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

Passed

Push — main ( 4b9dc0...1b55d1 )

by Douglas

created 2021-11-05 00:26 UTC

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

↳ Parent: mandos.model.settings

Complexity

Conditions

Size

Total Lines	61
Code Lines	55

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	5
eloc	55
nop	2
dl	0
loc	61
rs	8.006
c	0
b	0
f	0

How to fix Long Method

from __future__ import annotations


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

from pocketutils.core.dot_dict import NestedDotDict

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

from pocketutils.core.query_utils import QueryExecutor

from pocketutils.tools.common_tools import CommonTools

from pocketutils.tools.sys_tools import SystemTools

from suretime import Suretime

from typeddfs import FileFormat, FrozeDict


from mandos.model.utils.globals import Globals
from mandos.model.utils.setup import LOG_SETUP, MandosResources, logger

defaults: Mapping[str, Any] = FrozeDict(MandosResources.json_dict("default_settings.json"))
max_coeff = 1.1

T = TypeVar("T")



@dataclass(frozen=True, repr=True)

class Settings:
    """ """

    is_testing: bool
    ntp_continent: str
    table_suffix: str
    log_suffix: str
    cache_path: Path
    cache_gzip: bool
    save_every: int
    sanitize_paths: 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
    selenium_driver: str
    selenium_driver_path: Optional[Path]
    log_signals: bool
    log_exit: bool

    @property
    def as_dict(self) -> Mapping[str, Any]:

        return dataclasses.asdict(self)

    @property
    def all_cache_paths(self) -> AbstractSet[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({}))

    def __post_init__(self):
        # check these things
        FileFormat.from_suffix(self.table_suffix)
        FileFormat.from_suffix(self.archive_filename_suffix)
        LOG_SETUP.guess_file_sink_info(self.log_suffix)
        for k, v in self.as_dict.items():

            # this happens to work for now -- we have none that can be < 0
            if isinstance(v, (int, float)) and v < 0:
                raise XValueError(f"{k} = {v} < 0")

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

        extra_default_keys = dict(defaults)

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

            if s in extra_default_keys:  # could be accessed more than once
                del extra_default_keys[s]
            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
        _selenium_path = get("query.selenium_driver_path", Path)
        if _selenium_path is not None:
            _selenium_path = _selenium_path.expanduser()
        chembl_delay = get("query.chembl.delay_sec", float)
        pubchem_delay = get("query.pubchem.delay_sec", float)
        hmdb_delay = get("query.hmdb.delay_sec", float)
        data = cls(
            is_testing=get("is_testing", bool),
            ntp_continent=get("search.ntp_continent_code", _continent),
            table_suffix=get("search.default_table_suffix", str),
            log_suffix=get("search.default_log_suffix", str),
            save_every=get("search.save_every", int),
            sanitize_paths=get("search.sanitize_paths", bool),
            cache_path=Path(get("cache.path", str)).expanduser(),
            chembl_expire_sec=get("cache.chembl.expire_sec", int),
            pubchem_expire_sec=get("cache.pubchem.expire_sec", int),
            taxon_expire_sec=get("cache.taxa.expire_sec", int),
            cache_gzip=get("cache.gzip", bool),
            archive_filename_suffix=get("cache.archive_filename_suffix", str),
            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=chembl_delay,
            chembl_query_delay_max=chembl_delay * max_coeff,
            pubchem_timeout_sec=get("query.pubchem.timeout_sec", int),
            hmdb_expire_sec=get("cache.hmdb.expire_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=pubchem_delay * max_coeff,
            pubchem_n_tries=get("query.pubchem.n_tries", int),
            hmdb_timeout_sec=get("query.hmdb.timeout_sec", int),
            hmdb_backoff_factor=get("query.hmdb.backoff_factor", float),
            hmdb_query_delay_min=hmdb_delay,
            hmdb_query_delay_max=hmdb_delay * max_coeff,
            selenium_driver=get("query.selenium_driver", str).title(),
            selenium_driver_path=_selenium_path,
            log_signals=get("cli.log_signals", bool),
            log_exit=get("cli.log_exit", bool),
        )
        # we got all the required fields
        # make sure we don't have extra keys in defaults
        if len(extra_default_keys) > 0:
            raise AssertionError(
                f"There are {len(extra_default_keys)} extra defaults"
                + f"in {defaults}: {extra_default_keys}"
            )
        return data

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

        return defaults

    def configure(self):

