Merge remote-tracking branch 'origin/master' into feat/ref-minimizer

.env.example

@@ -32,6 +32,10 @@ SYNC_DESTINATION=123.456.789.123:~/nextclade
 DATA_FULL_DOMAIN=https://data.master.clades.nextstrain.org/v3
 # DATA_FULL_DOMAIN=http://localhost:27722
 
+# If enabled, Nextclade Web will first attempt to fetch datasets from the corresponding GitHub branch. If this attempt
+# fails, it will use `DATA_FULL_DOMAIN` as usual.
+DATA_TRY_GITHUB_BRANCH=0
+
 # Directory path (relative to the root of the project) from which local data server takes the data.
 # Useful for local testing on new datasets. See: https://github.com/neherlab/nextclade_data
 # It is recommended to keep the `nextclade_data` git repo in a sibling directory of `nextclade` git repo.

packages_rs/nextclade-web/config/next/lib/getEnvVars.ts

@@ -10,6 +10,7 @@ export function getEnvVars() {
   const DOMAIN = getDomain()
   const DOMAIN_STRIPPED = DOMAIN.replace('https://', '').replace('http://', '')
   const DATA_FULL_DOMAIN = getenv('DATA_FULL_DOMAIN')
+  const DATA_TRY_GITHUB_BRANCH = getenv('DATA_TRY_GITHUB_BRANCH')
 
   const common = {
     BABEL_ENV,
@@ -20,6 +21,7 @@ export function getEnvVars() {
     DOMAIN,
     DOMAIN_STRIPPED,
     DATA_FULL_DOMAIN,
+    DATA_TRY_GITHUB_BRANCH,
   }
 
   if (PRODUCTION) {

packages_rs/nextclade-web/config/next/next.config.ts

@@ -46,6 +46,7 @@ const {
   DOMAIN,
   DOMAIN_STRIPPED,
   DATA_FULL_DOMAIN,
+  DATA_TRY_GITHUB_BRANCH,
 } = getEnvVars()
 
 const BRANCH_NAME = getGitBranch()
@@ -61,6 +62,7 @@ const clientEnv = {
   DOMAIN,
   DOMAIN_STRIPPED,
   DATA_FULL_DOMAIN,
+  DATA_TRY_GITHUB_BRANCH,
   BLOCK_SEARCH_INDEXING: DOMAIN === RELEASE_URL ? '0' : '1',
 }
 

packages_rs/nextclade-web/src/constants.ts

@@ -31,6 +31,8 @@ export const URL_GITHUB_COMMITS = 'https://github.com/nextstrain/nextclade/commi
 export const URL_CLADE_SCHEMA_REPO = 'https://github.com/nextstrain/ncov-clades-schema/'
 export const URL_CLADE_SCHEMA_SVG = 'https://raw.githubusercontent.com/nextstrain/ncov-clades-schema/master/clades.svg'
 
+export const URL_GITHUB_DATA_RAW = 'https://raw.githubusercontent.com/nextstrain/nextclade_data' as const
+
 export const SUPPORT_EMAIL = '[email protected]'
 
 export const TWITTER_USERNAME_RAW = 'nextstrain' as const

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

@@ -68,20 +68,25 @@ export async function axiosFetchRawMaybe(url?: string): Promise<string | undefin
   return axiosFetchRaw(url)
 }
 
-export async function axiosHead<TData = unknown>(
-  url: string | undefined,
-  options?: AxiosRequestConfig,
-): Promise<TData> {
+export async function axiosHead(url: string | undefined, options?: AxiosRequestConfig): Promise<AxiosResponse> {
   if (isNil(url)) {
     throw new ErrorInternal(`Attempted to fetch from an invalid URL: '${url}'`)
   }
 
-  let res
   try {
-    res = await axios.head(url, options)
+    return await axios.head(url, options)
   } catch (error) {
     throw axios.isAxiosError(error) ? new HttpRequestError(error) : sanitizeError(error)
   }
+}
 
