W-ASAP: Use collections

[chaoran-chen]

From the existing CoV-Spectrum collections or the future generalized collections (#938), we can get for SARS-CoV-2 a set of collections where each collection has a list of variants. We can show them in the Wastewater COVID dashboard by adding a new exploration mode similar to the current Resistance Mutations mode.

For example, we can have a drop down with showing the list of (suitable) collections and once a collection is selected, we show the over-time heatmap where each row is is one entry in the collection. As label, we can show the user-specified name of the entry. Ideally, when the user hovers over the label, they would see the description and/or variant query, and when they click on it, they can be forwarded to the clinical dashboard.

There are different types of collections that one can create. Entries of a collection can just individual mutations, but they can also be complex queries.

Many collections (espcially the already existing collections on CoV-Spectrum) are not suitable as they also filter for Pango lineages or mutations that are far away and not covered by the same amplicon. To only show relevant collections, we can filter for those where in the description is a certain text like [For wastewater].

[chaoran-chen]

@fhennig, this issue is not necessarily blocked by #938 because, for the SARS-CoV-2 wastewater page, we can start with the existing CoV-Spectrum collections.

[fhennig]

Ahh I see ok cool.

[gordonkoehn]

Sounds like an elegant solution. The [For wastewater] marker is a good idea. Beyond that, we might also want to filter by maintainer (e.g., CBG/GenSpectrum) for specialised modes like resistance mutations — users can trust the curation of these.

This could also scale nicely to co-occurring mutations using arbitrary queries, which we'd want to define and store somewhere centrally.

[fhennig]

The way I see it, we need:

• changes in the frontend, to add the new mode
• a new component to display this stuff: feat: New "mutation-group"-over-time component dashboard-components#65
• a new LAPIS endpoint to allow us to query this

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also useful:

• cov-spectrum api docs: https://github.com/GenSpectrum/cov-spectrum-server/blob/develop/docs/api.md
• and example of a collection: https://open.cov-spectrum.org/collections/194 (check network to see API calls)