mandos.model

Complexity

Total Complexity

7

Size/Duplication

Total Lines	93
Duplicated Lines	0 %

Importance

Changes

0

5 Methods

Rating	Name	Duplication	Size	Complexity
A	MandosResources.path()	0	5	2
A	MandosResources.json()	0	4	1
A	CompoundStruct.simple_str()	0	4	2
A	MandosResources.a_path()	0	9	1
A	MandosResources.contains()	0	4	1

from __future__ import annotations

Missing module docstring

import abc
import typing
from dataclasses import dataclass
from pathlib import Path
from typing import Optional, TypeVar, Union

from pocketutils.core.dot_dict import NestedDotDict

Unable to import 'pocketutils.core.dot_dict'

from pocketutils.core.hashers import Hasher

Unable to import 'pocketutils.core.hashers'

from pocketutils.tools.common_tools import CommonTools

Unable to import 'pocketutils.tools.common_tools'

from mandos.model.settings import MANDOS_SETTINGS
from mandos.model.utils import MiscUtils


class Api(metaclass=abc.ABCMeta):

Empty class docstring

    """ """


class CompoundNotFoundError(LookupError):

Empty class docstring

    """ """


class MultipleMatchesError(ValueError):

Empty class docstring

    """ """


T = TypeVar("T", covariant=True)

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

@dataclass(frozen=True, repr=True, order=True)
class CompoundStruct:
    """
    Uniform data view for ChEMBL, PubChem, etc.
    Contains the source db (e.g. "pubchem"), the ID as a str, the inchi, and the inchikey.
    """

    db: str

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

    id: str

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

    inchi: str
    inchikey: str

    @property
    def simple_str(self) -> str:

Missing function or method docstring

        db = "" if self.db.lower() == "chembl" else self.db + " "

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

        return f"[{db}{self.id} : {self.inchikey}]"


class MandosResources:

Missing class docstring

    start_time = MiscUtils.utc()
    start_time_local = start_time.astimezone()
    start_timestamp = start_time.isoformat(timespec="milliseconds")
    start_timestamp_filesys = start_time_local.strftime("%Y-%m-%d_%H-%M-%S")
    hasher: Hasher = Hasher("sha256", buffer_size=16 * 1024)

    @classmethod
    def contains(cls, *nodes: Union[Path, str], suffix: Optional[str] = None) -> bool:
        """Returns whether a resource file (or dir) exists."""
        return cls.path(*nodes, suffix=suffix).exists()

    @classmethod
    def path(cls, *nodes: Union[Path, str], suffix: Optional[str] = None) -> Path:
        """Gets a path of a test resource file under ``resources/``."""
        path = Path(Path(__file__).parent.parent, "resources", *nodes)
        return path.with_suffix(path.suffix if suffix is None else suffix)

    @classmethod
    def a_path(cls, *nodes: Union[Path, str], suffixes: Optional[typing.Set[str]] = None) -> Path:
        """Gets a path of a test resource file under ``resources/``, ignoring suffix."""
        path = Path(Path(__file__).parent.parent, "resources", *nodes)
        return CommonTools.only(
            [
                p
                for p in path.parent.glob(path.stem + "*")
                if p.is_file() and (suffixes is None or p.suffix in suffixes)
            ]
        )

    @classmethod
    def json(cls, *nodes: Union[Path, str], suffix: Optional[str] = None) -> NestedDotDict:
        """Reads a JSON file under ``resources/``."""
        return NestedDotDict.read_json(cls.path(*nodes, suffix=suffix))


__all__ = [
    "Api",
    "CompoundStruct",
    "CompoundNotFoundError",
    "MultipleMatchesError",
    "MandosResources",
]