33 lines
948 B
Python
33 lines
948 B
Python
from abc import abstractmethod
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from contextlib import AbstractAsyncContextManager
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from typing import AsyncGenerator, AsyncIterable, Generator, Iterable, Mapping, Union
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from aiohttp import ClientSession
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from automlst.engine.data.mlst import Allele, MLSTProfile
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MLST_DATABASES = [
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"https://bigsdb.pasteur.fr/api/db",
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"https://rest.pubmlst.org/db"
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]
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class MLSTProfiler(AbstractAsyncContextManager):
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@abstractmethod
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def fetch_mlst_allele_variants(self, schema_id: int, sequence_string: str) -> AsyncGenerator[Allele]:
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pass
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@abstractmethod
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async def fetch_mlst_st(self, schema_id: int, alleles: AsyncIterable[Allele]) -> MLSTProfile:
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pass
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@abstractmethod
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async def profile_string(self, schema_id: int, string: str) -> MLSTProfile:
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pass
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@abstractmethod
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async def close(self):
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pass
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@abstractmethod
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async def get_scheme_ids(self) -> Mapping[str, int]:
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pass |