mandos.model.settings.Settings.add_to_path() - Code Metrics - Inspection of "fix: various" - dmyersturnbull/mandos - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Push — main ( 2b775d...83a9fb )

by Douglas

created 2021-09-23 02:56 UTC

mandos.model.settings.Settings.add_to_path() B

↳ Parent: mandos.model.settings

Complexity

Conditions

Size

Total Lines	10
Code Lines	10

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	6
eloc	10
nop	2
dl	0
loc	10
rs	8.6666
c	0
b	0
f	0

from __future__ import annotations


import os
from collections import Set

from dataclasses import dataclass
from pathlib import Path
from typing import Type, TypeVar, Any, Mapping, Optional, Collection, Union

import orjson

from chembl_webresource_client.settings import Settings as ChemblSettings

from mandos.model.utils.resources import MandosResources
from pocketutils.core.dot_dict import NestedDotDict

from pocketutils.core.query_utils import QueryExecutor

from pocketutils.core.exceptions import DirDoesNotExistError, FileDoesNotExistError, ConfigError

from pocketutils.tools.common_tools import CommonTools

from suretime import Suretime


from mandos.model.utils.setup import logger


defaults: Mapping[str, Any] = orjson.loads(
    MandosResources.path("default_settings.json").read_text(encoding="utf8")
)
T = TypeVar("T")



class Globals:

    chembl_settings = ChemblSettings.Instance()
    cwd = os.getcwd()
    where_am_i_installed = Path(__file__).parent.parent.parent
    is_in_ci = CommonTools.parse_bool(os.environ.get("IS_IN_CI", "false"))
    if is_in_ci:
        mandos_path = Path(__file__).parent.parent.parent / "tests" / "resources" / ".mandos-cache"
    else:
        _default_mandos_home = Path.home() / ".mandos"
        env_vars = {k.lower(): v for k, v in os.environ.items()}
        mandos_path = Path(env_vars.get("MANDOS_HOME", _default_mandos_home))
    settings_path = mandos_path / "settings.toml"
    disable_chembl = CommonTools.parse_bool(os.environ.get("MANDOS_NO_CHEMBL", "false"))
    disable_pubchem = CommonTools.parse_bool(os.environ.get("MANDOS_NO_PUBCHEM", "false"))


@dataclass(frozen=True, repr=True)

class Settings:
    """ """

    is_testing: bool
    ntp_continent: str
    cache_path: Path
    cache_gzip: bool
    chembl_expire_sec: int
    chembl_n_tries: int
    chembl_timeout_sec: int
    chembl_backoff_factor: float
    chembl_query_delay_min: float
    chembl_query_delay_max: float
    chembl_fast_save: bool
    pubchem_expire_sec: int
    pubchem_n_tries: int
    pubchem_timeout_sec: float
    pubchem_backoff_factor: float
    pubchem_query_delay_min: float
    pubchem_query_delay_max: float
    hmdb_expire_sec: int
    hmdb_timeout_sec: float
    hmdb_backoff_factor: float
    hmdb_query_delay_min: float
    hmdb_query_delay_max: float
    taxon_expire_sec: int
    archive_filename_suffix: str
    default_table_suffix: str
    selenium_driver: str
    selenium_driver_path: Optional[Path]

    def __post_init__(self):
        pass

    @property
    def all_cache_paths(self) -> Set[Path]:

        return {
            self.chembl_cache_path,
            self.pubchem_cache_path,
            self.g2p_cache_path,
            self.hmdb_cache_path,
            self.taxonomy_cache_path,
        }

    @property
    def driver_path(self) -> Path:

        return self.cache_path / "driver"

    @property
    def chembl_cache_path(self) -> Path:

        return self.cache_path / "chembl"

    @property
    def chembl_scrape_path(self) -> Path:

        return self.chembl_cache_path / "scrape"

    @property
    def pubchem_cache_path(self) -> Path:

        return self.cache_path / "pubchem"

    @property
    def g2p_cache_path(self) -> Path:

        return self.cache_path / "g2p"

    @property
    def hmdb_cache_path(self) -> Path:

        return self.cache_path / "hmdb"

