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GenSpectrum / LAPIS-SILO

Sequence Indexing engine for Large Order of genomic data
GNU Affero General Public License v3.0
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Q: Is pangoLienageDefinitionFilename mandatory config field? #369

Closed corneliusroemer closed 2 months ago

corneliusroemer commented 8 months ago

Only SARS-CoV-2 has pango lineages per se, there's something a bit like pango for mpox, and similar (but different) systems for flu, rsv etc

Is the lineage config field required? That would not make much sense, making it optional would be better.

In general, it might be good to come up with a general way of dealing with aliases that isn't pango specific.

I can help come up with something for the ones that works at least for those nomenclature schemes that are quite similar to pango: mpox, flu, rsv

Taepper commented 8 months ago

I would gladly discuss this with you! I had quite clear plans that @JonasKellerer partly implemented, but was left in a WIP state. It would be great to discuss whether it is sensible and your thoughts on this.

Overall: I would like to turn the Pango Alias system into a generic format for tree/hierarchical column types that are also possible to have multiple roots (i.e. more a forest than a tree)

fengelniederhammer commented 8 months ago

You're referring to the pangoLineageDefinitionFilename in the "preprocessing config", correct? It's not mandatory there.

corneliusroemer commented 8 months ago

Ok, so I get this error only because it's specified but then empty.

I was thinking that the preprocessing config uses default values - so how does one overwrite it to not need to exist? set to null?

lapis-silo-1  | [2024-03-26 10:56:37.928] [logger] [error] [api.cpp:297] filesystem error: Alias key file /preprocessing/input/pangolineage_alias.json does not exist: No error information
fengelniederhammer commented 8 months ago

Not specifying at all should work.

But we should check as part of #129 what other versions of "not setting it" do.

corneliusroemer commented 8 months ago

Indeed it does seem to work without setting that field - so it seems that by default this isn't set?

fengelniederhammer commented 8 months ago

Indeed it does seem to work without setting that field - so it seems that by default this isn't set?

Yes - as the docs state, by default it's unset. ;)

fengelniederhammer commented 2 months ago

The question was answered, it's currently mentioned in the docs. And #458 will remove the config value.