@openneuro/app 4.47.7 → 5.0.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@openneuro/app",
-  "version": "4.47.7",
+  "version": "5.0.0",
   "description": "React JS web frontend for the OpenNeuro platform.",
   "license": "MIT",
   "main": "public/client.js",
@@ -79,5 +79,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "af17c267fa700dff5b13d1b31aaf4f89c0853165"
+  "gitHead": "437b7f1a10abf79d6e49058b86cf0ddb625de684"
 }

package/src/client.jsx

@@ -35,6 +35,9 @@ const client = new ApolloClient({
           advancedSearch: relayStylePagination(),
         },
       },
+      DatasetFile: {
+        keyFields: false,
+      },
     },
   }),
   connectToDevTools: config.sentry.environment !== "production",

package/src/scripts/contributors/contributor.tsx

@@ -2,11 +2,12 @@ import React from "react"
 import { Link } from "react-router-dom"
 import { useUser } from "../queries/user"
 import type { Contributor } from "../types/datacite"
+import type { RequestStatus } from "../types/event-types.ts"
 import ORCIDiDLogo from "../../assets/ORCIDiD_iconvector.svg"
 
 interface SingleContributorDisplayProps {
   contributor: Contributor & {
-    resolutionStatus?: "pending" | "accepted" | "denied"
+    resolutionStatus?: RequestStatus
   }
   isLast: boolean
   separator: React.ReactNode
@@ -34,7 +35,7 @@ export const SingleContributorDisplay: React.FC<SingleContributorDisplayProps> =
     const userExists = !!user?.id
 
     // TODO get resolutionStatus from event/contributor
-    const resolutionAccepted = true //contributor.resolutionStatus === "accepted"
+    const resolutionAccepted = true //contributor.resolutionStatus === "ACCEPTED"
 
     return (
       <>

package/src/scripts/contributors/contributors-list.tsx

@@ -44,7 +44,6 @@ const UPDATE_CONTRIBUTORS = gql`
           files {
             id
             filename
-            key
             size
             annexed
             urls

package/src/scripts/datalad/dataset/dataset-query-fragments.js

@@ -77,7 +77,6 @@ export const DRAFT_FILES_FRAGMENT = gql`
       id
       files {
         id
-        key
         filename
         size
         directory
@@ -202,7 +201,6 @@ export const SNAPSHOT_FIELDS = gql`
     }
     files {
       id
-      key
       filename
       size
       directory

package/src/scripts/datalad/mutations/delete-comment.jsx

@@ -2,7 +2,7 @@ import React from "react"
 import PropTypes from "prop-types"
 import { gql } from "@apollo/client"
 import { Mutation } from "@apollo/client/react/components"
-import { DATASET_COMMENTS } from "../dataset/comments-fragments.js"
+import { DATASET_COMMENTS } from "../../dataset/fragments/comments-fragments.js"
 import { datasetCacheId } from "./cache-id.js"
 
 const deleteComment = gql`

package/src/scripts/dataset/__tests__/dataset-canonical-url.spec.ts

@@ -0,0 +1,20 @@
+import { datasetCanonicalUrl } from "../dataset-canonical-url"
+import { dataset } from "../../fixtures/dataset-query"
+import { vitest } from "vitest"
+
+vitest.mock("../../config", () => ({
+  config: { url: "http://localhost:9876" },
+}))
+
+describe("datasetCanonicalUrl", () => {
+  it("returns the canonical URL for a dataset with snapshots", () => {
+    const url = datasetCanonicalUrl(dataset)
+    expect(url.href).toBe("http://localhost:9876/datasets/ds001032/versions/2.0.0")
+  })
+
+  it("returns the canonical URL for a draft dataset", () => {
+    const draftDataset = { ...dataset, snapshots: [] }
+    const url = datasetCanonicalUrl(draftDataset)
+    expect(url.href).toBe("http://localhost:9876/datasets/ds001032")
+  })
+})

package/src/scripts/dataset/components/dataset-event-item.tsx

@@ -102,7 +102,7 @@ export const DatasetEventItem: React.FC<DatasetEventItemProps> = ({
       )
     } else {
       if (event.event.type === "contributorResponse") {
-        const statusText = event.event.resolutionStatus === "accepted"
+        const statusText = event.event.resolutionStatus === "ACCEPTED"
           ? "Accepted"
           : "Denied"
         return (
@@ -160,7 +160,7 @@ export const DatasetEventItem: React.FC<DatasetEventItemProps> = ({
     }
   }
 
