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feat: fetch sidecar Auspice JSON if .root_sequence is not on the tree #1460

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merged 7 commits into from
May 30, 2024
Merged

feat: fetch sidecar Auspice JSON if .root_sequence is not on the tree #1460

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8495372
feat: fetch sidecar Auspice JSON if `.root_sequence` is not on the tree
ivan-aksamentov May 30, 2024
27825f5
feat: use main dataset JSON media type, with quality factors
ivan-aksamentov May 30, 2024
9ed52a2
fix: check response mime type when requesting sidecar JSON
ivan-aksamentov May 30, 2024
7aadabd
refactor: format & lint
ivan-aksamentov May 30, 2024
0f80824
refactor: var name
ivan-aksamentov May 30, 2024
0de953e
fix: error message
ivan-aksamentov May 30, 2024
6e964be
refactor: ensure consistent naming
ivan-aksamentov May 30, 2024
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13 changes: 12 additions & 1 deletion packages/nextclade-web/src/io/fetchSingleDatasetAuspice.ts
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Original file line number Diff line number Diff line change
@@ -1,13 +1,24 @@
import { isEmpty } from 'lodash'
import { attrStrMaybe, AuspiceTree, Dataset } from 'src/types'
import { removeTrailingSlash } from 'src/io/url'
import { axiosFetch } from 'src/io/axiosFetch'
import { axiosFetch, axiosFetchOrUndefined } from 'src/io/axiosFetch'

export async function fetchSingleDatasetAuspice(datasetJsonUrl_: string) {
const datasetJsonUrl = removeTrailingSlash(datasetJsonUrl_)

const auspiceJson = await axiosFetch<AuspiceTree>(datasetJsonUrl, {
headers: { Accept: 'application/json, text/plain, */*' },
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})

if (isEmpty(auspiceJson.root_sequence)) {
const sidecar = await axiosFetchOrUndefined<Record<string, string>>(datasetJsonUrl, {
headers: { Accept: 'application/vnd.nextstrain.dataset.root-sequence+json' },
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})
if (!isEmpty(sidecar)) {
auspiceJson.root_sequence = sidecar
}
}
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const pathogen = auspiceJson.meta.extensions?.nextclade?.pathogen

const name =
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