-  return res.data as TData
+export async function axiosHeadOrUndefined(
+  url: string | undefined,
+  options?: AxiosRequestConfig,
+): Promise<AxiosResponse | undefined> {
+  try {
+    return await axiosHead(url, options)
+  } catch {
+    return undefined
+  }
 }

packages_rs/nextclade-web/src/io/fetchDatasets.ts

@@ -1,5 +1,8 @@
+/* eslint-disable prefer-destructuring */
 import type { ParsedUrlQuery } from 'querystring'
 import { findSimilarStrings } from 'src/helpers/string'
+import { axiosHeadOrUndefined } from 'src/io/axiosFetch'
+import { isGithubUrlOrShortcut, parseGitHubRepoUrlOrShortcut } from 'src/io/fetchSingleDatasetFromGithub'
 
 import { Dataset } from 'src/types'
 import {
@@ -10,9 +13,11 @@ import {
 } from 'src/io/fetchDatasetsIndex'
 import { getQueryParamMaybe } from 'src/io/getQueryParamMaybe'
 import { useRecoilValue, useSetRecoilState } from 'recoil'
-import { datasetCurrentAtom, datasetsAtom, datasetServerUrlAtom, datasetUpdatedAtom } from 'src/state/dataset.state'
+import { datasetCurrentAtom, datasetsAtom, datasetUpdatedAtom } from 'src/state/dataset.state'
 import { useQuery } from 'react-query'
 import { isNil } from 'lodash'
+import urljoin from 'url-join'
+import { URL_GITHUB_DATA_RAW } from 'src/constants'
 
 export async function getDatasetFromUrlParams(urlQuery: ParsedUrlQuery, datasets: Dataset[]) {
   // Retrieve dataset-related URL params and try to find a dataset based on these params
@@ -41,8 +46,62 @@ export async function getDatasetFromUrlParams(urlQuery: ParsedUrlQuery, datasets
   return dataset
 }
 
-export async function initializeDatasets(urlQuery: ParsedUrlQuery, datasetServerUrlDefault: string) {
-  const datasetServerUrl = getQueryParamMaybe(urlQuery, 'dataset-server') ?? datasetServerUrlDefault
+export async function getGithubDatasetServerUrl(): Promise<string | undefined> {
+  const BRANCH_NAME = process.env.BRANCH_NAME
+  if (!BRANCH_NAME) {
+    return undefined
+  }
+
+  const githubDatasetServerUrl = urljoin(URL_GITHUB_DATA_RAW, BRANCH_NAME, 'data_output')
+  const githubIndexJsonUrl = urljoin(githubDatasetServerUrl, 'index.json')
+
+  const headRes = await axiosHeadOrUndefined(githubIndexJsonUrl)
+
+  if (headRes) {
+    return githubDatasetServerUrl
+  }
+
+  return undefined
+}
+
+export function toAbsoluteUrl(url: string): string {
+  if (typeof window !== 'undefined' && url.slice(0) === '/') {
+    return urljoin(window.location.origin, url)
+  }
+  return url
+}
+
+export async function getDatasetServerUrl(urlQuery: ParsedUrlQuery) {
+  // Get dataset URL from query URL params.
+  let datasetServerUrl = getQueryParamMaybe(urlQuery, 'dataset-server')
+
+  // If the URL is formatted as a GitHub URL or as a GitHub URL shortcut, use it without any checking
+  if (datasetServerUrl && isGithubUrlOrShortcut(datasetServerUrl)) {
+    const { owner, repo, branch, path } = await parseGitHubRepoUrlOrShortcut(datasetServerUrl)
+    return urljoin('https://raw.githubusercontent.com', owner, repo, branch, path)
+  }
+
+  // If requested to try GitHub-hosted datasets either using `DATA_TRY_GITHUB_BRANCH` env var (e.g. from
+  // `.env` file), or using `&dataset-server=gh` or `&dataset-server=github` URL parameters, then check if the
+  // corresponding branch in the default data repo on GitHub contains an `index.json` file. And and if yes, use it.
+  const datasetServerTryGithubBranch =
+    process.env.DATA_TRY_GITHUB_BRANCH === '1' || (datasetServerUrl && ['gh', 'github'].includes(datasetServerUrl))
+  if (datasetServerTryGithubBranch) {
+    const githubDatasetServerUrl = await getGithubDatasetServerUrl()
+    if (githubDatasetServerUrl) {
+      datasetServerUrl = githubDatasetServerUrl
+    }
+  }
+
+  // If none of the above, use hardcoded default URL (from `.env` file)
+  datasetServerUrl = datasetServerUrl ?? process.env.DATA_FULL_DOMAIN ?? '/'
+
+  // If the URL happens to be a relative path, then convert to absolute URL (on the app's current host)
+  return toAbsoluteUrl(datasetServerUrl)
+}
+
+export async function initializeDatasets(urlQuery: ParsedUrlQuery) {
+  const datasetServerUrl = await getDatasetServerUrl(urlQuery)
 
   const datasetsIndexJson = await fetchDatasetsIndex(datasetServerUrl)
 
