@openneuro/app 4.23.0 → 4.24.0-alpha.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@openneuro/app",
-  "version": "4.23.0",
+  "version": "4.24.0-alpha.2",
   "description": "React JS web frontend for the OpenNeuro platform.",
   "license": "MIT",
   "main": "public/client.js",
@@ -16,14 +16,14 @@
   "dependencies": {
     "@apollo/client": "3.7.2",
     "@artsy/fresnel": "^1.3.1",
-    "@elastic/apm-rum": "5.11.0",
+    "@elastic/apm-rum": "5.16.0",
     "@emotion/react": "11.11.1",
     "@emotion/styled": "11.11.0",
     "@niivue/niivue": "0.34.0",
-    "@openneuro/client": "^4.23.0",
-    "@openneuro/components": "^4.23.0",
+    "@openneuro/client": "^4.24.0-alpha.2",
+    "@openneuro/components": "^4.24.0-alpha.2",
     "@tanstack/react-table": "^8.9.3",
-    "bids-validator": "1.13.0",
+    "bids-validator": "1.14.6",
     "bytes": "^3.0.0",
     "comlink": "^4.0.5",
     "date-fns": "^2.16.1",
@@ -54,7 +54,7 @@
     "@testing-library/react": "^14.2.1",
     "@types/dompurify": "^3",
     "@types/jsdom": "^16",
-    "@types/node": "18.11.9",
+    "@types/node": "20.12.7",
     "@types/react": "^17.0.8",
     "@types/react-dom": "^18.2.19",
     "@types/react-router-dom": "5.3.3",
@@ -62,17 +62,17 @@
     "core-js": "3.25.1",
     "esbuild-plugin-globals": "^0.1.1",
     "history": "5.3.0",
-    "jsdom": "^16.5.3",
+    "jsdom": "24.0.0",
     "object.fromentries": "^2.0.0",
     "rollup-plugin-polyfill-node": "0.12.0",
     "sass": "^1.32.8",
     "stream-browserify": "^3.0.0",
     "typescript": "5.1.6",
-    "vite": "4.5.2",
-    "vitest": "0.34.4"
+    "vite": "4.5.3",
+    "vitest": "1.5.0"
   },
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "e86df78635d7ac6cfa03a2add5760b8539103583"
+  "gitHead": "aa9717595d41e5e0eb55328c62fa59c80847b95e"
 }

package/src/scripts/dataset/__tests__/__snapshots__/snapshot-container.spec.tsx.snap

