mandos.entries.entries

Complexity

Total Complexity

59

Size/Duplication

Total Lines	1054
Duplicated Lines	8.92 %

Importance

Changes

0

47 Methods

Rating	Name	Duplication	Size	Complexity
A	EntryTransporterGeneralFunction.run()	26	26	1
A	EntryPubchemAssay.run()	0	28	1
A	Entry.get_search_type()	0	4	1
A	EntryPubchemReact.run()	0	20	1
A	Entry._get_default_key()	0	8	2
A	_EntryPubchemCoOccurrence.get_cooccurrence_type()	0	4	1
A	EntryChemblMechanism.run()	0	40	1
A	EntryChemblBinding.run()	0	54	1
A	EntryDrugbankDosage.run()	0	13	1
A	EntryHmdbComputed.run()	0	23	1
A	EntryHmdbTissue.run()	0	21	1
A	EntryPubchemComputed.run()	0	33	1
A	EntryDeaClass.run()	0	20	1
A	EntryDrugbankTransporter.run()	26	26	1
A	EntryGoFunction.go_type()	0	3	1
A	Utils.get_flags()	0	3	1
A	EntryPubchemDisease.run()	0	23	1
A	EntryDrugbankDdi.run()	0	24	1
A	Entry._get_searcher()	0	8	1
A	EntryGeneralFunction.run()	21	21	1
A	EntryChemblAtc.run()	0	24	1
A	EntryGoComponent.go_type()	0	3	1
A	EntryMetaRandom.run()	0	20	1
A	Entry.default_param_values()	0	6	1
A	_EntryPubchemCoOccurrence.cmd()	0	4	1
A	EntryDeaSchedule.run()	0	20	1
A	Utils.get_target_types()	0	3	1
A	_EntryChemblGo.go_type()	0	3	1
A	EntryGoProcess.go_type()	0	3	1
A	Utils.get_taxa()	0	5	1
A	Entry.run()	0	3	1
A	Entry._run()	0	22	3
A	EntryDrugbankMetabolites.run()	0	13	1
A	Utils.split()	0	3	1
B	_EntryChemblGo.run()	0	59	5
A	Entry.test()	0	5	1
A	_EntryChemblGo.cmd()	0	4	1
A	EntryPubchemCgi.run()	0	25	1
A	EntryPubchemDgi.run()	0	24	1
A	_EntryPubchemCoOccurrence.run()	0	38	3
A	Entry.cmd()	0	8	4
A	EntryDrugbankTarget.run()	21	21	1
A	Utils.get_trial_statuses()	0	3	1
A	EntryDrugbankAdmet.run()	0	13	1
A	EntryChemidPlusAcute.run()	0	34	1
A	EntryChemidPlusLd50.run()	0	26	1
A	EntryChemblTrials.run()	0	22	1

"""

Too many lines in module (1054/1000)

Run searches and write files.
"""

from __future__ import annotations

import abc
from pathlib import Path
from typing import TypeVar, Generic, Union, Mapping, Set, Sequence, Type, Optional

import typer

Unable to import 'typer'

from mandos.entries import EntryMeta
from mandos.entries.args import EntryArgs
from mandos.model import ReflectionUtils, InjectionError
from mandos.model.chembl_api import ChemblApi
from mandos.model.chembl_support import DataValidityComment
from mandos.model.chembl_support.chembl_targets import TargetType
from mandos.model.pubchem_support.pubchem_models import (
    ClinicalTrialsGovUtils,
    CoOccurrenceType,
    DrugbankTargetType,
)
from mandos.model.searches import Search
from mandos.model.settings import MANDOS_SETTINGS
from mandos.model.taxonomy import Taxonomy
from mandos.model.taxonomy_caches import TaxonomyFactories
from mandos.entries.api_singletons import Apis
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.dgidb_search import DgiSearch
from mandos.search.pubchem.ctd_gene_search import CtdGeneSearch
from mandos.entries.searcher import Searcher
from mandos.search.pubchem.drugbank_ddi_search import DrugbankDdiSearch
from mandos.search.pubchem.drugbank_interaction_search import (
    DrugbankTargetSearch,
    DrugbankGeneralFunctionSearch,
)

