@openneuro/app 4.5.0 → 4.6.0-alpha.1

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

@@ -0,0 +1,148 @@
+import React, { useState } from 'react'
+import PropTypes from 'prop-types'
+import semver from 'semver'
+import SnapshotDataset from '../mutations/snapshot'
+import EditList from '../fragments/edit-list.jsx'
+import { Button } from '@openneuro/components/button'
+import { DatasetPageBorder } from './styles/dataset-page-border'
+import { HeaderRow4 } from './styles/header-row'
+import FileView from '../files/file-view'
+import styled from '@emotion/styled'
+
+const FormRow = styled.div`
+  margin-top: 0;
+  margin-bottom: 1.3em;
+`
+
+export const NoErrors = ({ issues, children }) => {
+  const noErrors =
+    issues && issues.filter(issue => issue.severity === 'error').length === 0
+  // zero authors will cause DOI minting to fail
+  const hasAuthor =
+    issues && issues.filter(issue => issue.code === 113).length === 0
+  if (noErrors && hasAuthor) {
+    return children
+  } else {
+    const correctErrorsMessage =
+      'BIDS validation must be complete and all errors corrected'
+    const noAuthorMessage =
+      '"Authors" must include at least one entry in dataset_description.json'
+    const includedMessages = []
+    if (!noErrors) includedMessages.push(correctErrorsMessage)
+    if (!hasAuthor) includedMessages.push(noAuthorMessage)
+    return (
+      <span className="text-danger">
+        {`${includedMessages.join(' and ')} to create a version`}
+      </span>
+    )
+  }
+}
+
+const SnapshotRoute = ({ datasetId, snapshots, issues, description }) => {
+  const [changes, setChanges] = useState([])
+  const [semanticLevel, setSemanticLevel] = useState('patch')
+  const draftLicense = (description && description.License) || 'none'
+  const requiredLicense = 'CC0'
+  const updateToCC0 = draftLicense !== requiredLicense
+
+  const latestSnapshot = snapshots.length && snapshots[snapshots.length - 1]
+  const newVersion =
+    snapshots.length && semver.valid(latestSnapshot.tag)
+      ? semver.inc(latestSnapshot.tag, semanticLevel)
+      : '1.0.0'
+
+  const majorActive = semanticLevel === 'major' && 'active'
+  const minorActive = semanticLevel === 'minor' && 'active'
+  const patchActive = semanticLevel === 'patch' && 'active'
+
+  return (
+    <DatasetPageBorder>
+      <div className="dataset-snapshot-form">
+        <div className="dataset-form-body">
+          <HeaderRow4>New Version</HeaderRow4>
+          {updateToCC0 && (
+            <p>
+              <strong>Notice:</strong> The current license{' '}
+              <i>&quote;{draftLicense}&quote;</i> will be updated to
+              &quote;CC0&quote; when the version is created. Please see FAQ item
+              &quote;Are there any restrictions on the uploaded data?&quote; for
+              details.
+            </p>
+          )}
+          <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.
+          </p>
+          <FormRow className="snapshot-input-group">
+            {newVersion}
+            <div className="input-group-btn">
+              <Button
+                secondary={true}
+                label="Major"
+                size="xsmall"
+                className={`btn btn-default ${majorActive}`}
+                onClick={() => setSemanticLevel('major')}
+              />
+              <Button
+                secondary={true}
+                label="Minor"
+                size="xsmall"
+                className={`btn btn-default ${minorActive}`}
+                onClick={() => setSemanticLevel('minor')}
+              />
+              <Button
+                secondary={true}
+                label="Patch"
+                size="xsmall"
+                className={`btn btn-default ${patchActive}`}
+                onClick={() => setSemanticLevel('patch')}
+              />
+            </div>
+          </FormRow>
+          {latestSnapshot ? (
+            <FormRow>
+              <HeaderRow4>Current Changelog</HeaderRow4>
+              <FileView
+                datasetId={datasetId}
+                snapshotTag={latestSnapshot.tag}
+                path="CHANGES"
+              />
+            </FormRow>
+          ) : null}
+          <HeaderRow4>New Changelog</HeaderRow4>
+          <p>Add CHANGES file lines describing the new version.</p>
+          <EditList
+            placeholder="Enter new changes here..."
+            elements={changes}
+            setElements={setChanges}
+          />
+        </div>
+        <NoErrors issues={issues}>
+          {changes.length ? null : (
+            <small className="text-danger">
+              You must add at least one change message to create a new version
+            </small>
+          )}
+        </NoErrors>
+        <div className="dataset-form-controls">
+          <SnapshotDataset
+            datasetId={datasetId}
+            tag={newVersion}
+            changes={changes}
+            disabled={changes.length < 1}
+          />
+        </div>
+      </div>
+    </DatasetPageBorder>
+  )
+}
+
+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

