@openneuro/app 4.30.2 → 4.31.0

package/src/scripts/dataset/routes/delete-page.tsx

@@ -1,22 +1,16 @@
 import React, { useState } from "react"
-import { useCookies } from "react-cookie"
 import DeleteDatasetForm from "../mutations/delete-dataset-form.jsx"
 import DeleteDataset from "../mutations/delete.jsx"
 import LoggedIn from "../../authentication/logged-in.jsx"
-import { getProfile } from "../../authentication/profile"
-import AdminUser from "../../authentication/admin-user.jsx"
-import { RegularUser } from "../../authentication/regular-user"
 import { DatasetPageBorder } from "./styles/dataset-page-border"
 import { HeaderRow3 } from "./styles/header-row"
 
-interface DeletePageProps {
-  dataset: {
-    permissions: Record<string, object>
-    id: string
-  }
+interface DeletePageAction {
+  datasetId: string
+  hasEdit: boolean
 }
 
-const DeletePage = ({ dataset }: DeletePageProps): React.ReactElement => {
+export function DeletePageAction({ datasetId, hasEdit }: DeletePageAction) {
   const [values, setValues] = useState({
     reason: "",
     redirect: "",
@@ -28,40 +22,79 @@ const DeletePage = ({ dataset }: DeletePageProps): React.ReactElement => {
     }
     setValues(newValues)
   }
-  const [cookies] = useCookies()
-  const user = getProfile(cookies)
-  const hasEdit = user && user.admin
-  const datasetId = dataset.id
   return (
-    <DatasetPageBorder>
-      <HeaderRow3>Delete Dataset</HeaderRow3>
-      <AdminUser>
-        <DeleteDatasetForm
-          values={values}
-          onChange={handleInputChange}
-          hideDisabled={false}
-          hasEdit={hasEdit}
-        />
+    <>
+      <DeleteDatasetForm
+        values={values}
+        onChange={handleInputChange}
+        hideDisabled={false}
+        hasEdit={hasEdit}
+      />
+      <p>
+        <small className="warning-text">
+          * Warning: this action will permanently remove this dataset along with
+          associated snapshots.
+        </small>
+      </p>
+      <div className="dataset-form-controls">
+        <LoggedIn>
+          <DeleteDataset datasetId={datasetId} metadata={values} />
+        </LoggedIn>
+      </div>
+    </>
+  )
+}
+
+interface DeletePageMessageProps {
+  hasEdit: boolean
+}
+
+export function DeletePageMessage({ hasEdit }: DeletePageMessageProps) {
+  if (hasEdit) {
+    return (
+      <>
         <p>
-          <small className="warning-text">
-            * Warning: this action will permanently remove this dataset along
-            with associated snapshots.
-          </small>
+          This dataset has versions with DOIs that would be orphaned by
+          deletion.
         </p>
-        <div className="dataset-form-controls">
-          <LoggedIn>
-            <DeleteDataset datasetId={datasetId} metadata={values} />
-          </LoggedIn>
-        </div>
-      </AdminUser>
-      <RegularUser>
         <p>
-          Please contact support to permanently remove a dataset and all
-          versions of it. Provide a reason for the removal request and if the
-          dataset is a duplicate or has been supplanted by another provide that
-          information for a redirect to be created.
+          If deletion is required please contact support to permanently remove a
+          dataset and all versions of it. Provide a reason for the removal
+          request and if the dataset is a duplicate or has been supplanted by
+          another provide that information for a redirect to be created.
         </p>
-      </RegularUser>
+      </>
+    )
+  } else {
+    return (
+      <p>
+        Login or request dataset admin permissions from a dataset admin to
+        delete this dataset.
+      </p>
+    )
+  }
+}
+
+interface DeletePageProps {
+  dataset: {
+    permissions: Record<string, object>
+    id: string
+    snapshots: object[]
+  }
+  hasEdit: boolean
+}
+
+const DeletePage = (
+  { dataset, hasEdit }: DeletePageProps,
+): React.ReactElement => {
+  const datasetId = dataset.id
+  const canBeDeleted = dataset.snapshots.length === 0 && hasEdit
+  return (
+    <DatasetPageBorder>
+      <HeaderRow3>Delete Dataset</HeaderRow3>
+      {canBeDeleted
+        ? <DeletePageAction datasetId={datasetId} hasEdit={hasEdit} />
+        : <DeletePageMessage hasEdit={hasEdit} />}
     </DatasetPageBorder>
   )
 }

