mandos.entries.entries

Complexity

Total Complexity

45

Size/Duplication

Total Lines	1194
Duplicated Lines	50.17 %

Importance

Changes

0

41 Methods

Rating	Name	Duplication	Size	Complexity
A	EntryTransporterGeneralFunction.run()	27	27	1
A	EntryPubchemChemicalCoOccurrence.run()	35	35	1
A	EntryPubchemAssay.run()	0	30	1
B	EntryGoProcess.run()	45	45	1
A	_EntryPubchemCoOccurrence.get_cooccurrence_type()	0	4	1
A	EntryChemblBinding.run()	0	46	1
A	EntryChemblMechanism.run()	33	33	1
A	EntryDrugbankDosage.run()	0	14	1
A	EntryHmdbComputed.run()	0	24	1
A	EntryHmdbTissue.run()	4	22	1
A	EntryG2pInteractions.run()	26	24	1
A	EntryPubchemComputed.run()	0	34	1
A	EntryDeaClass.run()	0	19	1
A	EntryDrugbankTransporter.run()	27	27	1
A	EntryGoFunction.go_type()	3	3	1
A	EntryPubchemDisease.run()	23	23	1
A	EntryDrugbankDdi.run()	25	25	1
A	EntryGeneralFunction.run()	22	22	1
A	ChemblQsarPredictions.run()	38	38	1
A	EntryChemblAtc.run()	0	23	1
A	EntryGoComponent.go_type()	3	3	1
B	EntryGoComponent.run()	45	45	1
A	EntryMetaRandom.run()	0	21	1
A	_EntryPubchemCoOccurrence.cmd()	0	4	1
A	EntryDeaSchedule.run()	0	19	1
A	_EntryChemblGo.go_type()	0	3	1
A	EntryGoProcess.go_type()	3	3	1
A	EntryDrugbankMetabolites.run()	0	14	1
B	EntryGoFunction.run()	45	45	1
B	_EntryChemblGo.run()	0	48	5
A	EntryPubchemGeneCoOccurrence.run()	35	35	1
A	_EntryChemblGo.cmd()	0	4	1
A	EntryPubchemCgi.run()	25	25	1
A	EntryPubchemDgi.run()	25	25	1
A	_EntryPubchemCoOccurrence.run()	0	19	1
A	EntryDrugbankTarget.run()	22	22	1
A	EntryDrugbankAdmet.run()	0	14	1
A	EntryPubchemDiseaseCoOccurrence.run()	35	35	1
A	EntryChemidPlusAcute.run()	0	25	1
A	EntryChemidPlusLd50.run()	22	22	1
A	EntryChemblTrials.run()	0	21	1

"""

Too many lines in module (1194/1000)

Run searches and write files.
"""

from __future__ import annotations

import abc
from pathlib import Path
from typing import Optional, TypeVar

from mandos import logger
from mandos.entries._entry_args import EntryArgs
from mandos.entries._entry_utils import EntryUtils
from mandos.entries.abstract_entries import Entry
from mandos.entries.api_singletons import Apis
from mandos.entries.common_args import CommonArgs
from mandos.entries.searcher import Searcher
from mandos.model.utils import ReflectionUtils, InjectionError
from mandos.model.apis.chembl_api import ChemblApi
from mandos.model.apis.pubchem_support.pubchem_models import (
    CoOccurrenceType,
    DrugbankTargetType,
)
from mandos.model.searches import Search

Unused Search imported from mandos.model.searches

from mandos.search.chembl.atc_search import AtcSearch
from mandos.search.chembl.binding_search import BindingSearch
from mandos.search.chembl.go_search import GoSearch
from mandos.model.concrete_hits import GoType
from mandos.search.chembl.indication_search import IndicationSearch
from mandos.search.chembl.mechanism_search import MechanismSearch
from mandos.search.chembl.target_prediction_search import TargetPredictionSearch
from mandos.search.g2p.g2p_interaction_search import G2pInteractionSearch
from mandos.search.pubchem.acute_effects_search import AcuteEffectSearch, Ld50Search
from mandos.search.pubchem.bioactivity_search import BioactivitySearch
from mandos.search.pubchem.computed_property_search import ComputedPropertySearch
from mandos.search.pubchem.cooccurrence_search import (
    ChemicalCoOccurrenceSearch,
    CoOccurrenceSearch,
    DiseaseCoOccurrenceSearch,
    GeneCoOccurrenceSearch,
)
from mandos.search.pubchem.ctd_gene_search import CtdGeneSearch
from mandos.search.pubchem.dgidb_search import DgiSearch
from mandos.search.pubchem.disease_search import DiseaseSearch
from mandos.search.pubchem.drugbank_ddi_search import DrugbankDdiSearch
from mandos.search.pubchem.drugbank_interaction_search import (
    DrugbankGeneralFunctionSearch,
    DrugbankTargetSearch,
)

U = TypeVar("U", covariant=True, bound=CoOccurrenceSearch)

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class EntryChemblBinding(Entry[BindingSearch]):

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    @classmethod
    def run(

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        cls,

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        path: Path = CommonArgs.compounds,

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        key: str = EntryArgs.key("chembl:binding"),

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        to: Optional[Path] = CommonArgs.to_single,

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        taxa: str = CommonArgs.taxa,

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        traversal: str = EntryArgs.traversal_strategy,

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        target_types: str = EntryArgs.target_types,

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        confidence: int = EntryArgs.min_confidence,

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        binding: float = EntryArgs.binds_cutoff,

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        nonbinding: float = EntryArgs.does_not_bind_cutoff,

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        relations: str = EntryArgs.relations,

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        min_pchembl: float = EntryArgs.min_pchembl,

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        banned_flags: str = EntryArgs.banned_flags,

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        as_of: Optional[str] = CommonArgs.as_of,

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        check: bool = EntryArgs.check,

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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        no_setup: bool = CommonArgs.no_setup,

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    ) -> Searcher:
        """
        Binding data from ChEMBL.