@@ -0,0 +1,8 @@
+import styled from '@emotion/styled'
+
+export const DatasetPageBorder = styled.div`
+  border: 1px solid #ccc;
+  border-radius: 4px;
+  padding: 20px 15px;
+  margin-bottom: 25px;
+`

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

@@ -0,0 +1,8 @@
+import styled from '@emotion/styled'
+
+export const DatasetPageTabContainer = styled.div`
+  display: flex;
+  justify-content: space-between;
+  margin-bottom: 50px;
+  flex-direction: column;
+`

package/src/scripts/dataset/routes/styles/draft-background.tsx

@@ -0,0 +1,7 @@
+import styled from '@emotion/styled'
+
+export const DraftBackground = styled.div`
+  background: #fff;
+  background-image: radial-gradient(#ddd 1px, #fff 1px);
+  background-size: 20px 20px;
+`

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

@@ -0,0 +1,12 @@
+import styled from '@emotion/styled'
+
+const headerRowStyle = `
+  margin-top: 0;
+  margin-bottom: 1.3em;
+`
+
+export const HeaderRow2 = styled.h2(headerRowStyle)
+
+export const HeaderRow3 = styled.h3(headerRowStyle)
+
+export const HeaderRow4 = styled.h4(headerRowStyle)

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

@@ -0,0 +1,88 @@
+import React from 'react'
+import { Route, Switch } from 'react-router-dom'
+import { DatasetDefault } from './dataset-default'
+import AdminDataset from './admin-datalad'
+import DeletePage from './delete-page'
+import DownloadDataset from './download-dataset'
+import Publish from './publish'
+import Share from './manage-permissions'
+import Snapshot from './snapshot'
+import AddMetadata from './add-metadata'
+import FileDisplay from '../files/file-display'
+
+export const TabRoutesDraft = ({ dataset, hasEdit }) => {
+  return (
+    <Switch>
+      <Route
+        exact
+        path="/datasets/:datasetId"
+        component={() => <DatasetDefault dataset={dataset} hasEdit={hasEdit} />}
+      />
+      <Route
+        exact
+        path="/datasets/:datasetId/download"
+        component={() => (
+          <DownloadDataset
+            worker={dataset.worker}
+            datasetPermissions={dataset.permissions}
+          />
+        )}
+      />
+      <Route
+        exact
+        path="/datasets/:datasetId/delete"
+        component={() => <DeletePage dataset={dataset} />}
+      />
+      <Route
+        exact
+        path="/datasets/:datasetId/admin"
+        component={() => <AdminDataset dataset={dataset} />}
+      />
+      <Route
+        exact
+        path="/datasets/:datasetId/publish"
+        component={() => (
+          <Publish datasetId={dataset.id} metadata={dataset.metadata} />
+        )}
+      />
+      <Route
+        exact
+        path="/datasets/:datasetId/snapshot"
+        component={() => (
+          <Snapshot
+            datasetId={dataset.id}
+            snapshots={dataset.snapshots}
+            issues={dataset.draft.issues}
+            description={dataset.draft.description}
+          />
+        )}
+      />
+      <Route
+        exact
+        path="/datasets/:datasetId/share"
+        component={() => (
+          <Share
+            datasetId={dataset.id}
+            permissions={dataset.permissions}
+            reviewers={dataset.reviewers}
+          />
+        )}
+      />
+      <Route
+        path="/datasets/:datasetId/file-display/:filePath"
+        render={({
+          match: {
+            params: { datasetId, filePath },
+          },
+        }) => {
+          return <FileDisplay datasetId={datasetId} filePath={filePath} />
+        }}
+      />
+      <Route
+        exact
+        path="/datasets/:datasetId/metadata"
+        component={() => <AddMetadata dataset={dataset} />}
+      />
+    </Switch>
+  )
+}

