Merge pull request #1460 from nextstrain/feat/fetch-auspice-sidecar-json

packages/nextclade-web/package.json

@@ -87,6 +87,8 @@
   },
   "dependencies": {
     "@floating-ui/react": "0.26.1",
+    "@hapi/accept": "6.0.3",
+    "@hapi/content": "6.0.0",
     "animate.css": "4.1.1",
     "auspice": "2.53.0",
     "autoprefixer": "10.4.5",
@@ -200,6 +202,7 @@
     "@types/friendly-errors-webpack-plugin": "0.1.4",
     "@types/fs-extra": "9.0.13",
     "@types/glob": "7.2.0",
+    "@types/hapi__content": "6.0.3",
     "@types/history": "4.7.11",
     "@types/intercept-stdout": "0.1.0",
     "@types/jest": "27.4.1",

packages/nextclade-web/src/io/axiosFetch.ts

@@ -1,8 +1,15 @@
 import axios, { AxiosError, AxiosRequestConfig, AxiosResponse } from 'axios'
-import { isNil } from 'lodash'
+import { isNil, isString } from 'lodash'
+import { mediaTypes as parseAcceptHeader } from '@hapi/accept'
+import { ContentType, type as parseContentTypeHeader } from '@hapi/content'
 import { ErrorFatal } from 'src/helpers/ErrorFatal'
 import { sanitizeError } from 'src/helpers/sanitizeError'
 
+export interface RequestConfig extends AxiosRequestConfig {
+  // Check that MIME type of response's Content-Type header is compatible with at least one of MIME types in the request's Accept header
+  strictAccept?: boolean
+}
+
 export class HttpRequestError extends Error {
   public readonly url?: string
   public readonly status?: number | string
@@ -36,10 +43,27 @@ export function validateUrl(url?: string): string {
   return url
 }
 
-export async function axiosFetch<TData = unknown>(
-  url_: string | undefined,
-  options?: AxiosRequestConfig,
-): Promise<TData> {
+export interface CheckMimeTypesResult {
+  isCompatible: boolean
+  acceptTypes?: string[]
+  contentType?: ContentType
+  acceptHeader?: string | number | boolean
+  contentTypeHeader?: string
+}
+
+export function checkMimeTypes(req?: RequestConfig, res?: AxiosResponse): CheckMimeTypesResult {
+  const acceptHeader = req?.headers?.Accept
+  const contentTypeHeader = res?.headers['content-type']
+  if (isString(acceptHeader) && isString(contentTypeHeader)) {
+    const acceptTypes = parseAcceptHeader(acceptHeader)
+    const contentType = parseContentTypeHeader(contentTypeHeader)
+    const isCompatible = acceptTypes.includes(contentType.mime)
+    return { isCompatible, acceptTypes, contentType, acceptHeader, contentTypeHeader }
+  }
+  return { isCompatible: false, acceptHeader, contentTypeHeader }
+}
+
+export async function axiosFetch<TData = unknown>(url_: string | undefined, options?: RequestConfig): Promise<TData> {
   const url = validateUrl(url_)
 
   let res
@@ -53,6 +77,17 @@ export async function axiosFetch<TData = unknown>(
     throw new Error(`Unable to fetch: request to URL "${url}" resulted in no data`)
   }
 
+  if (options?.strictAccept) {
+    const mime = checkMimeTypes(options, res)
+    if (!mime.isCompatible) {
+      const accept = mime.acceptHeader ?? ''
+      const contentType = mime.contentTypeHeader ?? ''
+      throw new Error(
+        `Unable to fetch: request to URL "${url}" resulted in incompatible MIME type: Content-Type was "${contentType}", while Accept was "${accept}"`,
+      )
+    }
+  }
+
   return res.data as TData
 }
 
@@ -65,7 +100,7 @@ export async function axiosFetchMaybe(url?: string): Promise<string | undefined>
 
 export async function axiosFetchOrUndefined<TData = unknown>(
   url: string | undefined,
-  options?: AxiosRequestConfig,
+  options?: RequestConfig,
 ): Promise<TData | undefined> {
   try {
     return await axiosFetch<TData>(url, options)
@@ -77,7 +112,7 @@ export async function axiosFetchOrUndefined<TData = unknown>(
 /**
  * This version skips any transforms (such as JSON parsing) and returns plain string
  */
-export async function axiosFetchRaw(url: string | undefined, options?: AxiosRequestConfig): Promise<string> {
+export async function axiosFetchRaw(url: string | undefined, options?: RequestConfig): Promise<string> {
   return axiosFetch(url, { ...options, transformResponse: [] })
 }
 
@@ -88,7 +123,7 @@ export async function axiosFetchRawMaybe(url?: string): Promise<string | undefin
   return axiosFetchRaw(url)
 }
 