from mandos import logger, MandosMetadata, MandosLogging

Unused MandosMetadata imported from mandos

Unused MandosLogging imported from mandos

from mandos.search.chembl.binding_search import BindingSearch
from mandos.search.chembl.atc_search import AtcSearch
from mandos.search.chembl.go_search import GoType, GoSearch
from mandos.search.chembl.indication_search import IndicationSearch
from mandos.search.chembl.mechanism_search import MechanismSearch
from mandos.search.pubchem.cooccurrence_search import (
    GeneCoOccurrenceSearch,
    ChemicalCoOccurrenceSearch,
    CoOccurrenceSearch,
    DiseaseCoOccurrenceSearch,
)
from mandos.search.pubchem.disease_search import DiseaseSearch

S = TypeVar("S", bound=Search, covariant=True)

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

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

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

class Utils:

Empty class docstring

    """"""

    @staticmethod
    def split(st: str) -> Set[str]:

Missing function or method docstring

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

        return {s.strip() for s in st.split(",")}

    @staticmethod
    def get_taxa(taxa: str) -> Sequence[Taxonomy]:

Missing function or method docstring

        return [
            TaxonomyFactories.from_uniprot(MANDOS_SETTINGS.taxonomy_cache_path).load(int(taxon))
            for taxon in taxa.split(",")
        ]

    @staticmethod
    def get_trial_statuses(st: str) -> Set[str]:

Missing function or method docstring

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

        return ClinicalTrialsGovUtils.resolve_statuses(st)

    @staticmethod
    def get_target_types(st: str) -> Set[str]:

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

Missing function or method docstring

        return {s.name for s in TargetType.resolve(st)}

    @staticmethod
    def get_flags(st: str) -> Set[str]:

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

Missing function or method docstring

        return {s.name for s in DataValidityComment.resolve(st)}


class Entry(Generic[S], metaclass=abc.ABCMeta):

Missing class docstring

    @classmethod
    def cmd(cls) -> str:

Missing function or method docstring

        key = cls._get_default_key()
        if isinstance(key, typer.models.OptionInfo):
            key = key.default
        if key is None or not isinstance(key, str):
            raise AssertionError(f"Key for {cls.__name__} is {key}")
        return key

    @classmethod
    def run(cls, path: Path, **params) -> None:

Missing function or method docstring

        raise NotImplementedError()

    @classmethod
    def get_search_type(cls) -> Type[S]:

Missing function or method docstring

        # noinspection PyTypeChecker
        return ReflectionUtils.get_generic_arg(cls, Search)

    # noinspection PyUnusedLocal
    @classmethod
    def test(cls, path: Path, **params) -> None:

Missing function or method docstring

The argument path seems to be unused.

        params = dict(params)
        params["test"] = True
        cls.run(**params)

    @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,

Wrong hanging indentation before block (add 4 spaces).

        built: S,

Wrong hanging indentation before block (add 4 spaces).

        path: Path,

Wrong hanging indentation before block (add 4 spaces).

        to: Optional[Path],

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        check: bool,

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        log: Optional[Path],

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        quiet: bool,

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        verbose: bool,

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        no_setup: bool,

Wrong hanging indentation before block (add 4 spaces).

    ):
        if not no_setup:
            level = EntryMeta.set_logging(verbose, quiet, log)
            logger.notice(f"Ready. Set log level to {level}")
        searcher = cls._get_searcher(built, path, to)
        logger.notice(f"Searching {built.key} [{built.search_class}] on {path}")
        out = searcher.output_paths[built.key]
        if not check:
            searcher.search()
        logger.notice(f"Done! Wrote to {out}")
        return searcher

    @classmethod
    def _get_searcher(

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).

        built: S,

Wrong hanging indentation before block (add 4 spaces).

        path: Path,

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        to: Optional[Path],

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    ):
        return Searcher([built], [to], path)

