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

    def get_subseq(self, start, end, strand=PolymerStrand.positive):
        """ Get a subsequence

        Args:
            start (:obj:`int`): start coordinate (1-indexed)
Severity: Minor
Found in wc_kb/core.py - About 35 mins to fix

Cognitive Complexity

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

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

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

Further reading

Similar blocks of code found in 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

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

    type = obj_tables.sci.onto.OntoTermAttribute(kbOnt,
                                  terms=kbOnt['WC:RNA'].subclasses(),
Severity: Minor
Found in wc_kb/prokaryote.py and 2 other locations - About 30 mins to fix
wc_kb/prokaryote.py on lines 153..154
wc_kb/prokaryote.py on lines 329..330

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

Avoid too many return statements within this function.
Open

            return float(self.value)
Severity: Major
Found in wc_kb/core.py - About 30 mins to fix

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

        type = obj_tables.sci.onto.OntoTermAttribute(kbOnt,
                                  terms = kbOnt['WC:protein'].subclasses(),
    Severity: Minor
    Found in wc_kb/prokaryote.py and 2 other locations - About 30 mins to fix
    wc_kb/prokaryote.py on lines 40..41
    wc_kb/prokaryote.py on lines 329..330

    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 3 locations. Consider refactoring.
    Open

        cog = obj_tables.sci.onto.OntoTermAttribute(kbOnt,
                                  terms = kbOnt['WC:COG'].subclasses(),
    Severity: Minor
    Found in wc_kb/prokaryote.py and 2 other locations - About 30 mins to fix
    wc_kb/prokaryote.py on lines 40..41
    wc_kb/prokaryote.py on lines 153..154

    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

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

        def _default(self):
        args = self.app.pargs

        if args.compare_files:
            kb1 = wc_utils.workbook.io.read(args.core_path_1)
    Severity: Minor
    Found in wc_kb/__main__.py - About 25 mins to fix

    Cognitive Complexity

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

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

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

    Further reading

    Function 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

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

        def get_value(self):
        """ SpeciesType property values are stored as strings, this function returns the value as the correct type. """

        if self.value == '':
            return None
    Severity: Minor
    Found in wc_kb/core.py - About 25 mins to fix

    Cognitive Complexity

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

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

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

    Further reading

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

        def _parse_EviNExperiment(self, metadataObjs):
        if hasattr(self, 'evidence'):
            for evidence in self.evidence:
                metadataObjs = evidence._append_metadata_entries(key=Evidence, metadataObjs=metadataObjs)
                if evidence.experiment is not None:
    Severity: Minor
    Found in wc_kb/core.py - About 25 mins to fix

    Cognitive Complexity

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

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

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

    Further reading

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

        def gen_id(species_type, compartment):
        """ Generate a Species' primary identifier

        Args:
            species_type (:obj:`object`): a `SpeciesType`, or its id
    Severity: Minor
    Found in wc_kb/core.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

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