-  const handleSaveOrProcessRequest = async (status?: "accepted" | "denied") => {
+  const handleSaveOrProcessRequest = async (status?: "ACCEPTED" | "DENIED") => {
     if (status) {
       if (!event.user?.id) {
         toast.error("Cannot process request: User ID not found.")
@@ -239,14 +239,14 @@ export const DatasetEventItem: React.FC<DatasetEventItemProps> = ({
               {editingNoteId === event.id && (
                 <>
                   <button
-                    onClick={() => handleSaveOrProcessRequest("accepted")}
+                    onClick={() => handleSaveOrProcessRequest("ACCEPTED")}
                     className={`${styles.eventActionButton} on-button on-button--small on-button--secondary`}
                     style={{ marginBottom: "5px" }}
                   >
                     Accept
                   </button>
                   <button
-                    onClick={() => handleSaveOrProcessRequest("denied")}
+                    onClick={() => handleSaveOrProcessRequest("DENIED")}
                     className={`${styles.eventActionButton} on-button on-button--small`}
                   >
                     Deny

package/src/scripts/dataset/dataset-canonical-url.ts

@@ -0,0 +1,14 @@
+import { config } from "../config"
+
+export function datasetCanonicalUrl(dataset): URL {
+  const siteUrl = config.url
+  if (dataset.snapshots.length) {
+    const latestSnapshot = dataset.snapshots.slice(-1)[0]
+    return new URL(
+      `/datasets/${dataset.id}/versions/${latestSnapshot.tag}`,
+      siteUrl,
+    )
+  } else {
+    return new URL(`/datasets/${dataset.id}`, siteUrl)
+  }
+}

package/src/scripts/dataset/dataset-query.jsx

@@ -3,6 +3,7 @@ import * as Sentry from "@sentry/react"
 import PropTypes from "prop-types"
 import { useNavigate, useParams } from "react-router-dom"
 import { useApolloClient, useQuery } from "@apollo/client"
+import Helmet from "react-helmet"
 import { Loading } from "../components/loading/Loading"
 
 import DatasetQueryContext from "../datalad/dataset/dataset-query-context.js"
@@ -16,6 +17,7 @@ import { trackAnalytics } from "../utils/datalad"
 import FourOFourPage from "../errors/404page"
 import FourOThreePage from "../errors/403page"
 import { getDatasetPage, getDraftPage } from "../queries/dataset"
+import { datasetCanonicalUrl } from "./dataset-canonical-url"
 
 /**
  * Query to load and render dataset page - most dataset loading is done here
@@ -63,6 +65,12 @@ export const DatasetQueryHook = ({ datasetId, draft }) => {
   }
   return (
     <DatasetContext.Provider value={data.dataset}>
+      <Helmet>
+        <link
+          rel="canonical"
+          href={datasetCanonicalUrl(data.dataset).toString()}
+        />
+      </Helmet>
       <ErrorBoundary subject={"error in dataset page"}>
         <DatasetQueryContext.Provider
           value={{

package/src/scripts/dataset/download/__tests__/download-script.spec.tsx

@@ -11,7 +11,7 @@ describe("DownloadScript", () => {
   const mockData = {
     snapshot: {
       id: "ds000001:1.0.0",
-      downloadFiles: [
+      files: [
         {
           id: "a2776e2e194d72419638d7611ddef7efa9c9f643",
           directory: false,