        These are 'activity' annotations of the type 'B' that have a pCHEMBL value.
        https://mandos-chem.readthedocs.io/en/latest/binding.html

        OBJECT: The target name

        WEIGHT: The PCHEMBL value
        """
        built = BindingSearch(
            key=key,
            api=Apis.Chembl,
            taxa=EntryUtils.get_taxa(taxa),
            traversal=traversal,
            target_types=EntryUtils.get_target_types(target_types),
            min_conf_score=confidence,
            allowed_relations=EntryUtils.split(relations),
            min_pchembl=min_pchembl,
            banned_flags=EntryUtils.get_flags(banned_flags),
            binds_cutoff=binding,
            does_not_bind_cutoff=nonbinding,
        )
        return cls._run(built, path, to, check, log, quiet, verbose, no_setup)


class EntryChemblMechanism(Entry[MechanismSearch]):

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    @classmethod
    def run(

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        cls,

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        path: Path = CommonArgs.compounds,

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        key: str = EntryArgs.key("chembl:mechanism"),

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        to: Optional[Path] = CommonArgs.to_single,

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        taxa: Optional[str] = CommonArgs.taxa,

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        traversal: str = EntryArgs.traversal_strategy,

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        target_types: str = EntryArgs.target_types,

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        min_confidence: Optional[int] = EntryArgs.min_confidence,

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        as_of: Optional[str] = CommonArgs.as_of,

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        check: bool = EntryArgs.check,

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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        no_setup: bool = CommonArgs.no_setup,

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    ) -> Searcher:
        """
        Mechanism of action (MoA) data from ChEMBL.

        OBJECT: The target name

        PREDICATE: The target action (e.g. "agonist")
        """
        built = MechanismSearch(
            key=key,
            api=Apis.Chembl,
            taxa=EntryUtils.get_taxa(taxa),
            traversal_strategy=traversal,
            allowed_target_types=EntryUtils.get_target_types(target_types),
            min_confidence_score=min_confidence,
        )
        return cls._run(built, path, to, check, log, quiet, verbose, no_setup)


class ChemblQsarPredictions(Entry[TargetPredictionSearch]):

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    @classmethod
    def run(

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        cls,

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        path: Path = CommonArgs.compounds,

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        key: str = EntryArgs.key("chembl:predictions"),

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        to: Optional[Path] = CommonArgs.to_single,

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        taxa: str = CommonArgs.taxa,

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        traversal: str = EntryArgs.traversal_strategy,

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        target_types: str = EntryArgs.target_types,

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        min_threshold: float = EntryArgs.min_threshold,

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        as_of: Optional[str] = CommonArgs.as_of,

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        check: bool = EntryArgs.check,

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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        no_setup: bool = CommonArgs.no_setup,

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    ) -> Searcher:
        """
        Predicted target binding from ChEMBL.

        https://mandos-chem.readthedocs.io/en/latest/binding.html
        These are from a QSAR model by ChEMBL.

        OBJECT: The target name

        WEIGHT: The square root of the PCHEMBL threshold
                multiplied by a prediction odds-ratio, normalized
        """
        built = TargetPredictionSearch(
            key=key,
            api=Apis.Chembl,
            scrape=Apis.ChemblScrape,
            taxa=EntryUtils.get_taxa(taxa),
            traversal=traversal,
            target_types=EntryUtils.get_target_types(target_types),
            min_threshold=min_threshold,
        )
        return cls._run(built, path, to, check, log, quiet, verbose, no_setup)


class EntryChemblTrials(Entry[IndicationSearch]):

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    @classmethod
    def run(

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        cls,

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        path: Path = CommonArgs.compounds,

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        key: str = EntryArgs.key("chembl:trial"),

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        to: Optional[Path] = CommonArgs.to_single,

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        min_phase: Optional[int] = EntryArgs.chembl_trial,

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        as_of: Optional[str] = CommonArgs.as_of,

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        check: bool = EntryArgs.check,

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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        no_setup: bool = CommonArgs.no_setup,

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    ) -> Searcher:
        """
        Diseases from clinical trials listed in ChEMBL.

        OBJECT: The name of the disease (in MeSH)
        """
        built = IndicationSearch(key=key, api=Apis.Chembl, min_phase=min_phase)
        return cls._run(built, path, to, check, log, quiet, verbose, no_setup)


class EntryChemblAtc(Entry[AtcSearch]):

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    @classmethod
    def run(

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        cls,

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        path: Path = CommonArgs.compounds,

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        key: str = EntryArgs.key("chembl:atc"),

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        to: Optional[Path] = CommonArgs.to_single,

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        levels: str = EntryArgs.atc_level,

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        as_of: Optional[str] = CommonArgs.as_of,

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        check: bool = EntryArgs.check,

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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        no_setup: bool = CommonArgs.no_setup,

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    ) -> Searcher:
        """
        ATC codes from ChEMBL.

        OBJECT: The ATC code name
        """
        built = AtcSearch(
            key=key, api=Apis.Chembl, levels={int(x.strip()) for x in levels.split(",")}
        )
        return cls._run(built, path, to, check, log, quiet, verbose, no_setup)


class _EntryChemblGo(Entry[GoSearch], metaclass=abc.ABCMeta):
    @classmethod
    def go_type(cls) -> GoType:

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        raise NotImplementedError()

    @classmethod
    def cmd(cls) -> str:

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        me = str(cls.go_type().name)

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        return f"chembl:go.{me.lower()}"

    @classmethod
    def run(

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        cls,

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        path: Path = CommonArgs.compounds,

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        key: str = EntryArgs.key("<see above>"),

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        to: Optional[Path] = CommonArgs.to_single,

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        taxa: Optional[str] = CommonArgs.taxa,

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        traversal_strategy: str = EntryArgs.traversal_strategy,

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        target_types: str = EntryArgs.target_types,

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        confidence: Optional[int] = EntryArgs.min_confidence,

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        relations: str = EntryArgs.relations,

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        min_pchembl: float = EntryArgs.min_pchembl,

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        banned_flags: Optional[str] = EntryArgs.banned_flags,

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        binding_search: Optional[str] = EntryArgs.binding_search_name,

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        as_of: Optional[str] = CommonArgs.as_of,

