@openneuro/app 4.19.2 → 4.20.0-alpha.0

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

@@ -0,0 +1,18 @@
+import React from 'react'
+import { DataTable } from '../../../components/data-table'
+import styled from '@emotion/styled'
+
+const TableOverlow = styled.div`
+  overflow-x: scroll;
+  height: 64vh;
+`
+
+const FileViewerTable = ({ tableData }): React.ReactElement => {
+  return (
+    <TableOverlow>
+      <DataTable data={tableData}></DataTable>
+    </TableOverlow>
+  )
+}
+
+export default FileViewerTable

package/src/scripts/dataset/files/viewers/file-viewer-tsv.jsx

@@ -1,7 +1,7 @@
 import React from 'react'
 import PropTypes from 'prop-types'
 import parseTabular from './parse-tabular.js'
-import FileViewerTable from './file-viewer-table.jsx'
+import FileViewerTable from './file-viewer-table'
 
 const FileViewerTsv = ({ data }) => {
   const decoder = new TextDecoder()

package/src/scripts/dataset/fragments/__tests__/__snapshots__/cancel-button.spec.tsx.snap

@@ -1,4 +1,4 @@
-// Vitest Snapshot v1
+// Vitest Snapshot v1, https://vitest.dev/guide/snapshot.html
 
 exports[`CancelButton component > renders with default props 1`] = `
 <DocumentFragment>

package/src/scripts/dataset/fragments/__tests__/__snapshots__/edit-button.spec.tsx.snap

@@ -1,4 +1,4 @@
-// Vitest Snapshot v1
+// Vitest Snapshot v1, https://vitest.dev/guide/snapshot.html
 
 exports[`EditButton component > renders with default props 1`] = `
 <DocumentFragment>

package/src/scripts/dataset/fragments/__tests__/__snapshots__/edit-list.spec.jsx.snap

@@ -1,4 +1,4 @@
-// Vitest Snapshot v1
+// Vitest Snapshot v1, https://vitest.dev/guide/snapshot.html
 
 exports[`EditList component > renders with default props 1`] = `
 <DocumentFragment>

package/src/scripts/dataset/fragments/__tests__/__snapshots__/save-button.spec.tsx.snap

@@ -1,4 +1,4 @@
-// Vitest Snapshot v1
+// Vitest Snapshot v1, https://vitest.dev/guide/snapshot.html
 
 exports[`SaveButton component > renders with default props 1`] = `
 <DocumentFragment>

package/src/scripts/dataset/fragments/__tests__/__snapshots__/select-input.spec.tsx.snap

@@ -1,4 +1,4 @@
-// Vitest Snapshot v1
+// Vitest Snapshot v1, https://vitest.dev/guide/snapshot.html
 
 exports[`SelectInput > handles boolean display 1`] = `
 <DocumentFragment>

package/src/scripts/dataset/fragments/comments-fragments.js

@@ -8,7 +8,8 @@ export const DATASET_COMMENTS = gql`
       text
       createDate
       user {
-        email
+        name
+        orcid
       }
       parent {
         id

package/src/scripts/dataset/fragments/text-input.tsx

@@ -107,7 +107,7 @@ const TextInput = ({
   required,
   onChange,
 }): React.ReactElement => {
-  if (value === null) {
+  if (value === null || value === undefined) {
     if (nullMessage) value = nullMessage
     else value = ''
   } else value = value.toString()

package/src/scripts/dataset/mutations/__tests__/__snapshots__/delete.spec.jsx.snap

@@ -1,4 +1,4 @@
-// Vitest Snapshot v1
+// Vitest Snapshot v1, https://vitest.dev/guide/snapshot.html
 
 exports[`DeleteDataset mutation > renders with common props 1`] = `
 <DocumentFragment>

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

@@ -1,4 +1,4 @@
-// Vitest Snapshot v1
+// Vitest Snapshot v1, https://vitest.dev/guide/snapshot.html
 
 exports[`DeprecateVersion mutation > renders with typical props 1`] = `
 <DocumentFragment>

package/src/scripts/dataset/mutations/__tests__/__snapshots__/deprecate-version.spec.tsx.snap

@@ -1,4 +1,4 @@
-// Vitest Snapshot v1
+// Vitest Snapshot v1, https://vitest.dev/guide/snapshot.html
 
 exports[`DeprecateVersion mutation > renders with typical props 1`] = `
 <DocumentFragment>

package/src/scripts/dataset/mutations/__tests__/__snapshots__/description.spec.jsx.snap