@@ -13,7 +13,7 @@ exports[`SnapshotContainer component > includes JSON-LD data in the header 1`] =
   "onChangeClientState": [Function],
   "scriptTags": [
     {
-      "innerHTML": "{\\"@context\\":\\"http://schema.org\\",\\"@type\\":\\"Dataset\\",\\"name\\":\\"DS003-downsampled (only T1)\\",\\"author\\":[{\\"@type\\":\\"Person\\",\\"name\\":\\"J. Doe\\",\\"givenName\\":\\"J.\\",\\"familyName\\":\\"Doe\\"},{\\"@type\\":\\"Person\\",\\"name\\":\\"J. Doe\\",\\"givenName\\":\\"J.\\",\\"familyName\\":\\"Doe\\"},{\\"@type\\":\\"Person\\",\\"name\\":\\"J. Doe\\",\\"givenName\\":\\"J.\\",\\"familyName\\":\\"Doe\\"}],\\"datePublished\\":\\"2021-12-17T22:32:08.000Z\\",\\"dateModified\\":\\"2021-12-17T22:32:08.000Z\\",\\"license\\":\\"https://creativecommons.org/publicdomain/zero/1.0/\\",\\"publisher\\":{\\"@type\\":\\"Organization\\",\\"name\\":\\"OpenNeuro\\"},\\"description\\":\\"This dataset was obtained from the OpenfMRI project (http://www.openfmri.org).\\\\nAccession #: ds003\\\\nDescription: Rhyme judgment\\\\n\\\\nRelease history:\\\\n10/06/2011: initial release\\\\n3/21/2013: Updated release with QA information\\\\n\\\\nThis dataset is made available under the Public Domain Dedication and License \\\\nv1.0, whose full text can be found at \\\\nhttp://www.opendatacommons.org/licenses/pddl/1.0/. \\\\nWe hope that all users will follow the ODC Attribution/Share-Alike \\\\nCommunity Norms (http://www.opendatacommons.org/norms/odc-by-sa/); \\\\nin particular, while not legally required, we hope that all users \\\\nof the data will acknowledge the OpenfMRI project and NSF Grant \\\\nOCI-1131441 (R. Poldrack, PI) in any publications.\\\\n\\",\\"version\\":\\"1.0.0\\",\\"url\\":\\"https://openneuro.org/datasets/ds001032/versions/1.0.0\\"}",
+      "innerHTML": "{"@context":"http://schema.org","@type":"Dataset","name":"DS003-downsampled (only T1)","author":[{"@type":"Person","name":"J. Doe","givenName":"J.","familyName":"Doe"},{"@type":"Person","name":"J. Doe","givenName":"J.","familyName":"Doe"},{"@type":"Person","name":"J. Doe","givenName":"J.","familyName":"Doe"}],"datePublished":"2021-12-17T22:32:08.000Z","dateModified":"2021-12-17T22:32:08.000Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","publisher":{"@type":"Organization","name":"OpenNeuro"},"description":"This dataset was obtained from the OpenfMRI project (http://www.openfmri.org).\\nAccession #: ds003\\nDescription: Rhyme judgment\\n\\nRelease history:\\n10/06/2011: initial release\\n3/21/2013: Updated release with QA information\\n\\nThis dataset is made available under the Public Domain Dedication and License \\nv1.0, whose full text can be found at \\nhttp://www.opendatacommons.org/licenses/pddl/1.0/. \\nWe hope that all users will follow the ODC Attribution/Share-Alike \\nCommunity Norms (http://www.opendatacommons.org/norms/odc-by-sa/); \\nin particular, while not legally required, we hope that all users \\nof the data will acknowledge the OpenfMRI project and NSF Grant \\nOCI-1131441 (R. Poldrack, PI) in any publications.\\n","version":"1.0.0","url":"https://openneuro.org/datasets/ds001032/versions/1.0.0"}",
       "type": "application/ld+json",
     },
   ],

package/src/scripts/dataset/components/NemarButton.tsx

@@ -16,7 +16,11 @@ export const NemarButton: React.FC<NemarButtonProps> = ({
     <>
       {onNemar && (
         <div className="brainlife-block">
-          <Tooltip tooltip="View and analyze on NEMAR" flow="up">
+          <Tooltip
+            tooltip="View and analyze this dataset on the NEMAR OpenNeuro portal for MEG, iEEG, and EEG data"
+            flow="up"
+            wrapText={true}
+          >
             <Button
               className="brainlife-link"
               primary={true}

package/src/scripts/dataset/files/viewers/file-viewer-nifti.tsx

@@ -14,14 +14,23 @@ const FileViewerNifti = ({
         url: imageUrl,
         colorMap: "gray",
         opacity: 1,
-        visible: true,
         limitFrames4D: 5,
       },
     ]
     const nv = new Niivue({ dragAndDropEnabled: false })
     ;(window as any).niivue = nv
     nv.attachToCanvas(canvas.current)
-    nv.loadVolumes(volumeList) // press the "v" key to cycle through volumes
+    nv.loadVolumes(volumeList) // press the "v" key to cycle through views (axial, coronal, sagittal, 3D, etc.)
+    nv.graph.autoSizeMultiplanar = true // use autosizing
+    nv.opts.multiplanarForceRender = true // ensure that we draw the time series graph in the tile usually reserved for the 3D render
+    nv.graph.normalizeValues = false // use raw data values on y-axis
+    nv.graph.opacity = 1.0 // show the graph
+    // Notes: 
+    // 1.   If an image only has one volume, the timeseries graph will not be visible.
+    //      The 3D render will be placed in the graph tile instead. 
+    // 2.   Users can navigate volumes forward and backward in the series using the left and right arrow keys on desktop devices
+    // 3.   On touch screens, users can tap on the timeseries graph to jump to a volume index
+    // 4.   Users can load all volumes by clicking on the "..." displayed on the timeseries graph
   }, [imageUrl])
 