    @classmethod
    def default_param_values(cls) -> Mapping[str, Union[str, float, int]]:

Missing function or method docstring

        return {
            param: value
            for param, value in ReflectionUtils.default_arg_values(cls.run).items()
            if param not in {"key", "path"}
        }

    @classmethod
    def _get_default_key(cls) -> str:
        vals = ReflectionUtils.default_arg_values(cls.run)
        try:
            return vals["key"]
        except KeyError:
            logger.error(f"key not in {vals.keys()} for {cls.__name__}")
            raise


class EntryChemblBinding(Entry[BindingSearch]):

Missing class docstring

Value 'Entry' is unsubscriptable

    @classmethod
    def run(

This function exceeds the maximum number of variables (17/15).

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 (16/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = EntryArgs.path,

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

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        to: Optional[Path] = EntryArgs.to,

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        taxa: Optional[str] = EntryArgs.taxa,

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        traversal=EntryArgs.traversal_strategy,

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        target_types=EntryArgs.target_types,

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        confidence=EntryArgs.min_confidence,

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        relations=EntryArgs.relations,

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        min_pchembl=EntryArgs.min_pchembl,

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        banned_flags=EntryArgs.banned_flags,

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        check: bool = EntryArgs.test,

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        log: Optional[Path] = EntryArgs.log_path,

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        quiet: bool = EntryArgs.quiet,

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        verbose: bool = EntryArgs.verbose,

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        no_setup: bool = EntryArgs.no_setup,

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    ) -> Searcher:
        """
        Binding data from ChEMBL.
        These are 'activity' annotations of the type 'B' that have a pCHEMBL value.
        There is extended documentation on this search; see:

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

        OBJECT: ChEMBL preferred target name

        PREDICATE: "binds to"

        OTHER COLUMNS:

        - taxon_id: From UniProt

        - taxon_name: From Uniprot (scientific name)

        - pchembl: Negative base-10 log of activity value (see docs on ChEMBL)

        - standard_relation: One of '<', '<=', '=', '>=', '>', '~'. Consider using <, <=, and = to indicate hits.

This line is too long as per the coding-style (113/100).

        - std_type: e.g. EC50, Kd
        """
        built = BindingSearch(
            key=key,
            api=Apis.Chembl,
            taxa=Utils.get_taxa(taxa),
            traversal_strategy=traversal,
            allowed_target_types=Utils.get_target_types(target_types),
            min_confidence_score=confidence,
            allowed_relations=Utils.split(relations),
            min_pchembl=min_pchembl,
            banned_flags=Utils.get_flags(banned_flags),
        )
        return cls._run(built, path, to, check, log, quiet, verbose, no_setup)


class EntryChemblMechanism(Entry[MechanismSearch]):

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)

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        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = EntryArgs.path,

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

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        to: Optional[Path] = EntryArgs.to,

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        taxa: Optional[str] = EntryArgs.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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        check: bool = EntryArgs.test,

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        log: Optional[Path] = EntryArgs.log_path,

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        quiet: bool = EntryArgs.quiet,

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        verbose: bool = EntryArgs.verbose,

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        no_setup: bool = EntryArgs.no_setup,

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

        OBJECT: ChEMBL preferred target name

        PREDICATE: Target action; e.g. "agonist of" or "positive allosteric modulator of"

        OTHER COLUMNS:

        - direct_interaction: true or false

        - description: From ChEMBL

        - exact_target_id: the specifically annotated target, before traversal
        """
        built = MechanismSearch(
            key=key,
            api=Apis.Chembl,
            taxa=Utils.get_taxa(taxa),
            traversal_strategy=traversal,
            allowed_target_types=Utils.get_target_types(target_types),
            min_confidence_score=min_confidence,
        )
        return cls._run(built, path, to, check, log, quiet, verbose, no_setup)


class EntryChemblTrials(Entry[IndicationSearch]):

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)

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        cls,

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        path: Path = EntryArgs.path,

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

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        to: Optional[Path] = EntryArgs.to,

