mandos.model.utils.MiscUtils.ntp_utc() - Code Metrics - Inspection of "feat: add prediction search; improve taxa" - dmyersturnbull/mandos - Measure and Improve Code Quality continuously with Scrutinizer

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Push — main ( 9813db...5006f2 )

by Douglas

created 2021-08-07 00:13 UTC

mandos.model.utils.MiscUtils.ntp_utc() A

↳ Parent: mandos.model.utils

Complexity

Conditions

Size

Total Lines	6
Code Lines	5

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	1
eloc	5
nop	1
dl	0
loc	6
rs	10
c	0
b	0
f	0

import enum

import inspect
import sys
import typing
from datetime import datetime
from pathlib import Path
from typing import Type, TypeVar, Optional, Mapping, Any, Union, Sequence

from mandos import logger
from suretime import Suretime

from typeddfs import TypedDf


from mandos.model.settings import MANDOS_SETTINGS


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



class InjectionError(LookupError):

    """ """


class ReflectionUtils:

    @classmethod
    def get_generic_arg(cls, clazz: Type[T], bound: Optional[Type[T]] = None) -> Type:
        """
        Finds the generic argument (specific TypeVar) of a :py:class:`~typing.Generic` class.
        **Assumes that ``clazz`` only has one type parameter. Always returns the first.**

        Args:
            clazz: The Generic class
            bound: If non-None, requires the returned type to be a subclass of ``bound`` (or equal to it)


        Returns:
            The class

        Raises:
            AssertionError: For most errors
        """
        bases = clazz.__orig_bases__
        try:
            param = typing.get_args(bases[0])[0]

        except KeyError:
            raise AssertionError(f"Failed to get generic type on {cls}")
        if not issubclass(param, bound):
            raise AssertionError(f"{param} is not a {bound}")
        return param

    @classmethod
    def subclass_dict(cls, clazz: Type[T], concrete: bool = False) -> Mapping[str, Type[T]]:

        return {c.__name__: c for c in cls.subclasses(clazz, concrete=concrete)}

    @classmethod
    def subclasses(cls, clazz, concrete: bool = False):

        for subclass in clazz.__subclasses__():
            yield from cls.subclasses(subclass, concrete=concrete)
            if (
                not concrete

                or not inspect.isabstract(subclass)

                and not subclass.__name__.startswith("_")

            ):
                yield subclass

    @classmethod
    def default_arg_values(cls, func) -> Mapping[str, Optional[Any]]:

        return {k: v.default for k, v in cls.optional_args(func).items()}

    @classmethod
    def required_args(cls, func):
        """
        Finds parameters that lack default values.

        Args:
            func: A function or method

        Returns:
            A dict mapping parameter names to instances of ``MappingProxyType``,
            just as ``inspect.signature(func).parameters`` does.
        """
        return cls._args(func, True)

    @classmethod
    def optional_args(cls, func):
        """
        Finds parameters that have default values.

        Args:
            func: A function or method

        Returns:
            A dict mapping parameter names to instances of ``MappingProxyType``,
            just as ``inspect.signature(func).parameters`` does.
        """
        return cls._args(func, False)

    @classmethod
    def _args(cls, func, req):
        signature = inspect.signature(func)
        return {
            k: v
            for k, v in signature.parameters.items()
            if req
            and v.default is inspect.Parameter.empty
            or not req
            and v.default is not inspect.Parameter.empty
        }

    @classmethod
    def injection(cls, fully_qualified: str, clazz: Type[T]) -> Type[T]:
        """
        Gets a **class** by its fully-resolved class name.

        Args:
            fully_qualified:
            clazz:

        Returns:
            The Type

        Raises:
            InjectionError: If the class was not found
        """
        s = fully_qualified

        mod = s[: s.rfind(".")]
        clz = s[s.rfind(".") :]
        try:
            return getattr(sys.modules[mod], clz)
        except AttributeError:
            raise InjectionError(
                f"Did not find {clazz} by fully-qualified class name {fully_qualified}"
            ) from None


class MiscUtils:
    """
    These are here to make sure I always use the same NTP server, etc.
    """

    @classmethod
    def empty_df(cls, clazz: Type[T], reserved: bool = False) -> T:

        if issubclass(clazz, TypedDf):

            if reserved:
                req = clazz.known_names()
            else:
                req = [*clazz.required_index_names(), *clazz.required_columns]
            return clazz({r: [] for r in req})
        else:
            return clazz({})

