mandos.entries.searcher.SearcherUtils.dl()

Complexity

Conditions

8

Size

Total Lines	46
Code Lines	33

Duplication

Lines	0
Ratio	0 %

Importance

Changes

0

"""
    @classmethod
    def dl(

Method name "dl" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

Missing function or method docstring

Either all return statements in a function should return an expression, or none of them should.

        cls,

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        inchikeys: Sequence[str],

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        pubchem: bool = True,

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        chembl: bool = True,

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        hmdb: bool = True,

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The argument hmdb seems to be unused.

    ) -> IdMatchFrame:
        # we actually cache the results, even though the underlying APIs cache
        # the reasons for this are a little obscure --
        # when running a Searcher, we want to run before the FIRST search
        # for the typer commands to be replicas of the ``Entry.run`` methods, Searcher fetches before running a search

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        # but if we have multiple searches (as in ``mandos search --config``), we only want that at the beginning

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        # the alternative was having ``mandos search`` dynamically subclass each ``Entry`` -- which was really hard

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        # this is much cleaner, even though it's redundant
        # if the cached results under /pubchem and /chembl are deleted, we unfortunately won't cache the results

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        # when running this command
        # to fix that, we need to delete the cached /match dataframes
        # now that I'm writing this down, I realize this is pretty bad
        # TODO

TODO and FIXME comments should generally be avoided.

        key = hash(",".join(inchikeys))
        cached_path = (MANDOS_SETTINGS.match_cache_path / str(key)).with_suffix(".feather")
        if cached_path.exists():
            logger.info(f"Found ID matching results at {cached_path}")

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            return IdMatchFrame.read_feather(cached_path)
        found_chembl: Dict[str, str] = {}
        found_pubchem: Dict[str, str] = {}
        if pubchem:
            for inchikey in inchikeys:
                try:
                    found_pubchem[inchikey] = str(Pubchem.fetch_data(inchikey).cid)
                except CompoundNotFoundError:
                    logger.error(f"Did not find compound {inchikey}")

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                    logger.debug(f"Did not find compound {inchikey}", exc_info=True)

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        if chembl:
            for inchikey in inchikeys:
                try:
                    found_chembl[inchikey] = ChemblUtils(Chembl).get_compound(inchikey).chid
                except CompoundNotFoundError:
                    logger.error(f"Did not find compound {inchikey}")

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                    logger.debug(f"Did not find compound {inchikey}", exc_info=True)

Use lazy % formatting in logging functions

        df = pd.DataFrame([pd.Series(dict(inchikey=c)) for c in inchikeys])

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        df["chembl_id"] = df["inchikey"].map(found_chembl.get)
        df["pubchem_id"] = df["inchikey"].map(found_pubchem.get)
        df = IdMatchFrame(df)

Variable name "df" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        df.to_feather(cached_path)