Merge pull request #1637 from nextstrain/fix/web-crash-dataset-json

Author: ivan-aksamentov

packages/nextclade-web/package.json

@@ -126,6 +126,7 @@
     "next-compose-plugins": "2.2.1",
     "numbro": "2.3.6",
     "p-memoize": "4.0.4",
+    "p-props": "4.0.0",
     "polished": "4.2.2",
     "pretty-bytes": "5.6.0",
     "prop-types": "15.8.1",

packages/nextclade-web/src/helpers/notUndefined.ts

@@ -10,15 +10,14 @@ export function notUndefinedOrNull<T>(x: T | undefined | null): x is NonNullable
   return x !== undefined && x !== null
 }
 
-export function filterValuesNotUndefinedOrNull<T extends object>(obj: T): T {
-  return Object.fromEntries(Object.entries(obj).filter(([_, value]) => notUndefinedOrNull(value))) as T
-}
-
 export function pairValueNotUndefinedOrNull<K, V>(pair: [K, V | undefined | null]): pair is [K, V] {
   return notUndefinedOrNull(pair[1])
 }
 
-/** If value is not undefined, map it according to a fn, otherwise return unmodified (i.e. undefined) */
-export function mapMaybe<T, U>(value: T | undefined, fn: (v: T) => U): U | undefined {
-  return !isNil(value) ? fn(value) : value
+/** If value is not undefined or null, map it according to a fn, otherwise return undefined */
+export function mapMaybe<T, U>(value: T | undefined | null, fn: (v: NonNullable<T>) => U): U | undefined {
+  if (isNil(value)) {
+    return undefined
+  }
+  return fn(value as NonNullable<T>)
 }

packages/nextclade-web/src/helpers/promise.ts

@@ -1,12 +1,11 @@
 import type { AuspiceJsonV2 } from 'auspice'
 import { concurrent } from 'fasy'
-import { isEmpty, isNil } from 'lodash'
+import { isEmpty, isNil, omitBy } from 'lodash'
+import pProps from 'p-props'
 import { useRouter } from 'next/router'
 import { useRecoilCallback } from 'recoil'
 import { REF_NODE_CLADE_FOUNDER, REF_NODE_PARENT, REF_NODE_ROOT } from 'src/constants'
 import { ErrorInternal } from 'src/helpers/ErrorInternal'
-import { filterValuesNotUndefinedOrNull } from 'src/helpers/notUndefined'
-import { promiseAllObject } from 'src/helpers/promise'
 import {
   seqIndexToTopDatasetNameAtom,
   seqIndicesWithoutDatasetSuggestionsAtom,
@@ -237,24 +236,31 @@ async function resolveParams(
   datasets: Dataset[] | undefined,
 ): Promise<NextcladeParamsRaw> {
   if (tree) {
-    return resolveInputsForAuspiceDataset(tree, overrides)
+    if (!datasets?.[0]) {
+      throw new ErrorInternal('Attempted to start analysis with Auspice JSON, but without dataset info resolved')
+    }
+    return resolveInputsForAuspiceDataset(tree, overrides, datasets[0].path)
   }
   return resolveInputsForNextcladeDataset(overrides, datasets)
 }
 
-async function resolveInputsForAuspiceDataset(tree: AuspiceTree | undefined, overrides: DatasetFilesOverrides) {
-  const resolvedOverrides = await promiseAllObject({
-    genomeAnnotation: async () => resolveOverride(overrides.genomeAnnotation),
-    reference: async () => resolveOverride(overrides.reference),
-    treeJson: async () => resolveOverride(overrides.treeJson),
-    pathogenJson: async () => resolveOverride(overrides.pathogenJson),
+async function resolveInputsForAuspiceDataset(
+  tree: AuspiceTree | undefined,
+  overrides: DatasetFilesOverrides,
+  datasetName: string,
+): Promise<NextcladeParamsRaw> {
+  const resolvedOverrides = await pProps({
+    genomeAnnotation: resolveOverride(overrides.genomeAnnotation),
+    reference: resolveOverride(overrides.reference),
+    treeJson: resolveOverride(overrides.treeJson),
+    pathogenJson: resolveOverride(overrides.pathogenJson),
   })
-  const filteredOverrides = filterValuesNotUndefinedOrNull(resolvedOverrides)
+  const filteredOverrides = omitBy(resolvedOverrides, isNil)
   return {
     Auspice: {
       auspiceJson: JSON.stringify(tree),
       ...filteredOverrides,
-      datasetName: 'Auspice JSON',
+      datasetName,
     },
   }
 }
@@ -281,13 +287,13 @@ async function getDatasetsFiles(
 /** Resolves all dataset files into strings */
 async function getDatasetFiles(datasets: Dataset[]): Promise<NextcladeParamsRawDir[]> {
   return concurrent.map(async (dataset) => {
-    return promiseAllObject({
+    return {
       datasetName: dataset.path,
       genomeAnnotation: await axiosFetchRawMaybe(dataset.files?.genomeAnnotation),
       reference: await axiosFetchRaw(dataset.files?.reference),
       treeJson: await axiosFetchRawMaybe(dataset.files?.treeJson),
       pathogenJson: await axiosFetchRaw(dataset.files?.pathogenJson),
-    })
+    }
   }, datasets)
 }
 
