ENH: Make `sample type` an Auspice filter

[corneliusroemer]

I think it would be nice to have sample type enabled as an Auspice filter.

It should be as easy as adding a few lines to the auspice_config.json that's used for exporting.

That way, one could quickly filter down to new samples as opposed to reference tree samples.

[yatisht]

@jmcbroome would this be easy to add?

[jmcbroome]

I'm afraid I'm lacking some context for this request. We don't use an "Auspice_config" json, we have a simple Nextstrain json format hardcoded into matUtils. Would "sample type" be some kind of metadata tagging that we could set a coloring by, similar to country? How would "sample type" be determined? Would this be part of an output from calling an UShER placement, and the samples would be tagged by whether they were added in that call?

[corneliusroemer]

Happy to explain @jmcbroome :)

You already have it as a color by:

All that's needed is to add a little bit of code to the hardcoded auspice.json part here: https://github.com/yatisht/usher/blob/728b739a27613e8277988a504743c58e09bc233e/src/matUtils/convert.cpp#L481

I'll see what needs to be added to get it to work - it should just be a very small code change.

[corneliusroemer]

Right now, filters seems to be empty, at least in the auspice.json produced by online Usher:

Maybe a bug? Or maybe I'm looking at the wrong part of the code.

[corneliusroemer]

Alright, so all you have to do is add the following inside filter:

"filters": ["country","userOrOld"]

That's it!

I manually edited an auspice.json produced by usher conforming with the above and it works 🎉

[corneliusroemer]

Here's an auspice config.json I found in this repo. Not sure whether it's used at all.

https://github.com/yatisht/usher/blob/master/workflows/config/config.json

[corneliusroemer]

@jmcbroome what I don't understand is why the filters array was empty. It should have already contained country but didn't. Any idea why?

The weird thing is, that I can only find a description mentioning matUtils while the description of the web produced auspice.json has a different description. So that may be why country isn't showing in the filter. https://github.com/yatisht/usher/blob/a37da007af2cb04c8d1942e0e8aac051b0e1b64d/src/matUtils/convert.cpp#L474

@AngieHinrichs do you have an idea where the web version of auspice meta comes from?