mandos.cli.main() - Code Metrics - Inspection of "fix: various" - dmyersturnbull/mandos - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Push — main ( 4074a3...6b8d16 )

by Douglas

created 2021-11-02 03:03 UTC

mandos.cli.main() A

↳ Parent: mandos.cli

Complexity

Conditions

Size

Total Lines	16
Code Lines	15

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	4
eloc	15
nop	0
dl	0
loc	16
rs	9.65
c	0
b	0
f	0

"""
Command-line interface for mandos.
"""

from __future__ import annotations

import os
import traceback
from pathlib import Path
from typing import Optional, Type

import orjson

import typer

from pocketutils.core import DictNamespace

from pocketutils.misc.loguru_utils import FancyLoguru

from typer.models import CommandInfo


from mandos.model.utils.globals import Globals

cli = typer.Typer()


class CmdNamespace(DictNamespace):

    @classmethod
    def make(cls) -> CmdNamespace:

        from mandos.entry.calc_commands import CalcCommands

        from mandos.entry.entry_commands import Entries

        from mandos.entry.misc_commands import (

            MiscCommands,
            _InsertedCommandListSingleton,
        )
        from mandos.entry.plot_commands import PlotCommands


        cli.registered_commands += [
            CommandInfo(":document", callback=MiscCommands.document),
            CommandInfo(":search", callback=MiscCommands.search),
            CommandInfo(":init", callback=MiscCommands.init, hidden=True),
            CommandInfo(":settings", callback=MiscCommands.list_settings, hidden=True),
            CommandInfo(":fill", callback=MiscCommands.fill),
            CommandInfo(":cache:data", callback=MiscCommands.cache_data),
            CommandInfo(":cache:taxa", callback=MiscCommands.cache_taxa),
            CommandInfo(":cache:g2p", callback=MiscCommands.cache_g2p),
            CommandInfo(":cache:clear", callback=MiscCommands.cache_clear),
            CommandInfo(":export:taxa", callback=MiscCommands.export_taxa),
            CommandInfo(":concat", callback=MiscCommands.concat),
            CommandInfo(":filter", callback=MiscCommands.filter),
            CommandInfo(":export:copy", callback=MiscCommands.export_copy),
            CommandInfo(":export:state", callback=MiscCommands.export_state),
            CommandInfo(":export:reify", callback=MiscCommands.export_reify),
            CommandInfo(":export:db", callback=MiscCommands.export_db, hidden=True),
            CommandInfo(":init-db", callback=MiscCommands.init_db, hidden=True),
            CommandInfo(":serve", callback=MiscCommands.serve, hidden=True),
            CommandInfo(":calc:enrichment", callback=CalcCommands.calc_enrichment),
            CommandInfo(":calc:phi", callback=CalcCommands.calc_phi),
            CommandInfo(":calc:psi", callback=CalcCommands.calc_psi),
            CommandInfo(":calc:ecfp", callback=CalcCommands.calc_ecfp, hidden=True),
            CommandInfo(":calc:psi-projection", callback=CalcCommands.calc_projection),
            CommandInfo(":calc:tau", callback=CalcCommands.calc_tau),
            CommandInfo(":plot:enrichment", callback=PlotCommands.plot_enrichment),
            CommandInfo(":plot:psi-projection", callback=PlotCommands.plot_projection),
            CommandInfo(":plot:psi-heatmap", callback=PlotCommands.plot_heatmap),
            CommandInfo(":plot:phi-vs-psi", callback=PlotCommands.plot_phi_psi),
            CommandInfo(":plot:tau", callback=PlotCommands.plot_tau),
        ]
        commands = {c.name: c for c in cli.registered_commands}
        # Oh dear this is a nightmare
        # it's really hard to create typer commands with dynamically configured params --
        # we really need to rely on its inferring of params
        # that makes this really hard to do well
        for entry in Entries:
            cmd = entry.cmd()
            info = CommandInfo(cmd, callback=entry.run)
            cli.registered_commands.append(info)
            # print(f"Registered {entry.cmd()} to {entry}")
            commands[cmd] = entry.run
        _InsertedCommandListSingleton.commands = cli.registered_commands
        return cls(**commands)