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        check: bool = EntryArgs.check,

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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        no_setup: bool = CommonArgs.no_setup,

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    ) -> Searcher:
        """
        See the docs for the specific entries.
        """
        if key is None or key == "<see above>":
            key = cls.cmd()
        api = ChemblApi.wrap(Apis.Chembl)
        if binding_search is None:
            binding_clazz = BindingSearch
        else:
            binding_clazz = ReflectionUtils.injection(binding_search, BindingSearch)
            logger.info(f"Passing parameters to {binding_clazz.__qualname__}")
        try:
            binding_search = binding_clazz(
                key=key,
                api=Apis.Chembl,
                taxa=EntryUtils.get_taxa(taxa),
                traversal=traversal_strategy,
                target_types=EntryUtils.get_target_types(target_types),
                min_conf_score=confidence,
                allowed_relations=EntryUtils.split(relations),
                min_pchembl=min_pchembl,
                banned_flags=EntryUtils.get_flags(banned_flags),
            )
        except (TypeError, ValueError):
            raise InjectionError(f"Failed to build {binding_clazz.__qualname__}")
        built = GoSearch(key, api, cls.go_type(), binding_search)
        return cls._run(built, path, to, check, log, quiet, verbose, no_setup)


class EntryGoFunction(_EntryChemblGo):

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    @classmethod
    def go_type(cls) -> GoType:
        return GoType.function

    @classmethod
    def run(

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        cls,

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        path: Path = CommonArgs.compounds,

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        key: str = EntryArgs.key("chembl:go.function"),

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        to: Optional[Path] = CommonArgs.to_single,

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        taxa: Optional[str] = CommonArgs.taxa,

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        traversal_strategy: str = EntryArgs.traversal_strategy,

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        target_types: str = EntryArgs.target_types,

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        confidence: Optional[int] = EntryArgs.min_confidence,

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        relations: str = EntryArgs.relations,

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        min_pchembl: float = EntryArgs.min_pchembl,

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        banned_flags: Optional[str] = EntryArgs.banned_flags,

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        binding_search: Optional[str] = EntryArgs.binding_search_name,

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        as_of: Optional[str] = CommonArgs.as_of,

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        check: bool = EntryArgs.check,

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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        no_setup: bool = CommonArgs.no_setup,

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    ) -> Searcher:
        """
        GO Function terms associated with ChEMBL binding targets.

        OBJECT: The GO Function term name

        WEIGHT: The sum of the PCHEMBL values
        """
        return super().run(
            path=path,
            key=key,
            to=to,
            taxa=taxa,
            traversal_strategy=traversal_strategy,
            target_types=target_types,
            confidence=confidence,
            relations=relations,
            min_pchembl=min_pchembl,
            banned_flags=banned_flags,
            binding_search=binding_search,
            as_of=as_of,
            check=check,
            log=log,
            quiet=quiet,
            verbose=verbose,
        )


class EntryGoProcess(_EntryChemblGo):

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    @classmethod
    def go_type(cls) -> GoType:
        return GoType.process

    @classmethod
    def run(

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        cls,

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        path: Path = CommonArgs.compounds,

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        key: str = EntryArgs.key("chembl:go.process"),

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        to: Optional[Path] = CommonArgs.to_single,

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        taxa: Optional[str] = CommonArgs.taxa,

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        traversal_strategy: str = EntryArgs.traversal_strategy,

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        target_types: str = EntryArgs.target_types,

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        confidence: Optional[int] = EntryArgs.min_confidence,

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        relations: str = EntryArgs.relations,

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        min_pchembl: float = EntryArgs.min_pchembl,

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        banned_flags: Optional[str] = EntryArgs.banned_flags,

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        binding_search: Optional[str] = EntryArgs.binding_search_name,

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        as_of: Optional[str] = CommonArgs.as_of,

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        check: bool = EntryArgs.check,

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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        no_setup: bool = CommonArgs.no_setup,

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    ) -> Searcher:
        """
        GO Process terms associated with ChEMBL binding targets.

        OBJECT: The GO Process term name

        WEIGHT: The sum of the PCHEMBL values
        """
        return super().run(
            path=path,
            key=key,
            to=to,
            taxa=taxa,
            traversal_strategy=traversal_strategy,
            target_types=target_types,
            confidence=confidence,
            relations=relations,
            min_pchembl=min_pchembl,
            banned_flags=banned_flags,
            binding_search=binding_search,
            as_of=as_of,
            check=check,
            log=log,
            quiet=quiet,
            verbose=verbose,
        )


class EntryGoComponent(_EntryChemblGo):

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    @classmethod
    def go_type(cls) -> GoType:
        return GoType.component

    @classmethod
    def run(

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        cls,

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        path: Path = CommonArgs.compounds,

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        key: str = EntryArgs.key("chembl:go.component"),

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        to: Optional[Path] = CommonArgs.to_single,

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        taxa: Optional[str] = CommonArgs.taxa,

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        traversal_strategy: str = EntryArgs.traversal_strategy,

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        target_types: str = EntryArgs.target_types,

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        confidence: Optional[int] = EntryArgs.min_confidence,

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        relations: str = EntryArgs.relations,

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        min_pchembl: float = EntryArgs.min_pchembl,

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        banned_flags: Optional[str] = EntryArgs.banned_flags,

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        binding_search: Optional[str] = EntryArgs.binding_search_name,

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        as_of: Optional[str] = CommonArgs.as_of,

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        check: bool = EntryArgs.check,

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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        no_setup: bool = CommonArgs.no_setup,

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    ) -> Searcher:
        """
        GO Component terms associated with ChEMBL binding targets.