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

@@ -0,0 +1,57 @@
+import React from 'react'
+import { Route, Switch } from 'react-router-dom'
+import { SnapshotDefault } from './snapshot-default'
+import DownloadDataset from './download-dataset'
+import { DeprecateSnapshotPage } from './deprecate-snapshot-page'
+import FileDisplay from '../files/file-display'
+import AddMetadata from './add-metadata'
+
+export const TabRoutesSnapshot = ({ dataset, snapshot }) => {
+  return (
+    <Switch>
+      <Route
+        exact
+        path="/datasets/:datasetId/versions/:snapshotId"
+        component={() => (
+          <SnapshotDefault dataset={dataset} snapshot={snapshot} />
+        )}
+      />
+      <Route
+        exact
+        path="/datasets/:datasetId/versions/:snapshotId/download"
+        component={() => (
+          <DownloadDataset
+            worker={dataset.worker}
+            datasetPermissions={dataset.permissions}
+          />
+        )}
+      />
+      <Route
+        exact
+        path="/datasets/:datasetId/versions/:snapshotTag/deprecate"
+        component={() => <DeprecateSnapshotPage />}
+      />
+      <Route
+        path="/datasets/:datasetId/versions/:snapshotTag/file-display/:filePath"
+        render={({
+          match: {
+            params: { datasetId, filePath, snapshotTag },
+          },
+        }) => {
+          return (
+            <FileDisplay
+              datasetId={datasetId}
+              snapshotTag={snapshotTag}
+              filePath={filePath}
+            />
+          )
+        }}
+      />
+      <Route
+        exact
+        path="/datasets/:datasetId/versions/:snapshotTag/metadata"
+        component={() => <AddMetadata dataset={dataset} />}
+      />
+    </Switch>
+  )
+}

package/src/scripts/{refactor_2021/dataset → dataset}/snapshot-container.tsx

@@ -1,16 +1,14 @@
 import React from 'react'
 import { gql, useQuery } from '@apollo/client'
-import DatasetQueryContext from '../../datalad/dataset/dataset-query-context.js'
-import Markdown from 'markdown-to-jsx'
+import { DatasetPageTabContainer } from './routes/styles/dataset-page-tab-container'
+import DatasetQueryContext from '../datalad/dataset/dataset-query-context.js'
 import { Link, useLocation } from 'react-router-dom'
 import pluralize from 'pluralize'
 import formatDistanceToNow from 'date-fns/formatDistanceToNow'
 import parseISO from 'date-fns/parseISO'
 
-import Files from './files'
 import Validation from '../validation/validation.jsx'
-import { config } from '../../config'
-import Comments from './comments/comments.jsx'
+import { config } from '../config'
 import DatasetCitation from './fragments/dataset-citation.jsx'
 import { DatasetAlertVersion } from './fragments/dataset-alert-version'
 
@@ -35,13 +33,12 @@ import {
 } from '../authentication/profile'
 import { useCookies } from 'react-cookie'
 
-import { ReadMore } from '@openneuro/components/read-more'
-
 import { FollowDataset } from './mutations/follow'
 import { StarDataset } from './mutations/star'
 
-import { SNAPSHOT_FIELDS } from '../../datalad/dataset/dataset-query-fragments.js'
+import { SNAPSHOT_FIELDS } from '../datalad/dataset/dataset-query-fragments.js'
 import { DOILink } from './fragments/doi-link'
+import { TabRoutesSnapshot } from './routes/tab-routes-snapshot'
 