class MandosCli:
    """
    Global entry point for various stuff.
    """

    cli = cli

    commands = None
    log_setup: FancyLoguru = None

    @classmethod
    def as_library(cls) -> Type[MandosCli]:

        from mandos.model.utils.setup import LOG_SETUP


        Globals.is_cli = False
        cls.log_setup = (
            LOG_SETUP.set_control(False)
            .config_levels(
                levels=LOG_SETUP.defaults.levels_extended,
                icons=LOG_SETUP.defaults.icons_extended,
                colors=LOG_SETUP.defaults.colors_extended,
            )
            .add_log_methods()
        )
        cls.start()
        cls.commands = CmdNamespace.make()
        return cls

    @classmethod
    def as_cli(cls) -> Type[MandosCli]:

        from mandos.model.utils.setup import LOG_SETUP


        Globals.is_cli = True
        cls.log_setup = LOG_SETUP.logger.remove(None)
        (
            LOG_SETUP.set_control(True)
            .disable("chembl_webresource_client", "requests_cache", "urllib3", "numba")
            .config_levels(
                levels=LOG_SETUP.defaults.levels_extended,
                icons=LOG_SETUP.defaults.icons_extended,
                colors=LOG_SETUP.defaults.colors_red_green_safe,
            )
            .add_log_methods()
            .config_main(fmt=LOG_SETUP.defaults.fmt_simplified)
            .intercept_std()
        )
        cls.start()
        cls.commands = CmdNamespace.make()
        cls.init_apis()
        return cls

    @classmethod
    def init_apis(cls):

        from mandos.entry.api_singletons import Apis


        Apis.set_default()

    @classmethod
    def start(cls):

        from mandos import MandosMetadata

        from mandos.model.utils.setup import logger


        if MandosMetadata.version is None:
            logger.error("Could not load package metadata for mandos. Is it installed?")
        else:
            logger.info(f"Mandos v{MandosMetadata.version}")


def _write_exc_info(mandos_: Type[MandosCli], e: BaseException) -> Path:

    s_ = mandos_.log_setup

    s_.logger.exception(f"Command failed: {str(e)}")
    log_path_: Optional[Path] = next(iter(s_.paths)) if len(s_.paths) > 0 else None
    if log_path_ is None:
        log_path_ = Path(f"mandos-err-{Globals.start_timestamp_filesys}.log")
        log_path_.write_text(str(e) + os.linesep + traceback.format_exc(), encoding="utf8")
    return log_path_.resolve()


def _write_sys_info() -> Optional[Path]:
    try:
        from pocketutils.tools.filesys_tools import FilesysTools


        info_ = FilesysTools.get_env_info()
        info_path_ = Path(f"mandos-err-{Globals.start_timestamp_filesys}-sys.json")
        info_ = orjson.dumps(info_, option=orjson.OPT_INDENT_2).decode(encoding="utf8")
        info_path_.write_text(info_, encoding="utf8")
        return info_path_.resolve()
    except BaseException:

        return None


def main() -> None:

    mandos_ = MandosCli.as_cli()
    try:
        mandos_.cli()
    except KeyboardInterrupt:
        raise typer.Abort()
    except BaseException as e:

        typer.echo(f"Command failed: {str(e)}", err=True)
        lg_path_ = _write_exc_info(mandos_, e)
        typer.echo(f"See {lg_path_} for details", err=True)
        inf_path_ = _write_sys_info()
        if inf_path_ is None:
            typer.echo(f"Could not get system info", err=True)

        else:
            typer.echo(f"Wrote system info to {inf_path_}")
        raise typer.Exit(code=1)


if __name__ == "__main__":
    main()