package/src/scripts/dataset/routes/snapshot.tsx

@@ -15,12 +15,10 @@ const FormRow = styled.div`
   margin-bottom: 1.3em;
 `
 
-export const NoErrors = ({ issues, children }) => {
-  const noErrors = issues &&
-    issues.filter((issue) => issue.severity === "error").length === 0
+export const NoErrors = ({ validation, authors, children }) => {
+  const noErrors = validation?.errors === 0
   // zero authors will cause DOI minting to fail
-  const hasAuthor = issues &&
-    issues.filter((issue) => issue.code === 113).length === 0
+  const hasAuthor = authors.length > 0
   if (noErrors && hasAuthor) {
     return children
   } else {
@@ -42,7 +40,7 @@ export const NoErrors = ({ issues, children }) => {
 const SnapshotRoute = ({
   datasetId,
   snapshots,
-  issues,
+  validation,
   description,
 }): React.ReactElement => {
   const [changes, setChanges] = useState([])
@@ -76,8 +74,8 @@ const SnapshotRoute = ({
           )}
           <p>
             Create a new version of this dataset for download and public access.
-            This will begin an export of this dataset to GitHub and S3 if it has
-            been made public.
+            DOIs are assigned to versions created. This will begin an export of
+            this dataset to GitHub and S3 if it has been made public.
           </p>
           <FormRow className="snapshot-input-group">
             {newVersion}
@@ -124,21 +122,29 @@ const SnapshotRoute = ({
             setElements={setChanges}
           />
         </div>
-        <NoErrors issues={issues}>
+        <NoErrors validation={validation} authors={description.Authors}>
           {changes.length ? null : (
             <small className="text-danger">
               You must add at least one change message to create a new version
             </small>
           )}
+          {snapshots.length === 0
+            ? (
+              <p>
+                Once a version has been created and DOI assigned, the dataset
+                can no longer be deleted.
+              </p>
+            )
+            : null}
+          <div className="dataset-form-controls">
+            <SnapshotDataset
+              datasetId={datasetId}
+              tag={newVersion}
+              changes={changes}
+              disabled={changes.length < 1}
+            />
+          </div>
         </NoErrors>
-        <div className="dataset-form-controls">
-          <SnapshotDataset
-            datasetId={datasetId}
-            tag={newVersion}
-            changes={changes}
-            disabled={changes.length < 1}
-          />
-        </div>
       </div>
     </DatasetPageBorder>
   )

package/src/scripts/dataset/routes/tab-routes-draft.tsx

@@ -31,7 +31,10 @@ export const TabRoutesDraft = ({ dataset, hasEdit }) => {
         path="derivatives"
         element={<Derivatives derivatives={dataset.derivatives} />}
       />
-      <Route path="delete" element={<DeletePage dataset={dataset} />} />
+      <Route
+        path="delete"
+        element={<DeletePage dataset={dataset} hasEdit={hasEdit} />}
+      />
       <Route path="admin" element={<AdminDataset dataset={dataset} />} />
       <Route
         path="publish"
@@ -43,7 +46,7 @@ export const TabRoutesDraft = ({ dataset, hasEdit }) => {
           <Snapshot
             datasetId={dataset.id}
             snapshots={dataset.snapshots}
-            issues={dataset.draft.issues}
+            validation={dataset.draft.validation}
             description={dataset.draft.description}
           />
         }

package/src/scripts/dataset/snapshot-container.tsx

@@ -9,6 +9,7 @@ import { pageTitle } from "../resources/strings.js"
 import { config } from "../config"
 import DatasetCitation from "./fragments/dataset-citation.jsx"
 import { DatasetAlertVersion } from "./fragments/dataset-alert-version"
+import { DatasetAlertPrivate } from "./fragments/dataset-alert"
 import { AnalyzeDropdown } from "./components/AnalyzeDropdown"
 import { CloneDropdown } from "./components/CloneDropdown"
 import { DatasetGitAccess } from "./components/DatasetGitAccess"
@@ -74,6 +75,9 @@ export const SnapshotContainer: React.FC<SnapshotContainerProps> = ({
     isAdmin
   const isDatasetAdmin =
     hasDatasetAdminPermissions(dataset.permissions, profile?.sub) || isAdmin
+  const hasDraftChanges = dataset.snapshots.length === 0 ||
+    dataset.draft.head !==
+      dataset.snapshots[dataset.snapshots.length - 1].hexsha
   const modality: string = summary?.modalities[0] || ""
   const hasDerivatives = dataset?.derivatives.length > 0
 