    @property
    def taxonomy_cache_path(self) -> Path:

        return self.cache_path / "taxonomy"

    @classmethod
    def from_file(cls, path: Path) -> Settings:

        return cls.load(NestedDotDict.read_toml(path))

    @classmethod
    def empty(cls) -> Settings:

        return cls.load(NestedDotDict({}))

    @classmethod
    def load(cls, data: NestedDotDict) -> Settings:

        def get(s: str, t: Type[T]) -> T:

            try:
                return data.get_as(s, t, defaults[s])
            except TypeError:
                raise ConfigError(f"Key {s}={data.get(s), defaults[s]} is not of type {t}")

        _continent = Suretime.Types.NtpContinents.of
        return cls(
            is_testing=get("is_testing", bool),
            ntp_continent=get("continent_code", _continent),
            cache_path=Path(get("cache.path", str)).expanduser(),
            cache_gzip=get("cache.gzip", bool),
            chembl_expire_sec=get("query.chembl.expire_sec", int),
            chembl_n_tries=get("query.chembl.n_tries", int),
            chembl_fast_save=get("query.chembl.fast_save", bool),
            chembl_timeout_sec=get("query.chembl.timeout_sec", int),
            chembl_backoff_factor=get("query.chembl.backoff_factor", float),
            chembl_query_delay_min=get("query.chembl.delay_sec", float),
            chembl_query_delay_max=get("query.chembl.delay_sec", float),
            pubchem_expire_sec=get("query.pubchem.expire_sec", int),
            pubchem_timeout_sec=get("query.pubchem.timeout_sec", int),
            pubchem_backoff_factor=get("query.pubchem.backoff_factor", float),
            pubchem_query_delay_min=get("query.pubchem.delay_sec", float),
            pubchem_query_delay_max=get("query.pubchem.delay_sec", float),
            pubchem_n_tries=get("query.pubchem.n_tries", int),
            hmdb_expire_sec=get("query.hmdb.expire_sec", int),
            hmdb_timeout_sec=get("query.hmdb.timeout_sec", int),
            hmdb_backoff_factor=get("query.hmdb.backoff_factor", float),
            hmdb_query_delay_min=get("query.hmdb.delay_sec", float),
            hmdb_query_delay_max=get("query.hmdb.delay_sec", float),
            taxon_expire_sec=get("query.taxa.expire_sec", int),
            archive_filename_suffix=get("cache.archive_filename_suffix", str),
            default_table_suffix=get("default_table_suffix", str),
            selenium_driver=get("selenium_driver", str).title(),
            selenium_driver_path=get("selenium_driver_path", Path),
        )

    @classmethod
    def defaults(cls) -> Mapping[str, Any]:

        return dict(defaults)

    def configure(self):

        """ """
        if not Globals.disable_chembl:
            instance = Globals.chembl_settings
            instance.CACHING = True
            instance.CACHE_NAME = str(self.chembl_cache_path / "chembl.sqlite")
            instance.TOTAL_RETRIES = self.chembl_n_tries
            instance.FAST_SAVE = self.chembl_fast_save
            instance.TIMEOUT = self.chembl_timeout_sec
            instance.BACKOFF_FACTOR = self.chembl_backoff_factor
            instance.CACHE_EXPIRE = self.chembl_expire_sec

    @classmethod
    def set_path_for_selenium(cls) -> None:

        cls.add_to_path(
            [MANDOS_SETTINGS.driver_path, MandosResources.dir(), Globals.where_am_i_installed]
        )

    @classmethod
    def add_to_path(cls, paths: Collection[Union[None, str, Path]]) -> None:

        paths = {Path(p) for p in paths if p is not None}
        for path in paths:
            if path.exists() and not path.is_dir() and not path.is_mount():
                raise DirDoesNotExistError(f"Path {path} is not a directory or mount")
        paths = os.pathsep.join({str(p) for p in paths})
        if len(paths) > 0:
            os.environ["PATH"] += os.pathsep + paths
        logger.debug(f"Added to PATH: {paths}")