 const formatDate = dateObject =>
   new Date(dateObject).toISOString().split('T')[0]
@@ -111,7 +108,7 @@ const SnapshotContainer: React.FC<SnapshotContainerProps> = ({
           <div className="col col-8 col-lg">
             {summary && (
               <DatasetHeaderMeta
-                size={summary.size}
+                size={snapshot.size}
                 totalFiles={summary.totalFiles}
                 datasetId={datasetId}
               />
@@ -168,39 +165,9 @@ const SnapshotContainer: React.FC<SnapshotContainerProps> = ({
                 isDatasetAdmin={isDatasetAdmin}
               />
             </div>
-            <ReadMore
-              fileTree={true}
-              id="collapse-tree"
-              expandLabel="Read More"
-              collapseLabel="Collapse">
-              <Files
-                datasetId={datasetId}
-                snapshotTag={snapshot.tag}
-                datasetName={description.Name}
-                files={snapshot.files}
-                editMode={false}
-                datasetPermissions={dataset.permissions}
-              />
-            </ReadMore>
-            <MetaDataBlock
-              heading="README"
-              item={
-                <ReadMore
-                  id="readme"
-                  expandLabel="Read More"
-                  collapseLabel="Collapse">
-                  <Markdown>
-                    {snapshot.readme == null ? 'N/A' : snapshot.readme}
-                  </Markdown>
-                </ReadMore>
-              }
-              className="dataset-readme markdown-body"
-            />
-            <Comments
-              datasetId={dataset.id}
-              uploader={dataset.uploader}
-              comments={dataset.comments}
-            />
+            <DatasetPageTabContainer>
+              <TabRoutesSnapshot dataset={dataset} snapshot={snapshot} />
+            </DatasetPageTabContainer>
           </div>
           <div className="col sidebar">
             <MetaDataBlock

package/src/scripts/{refactor_2021 → errors}/freshdesk-widget.jsx

@@ -1,7 +1,7 @@
 import React from 'react'
 import PropTypes from 'prop-types'
 import { useCookies } from 'react-cookie'
-import { getProfile } from './authentication/profile'
+import { getProfile } from '../authentication/profile'
 import { config } from '../config'
 
 const buildCustomQuery = (customText, prepopulatedFields) => {

package/src/scripts/errors/freshdeskInterface.jsx

@@ -1,5 +1,5 @@
 import React, { useState } from 'react'
-import FreshdeskWidget from '../datalad/fragments/freshdesk-widget.jsx'
+import FreshdeskWidget from './freshdesk-widget.jsx'
 import {
   Overlay,
   ModalContainer,

package/src/scripts/index.tsx

@@ -1,10 +1,10 @@
 import React from 'react'
-import Uploader from './refactor_2021/uploader/uploader.jsx'
+import Uploader from './uploader/uploader.jsx'
 import Routes from './routes'
-import HeaderContainer from './refactor_2021/containers/header'
-import FooterContainer from './refactor_2021/containers/footer'
-import { SearchParamsProvider } from './refactor_2021/search/search-params-ctx'
-import { UserModalOpenProvider } from './refactor_2021/user-login-modal-ctx'
+import HeaderContainer from './common/containers/header'
+import FooterContainer from './common/containers/footer'
+import { SearchParamsProvider } from './search/search-params-ctx'
+import { UserModalOpenProvider } from './utils/user-login-modal-ctx'
 
 import '../assets/email-header.png'
 

package/src/scripts/pages/admin/admin.jsx

@@ -4,7 +4,7 @@ import React from 'react'
 import { Redirect, Switch, Route, NavLink } from 'react-router-dom'
 import Users from './users.jsx'
 import FlaggedFiles from './flagged-files.jsx'
-import AdminUser from '../../refactor_2021/authentication/admin-user.jsx'
+import AdminUser from '../../authentication/admin-user.jsx'
 
 class Dashboard extends React.Component {
   // life cycle events --------------------------------------------------

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 '../../refactor_2021/authentication/profile.js'
+import { getProfile } from '../../authentication/profile.js'
 import { useCookies } from 'react-cookie'
 import { USER_FRAGMENT } from './user-fragment'
 

package/src/scripts/{refactor_2021/user → pages}/api.jsx

@@ -2,9 +2,9 @@ import React from 'react'
 import { Loading } from '@openneuro/components/loading'
 import { CopyToClipboard } from 'react-copy-to-clipboard'
 import Helmet from 'react-helmet'
-import { pageTitle } from '../../resources/strings.js'
+import { pageTitle } from '../resources/strings.js'
 import { Button } from '@openneuro/components/button'
-import { config } from '../../config'
+import { config } from '../config'
 