@@ -111,6 +115,12 @@ export const SnapshotContainer: React.FC<SnapshotContainerProps> = ({
             </DatasetHeader>
           </>
         )}
+        {!dataset.public && isDatasetAdmin && (
+          <DatasetAlertPrivate
+            datasetId={dataset.id}
+            hasDraftChanges={hasDraftChanges}
+          />
+        )}
         {snapshot?.deprecated && (
           <DatasetAlertVersion
             datasetId={dataset.id}
@@ -125,6 +135,7 @@ export const SnapshotContainer: React.FC<SnapshotContainerProps> = ({
               <div className="dataset-validation">
                 <ValidationBlock
                   datasetId={datasetId}
+                  version={snapshot.tag}
                   issues={snapshot.issues}
                   validation={snapshot.validation}
                 />

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

@@ -41,6 +41,9 @@ describe("SearchParamsProvider", () => {
       </SearchParamsCtx.Consumer>,
       { wrapper },
     )
+    // Open the author dropdown
+    const authorDropdown = screen.getByRole("switch")
+    fireEvent.click(authorDropdown)
     const textInput = screen.getByRole("textbox")
     const button = screen.getByRole("button")
     fireEvent.change(textInput, { target: { value: "New Author" } })

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

@@ -157,6 +157,7 @@ export interface SearchParams {
   sortBy_selected
   bidsDatasetType_available: string[]
   bidsDatasetType_selected: string | null
+  brain_initiative: string | null
 }
 
 const initialSearchParams: SearchParams = {
@@ -204,6 +205,7 @@ const initialSearchParams: SearchParams = {
   sortBy_selected: sortBy[0],
   bidsDatasetType_available: ["raw", "derivative"],
   bidsDatasetType_selected: null,
+  brain_initiative: null,
 }
 
 export default initialSearchParams

package/src/scripts/search/inputs/__tests__/nihselect.spec.tsx

@@ -0,0 +1,36 @@
+import React from "react"
+import { fireEvent, render, screen, waitFor } from "@testing-library/react"
+import { MemoryRouter, Route, Routes } from "react-router-dom"
+import { SearchParamsCtx } from "../../search-params-ctx"
+import NIHSelect from "../nih-select"
+
+const customRender = (
+  ui,
+  { searchParams = {}, initialRoute = "/search" } = {},
+) => {
+  return render(
+    <SearchParamsCtx.Provider
+      value={{ searchParams, setSearchParams: () => {} }}
+    >
+      <MemoryRouter initialEntries={[initialRoute]}>
+        <Routes>
+          <Route path="/search" element={ui} />
+          <Route path="/search/nih" element={<h1>NIH Brain Initiative</h1>} />
+        </Routes>
+      </MemoryRouter>
+    </SearchParamsCtx.Provider>,
+  )
+}
+
+describe("NIHSelect Component", () => {
+  it("updates search params when NIH is selected and navigates to the NIH page", async () => {
+    customRender(<NIHSelect label="NIH Funding" />)
+
+    const nihOption = screen.getByText("NIH Funding")
+    fireEvent.click(nihOption)
+
+    await waitFor(() => {
+      expect(screen.getByText("NIH Brain Initiative")).toBeInTheDocument()
+    })
+  })
+})

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

@@ -1,6 +1,7 @@
 import KeywordInput from "./keyword-input"
 import AllDatasetsToggle from "./admin-allDatasets-toggle"
 import ModalitySelect from "./modality-select"
+import NIHSelect from "./nih-select"
 import ShowDatasetRadios from "./show-datasets-radios"
 import AgeRangeInput from "./age-range-input"
 import SubjectCountRangeInput from "./subject-count-range-input"
@@ -30,6 +31,7 @@ export {
   DiagnosisSelect,
   KeywordInput,
   ModalitySelect,
+  NIHSelect,
   ScannerManufacturers,
   ScannerManufacturersModelNames,
   SectionSelect,

