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""" |
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Runner. |
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""" |
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from __future__ import annotations |
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7
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import typing |
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from pathlib import Path |
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from typing import Optional, Type, Union |
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10
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import typer |
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from pocketutils.core.dot_dict import NestedDotDict |
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14
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from mandos import MandosLogging |
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from mandos.entries import EntryMeta |
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from mandos.entries.api_singletons import Apis |
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from mandos.entries.entries import Entries, Entry |
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from mandos.model import InjectionError, ReflectionUtils |
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from mandos.model.settings import MANDOS_SETTINGS |
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cli = typer.Typer() |
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Apis.set_default() |
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Chembl, Pubchem = Apis.Chembl, Apis.Pubchem |
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EntriesByCmd: typing.Dict[str, Type[Entry]] = {e.cmd(): e for e in Entries} |
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# these are only permitted in 'meta', not individual searches |
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meta_keys = {"verbose", "quiet", "check", "log", "to"} |
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class MultiSearch: |
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""" |
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Ugh. |
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""" |
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# ------------------------ |
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# TODO: This code is nightmarishly complex. |
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# ------------------------ |
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def __init__(self, path: Path, config: str): |
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self.path = path |
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toml = NestedDotDict.read_toml(config) |
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self.toml_searches = toml.get_as("search", list, []) |
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# 'meta' allows us to set defaults |
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# for now, I'm only allowing true "metadata" keys |
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self.meta = toml.sub("meta") |
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# TODO: allow specifying a directory, not just format (suffix) |
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self.format = self.meta.get_as("to", str, MANDOS_SETTINGS.default_table_suffix) |
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if not self.format.startswith("."): |
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raise ValueError( |
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f"Value to='{self.format}' does not start with '.'. Only a filename extension is permitted." |
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) |
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for key, value in self.meta.items(): |
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if key not in meta_keys: |
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raise ValueError( |
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f"Found {key}={value} in 'meta' of TOML. Only {', '.join(meta_keys)} are supported." |
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57
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) |
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def search(self) -> None: |
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60
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cmds = self._build_commands() |
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# this is terrible |
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EntryMeta.set_logging( |
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quiet=self.meta.get("quiet", False), |
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verbose=self.meta.get("verbose", False), |
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log=self.meta.get("log", None), |
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) |
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for key, (ent, params) in cmds.items(): |
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68
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ent.run(self.path, **{**params, **dict(no_setup=True, check=False)}) |
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70
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def _build_commands( |
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self, |
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) -> typing.Dict[str, typing.Tuple[Type[Entry], typing.Mapping[str, Union[int, str, float]]]]: |
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commands: typing.Dict[ |
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str, typing.Tuple[Type[Entry], typing.Mapping[str, Union[int, str, float]]] |
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] = {} |
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# build up the lit of Entry classes first, and run ``test`` on each one |
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# that's to check that the parameters are correct before running anything |
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for e in self.toml_searches: |
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e = NestedDotDict(e) |
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80
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cmd = e.req_as("source", str) |
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key = e.get_as("key", str, cmd) |
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try: |
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cmd = EntriesByCmd[cmd] |
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except KeyError: |
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raise InjectionError(f"Search command {cmd} (key {key}) does not exist") |
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# use defaults |
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params = dict(self.meta) |
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# they shouldn't pass any of these args |
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if "path" in e: |
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raise ValueError(f"Cannot set 'path' in [[search]]") |
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91
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for bad in {*meta_keys, "no_setup"}: |
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if bad in e: |
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raise ValueError(f"Cannot set '{bad}' in [[search]]; set in meta") |
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# update the defaults from 'meta' (e.g. 'verbose') |
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# skip the source -- it's the command name |
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# stupidly, we need to explicitly add the defaults from the OptionInfo instances |
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params.update(cmd.default_param_values().items()) |
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# do this after: the defaults had path, key, and to |
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# params["path"] = self.path |
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params["key"] = key |
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params["to"] = self.format |
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params.update({k: v for k, v in e.items() if k != "source"}) |
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del params["check"] |
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cmd.test(self.path, **{**params, **dict(quiet=True)}) |
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105
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if key in commands: |
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raise ValueError(f"Repeated search key '{key}'") |
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107
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commands[key] = (cmd, params) |
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108
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if self.meta.get("check", False): |
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109
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# we already ran check on all of them |
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110
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return {} |
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111
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else: |
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112
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return commands |
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113
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114
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115
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__all__ = ["MultiSearch"] |
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116
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dmyersturnbull /
mandos
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