@@ -1,4 +1,4 @@
-// Vitest Snapshot v1
+// Vitest Snapshot v1, https://vitest.dev/guide/snapshot.html
 
 exports[`UpdateDescription mutation > renders with common props 1`] = `
 <DocumentFragment>

package/src/scripts/dataset/mutations/__tests__/__snapshots__/update-permissions.spec.jsx.snap

@@ -1,4 +1,4 @@
-// Vitest Snapshot v1
+// Vitest Snapshot v1, https://vitest.dev/guide/snapshot.html
 
 exports[`UpdateDatasetPermissions mutation > renders with default props 1`] = `
 <DocumentFragment>

package/src/scripts/dataset/mutations/comment.jsx

@@ -70,7 +70,7 @@ export const newCommentsReducer = (
 }
 
 /**
- * Modify an exsiting comment and return new state based on arguments
+ * Modify an existing comment and return new state based on arguments
  * @param {Object[]} comments
  * @param {Object} arguments
  * @param {string} arguments.commentId

package/src/scripts/dataset/mutations/delete-anonymous-reviewer.tsx

@@ -20,10 +20,13 @@ interface DeleteReviewerLinkProps {
 export const DeleteReviewerLink: FC<DeleteReviewerLinkProps> = ({
   datasetId,
   id,
+}: {
+  datasetId: string
+  id: string
 }) => {
   const [DeleteReviewerLink] = useMutation(DELETE_REVIEWER, {
     update(cache, { data: { deleteReviewer } }) {
-      const { reviewers } = cache.readFragment({
+      const { reviewers } = cache.readFragment<{ reviewers: any[] }>({
         id: `Dataset:${datasetId}`,
         fragment: DATASET_REVIEWERS,
       })

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

@@ -4,12 +4,15 @@ import { gql, useMutation } from '@apollo/client'
 import { useNavigate } from 'react-router-dom'
 import ErrorBoundary from '../../errors/errorBoundary.jsx'
 import { Button } from '@openneuro/components/button'
+import { getDatasetPage, getDraftPage } from '../../queries/dataset'
 
 const CREATE_SNAPSHOT = gql`
   mutation createSnapshot($datasetId: ID!, $tag: String!, $changes: [String!]) {
     createSnapshot(datasetId: $datasetId, tag: $tag, changes: $changes) {
       id
       tag
+      created
+      hexsha
     }
   }
 `
@@ -28,7 +31,9 @@ const CreateSnapshotMutation = ({
   disabled,
 }: CreateSnapshotMutationProps) => {
   const navigate = useNavigate()
-  const [snapshotDataset, { loading, error }] = useMutation(CREATE_SNAPSHOT)
+  const [snapshotDataset, { loading, error }] = useMutation(CREATE_SNAPSHOT, {
+    refetchQueries: [getDatasetPage, getDraftPage],
+  })
 
   if (error) throw error
 
@@ -42,7 +47,10 @@ const CreateSnapshotMutation = ({
         onClick={(): void => {
           void snapshotDataset({
             variables: { datasetId, tag, changes },
-          }).then(() => navigate(`/datasets/${datasetId}/versions/${tag}`))
+          }).then(data => {
+            console.log(data)
+            navigate(`/datasets/${datasetId}/versions/${tag}`)
+          })
         }}
         disabled={disabled}
         label="Create Version"

package/src/scripts/dataset/routes/add-metadata.jsx

@@ -6,7 +6,7 @@ import MetadataForm from '../mutations/metadata-form.jsx'
 import { DatasetRelations } from '../mutations/dataset-relations'
 import SubmitMetadata from '../mutations/submit-metadata.jsx'
 import LoggedIn from '../../authentication/logged-in.jsx'
-import { hasEditPermissions, getProfile } from '../../authentication/profile.js'
+import { hasEditPermissions, getProfile } from '../../authentication/profile'
 import { DatasetPageBorder } from './styles/dataset-page-border'
 import { HeaderRow3, HeaderRow4 } from './styles/header-row'
 

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

@@ -3,7 +3,7 @@ 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.js'
+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'

package/src/scripts/dataset/routes/manage-permissions.jsx

@@ -1,6 +1,5 @@
 import React, { useState } from 'react'
 import PropTypes from 'prop-types'
-import { Link } from 'react-router-dom'
 import { Button } from '@openneuro/components/button'
 
 import { RemovePermissions } from '../mutations/remove-permissions'
@@ -140,7 +139,7 @@ Share.propTypes = {
   datasetId: PropTypes.string,
   permissions: PropTypes.object,
   reviewers: PropTypes.array,
-  hasSnapshot: PropTypes.boolean,
+  hasSnapshot: PropTypes.bool,
 }
 
 export default Share

package/src/scripts/dataset/routes/{snapshot.jsx → snapshot.tsx}

@@ -1,6 +1,5 @@
 import React, { useState } from 'react'
-import PropTypes from 'prop-types'
-import semver from 'semver'
+import semver, { ReleaseType } from 'semver'
 import SnapshotDataset from '../mutations/snapshot'
 import EditList from '../fragments/edit-list.jsx'
 import { Button } from '@openneuro/components/button'
@@ -38,7 +37,12 @@ export const NoErrors = ({ issues, children }) => {
   }
 }
 
