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Add v3 mpxv datasets, still some wip #104

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merged 5 commits into from
Nov 21, 2023
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corneliusroemer
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@corneliusroemer corneliusroemer commented Nov 16, 2023

Some of the strings still need to be changed, might tweak some things in pathogen.json - but this is 80% ready and works without error now

New paths are:

  • nextstrain/mpox/lineage-b.1
  • nextstrain/mpox/clade-iib
  • nextstrain/mpox/all-clades

Can be tested via: https://master.clades.nextstrain.org/?dataset-server=gh:nextstrain/nextclade_data@mpxv-update-draft@/data_output

@ivan-aksamentov
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Looks good. I find paths a bit long (especially for CLI usage), but if it suits you, then it's fine for me too.

The format for recognized pathogen.json attributes (to get friendly names in the UI) is like this:
https://github.com/nextstrain/nextclade_data/blob/bd6d9d159970dc2895eb833e1e16d7206de67f7a/data/nextstrain/flu/h1n1pdm/ha/CY121680/pathogen.json#L80C1-L84
But you can also put anything else there, and of any type. For example, Richard have added "segment" attribute to some of the flus.

@corneliusroemer
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Thanks for the comments @ivan-aksamentov! I'll reconsider the path verbosity

@corneliusroemer
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I've shortened paths and dropped the last component, the reference, after consultation with Richard, as it is not required to disambiguate and takes a lot of space

@corneliusroemer corneliusroemer merged commit 2008684 into master Nov 21, 2023
@corneliusroemer corneliusroemer deleted the mpxv-update-draft branch November 21, 2023 17:07
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3 participants