        OBJECT: The GO Component term name

        WEIGHT: The sum of the PCHEMBL values
        """
        return super().run(
            path=path,
            key=key,
            to=to,
            taxa=taxa,
            traversal_strategy=traversal_strategy,
            target_types=target_types,
            confidence=confidence,
            relations=relations,
            min_pchembl=min_pchembl,
            banned_flags=banned_flags,
            binding_search=binding_search,
            as_of=as_of,
            check=check,
            log=log,
            quiet=quiet,
            verbose=verbose,
        )


class EntryPubchemDisease(Entry[DiseaseSearch]):

Value 'Entry' is unsubscriptable

Missing class docstring

    @classmethod

This code seems to be duplicated in your project.

    def run(

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

Too many arguments (10/5)

        cls,

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        path: Path = CommonArgs.compounds,

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        key: str = EntryArgs.key("disease.ctd:mesh"),

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        to: Optional[Path] = CommonArgs.to_single,

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        as_of: Optional[str] = CommonArgs.as_of,

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The argument as_of seems to be unused.

        check: bool = EntryArgs.check,

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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        no_setup: bool = CommonArgs.no_setup,

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    ) -> Searcher:
        """
        Diseases in the CTD.

        (Comparative Toxicogenomics Database.)

        OBJECT: The MeSH code of the disease

        """
        built = DiseaseSearch(key, Apis.Pubchem)
        return cls._run(built, path, to, check, log, quiet, verbose, no_setup)


class _EntryPubchemCoOccurrence(Entry[U], metaclass=abc.ABCMeta):
    @classmethod
    def cmd(cls) -> str:

Missing function or method docstring

        me = str(cls.get_cooccurrence_type().name)

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

        return f"lit.pubchem:{me.lower()}"

    @classmethod
    def get_cooccurrence_type(cls) -> CoOccurrenceType:

Missing function or method docstring

        s: CoOccurrenceSearch = cls.get_search_type()

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

        return s.cooccurrence_type()

    @classmethod
    def run(

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

Too many arguments (12/5)

        cls,

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        path: Path = CommonArgs.compounds,

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        key: str = EntryArgs.key("<see above>"),

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        to: Optional[Path] = CommonArgs.to_single,

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        min_score: float = EntryArgs.min_cooccurrence_score,

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        min_articles: int = EntryArgs.min_cooccurring_articles,

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        as_of: Optional[str] = CommonArgs.as_of,

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        log: Optional[Path] = CommonArgs.log_path,

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        check: bool = EntryArgs.check,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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        no_setup: bool = CommonArgs.no_setup,

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    ) -> Searcher:
        """See the docstrings for the individual entries."""
        clazz = cls.get_search_type()
        built = clazz(key, Apis.Pubchem, min_score=min_score, min_articles=min_articles)
        return cls._run(built, path, to, check, log, quiet, verbose, no_setup)


class EntryPubchemGeneCoOccurrence(_EntryPubchemCoOccurrence[GeneCoOccurrenceSearch]):

Empty class docstring

This code seems to be duplicated in your project.

    """ """

    @classmethod
    def run(

Too many arguments (12/5)

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

        cls,

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        path: Path = CommonArgs.compounds,

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        key: str = EntryArgs.key(f"lit.pubchem:{CoOccurrenceType.gene.name.lower()}"),

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        to: Optional[Path] = CommonArgs.to_single,

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        min_score: float = EntryArgs.min_cooccurrence_score,

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        min_articles: int = EntryArgs.min_cooccurring_articles,

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        as_of: Optional[str] = CommonArgs.as_of,

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        log: Optional[Path] = CommonArgs.log_path,

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        check: bool = EntryArgs.check,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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The argument verbose seems to be unused.

        no_setup: bool = CommonArgs.no_setup,

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    ) -> Searcher:
        """
        Co-occurrences of genes from PubMed articles.

        https://mandos-chem.readthedocs.io/en/latest/co-occurrences.html

        OBJECT: The name of the gene

        WEIGHT: The co-occurrence score (refer to the docs)
        """
        return super().run(
            path=path,
            key=key,
            to=to,
            min_score=min_score,
            min_articles=min_articles,
            as_of=as_of,
            log=log,
            check=check,
            quiet=quiet,
            no_setup=no_setup,
        )


class EntryPubchemDiseaseCoOccurrence(_EntryPubchemCoOccurrence[DiseaseCoOccurrenceSearch]):

This code seems to be duplicated in your project.

Empty class docstring

    """ """

    @classmethod
    def run(

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

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        cls,

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        path: Path = CommonArgs.compounds,

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        key: str = EntryArgs.key(f"lit.pubchem:{CoOccurrenceType.disease.name.lower()}"),

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        to: Optional[Path] = CommonArgs.to_single,

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        min_score: float = EntryArgs.min_cooccurrence_score,

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        min_articles: int = EntryArgs.min_cooccurring_articles,

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        as_of: Optional[str] = CommonArgs.as_of,

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        log: Optional[Path] = CommonArgs.log_path,

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        check: bool = EntryArgs.check,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

The argument verbose seems to be unused.

        no_setup: bool = CommonArgs.no_setup,

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    ) -> Searcher:
        """
        Co-occurrences of diseases from PubMed articles.

        https://mandos-chem.readthedocs.io/en/latest/co-occurrences.html

        OBJECT: The name of the disease

        WEIGHT: The co-occurrence score (refer to the docs)
        """
        return super().run(
            path=path,
            key=key,
            to=to,
            min_score=min_score,
            min_articles=min_articles,
            as_of=as_of,
            log=log,
            check=check,
            quiet=quiet,
            no_setup=no_setup,
        )


class EntryPubchemChemicalCoOccurrence(_EntryPubchemCoOccurrence[ChemicalCoOccurrenceSearch]):

Empty class docstring

This code seems to be duplicated in your project.