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        min_phase: Optional[int] = EntryArgs.chembl_trial,

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        check: bool = EntryArgs.test,

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        log: Optional[Path] = EntryArgs.log_path,

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        quiet: bool = EntryArgs.quiet,

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        verbose: bool = EntryArgs.verbose,

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        no_setup: bool = EntryArgs.no_setup,

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

        OBJECT: MeSH code

        PREDICATE: "phase <level> trial"
        """
        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]):

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)

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        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = EntryArgs.path,

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

Wrong hanging indentation before block (add 4 spaces).

        to: Optional[Path] = EntryArgs.to,

Wrong hanging indentation before block (add 4 spaces).

        levels: str = EntryArgs.atc_level,

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        check: bool = EntryArgs.test,

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        log: Optional[Path] = EntryArgs.log_path,

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        quiet: bool = EntryArgs.quiet,

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        verbose: bool = EntryArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = EntryArgs.no_setup,

Wrong hanging indentation before block (add 4 spaces).

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

        OBJECT: ATC Code

        PREDICATE: "ATC L<leveL> code"
        """
        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:

Missing function or method docstring

        raise NotImplementedError()

    @classmethod
    def cmd(cls) -> str:

Missing function or method docstring

        me = str(cls.go_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"chembl:go.{me.lower()}"

    @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)

This function exceeds the maximum number of variables (20/15).

Too many arguments (17/5)

        cls,

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        path: Path = EntryArgs.path,

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

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        to: Optional[Path] = EntryArgs.to,

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        taxa: Optional[str] = EntryArgs.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,

Wrong hanging indentation before block (add 4 spaces).

        banned_flags: Optional[str] = EntryArgs.banned_flags,

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        binding_search: Optional[str] = EntryArgs.binding_search_name,

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        check: bool = EntryArgs.test,

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        log: Optional[Path] = EntryArgs.log_path,

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        quiet: bool = EntryArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = EntryArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = EntryArgs.no_setup,

Wrong hanging indentation before block (add 4 spaces).

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

        OBJECT: GO Term name

        PREDICATE: "associated with ""Function"|"Process"|"Component"" term"

        OTHER COLUMNS:
            See the docs for ``mandos chembl:binding``

        Note:

            By default, the key is the "chembl:go.function", "chembl:go.process", or "chembl:go.component".

This line is too long as per the coding-style (107/100).

        """
        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"NOTICE: Passing parameters to {binding_clazz.__qualname__}")
        try:
            binding_search = binding_clazz(
                key=key,
                api=Apis.Chembl,
                taxa=Utils.get_taxa(taxa),
                traversal_strategy=traversal_strategy,
                allowed_target_types=Utils.get_target_types(target_types),
                min_confidence_score=confidence,
                allowed_relations=Utils.split(relations),
                min_pchembl=min_pchembl,
                banned_flags=Utils.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):

Missing class docstring

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


class EntryGoProcess(_EntryChemblGo):

Missing class docstring

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


class EntryGoComponent(_EntryChemblGo):

Missing class docstring

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


class EntryPubchemDisease(Entry[DiseaseSearch]):

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 (9/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = EntryArgs.path,

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

Wrong hanging indentation before block (add 4 spaces).

        to: Optional[Path] = EntryArgs.to,

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        check: bool = EntryArgs.test,

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        log: Optional[Path] = EntryArgs.log_path,

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        quiet: bool = EntryArgs.quiet,

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        verbose: bool = EntryArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = EntryArgs.no_setup,

Wrong hanging indentation before block (add 4 spaces).

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

        Comparative Toxicogenomics Database.

        OBJECT: MeSH code of disease

        PREDICATE: "marker/mechanism evidence for" or "disease evidence for"
        """
        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 (11/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = EntryArgs.path,

Wrong hanging indentation before block (add 4 spaces).