package/src/scripts/search/inputs/nih-select.tsx

@@ -0,0 +1,63 @@
+import React, { useContext, useEffect } from "react"
+import type { FC } from "react"
+import { useLocation, useNavigate } from "react-router-dom"
+import { SearchParamsCtx } from "../search-params-ctx"
+import { SingleSelect } from "@openneuro/components/facets"
+
+interface NIHSelectProps {
+  label?: string
+}
+
+const NIHSelect: FC<NIHSelectProps> = ({ label }) => {
+  const { searchParams, setSearchParams } = useContext(SearchParamsCtx)
+  const navigate = useNavigate()
+  const location = useLocation()
+
+  const { brain_initiative } = searchParams
+
+  const setBrainInitiative = (selectedValue: string): void => {
+    const newSelectedFunding = selectedValue === "NIH" ? "true" : ""
+
+    // Update only brain_initiative in the search params context
+    setSearchParams((prevState) => ({
+      ...prevState,
+      brain_initiative: newSelectedFunding,
+    }))
+
+    const params = new URLSearchParams(location.search)
+
+    if (newSelectedFunding) {
+      params.set(
+        "query",
+        JSON.stringify({ brain_initiative: newSelectedFunding }),
+      )
+    } else {
+      params.delete("query")
+    }
+
+    navigate(`/search/nih?${params.toString()}`, { replace: true })
+  }
+
+  useEffect(() => {
+    if (
+      brain_initiative === "true" &&
+      !location.search.includes("brain_initiative")
+    ) {
+      const params = new URLSearchParams(location.search)
+      params.set("query", JSON.stringify({ brain_initiative: "true" }))
+      navigate(`/search/nih?${params.toString()}`, { replace: true })
+    }
+  }, [brain_initiative, location.search, navigate])
+
+  return (
+    <SingleSelect
+      className="nih-facet facet-open"
+      label={label}
+      selected={brain_initiative === "true" ? "NIH" : ""}
+      setSelected={setBrainInitiative}
+      items={["NIH"]}
+    />
+  )
+}
+
+export default NIHSelect

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

@@ -1,4 +1,4 @@
-import React, { useContext } from "react"
+import React, { useContext, useEffect } from "react"
 import type { FC } from "react"
 import { useLocation } from "react-router-dom"
 import {
@@ -22,6 +22,7 @@ import {
   DiagnosisSelect,
   KeywordInput,
   ModalitySelect,
+  NIHSelect,
   ScannerManufacturers,
   ScannerManufacturersModelNames,
   SectionSelect,
@@ -83,6 +84,7 @@ export const setDefaultSearch = (
     EEG: ["EEG"],
     iEEG: ["iEEG"],
     MEG: ["MEG"],
+    NIH: ["NIH"],
   }
   if (
     modality &&
@@ -106,12 +108,16 @@ const SearchContainer: FC<SearchContainerProps> = ({ portalContent }) => {
 
   const { searchParams, setSearchParams } = useContext(SearchParamsCtx)
   const modality = portalContent?.modality || null
-  setDefaultSearch(
-    modality,
-    searchParams,
-    setSearchParams,
-    new URLSearchParams(location.search),
-  )
+  const selected_grant = portalContent?.portalName || null
+
+  useEffect(() => {
+    setDefaultSearch(
+      modality,
+      searchParams,
+      setSearchParams,
+      new URLSearchParams(location.search),
+    )
+  }, [modality, searchParams, setSearchParams, location.search])
 
   const { loading, data, fetchMore, variables } = useSearchResults()
   const loadMore = loading ? () => {} : () => {
@@ -136,13 +142,14 @@ const SearchContainer: FC<SearchContainerProps> = ({ portalContent }) => {
   return (
     <>
       <Helmet>
-        <title>OpenNeuro - {portalContent ? modality : ""} Search</title>
+        <title>OpenNeuro - {modality || selected_grant || ""} Search</title>
       </Helmet>
       <SearchPage
         portalContent={portalContent}
-        renderAggregateCounts={() => (
-          <AggregateCountsContainer modality={portalContent.modality} />
-        )}
+        renderAggregateCounts={() =>
+          portalContent.modality
+            ? <AggregateCountsContainer modality={portalContent.modality} />
+            : null}
         renderFilterBlock={() => (
           <FiltersBlockContainer
             loading={loading}
@@ -153,12 +160,13 @@ const SearchContainer: FC<SearchContainerProps> = ({ portalContent }) => {
         renderSearchHeader={() => (
           <>
             {portalContent
-              ? "Search " + modality + " Portal"
+              ? "Search " + (modality || selected_grant || "") + " Portal"
               : "Search All Datasets"}
           </>
         )}
         renderSearchFacets={() => (
           <>
+            <NIHSelect label={"Search NIH Brain Initiative Datasets"} />
             <NeurobagelSearch />
             <KeywordInput />
             <AdminUser>