    """ """

    @classmethod
    def run(

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

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        cls,

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        path: Path = CommonArgs.compounds,

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        key: str = EntryArgs.key(f"lit.pubchem:{CoOccurrenceType.chemical.name.lower()}"),

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        to: Optional[Path] = CommonArgs.to_single,

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        min_score: float = EntryArgs.min_cooccurrence_score,

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        min_articles: int = EntryArgs.min_cooccurring_articles,

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        as_of: Optional[str] = CommonArgs.as_of,

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        log: Optional[Path] = CommonArgs.log_path,

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        check: bool = EntryArgs.check,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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The argument verbose seems to be unused.

        no_setup: bool = CommonArgs.no_setup,

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    ) -> Searcher:
        """
        Co-occurrences of chemicals from PubMed articles.

        https://mandos-chem.readthedocs.io/en/latest/co-occurrences.html

        OBJECT: The name of the chemical (e.g. "cocaine")

        WEIGHT: The co-occurrence score (refer to the docs)
        """
        return super().run(
            path=path,
            key=key,
            to=to,
            min_score=min_score,
            min_articles=min_articles,
            as_of=as_of,
            log=log,
            check=check,
            quiet=quiet,
            no_setup=no_setup,
        )


class EntryPubchemDgi(Entry[DgiSearch]):

Value 'Entry' is unsubscriptable

Missing class docstring

    @classmethod

This code seems to be duplicated in your project.

    def run(

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

Too many arguments (10/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = CommonArgs.compounds,

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        key: str = EntryArgs.key("inter.dgidb:gene"),

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        to: Optional[Path] = CommonArgs.to_single,

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        as_of: Optional[str] = CommonArgs.as_of,

The argument as_of seems to be unused.

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        log: Optional[Path] = CommonArgs.log_path,

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        check: bool = EntryArgs.check,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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        no_setup: bool = CommonArgs.no_setup,

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    ) -> Searcher:
        """
        Drug/gene interactions in the DGIDB.

        Drug Gene Interaction Database.
        Also see disease.dgidb:int.

        OBJECT: The name of the gene

        PREDICATE: "interaction:generic" or "interaction:<type>"
        """
        built = DgiSearch(key, Apis.Pubchem)
        return cls._run(built, path, to, check, log, quiet, verbose, no_setup)


class EntryPubchemCgi(Entry[CtdGeneSearch]):

Value 'Entry' is unsubscriptable

Missing class docstring

    @classmethod

This code seems to be duplicated in your project.

    def run(

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

Too many arguments (10/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = CommonArgs.compounds,

Wrong hanging indentation before block (add 4 spaces).

        key: str = EntryArgs.key("inter.ctd:gene"),

Wrong hanging indentation before block (add 4 spaces).

        as_of: Optional[str] = CommonArgs.as_of,

The argument as_of seems to be unused.

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        to: Optional[Path] = CommonArgs.to_single,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = CommonArgs.log_path,

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        check: bool = EntryArgs.check,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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        no_setup: bool = CommonArgs.no_setup,

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    ) -> Searcher:
        """
        Compound/gene interactions in the DGIDB.

        Drug Gene Interaction Database.
        Also see ``interact.dgidb:int``.

        OBJECT: The name of the gene

        PREDICATE: derived from the interaction type (e.g. "downregulation")
        """
        built = CtdGeneSearch(key, Apis.Pubchem)
        return cls._run(built, path, to, check, log, quiet, verbose, no_setup)


class EntryDrugbankTarget(Entry[DrugbankTargetSearch]):

Value 'Entry' is unsubscriptable

This code seems to be duplicated in your project.

Missing class docstring

    @classmethod
    def run(

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

Too many arguments (10/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = CommonArgs.compounds,

Wrong hanging indentation before block (add 4 spaces).

        key: str = EntryArgs.key("inter.drugbank:targ"),

Wrong hanging indentation before block (add 4 spaces).

        as_of: Optional[str] = CommonArgs.as_of,

The argument as_of seems to be unused.

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        to: Optional[Path] = CommonArgs.to_single,

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        check: bool = EntryArgs.check,

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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        no_setup: bool = CommonArgs.no_setup,

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    ) -> Searcher:
        """
        Protein targets from DrugBank.

        OBJECT: The target name (e.g. "Solute carrier family 22 member 11")

        PREDICATE: "<target_type>:<action>"
        """
        built = DrugbankTargetSearch(key, Apis.Pubchem, {DrugbankTargetType.target})
        return cls._run(built, path, to, check, log, quiet, verbose, no_setup)


class EntryGeneralFunction(Entry[DrugbankGeneralFunctionSearch]):

Missing class docstring

Value 'Entry' is unsubscriptable

This code seems to be duplicated in your project.

    @classmethod
    def run(

Too many arguments (10/5)

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

        cls,

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        path: Path = CommonArgs.compounds,

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        key: str = EntryArgs.key("inter.drugbank:targ-fn"),

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        as_of: Optional[str] = CommonArgs.as_of,

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The argument as_of seems to be unused.

        to: Optional[Path] = CommonArgs.to_single,

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        check: bool = EntryArgs.check,

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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        no_setup: bool = CommonArgs.no_setup,

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    ) -> Searcher:
        """
        General functions from DrugBank targets.

        OBJECT: The name of the "general function" (e.g. "Toxic substance binding")

        PREDICATE: "<target_type>:<action>"
        """
        built = DrugbankGeneralFunctionSearch(key, Apis.Pubchem, {DrugbankTargetType.target})
        return cls._run(built, path, to, check, log, quiet, verbose, no_setup)


class EntryDrugbankTransporter(Entry[DrugbankTargetSearch]):

Missing class docstring

Value 'Entry' is unsubscriptable

This code seems to be duplicated in your project.

    @classmethod
    def run(

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

Too many arguments (10/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = CommonArgs.compounds,

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        key: str = EntryArgs.key("inter.drugbank:pk"),

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        as_of: Optional[str] = CommonArgs.as_of,

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The argument as_of seems to be unused.

        to: Optional[Path] = CommonArgs.to_single,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.check,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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        no_setup: bool = CommonArgs.no_setup,

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    ) -> Searcher:
        """
        PK-related proteins from DrugBank.

        OBJECT: The transporter name (e.g. "Solute carrier family 22 member 11")

        PREDICATE: "<target_type>:<action>" (e.g. metabolized, transported, etc.)
        """
        target_types = {
            DrugbankTargetType.transporter,
            DrugbankTargetType.carrier,
            DrugbankTargetType.enzyme,
        }
        built = DrugbankTargetSearch(key, Apis.Pubchem, target_types)
        return cls._run(built, path, to, check, log, quiet, verbose, no_setup)


class EntryTransporterGeneralFunction(Entry[DrugbankGeneralFunctionSearch]):

Value 'Entry' is unsubscriptable

Missing class docstring

This code seems to be duplicated in your project.

