feat: fetch sidecar Auspice JSON if .root_sequence is not on the tree
#1460
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Followup of #1455 If `.root_sequence` is not available on Auspice JSON, let's attempt to fetch ref sequence from sidecar Auspice JSON. For that let's GET from the same URL, but with `Accept: application/vnd.nextstrain.dataset.root-sequence+json` header.
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Attempt to run with a very large SC2 tree has hit the local storage limit. Well, I should not store the dataset in the local storage in the first place. Need to rethink my decisions about how to persist the datasets from Not related to this PR, but something to address ASAP. |
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It's unclear how to implement a symmetric functionality in CLI. I guess we can tell users to paste their sidecar into the main JSON? Does it make sense to introduce a new CLI arg for a new file type? |
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@ivan-aksamentov The root sequence sidecar for Maybe the CLI could also support fetching a dataset specified as a URL directly, and then make the same content-nego request behind the scenes in that case? |
#1460 (comment) Co-authored-by: Thomas Sibley <[email protected]>
Most discussion about this functionality has been happening within the nextclade repo, see <nextstrain/nextclade#1455> and <nextstrain/nextclade#1460> for a good summary.
Most discussion about this functionality has been happening within the nextclade repo, see <nextstrain/nextclade#1455> and <nextstrain/nextclade#1460> for a good summary.
Followup of #1455
If
.root_sequenceis not available on Auspice JSON, let's attempt to fetch ref sequence from sidecar Auspice JSON. For that let's GET from the same URL, but withAccept: application/vnd.nextstrain.dataset.root-sequence+jsonheader.