Include submissionId in displayName

[theosanderson]

The definitive sample ID (a la Hu-1 for SARS-CoV-2) for the recent ebola genome is CL292200, which was used as the submissionId.

IMO we should include it in the displayName, which we don't currently:

I expect this to apply in many future instances.

[chaoran-chen]

But in case Pathoplexus, for CCHF (example), the submisison IDs of INSDC-ingested sequences are really long. For Influenza on GenSpectrum (example), that's even worse.

[theosanderson]

👍 one could treat insdc_ingest_user specially here and exclude the submission ID (it's not a real submission ID from a user).

[theosanderson]

(For GenSpectrum of course you could make any choice you want about what to include, which is already configurable)

[chaoran-chen]

That could be one option. It will probably work well in many cases but not in all. We have in Pathoplexus https://pathoplexus.org/seq/PP_0013N8P.1 with a Submission ID "Monkeypox/PT0836/2025". If we do this, we may want to adapt our Pathoplexus submission documentation to make users aware of how the submission ID is going to be used.

[theosanderson]

👍 there could be a general case for stripping /s as part of this (converting them to - or _) to maintain the delimiter. And yes, definitely not against documenting whatever we decide on!

[fhennig]

Maybe the display name format could be configurable on a per-organism basis?

i.e.

displayNameFormat: "${sampleId}/${accession}/${version}/${collectionCountry}"

The display name is mostly useful for website navigation etc, and I think depending on how one uses Loculus, different things might be useful to have in the display name (maybe one might opt to only use the sample ID and not even care about Loculus accessions or anything else!).

What exactly is done for PPX can then be a separate discussion

[theosanderson]

Maybe the display name format could be configurable on a per-organism basis?

It already is - it's made by the preprocessing pipeline subject to configuration in the YAML.

I still think this is a useful place to have the discussion as, for example, it does impact on this Q about potential specific behaviour for the insdc_ingest_user