    @classmethod
    def run(

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

Too many arguments (10/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = CommonArgs.compounds,

Wrong hanging indentation before block (add 4 spaces).

        key: str = EntryArgs.key("inter.drugbank:pk-fn"),

Wrong hanging indentation before block (add 4 spaces).

        as_of: Optional[str] = CommonArgs.as_of,

Wrong hanging indentation before block (add 4 spaces).

The argument as_of seems to be unused.

        to: Optional[Path] = CommonArgs.to_single,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.check,

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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        no_setup: bool = CommonArgs.no_setup,

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    ) -> Searcher:
        """
        DrugBank PK-related protein functions.

        OBJECT: The name of the general function (e.g. "Toxic substance binding")

        PREDICATE: "<target_type>:<action>" (e.g. metabolized, transported, etc.)
        """
        target_types = {
            DrugbankTargetType.transporter,
            DrugbankTargetType.carrier,
            DrugbankTargetType.enzyme,
        }
        built = DrugbankGeneralFunctionSearch(key, Apis.Pubchem, target_types)
        return cls._run(built, path, to, check, log, quiet, verbose, no_setup)


class EntryDrugbankDdi(Entry[DrugbankDdiSearch]):

Value 'Entry' is unsubscriptable

Missing class docstring

    @classmethod

This code seems to be duplicated in your project.

    def run(

Too many arguments (10/5)

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

        cls,

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        path: Path = CommonArgs.compounds,

Wrong hanging indentation before block (add 4 spaces).

        key: str = EntryArgs.key("inter.drugbank:ddi"),

Wrong hanging indentation before block (add 4 spaces).

        to: Optional[Path] = CommonArgs.to_single,

Wrong hanging indentation before block (add 4 spaces).

        as_of: Optional[str] = CommonArgs.as_of,

Wrong hanging indentation before block (add 4 spaces).

The argument as_of seems to be unused.

        check: bool = EntryArgs.check,

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        log: Optional[Path] = CommonArgs.log_path,

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        quiet: bool = CommonArgs.quiet,

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        verbose: bool = CommonArgs.verbose,

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        no_setup: bool = CommonArgs.no_setup,

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    ) -> Searcher:
        """
        Drug/drug interactions listed by DrugBank.

        The "description" column includes useful information about the interaction,
        such as diseases and whether a risk is increased or decreased.

        OBJECT: The name of the drug (e.g. "ibuprofen")

        PREDICATE: typically increase/decrease/change followed by risk/activity/etc.
        """
        built = DrugbankDdiSearch(key, Apis.Pubchem)
        return cls._run(built, path, to, check, log, quiet, verbose, no_setup)


class EntryPubchemAssay(Entry[BioactivitySearch]):

Missing class docstring

Value 'Entry' is unsubscriptable

    @classmethod
    def run(

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

Too many arguments (12/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = CommonArgs.compounds,

Wrong hanging indentation before block (add 4 spaces).

        key: str = EntryArgs.key("assay.pubchem:act"),

Wrong hanging indentation before block (add 4 spaces).

        to: Optional[Path] = CommonArgs.to_single,

Wrong hanging indentation before block (add 4 spaces).

        name_must_match: bool = EntryArgs.name_must_match,

Wrong hanging indentation before block (add 4 spaces).

        ban_sources: Optional[str] = EntryArgs.banned_sources,

The argument ban_sources seems to be unused.

Wrong hanging indentation before block (add 4 spaces).

        as_of: Optional[str] = CommonArgs.as_of,

Wrong hanging indentation before block (add 4 spaces).

The argument as_of seems to be unused.

        check: bool = EntryArgs.check,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = CommonArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = CommonArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = CommonArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = CommonArgs.no_setup,

Wrong hanging indentation before block (add 4 spaces).

    ) -> Searcher:
        """
        PubChem bioactivity results.

        Note: The species name, if present, is taken from the target name.
        The taxon ID is what was curated in PubChem.

        OBJECT: The name of the target without species suffix
                (e.g. "Slc6a3 - solute carrier family 6 member 3")

        PREDICATE: "active", "inactive", "inconclusive", or "undetermined"

        WEIGHT: 2 for confirmatory; 1 otherwise
        """
        built = BioactivitySearch(key, Apis.Pubchem, compound_name_must_match=name_must_match)
        return cls._run(built, path, to, check, log, quiet, verbose, no_setup)


class EntryDeaSchedule(Entry[BioactivitySearch]):

Missing class docstring

Value 'Entry' is unsubscriptable

    @classmethod
    def run(

Too many arguments (10/5)

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

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = CommonArgs.compounds,

Wrong hanging indentation before block (add 4 spaces).

        key: str = EntryArgs.key("drug.dea:schedule"),

Wrong hanging indentation before block (add 4 spaces).

        to: Optional[Path] = CommonArgs.to_single,

Wrong hanging indentation before block (add 4 spaces).

        as_of: Optional[str] = CommonArgs.as_of,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.check,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = CommonArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = CommonArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = CommonArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = CommonArgs.no_setup,

Wrong hanging indentation before block (add 4 spaces).

    ) -> Searcher:
        """
        DEA schedules (PENDING).

        OBJECT: The DEA schedule (1 to 4, or "unscheduled")
        """
        pass

Unnecessary pass statement

class EntryDeaClass(Entry[BioactivitySearch]):

Value 'Entry' is unsubscriptable

Missing class docstring

    @classmethod
    def run(

Too many arguments (10/5)

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

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = CommonArgs.compounds,

Wrong hanging indentation before block (add 4 spaces).

        key: str = EntryArgs.key("drug.dea:class"),

Wrong hanging indentation before block (add 4 spaces).

        to: Optional[Path] = CommonArgs.to_single,

Wrong hanging indentation before block (add 4 spaces).

        as_of: Optional[str] = CommonArgs.as_of,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.check,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = CommonArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = CommonArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = CommonArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = CommonArgs.no_setup,

Wrong hanging indentation before block (add 4 spaces).

