Avoid deeply nested control flow statements.

Open

                    if arg.get("optional", False) and arg.get("multiple", False) is False:
                        args_summary += "?"
                        if arg["type"] in ["NSArg"]:
                            text = f'Zero or one namespace argument of following type(s): {", ".join([val for val in arg["values"]])}'
                        elif arg["type"] == "StrArgNSArg":

Function get_term_completions has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

def get_term_completions(

Avoid deeply nested control flow statements.

Open

                    if arg["type"] in ["Function", "Modifier"]:
                        opt_args.extend(arg.get("values", []))
                    elif arg["type"] in ["StrArgNSArg", "NSArg", "StrArg"]:
                        opt_args.append(arg["type"])

Function ordered_pairs has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

def ordered_pairs(left: List[int], right: List[int]) -> List[Union[int, None]]:
    """Return ordered pairs such that every left, right pair has left < right"""

    alt = {"left": "right", "right": "left"}

• Read up
  Read up

Avoid deeply nested control flow statements.

Open

                    if arg.get("optional", False) and arg.get("multiple", False) is False:
                        args_summary += "?"
                        text = f'Zero or one of each function(s): {", ".join([val for val in arg["values"]])}'
                    elif arg.get("optional", False):
                        args_summary += "*"

Avoid deeply nested control flow statements.

Open

                    if not assertion.get("relation") in counts["assertions"]["relations"]:
                        counts["assertions"]["relations"][assertion.get("relation")] = 1
                    else:
                        counts["assertions"]["relations"][assertion.get("relation")] += 1

Function get_term_completions has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

def get_term_completions(

Function __init__ has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def __init__(

Function subcomponents has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def subcomponents(self, subcomponents=None):
        """Generate subcomponents of the BEL subject or object

        Args:
            AST

• Read up
  Read up

Function load_resource has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

def load_resource(resource_url: str = None, force: bool = False):
    """Load BEL Resource file

    Forceupdate will create a new index in Elasticsearch regardless of whether
    an index with the resource version already exists.

• Read up
  Read up

Avoid deeply nested control flow statements.

Open

                    if re.match("\s*\(", assertion["object"]):
                        counts["assertions"]["nested"] += 1

Avoid deeply nested control flow statements.

Open

                    if arg["type"] in ["Function", "Modifier"]:
                        mult_args.extend(arg.get("values", []))
                    elif arg["type"] in ["NSArg"]:
                        # Complex and Composite signature has this
                        mult_args.extend(arg.get("values", []))

Function get_term_search has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

def get_term_search(search_term, size, entity_types, annotation_types, species, namespaces):

Avoid deeply nested control flow statements.

Open

                    if arg["type"] in ["Function", "Modifier"]:
                        pos_args.append(arg.get("values", []))
                    elif arg["type"] in ["StrArgNSArg", "NSArg", "StrArg"]:
                        pos_args.append(arg["type"])

Function set_single_line has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

def set_single_line(lines):

    flag = False
    hold = ""

• Read up
  Read up

Avoid deeply nested control flow statements.

Open

                    if arg["type"] in ["Function", "Modifier"]:
                        req_args.append(arg.get("values", []))
                    elif arg["type"] in ["StrArgNSArg", "NSArg", "StrArg"]:
                        req_args.append(arg["type"])

Function collect_orthologs has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def collect_orthologs(self, species_keys: List[Key] = settings.BEL_ORTHOLOGIZE_TARGETS):
        """Get orthologs for BelEntity is orthologizable"""

        self.add_entity_types()
        self.normalize()

• Read up
  Read up

Consider simplifying this complex logical expression.

Open

        if fn_arg.type == "Function" and fn_arg.name not in opt_and_mult_args:
            errors.append(
                ValidationError(
                    type="Assertion",
                    severity="Error",

Consider simplifying this complex logical expression.

Open

        if self.subject or self.relation or self.object:
            if self.relation and not self.object:
                msg = "Missing Assertion Object"
                self.errors.append(ValidationError(type="Assertion", severity="Error", msg=msg))
            elif self.object and (not self.subject or not self.relation):

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

Open

    def __init__(