   return <canvas ref={canvas} height={800} />

package/src/scripts/errors/errorRoute.jsx

@@ -7,22 +7,22 @@ import OrcidGeneral from "./orcid/general.jsx"
 import OrcidEmail from "./orcid/email.jsx"
 import OrcidGiven from "./orcid/given.jsx"
 import OrcidFamily from "./orcid/family.jsx"
+import FourOFourPage from "./404page"
 
-class ErrorRoute extends React.Component {
-  render() {
-    return (
-      <div className="container errors">
-        <div className="panel">
-          <Routes>
-            <Route path="orcid" element={<OrcidGeneral />} />
-            <Route path="orcid/email" element={<OrcidEmail />} />
-            <Route path="orcid/given" element={<OrcidGiven />} />
-            <Route path="orcid/family" element={<OrcidFamily />} />
-          </Routes>
-        </div>
+function ErrorRoute() {
+  return (
+    <div className="container errors">
+      <div className="panel">
+        <Routes>
+          <Route path="orcid" element={<OrcidGeneral />} />
+          <Route path="orcid/email" element={<OrcidEmail />} />
+          <Route path="orcid/given" element={<OrcidGiven />} />
+          <Route path="orcid/family" element={<OrcidFamily />} />
+          <Route path="*" element={<FourOFourPage />} />
+        </Routes>
       </div>
-    )
-  }
+    </div>
+  )
 }
 
 export default ErrorRoute

package/src/scripts/routes.tsx

@@ -39,7 +39,7 @@ const AppRoutes: React.VoidFunctionComponent = () => (
       path="/dashboard"
       element={<Navigate to="/search?mydatasets" replace />}
     />
-    <Route element={<FourOFourPage />} />
+    <Route path="/*" element={<FourOFourPage />} />
   </Routes>
 )
 

package/src/scripts/search/initial-search-params.tsx

@@ -155,46 +155,11 @@ export interface SearchParams {
   tracerRadionuclides: string[]
   sortBy_available
   sortBy_selected
+  bidsDatasetType_available: string[]
+  bidsDatasetType_selected: string | null
 }
 
-// TODO: move to this initial state
-//       and load dynamic options on mount
 const initialSearchParams: SearchParams = {
-  keywords: [],
-  searchAllDatasets: false,
-  datasetType_available,
-  datasetType_selected: null,
-  datasetStatus_available,
-  datasetStatus_selected: null,
-  modality_available,
-  modality_selected: null,
-  ageRange: [null, null],
-  subjectCountRange: [null, null],
-  diagnosis_available: [],
-  diagnosis_selected: null,
-  tasks: [],
-  authors: [],
-  // more
-  sex_available: [],
-  sex_selected: null,
-  date_available: [],
-  date_selected: null,
-  species_available: [],
-  species_selected: null,
-  section_available: [],
-  section_selected: null,
-  studyDomains: [],
-  bodyParts: [],
-  scannerManufacturers: [],
-  scannerManufacturersModelNames: [],
-  tracerNames: [],
-  tracerRadionuclides: [],
-  sortBy_available: sortBy,
-  sortBy_selected: sortBy[0],
-}
-
-// TODO: (stretch) delete and move to dynamically loaded initialSearchParams
-const TEMPORARY_initialSearchParams: SearchParams = {
   keywords: [],
   searchAllDatasets: false,
   datasetType_available,
@@ -237,6 +202,8 @@ const TEMPORARY_initialSearchParams: SearchParams = {
   tracerRadionuclides: [],
   sortBy_available: sortBy,
   sortBy_selected: sortBy[0],
+  bidsDatasetType_available: ["raw", "derivative"],
+  bidsDatasetType_selected: null,
 }
 
