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

def get_pubtator(pmid):
    """Get Pubtator Bioconcepts from Pubmed Abstract

    Re-configure the denotations into an annotation dictionary format
    and collapse duplicate terms so that their spans are in a list.
Severity: Minor
Found in bel/nanopub/pubmed.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

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

    def get_orthologs(
        self, orthologs: List[dict] = None, orthologize_targets_keys: List[Key] = None
    ):
        """Collect orthologs associated with NSArgs"""
Severity: Minor
Found in bel/lang/ast.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

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

def get_term(term_key: Key) -> Optional[Term]:
    """Expect one term to match term_key

    Term Key can match the main key, alt_keys or obsolete_keys
    """
Severity: Minor
Found in bel/terms/terms.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 __init__ has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def __init__(self, term_key: Key = "", nsval: Optional[NsVal] = None):
        """Create BelEntity via a term_key or a NsVal object

        You cannot provide a term_key_label string (e.g. NS:ID:LABEL) as a term_key
        """
Severity: Minor
Found in bel/schemas/bel.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 process_set has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

def process_set(line, annotations):
    """Convert annotations into nanopub_bel annotations format"""

    matches = re.match('SET\s+(\w+)\s*=\s*"?(.*?)"?\s*$', line)
Severity: Minor
Found in bel/nanopub/belscripts.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 validate has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def validate(self):
        """Validate BEL Assertion"""

        # Process AST top-level args or Function args
        if hasattr(self, "args"):
Severity: Minor
Found in bel/lang/ast.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 to_string has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def to_string(self, fmt: str = "medium") -> str:
        """Convert AST object to string

        Args:
            fmt (str): short, medium, long formatted BEL statements
Severity: Minor
Found in bel/lang/ast.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 add_namespaces has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

def add_namespaces(specification):
    """Add namespace convenience keys, list, list_{short|long}, to_{short|long}"""

    for ns in specification["namespaces"]:
        specification["namespaces"][ns]["list"] = []
Severity: Minor
Found in bel/belspec/enhance.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 add_entity_types has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def add_entity_types(self):
        """get entity_types to BEL Entity"""

        if self.entity_types:
            return self
Severity: Minor
Found in bel/schemas/bel.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_term_search has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

def get_term_search(search_term, size, entity_types, annotation_types, species, namespaces):
    """Search for terms given search term"""

    if not size:
        size = 10
Severity: Minor
Found in bel/terms/terms.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 orthologize has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def orthologize(self, species_key: Key):
        """Orthologize any orthologizable element

        Run orthologizable() method first to confirm that entire Assertion is
        orthologizable.
Severity: Minor
Found in bel/lang/ast.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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