[BUG] taxpasta deletes nodes/names.dmp from --taxonomy dir about taxpasta

[kdm9]

@Midnighter hmm, I did check the version of taxprofiler was up-to-date, but I had initially installed v0.2.3 and so it is possible that I checked the version e.g. in a different conda env from the jobs that rm'd the files.

Given that this was a recently fixed bug, I suspect that is what happened. I've recreated all conda envs to update taxprofiler, so we'll see if the issues recur.

In the mean time I'm happy to close this issue, and will reopen if I find this happening again with v0.3.0 or higher.

[kdm9]

I should have made this clear: this doesn't happen every single time I ctrl-c taxpasta. I'd estimate about a quarter of the times

[Midnighter]

It indeed sounds like an upstream issue in taxopy to me. Not sure why this would happen when only reading content. @maxibor do you have some capacity to investigate?

[apcamargo]

I'm not exactly sure how taxopy is called within taxpasta, but this is the part of the code that controls the deletion of the files: https://github.com/apcamargo/taxopy/blob/437f94be6b592cc5638e45c10804760191ddffc8/taxopy/core.py#L128-L129

If nodes.dmp or names.dmp are manually supplied, the files shouldn't be deleted.

[Midnighter]

The taxopy.TaxDb is created in this piece of code:

class TaxopyTaxonomyService(TaxonomyService):
    """Define the taxonomy service based on taxopy."""

    def __init__(self, *, tax_db: taxopy.TaxDb, **kwargs) -> None:
        """Initialize a taxonomy service instance with a taxopy database."""
        super().__init__(**kwargs)
        self._tax_db = tax_db

    @classmethod
    def from_taxdump(cls, source: Path) -> TaxopyTaxonomyService:
        """Create a service instance from a directory path containing taxdump info."""
        merged = source / "merged.dmp"
        return cls(
            tax_db=taxopy.TaxDb(
                names_dmp=str(source / "names.dmp"),
                nodes_dmp=str(source / "nodes.dmp"),
                merged_dmp=str(merged) if merged.is_file() else None,
                keep_files=True,
            )
        )

So I don't see why the files should ever get deleted. Unless, @kdm9 you were using an earlier version of taxpasta which indeed had a bug in this code.