if Globals.settings_path.exists():
    MANDOS_SETTINGS = Settings.from_file(Globals.settings_path)
    logger.info(f"Read settings at {Globals.settings_path}")
else:
    MANDOS_SETTINGS = Settings.empty()
    logger.info(f"Using defaults (no file at {Globals.settings_path})")
MANDOS_SETTINGS.configure()
logger.debug(f"Setting ChEMBL cache to {MANDOS_SETTINGS.chembl_cache_path}")


class QueryExecutors:

    chembl = QueryExecutor(
        MANDOS_SETTINGS.chembl_query_delay_min, MANDOS_SETTINGS.chembl_query_delay_max
    )
    pubchem = QueryExecutor(
        MANDOS_SETTINGS.pubchem_query_delay_min, MANDOS_SETTINGS.pubchem_query_delay_max
    )
    hmdb = QueryExecutor(
        MANDOS_SETTINGS.pubchem_query_delay_min, MANDOS_SETTINGS.pubchem_query_delay_max
    )


QUERY_EXECUTORS = QueryExecutors



__all__ = ["MANDOS_SETTINGS", "QUERY_EXECUTORS"]


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
3			import os
4			from collections import Set
			0 ignored issues – show Bug introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report The name `Set` does not seem to exist in module `collections`. Loading history...
5			from dataclasses import dataclass
6			from pathlib import Path
7			from typing import Type, TypeVar, Any, Mapping, Optional, Collection, Union
8
9			import orjson
			0 ignored issues – show introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Unable to import 'orjson' Loading history...
10			from chembl_webresource_client.settings import Settings as ChemblSettings
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Unable to import 'chembl_webresource_client.settings' Loading history...
11			from mandos.model.utils.resources import MandosResources
12			from pocketutils.core.dot_dict import NestedDotDict
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Unable to import 'pocketutils.core.dot_dict' Loading history...
13			from pocketutils.core.query_utils import QueryExecutor
			0 ignored issues – show introduced 2021-08-02 23:39 UTC by Report Bug Copy Issue Report Unable to import 'pocketutils.core.query_utils' Loading history...
14			from pocketutils.core.exceptions import DirDoesNotExistError, FileDoesNotExistError, ConfigError
			0 ignored issues – show introduced 2021-09-23 03:01 UTC by Report Bug Copy Issue Report Unable to import 'pocketutils.core.exceptions' Loading history... Unused Code introduced 2021-09-23 03:01 UTC by Report Bug Copy Issue Report Unused FileDoesNotExistError imported from pocketutils.core.exceptions Loading history...
15			from pocketutils.tools.common_tools import CommonTools
			0 ignored issues – show introduced 2021-04-03 02:07 UTC by Report Bug Copy Issue Report Unable to import 'pocketutils.tools.common_tools' Loading history...
16			from suretime import Suretime
			0 ignored issues – show introduced 2021-06-30 04:51 UTC by Report Bug Copy Issue Report Unable to import 'suretime' Loading history...
17
18			from mandos.model.utils.setup import logger
			0 ignored issues – show introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Imports from package mandos are not grouped Loading history...
19
20			defaults: Mapping[str, Any] = orjson.loads(
21			MandosResources.path("default_settings.json").read_text(encoding="utf8")
22			)
23			T = TypeVar("T")
			0 ignored issues – show Coding Style Naming introduced 2021-09-06 00:54 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...
24
25
26			class Globals:
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27			chembl_settings = ChemblSettings.Instance()
28			cwd = os.getcwd()
29			where_am_i_installed = Path(__file__).parent.parent.parent
30			is_in_ci = CommonTools.parse_bool(os.environ.get("IS_IN_CI", "false"))
31			if is_in_ci:
32			mandos_path = Path(__file__).parent.parent.parent / "tests" / "resources" / ".mandos-cache"
33			else:
34			_default_mandos_home = Path.home() / ".mandos"
35			env_vars = {k.lower(): v for k, v in os.environ.items()}
36			mandos_path = Path(env_vars.get("MANDOS_HOME", _default_mandos_home))
37			settings_path = mandos_path / "settings.toml"