package/src/scripts/dataset/download/download-script.tsx

@@ -24,7 +24,7 @@ export function generateDownloadScript(data): string {
   // ds000001:1.0.0 -> ds000001-1.0.0 for directories
   const directory = data.snapshot.id.split(":").join("-")
   let script = "#!/bin/sh\n"
-  for (const f of data.snapshot.downloadFiles) {
+  for (const f of data.snapshot.files) {
     script += `curl --create-dirs ${f.urls[0]} -o ${directory}/${f.filename}\n`
   }
   return script
@@ -39,7 +39,7 @@ export const getSnapshotDownload = gql`
   query snapshot($datasetId: ID!, $tag: String!) {
     snapshot(datasetId: $datasetId, tag: $tag) {
       id
-      downloadFiles {
+      files(recursive: true) {
         id
         directory
         filename
@@ -54,14 +54,17 @@ export const DownloadScript = ({
   datasetId,
   snapshotTag,
 }: DownloadS3DerivativesProps): JSX.Element => {
-  const [getDownload, { loading, data }] = useLazyQuery(getSnapshotDownload, {
-    variables: {
-      datasetId: datasetId,
-      tag: snapshotTag,
+  const [getDownload, { loading, data, error }] = useLazyQuery(
+    getSnapshotDownload,
+    {
+      variables: {
+        datasetId: datasetId,
+        tag: snapshotTag,
+      },
+      errorPolicy: "all",
     },
-    errorPolicy: "all",
-  })
-  if (data) {
+  )
+  if (data?.snapshot?.files) {
     const script = generateDownloadScript(data)
     inlineDownload(`${datasetId}-${snapshotTag}.sh`, script)
   }
@@ -76,10 +79,18 @@ export const DownloadScript = ({
           Node.js.
         </p>
         <p>
-          {loading
+          {error
+            ? (
+              "Failed to generate download script."
+            )
+            : loading
             ? (
               "Loading..."
             )
+            : data?.snapshot && !data.snapshot.files
+            ? (
+              "Download is not yet available for this version. Please try again later."
+            )
             : (
               <a
                 href="#"

package/src/scripts/dataset/files/__tests__/file-tree-unloaded-directory.spec.jsx

@@ -38,7 +38,7 @@ describe("FileTreeUnloadedDirectory component", () => {
       expect(
         mergeNewFiles(dir)(defaultObj, { fetchMoreResult: updatedObj }).dataset
           .draft.files,
-      ).toEqual([a, b, { ...c, id: "sub-01:91011", filename: "sub-01:c" }])
+      ).toEqual([a, b, { ...c, id: "91011", filename: "sub-01:c" }])
     })
     it("works with snapshots", () => {
       const dir = { filename: "sub-01", directory: true }
@@ -52,7 +52,7 @@ describe("FileTreeUnloadedDirectory component", () => {
           .snapshot.files,
       ).toEqual([dir, a, b, {
         ...c,
-        id: "sub-01:91011",
+        id: "91011",
         filename: "sub-01:c",
       }])
     })
@@ -67,7 +67,7 @@ describe("FileTreeUnloadedDirectory component", () => {
           .snapshot.files,
       ).toEqual([{
         ...c,
-        id: "sub-01:91011",
+        id: "91011",
         filename: "sub-01:c",
       }])
     })
@@ -83,7 +83,7 @@ describe("FileTreeUnloadedDirectory component", () => {
           .dataset.draft.files,
       ).toEqual([{
         ...c,
-        id: "sub-01:91011",
+        id: "91011",
         filename: "sub-01:c",
       }])
     })

package/src/scripts/dataset/files/file-tree-unloaded-directory.jsx

@@ -10,7 +10,6 @@ export const DRAFT_FILES_QUERY = gql`
       draft {
         files(tree: $tree) {
           id
-          key
           filename
           size
           directory
@@ -27,7 +26,6 @@ export const SNAPSHOT_FILES_QUERY = gql`
     snapshot(datasetId: $datasetId, tag: $snapshotTag) {
       files(tree: $tree) {
         id
-        key
         filename
         size
         directory
@@ -43,8 +41,7 @@ export const SNAPSHOT_FILES_QUERY = gql`
  */
 export const nestFiles = (path) => (file) => ({
   ...file,
-  // Generate a unique id for any nested files to avoid overwriting trees with two parents
-  id: `${path}:${file.id}`,
+  id: file.id,
   filename: `${path}:${file.filename}`,
 })
 