@@ -296,13 +302,13 @@ async function getDatasetFilesWithOverrides(
   overrides: DatasetFilesOverrides,
   dataset: Dataset,
 ): Promise<NextcladeParamsRawDir> {
-  return promiseAllObject({
+  return {
     datasetName: dataset.path,
-    genomeAnnotation: resolveOverrideOrDatasetFile(overrides.genomeAnnotation, dataset.files?.genomeAnnotation),
-    reference: resolveOverrideOrDatasetFileRequired(overrides.reference, dataset.files?.reference),
-    treeJson: resolveOverrideOrDatasetFile(overrides.treeJson, dataset.files?.treeJson),
-    pathogenJson: resolveOverrideOrDatasetFileRequired(overrides.pathogenJson, dataset.files?.pathogenJson),
-  })
+    genomeAnnotation: await resolveOverrideOrDatasetFile(overrides.genomeAnnotation, dataset.files?.genomeAnnotation),
+    reference: await resolveOverrideOrDatasetFileRequired(overrides.reference, dataset.files?.reference),
+    treeJson: await resolveOverrideOrDatasetFile(overrides.treeJson, dataset.files?.treeJson),
+    pathogenJson: await resolveOverrideOrDatasetFileRequired(overrides.pathogenJson, dataset.files?.pathogenJson),
+  }
 }
 
 async function resolveOverrideOrDatasetFileRequired(

packages/nextclade-web/src/hooks/useRunAnalysis.ts

@@ -4282,6 +4282,14 @@ agent-base@6:
   dependencies:
     debug "4"
 
+aggregate-error@^3.0.0:
+  version "3.1.0"
+  resolved "https://registry.yarnpkg.com/aggregate-error/-/aggregate-error-3.1.0.tgz#92670ff50f5359bdb7a3e0d40d0ec30c5737687a"
+  integrity sha512-4I7Td01quW/RpocfNayFdFVk1qSuoh0E7JrbRJ16nH01HhKFQ88INq9Sd+nd72zqRySlr9BmDA8xlEJ6vJMrYA==
+  dependencies:
+    clean-stack "^2.0.0"
+    indent-string "^4.0.0"
+
 ajv-formats@^2.1.1:
   version "2.1.1"
   resolved "https://registry.yarnpkg.com/ajv-formats/-/ajv-formats-2.1.1.tgz#6e669400659eb74973bbf2e33327180a0996b520"
@@ -5588,6 +5596,11 @@ clean-regexp@^1.0.0:
   dependencies:
     escape-string-regexp "^1.0.5"
 
+clean-stack@^2.0.0:
+  version "2.2.0"
+  resolved "https://registry.yarnpkg.com/clean-stack/-/clean-stack-2.2.0.tgz#ee8472dbb129e727b31e8a10a427dee9dfe4008b"
+  integrity sha512-4diC9HaTE+KRAMWhDhrGOECgWZxoevMc5TlkObMqNSsVU62PYzXZ/SMTjzyGAFF1YusgxGcSWTEXBhp0CPwQ1A==
+
 clean-webpack-plugin@^4.0.0:
   version "4.0.0"
   resolved "https://registry.yarnpkg.com/clean-webpack-plugin/-/clean-webpack-plugin-4.0.0.tgz#72947d4403d452f38ed61a9ff0ada8122aacd729"
@@ -12514,6 +12527,13 @@ p-map@^2.0.0:
   resolved "https://registry.yarnpkg.com/p-map/-/p-map-2.1.0.tgz#310928feef9c9ecc65b68b17693018a665cea175"
   integrity sha512-y3b8Kpd8OAN444hxfBbFfj1FY/RjtTd8tzYwhUqNYXx0fXx2iX4maP4Qr6qhIKbQXI02wTLAda4fYUbDagTUFw==
 
+p-map@^4.0.0:
+  version "4.0.0"
+  resolved "https://registry.yarnpkg.com/p-map/-/p-map-4.0.0.tgz#bb2f95a5eda2ec168ec9274e06a747c3e2904d2b"
+  integrity sha512-/bjOqmgETBYB5BoEeGVea8dmvHb2m9GLy1E9W43yeyfP6QQCZGFNa+XRceJEuDB6zqr+gKpIAmlLebMpykw/MQ==
+  dependencies:
+    aggregate-error "^3.0.0"
+
 p-memoize@4.0.4:
   version "4.0.4"
   resolved "https://registry.yarnpkg.com/p-memoize/-/p-memoize-4.0.4.tgz#90a4c4668866737fc5c8364c56b06f6ca44afb15"
@@ -12523,6 +12543,13 @@ p-memoize@4.0.4:
     mimic-fn "^3.0.0"
     p-settle "^4.1.1"
 
+p-props@4.0.0:
+  version "4.0.0"
+  resolved "https://registry.yarnpkg.com/p-props/-/p-props-4.0.0.tgz#f37c877a9a722057833e1dc38d43edf3906b3437"
+  integrity sha512-3iKFbPdoPG7Ne3cMA53JnjPsTMaIzE9gxKZnvKJJivTAeqLEZPBu6zfi6DYq9AsH1nYycWmo3sWCNI8Kz6T2Zg==
+  dependencies:
+    p-map "^4.0.0"
+
 p-reflect@^2.1.0:
   version "2.1.0"
   resolved "https://registry.yarnpkg.com/p-reflect/-/p-reflect-2.1.0.tgz#5d67c7b3c577c4e780b9451fc9129675bd99fe67"