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Function process_definition has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
Open

def process_definition(line, nanopubs_metadata):
    """Process DEFINE line in BEL script"""

    matches = re.match('DEFINE\s+(\w+)\s+(\w+)\s+AS\s+URL\s+"(.*?)"\s*$', line)
    if matches:
Severity: Minor
Found in bel/nanopub/belscripts.py - About 1 hr 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_annotations has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
Open

def add_annotations(pubmed):
    """Add nanopub annotations to pubmed doc

    Enhance MESH terms etc as full-fledged nanopub annotations for use by the BEL Nanopub editor
    """
Severity: Minor
Found in bel/nanopub/pubmed.py - About 1 hr 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_bel_handles has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
Open

def get_bel_handles(client, username=None, password=None):
    """Get BEL API arango db handle"""

    (username, password) = get_user_credentials(username, password)
Severity: Minor
Found in bel/db/arangodb.py - About 1 hr 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 load_terms has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
Open

def load_terms(
    f: IO, metadata: dict, force: bool = False, resource_download_url: Optional[str] = None
):
    """Load terms into Elasticsearch and ArangoDB
Severity: Minor
Found in bel/resources/namespace.py - About 1 hr 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 orthologizable has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
Open

    def orthologizable(self, species_key: Key) -> Optional[bool]:
        """Is this Assertion fully orthologizable?

        Is it possible to orthologize every gene/protein/RNA NSArg to the target species?
        """
Severity: Minor
Found in bel/lang/ast.py - About 1 hr 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_journal_article_record has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
Open

def parse_journal_article_record(doc: dict, root) -> dict:
    """Parse Pubmed Journal Article record"""

    doc["title"] = next(iter(root.xpath("//ArticleTitle/text()")), "")
Severity: Minor
Found in bel/nanopub/pubmed.py - About 1 hr 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 orthologizable has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
Open

    def orthologizable(self, species_key: Key):
        """Is this Assertion fully orthologizable?

        This method will detect if the orthologization will result
        in a partially orthologized Assertion.
Severity: Minor
Found in bel/lang/ast.py - About 1 hr 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 find_functions has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
Open

def find_functions(
    assertion_str: str,
    matched_quotes: List[Pair],
    matched_parens: List[Pair],
    errors: List[ValidationError],
Severity: Minor
Found in bel/lang/parse.py - About 1 hr 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 find_matching_parens has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
Open

def find_matching_parens(
    assertion_str, matched_quotes, errors: List[ValidationError]
) -> Tuple[List[Pair], List[ValidationError]]:
    """Find and return the location of the matching parentheses pairs in s.
Severity: Minor
Found in bel/lang/parse.py - About 1 hr 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_assertion has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

def validate_assertion(assertion_obj: AssertionStr, *, version: str = "latest"):
    """ Validate single assertion """

    bo = bel.lang.belobj.BEL(assertion_obj, version=version)
Severity: Minor
Found in bel/nanopub/validate.py - About 1 hr 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_citation has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

def process_citation(citation_str: str) -> dict:
    """Parse BEL Script Citation string into nanopub_bel citation object"""

    citation_obj = {}
Severity: Minor
Found in bel/nanopub/belscripts.py - About 1 hr 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_pub_date has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

def process_pub_date(year, mon, day, medline_date):
    """Create pub_date from what Pubmed provides in Journal PubDate entry"""

    if medline_date:
        year = "0000"
Severity: Minor
Found in bel/nanopub/pubmed.py - About 1 hr 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_belscript has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

def convert_belscript(ctx, input_fn, output_fn):
    """Convert belscript to nanopubs_bel format

    This will convert the OpenBEL BELScript file format to
    nanopub_bel-1.0.0 format.
Severity: Minor
Found in bel/cli/scripts.py - About 1 hr 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 find_matching_quotes has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

def find_matching_quotes(
    assertion_str: str, errors: List[ValidationError]
) -> Tuple[List[Pair], List[ValidationError]]:
    """Find matching quotes using BEL Assertion syntax"""
Severity: Minor
Found in bel/lang/parse.py - About 1 hr 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_unset has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

def process_unset(line, annotations):
    """Process UNSET lines in BEL Script"""

    matches = re.match('UNSET\s+"?(.*?)"?\s*$', line)
    if matches:
Severity: Minor
Found in bel/nanopub/belscripts.py - About 1 hr 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 check_str_arg has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

def check_str_arg(value: str, check_values: List[str]) -> Optional[str]:
    """Check StrArg value"""

    regex_flag = False
    for check_value in check_values:
Severity: Minor
Found in bel/lang/ast.py - About 55 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 subcomponents has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

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

        Args:
            AST
Severity: Minor
Found in bel/lang/ast.py - About 55 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 yield_nanopub has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

def yield_nanopub(assertions, annotations, line_num):
    """Yield nanopub object"""

    if not assertions:
        return {}
Severity: Minor
Found in bel/nanopub/belscripts.py - About 55 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_assertions has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

def validate_assertions(
    assertions: List[dict], *, version: str = "latest", validation_level: str = "complete"
):
    """Validate assertions
Severity: Minor
Found in bel/nanopub/validate.py - About 55 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 create_nanopubs_fh has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

def create_nanopubs_fh(output_fn: str):
    """Create Nanopubs output filehandle

    \b
    If output fn is '-' will write JSONlines to STDOUT
Severity: Minor
Found in bel/nanopub/files.py - About 55 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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