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from __future__ import annotations |
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2
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3
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import abc |
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import typing |
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from dataclasses import dataclass |
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from pathlib import Path |
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7
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from typing import Optional, TypeVar, Union |
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8
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9
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from pocketutils.core.dot_dict import NestedDotDict |
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from pocketutils.core.hashers import Hasher |
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from pocketutils.tools.common_tools import CommonTools |
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from mandos.model.settings import MANDOS_SETTINGS |
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from mandos.model.utils import MiscUtils |
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class Api(metaclass=abc.ABCMeta): |
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""" """ |
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class CompoundNotFoundError(LookupError): |
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""" """ |
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class MultipleMatchesError(ValueError): |
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""" """ |
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T = TypeVar("T", covariant=True) |
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30
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31
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@dataclass(frozen=True, repr=True, order=True) |
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class CompoundStruct: |
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""" |
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Uniform data view for ChEMBL, PubChem, etc. |
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Contains the source db (e.g. "pubchem"), the ID as a str, the inchi, and the inchikey. |
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""" |
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db: str |
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id: str |
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inchi: str |
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inchikey: str |
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@property |
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def simple_str(self) -> str: |
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db = "" if self.db.lower() == "chembl" else self.db + " " |
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return f"[{db}{self.id} : {self.inchikey}]" |
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48
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49
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50
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class MandosResources: |
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52
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start_time = MiscUtils.utc() |
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start_time_local = start_time.astimezone() |
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start_timestamp = start_time.isoformat(timespec="milliseconds") |
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start_timestamp_filesys = start_time_local.strftime("%Y-%m-%d_%H-%M-%S") |
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hasher: Hasher = Hasher("sha256", buffer_size=16 * 1024) |
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57
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58
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@classmethod |
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def contains(cls, *nodes: Union[Path, str], suffix: Optional[str] = None) -> bool: |
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"""Returns whether a resource file (or dir) exists.""" |
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return cls.path(*nodes, suffix=suffix).exists() |
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@classmethod |
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def path(cls, *nodes: Union[Path, str], suffix: Optional[str] = None) -> Path: |
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"""Gets a path of a test resource file under ``resources/``.""" |
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path = Path(Path(__file__).parent.parent, "resources", *nodes) |
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return path.with_suffix(path.suffix if suffix is None else suffix) |
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69
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@classmethod |
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def a_path(cls, *nodes: Union[Path, str], suffixes: Optional[typing.Set[str]] = None) -> Path: |
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"""Gets a path of a test resource file under ``resources/``, ignoring suffix.""" |
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path = Path(Path(__file__).parent.parent, "resources", *nodes) |
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return CommonTools.only( |
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[ |
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p |
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for p in path.parent.glob(path.stem + "*") |
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if p.is_file() and (suffixes is None or p.suffix in suffixes) |
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] |
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) |
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80
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81
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@classmethod |
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def json(cls, *nodes: Union[Path, str], suffix: Optional[str] = None) -> NestedDotDict: |
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"""Reads a JSON file under ``resources/``.""" |
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return NestedDotDict.read_json(cls.path(*nodes, suffix=suffix)) |
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85
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86
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87
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__all__ = [ |
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"Api", |
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"CompoundStruct", |
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"CompoundNotFoundError", |
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"MultipleMatchesError", |
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"MandosResources", |
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] |
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dmyersturnbull /
mandos
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