mandos.search.pubchem.acute_effects_search

Complexity

Total Complexity

10

Size/Duplication

Total Lines	101
Duplicated Lines	0 %

Importance

Changes

0

5 Methods

Rating	Name	Duplication	Size	Complexity
A	AcuteEffectSearch.find()	0	28	4
A	Ld50Search.data_source()	0	3	1
A	Ld50Search.find()	0	24	3
A	AcuteEffectSearch.data_source()	0	3	1
A	AcuteEffectSearch.__init__()	0	3	1

from dataclasses import dataclass

Missing module docstring

from typing import Sequence, Optional

Unused Optional imported from typing

from mandos.model.pubchem_api import PubchemApi
from mandos.search.pubchem import PubchemHit, PubchemSearch


@dataclass(frozen=True, order=True, repr=True)

Empty class docstring

class AcuteEffectHit(PubchemHit):
    """"""

    organism: str
    human: bool
    test_type: str
    route: str
    effect: str
    mg_per_kg: float


@dataclass(frozen=True, order=True, repr=True)

Empty class docstring

class Ld50Hit(PubchemHit):
    """"""

    organism: str
    human: bool


class AcuteEffectSearch(PubchemSearch[AcuteEffectHit]):

Empty class docstring

    """"""

    def __init__(self, key: str, api: PubchemApi, top_level: bool):
        super().__init__(key, api)
        self.top_level = top_level

    @property
    def data_source(self) -> str:

Missing function or method docstring

        return "ChemIDplus"

    def find(self, inchikey: str) -> Sequence[AcuteEffectHit]:

Missing function or method docstring

        data = self.api.fetch_data(inchikey)
        results = []
        for dd in data.toxicity.acute_effects:

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

            for effect in dd.effects:
                effect_name = effect.category.lower() if self.top_level else effect.lower()
                results.append(
                    AcuteEffectHit(
                        record_id=str(dd.gid),
                        origin_inchikey=inchikey,
                        matched_inchikey=data.names_and_identifiers.inchikey,
                        compound_id=str(data.cid),
                        compound_name=data.name,
                        predicate="causes acute effect",
                        object_id=effect_name,
                        object_name=effect_name,
                        search_key=self.key,
                        search_class=self.search_class,
                        data_source=self.data_source,
                        effect=effect.lower(),
                        organism=dd.organism,
                        human=dd.organism.is_human,
                        route=dd.route,
                        mg_per_kg=dd.mg_per_kg,
                        test_type=dd.test_type,
                    )
                )
        return results


class Ld50Search(PubchemSearch[Ld50Hit]):

Missing class docstring

    @property
    def data_source(self) -> str:

Missing function or method docstring

        return "ChemIDplus"

    def find(self, inchikey: str) -> Sequence[Ld50Hit]:

Missing function or method docstring

        data = self.api.fetch_data(inchikey)
        results = []
        for dd in data.toxicity.acute_effects:

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

            if dd.test_type != "LD50":
                continue
            results.append(
                Ld50Hit(
                    record_id=str(dd.gid),
                    origin_inchikey=inchikey,
                    matched_inchikey=data.names_and_identifiers.inchikey,
                    compound_id=str(data.cid),
                    compound_name=data.name,
                    predicate="has LD50 for " + dd.organism,
                    object_id=str(dd.mg_per_kg),
                    object_name=str(dd.mg_per_kg),
                    search_key=self.key,
                    search_class=self.search_class,
                    data_source=self.data_source,
                    organism=dd.organism,
                    human=dd.organism.is_human,
                )
            )
        return results


__all__ = ["AcuteEffectHit", "AcuteEffectSearch", "Ld50Hit", "Ld50Search"]