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

@@ -128,6 +128,7 @@ export const getSelectParams = ({
   tracerNames,
   tracerRadionuclides,
   bidsDatasetType_selected,
+  brain_initiative,
 }) => ({
   keywords,
   modality_selected,
@@ -150,6 +151,7 @@ export const getSelectParams = ({
   tracerNames,
   tracerRadionuclides,
   bidsDatasetType_selected,
+  brain_initiative,
 })
 
 /**

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

@@ -2,31 +2,39 @@ import React from "react"
 import type { FC } from "react"
 import { Route, Routes } from "react-router-dom"
 import SearchContainer from "./search-container"
-import { portalContent } from "@openneuro/components/content"
+import {
+  portalContent,
+  portalGrantContent,
+} from "@openneuro/components/content"
 
 const SearchRoutes: FC = () => (
   <Routes>
     <Route path="/" element={<SearchContainer />} />
     <Route
-      path="modality/mri"
+      path="/modality/mri"
       element={<SearchContainer portalContent={portalContent.mri} />}
     />
     <Route
-      path="modality/eeg"
+      path="/modality/eeg"
       element={<SearchContainer portalContent={portalContent.eeg} />}
     />
     <Route
-      path="modality/ieeg"
+      path="/modality/ieeg"
       element={<SearchContainer portalContent={portalContent.ieeg} />}
     />
     <Route
-      path="modality/meg"
+      path="/modality/meg"
       element={<SearchContainer portalContent={portalContent.meg} />}
     />
     <Route
-      path="modality/pet"
+      path="/modality/pet"
       element={<SearchContainer portalContent={portalContent.pet} />}
     />
+    <Route
+      path="/nih"
+      element={<SearchContainer portalContent={portalGrantContent.nih} />}
+    />
   </Routes>
 )
+
 export default SearchRoutes

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

@@ -87,6 +87,10 @@ const searchQuery = gql`
             issues {
               severity
             }
+            validation {
+              errors
+              warnings
+            }
             description {
               Name
               Authors
@@ -150,6 +154,7 @@ export const useSearchResults = () => {
     tracerRadionuclides,
     sortBy_selected,
     bidsDatasetType_selected,
+    brain_initiative,
   } = searchParams
 
   const boolQuery = new BoolQuery()
@@ -206,6 +211,7 @@ export const useSearchResults = () => {
       )
     }
   }
+
   if (isActiveRange(ageRange)) {
     boolQuery.addClause(
       "filter",
@@ -237,6 +243,15 @@ export const useSearchResults = () => {
       ),
     )
   }
+  if (brain_initiative) {
+    boolQuery.addClause(
+      "filter",
+      matchQuery(
+        "brainInitiative",
+        brain_initiative,
+      ),
+    )
+  }
   if (tasks.length) {
     boolQuery.addClause(
       "must",

package/src/scripts/types/user-types.ts

@@ -0,0 +1,72 @@
+export interface User {
+  id: string
+  name: string
+  location?: string
+  github?: string
+  institution?: string
+  email: string
+  avatar?: string
+  orcid?: string
+  links?: string[]
+}
+
+export interface UserRoutesProps {
+  user: User
+  hasEdit: boolean
+}
+export interface UserCardProps {
+  user: User
+}
+
+export interface UserAccountViewProps {
+  user: {
+    name: string
+    email: string
+    orcid?: string
+    links?: string[]
+    location?: string
+    institution?: string
+    github?: string
+  }
+}
+
+export interface Dataset {
+  id: string
+  created: string
+  name: string
+  public: boolean
+  analytics: {
+    views: number
+    downloads: number
+  }
+  stars?: { userId: string; datasetId: string }[]
+  followers?: { userId: string; datasetId: string }[]
+  latestSnapshot?: {
+    id: string
+    size: number
+    issues: { severity: string }[]
+    created?: string
+    description?: {
+      Authors: string[]
+    }
+  }
+  draft?: {
+    size?: number
+    created?: string
+  }
+}
+
+export interface DatasetCardProps {
+  dataset: Dataset
+  hasEdit: boolean
+}
+
+export interface UserDatasetsViewProps {
+  user: User
+  hasEdit: boolean
+}
+
+export interface AccountContainerProps {
+  user: User
+  hasEdit: boolean
+}