        """ """
        if self.log_exit:
            SystemTools.trace_exit(CommonTools.make_writer(logger.trace))
        if self.log_signals:
            SystemTools.trace_signals(CommonTools.make_writer(logger.trace))

    def configure_chembl(self):

        from chembl_webresource_client.settings import Settings as ChemblSettings


        if not Globals.disable_chembl:
            instance = ChemblSettings.Instance()
            instance.CACHING = True
            instance.CACHE_NAME = str(self.chembl_cache_path.resolve() / "chembl.sqlite")
            logger.debug(f"ChEMBL cache is at {instance.CACHE_NAME}")
            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([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():
    SETTINGS = Settings.from_file(Globals.settings_path)
    logger.success(f"Read settings at {Globals.settings_path}")
else:
    SETTINGS = Settings.empty()
    logger.success(f"Using defaults (no file at {Globals.settings_path})")
SETTINGS.configure()


class QueryExecutors:

    chembl = QueryExecutor(SETTINGS.chembl_query_delay_min, SETTINGS.chembl_query_delay_max)
    pubchem = QueryExecutor(SETTINGS.pubchem_query_delay_min, SETTINGS.pubchem_query_delay_max)
    hmdb = QueryExecutor(SETTINGS.hmdb_query_delay_min, SETTINGS.hmdb_query_delay_max)


