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CIMAC-CIDC/cidc-schemas

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cidc_schemas/unprism.py

Summary

Maintainability
B
4 hrs
Test Coverage
A
96%

File unprism.py has 290 lines of code (exceeds 250 allowed). Consider refactoring.
Open

"""Tools from extracting information from trial metadata blobs."""
from io import StringIO, BytesIO
from typing import Callable, Dict, List, NamedTuple, Optional, Union

import pandas as pd
Severity: Minor
Found in cidc_schemas/unprism.py - About 2 hrs to fix

    Function _build_artifact has 7 arguments (exceeds 4 allowed). Consider refactoring.
    Open

    def _build_artifact(
    Severity: Major
    Found in cidc_schemas/unprism.py - About 50 mins to fix

      Function _olink_derivation has a Cognitive Complexity of 12 (exceeds 10 allowed). Consider refactoring.
      Open

      def _olink_derivation(context: DeriveFilesContext) -> DeriveFilesResult:
    """Generate a single analysis-ready NPX file across the entire trial for only samples/analytes"""
    olink = context.trial_metadata.get("assays", {}).get("olink", {})

    def download_and_parse_npx(npx_url: str) -> Optional[pd.DataFrame]:
      Severity: Minor
      Found in cidc_schemas/unprism.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"

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