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""" |
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Command-line interface for mandos. |
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3
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""" |
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5
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from __future__ import annotations |
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import logging |
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from pathlib import Path |
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import typer |
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from mandos.model.settings import MANDOS_SETTINGS |
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from mandos.model.taxonomy_caches import TaxonomyFactories |
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from mandos.entries.entries import Entries, _Typer |
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14
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from mandos.entries.api_singletons import Apis |
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from mandos.entries.multi_searches import MultiSearch |
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from mandos.entries.searcher import SearcherUtils |
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logger = logging.getLogger(__package__) |
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# IMPORTANT! |
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Apis.set_default() |
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cli = typer.Typer() |
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class Commands: |
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""" |
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Entry points for mandos. |
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""" |
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@staticmethod |
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def search( |
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path: Path = _Typer.path, |
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config: Path = typer.Argument( |
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33
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None, |
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help=".toml config file. See docs.", |
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exists=True, |
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dir_okay=False, |
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readable=True, |
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), |
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) -> None: |
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""" |
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Run multiple searches. |
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""" |
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MultiSearch(path, config).search() |
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45
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@staticmethod |
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def find( |
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path: Path = _Typer.path, |
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48
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pubchem: bool = typer.Option(True, help="Download data from PubChem"), |
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49
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chembl: bool = typer.Option(True, help="Download data from ChEMBL"), |
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50
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hmdb: bool = typer.Option(True, help="Download data from HMDB"), |
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51
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) -> None: |
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52
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""" |
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Fetches and caches compound data. |
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Useful to check what you can see before running a search. |
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""" |
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out_path = path.with_suffix(".ids.csv") |
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if out_path.exists(): |
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raise FileExistsError(out_path) |
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inchikeys = SearcherUtils.read(path) |
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df = SearcherUtils.dl(inchikeys, pubchem=pubchem, chembl=chembl, hmdb=hmdb) |
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61
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df.to_csv(out_path) |
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typer.echo(f"Wrote to {out_path}") |
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@staticmethod |
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def dl_tax( |
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taxon: int, |
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67
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) -> None: |
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68
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""" |
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69
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Preps a new taxonomy file for use in mandos. |
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70
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Just returns if a corresponding file already exists in the resources dir or mandos cache (``~/.mandos``). |
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71
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Otherwise, downloads a tab-separated file from UniProt. |
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(To find manually, follow the ``All lower taxonomy nodes`` link and click ``Download``.) |
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Then applies fixes and reduces the file size, creating a new file alongside. |
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Puts both the raw data and fixed data in the cache under ``~/.mandos/taxonomy/``. |
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Args: |
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taxon: The **ID** of the UniProt taxon |
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78
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""" |
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TaxonomyFactories.from_uniprot(MANDOS_SETTINGS.taxonomy_cache_path).load(taxon) |
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80
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81
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82
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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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from typer.models import CommandInfo |
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88
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89
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info = CommandInfo(entry.cmd(), callback=entry.run) |
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cli.registered_commands.append(info) |
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setattr(Commands, entry.cmd(), entry.run) |
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cli.registered_commands.extend( |
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[ |
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CommandInfo("@search", callback=Commands.search), |
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96
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CommandInfo("@dl-tax", callback=Commands.dl_tax, hidden=True), |
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] |
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98
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) |
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99
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100
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101
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if __name__ == "__main__": |
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cli() |
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103
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104
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105
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__all__ = ["Commands"] |
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dmyersturnbull /
mandos
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