QUERY_EXECUTORS = QueryExecutors



__all__ = ["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 dataclasses
4			import os
5			from dataclasses import dataclass
6			from pathlib import Path
7			from typing import AbstractSet, Any, Collection, Mapping, Optional, Type, TypeVar, Union
8
9			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...
10			from pocketutils.core.exceptions import ConfigError, DirDoesNotExistError, XValueError
			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...
11			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...
12			from pocketutils.tools.common_tools import CommonTools
			0 ignored issues – show introduced 2021-08-07 00:15 UTC by Report Bug Copy Issue Report Unable to import 'pocketutils.tools.common_tools' Loading history...
13			from pocketutils.tools.sys_tools import SystemTools
			0 ignored issues – show introduced 2021-11-05 00:32 UTC by Report Bug Copy Issue Report Unable to import 'pocketutils.tools.sys_tools' Loading history...
14			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...
15			from typeddfs import FileFormat, FrozeDict
			0 ignored issues – show introduced 2021-09-29 03:10 UTC by Report Bug Copy Issue Report Unable to import 'typeddfs' Loading history...
16
17			from mandos.model.utils.globals import Globals
18			from mandos.model.utils.setup import LOG_SETUP, MandosResources, logger
19
20			defaults: Mapping[str, Any] = FrozeDict(MandosResources.json_dict("default_settings.json"))
21			max_coeff = 1.1
			0 ignored issues – show Coding Style Naming introduced 2021-10-28 02:14 UTC by Report Bug Copy Issue Report Constant name "max_coeff" doesn't conform to UPPER_CASE naming style ('([^\\W\\da-z][^\\Wa-z]\|__.__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
22			T = TypeVar("T")
			0 ignored issues – show Coding Style Naming introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Class name "T" doesn't conform to PascalCase naming style ('[^\\W\\da-z][^\\W_]+$' 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...
23
24
25			@dataclass(frozen=True, repr=True)
			0 ignored issues – show Documentation introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Empty class docstring Loading history... best-practice introduced 2021-10-02 18:29 UTC by Report Bug Copy Issue Report Too many instance attributes (32/7) Loading history...
26			class Settings:
27			""" """
28
29			is_testing: bool
30			ntp_continent: str
31			table_suffix: str
32			log_suffix: str
33			cache_path: Path
34			cache_gzip: bool
35			save_every: int
36			sanitize_paths: bool
37			chembl_expire_sec: int
38			chembl_n_tries: int
39			chembl_timeout_sec: int
40			chembl_backoff_factor: float
41			chembl_query_delay_min: float
42			chembl_query_delay_max: float
43			chembl_fast_save: bool
44			pubchem_expire_sec: int
45			pubchem_n_tries: int
46			pubchem_timeout_sec: float
47			pubchem_backoff_factor: float
48			pubchem_query_delay_min: float
49			pubchem_query_delay_max: float
50			hmdb_expire_sec: int
51			hmdb_timeout_sec: float
52			hmdb_backoff_factor: float
53			hmdb_query_delay_min: float
54			hmdb_query_delay_max: float
55			taxon_expire_sec: int
56			archive_filename_suffix: str
57			selenium_driver: str
58			selenium_driver_path: Optional[Path]
59			log_signals: bool
60			log_exit: bool
61
62			@property
63			def as_dict(self) -> Mapping[str, Any]:
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64			return dataclasses.asdict(self)
65
66			@property
67			def all_cache_paths(self) -> AbstractSet[Path]:
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68			return {
69			self.chembl_cache_path,
70			self.pubchem_cache_path,
71			self.g2p_cache_path,
72			self.hmdb_cache_path,
73			self.taxonomy_cache_path,
74			}
75
76			@property
77			def driver_path(self) -> Path:
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78			return self.cache_path / "driver"
79
80			@property
81			def chembl_cache_path(self) -> Path:
			0 ignored issues – show introduced 2021-03-24 04:52 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
82			return self.cache_path / "chembl"
83
84			@property
85			def chembl_scrape_path(self) -> Path:
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
86			return self.chembl_cache_path / "scrape"
87
88			@property
89			def pubchem_cache_path(self) -> Path:
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
90			return self.cache_path / "pubchem"
91
92			@property
93			def g2p_cache_path(self) -> 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...
94			return self.cache_path / "g2p"
95
96			@property
97			def hmdb_cache_path(self) -> Path:
			0 ignored issues – show introduced 2021-03-10 02:41 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
98			return self.cache_path / "hmdb"
99
100			@property
101			def taxonomy_cache_path(self) -> Path:
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102			return self.cache_path / "taxonomy"
103
104			@classmethod
105			def from_file(cls, path: Path) -> Settings:
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106			return cls.load(NestedDotDict.read_toml(path))
107
108			@classmethod
109			def empty(cls) -> Settings:
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
110			return cls.load(NestedDotDict({}))
111
112			def __post_init__(self):
113			# check these things
114			FileFormat.from_suffix(self.table_suffix)
115			FileFormat.from_suffix(self.archive_filename_suffix)
116			LOG_SETUP.guess_file_sink_info(self.log_suffix)
117			for k, v in self.as_dict.items():
			0 ignored issues – show Coding Style Naming introduced 2021-09-29 03:10 UTC by Report Bug Copy Issue Report Variable name "v" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
118			# this happens to work for now -- we have none that can be < 0
119			if isinstance(v, (int, float)) and v < 0:
120			raise XValueError(f"{k} = {v} < 0")
121
122			@classmethod
123			def load(cls, data: NestedDotDict) -> Settings:
			0 ignored issues – show introduced 2021-09-23 03:01 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
124			extra_default_keys = dict(defaults)
125
126			def get(s: str, t: Type[T]) -> T:
			0 ignored issues – show Coding Style Naming introduced 2021-09-06 00:54 UTC by Report Bug Copy Issue Report Argument name "t" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' 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...
127			if s in extra_default_keys: # could be accessed more than once
128			del extra_default_keys[s]
129			try:
130			return data.get_as(s, t, defaults[s])
131			except TypeError:
132			raise ConfigError(f"Key {s}={data.get(s), defaults[s]} is not of type {t}")
133
134			_continent = Suretime.Types.NtpContinents.of
135			_selenium_path = get("query.selenium_driver_path", Path)
136			if _selenium_path is not None:
137			_selenium_path = _selenium_path.expanduser()
138			chembl_delay = get("query.chembl.delay_sec", float)
139			pubchem_delay = get("query.pubchem.delay_sec", float)
140			hmdb_delay = get("query.hmdb.delay_sec", float)
141			data = cls(
142			is_testing=get("is_testing", bool),
143			ntp_continent=get("search.ntp_continent_code", _continent),
144			table_suffix=get("search.default_table_suffix", str),
145			log_suffix=get("search.default_log_suffix", str),
146			save_every=get("search.save_every", int),
147			sanitize_paths=get("search.sanitize_paths", bool),
148			cache_path=Path(get("cache.path", str)).expanduser(),
149			chembl_expire_sec=get("cache.chembl.expire_sec", int),
150			pubchem_expire_sec=get("cache.pubchem.expire_sec", int),
151			taxon_expire_sec=get("cache.taxa.expire_sec", int),
152			cache_gzip=get("cache.gzip", bool),
153			archive_filename_suffix=get("cache.archive_filename_suffix", str),
154			chembl_n_tries=get("query.chembl.n_tries", int),
155			chembl_fast_save=get("query.chembl.fast_save", bool),
156			chembl_timeout_sec=get("query.chembl.timeout_sec", int),
157			chembl_backoff_factor=get("query.chembl.backoff_factor", float),
158			chembl_query_delay_min=chembl_delay,
159			chembl_query_delay_max=chembl_delay * max_coeff,
160			pubchem_timeout_sec=get("query.pubchem.timeout_sec", int),
161			hmdb_expire_sec=get("cache.hmdb.expire_sec", int),
162			pubchem_backoff_factor=get("query.pubchem.backoff_factor", float),
163			pubchem_query_delay_min=get("query.pubchem.delay_sec", float),
164			pubchem_query_delay_max=pubchem_delay * max_coeff,
165			pubchem_n_tries=get("query.pubchem.n_tries", int),
166			hmdb_timeout_sec=get("query.hmdb.timeout_sec", int),
167			hmdb_backoff_factor=get("query.hmdb.backoff_factor", float),
168			hmdb_query_delay_min=hmdb_delay,
169			hmdb_query_delay_max=hmdb_delay * max_coeff,
170			selenium_driver=get("query.selenium_driver", str).title(),
171			selenium_driver_path=_selenium_path,
172			log_signals=get("cli.log_signals", bool),
173			log_exit=get("cli.log_exit", bool),
174			)
175			# we got all the required fields
176			# make sure we don't have extra keys in defaults
177			if len(extra_default_keys) > 0:
178			raise AssertionError(
179			f"There are {len(extra_default_keys)} extra defaults"
180			+ f"in {defaults}: {extra_default_keys}"
181			)
182			return data
183
184			@classmethod
185			def defaults(cls) -> Mapping[str, Any]:
			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			return defaults
187
188			def configure(self):
			0 ignored issues – show Documentation introduced 2021-04-03 02:07 UTC by Report Bug Copy Issue Report Empty method docstring Loading history...
189			""" """
190			if self.log_exit:
191			SystemTools.trace_exit(CommonTools.make_writer(logger.trace))
192			if self.log_signals:
193			SystemTools.trace_signals(CommonTools.make_writer(logger.trace))
194
195			def configure_chembl(self):
			0 ignored issues – show introduced 2021-09-23 03:01 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
196			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... introduced 2021-11-05 00:32 UTC by Report Bug Copy Issue Report Import outside toplevel (chembl_webresource_client.settings.Settings) Loading history...
197
198			if not Globals.disable_chembl:
199			instance = ChemblSettings.Instance()
200			instance.CACHING = True
201			instance.CACHE_NAME = str(self.chembl_cache_path.resolve() / "chembl.sqlite")
202			logger.debug(f"ChEMBL cache is at {instance.CACHE_NAME}")
203			instance.TOTAL_RETRIES = self.chembl_n_tries
204			instance.FAST_SAVE = self.chembl_fast_save
205			instance.TIMEOUT = self.chembl_timeout_sec
206			instance.BACKOFF_FACTOR = self.chembl_backoff_factor
207			instance.CACHE_EXPIRE = self.chembl_expire_sec
208
209			@classmethod
210			def set_path_for_selenium(cls) -> None:
			0 ignored issues – show introduced 2021-09-29 03:10 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
211			cls.add_to_path([SETTINGS.driver_path, MandosResources.dir(), Globals.where_am_i_installed])
212
213			@classmethod
214			def add_to_path(cls, paths: Collection[Union[None, str, Path]]) -> None:
			0 ignored issues – show introduced 2021-11-05 00:32 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
215			paths = {Path(p) for p in paths if p is not None}
216			for path in paths:
217			if path.exists() and not path.is_dir() and not path.is_mount():
218			raise DirDoesNotExistError(f"Path {path} is not a directory or mount")
219			paths = os.pathsep.join({str(p) for p in paths})
220			if len(paths) > 0:
221			os.environ["PATH"] += os.pathsep + paths
222			logger.debug(f"Added to PATH: {paths}")
223
224
225			if Globals.settings_path.exists():
226			SETTINGS = Settings.from_file(Globals.settings_path)
227			logger.success(f"Read settings at {Globals.settings_path}")
228			else:
229			SETTINGS = Settings.empty()
230			logger.success(f"Using defaults (no file at {Globals.settings_path})")
231			SETTINGS.configure()
232
233
234			class QueryExecutors:
			0 ignored issues – show introduced 2021-03-10 02:41 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
235			chembl = QueryExecutor(SETTINGS.chembl_query_delay_min, SETTINGS.chembl_query_delay_max)
236			pubchem = QueryExecutor(SETTINGS.pubchem_query_delay_min, SETTINGS.pubchem_query_delay_max)
237			hmdb = QueryExecutor(SETTINGS.hmdb_query_delay_min, SETTINGS.hmdb_query_delay_max)
238
239
240			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...
241
242
243			__all__ = ["SETTINGS", "QUERY_EXECUTORS"]
244

dmyersturnbull / mandos

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