Source code for modos.codes

"""Utilities to automatically find / recommend terminology codes from text."""
from dataclasses import dataclass
from typing import Optional, Protocol

from pathlib import Path
import requests



[docs]
SLOT_TERMINOLOGIES = {
    "cell_type": ["https://purl.obolibrary.org/obo/cl.owl"],
    "source_material": ["https://purl.obolibrary.org/obo/uberon.owl"],
    "taxon_id": [
        "https://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl"
    ],
}



@dataclass

[docs]
class Code:

[docs]
    label: str


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    uri: str





[docs]
class CodeMatcher(Protocol):

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    endpoint: Optional[str]


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    slot: str


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    top: int



[docs]
    def find_codes(self, query: str) -> list[Code]:
        ...





[docs]
class LocalCodeMatcher(CodeMatcher):
    """Find ontology codes for a given text by running a local term matcher."""

    def __init__(self, slot: str, top: int = 50):

[docs]
        self.endpoint = None


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        self.slot = slot


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        self.top = top


        try:
            from pyfuzon import cache
        except ImportError:
            raise ModuleNotFoundError(
                "pyfuzon must be installed to perform local code matching."
            )

        sources = SLOT_TERMINOLOGIES[slot]
        try:
            self.matcher = cache.load_by_source(sources)
        except RuntimeError:
            Path(cache.get_cache_path(sources)).parent.mkdir(
                parents=True, exist_ok=True
            )
            cache.cache_by_source(sources)
            self.matcher = cache.load_by_source(sources)


[docs]
    def find_codes(self, query: str) -> list[Code]:
        return self.matcher.top(query, self.top)





[docs]
class RemoteCodeMatcher(CodeMatcher):
    """Find ontology codes for a given text relying on a remote term matcher."""

    def __init__(self, slot: str, endpoint: str, top: int = 50):

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        self.endpoint = endpoint


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        self.slot = slot


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        self.top = top



[docs]
    def find_codes(self, query: str) -> list[Code]:
        codes = requests.get(
            f"{self.endpoint}/top?collection={self.slot}&query={query}&top={self.top}"
        ).json()["codes"]
        return [Code(label=code["label"], uri=code["uri"]) for code in codes]





[docs]
def get_slot_matcher(
    slot: str,
    endpoint: Optional[str] = None,
) -> CodeMatcher:
    """Instantiates a code matcher based on input slot name."""
    if endpoint:
        matcher = RemoteCodeMatcher(slot, endpoint)
    else:
        matcher = LocalCodeMatcher(slot)
    return matcher




[docs]
def get_slot_matchers(
    endpoint: Optional[str] = None,
) -> dict[str, CodeMatcher]:
    """Instantiates a code matcher for each slot. If the endpoint is provided, remote matchers are used."""
    matchers = {}
    for slot in SLOT_TERMINOLOGIES.keys():
        matchers[slot] = get_slot_matcher(slot, endpoint)
    return matchers