mandos.search.pubchem.pubchem_searches

Complexity

Total Complexity

9

Size/Duplication

Total Lines	110
Duplicated Lines	0 %

Importance

Changes

0

5 Methods

Rating	Name	Duplication	Size	Complexity
B	PubchemSearchFactory.cat()	0	40	5
A	PubchemSearch.__init__()	0	3	1
A	PubchemClassHit.predicate()	0	3	1
A	PubchemSearch.find()	0	3	1
A	PubchemSearch.process()	0	2	1

from __future__ import annotations

Missing module docstring

import abc
import enum

The import enum seems to be unused.

import logging

The import logging seems to be unused.

import re
from dataclasses import dataclass
from typing import Sequence, Type, Union, FrozenSet, Optional, TypeVar, Any

Unused Union imported from typing

Unused FrozenSet imported from typing

Unused Any imported from typing

from pocketutils.core.dot_dict import NestedDotDict

Unable to import 'pocketutils.core.dot_dict'

Unused NestedDotDict imported from pocketutils.core.dot_dict

from mandos.model import AbstractHit, Search
from mandos.chembl_api import ChemblApi
from mandos.model.settings import Settings
from mandos.model.taxonomy import Taxonomy
from mandos.pubchem_api import (

The name TitleAndSummary does not seem to exist in module mandos.pubchem_api.

The name RelatedRecords does not seem to exist in module mandos.pubchem_api.

The name ChemicalAndPhysicalProperties does not seem to exist in module mandos.pubchem_api.

The name DrugAndMedicationInformation does not seem to exist in module mandos.pubchem_api.

The name PharmacologyAndBiochemistry does not seem to exist in module mandos.pubchem_api.

The name SafetyAndHazards does not seem to exist in module mandos.pubchem_api.

The name Toxicity does not seem to exist in module mandos.pubchem_api.

The name AssociatedDisordersAndDiseases does not seem to exist in module mandos.pubchem_api.

The name Literature does not seem to exist in module mandos.pubchem_api.

The name BiomolecularInteractionsAndPathways does not seem to exist in module mandos.pubchem_api.

The name Classification does not seem to exist in module mandos.pubchem_api.

Unused TitleAndSummary imported from mandos.pubchem_api

Unused RelatedRecords imported from mandos.pubchem_api

Unused ChemicalAndPhysicalProperties imported from mandos.pubchem_api

Unused PharmacologyAndBiochemistry imported from mandos.pubchem_api

Unused SafetyAndHazards imported from mandos.pubchem_api

Unused Toxicity imported from mandos.pubchem_api

Unused AssociatedDisordersAndDiseases imported from mandos.pubchem_api

Unused Literature imported from mandos.pubchem_api

Unused BiomolecularInteractionsAndPathways imported from mandos.pubchem_api

Unused Classification imported from mandos.pubchem_api

    CachingPubchemApi,
    QueryingPubchemApi,
    PubchemData,
    TitleAndSummary,
    RelatedRecords,
    ChemicalAndPhysicalProperties,
    DrugAndMedicationInformation,
    PharmacologyAndBiochemistry,
    SafetyAndHazards,
    Toxicity,
    AssociatedDisordersAndDiseases,
    Literature,
    BiomolecularInteractionsAndPathways,
    Classification,
)


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

Missing class docstring

class PubchemClassHit(AbstractHit):
    @property
    def predicate(self) -> str:
        return "is in"


H = TypeVar("H", bound=AbstractHit, covariant=True)

Class name "H" doesn't conform to PascalCase naming style ('[^\\W\\da-z][^\\W_]+$' pattern)

class PubchemSearch(Search[H], metaclass=abc.ABCMeta):

Missing class docstring

    def __init__(self, chembl_api: ChemblApi, config: Settings, tax: Taxonomy):
        super().__init__(chembl_api, config, tax)
        self.pubchem_api = CachingPubchemApi(config.cache_path, QueryingPubchemApi(), compress=True)

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

Missing function or method docstring

        data = self.pubchem_api.fetch_data(lookup)
        return self.process(lookup, data)

    def process(self, lookup: str, data: PubchemData) -> Sequence[H]:

Missing function or method docstring

        raise NotImplementedError()


class PubchemSearchFactory:

Missing class docstring

    pattern = re.compile(r"(?<!^)(?=[A-Z])")

    @classmethod
    def cat(

Missing function or method docstring

        cls, full_field, name: Optional[str] = None, object_field: Optional[str] = None

Wrong hanging indentation before block (add 4 spaces).

    ) -> Type[PubchemSearch]:
        clazz_name, field_name = str(full_field).split(" ", 3)[-2].split(".")
        clazz_name = PubchemSearchFactory.pattern.sub("_", clazz_name.__name__).lower()
        if name is None:
            name = field_name.replace("_", " ")

        class MyClassSearch(PubchemSearch[PubchemClassHit]):

Missing class docstring

            def process(self, lookup: str, data: PubchemData) -> Sequence[PubchemClassHit]:

Missing function or method docstring

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

                values = getattr(getattr(data, clazz_name), field_name)
                if object_field is not None:
                    values = frozenset([getattr(x, object_field) for x in values])
                if not isinstance(values, frozenset):
                    values = frozenset({values})
                hits = []
                for value in values:
                    """
                    record_id: Optional[str]
                    compound_id: str
                    inchikey: str
                    compound_lookup: str
                    compound_name: str
                    object_id: str
                    object_name: str
                    """

This string statement has no effect and could be removed.

                    hit = PubchemClassHit(

The variable hit seems to be unused.

                        record_id=None,
                        compound_id=str(data.cid),
                        inchikey=data.chemical_and_physical_properties.inchikey,
                        compound_lookup=lookup,
                        compound_name=data.name,
                        object_id=str(value),
                        object_name=str(value),
                    )
                return hits

        MyClassSearch.__name__ = name
        return MyClassSearch


F = PubchemSearchFactory

Class name "F" doesn't conform to PascalCase naming style ('[^\\W\\da-z][^\\W_]+$' pattern)

P = PubchemData

Class name "P" doesn't conform to PascalCase naming style ('[^\\W\\da-z][^\\W_]+$' pattern)

DeaClassSearch = F.cat(DrugAndMedicationInformation.dea_class)
DeaScheduleSearch = F.cat(DrugAndMedicationInformation.dea_schedule)
HsdbUsesSearch = F.cat(DrugAndMedicationInformation.hsdb_uses)
ClinicalTrialsSearch = F.cat(DrugAndMedicationInformation.clinical_trials)