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

Wrong hanging indentation before block (add 4 spaces).

        to: Optional[Path] = EntryArgs.to,

Wrong hanging indentation before block (add 4 spaces).

        min_score: float = EntryArgs.min_cooccurrence_score,

Wrong hanging indentation before block (add 4 spaces).

        min_articles: int = EntryArgs.min_cooccurring_articles,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = EntryArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.test,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = EntryArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = EntryArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = EntryArgs.no_setup,

Wrong hanging indentation before block (add 4 spaces).

    ) -> Searcher:
        """
        Co-occurrences from PubMed articles.
        There is extended documentation on this search.
        Also refer to https://pubchemdocs.ncbi.nlm.nih.gov/knowledge-panels

        OBJECT: Name of gene/chemical/disease

        PREDICATE: "co-occurs with <gene/chemical/disease>"

        OTHER COLUMNS:

        - score: enrichment score; see PubChem docs

        - intersect_count: Number of articles co-occurring

        - query_count: Total number of articles for query compound

        - neighbor_count: Total number of articles for target (co-occurring) compound
        """
        if key is None or key == "<see above>":
            key = cls.cmd()
        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

    """"""


class EntryPubchemDiseaseCoOccurrence(_EntryPubchemCoOccurrence[DiseaseCoOccurrenceSearch]):

Empty class docstring

    """"""


class EntryPubchemChemicalCoOccurrence(_EntryPubchemCoOccurrence[ChemicalCoOccurrenceSearch]):

Empty class docstring

    """"""


class EntryPubchemDgi(Entry[DgiSearch]):

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 (9/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = EntryArgs.path,

Wrong hanging indentation before block (add 4 spaces).

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

Wrong hanging indentation before block (add 4 spaces).

        to: Optional[Path] = EntryArgs.to,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = EntryArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.test,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = EntryArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = EntryArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = EntryArgs.no_setup,

Wrong hanging indentation before block (add 4 spaces).

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

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

        OBJECT: Name of the gene

        PREDICATE: "interacts with gene"
        """
        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
    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 (9/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = EntryArgs.path,

Wrong hanging indentation before block (add 4 spaces).

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

Wrong hanging indentation before block (add 4 spaces).

        to: Optional[Path] = EntryArgs.to,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = EntryArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.test,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = EntryArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = EntryArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = EntryArgs.no_setup,

Wrong hanging indentation before block (add 4 spaces).

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

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

        OBJECT: Name of the gene

        PREDICATE: "compound/gene interaction"

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


class EntryDrugbankTarget(Entry[DrugbankTargetSearch]):

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 (9/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = EntryArgs.path,

Wrong hanging indentation before block (add 4 spaces).

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

Wrong hanging indentation before block (add 4 spaces).

        to: Optional[Path] = EntryArgs.to,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.test,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = EntryArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = EntryArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = EntryArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = EntryArgs.no_setup,

Wrong hanging indentation before block (add 4 spaces).

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

        OBJECT: Target name (e.g. "Solute carrier family 22 member 11") from DrugBank

        PREDICATE: Action (e.g. "binder", "downregulator", or "agonist")
        """
        built = DrugbankTargetSearch(key, Apis.Pubchem, {DrugbankTargetType.target})
        return cls._run(built, path, to, check, log, quiet, verbose, no_setup)


class EntryGeneralFunction(Entry[DrugbankGeneralFunctionSearch]):

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 (9/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = EntryArgs.path,

Wrong hanging indentation before block (add 4 spaces).

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

Wrong hanging indentation before block (add 4 spaces).

        to: Optional[Path] = EntryArgs.to,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.test,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = EntryArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = EntryArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = EntryArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = EntryArgs.no_setup,

Wrong hanging indentation before block (add 4 spaces).

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

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

        PREDICATE: against on target (e.g. "binder", "downregulator", or "agonist").
        """
        built = DrugbankGeneralFunctionSearch(key, Apis.Pubchem, {DrugbankTargetType.target})
        return cls._run(built, path, to, check, log, quiet, verbose, no_setup)


class EntryDrugbankTransporter(Entry[DrugbankTargetSearch]):

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 (9/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = EntryArgs.path,

Wrong hanging indentation before block (add 4 spaces).