    @classmethod
    def adjust_filename(cls, to: Optional[Path], default: Union[str, Path], replace: bool) -> Path:

        if to is None:
            path = Path(default)
        elif str(to).startswith("."):
            path = Path(default).with_suffix(str(to))
        elif to.is_dir() or to.suffix == "":
            path = to / default
        else:
            raise AssertionError(str(to))
        path = Path(path)
        if path.exists() and not replace:

            raise FileExistsError(f"File {path} already exists")
        elif replace:
            logger.info(f"Overwriting existing file {path}.")
        return path

    @classmethod
    def ntp_utc(cls) -> datetime:

        ntp = Suretime.tagged.now_utc_ntp(
            ntp_server=MANDOS_SETTINGS.ntp_continent, ntp_clock="client-sent"
        )
        return ntp.use_clock_as_dt.dt

    @classmethod
    def utc(cls) -> datetime:

        return Suretime.tagged.now_utc_sys().dt

    @classmethod
    def serialize_list(cls, lst: Sequence[str]) -> str:

        return " || ".join([str(x) for x in lst])

    @classmethod
    def deserialize_list(cls, s: str) -> Sequence[str]:

        return s.split(" || ")


class TrueFalseUnknown(enum.Enum):

    true = enum.auto()
    false = enum.auto()
    unknown = enum.auto()

    @classmethod
    def parse(cls, s: str):

        tf_map = {
            "t": TrueFalseUnknown.true,
            "f": TrueFalseUnknown.false,
            "true": TrueFalseUnknown.true,
            "false": TrueFalseUnknown.false,
        }
        return tf_map.get(s.lower().strip(), TrueFalseUnknown.unknown)


class CleverEnum(enum.Enum):
    """
    An enum with a ``.of`` method that finds values
    with limited string/value fixing.
    May support an "unmatched" type -- a fallback value when there is no match.
    This is similar to pocketutils' simpler ``SmartEnum``.
    It is mainly useful for enums corresponding to concepts in ChEMBL and PubChem,
    where it's acceptable for the user to input spaces (like the database concepts use)
    rather than the underscores that Python requires.
    """

    @classmethod
    def _unmatched_type(cls) -> Optional[__qualname__]:
        return None

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

        """
        Turns a string or int into this type.
        Case-insensitive. Replaces `` ``, ``.``, and ``-`` with ``_``.
        """
        if isinstance(s, cls):
            return s
        key = s.strip().replace(" ", "_").replace(".", "_").replace("-", "_").lower()
        try:
            if isinstance(s, str):

                return cls[key]
            elif isinstance(key, int):
                return cls(key)
            else:
                raise TypeError(f"Lookup type {type(s)} for value {s} not a str or int")
        except KeyError:
            unk = cls._unmatched_type()
            if unk is None:
                raise
            logger.error(f"Value {key} not found. Using {unk}")
            if not isinstance(unk, cls):
                raise AssertionError(f"Wrong type {type(unk)} (lookup: {s})")
            return unk


