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Showing 111 of 113 total issues

Function find_functions has 5 arguments (exceeds 4 allowed). Consider refactoring.
Open

def find_functions(
Severity: Minor
Found in bel/lang/parse.py - About 35 mins to fix

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

        def normalize(
        self,
        canonical_targets: Mapping[str, List[str]] = settings.BEL_CANONICALIZE,
        decanonical_targets: Mapping[str, List[str]] = settings.BEL_DECANONICALIZE,
    ):
    Severity: Minor
    Found in bel/schemas/bel.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 add_term has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
    Open

        def add_term(self):
        """Add term info"""

        if self.namespace_metadata and self.namespace_metadata.namespace_type == "complete":
            self.term = bel.terms.terms.get_term(self.nsval.key)
    Severity: Minor
    Found in bel/schemas/bel.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 update_index_state has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
    Open

    def update_index_state(collection, desired_indexes: List[IndexDefinition]):
    """Update index state

    desired_indexes keys = f"{index_type}_{'_'.join(sorted(fields))}", e.g. persistent_firstname_lastname
    Severity: Minor
    Found in bel/db/arangodb.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 html_wrap_span has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
    Open

    def html_wrap_span(
    string: str, pairs: List[Tuple[int, int]], css_class: Optional[str] = "accentuate"
) -> str:
    """Wrap targeted area of Assertion with html highlighting
    Severity: Minor
    Found in bel/core/utils.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 decanonicalize has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
    Open

        def decanonicalize(
        self,
        canonical_targets: Mapping[str, List[str]] = settings.BEL_CANONICALIZE,
        decanonical_targets: Mapping[str, List[str]] = settings.BEL_DECANONICALIZE,
    ):
    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 preprocess_belscript has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
    Open

    def preprocess_belscript(lines):
    """ Convert any multi-line SET statements into single line SET statements"""

    set_flag = False
    for line in lines:
    Severity: Minor
    Found in bel/nanopub/belscripts.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 migrate_ast has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
    Open

    def migrate_ast(ast: BELAst) -> BELAst:

    # Process Subject
    bo.ast.subject = convert(bo.ast.subject)
    Severity: Minor
    Found in bel/lang/migrate_1_2.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 intersect has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
    Open

    def intersect(pos: int, spans: List[Optional[Span]]) -> bool:
    """Check to see if pos intersects the provided spans - e.g. quotes"""

    if spans:
        for span in spans:
    Severity: Minor
    Found in bel/lang/parse.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,
    ):
    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_species_keys has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
    Open

        def get_species_keys(self, species_keys: List[str] = None):
        """Collect species associated with NSArgs

        Can have multiple species related to single Assertion
        """
    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 parse_book_record has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
    Open

    def parse_book_record(doc: dict, root) -> dict:
    """Parse Pubmed Book entry"""

    doc["title"] = next(iter(root.xpath("//BookTitle/text()")))
    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_cached_assertion_validations has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
    Open

    def get_cached_assertion_validations(assertions, validation_level):
    """ Collect cached validations for assertions"""

    # Get hash keys for missing validations
    hashes = []
    Severity: Minor
    Found in bel/nanopub/validate.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 decanonicalize has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
    Open

        def decanonicalize(
        self,
        canonical_targets: Mapping[str, List[str]] = settings.BEL_CANONICALIZE,
        decanonical_targets: Mapping[str, List[str]] = settings.BEL_DECANONICALIZE,
    ):
    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 canonicalize has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
    Open

        def canonicalize(
        self,
        canonical_targets: Mapping[str, List[str]] = settings.BEL_CANONICALIZE,
        decanonical_targets: Mapping[str, List[str]] = settings.BEL_DECANONICALIZE,
    ):
    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_cached_annotation_validations has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
    Open

    def get_cached_annotation_validations(annotations):
    """ Collect cached validations for annotations"""

    # Get hash keys for missing validations
    hashes = []
    Severity: Minor
    Found in bel/nanopub/validate.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 convert_fus has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
    Open

    def convert_fus(ast):
    """Convert BEL1 fus() to BEL2 fus()"""

    parent_fn_name = ast.name_short
    prefix_list = {"p": "p.", "r": "r.", "g": "c."}
    Severity: Minor
    Found in bel/lang/migrate_1_2.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 canonicalize has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
    Open

        def canonicalize(
        self,
        canonical_targets: Mapping[str, List[str]] = settings.BEL_CANONICALIZE,
        decanonical_targets: Mapping[str, List[str]] = settings.BEL_DECANONICALIZE,
    ):
    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_terms has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
    Open

    def get_terms(term_key: Key) -> List[Term]:
    """Get term(s) using term_key - given term_key may match multiple term records

    Term Key can match the main key, alt_keys or obsolete_keys
    """
    Severity: Minor
    Found in bel/terms/terms.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_species_keys has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
    Open

        def get_species_keys(self, species_keys: List[str] = None):
        """Collect species associated with NSArgs

        Can have multiple species related to single Assertion
        """
    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

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