38			disable_chembl = CommonTools.parse_bool(os.environ.get("MANDOS_NO_CHEMBL", "false"))
39			disable_pubchem = CommonTools.parse_bool(os.environ.get("MANDOS_NO_PUBCHEM", "false"))
40
41
42			@dataclass(frozen=True, repr=True)
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43			class Settings:
44			""" """
45
46			is_testing: bool
47			ntp_continent: str
48			cache_path: Path
49			cache_gzip: bool
50			chembl_expire_sec: int
51			chembl_n_tries: int
52			chembl_timeout_sec: int
53			chembl_backoff_factor: float
54			chembl_query_delay_min: float
55			chembl_query_delay_max: float
56			chembl_fast_save: bool
57			pubchem_expire_sec: int
58			pubchem_n_tries: int
59			pubchem_timeout_sec: float
60			pubchem_backoff_factor: float
61			pubchem_query_delay_min: float
62			pubchem_query_delay_max: float
63			hmdb_expire_sec: int
64			hmdb_timeout_sec: float
65			hmdb_backoff_factor: float
66			hmdb_query_delay_min: float
67			hmdb_query_delay_max: float
68			taxon_expire_sec: int
69			archive_filename_suffix: str
70			default_table_suffix: str
71			selenium_driver: str
72			selenium_driver_path: Optional[Path]
73
74			def __post_init__(self):
75			pass
76
77			@property
78			def all_cache_paths(self) -> Set[Path]:
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79			return {
80			self.chembl_cache_path,
81			self.pubchem_cache_path,
82			self.g2p_cache_path,
83			self.hmdb_cache_path,
84			self.taxonomy_cache_path,
85			}
86
87			@property
88			def driver_path(self) -> Path:
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89			return self.cache_path / "driver"
90
91			@property
92			def chembl_cache_path(self) -> Path:
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93			return self.cache_path / "chembl"
94
95			@property
96			def chembl_scrape_path(self) -> Path:
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97			return self.chembl_cache_path / "scrape"
98
99			@property
100			def pubchem_cache_path(self) -> Path:
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101			return self.cache_path / "pubchem"
102
103			@property
104			def g2p_cache_path(self) -> Path:
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105			return self.cache_path / "g2p"
106
107			@property
108			def hmdb_cache_path(self) -> Path:
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109			return self.cache_path / "hmdb"
110
111			@property
112			def taxonomy_cache_path(self) -> Path:
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113			return self.cache_path / "taxonomy"
114
115			@classmethod
116			def from_file(cls, path: Path) -> Settings:
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117			return cls.load(NestedDotDict.read_toml(path))
118
119			@classmethod
120			def empty(cls) -> Settings:
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121			return cls.load(NestedDotDict({}))
122
123			@classmethod
124			def load(cls, data: NestedDotDict) -> Settings:
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125			def get(s: str, t: Type[T]) -> T:
			0 ignored issues – show Coding Style Naming introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Argument name "t" 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 2021-09-06 00:54 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...
126			try:
127			return data.get_as(s, t, defaults[s])
128			except TypeError:
129			raise ConfigError(f"Key {s}={data.get(s), defaults[s]} is not of type {t}")
130
131			_continent = Suretime.Types.NtpContinents.of
132			return cls(
133			is_testing=get("is_testing", bool),
134			ntp_continent=get("continent_code", _continent),
135			cache_path=Path(get("cache.path", str)).expanduser(),
136			cache_gzip=get("cache.gzip", bool),
137			chembl_expire_sec=get("query.chembl.expire_sec", int),
138			chembl_n_tries=get("query.chembl.n_tries", int),
139			chembl_fast_save=get("query.chembl.fast_save", bool),
140			chembl_timeout_sec=get("query.chembl.timeout_sec", int),
141			chembl_backoff_factor=get("query.chembl.backoff_factor", float),
142			chembl_query_delay_min=get("query.chembl.delay_sec", float),