__all__ = ["InjectionError", "ReflectionUtils", "MiscUtils", "TrueFalseUnknown", "CleverEnum"]


1			import enum
			0 ignored issues – show introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Missing module docstring Loading history...
2			import inspect
3			import sys
4			import typing
5			from datetime import datetime
6			from pathlib import Path
7			from typing import Type, TypeVar, Optional, Mapping, Any, Union, Sequence
8
9			from mandos import logger
10			from suretime import Suretime
			0 ignored issues – show introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Unable to import 'suretime' Loading history...
11			from typeddfs import TypedDf
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12
13			from mandos.model.settings import MANDOS_SETTINGS
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14
15			T = TypeVar("T", covariant=True)
			0 ignored issues – show Coding Style Naming introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Class name "T" doesn't conform to PascalCase naming style ('[^\\W\\da-z][^\\W_]+$' 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...
16
17
18			class InjectionError(LookupError):
			0 ignored issues – show Documentation introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Empty class docstring Loading history...
19			""" """
20
21
22			class ReflectionUtils:
			0 ignored issues – show introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
23			@classmethod
24			def get_generic_arg(cls, clazz: Type[T], bound: Optional[Type[T]] = None) -> Type:
25			"""
26			Finds the generic argument (specific TypeVar) of a :py:class:`~typing.Generic` class.
27			Assumes that ``clazz`` only has one type parameter. Always returns the first.
28
29			Args:
30			clazz: The Generic class
31			bound: If non-None, requires the returned type to be a subclass of ``bound`` (or equal to it)
			0 ignored issues – show Coding Style introduced 2021-03-22 20:05 UTC by Report Bug Copy Issue Report This line is too long as per the coding-style (105/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history...
32
33			Returns:
34			The class
35
36			Raises:
37			AssertionError: For most errors
38			"""
39			bases = clazz.__orig_bases__
40			try:
41			param = typing.get_args(bases[0])[0]
			0 ignored issues – show Bug introduced 2021-03-21 02:08 UTC by Report Bug Copy Issue Report The Module `typing` does not seem to have a member named `get_args`. This check looks for calls to members that are non-existent. These calls will fail. The member could have been renamed or removed. Loading history...
42			except KeyError:
43			raise AssertionError(f"Failed to get generic type on {cls}")
44			if not issubclass(param, bound):
45			raise AssertionError(f"{param} is not a {bound}")
46			return param
47
48			@classmethod
49			def subclass_dict(cls, clazz: Type[T], concrete: bool = False) -> Mapping[str, Type[T]]:
			0 ignored issues – show introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
50			return {c.__name__: c for c in cls.subclasses(clazz, concrete=concrete)}
51
52			@classmethod
53			def subclasses(cls, clazz, concrete: bool = False):
			0 ignored issues – show introduced 2021-06-30 04:51 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
54			for subclass in clazz.__subclasses__():
55			yield from cls.subclasses(subclass, concrete=concrete)
56			if (
57			not concrete
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58			or not inspect.isabstract(subclass)
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59			and not subclass.__name__.startswith("_")
			0 ignored issues – show Coding Style introduced 2021-08-02 23:39 UTC by Report Bug Copy Issue Report Wrong hanging indentation before block (add 4 spaces). Loading history...
60			):
61			yield subclass
62
63			@classmethod
64			def default_arg_values(cls, func) -> Mapping[str, Optional[Any]]:
			0 ignored issues – show introduced 2021-06-30 04:51 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
65			return {k: v.default for k, v in cls.optional_args(func).items()}
66
67			@classmethod
68			def required_args(cls, func):
69			"""
70			Finds parameters that lack default values.
71
72			Args:
73			func: A function or method
74
75			Returns:
76			A dict mapping parameter names to instances of ``MappingProxyType``,
77			just as ``inspect.signature(func).parameters`` does.
78			"""
79			return cls._args(func, True)
80
81			@classmethod
82			def optional_args(cls, func):
83			"""
84			Finds parameters that have default values.
85
86			Args:
87			func: A function or method
88
89			Returns:
90			A dict mapping parameter names to instances of ``MappingProxyType``,
91			just as ``inspect.signature(func).parameters`` does.
92			"""
93			return cls._args(func, False)
94
95			@classmethod
96			def _args(cls, func, req):
97			signature = inspect.signature(func)
98			return {
99			k: v
100			for k, v in signature.parameters.items()
101			if req
102			and v.default is inspect.Parameter.empty
103			or not req
104			and v.default is not inspect.Parameter.empty
105			}
106
107			@classmethod
108			def injection(cls, fully_qualified: str, clazz: Type[T]) -> Type[T]:
109			"""
110			Gets a class by its fully-resolved class name.
111
112			Args:
113			fully_qualified:
114			clazz:
115
116			Returns:
117			The Type
118
119			Raises:
120			InjectionError: If the class was not found
121			"""
122			s = fully_qualified
			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...
123			mod = s[: s.rfind(".")]
124			clz = s[s.rfind(".") :]
125			try:
126			return getattr(sys.modules[mod], clz)
127			except AttributeError:
128			raise InjectionError(
129			f"Did not find {clazz} by fully-qualified class name {fully_qualified}"
130			) from None
131
132
133			class MiscUtils:
134			"""
135			These are here to make sure I always use the same NTP server, etc.
136			"""
137