-export default TEMPORARY_initialSearchParams
+export default initialSearchParams

package/src/scripts/search/inputs/dataset-type-select.tsx

@@ -0,0 +1,33 @@
+import React, { FC, useContext } from "react"
+import { SearchParamsCtx } from "../search-params-ctx"
+import { FacetSelect } from "@openneuro/components/facets"
+import { AccordionTab, AccordionWrap } from "@openneuro/components/accordion"
+
+const DatasetTypeSelect: FC = () => {
+  const { searchParams, setSearchParams } = useContext(SearchParamsCtx)
+
+  const { bidsDatasetType_selected, bidsDatasetType_available } = searchParams
+  const setDatasetType = (bidsDatasetType_selected) =>
+    setSearchParams((prevState) => ({
+      ...prevState,
+      bidsDatasetType_selected,
+    }))
+
+  return (
+    <AccordionWrap className="facet-accordion">
+      <AccordionTab
+        accordionStyle="plain"
+        label="Dataset Type"
+        startOpen={false}
+      >
+        <FacetSelect
+          selected={bidsDatasetType_selected}
+          setSelected={setDatasetType}
+          items={bidsDatasetType_available}
+        />
+      </AccordionTab>
+    </AccordionWrap>
+  )
+}
+
+export default DatasetTypeSelect

package/src/scripts/search/inputs/index.ts

@@ -4,6 +4,7 @@ import ModalitySelect from "./modality-select"
 import ShowDatasetRadios from "./show-datasets-radios"
 import AgeRangeInput from "./age-range-input"
 import SubjectCountRangeInput from "./subject-count-range-input"
+import DatasetTypeSelect from "./dataset-type-select"
 import DiagnosisSelect from "./diagnosis-select"
 import TaskInput from "./task-input"
 import AuthorInput from "./author-input"
@@ -24,6 +25,7 @@ export {
   AllDatasetsToggle,
   AuthorInput,
   BodyPartsInput,
+  DatasetTypeSelect,
   DateRadios,
   DiagnosisSelect,
   KeywordInput,

package/src/scripts/search/search-container.tsx

@@ -16,6 +16,7 @@ import {
   AllDatasetsToggle,
   AuthorInput,
   BodyPartsInput,
+  DatasetTypeSelect,
   DateRadios,
   DiagnosisSelect,
   KeywordInput,
@@ -101,14 +102,12 @@ const SearchContainer: FC<SearchContainerProps> = ({ portalContent }) => {
 
   const { searchParams, setSearchParams } = useContext(SearchParamsCtx)
   const modality = portalContent?.modality || null
-  useEffect(() => {
-    setDefaultSearch(
-      modality,
-      searchParams,
-      setSearchParams,
-      new URLSearchParams(location.search),
-    )
-  }, [modality, searchParams.modality_selected, setSearchParams, location])
+  setDefaultSearch(
+    modality,
+    searchParams,
+    setSearchParams,
+    new URLSearchParams(location.search),
+  )
 
   const { loading, data, fetchMore, refetch, variables, error } =
     useSearchResults()
@@ -166,6 +165,7 @@ const SearchContainer: FC<SearchContainerProps> = ({ portalContent }) => {
             {!portalContent
               ? <ModalitySelect portalStyles={true} label="Modalities" />
               : <ModalitySelect portalStyles={false} label="Choose Modality" />}
+            <DatasetTypeSelect />
             <AgeRangeInput />
             <SubjectCountRangeInput />
             <DiagnosisSelect />

package/src/scripts/search/search-params-ctx.tsx

@@ -123,6 +123,7 @@ export const getSelectParams = ({
   scannerManufacturersModelNames,
   tracerNames,
   tracerRadionuclides,
+  bidsDatasetType_selected,
 }) => ({
   keywords,
   modality_selected,
@@ -144,6 +145,7 @@ export const getSelectParams = ({
   scannerManufacturersModelNames,
   tracerNames,
   tracerRadionuclides,
+  bidsDatasetType_selected,
 })
 
 /**

package/src/scripts/search/use-search-results.tsx

@@ -12,7 +12,6 @@ import {
   simpleQueryString,
   sqsJoinWithAND,
 } from "./es-query-builders"
-import { species_list } from "@openneuro/components/content"
 
 const searchQuery = gql`
   query advancedSearchDatasets(