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kg_covid_19/transform_utils/sars_cov_2_gene_annot/sars_cov_2_gene_annot.py

Summary

Maintainability
B
6 hrs
Test Coverage
D
66%

File sars_cov_2_gene_annot.py has 258 lines of code (exceeds 250 allowed). Consider refactoring.
Open

"""Transform for SARS-CoV-2 gene annotation data."""

import logging
import os
from typing import Generator, List, Optional, TextIO
Severity: Minor
Found in kg_covid_19/transform_utils/sars_cov_2_gene_annot/sars_cov_2_gene_annot.py - About 2 hrs to fix

    Function gpi_to_gene_node_data has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.
    Open

        def gpi_to_gene_node_data(self, rec: dict) -> list:
        """Return node that can be passed to write_node_edge_item().

        Uses a parsed gpi entry.
        :param rec: record from gpi iterator
    Severity: Minor
    Found in kg_covid_19/transform_utils/sars_cov_2_gene_annot/sars_cov_2_gene_annot.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 _gpi12iterator has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
    Open

    def _gpi12iterator(handle: TextIO) -> Generator:
    # Partly cribbed from Biopython GPI 1.1 parser
    # There is no GPI 1.2 parser yet, so I made this
    """Read GPI 1.2 format files (PRIVATE).
    Severity: Minor
    Found in kg_covid_19/transform_utils/sars_cov_2_gene_annot/sars_cov_2_gene_annot.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 gpa_to_edge_data has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
    Open

        def gpa_to_edge_data(self, rec: dict) -> list:
        """Return an edge with annotations given a parsed gpa entry.

        :param rec: record from gpa iterator
        :return:
    Severity: Minor
    Found in kg_covid_19/transform_utils/sars_cov_2_gene_annot/sars_cov_2_gene_annot.py - About 45 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 run has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
    Open

        def run(self, data_file: Optional[str] = None):
        """Run the transform."""
        # file housekeeping
        os.makedirs(self.output_dir, exist_ok=True)
    Severity: Minor
    Found in kg_covid_19/transform_utils/sars_cov_2_gene_annot/sars_cov_2_gene_annot.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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