@@ -85,7 +82,7 @@ export const fetchMoreDirectory = (
 ) =>
   fetchMore({
     query: snapshotTag ? SNAPSHOT_FILES_QUERY : DRAFT_FILES_QUERY,
-    variables: { datasetId, snapshotTag, tree: directory.key },
+    variables: { datasetId, snapshotTag, tree: directory.id },
     updateQuery: mergeNewFiles(directory, snapshotTag),
   })
 

package/src/scripts/dataset/files/file-tree.tsx

@@ -146,7 +146,7 @@ const FileTree = ({
                   toggleFileToDelete={toggleFileToDelete}
                   isFileToBeDeleted={isFileToBeDeleted}
                   filename={file.filename.split(":").pop()}
-                  annexKey={file.key}
+                  annexKey={file.id}
                   datasetPermissions={datasetPermissions}
                   annexed={file.annexed}
                   isMobile={false}

package/src/scripts/dataset/mutations/delete-file.jsx

@@ -9,6 +9,15 @@ const DELETE_FILE = gql`
   }
 `
 
+const DELETED_FILE_FRAGMENT = gql`
+  fragment DeletedFile on DatasetFile {
+    id
+    key
+    filename
+    directory
+  }
+`
+
 /**
  * Given a file object, path/filename for deletion, and a list of currently loaded files, filter any that will be deleted and orphan directories
  */
@@ -48,28 +57,14 @@ const DeleteFile = ({ datasetId, path, filename }) => {
               const cachedFileObjects = cachedFiles.map((f) =>
                 cache.readFragment({
                   id: cache.identify(f),
-                  fragment: gql`
-                    fragment DeletedFile on DatasetFile {
-                      id
-                      key
-                      filename
-                      directory
-                    }
-                  `,
+                  fragment: DELETED_FILE_FRAGMENT,
                 })
               )
               const remainingFiles = cachedFiles.filter((f) => {
                 // Get the cache key for each file we have loaded
                 const file = cache.readFragment({
                   id: cache.identify(f),
-                  fragment: gql`
-                    fragment DeletedFile on DatasetFile {
-                      id
-                      key
-                      filename
-                      directory
-                    }
-                  `,
+                  fragment: DELETED_FILE_FRAGMENT,
                 })
                 return fileCacheDeleteFilter(
                   file,

package/src/scripts/dataset/mutations/hold-deletion.tsx

@@ -0,0 +1,57 @@
+import React from "react"
+import { gql, useMutation, useQuery } from "@apollo/client"
+import { Button } from "../../components/button/Button"
+
+const GET_HOLD_DELETION = gql`
+  query getHoldDeletion($datasetId: ID!) {
+    dataset(id: $datasetId) {
+      id
+      holdDeletion
+    }
+  }
+`
+
+const HOLD_DELETION = gql`
+  mutation holdDeletion($datasetId: ID!, $hold: Boolean!) {
+    holdDeletion(datasetId: $datasetId, hold: $hold)
+  }
+`
+
+export const HoldDeletion = ({ datasetId }: { datasetId: string }) => {
+  const { data, loading: queryLoading } = useQuery(GET_HOLD_DELETION, {
+    variables: { datasetId },
+  })
+  const [holdDeletion, { loading: mutationLoading }] = useMutation(
+    HOLD_DELETION,
+    {
+      refetchQueries: [{ query: GET_HOLD_DELETION, variables: { datasetId } }],
+    },
+  )
+
+  const held = data?.dataset?.holdDeletion ?? false
+  const loading = queryLoading || mutationLoading
+
+  return (
+    <span>
+      <Button
+        icon={loading
+          ? "fa fa-spin fa-repeat"
+          : held
+          ? "fa fa-lock"
+          : "fa fa-unlock"}
+        label={loading
+          ? "Updating..."
+          : held
+          ? "Deletion Held"
+          : "Hold Deletion"}
+        primary={!held}
+        secondary={held}
+        size="small"
+        disabled={loading}
+        onClick={() => {
+          holdDeletion({ variables: { datasetId, hold: !held } })
+        }}
+      />
+    </span>
+  )
+}