    ) -> Searcher:
        """
        DEA classes (PENDING).

        OBJECT: The DEA class name (e.g. "hallucinogen")
        """
        pass

Unnecessary pass statement

class EntryChemidPlusAcute(Entry[AcuteEffectSearch]):

Value 'Entry' is unsubscriptable

Missing class docstring

    @classmethod
    def run(

Too many arguments (11/5)

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

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = CommonArgs.compounds,

Wrong hanging indentation before block (add 4 spaces).

        key: str = EntryArgs.key("tox.chemidplus:acute"),

Wrong hanging indentation before block (add 4 spaces).

        to: Optional[Path] = CommonArgs.to_single,

Wrong hanging indentation before block (add 4 spaces).

        level: int = EntryArgs.acute_effect_level,

Wrong hanging indentation before block (add 4 spaces).

        as_of: Optional[str] = CommonArgs.as_of,

Wrong hanging indentation before block (add 4 spaces).

The argument as_of seems to be unused.

        check: bool = EntryArgs.check,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = CommonArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = CommonArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = CommonArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = CommonArgs.no_setup,

Wrong hanging indentation before block (add 4 spaces).

    ) -> Searcher:
        """
        Acute effect codes from ChemIDPlus.

        OBJECT: The code name (e.g. "behavioral: excitement")
        """
        built = AcuteEffectSearch(
            key,
            Apis.Pubchem,
            top_level=level == 1,
        )
        return cls._run(built, path, to, check, log, quiet, verbose, no_setup)


class EntryChemidPlusLd50(Entry[Ld50Search]):

Missing class docstring

Value 'Entry' is unsubscriptable

    @classmethod

This code seems to be duplicated in your project.

    def run(

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

Too many arguments (10/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = CommonArgs.compounds,

Wrong hanging indentation before block (add 4 spaces).

        key: str = EntryArgs.key("tox.chemidplus:ld50"),

Wrong hanging indentation before block (add 4 spaces).

        to: Optional[Path] = CommonArgs.to_single,

Wrong hanging indentation before block (add 4 spaces).

        as_of: Optional[str] = CommonArgs.as_of,

The argument as_of seems to be unused.

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.check,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = CommonArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = CommonArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = CommonArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = CommonArgs.no_setup,

Wrong hanging indentation before block (add 4 spaces).

    ) -> Searcher:
        """
        LD50 acute effects from ChemIDPlus.

        OBJECT: The negative log10 of the dose in mg/kg

        PREDICATE: "LD50:<route>" (e.g. "LD50:intravenous")
        """
        built = Ld50Search(key, Apis.Pubchem)
        return cls._run(built, path, to, check, log, quiet, verbose, no_setup)


class EntryG2pInteractions(Entry[G2pInteractionSearch]):

Missing class docstring

Value 'Entry' is unsubscriptable

    @classmethod

This code seems to be duplicated in your project.

    def run(

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

Too many arguments (10/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = CommonArgs.compounds,

Wrong hanging indentation before block (add 4 spaces).

        key: str = EntryArgs.key("g2p:interactions"),

Wrong hanging indentation before block (add 4 spaces).

        to: Optional[Path] = CommonArgs.to_single,

Wrong hanging indentation before block (add 4 spaces).

        as_of: Optional[str] = CommonArgs.as_of,

The argument as_of seems to be unused.

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.check,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = CommonArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = CommonArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = CommonArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = CommonArgs.no_setup,

Wrong hanging indentation before block (add 4 spaces).

    ) -> Searcher:
        """
        Target interactions with affinities from Guide to Pharmacology.

        OBJECT: A molecular target

        PREDICATE: "interaction:agonism", etc.

        WEIGHT: 1.0
        """
        built = G2pInteractionSearch(key, Apis.G2p)
        return cls._run(built, path, to, check, log, quiet, verbose, no_setup)


class EntryHmdbTissue(Entry[BioactivitySearch]):

Value 'Entry' is unsubscriptable

Missing class docstring

    @classmethod
    def run(

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

Too many arguments (11/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = CommonArgs.compounds,

Wrong hanging indentation before block (add 4 spaces).

        key: str = EntryArgs.key("hmdb:tissue"),

Wrong hanging indentation before block (add 4 spaces).

        to: Optional[Path] = CommonArgs.to_single,

Wrong hanging indentation before block (add 4 spaces).

        min_nanomolar: Optional[float] = EntryArgs.min_nanomolar,

Wrong hanging indentation before block (add 4 spaces).

        as_of: Optional[str] = CommonArgs.as_of,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.check,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = CommonArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = CommonArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = CommonArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = CommonArgs.no_setup,

Wrong hanging indentation before block (add 4 spaces).

    ) -> Searcher:
        """
        Tissue concentrations from HMDB (PENDING).

        OBJECT:

        PREDICATE: "tissue:..."
        """
        pass

Unnecessary pass statement

class EntryHmdbComputed(Entry[BioactivitySearch]):

Value 'Entry' is unsubscriptable

Missing class docstring

    @classmethod
    def run(

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

Too many arguments (11/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = CommonArgs.compounds,

Wrong hanging indentation before block (add 4 spaces).

        key: str = EntryArgs.key("hmdb:computed"),

Wrong hanging indentation before block (add 4 spaces).

        to: Optional[Path] = CommonArgs.to_single,

Wrong hanging indentation before block (add 4 spaces).

        min_nanomolar: Optional[float] = None,

Wrong hanging indentation before block (add 4 spaces).

        as_of: Optional[str] = CommonArgs.as_of,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.check,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = CommonArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = CommonArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = CommonArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = CommonArgs.no_setup,

Wrong hanging indentation before block (add 4 spaces).

    ) -> Searcher:
        """
        Computed properties from HMDB (PENDING).

        Keys include pKa, logP, logS, etc.

