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""" |
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Runner. |
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3
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""" |
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4
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5
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from __future__ import annotations |
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6
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7
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import typing |
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8
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from pathlib import Path |
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9
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from typing import Optional, Union, Type |
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10
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import typer |
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11
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from pocketutils.core.dot_dict import NestedDotDict |
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12
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13
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from mandos import logger |
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14
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from mandos.entries.paths import EntryPaths |
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15
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from mandos.model import InjectionError |
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from mandos.entries.entries import Entries, Entry |
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from mandos.entries.api_singletons import Apis |
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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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22
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23
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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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27
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28
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class MultiSearch: |
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""" |
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Ugh. |
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""" |
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34
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def __init__(self, path: Path, config: Optional[Path]): |
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35
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if config is None: |
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36
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config = path.with_suffix(".toml") |
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self.path = path |
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38
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if not self.path.exists(): |
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raise FileNotFoundError(f"File {path} not found") |
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40
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if not config.exists(): |
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raise FileNotFoundError(f"File {config} not found") |
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42
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toml = NestedDotDict.read_toml(config) |
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43
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self.toml_searches = toml.get_as("search", list, []) |
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44
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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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47
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# TODO: allow specifying a directory, not just format (suffix) |
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48
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self.format = self.meta.get_as("to", str, ".feather") |
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49
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if not self.format.startswith("."): |
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raise ValueError( |
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51
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f"Value to='{self.format}' does not start with '.'. Only a filename extension is permitted." |
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52
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) |
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53
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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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55
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raise ValueError( |
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56
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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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58
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59
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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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61
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for key, (ent, params) in cmds.items(): |
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62
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ent.run(self.path, no_setup=True, **params) |
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63
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64
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def _build_commands( |
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65
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self, |
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66
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) -> typing.Dict[str, typing.Tuple[Type[Entry], typing.Mapping[str, Union[int, str, float]]]]: |
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67
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commands: typing.Dict[ |
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68
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str, typing.Tuple[Type[Entry], typing.Mapping[str, Union[int, str, float]]] |
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69
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] = {} |
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70
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# build up the lit of Entry classes first, and run ``test`` on each one |
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71
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# that's to check that the parameters are correct before running anything |
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72
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for e in self.toml_searches: |
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73
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cmd = e.req_as("source", str) |
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74
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key = e.req_as("key", str) |
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75
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# use defaults |
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76
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params = dict(self.meta) |
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77
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# they shouldn't pass any of these args |
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78
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if "path" in e: |
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79
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raise ValueError(f"Cannot set 'path' in [[search]]") |
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80
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for bad in {*meta_keys, "no_setup"}: |
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81
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if bad in e: |
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82
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raise ValueError(f"Cannot set '{bad}' in [[search]]; set in meta") |
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83
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# update the defaults from 'meta' (e.g. 'verbose') |
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84
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# skip the source -- it's the command name |
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85
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params.update({k: v for k, v in e.items() if k != "source"}) |
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86
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try: |
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87
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cmd = EntriesByCmd[cmd] |
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88
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except KeyError: |
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89
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raise InjectionError(f"Search command {cmd} (key {key}) does not exist") |
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90
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cmd.test(self.path, **params) |
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91
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if key in commands: |
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92
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raise ValueError(f"Repeated search key '{key}'") |
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93
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commands[key] = (cmd, params) |
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94
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if self.meta.get("check", False): |
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95
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# we already ran check on all of them |
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96
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return {} |
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97
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else: |
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98
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return commands |
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99
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100
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101
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__all__ = ["MultiSearch"] |
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102
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dmyersturnbull /
mandos
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