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

Wrong hanging indentation before block (add 4 spaces).

        to: Optional[Path] = EntryArgs.to,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.test,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = EntryArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = EntryArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = EntryArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = EntryArgs.no_setup,

Wrong hanging indentation before block (add 4 spaces).

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

        OBJECT: Transporter name (e.g. "Solute carrier family 22 member 11") from DrugBank

        PREDICATE: "transported by", "carried by", or "metabolized by"
        """
        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]):

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 (9/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = EntryArgs.path,

Wrong hanging indentation before block (add 4 spaces).

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

Wrong hanging indentation before block (add 4 spaces).

        to: Optional[Path] = EntryArgs.to,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.test,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = EntryArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = EntryArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = EntryArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = EntryArgs.no_setup,

Wrong hanging indentation before block (add 4 spaces).

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

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

        PREDICATE: "transported by", "carried by", or "metabolized by"
        """
        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]):

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 (9/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = EntryArgs.path,

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] = EntryArgs.to,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.test,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = EntryArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = EntryArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = EntryArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = EntryArgs.no_setup,

Wrong hanging indentation before block (add 4 spaces).

    ) -> 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: name of the drug (e.g. "ibuprofen")

        PREDICATE: "ddi"
        """
        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 (11/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = EntryArgs.path,

Wrong hanging indentation before block (add 4 spaces).

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

Wrong hanging indentation before block (add 4 spaces).

        to: Optional[Path] = EntryArgs.to,

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] = None,

The argument ban_sources seems to be unused.

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.test,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = EntryArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = EntryArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = EntryArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = EntryArgs.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: Name of the target without species suffix (e.g. "Slc6a3 - solute carrier family 6 member 3")

This line is too long as per the coding-style (108/100).

        PREDICATE: "active"|"inactive"|"inconclusive"|"undetermined"

        SOURCE: "PubChem: <referrer> "(""confirmatory"|"literature"|"other"")"
        """
        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]):

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 (9/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = EntryArgs.path,

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] = EntryArgs.to,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.test,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = EntryArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = EntryArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = EntryArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = EntryArgs.no_setup,

Wrong hanging indentation before block (add 4 spaces).

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

        OBJECT: (1 to 4, or "unscheduled")

        PREDICATE: "has DEA schedule"
        """
        pass

Unnecessary pass statement

class EntryDeaClass(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 (9/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = EntryArgs.path,

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] = EntryArgs.to,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.test,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = EntryArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = EntryArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = EntryArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = EntryArgs.no_setup,

Wrong hanging indentation before block (add 4 spaces).

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

        OBJECT: e.g. "hallucinogen"

        PREDICATE: "is in DEA class"
        """
        pass

Unnecessary pass statement

class EntryChemidPlusAcute(Entry[AcuteEffectSearch]):

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 (10/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = EntryArgs.path,

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] = EntryArgs.to,

Wrong hanging indentation before block (add 4 spaces).

        level: int = EntryArgs.acute_effect_level,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.test,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = EntryArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = EntryArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = EntryArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = EntryArgs.no_setup,

Wrong hanging indentation before block (add 4 spaces).

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

        OBJECT: E.g. "behavioral: excitement"

        PREDICATE: "causes acute effect"

        OTHER COLUMNS:

            - organism: e.g. 'women', 'infant', 'men', 'human', 'dog', 'domestic animals - sheep and goats'

This line is too long as per the coding-style (107/100).

            - human: true or false
            - test_type: e.g. 'TDLo'
            - route: e.g. 'skin'
            - mg_per_kg: e.g. 17.5
        """
        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
    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 (9/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = EntryArgs.path,

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] = EntryArgs.to,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.test,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = EntryArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = EntryArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = EntryArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = EntryArgs.no_setup,

Wrong hanging indentation before block (add 4 spaces).