-const SnapshotRoute = ({ datasetId, snapshots, issues, description }) => {
+const SnapshotRoute = ({
+  datasetId,
+  snapshots,
+  issues,
+  description,
+}): React.ReactElement => {
   const [changes, setChanges] = useState([])
   const [semanticLevel, setSemanticLevel] = useState('patch')
   const draftLicense = (description && description.License) || 'none'
@@ -48,7 +52,7 @@ const SnapshotRoute = ({ datasetId, snapshots, issues, description }) => {
   const latestSnapshot = snapshots.length && snapshots[snapshots.length - 1]
   const newVersion =
     snapshots.length && semver.valid(latestSnapshot.tag)
-      ? semver.inc(latestSnapshot.tag, semanticLevel)
+      ? semver.inc(latestSnapshot.tag, semanticLevel as ReleaseType)
       : '1.0.0'
 
   const majorActive = semanticLevel === 'major' && 'active'
@@ -138,11 +142,4 @@ const SnapshotRoute = ({ datasetId, snapshots, issues, description }) => {
   )
 }
 
-SnapshotRoute.propTypes = {
-  datasetId: PropTypes.string,
-  snapshots: PropTypes.array,
-  issues: PropTypes.array,
-  description: PropTypes.object,
-}
-
 export default SnapshotRoute

package/src/scripts/dataset/routes/styles/dataset-page-border.tsx

@@ -1,4 +1,6 @@
+import React from 'react'
 import styled from '@emotion/styled'
+import '@emotion/react'
 
 export const DatasetPageBorder = styled.div`
   border: 1px solid #ccc;

package/src/scripts/dataset/routes/styles/dataset-page-tab-container.tsx

@@ -1,4 +1,6 @@
+import React from 'react'
 import styled from '@emotion/styled'
+import '@emotion/react'
 
 export const DatasetPageTabContainer = styled.div`
   display: flex;

package/src/scripts/dataset/routes/styles/header-row.tsx

@@ -1,4 +1,6 @@
+import React from 'react'
 import styled from '@emotion/styled'
+import '@emotion/react'
 
 const headerRowStyle = `
   margin-top: 0;

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

@@ -55,7 +55,7 @@ export const TabRoutesDraft = ({ dataset, hasEdit }) => {
             datasetId={dataset.id}
             permissions={dataset.permissions}
             reviewers={dataset.reviewers}
-            hasSnapshot={dataset.snapshots.length}
+            hasSnapshot={dataset.snapshots.length !== 0}
           />
         }
       />

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

@@ -108,13 +108,13 @@ export const SnapshotContainer: React.FC<SnapshotContainerProps> = ({
               modality={summary?.modalities[0]}>
               <FollowToggles>
                 <FollowDataset
-                  profile={profile}
+                  profile={profile !== null}
                   datasetId={dataset.id}
                   following={dataset.following}
                   followers={dataset.followers.length}
                 />
                 <StarDataset
-                  profile={profile}
+                  profile={profile !== null}
                   datasetId={dataset.id}
                   starred={dataset.starred}
                   stars={dataset.stars.length}

package/src/scripts/pages/admin/user-tools.tsx

@@ -2,7 +2,7 @@ import React, { FC, ReactElement } from 'react'
 import { gql } from '@apollo/client'
 import { Mutation } from '@apollo/client/react/components'
 import { WarnButton } from '@openneuro/components/warn-button'
-import { getProfile } from '../../authentication/profile.js'
+import { getProfile } from '../../authentication/profile'
 import { useCookies } from 'react-cookie'
 import { USER_FRAGMENT } from './user-fragment'
 

package/src/scripts/pages/faq/faq.tsx

@@ -0,0 +1,8 @@
+import React from 'react'
+
+const Faq = (): React.ReactElement => {
+  window.location.replace('https://docs.openneuro.org/faq')
+  return null
+}
+
+export default Faq