__all__ = ["CmdNamespace", "MandosCli"]


1			"""
2			Command-line interface for mandos.
3			"""
4
5			from __future__ import annotations
6
7			import os
8			import traceback
9			from pathlib import Path
10			from typing import Optional, Type
11
12			import orjson
			0 ignored issues – show introduced 2021-11-02 03:04 UTC by Report Bug Copy Issue Report Unable to import 'orjson' Loading history...
13			import typer
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Unable to import 'typer' Loading history...
14			from pocketutils.core import DictNamespace
			0 ignored issues – show introduced 2021-10-28 02:14 UTC by Report Bug Copy Issue Report Unable to import 'pocketutils.core' Loading history...
15			from pocketutils.misc.loguru_utils import FancyLoguru
			0 ignored issues – show introduced 2021-11-02 03:04 UTC by Report Bug Copy Issue Report Unable to import 'pocketutils.misc.loguru_utils' Loading history...
16			from typer.models import CommandInfo
			0 ignored issues – show introduced 2021-03-21 02:08 UTC by Report Bug Copy Issue Report Unable to import 'typer.models' Loading history...
17
18			from mandos.model.utils.globals import Globals
19
20			cli = typer.Typer()
21
22
23			class CmdNamespace(DictNamespace):
			0 ignored issues – show introduced 2021-10-28 02:14 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
24			@classmethod
25			def make(cls) -> CmdNamespace:
			0 ignored issues – show introduced 2021-04-03 02:07 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
26			from mandos.entry.calc_commands import CalcCommands
			0 ignored issues – show introduced 2021-10-28 02:14 UTC by Report Bug Copy Issue Report Import outside toplevel (mandos.entry.calc_commands.CalcCommands) Loading history...
27			from mandos.entry.entry_commands import Entries
			0 ignored issues – show introduced 2021-10-28 02:14 UTC by Report Bug Copy Issue Report Import outside toplevel (mandos.entry.entry_commands.Entries) Loading history...
28			from mandos.entry.misc_commands import (
			0 ignored issues – show introduced 2021-10-28 02:14 UTC by Report Bug Copy Issue Report Import outside toplevel (mandos.entry.misc_commands.MiscCommands, mandos.entry.misc_commands._InsertedCommandListSingleton) Loading history...
29			MiscCommands,
30			_InsertedCommandListSingleton,
31			)
32			from mandos.entry.plot_commands import PlotCommands
			0 ignored issues – show introduced 2021-10-28 02:14 UTC by Report Bug Copy Issue Report Import outside toplevel (mandos.entry.plot_commands.PlotCommands) Loading history...
33
34			cli.registered_commands += [
35			CommandInfo(":document", callback=MiscCommands.document),
36			CommandInfo(":search", callback=MiscCommands.search),
37			CommandInfo(":init", callback=MiscCommands.init, hidden=True),
38			CommandInfo(":settings", callback=MiscCommands.list_settings, hidden=True),
39			CommandInfo(":fill", callback=MiscCommands.fill),
40			CommandInfo(":cache:data", callback=MiscCommands.cache_data),
41			CommandInfo(":cache:taxa", callback=MiscCommands.cache_taxa),
42			CommandInfo(":cache:g2p", callback=MiscCommands.cache_g2p),
43			CommandInfo(":cache:clear", callback=MiscCommands.cache_clear),
44			CommandInfo(":export:taxa", callback=MiscCommands.export_taxa),
45			CommandInfo(":concat", callback=MiscCommands.concat),
46			CommandInfo(":filter", callback=MiscCommands.filter),
47			CommandInfo(":export:copy", callback=MiscCommands.export_copy),
48			CommandInfo(":export:state", callback=MiscCommands.export_state),
49			CommandInfo(":export:reify", callback=MiscCommands.export_reify),
50			CommandInfo(":export:db", callback=MiscCommands.export_db, hidden=True),
51			CommandInfo(":init-db", callback=MiscCommands.init_db, hidden=True),
52			CommandInfo(":serve", callback=MiscCommands.serve, hidden=True),
53			CommandInfo(":calc:enrichment", callback=CalcCommands.calc_enrichment),
54			CommandInfo(":calc:phi", callback=CalcCommands.calc_phi),
55			CommandInfo(":calc:psi", callback=CalcCommands.calc_psi),