-export async function axiosHead(url: string | undefined, options?: AxiosRequestConfig): Promise<AxiosResponse> {
+export async function axiosHead(url: string | undefined, options?: RequestConfig): Promise<AxiosResponse> {
   if (isNil(url)) {
     throw new ErrorFatal(`Attempted to fetch from an invalid URL: '${url}'`)
   }
@@ -102,7 +137,7 @@ export async function axiosHead(url: string | undefined, options?: AxiosRequestC
 
 export async function axiosHeadOrUndefined(
   url: string | undefined,
-  options?: AxiosRequestConfig,
+  options?: RequestConfig,
 ): Promise<AxiosResponse | undefined> {
   try {
     return await axiosHead(url, options)

packages/nextclade-web/src/io/fetchSingleDatasetAuspice.ts

@@ -1,13 +1,27 @@
+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, */*' },
+    headers: {
+      Accept: 'application/vnd.nextstrain.dataset.main+json;q=1, application/json;q=0.9, text/plain;q=0.8, */*;q=0.1',
+    },
   })
+
+  if (isEmpty(auspiceJson.root_sequence)) {
+    const sidecar = await axiosFetchOrUndefined<Record<string, string>>(datasetJsonUrl, {
+      headers: { Accept: 'application/vnd.nextstrain.dataset.root-sequence+json' },
+      strictAccept: true,
+    })
+    if (!isEmpty(sidecar)) {
+      auspiceJson.root_sequence = sidecar
+    }
+  }
+
   const pathogen = auspiceJson.meta.extensions?.nextclade?.pathogen
 
   const name =

packages/nextclade-web/src/styles/global.scss

@@ -11,7 +11,9 @@
 
 @import './components/Results';
 
-html, body, #__next {
+html,
+body,
+#__next {
   overflow: hidden;
   height: 100%;
   width: 100%;

packages/nextclade-web/yarn.lock

@@ -2365,6 +2365,33 @@
     protobufjs "^7.0.0"
     yargs "^16.2.0"
 
+"@hapi/[email protected]":
+  version "6.0.3"
+  resolved "https://registry.yarnpkg.com/@hapi/accept/-/accept-6.0.3.tgz#eef0800a4f89cd969da8e5d0311dc877c37279ab"
+  integrity sha512-p72f9k56EuF0n3MwlBNThyVE5PXX40g+aQh+C/xbKrfzahM2Oispv3AXmOIU51t3j77zay1qrX7IIziZXspMlw==
+  dependencies:
+    "@hapi/boom" "^10.0.1"
+    "@hapi/hoek" "^11.0.2"
+
+"@hapi/boom@^10.0.0", "@hapi/boom@^10.0.1":
+  version "10.0.1"
+  resolved "https://registry.yarnpkg.com/@hapi/boom/-/boom-10.0.1.tgz#ebb14688275ae150aa6af788dbe482e6a6062685"
+  integrity sha512-ERcCZaEjdH3OgSJlyjVk8pHIFeus91CjKP3v+MpgBNp5IvGzP2l/bRiD78nqYcKPaZdbKkK5vDBVPd2ohHBlsA==
+  dependencies:
+    "@hapi/hoek" "^11.0.2"
+
+"@hapi/[email protected]":
+  version "6.0.0"
+  resolved "https://registry.yarnpkg.com/@hapi/content/-/content-6.0.0.tgz#2427af3bac8a2f743512fce2a70cbdc365af29df"
+  integrity sha512-CEhs7j+H0iQffKfe5Htdak5LBOz/Qc8TRh51cF+BFv0qnuph3Em4pjGVzJMkI2gfTDdlJKWJISGWS1rK34POGA==
+  dependencies:
+    "@hapi/boom" "^10.0.0"
+
+"@hapi/hoek@^11.0.2":
+  version "11.0.4"
+  resolved "https://registry.yarnpkg.com/@hapi/hoek/-/hoek-11.0.4.tgz#42a7f244fd3dd777792bfb74b8c6340ae9182f37"
+  integrity sha512-PnsP5d4q7289pS2T2EgGz147BFJ2Jpb4yrEdkpz2IhgEUzos1S7HTl7ezWh1yfYzYlj89KzLdCRkqsP6SIryeQ==
+
 "@hot-loader/react-dom@^16.13.0":
   version "16.14.0"
   resolved "https://registry.yarnpkg.com/@hot-loader/react-dom/-/react-dom-16.14.0.tgz#3cfc64e40bb78fa623e59b582b8f09dcdaad648a"
@@ -3434,6 +3461,13 @@
   dependencies:
     "@types/node" "*"
 
+"@types/[email protected]":
+  version "6.0.3"
+  resolved "https://registry.yarnpkg.com/@types/hapi__content/-/hapi__content-6.0.3.tgz#4e3820d8d07ae90de955263622e9c56ee177bd01"
+  integrity sha512-J0TOzZIy99b9G2ujGXpC7369wohXLCLwNfxEFN+X1w0oYOEhQ5+ViKweCZ919fGVp9U40QAjUc/LD1h1CVFCpQ==
+  dependencies:
+    "@types/node" "*"
+
 "@types/hast@^2.0.0":
   version "2.3.4"
   resolved "https://registry.yarnpkg.com/@types/hast/-/hast-2.3.4.tgz#8aa5ef92c117d20d974a82bdfb6a648b08c0bafc"