package/src/scripts/pages/metadata/dataset-metadata.tsx

@@ -0,0 +1,86 @@
+import React from 'react'
+import styled from '@emotion/styled'
+import { DataTable } from '../../components/data-table'
+import { gql, useQuery } from '@apollo/client'
+import { Loading } from '@openneuro/components/loading'
+import { makeCsv } from '../../utils/csv'
+
+const MetadataPageStyle = styled.div`
+  background: white;
+  overflow-x: scroll;
+  padding: 1em;
+  height: calc(100vh - 125px);
+  white-space: nowrap;
+`
+
+const MetadataPageButton = styled.button`
+  display: inline-block;
+  margin-right: 1em;
+`
+
+const METADATA_QUERY = gql`
+  query {
+    publicMetadata {
+      datasetId
+      datasetUrl
+      datasetName
+      firstSnapshotCreatedAt
+      latestSnapshotCreatedAt
+      dxStatus
+      tasksCompleted
+      trialCount
+      grantFunderName
+      grantIdentifier
+      studyDesign
+      studyDomain
+      studyLongitudinal
+      dataProcessed
+      species
+      associatedPaperDOI
+      openneuroPaperDOI
+      seniorAuthor
+      adminUsers
+      ages
+      modalities
+      affirmedDefaced
+      affirmedConsent
+    }
+  }
+`
+
+export function DatasetMetadata(): React.ReactElement {
+  const { loading, error, data } = useQuery(METADATA_QUERY, {
+    errorPolicy: 'all',
+  })
+  if (loading || error) {
+    return <Loading />
+  } else {
+    return (
+      <MetadataPageStyle>
+        <p>
+          <MetadataPageButton
+            role="button"
+            type="button"
+            className="on-button on-button--small on-button--primary icon-text"
+            aria-label="Download"
+            onClick={() =>
+              makeCsv(data?.publicMetadata, 'openneuro-metadata.csv')
+            }>
+            <i className="fa fa-download css-0" aria-hidden="true"></i>Download
+            CSV
+          </MetadataPageButton>
+          Metadata collected for all public datasets on OpenNeuro.
+        </p>
+        <DataTable
+          data={data?.publicMetadata}
+          downloadFilename="openneuro-metadata.csv"
+          hideColumns={[
+            '__typename',
+            'datasetUrl',
+            'affirmedDefaced',
+            'affirmedConsent',
+          ]}></DataTable>
+      </MetadataPageStyle>
+    )
+  }
+}

package/src/scripts/queries/dataset.ts

@@ -0,0 +1,113 @@
+/**
+ * Top level dataset queries only, mutations may cause refetches of these
+ */
+import { gql } from '@apollo/client'
+import * as DatasetQueryFragments from '../datalad/dataset/dataset-query-fragments.js'
+import { DATASET_COMMENTS } from '../datalad/dataset/comments-fragments.js'
+
+/**
+ * Generate the dataset page query
+ */
+export const getDatasetPage = gql`
+  query dataset($datasetId: ID!) {
+    dataset(id: $datasetId) {
+      id
+      created
+      public
+      following
+      followers {
+        userId
+      }
+      starred
+      stars {
+        userId
+      }
+      worker
+      ...DatasetDraft
+      ...DatasetPermissions
+      ...DatasetSnapshots
+      ...DatasetIssues
+      ...DatasetMetadata
+      ...DatasetComments
+      uploader {
+        id
+        name
+        email
+        orcid
+      }
+      analytics {
+        downloads
+        views
+      }
+      derivatives {
+        name
+        s3Url
+        dataladUrl
+        local
+      }
+      onBrainlife
+    }
+  }
+  ${DatasetQueryFragments.DRAFT_FRAGMENT}
+  ${DatasetQueryFragments.PERMISSION_FRAGMENT}
+  ${DatasetQueryFragments.DATASET_SNAPSHOTS}
+  ${DatasetQueryFragments.DATASET_ISSUES}
+  ${DatasetQueryFragments.DATASET_METADATA}
+  ${DATASET_COMMENTS}
+`
+
+/**
+ * Add files fragment for draft route
+ */
+export const getDraftPage = gql`
+  query dataset($datasetId: ID!) {
+    dataset(id: $datasetId) {
+      id
+      created
+      public
+      following
+      followers {
+        userId
+      }
+      starred
+      stars {
+        userId
+      }
+      reviewers {
+        id
+        expiration
+      }
+      worker
+      ...DatasetDraft
+      ...DatasetDraftFiles
+      ...DatasetPermissions
+      ...DatasetSnapshots
+      ...DatasetIssues
+      ...DatasetMetadata
+      ...DatasetComments
+      uploader {
+        id
+        name
+        email
+        orcid
+      }
+      analytics {
+        downloads
+        views
+      }
+      derivatives {
+        name
+        s3Url
+        dataladUrl
+        local
+      }
+    }
+  }
+  ${DatasetQueryFragments.DRAFT_FRAGMENT}
+  ${DatasetQueryFragments.DRAFT_FILES_FRAGMENT}
+  ${DatasetQueryFragments.PERMISSION_FRAGMENT}
+  ${DatasetQueryFragments.DATASET_SNAPSHOTS}
+  ${DatasetQueryFragments.DATASET_ISSUES}
+  ${DatasetQueryFragments.DATASET_METADATA}
+  ${DATASET_COMMENTS}
+`

