mandos.model.apis.chembl_support.DataValidityComment.resolve() - Code Metrics - Inspection of "feat: massive changes" - dmyersturnbull/mandos - Measure and Improve Code Quality continuously with Scrutinizer

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Push — main ( ddff4b...7b3fbc )

by Douglas

created 2021-06-30 04:47 UTC

DataValidityComment.resolve() B

↳ Parent: mandos.model.apis.chembl_support

Complexity

Conditions

Size

Total Lines	16
Code Lines	15

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	6
eloc	15
nop	2
dl	0
loc	16
rs	8.6666
c	0
b	0
f	0

from __future__ import annotations

import enum
from dataclasses import dataclass
from typing import Set, Union

from mandos.model import CleverEnum, CompoundNotFoundError


class ChemblCompoundLookupError(CompoundNotFoundError):

    """ """


class ActivityRelation(CleverEnum):

    lt = enum.auto()
    gt = enum.auto()
    le = enum.auto()
    ge = enum.auto()
    eq = enum.auto()
    approx = enum.auto()

    @classmethod
    def of(cls, name: Union[int, str]) -> CleverEnum:

        return super().of(
            {
                "<": "lt",
                ">": "gt",
                "=": "eq",
                "~": "approx",
                "<=": "le",
                ">=": "ge",
            }.get(name, name)
        )


class DataValidityComment(CleverEnum):

    potential_missing_data = enum.auto()
    potential_transcription_error = enum.auto()
    potential_author_error = enum.auto()
    manually_validated = enum.auto()
    outside_typical_range = enum.auto()
    non_standard_unit_for_type = enum.auto()
    author_confirmed_error = enum.auto()

    @classmethod
    def resolve(cls, st: str) -> Set[DataValidityComment]:

        found = set()
        for s in st.lower().split(","):

            s = s.strip()

            if s == "@all":
                return set(cls)
            if s == "@negative":
                match = DataValidityComment.negative_comments()
            elif s == "@positive":
                match = DataValidityComment.positive_comments()
            else:
                match = {DataValidityComment.of(s)}
            for m in match:

                found.add(m)
        return found

    @property
    def is_positive(self) -> bool:

        return self in DataValidityComment.positive_comments()

    @property
    def is_negative(self) -> bool:

        return self in DataValidityComment.negative_comments()

    @classmethod
    def positive_comments(cls) -> Set[DataValidityComment]:

        return {DataValidityComment.manually_validated}

    @classmethod
    def negative_comments(cls) -> Set[DataValidityComment]:

        return {
            DataValidityComment.potential_missing_data,
            DataValidityComment.potential_transcription_error,
            DataValidityComment.potential_author_error,
            DataValidityComment.outside_typical_range,
            DataValidityComment.non_standard_unit_for_type,
            DataValidityComment.author_confirmed_error,
        }


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

class ChemblCompound:
    """ """

    chid: str
    inchikey: str
    name: str


class AssayType(enum.Enum):

    binding = enum.auto()
    functional = enum.auto()
    adme = enum.auto()
    physicochemical = enum.auto()

    @property
    def character(self) -> str:

        return {
            AssayType.binding: "B",
            AssayType.functional: "F",
            AssayType.adme: "A",
            AssayType.physicochemical: "P",
        }[self]


__all__ = [
    "ChemblCompound",
    "ChemblCompoundLookupError",
    "DataValidityComment",
    "ActivityRelation",
    "AssayType",
]


