dmyersturnbull / mandos

        return super().run(**{a: locs[a] for a in args if a != "cls"})

class EntryPubchemChemicalCoOccurrence(_EntryPubchemCoOccurrence[ChemicalCoOccurrenceSearch]):

    @classmethod

    @entry()

    def run(

        cls,

        path: Path = CommonArgs.in_compound_table,

        key: str = EntryArgs.key(f"lit.pubchem:{CoOccurrenceType.chemical.name.lower()}"),

        to: Optional[Path] = CommonArgs.out_annotations_file,

        min_score: float = EntryArgs.min_cooccurrence_score,

        min_articles: int = EntryArgs.min_cooccurring_articles,

        as_of: Optional[str] = CommonArgs.as_of,

        replace: bool = CommonArgs.replace,

        proceed: bool = CommonArgs.proceed,

        check: bool = EntryArgs.check,

        log: Optional[Path] = CommonArgs.log,

        stderr: str = CommonArgs.stderr,

    ) -> Searcher:

        """

        Co-occurrences of chemicals from PubMed articles.

        https://mandos-chem.readthedocs.io/en/latest/co-occurrences.html

        OBJECT: The name of the chemical (e.g. "cocaine")

        WEIGHT: The co-occurrence score (refer to the docs)

        """

        args, _, _, locs = inspect.getargvalues(inspect.currentframe())

        return super().run(**{a: locs[a] for a in args if a != "cls"})

class EntryPubchemDgi(Entry[DgiSearch]):

        return super().run(**{a: locs[a] for a in args if a != "cls"})

class EntryPubchemDiseaseCoOccurrence(_EntryPubchemCoOccurrence[DiseaseCoOccurrenceSearch]):

    @classmethod

    @entry()

    def run(

        cls,

        path: Path = CommonArgs.in_compound_table,

        key: str = EntryArgs.key(f"lit.pubchem:{CoOccurrenceType.disease.name.lower()}"),

        to: Optional[Path] = CommonArgs.out_annotations_file,

        min_score: float = EntryArgs.min_cooccurrence_score,

        min_articles: int = EntryArgs.min_cooccurring_articles,

        as_of: Optional[str] = CommonArgs.as_of,

        replace: bool = CommonArgs.replace,

        proceed: bool = CommonArgs.proceed,

        check: bool = EntryArgs.check,

        log: Optional[Path] = CommonArgs.log,

        stderr: str = CommonArgs.stderr,

    ) -> Searcher:

        """

        Co-occurrences of diseases from PubMed articles.

        https://mandos-chem.readthedocs.io/en/latest/co-occurrences.html

        OBJECT: The name of the disease

        WEIGHT: The co-occurrence score (refer to the docs)

        """

        args, _, _, locs = inspect.getargvalues(inspect.currentframe())

        return super().run(**{a: locs[a] for a in args if a != "cls"})

class EntryPubchemChemicalCoOccurrence(_EntryPubchemCoOccurrence[ChemicalCoOccurrenceSearch]):

        return cls._run(built, path, to, replace, proceed, check, log, stderr)

class EntryPubchemGeneCoOccurrence(_EntryPubchemCoOccurrence[GeneCoOccurrenceSearch]):

    @classmethod

    @entry()

    def run(

        cls,

        path: Path = CommonArgs.in_compound_table,

        key: str = EntryArgs.key(f"lit.pubchem:{CoOccurrenceType.gene.name.lower()}"),

        to: Optional[Path] = CommonArgs.out_annotations_file,

        min_score: float = EntryArgs.min_cooccurrence_score,

        min_articles: int = EntryArgs.min_cooccurring_articles,

        as_of: Optional[str] = CommonArgs.as_of,

        replace: bool = CommonArgs.replace,

        proceed: bool = CommonArgs.proceed,

        check: bool = EntryArgs.check,

        log: Optional[Path] = CommonArgs.log,

        stderr: str = CommonArgs.stderr,

    ) -> Searcher:

        """

        Co-occurrences of genes from PubMed articles.

        https://mandos-chem.readthedocs.io/en/latest/co-occurrences.html

        OBJECT: The name of the gene

        WEIGHT: The co-occurrence score (refer to the docs)

        """

        args, _, _, locs = inspect.getargvalues(inspect.currentframe())

        return super().run(**{a: locs[a] for a in args if a != "cls"})

class EntryPubchemDiseaseCoOccurrence(_EntryPubchemCoOccurrence[DiseaseCoOccurrenceSearch]):