56			CommandInfo(":calc:ecfp", callback=CalcCommands.calc_ecfp, hidden=True),
57			CommandInfo(":calc:psi-projection", callback=CalcCommands.calc_projection),
58			CommandInfo(":calc:tau", callback=CalcCommands.calc_tau),
59			CommandInfo(":plot:enrichment", callback=PlotCommands.plot_enrichment),
60			CommandInfo(":plot:psi-projection", callback=PlotCommands.plot_projection),
61			CommandInfo(":plot:psi-heatmap", callback=PlotCommands.plot_heatmap),
62			CommandInfo(":plot:phi-vs-psi", callback=PlotCommands.plot_phi_psi),
63			CommandInfo(":plot:tau", callback=PlotCommands.plot_tau),
64			]
65			commands = {c.name: c for c in cli.registered_commands}
66			# Oh dear this is a nightmare
67			# it's really hard to create typer commands with dynamically configured params --
68			# we really need to rely on its inferring of params
69			# that makes this really hard to do well
70			for entry in Entries:
71			cmd = entry.cmd()
72			info = CommandInfo(cmd, callback=entry.run)
73			cli.registered_commands.append(info)
74			# print(f"Registered {entry.cmd()} to {entry}")
75			commands[cmd] = entry.run
76			_InsertedCommandListSingleton.commands = cli.registered_commands
77			return cls(**commands)
78
79
80			class MandosCli:
81			"""
82			Global entry point for various stuff.
83			"""
84
85			cli = cli
			0 ignored issues – show Comprehensibility Best Practice introduced 2021-10-28 02:14 UTC by Report Bug Copy Issue Report The variable `cli` does not seem to be defined. Loading history...
86			commands = None
87			log_setup: FancyLoguru = None
88
89			@classmethod
90			def as_library(cls) -> Type[MandosCli]:
			0 ignored issues – show introduced 2021-10-28 02:14 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
91			from mandos.model.utils.setup import LOG_SETUP
			0 ignored issues – show introduced 2021-10-28 02:14 UTC by Report Bug Copy Issue Report Import outside toplevel (mandos.model.utils.setup.LOG_SETUP) Loading history...
92
93			Globals.is_cli = False
94			cls.log_setup = (
95			LOG_SETUP.set_control(False)
96			.config_levels(
97			levels=LOG_SETUP.defaults.levels_extended,
98			icons=LOG_SETUP.defaults.icons_extended,
99			colors=LOG_SETUP.defaults.colors_extended,
100			)
101			.add_log_methods()
102			)
103			cls.start()
104			cls.commands = CmdNamespace.make()
105			return cls
106
107			@classmethod
108			def as_cli(cls) -> Type[MandosCli]:
			0 ignored issues – show introduced 2021-10-28 02:14 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
109			from mandos.model.utils.setup import LOG_SETUP
			0 ignored issues – show introduced 2021-10-28 02:14 UTC by Report Bug Copy Issue Report Import outside toplevel (mandos.model.utils.setup.LOG_SETUP) Loading history...
110
111			Globals.is_cli = True
112			cls.log_setup = LOG_SETUP.logger.remove(None)
113			(
114			LOG_SETUP.set_control(True)
115			.disable("chembl_webresource_client", "requests_cache", "urllib3", "numba")
116			.config_levels(
117			levels=LOG_SETUP.defaults.levels_extended,
118			icons=LOG_SETUP.defaults.icons_extended,
119			colors=LOG_SETUP.defaults.colors_red_green_safe,
120			)
121			.add_log_methods()
122			.config_main(fmt=LOG_SETUP.defaults.fmt_simplified)
123			.intercept_std()
124			)
125			cls.start()
126			cls.commands = CmdNamespace.make()
127			cls.init_apis()
128			return cls
129
130			@classmethod
131			def init_apis(cls):
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132			from mandos.entry.api_singletons import Apis
			0 ignored issues – show introduced 2021-10-28 02:14 UTC by Report Bug Copy Issue Report Import outside toplevel (mandos.entry.api_singletons.Apis) Loading history...
133
134			Apis.set_default()
135
136			@classmethod
137			def start(cls):
			0 ignored issues – show introduced 2021-10-28 02:14 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
138			from mandos import MandosMetadata
			0 ignored issues – show introduced 2021-10-28 02:14 UTC by Report Bug Copy Issue Report Import outside toplevel (mandos.MandosMetadata) Loading history...
