mandos.entry.tools.searchers.Searcher.search()

Complexity

Conditions

10

Size

Total Lines	66
Code Lines	54

Duplication

Lines	0
Ratio	0 %

Importance

Changes

0

"""
    def search(self) -> SearchReturnInfo:

This function exceeds the maximum number of variables (16/15).

        """
        Performs the search, and writes data.
        """
        inchikeys = self.input_df["inchikey"].unique()
        if self.is_complete:
            logger.info(f"{self.to} already complete")
            return SearchReturnInfo(
                n_kept=len(inchikeys), n_processed=0, n_errored=0, time_taken=timedelta(seconds=0)
            )
        logger.info(f"Will save every {SETTINGS.save_every} compounds")
        logger.info(f"Writing {self.what.key} to {self.to}")
        annotes = []
        compounds_run = set()
        cache = SearchCache(self.to, inchikeys, restart=self.restart, proceed=self.proceed)
        # refresh so we know it's (no longer) complete
        # this would only happen if we're forcing this -- which is not currently allowed
        (
            Checksums()
            .load_dirsum_of_file(self.to, missing_ok=True)
            .remove(self.to, missing_ok=True)
            .write(rm_if_empty=True)
        )
        t0, n0, n_proc, n_err, n_annot = time.monotonic(), cache.at, 0, 0, 0

Variable name "n0" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

Variable name "t0" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        while True:
            try:
                compound = cache.next()

cache.next does not seem to be callable.

            except StopIteration:
                break
            try:
                with logger.contextualize(compound=compound):
                    x = self.what.find(compound)

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

                annotes.extend(x)
            except CompoundNotFoundError:
                logger.info(f"Compound {compound} not found for {self.what.key}")
                x = []

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

                n_err += 1
            except Exception:
                raise SearchError(
                    f"Failed {self.what.key} [{self.what.search_class}] on compound {compound}",
                    compound=compound,
                    search_key=self.what.key,
                    search_class=self.what.search_class,
                )
            compounds_run.add(compound)
            logger.debug(f"Found {len(x)} {self.what.search_name()} annotations for {compound}")
            n_annot += len(x)
            n_proc += 1
            # logging, caching, and such:
            on_nth = cache.at % SETTINGS.save_every == SETTINGS.save_every - 1
            is_last = cache.at == len(inchikeys) - 1
            if on_nth or is_last:
                logger.log(
                    "NOTICE" if is_last else "INFO",
                    f"Found {len(annotes)} {self.what.search_name()} annotations"
                    + f" for {cache.at} of {len(inchikeys)} compounds",
                )
                self._save(annotes, done=is_last)
            cache.save(*compounds_run)  # CRITICAL -- do this AFTER saving
        # done!
        i1, t1 = cache.at, time.monotonic()

Variable name "i1" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

Variable name "t1" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

        assert i1 == len(inchikeys)
        cache.kill()
        logger.success(f"Wrote {self.what.key} to {self.to}")
        return SearchReturnInfo(
            n_kept=n0, n_processed=n_proc, n_errored=n_err, time_taken=timedelta(seconds=t1 - t0)
        )