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

@@ -0,0 +1,56 @@
+import React from "react"
+import { cleanup, render, screen } from "@testing-library/react"
+import { vi } from "vitest"
+import { NoErrors } from "../snapshot"
+
+const mockUseUser = vi.fn()
+
+vi.mock("../../../queries/user", () => ({
+  useUser: () => mockUseUser(),
+}))
+
+vi.mock("../../mutations/fsck-dataset", () => ({
+  FsckDataset: ({ disabled }) => (
+    <button data-testid="mock-fsck-button" disabled={disabled}>
+      Rerun File Checks
+    </button>
+  ),
+}))
+
+vi.mock("../../fragments/file-check-list", () => ({
+  FileCheckList: () => <div>Mock File Check List</div>,
+}))
+
+describe("NoErrors Component", () => {
+  afterEach(() => {
+    cleanup()
+    vi.clearAllMocks()
+  })
+
+  const baseProps = {
+    datasetId: "ds000001",
+    modified: new Date().toISOString(), // Ensures recheckEnabled is false
+    validation: { errors: 0 },
+    authors: [{ name: "Author" }],
+    fileCheck: { annexFsck: ["badfile.nii.gz"] }, // Ensures !noBadFiles is true
+    children: <div data-testid="children">Children</div>,
+  }
+
+  it("does not disable FsckDataset for admin users", () => {
+    mockUseUser.mockReturnValue({ user: { admin: true } })
+    render(<NoErrors {...baseProps} />)
+    const fsckButton = screen.getByTestId("mock-fsck-button")
+    expect(fsckButton).not.toBeDisabled()
+    expect(screen.queryByText(/A recheck can be requested in/)).not
+      .toBeInTheDocument()
+  })
+
+  it("disables FsckDataset for non-admin users", () => {
+    mockUseUser.mockReturnValue({ user: { admin: false } })
+    render(<NoErrors {...baseProps} />)
+    const fsckButton = screen.getByTestId("mock-fsck-button")
+    expect(fsckButton).toBeDisabled()
+    expect(screen.getByText(/A recheck can be requested in/))
+      .toBeInTheDocument()
+  })
+})

package/src/scripts/dataset/routes/admin-datalad.jsx

@@ -2,6 +2,7 @@ import React from "react"
 import PropTypes from "prop-types"
 import DatasetHistory from "../fragments/dataset-history.jsx"
 import CacheClear from "../mutations/cache-clear.jsx"
+import { HoldDeletion } from "../mutations/hold-deletion"
 import AdminExports from "../mutations/admin-exports"
 import { DatasetPageBorder } from "./styles/dataset-page-border"
 import { HeaderRow3, HeaderRow4 } from "./styles/header-row"
@@ -19,6 +20,15 @@ const AdminDataset = ({ dataset }) => (
       <CacheClear datasetId={dataset.id} />
     </div>
     <hr />
+    <HeaderRow4>Hold Automated Draft Deletion</HeaderRow4>
+    <p>
+      Pause automated deletion of stale draft data and prevent sending a final
+      notice for this dataset.
+    </p>
+    <div className="dataset-form-controls">
+      <HoldDeletion datasetId={dataset.id} />
+    </div>
+    <hr />
     <HeaderRow4>Rerun Exports</HeaderRow4>
     <p>
       Correct most temporary issues with a dataset export by reattempting to