        OBJECT: A number; booleans are converted to 0/1

        PREDICATE: The name of the property
        """
        pass

Unnecessary pass statement

class EntryPubchemComputed(Entry[ComputedPropertySearch]):

Value 'Entry' is unsubscriptable

Missing class docstring

    @classmethod
    def run(

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

Too many arguments (11/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = CommonArgs.compounds,

Wrong hanging indentation before block (add 4 spaces).

        key: str = EntryArgs.key("chem.pubchem:computed"),

Wrong hanging indentation before block (add 4 spaces).

        keys: str = EntryArgs.pubchem_computed_keys,

Wrong hanging indentation before block (add 4 spaces).

        to: Optional[Path] = CommonArgs.to_single,

Wrong hanging indentation before block (add 4 spaces).

        as_of: Optional[str] = CommonArgs.as_of,

The argument as_of seems to be unused.

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.check,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = CommonArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = CommonArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = CommonArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = CommonArgs.no_setup,

Wrong hanging indentation before block (add 4 spaces).

    ) -> Searcher:
        """
        Computed properties from PubChem.

        OBJECT: Number

        PREDICATE: e.g. "complexity"
        """
        # replace acronyms, etc.
        # ComputedPropertySearch standardizes punctuation and casing
        known = {
            k: v
            for k, v in {
                **EntryArgs.KNOWN_USEFUL_KEYS,
                **EntryArgs.KNOWN_USELESS_KEYS,
            }.items()
            if v is not None
        }
        keys = {known.get(s.strip(), s) for s in keys.split(",")}
        built = ComputedPropertySearch(key, Apis.Pubchem, descriptors=keys)
        return cls._run(built, path, to, check, log, quiet, verbose, no_setup)


class EntryDrugbankAdmet(Entry[DrugbankTargetSearch]):

Missing class docstring

Value 'Entry' is unsubscriptable

    @classmethod
    def run(

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

Too many arguments (10/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = CommonArgs.compounds,

Wrong hanging indentation before block (add 4 spaces).

        key: str = EntryArgs.key("drugbank.admet:properties"),

Wrong hanging indentation before block (add 4 spaces).

        to: Optional[Path] = CommonArgs.to_single,

Wrong hanging indentation before block (add 4 spaces).

        as_of: Optional[str] = CommonArgs.as_of,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.check,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = CommonArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = CommonArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = CommonArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = CommonArgs.no_setup,

Wrong hanging indentation before block (add 4 spaces).

    ) -> Searcher:
        """
        Enzyme predictions from DrugBank (PENDING).

        OBJECT: Enzyme name

        PREDICATE: Action
        """


class EntryDrugbankMetabolites(Entry[DrugbankTargetSearch]):

Missing class docstring

Value 'Entry' is unsubscriptable

    @classmethod
    def run(

Too many arguments (10/5)

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

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = CommonArgs.compounds,

Wrong hanging indentation before block (add 4 spaces).

        key: str = EntryArgs.key("drugbank.admet:metabolites"),

Wrong hanging indentation before block (add 4 spaces).

        to: Optional[Path] = CommonArgs.to_single,

Wrong hanging indentation before block (add 4 spaces).

        as_of: Optional[str] = CommonArgs.as_of,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.check,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = CommonArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = CommonArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = CommonArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = CommonArgs.no_setup,

Wrong hanging indentation before block (add 4 spaces).

    ) -> Searcher:
        """
        Metabolites from DrugBank (PENDING).

        OBJECT: Compound name (e.g. "norcocaine").

        PREDICATE: "metabolized to"
        """


class EntryDrugbankDosage(Entry[DrugbankTargetSearch]):

Missing class docstring

Value 'Entry' is unsubscriptable

    @classmethod
    def run(

Too many arguments (10/5)

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

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = CommonArgs.compounds,

Wrong hanging indentation before block (add 4 spaces).

        key: str = EntryArgs.key("drugbank.admet:dosage"),

Wrong hanging indentation before block (add 4 spaces).

        to: Optional[Path] = CommonArgs.to_single,

Wrong hanging indentation before block (add 4 spaces).

        as_of: Optional[str] = CommonArgs.as_of,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.check,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = CommonArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = CommonArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = CommonArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = CommonArgs.no_setup,

Wrong hanging indentation before block (add 4 spaces).

    ) -> Searcher:
        """
        Dosage from DrugBank (PENDING).

        OBJECT: concentration in mg/mL

        PREDICATE: "dosage :: <route>"

        OTHER COLUMNS:

        - form (e.g. liquid)
        """


class EntryMetaRandom(Entry[BioactivitySearch]):

Value 'Entry' is unsubscriptable

Missing class docstring

    @classmethod
    def run(

Too many arguments (10/5)

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

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = CommonArgs.compounds,

Wrong hanging indentation before block (add 4 spaces).

        key: str = EntryArgs.key("meta:random"),

Wrong hanging indentation before block (add 4 spaces).

        to: Optional[Path] = CommonArgs.to_single,

Wrong hanging indentation before block (add 4 spaces).

        as_of: Optional[str] = CommonArgs.as_of,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.check,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = CommonArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = CommonArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = CommonArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = CommonArgs.no_setup,

Wrong hanging indentation before block (add 4 spaces).

    ) -> Searcher:
        """
        Random class assignment (PENDING).

        OBJECT: 1 thru n-compounds

        PREDICATE: "random"
        """
        pass

Unnecessary pass statement

Entries = [
    EntryChemblBinding,
    EntryChemblMechanism,
    EntryChemblAtc,
    EntryChemblTrials,
    EntryGoFunction,
    EntryGoProcess,
    EntryGoComponent,
    EntryPubchemComputed,
    EntryPubchemDisease,
    EntryPubchemGeneCoOccurrence,
    EntryPubchemDiseaseCoOccurrence,
    EntryPubchemChemicalCoOccurrence,
    EntryPubchemDgi,
    EntryPubchemCgi,
    EntryDrugbankTarget,
    EntryGeneralFunction,
    EntryDrugbankTransporter,
    EntryTransporterGeneralFunction,
    EntryDrugbankDdi,
    EntryPubchemAssay,
    EntryDeaSchedule,
    EntryDeaClass,
    EntryChemidPlusAcute,
    EntryChemidPlusLd50,
    EntryHmdbTissue,
    EntryMetaRandom,
]