143			chembl_query_delay_max=get("query.chembl.delay_sec", float),
144			pubchem_expire_sec=get("query.pubchem.expire_sec", int),
145			pubchem_timeout_sec=get("query.pubchem.timeout_sec", int),
146			pubchem_backoff_factor=get("query.pubchem.backoff_factor", float),
147			pubchem_query_delay_min=get("query.pubchem.delay_sec", float),
148			pubchem_query_delay_max=get("query.pubchem.delay_sec", float),
149			pubchem_n_tries=get("query.pubchem.n_tries", int),
150			hmdb_expire_sec=get("query.hmdb.expire_sec", int),
151			hmdb_timeout_sec=get("query.hmdb.timeout_sec", int),
152			hmdb_backoff_factor=get("query.hmdb.backoff_factor", float),
153			hmdb_query_delay_min=get("query.hmdb.delay_sec", float),
154			hmdb_query_delay_max=get("query.hmdb.delay_sec", float),
155			taxon_expire_sec=get("query.taxa.expire_sec", int),
156			archive_filename_suffix=get("cache.archive_filename_suffix", str),
157			default_table_suffix=get("default_table_suffix", str),
158			selenium_driver=get("selenium_driver", str).title(),
159			selenium_driver_path=get("selenium_driver_path", Path),
160			)
161
162			@classmethod
163			def defaults(cls) -> Mapping[str, Any]:
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164			return dict(defaults)
165
166			def configure(self):
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167			""" """
168			if not Globals.disable_chembl:
169			instance = Globals.chembl_settings
170			instance.CACHING = True
171			instance.CACHE_NAME = str(self.chembl_cache_path / "chembl.sqlite")
172			instance.TOTAL_RETRIES = self.chembl_n_tries
173			instance.FAST_SAVE = self.chembl_fast_save
174			instance.TIMEOUT = self.chembl_timeout_sec
175			instance.BACKOFF_FACTOR = self.chembl_backoff_factor
176			instance.CACHE_EXPIRE = self.chembl_expire_sec
177
178			@classmethod
179			def set_path_for_selenium(cls) -> None:
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180			cls.add_to_path(
181			[MANDOS_SETTINGS.driver_path, MandosResources.dir(), Globals.where_am_i_installed]
182			)
183
184			@classmethod
185			def add_to_path(cls, paths: Collection[Union[None, str, Path]]) -> None:
			0 ignored issues – show introduced 2021-09-23 03:01 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
186			paths = {Path(p) for p in paths if p is not None}
187			for path in paths:
188			if path.exists() and not path.is_dir() and not path.is_mount():
189			raise DirDoesNotExistError(f"Path {path} is not a directory or mount")
190			paths = os.pathsep.join({str(p) for p in paths})
191			if len(paths) > 0:
192			os.environ["PATH"] += os.pathsep + paths
193			logger.debug(f"Added to PATH: {paths}")
194
195
196			if Globals.settings_path.exists():
197			MANDOS_SETTINGS = Settings.from_file(Globals.settings_path)
198			logger.info(f"Read settings at {Globals.settings_path}")
199			else:
200			MANDOS_SETTINGS = Settings.empty()
201			logger.info(f"Using defaults (no file at {Globals.settings_path})")
202			MANDOS_SETTINGS.configure()
203			logger.debug(f"Setting ChEMBL cache to {MANDOS_SETTINGS.chembl_cache_path}")
204
205
206			class QueryExecutors:
			0 ignored issues – show introduced 2021-08-02 23:39 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
207			chembl = QueryExecutor(
208			MANDOS_SETTINGS.chembl_query_delay_min, MANDOS_SETTINGS.chembl_query_delay_max
209			)
210			pubchem = QueryExecutor(
211			MANDOS_SETTINGS.pubchem_query_delay_min, MANDOS_SETTINGS.pubchem_query_delay_max
212			)
213			hmdb = QueryExecutor(
214			MANDOS_SETTINGS.pubchem_query_delay_min, MANDOS_SETTINGS.pubchem_query_delay_max
215			)
216
217
218			QUERY_EXECUTORS = QueryExecutors
			0 ignored issues – show Coding Style Naming introduced 2021-08-02 23:39 UTC by Report Bug Copy Issue Report Class name "QUERY_EXECUTORS" 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...
219
220
221			__all__ = ["MANDOS_SETTINGS", "QUERY_EXECUTORS"]
222

dmyersturnbull / mandos

Push — main ( 2b775d...83a9fb )

mandos.model.settings.Settings.add_to_path() B

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