43 lines
1.4 KiB
Python
43 lines
1.4 KiB
Python
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from argparse import ArgumentParser
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import asyncio
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from automlst.engine.remote.databases.bigsdb import BIGSdbIndex
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def setup_parser(parser: ArgumentParser):
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parser.description = "Fetches the latest BIGSdb MLST database definitions."
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parser.add_argument(
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"--retrieve-bigsdbs", "-l",
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action="store_true",
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dest="list_dbs",
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required=False,
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default=False,
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help="Lists all known BIGSdb MLST databases (fetched from known APIs and cached)."
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)
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parser.add_argument(
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"--retrieve-bigsdb-schemas", "-lschemas",
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nargs="+",
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action="extend",
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dest="list_bigsdb_schemas",
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required=False,
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default=[],
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type=str,
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help="Lists the known schema IDs for a given BIGSdb sequence definition database name. The name, and then the ID of the schema is given."
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)
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parser.set_defaults(func=run_asynchronously)
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async def run(args):
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async with BIGSdbIndex() as bigsdb_index:
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if args.list_dbs:
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known_seqdef_dbs = await bigsdb_index.get_known_seqdef_dbs(force=False)
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print("\n".join(known_seqdef_dbs.keys()))
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for bigsdb_schema_name in args.list_bigsdb_schemas:
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schemas = await bigsdb_index.get_schemas_for_seqdefdb(bigsdb_schema_name)
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for schema_desc, schema_id in schemas.items():
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print(f"{schema_desc}: {schema_id}")
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def run_asynchronously(args):
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asyncio.run(run(args))
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