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

@@ -11,6 +11,7 @@ import styled from "@emotion/styled"
 import { apiPath } from "../files/file"
 import { FileCheckList } from "../fragments/file-check-list"
 import { FsckDataset } from "../mutations/fsck-dataset"
+import { useUser } from "../../queries/user"
 
 const FormRow = styled.div`
   margin-top: 0;
@@ -20,6 +21,8 @@ const FormRow = styled.div`
 export const NoErrors = (
   { datasetId, modified, validation, authors, fileCheck, children },
 ) => {
+  const { user } = useUser()
+  const adminUser = user?.admin || false
   const noErrors = validation?.errors === 0
   // zero authors will cause DOI minting to fail
   const hasAuthor = authors?.length > 0
@@ -58,8 +61,11 @@ export const NoErrors = (
         )}
         {!noBadFiles && (
           <span>
-            <FsckDataset datasetId={datasetId} disabled={!recheckEnabled} />
-            {!recheckEnabled && (
+            <FsckDataset
+              datasetId={datasetId}
+              disabled={!recheckEnabled && !adminUser}
+            />
+            {!recheckEnabled && !adminUser && (
               <p>A recheck can be requested in {minutesDiff} minutes.</p>
             )}
           </span>

package/src/scripts/pages/front-page/aggregate-queries/use-publicDatasets-count.ts

@@ -11,7 +11,7 @@ const PUBLIC_DATASETS_COUNT = gql`
 `
 
 const BRAIN_INITIATIVE_COUNT = gql`
-  query AdvancedSearch($query: JSON!, $datasetType: String!) {
+  query AdvancedSearch($query: DatasetSearchInput!, $datasetType: String!) {
     advancedSearch(query: $query, datasetType: $datasetType) {
       pageInfo {
         count
@@ -26,9 +26,7 @@ const usePublicDatasetsCount = (modality?: string) => {
   const query = isNIH ? BRAIN_INITIATIVE_COUNT : PUBLIC_DATASETS_COUNT
   const variables = isNIH
     ? {
-      query: {
-        bool: { filter: [{ match: { brainInitiative: { query: "true" } } }] },
-      },
+      query: { brainInitiative: true },
       datasetType: "public",
     }
     : { modality }

package/src/scripts/queries/dataset.ts

@@ -3,7 +3,7 @@
  */
 import { gql } from "@apollo/client"
 import * as DatasetQueryFragments from "../datalad/dataset/dataset-query-fragments.js"
-import { DATASET_COMMENTS } from "../datalad/dataset/comments-fragments.js"
+import { DATASET_COMMENTS } from "../dataset/fragments/comments-fragments.js"
 
 /**
  * Generate the dataset page query

package/src/scripts/queries/datasetEvents.ts

@@ -53,7 +53,7 @@ export const PROCESS_CONTRIBUTOR_REQUEST_MUTATION = gql`
     $datasetId: ID!
     $requestId: ID!
     $targetUserId: ID!
-    $resolutionStatus: String!
+    $resolutionStatus: ResponseStatusType!
     $reason: String
   ) {
     processContributorRequest(
@@ -153,7 +153,7 @@ export const CREATE_CONTRIBUTOR_CITATION_EVENT = gql`
 `
 
 export const PROCESS_CONTRIBUTOR_CITATION_MUTATION = gql`
-  mutation ProcessContributorCitation($eventId: ID!, $status: String!) {
+  mutation ProcessContributorCitation($eventId: ID!, $status: ResponseStatusType!) {
     processContributorCitation(eventId: $eventId, status: $status) {
       id
       timestamp

package/src/scripts/queries/user.ts

@@ -96,18 +96,16 @@ export const UPDATE_USER = gql`
 
 export const ADVANCED_SEARCH_DATASETS_QUERY = gql`
   query advancedSearchDatasets(
-    $query: JSON!
+    $query: DatasetSearchInput!
     $cursor: String
     $allDatasets: Boolean
     $datasetStatus: String
-    $sortBy: JSON
     $first: Int!
   ) {
     datasets: advancedSearch(
       query: $query
       allDatasets: $allDatasets
       datasetStatus: $datasetStatus
-      sortBy: $sortBy
       first: $first
       after: $cursor
     ) {