139			from mandos.model.utils.setup import logger
			0 ignored issues – show introduced 2021-10-28 02:14 UTC by Report Bug Copy Issue Report Import outside toplevel (mandos.model.utils.setup.logger) Loading history...
140
141			if MandosMetadata.version is None:
142			logger.error("Could not load package metadata for mandos. Is it installed?")
143			else:
144			logger.info(f"Mandos v{MandosMetadata.version}")
145
146
147			def _write_exc_info(mandos_: Type[MandosCli], e: BaseException) -> Path:
			0 ignored issues – show Coding Style Naming introduced 2021-11-02 03:04 UTC by Report Bug Copy Issue Report Argument name "e" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
148			s_ = mandos_.log_setup
			0 ignored issues – show Coding Style Naming introduced 2021-11-02 03:04 UTC by Report Bug Copy Issue Report Variable name "s_" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' 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...
149			s_.logger.exception(f"Command failed: {str(e)}")
150			log_path_: Optional[Path] = next(iter(s_.paths)) if len(s_.paths) > 0 else None
151			if log_path_ is None:
152			log_path_ = Path(f"mandos-err-{Globals.start_timestamp_filesys}.log")
153			log_path_.write_text(str(e) + os.linesep + traceback.format_exc(), encoding="utf8")
154			return log_path_.resolve()
155
156
157			def _write_sys_info() -> Optional[Path]:
158			try:
159			from pocketutils.tools.filesys_tools import FilesysTools
			0 ignored issues – show introduced 2021-11-02 03:04 UTC by Report Bug Copy Issue Report Unable to import 'pocketutils.tools.filesys_tools' Loading history... introduced 2021-11-02 03:04 UTC by Report Bug Copy Issue Report Import outside toplevel (pocketutils.tools.filesys_tools.FilesysTools) Loading history...
160
161			info_ = FilesysTools.get_env_info()
162			info_path_ = Path(f"mandos-err-{Globals.start_timestamp_filesys}-sys.json")
163			info_ = orjson.dumps(info_, option=orjson.OPT_INDENT_2).decode(encoding="utf8")
164			info_path_.write_text(info_, encoding="utf8")
165			return info_path_.resolve()
166			except BaseException:
			0 ignored issues – show Best Practice introduced 2021-11-02 03:04 UTC by Report Bug Copy Issue Report Catching very general exceptions such as `BaseException` is usually not recommended. Generally, you would want to handle very specific errors in the exception handler. This ensure that you do not hide other types of errors which should be fixed. So, unless you specifically plan to handle any error, consider adding a more specific exception. Loading history...
167			return None
168
169
170			def main() -> None:
			0 ignored issues – show introduced 2021-11-02 03:04 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
171			mandos_ = MandosCli.as_cli()
172			try:
173			mandos_.cli()
174			except KeyboardInterrupt:
175			raise typer.Abort()
176			except BaseException as e:
			0 ignored issues – show Coding Style Naming introduced 2021-11-02 03:04 UTC by Report Bug Copy Issue Report Variable name "e" 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...
177			typer.echo(f"Command failed: {str(e)}", err=True)
178			lg_path_ = _write_exc_info(mandos_, e)
179			typer.echo(f"See {lg_path_} for details", err=True)
180			inf_path_ = _write_sys_info()
181			if inf_path_ is None:
182			typer.echo(f"Could not get system info", err=True)
			0 ignored issues – show introduced 2021-11-02 03:04 UTC by Report Bug Copy Issue Report Using an f-string that does not have any interpolated variables Loading history...
183			else:
184			typer.echo(f"Wrote system info to {inf_path_}")
185			raise typer.Exit(code=1)
186
187
188			if __name__ == "__main__":
189			main()
190
191
192			__all__ = ["CmdNamespace", "MandosCli"]
193

dmyersturnbull / mandos

Push — main ( 4074a3...6b8d16 )

mandos.cli.main() A

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Importance

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