package/src/scripts/routes.tsx

@@ -15,6 +15,7 @@ import { PETRedirect } from './pages/pet-redirect'
 import Citation from './pages/citation-page'
 import FourOFourPage from './errors/404page'
 import { ImportDataset } from './pages/import-dataset'
+import { DatasetMetadata } from './pages/metadata/dataset-metadata'
 
 const AppRoutes: React.VoidFunctionComponent = () => (
   <Routes>
@@ -28,6 +29,7 @@ const AppRoutes: React.VoidFunctionComponent = () => (
     <Route path="/pet" element={<PETRedirect />} />
     <Route path="/cite" element={<Citation />} />
     <Route path="/import" element={<ImportDataset />} />
+    <Route path="/metadata" element={<DatasetMetadata />} />
     <Route path="/public" element={<Navigate to="/search" replace />} />
     <Route
       path="/saved"

package/src/scripts/search/__helpers__/search-render.tsx

@@ -1,6 +1,7 @@
 import React from 'react'
 import { SearchParamsCtx } from '../search-params-ctx'
 import { render } from '@testing-library/react'
+import { queries } from '@testing-library/dom'
 
 /**
  * Render with SearchParamsCtx state

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

@@ -1,4 +1,4 @@
-import { sortBy } from '@openneuro/components/mock-content'
+import { sortBy } from '@openneuro/components/content'
 
 const datasetType_available = [
   { label: 'All Public', value: 'All Public' },

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

@@ -1,7 +1,7 @@
 import React, { FC } from 'react'
 import { Route, Routes } from 'react-router-dom'
 import SearchContainer from './search-container'
-import { portalContent } from '@openneuro/components/mock-content'
+import { portalContent } from '@openneuro/components/content'
 
 const SearchRoutes: FC = () => (
   <Routes>

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

@@ -11,7 +11,7 @@ import {
   sqsJoinWithAND,
   joinWithOR,
 } from './es-query-builders'
-import { species_list } from '@openneuro/components/mock-content'
+import { species_list } from '@openneuro/components/content'
 
 const searchQuery = gql`
   query advancedSearchDatasets(

package/src/scripts/styles/media.tsx

@@ -1,4 +1,6 @@
+import React from 'react'
 import { createMedia } from '@artsy/fresnel'
+import '@artsy/fresnel/dist/Media'
 
 const AppMedia = createMedia({
   breakpoints: {

package/src/scripts/utils/__tests__/csv.spec.ts

@@ -0,0 +1,41 @@
+import { convertArrayToCSV } from '../csv'
+
+describe('utils/csv', () => {
+  it('converts to a valid CSV', () => {
+    const obj = [
+      { exampleCol: 'test', exampleCol2: 'test2', __typename: 'example' },
+      { exampleCol: 'test4', exampleCol2: 'test3', __typename: 'example' },
+    ]
+    expect(convertArrayToCSV(obj)).toEqual(
+      'exampleCol,exampleCol2\n"test","test2"\n"test4","test3"',
+    )
+  })
+  it('escapes comma values correctly', () => {
+    const obj = [
+      { exampleCol: 'test', modalities: 'PET,MRI', __typename: 'example' },
+      { exampleCol: 'test4', modalities: 'MRI', __typename: 'example' },
+    ]
+    expect(convertArrayToCSV(obj)).toEqual(
+      'exampleCol,modalities\n"test","PET,MRI"\n"test4","MRI"',
+    )
+  })
+  it('escapes double quotes', () => {
+    const obj = [
+      {
+        exampleCol: 'test',
+        modalities: 'PET,MRI',
+        name: 'A "Dataset"',
+        __typename: 'example',
+      },
+      {
+        exampleCol: 'test4',
+        modalities: 'MRI',
+        name: 'Another Dataset',
+        __typename: 'example',
+      },
+    ]
+    expect(convertArrayToCSV(obj)).toEqual(
+      'exampleCol,modalities,name\n"test","PET,MRI","A ""Dataset"""\n"test4","MRI","Another Dataset"',
+    )
+  })
+})