138			@classmethod
139			def empty_df(cls, clazz: Type[T], reserved: bool = False) -> T:
			0 ignored issues – show introduced 2021-06-30 04:51 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
140			if issubclass(clazz, TypedDf):
			0 ignored issues – show unused-code introduced 2021-08-02 23:39 UTC by Report Bug Copy Issue Report Unnecessary "else" after "return" Loading history...
141			if reserved:
142			req = clazz.known_names()
143			else:
144			req = [clazz.required_index_names(), clazz.required_columns]
145			return clazz({r: [] for r in req})
146			else:
147			return clazz({})
148
149			@classmethod
150			def adjust_filename(cls, to: Optional[Path], default: Union[str, Path], replace: bool) -> Path:
			0 ignored issues – show introduced 2021-06-30 04:51 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history... Coding Style Naming introduced 2021-06-30 04:51 UTC by Report Bug Copy Issue Report 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 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...
151			if to is None:
152			path = Path(default)
153			elif str(to).startswith("."):
154			path = Path(default).with_suffix(str(to))
155			elif to.is_dir() or to.suffix == "":
156			path = to / default
157			else:
158			raise AssertionError(str(to))
159			path = Path(path)
160			if path.exists() and not replace:
			0 ignored issues – show Unused Code introduced 2021-08-03 04:51 UTC by Report Bug Copy Issue Report Unnecessary "elif" after "raise" Loading history...
161			raise FileExistsError(f"File {path} already exists")
162			elif replace:
163			logger.info(f"Overwriting existing file {path}.")
164			return path
165
166			@classmethod
167			def ntp_utc(cls) -> datetime:
			0 ignored issues – show introduced 2021-08-02 23:39 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
168			ntp = Suretime.tagged.now_utc_ntp(
169			ntp_server=MANDOS_SETTINGS.ntp_continent, ntp_clock="client-sent"
170			)
171			return ntp.use_clock_as_dt.dt
172
173			@classmethod
174			def utc(cls) -> datetime:
			0 ignored issues – show introduced 2021-06-30 04:51 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
175			return Suretime.tagged.now_utc_sys().dt
176
177			@classmethod
178			def serialize_list(cls, lst: Sequence[str]) -> str:
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179			return " \|\| ".join([str(x) for x in lst])
180
181			@classmethod
182			def deserialize_list(cls, s: str) -> Sequence[str]:
			0 ignored issues – show introduced 2021-08-02 23:39 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history... Coding Style Naming introduced 2021-06-30 04:51 UTC by Report Bug Copy Issue Report Argument 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...
183			return s.split(" \|\| ")
184
185
186			class TrueFalseUnknown(enum.Enum):
			0 ignored issues – show introduced 2021-06-30 04:51 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
187			true = enum.auto()
188			false = enum.auto()
189			unknown = enum.auto()
190
191			@classmethod
192			def parse(cls, s: str):
			0 ignored issues – show introduced 2021-06-30 04:51 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history... Coding Style Naming introduced 2021-06-30 04:51 UTC by Report Bug Copy Issue Report Argument name "s" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
193			tf_map = {
194			"t": TrueFalseUnknown.true,
195			"f": TrueFalseUnknown.false,
196			"true": TrueFalseUnknown.true,
197			"false": TrueFalseUnknown.false,
198			}
199			return tf_map.get(s.lower().strip(), TrueFalseUnknown.unknown)
200
201
202			class CleverEnum(enum.Enum):
203			"""
204			An enum with a ``.of`` method that finds values
205			with limited string/value fixing.
206			May support an "unmatched" type -- a fallback value when there is no match.
207			This is similar to pocketutils' simpler ``SmartEnum``.
208			It is mainly useful for enums corresponding to concepts in ChEMBL and PubChem,
209			where it's acceptable for the user to input spaces (like the database concepts use)
210			rather than the underscores that Python requires.
211			"""
212
213			@classmethod
214			def _unmatched_type(cls) -> Optional[__qualname__]:
215			return None
216
217			@classmethod
218			def of(cls, s: Union[int, str, __qualname__]) -> __qualname__:
			0 ignored issues – show Coding Style Naming introduced 2021-03-16 18:40 UTC by Report Bug Copy Issue Report Argument name "s" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' 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... Coding Style Naming introduced 2021-03-16 18:40 UTC by Report Bug Copy Issue Report Method name "of" 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...
219			"""
220			Turns a string or int into this type.
221			Case-insensitive. Replaces `` ``, ``.``, and ``-`` with ``_``.
222			"""
223			if isinstance(s, cls):
224			return s
225			key = s.strip().replace(" ", "_").replace(".", "_").replace("-", "_").lower()
226			try:
227			if isinstance(s, str):
			0 ignored issues – show unused-code introduced 2021-03-16 18:40 UTC by Report Bug Copy Issue Report Unnecessary "elif" after "return" Loading history...
228			return cls[key]
229			elif isinstance(key, int):
230			return cls(key)
231			else:
232			raise TypeError(f"Lookup type {type(s)} for value {s} not a str or int")
233			except KeyError:
234			unk = cls._unmatched_type()
235			if unk is None:
236			raise
237			logger.error(f"Value {key} not found. Using {unk}")
238			if not isinstance(unk, cls):
239			raise AssertionError(f"Wrong type {type(unk)} (lookup: {s})")
240			return unk
241
242
243			__all__ = ["InjectionError", "ReflectionUtils", "MiscUtils", "TrueFalseUnknown", "CleverEnum"]
244

dmyersturnbull / mandos

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mandos.model.utils.MiscUtils.ntp_utc() A

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