = obj_tables.StringAttribute(verbose_name='ColumnID')
    column_string = obj_tables.StringAttribute(verbose_name='ColumnString')

    class Meta(obj_tables.Model.Meta):
Severity: Major
Found in examples/sbtab/SBtab.py and 2 other locations - About 3 hrs to fix
examples/sbtab/SBtab.py on lines 862..873
examples/sbtab/SBtab.py on lines 1048..1059

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 67.

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 SparseMatrixRow(obj_tables.Model):
    row_i_d = obj_tables.StringAttribute(verbose_name='RowID')
    row_string = obj_tables.StringAttribute(verbose_name='RowString')

    class Meta(obj_tables.Model.Meta):
Severity: Major
Found in examples/sbtab/SBtab.py and 2 other locations - About 3 hrs to fix
examples/sbtab/SBtab.py on lines 862..873
examples/sbtab/SBtab.py on lines 1062..1073

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 67.

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 default_cleaned_value is not None and \
                (not isinstance(default_cleaned_value, pronto.Term)
                    or default_cleaned_value not in ontology.terms()
                    or (isinstance(terms, list) and default_cleaned_value not in terms)):
            raise ValueError(
Severity: Major
Found in obj_tables/sci/onto.py and 1 other location - About 3 hrs to fix
obj_tables/sci/onto.py on lines 65..69

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 65.

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 default is not None and \
                (not isinstance(default, pronto.Term)
                    or default not in ontology.terms()
                    or (isinstance(terms, list) and default not in terms)):
            raise ValueError(
Severity: Major
Found in obj_tables/sci/onto.py and 1 other location - About 3 hrs to fix
obj_tables/sci/onto.py on lines 71..75

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 65.

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 __init__(self, default=None, none_value=None, verbose_name='', description='',
                 primary=False, unique=False, unique_case_insensitive=False):
        """
        Args:
            default (:obj:`sympy.Expr`, optional): default value
Severity: Major
Found in obj_tables/math/symbolic.py and 1 other location - About 3 hrs to fix
obj_tables/math/symbolic.py on lines 212..224

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 63.

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 Meta:
        label = 'init-schema'
        description = 'Initialize a Python schema from a declarative description of the schema in a table (XLSX, CSV, TSV)'
        help = 'Initialize a Python schema from a declarative description of the schema in a table (XLSX, CSV, TSV)'
        stacked_on = 'base'
Severity: Major
Found in obj_tables/__main__.py and 2 other locations - About 3 hrs to fix
obj_tables/__main__.py on lines 239..248
obj_tables/__main__.py on lines 269..278

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 63.

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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