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""" |
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Command-line interface for mandos. |
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""" |
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from __future__ import annotations |
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from typing import Type |
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import typer |
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from pocketutils.core import DictNamespace |
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from typer.models import CommandInfo |
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from mandos.model.utils.globals import Globals |
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cli = typer.Typer() |
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class CmdNamespace(DictNamespace): |
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@classmethod |
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def make(cls) -> CmdNamespace: |
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from mandos.entry.calc_commands import CalcCommands |
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from mandos.entry.entry_commands import Entries |
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from mandos.entry.misc_commands import ( |
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MiscCommands, |
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_InsertedCommandListSingleton, |
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) |
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from mandos.entry.plot_commands import PlotCommands |
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cli.registered_commands += [ |
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CommandInfo(":document", callback=MiscCommands.document), |
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CommandInfo(":search", callback=MiscCommands.search), |
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CommandInfo(":init", callback=MiscCommands.init, hidden=True), |
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CommandInfo(":settings", callback=MiscCommands.list_settings, hidden=True), |
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CommandInfo(":fill", callback=MiscCommands.fill), |
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CommandInfo(":cache:data", callback=MiscCommands.cache_data), |
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CommandInfo(":cache:taxa", callback=MiscCommands.cache_taxa), |
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CommandInfo(":cache:g2p", callback=MiscCommands.cache_g2p), |
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CommandInfo(":cache:clear", callback=MiscCommands.cache_clear), |
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CommandInfo(":export:taxa", callback=MiscCommands.export_taxa), |
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CommandInfo(":concat", callback=MiscCommands.concat), |
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CommandInfo(":filter", callback=MiscCommands.filter), |
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CommandInfo(":export:copy", callback=MiscCommands.export_copy), |
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CommandInfo(":export:state", callback=MiscCommands.export_state), |
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CommandInfo(":export:reify", callback=MiscCommands.export_reify), |
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CommandInfo(":export:db", callback=MiscCommands.export_db, hidden=True), |
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CommandInfo(":init-db", callback=MiscCommands.init_db, hidden=True), |
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CommandInfo(":serve", callback=MiscCommands.serve, hidden=True), |
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CommandInfo(":calc:enrichment", callback=CalcCommands.calc_enrichment), |
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CommandInfo(":calc:phi", callback=CalcCommands.calc_phi), |
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CommandInfo(":calc:psi", callback=CalcCommands.calc_psi), |
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CommandInfo(":calc:ecfp", callback=CalcCommands.calc_ecfp, hidden=True), |
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CommandInfo(":calc:psi-projection", callback=CalcCommands.calc_projection), |
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CommandInfo(":calc:tau", callback=CalcCommands.calc_tau), |
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CommandInfo(":plot:enrichment", callback=PlotCommands.plot_enrichment), |
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CommandInfo(":plot:psi-projection", callback=PlotCommands.plot_projection), |
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CommandInfo(":plot:psi-heatmap", callback=PlotCommands.plot_heatmap), |
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CommandInfo(":plot:phi-vs-psi", callback=PlotCommands.plot_phi_psi), |
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CommandInfo(":plot:tau", callback=PlotCommands.plot_tau), |
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] |
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commands = {c.name: c for c in cli.registered_commands} |
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# Oh dear this is a nightmare |
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# it's really hard to create typer commands with dynamically configured params -- |
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# we really need to rely on its inferring of params |
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# that makes this really hard to do well |
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for entry in Entries: |
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cmd = entry.cmd() |
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info = CommandInfo(cmd, callback=entry.run) |
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cli.registered_commands.append(info) |
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# print(f"Registered {entry.cmd()} to {entry}") |
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commands[cmd] = entry.run |
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_InsertedCommandListSingleton.commands = cli.registered_commands |
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return cls(**commands) |
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class MandosCli: |
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""" |
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Global entry point for various stuff. |
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""" |
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cli = cli |
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commands = None |
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@classmethod |
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def as_library(cls) -> Type[MandosCli]: |
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from mandos.model.utils.setup import LOG_SETUP |
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Globals.is_cli = False |
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( |
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LOG_SETUP.set_control(False) |
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.config_levels( |
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levels=LOG_SETUP.defaults.levels_extended, |
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icons=LOG_SETUP.defaults.icons_extended, |
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colors=LOG_SETUP.defaults.colors_extended, |
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) |
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.add_log_methods() |
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) |
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cls.start() |
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cls.commands = CmdNamespace.make() |
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return cls |
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101
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@classmethod |
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def as_cli(cls) -> Type[MandosCli]: |
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103
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from mandos.model.utils.setup import LOG_SETUP |
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104
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Globals.is_cli = True |
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LOG_SETUP.logger.remove(None) |
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( |
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LOG_SETUP.set_control(True) |
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.disable("chembl_webresource_client", "requests_cache", "urllib3") |
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.config_levels( |
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levels=LOG_SETUP.defaults.levels_extended, |
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icons=LOG_SETUP.defaults.icons_extended, |
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colors=LOG_SETUP.defaults.colors_red_green_safe, |
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) |
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.add_log_methods() |
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.config_main(fmt=LOG_SETUP.defaults.fmt_simplified) |
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) |
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cls.start() |
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cls.commands = CmdNamespace.make() |
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cls.init_apis() |
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return cls |
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123
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@classmethod |
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def init_apis(cls): |
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from mandos.entry.api_singletons import Apis |
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126
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127
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Apis.set_default() |
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128
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129
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@classmethod |
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def start(cls): |
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131
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from mandos import MandosMetadata |
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from mandos.model.utils.setup import logger |
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133
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134
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if MandosMetadata.version is None: |
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logger.error("Could not load package metadata for mandos. Is it installed?") |
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else: |
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logger.info(f"Mandos v{MandosMetadata.version}") |
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139
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if __name__ == "__main__": |
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MandosCli.as_cli().cli() |
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143
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__all__ = ["CmdNamespace", "MandosCli"] |
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dmyersturnbull /
mandos
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