1			from __future__ import annotations
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing module docstring Loading history...
2			import enum
3			from dataclasses import dataclass
4			from typing import Set, Union
5
6			from mandos.model import CleverEnum, CompoundNotFoundError
7
8
9			class ChemblCompoundLookupError(CompoundNotFoundError):
			0 ignored issues – show Documentation introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Empty class docstring Loading history...
10			""" """
11
12
13			class ActivityRelation(CleverEnum):
			0 ignored issues – show introduced 2021-03-21 02:08 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
14			lt = enum.auto()
15			gt = enum.auto()
16			le = enum.auto()
17			ge = enum.auto()
18			eq = enum.auto()
19			approx = enum.auto()
20
21			@classmethod
22			def of(cls, name: Union[int, str]) -> CleverEnum:
			0 ignored issues – show Bug introduced 2021-03-21 02:08 UTC by Report Bug Copy Issue Report Parameters differ from overridden 'of' method Loading history...
23			return super().of(
24			{
25			"<": "lt",
26			">": "gt",
27			"=": "eq",
28			"~": "approx",
29			"<=": "le",
30			">=": "ge",
31			}.get(name, name)
32			)
33
34
35			class DataValidityComment(CleverEnum):
			0 ignored issues – show introduced 2021-03-21 02:08 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
36			potential_missing_data = enum.auto()
37			potential_transcription_error = enum.auto()
38			potential_author_error = enum.auto()
39			manually_validated = enum.auto()
40			outside_typical_range = enum.auto()
41			non_standard_unit_for_type = enum.auto()
42			author_confirmed_error = enum.auto()
43
44			@classmethod
45			def resolve(cls, st: str) -> Set[DataValidityComment]:
			0 ignored issues – show Coding Style Naming introduced 2021-03-21 02:08 UTC by Report Bug Copy Issue Report Argument name "st" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history... introduced 2021-03-21 02:08 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
46			found = set()
47			for s in st.lower().split(","):
			0 ignored issues – show Coding Style Naming introduced 2021-03-21 02:08 UTC by Report Bug Copy Issue Report Variable name "s" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
48			s = s.strip()
			0 ignored issues – show Coding Style Naming introduced 2021-03-21 02:08 UTC by Report Bug Copy Issue Report Variable name "s" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
49			if s == "@all":
50			return set(cls)
51			if s == "@negative":
52			match = DataValidityComment.negative_comments()
53			elif s == "@positive":
54			match = DataValidityComment.positive_comments()
55			else:
56			match = {DataValidityComment.of(s)}
57			for m in match:
			0 ignored issues – show Coding Style Naming introduced 2021-03-21 02:08 UTC by Report Bug Copy Issue Report Variable name "m" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
58			found.add(m)
59			return found
60
61			@property
62			def is_positive(self) -> bool:
			0 ignored issues – show introduced 2021-03-21 02:08 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
63			return self in DataValidityComment.positive_comments()
64
65			@property
66			def is_negative(self) -> bool:
			0 ignored issues – show introduced 2021-03-21 02:08 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
67			return self in DataValidityComment.negative_comments()
68
69			@classmethod
70			def positive_comments(cls) -> Set[DataValidityComment]:
			0 ignored issues – show introduced 2021-03-21 02:08 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
71			return {DataValidityComment.manually_validated}
72
73			@classmethod
74			def negative_comments(cls) -> Set[DataValidityComment]:
			0 ignored issues – show introduced 2021-03-21 02:08 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
75			return {
76			DataValidityComment.potential_missing_data,
77			DataValidityComment.potential_transcription_error,
78			DataValidityComment.potential_author_error,
79			DataValidityComment.outside_typical_range,
80			DataValidityComment.non_standard_unit_for_type,
81			DataValidityComment.author_confirmed_error,
82			}
83
84
85			@dataclass(frozen=True, order=True, repr=True)
			0 ignored issues – show Documentation introduced 2021-06-30 04:51 UTC by Report Bug Copy Issue Report Empty class docstring Loading history...
86			class ChemblCompound:
87			""" """
88
89			chid: str
90			inchikey: str
91			name: str
92
93
94			class AssayType(enum.Enum):
			0 ignored issues – show introduced 2021-03-22 20:05 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
95			binding = enum.auto()
96			functional = enum.auto()
97			adme = enum.auto()
98			physicochemical = enum.auto()
99
100			@property
101			def character(self) -> str:
			0 ignored issues – show introduced 2021-03-22 20:05 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
102			return {
103			AssayType.binding: "B",
104			AssayType.functional: "F",
105			AssayType.adme: "A",
106			AssayType.physicochemical: "P",
107			}[self]
108
109
110			__all__ = [
111			"ChemblCompound",
112			"ChemblCompoundLookupError",
113			"DataValidityComment",
114			"ActivityRelation",
115			"AssayType",
116			]
117

dmyersturnbull / mandos

Push — main ( ddff4b...7b3fbc )

DataValidityComment.resolve() B

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