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dmyersturnbull/mandos

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mandos/model/apis/querying_pubchem_api.py

Summary

Maintainability
C
7 hrs
Test Coverage

File querying_pubchem_api.py has 326 lines of code (exceeds 250 allowed). Consider refactoring.
Open

"""
PubChem querying API.
"""
from __future__ import annotations
Severity: Minor
Found in mandos/model/apis/querying_pubchem_api.py - About 3 hrs to fix

    Function _strip_by_key_in_place has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
    Open

        def _strip_by_key_in_place(self, data: Union[dict, list], bad_key: str) -> None:
        if isinstance(data, list):
            for x in data:
                self._strip_by_key_in_place(x, bad_key)
        elif isinstance(data, dict):
    Severity: Minor
    Found in mandos/model/apis/querying_pubchem_api.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_metadata has 6 arguments (exceeds 4 allowed). Consider refactoring.
    Open

        def _get_metadata(
    Severity: Minor
    Found in mandos/model/apis/querying_pubchem_api.py - About 45 mins to fix

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

          def __init__(
      Severity: Minor
      Found in mandos/model/apis/querying_pubchem_api.py - About 35 mins to fix

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

            def fetch_properties(self, cid: int) -> Mapping[str, Any]:
        url = f"{self._pug}/compound/cid/{cid}/JSON"
        #
        try:
            matches: NestedDotDict = self._query_json(url)
        Severity: Minor
        Found in mandos/model/apis/querying_pubchem_api.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 _scrape_cid has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
        Open

            def _scrape_cid(self, inchikey: str) -> int:
        # This is awful
        # Every attempt to get the actual, correct, unique CID corresponding to the inchikey
        # failed with every proper PubChem API
        # We can't use <pug_view>/data/compound/<inchikey> -- we can only use a CID there
        Severity: Minor
        Found in mandos/model/apis/querying_pubchem_api.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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