# -*- coding: utf-8 -*-
"""High-level API for species."""
import logging
from functools import lru_cache
from typing import Mapping, Optional
from .alts import get_primary_identifier
from .utils import get_version
from ..getters import NoBuild, get_ontology
from ..identifier_utils import wrap_norm_prefix
from ..utils.cache import cached_mapping
from ..utils.path import prefix_cache_join
__all__ = [
"get_id_species_mapping",
"get_species",
]
logger = logging.getLogger(__name__)
[docs]@wrap_norm_prefix
def get_species(prefix: str, identifier: str) -> Optional[str]:
"""Get the species."""
if prefix == "uniprot":
raise NotImplementedError
try:
id_species = get_id_species_mapping(prefix)
except NoBuild:
logger.warning("unable to look up species for prefix %s", prefix)
return None
if not id_species:
logger.warning("no results produced for prefix %s", prefix)
return None
primary_id = get_primary_identifier(prefix, identifier)
return id_species.get(primary_id)
[docs]@lru_cache()
@wrap_norm_prefix
def get_id_species_mapping(
prefix: str,
force: bool = False,
strict: bool = True,
version: Optional[str] = None,
) -> Mapping[str, str]:
"""Get an identifier to species mapping."""
if prefix == "ncbigene":
from ..sources.ncbigene import get_ncbigene_id_to_species_mapping
logger.info("[%s] loading species mappings", prefix)
rv = get_ncbigene_id_to_species_mapping()
logger.info("[%s] done loading species mappings", prefix)
return rv
if version is None:
version = get_version(prefix)
path = prefix_cache_join(prefix, name="species.tsv", version=version)
@cached_mapping(path=path, header=[f"{prefix}_id", "species"], force=force)
def _get_id_species_mapping() -> Mapping[str, str]:
logger.info("[%s] no cached species found. getting from OBO loader", prefix)
ontology = get_ontology(prefix, force=force, strict=strict, version=version)
logger.info("[%s] loading species mappings", prefix)
return ontology.get_id_species_mapping()
return _get_id_species_mapping()