mandos.search.chembl.indication_search

Complexity

Total Complexity

5

Size/Duplication

Total Lines	76
Duplicated Lines	0 %

Importance

Changes

0

3 Methods

Rating	Name	Duplication	Size	Complexity
A	IndicationHit.predicate()	0	3	1
A	IndicationSearch.find()	0	19	3
A	IndicationSearch.process()	0	22	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 IndicationHit(AbstractHit):
    """
    An indication with a MESH term.
    """

    max_phase: int

    @property
    def predicate(self) -> str:
        return f"phase-{self.max_phase} indication"


class IndicationSearch(Search[IndicationHit]):

Empty class docstring

Value 'Search' is unsubscriptable

    """"""

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

        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)
        inds = self.api.drug_indication.filter(parent_molecule_chembl_id=compound.chid)
        hits = []
        for ind in inds:
            if ind.req_as("max_phase_for_ind", int) >= self.config.min_phase:
                hits.append(self.process(lookup, compound, ind))
        return hits

    def process(

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

        self, lookup: str, compound: ChemblCompound, indication: NestedDotDict

Wrong hanging indentation before block (add 4 spaces).

    ) -> IndicationHit:
        """

        Args:
            lookup:
            compound:
            indication:

        Returns:

        """
        return IndicationHit(
            indication.req_as("drugind_id", str),
            compound.chid,
            compound.inchikey,
            lookup,
            compound.name,
            object_id=indication.req_as("mesh_id", str),
            object_name=indication.req_as("mesh_heading", str).strip("\n"),
            max_phase=indication.req_as("max_phase_for_ind", int),
        )


__all__ = ["IndicationHit", "IndicationSearch"]