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

        OBJECT: A dose in mg/kg (e.g. 3100)

        PREDICATE: "LD50 :: <route>" (e.g. "LD50 :: intravenous)

        OTHER COLUMNS:

            - organism: e.g. 'women', 'infant', 'men', 'human', 'dog', 'domestic animals - sheep and goats'

This line is too long as per the coding-style (107/100).

            - human: true or false
        """
        built = Ld50Search(key, Apis.Pubchem)
        return cls._run(built, path, to, check, log, quiet, verbose, no_setup)


class EntryHmdbTissue(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 (10/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = EntryArgs.path,

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] = EntryArgs.to,

Wrong hanging indentation before block (add 4 spaces).

        min_nanomolar: Optional[float] = None,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.test,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = EntryArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = EntryArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = EntryArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = EntryArgs.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 (10/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = EntryArgs.path,

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] = EntryArgs.to,

Wrong hanging indentation before block (add 4 spaces).

        min_nanomolar: Optional[float] = None,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.test,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = EntryArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = EntryArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = EntryArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = EntryArgs.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 EntryPubchemReact(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 (9/5)

        cls,

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        path: Path = EntryArgs.path,

Wrong hanging indentation before block (add 4 spaces).

        key: str = EntryArgs.key("inter.pubchem:react"),

Wrong hanging indentation before block (add 4 spaces).

        to: Optional[Path] = EntryArgs.to,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.test,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = EntryArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = EntryArgs.quiet,

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        verbose: bool = EntryArgs.verbose,

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        no_setup: bool = EntryArgs.no_setup,

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    ) -> Searcher:
        """
        Metabolic reactions (PENDING).

        OBJECT: Equation

        PREDICATE: "<pathway>"
        """
        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 (10/5)

        cls,

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        path: Path = EntryArgs.path,

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] = EntryArgs.to,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.test,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = EntryArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = EntryArgs.quiet,

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        verbose: bool = EntryArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = EntryArgs.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,
            }
            if v is not None
        }
        keys = {known.get(s.strip(), s) for s in keys.split(",")}
        built = ComputedPropertySearch(key, Apis.Pubchem, descriptors=keys, source="PubChem")
        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 (9/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = EntryArgs.path,

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] = EntryArgs.to,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.test,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = EntryArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = EntryArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = EntryArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = EntryArgs.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(

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 (9/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = EntryArgs.path,

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] = EntryArgs.to,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.test,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = EntryArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = EntryArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = EntryArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = EntryArgs.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]):

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 (9/5)

        cls,

Wrong hanging indentation before block (add 4 spaces).

        path: Path = EntryArgs.path,

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] = EntryArgs.to,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.test,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = EntryArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = EntryArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = EntryArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = EntryArgs.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 (9/5)

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 = EntryArgs.path,

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] = EntryArgs.to,

Wrong hanging indentation before block (add 4 spaces).

        check: bool = EntryArgs.test,

Wrong hanging indentation before block (add 4 spaces).

        log: Optional[Path] = EntryArgs.log_path,

Wrong hanging indentation before block (add 4 spaces).

        quiet: bool = EntryArgs.quiet,

Wrong hanging indentation before block (add 4 spaces).

        verbose: bool = EntryArgs.verbose,

Wrong hanging indentation before block (add 4 spaces).

        no_setup: bool = EntryArgs.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,
    EntryPubchemDisease,
    EntryPubchemGeneCoOccurrence,
    EntryPubchemDiseaseCoOccurrence,
    EntryPubchemChemicalCoOccurrence,
    EntryPubchemDgi,
    EntryPubchemCgi,
    EntryDrugbankTarget,
    EntryGeneralFunction,
    EntryDrugbankTransporter,
    EntryTransporterGeneralFunction,
    EntryDrugbankDdi,
    EntryPubchemAssay,
    EntryDeaSchedule,
    EntryDeaClass,
    EntryChemidPlusAcute,
    EntryChemidPlusLd50,
    EntryHmdbTissue,
    EntryPubchemReact,
    EntryMetaRandom,
]