mandos.search.chembl.atc_search

Complexity

Total Complexity

6

Size/Duplication

Total Lines	78
Duplicated Lines	0 %

Importance

Changes

0

4 Methods

Rating	Name	Duplication	Size	Complexity
A	AtcSearch._code()	0	11	1
A	AtcSearch.find()	0	18	3
A	AtcSearch.process()	0	13	1
A	AtcHit.predicate()	0	3	1

from __future__ import annotations

Missing module docstring

import logging
from dataclasses import dataclass
from typing import Sequence

from pocketutils.core.dot_dict import NestedDotDict

Unable to import 'pocketutils.core.dot_dict'

from mandos.model import AbstractHit, ChemblCompound, Search

logger = logging.getLogger("mandos")


@dataclass(frozen=True, order=True, repr=True)
class AtcHit(AbstractHit):
    """
    An ATC code found for a compound.
    """

    level: int

    @property
    def predicate(self) -> str:
        return f"has ATC L-{self.level} code"


class AtcSearch(Search[AtcHit]):

Empty class docstring

Value 'Search' is unsubscriptable

    """"""

    def find(self, lookup: str) -> Sequence[AtcHit]:
        """

        Args:
            lookup:

        Returns:

        """
        # 'atc_classifications': ['S01HA01', 'N01BC01', 'R02AD03', 'S02DA02']
        # 'indication_class': 'Anesthetic (topical)'
        ch = self.get_compound_dot_dict(lookup)

Variable name "ch" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        compound = self.compound_dot_dict_to_obj(ch)
        hits = []
        if "atc_classifications" in ch:
            for atc in ch["atc_classifications"]:
                hits.extend(self.process(lookup, compound, atc))
        return hits

    def process(self, lookup: str, compound: ChemblCompound, atc: str) -> Sequence[AtcHit]:
        """

        Args:
            lookup:
            compound:
            atc:

        Returns:

        """
        dots = NestedDotDict(self.api.atc_class.get(atc))
        return [self._code(lookup, compound, dots, 3), self._code(lookup, compound, dots, 4)]

    def _code(self, lookup: str, compound: ChemblCompound, dots: NestedDotDict, level: int):

This method could be written as a function/class method.

        # 'level1': 'N', 'level1_description': 'NERVOUS SYSTEM', 'level2': 'N05', ...
        return AtcHit(
            None,
            compound.chid,
            compound.inchikey,
            lookup,
            compound.name,
            object_id=dots.get(f"level{level}"),
            object_name=dots.get(f"level{level}_description"),
            level=level,
        )


__all__ = ["AtcHit", "AtcSearch"]