@@ -57,11 +116,10 @@ export async function initializeDatasets(urlQuery: ParsedUrlQuery, datasetServer
 /** Refetch dataset index periodically and update the local copy of if */
 export function useUpdatedDatasetIndex() {
   const setDatasetsState = useSetRecoilState(datasetsAtom)
-  const datasetServerUrl = useRecoilValue(datasetServerUrlAtom)
   useQuery(
     'refetchDatasetIndex',
     async () => {
-      const { currentDataset: _, ...datasetsState } = await initializeDatasets({}, datasetServerUrl)
+      const { currentDataset: _, ...datasetsState } = await initializeDatasets({})
       setDatasetsState(datasetsState)
     },
     {
@@ -89,10 +147,9 @@ export function useUpdatedDataset() {
     'currentDatasetState',
     async () => {
       const path = datasetCurrent?.path
-      const refAccession = datasetCurrent?.attributes.reference.value
       const updatedAt = datasetCurrent?.version?.updatedAt
-      if (!isNil(refAccession) && !isNil(updatedAt)) {
-        const candidateDatasets = filterDatasets(datasets, path, refAccession)
+      if (!isNil(updatedAt)) {
+        const candidateDatasets = filterDatasets(datasets, path)
         const updatedDataset = candidateDatasets.find((candidate) => {
           const candidateTag = candidate.version?.updatedAt
           return candidateTag && candidateTag > updatedAt

packages_rs/nextclade-web/src/pages/_app.tsx

@@ -48,7 +48,7 @@ import { SEO } from 'src/components/Common/SEO'
 import { Plausible } from 'src/components/Common/Plausible'
 import i18n, { changeLocale, getLocaleWithKey } from 'src/i18n/i18n'
 import { theme } from 'src/theme'
-import { datasetCurrentAtom, datasetsAtom, datasetServerUrlAtom } from 'src/state/dataset.state'
+import { datasetCurrentAtom, datasetsAtom } from 'src/state/dataset.state'
 import { ErrorBoundary } from 'src/components/Error/ErrorBoundary'
 import { PreviewWarning } from 'src/components/Common/PreviewWarning'
 
@@ -99,8 +99,7 @@ export function RecoilStateInitializer() {
           return datasetInfo
         }
 
-        const datasetServerUrlDefault = await getPromise(datasetServerUrlAtom)
-        return initializeDatasets(urlQuery, datasetServerUrlDefault)
+        return initializeDatasets(urlQuery)
       })
       .catch((error) => {
         // Dataset error is fatal and we want error to be handled in the ErrorBoundary

packages_rs/nextclade-web/src/state/dataset.state.ts

@@ -1,6 +1,5 @@
 import { isNil } from 'lodash'
 import { atom, DefaultValue, selector } from 'recoil'
-import urljoin from 'url-join'
 
 import type { Dataset } from 'src/types'
 // import { GENE_OPTION_NUC_SEQUENCE } from 'src/constants'
@@ -10,20 +9,6 @@ import { persistAtom } from 'src/state/persist/localStorage'
 import { isDefaultValue } from 'src/state/utils/isDefaultValue'
 import { areDatasetsEqual } from 'src/types'
 
-export function getDefaultDatasetServer(): string {
-  let datasetServerUrl = process.env.DATA_FULL_DOMAIN ?? '/'
-  // Add HTTP Origin if datasetServerUrl is a relative path (start with '/')
-  if (typeof window !== 'undefined' && datasetServerUrl.slice(0) === '/') {
-    datasetServerUrl = urljoin(window.location.origin, datasetServerUrl)
-  }
-  return datasetServerUrl
-}
-
-export const datasetServerUrlAtom = atom<string>({
-  key: 'datasetServerUrl',
-  default: getDefaultDatasetServer(),
-})
-
 export interface Datasets {
   datasets: Dataset[]
 }

scripts/build_on_vercel.sh

@@ -115,6 +115,8 @@ sed -i'' "s|PROD_ENABLE_TYPE_CHECKS=1|PROD_ENABLE_TYPE_CHECKS=0|g" .env
 sed -i'' "s|PROD_ENABLE_ESLINT=1|PROD_ENABLE_ESLINT=0|g" .env
 sed -i'' "s|PROD_ENABLE_STYLELINT=1|PROD_ENABLE_STYLELINT=0|g" .env
 
+sed -i'' "s|DATA_TRY_GITHUB_BRANCH=0|DATA_TRY_GITHUB_BRANCH=1|g" .env
+
 cd packages_rs/nextclade-web
 
 yarn install --frozen-lockfile