 /**
  * Create API Key

package/src/scripts/{faq → pages/faq}/__tests__/__snapshots__/faq.spec.jsx.snap

@@ -221,7 +221,7 @@ exports[`faq/faq/Faq renders successfully 1`] = `
           <span>
             We offer two options for uploading data onto OpenNeuro. The first is to upload via the web interface. The second is to upload via our 
             <a
-              href="https://docs.openneuro.org/packages-openneuro-cli-readme"
+              href="https://docs.openneuro.org/openneuro-packages-openneuro-cli-readme"
             >
               command-line utility tool
             </a>

package/src/scripts/{faq → pages/faq}/faq-content.js

@@ -48,8 +48,7 @@ export const faq = [
       '[Ultimate consent form GDPR edition](https://open-brain-consent.readthedocs.io/en/stable/gdpr/ultimate_gdpr.html).',
   },
   {
-    faq:
-      'Do I need to format my data in some special way before uploading it to OpenNeuro?',
+    faq: 'Do I need to format my data in some special way before uploading it to OpenNeuro?',
     answer:
       'Yes! OpenNeuro only accepts data in the Brain Imaging Data Structure ' +
       '(BIDS) format. You can read about it more at ' +
@@ -58,8 +57,7 @@ export const faq = [
       'post them at [neurostars.org](https://neurostars.org/tags/bids).',
   },
   {
-    faq:
-      'Do I need to remove facial features from structural images before uploading the data?',
+    faq: 'Do I need to remove facial features from structural images before uploading the data?',
     answer:
       'OpenNeuro does not accept datasets that have not been defaced for ' +
       'privacy considerations. Datasets found to not have been defaced will ' +
@@ -80,7 +78,7 @@ export const faq = [
     answer:
       'We offer two options for uploading data onto OpenNeuro. ' +
       'The first is to upload via the web interface. ' +
-      'The second is to upload via our [command-line utility tool](https://docs.openneuro.org/packages-openneuro-cli-readme)',
+      'The second is to upload via our [command-line utility tool](https://docs.openneuro.org/openneuro-packages-openneuro-cli-readme)',
   },
   {
     faq: 'Why can I not use CC-BY (or other CC license)?',

package/src/scripts/{faq → pages/faq}/faq.jsx

@@ -4,7 +4,7 @@ import React from 'react'
 import Markdown from 'markdown-to-jsx'
 import { faq } from './faq-content'
 import Helmet from 'react-helmet'
-import { pageTitle } from '../resources/strings.js'
+import { pageTitle } from '../../resources/strings.js'
 
 class Faq extends React.Component {
   render() {

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

@@ -1,11 +1,11 @@
 import React, { useState } from 'react'
 import styled from '@emotion/styled'
-import { ImportDatasetMutation } from '../refactor_2021/dataset/mutations/import-dataset'
+import { ImportDatasetMutation } from '../dataset/mutations/import-dataset'
 import { useLocation } from 'react-router-dom'
-import LoggedIn from '../refactor_2021/authentication/logged-in'
-import LoggedOut from '../refactor_2021/authentication/logged-out'
-import { testAffirmed } from '../refactor_2021/uploader/upload-disclaimer'
-import { UploadDisclaimerInput } from '../refactor_2021/uploader/upload-disclaimer-input'
+import LoggedIn from '../authentication/logged-in'
+import LoggedOut from '../authentication/logged-out'
+import { testAffirmed } from '../uploader/upload-disclaimer'
+import { UploadDisclaimerInput } from '../uploader/upload-disclaimer-input'
 
 function useQuery() {
   const { search } = useLocation()

package/src/scripts/routes.tsx

@@ -2,14 +2,14 @@ import React from 'react'
 import { Route, Switch, Redirect } from 'react-router-dom'
 
 // TODO - Re-enable code splitting these when we can
-import Dataset from './refactor_2021/dataset/draft-snapshot-routes'
+import Dataset from './dataset/draft-snapshot-routes'
 //import PreRefactorDatasetProps from './dataset/dataset-pre-refactor-container'
 
 import { FAQS } from '@openneuro/components/faqs'
 import FrontPageContainer from './pages/front-page/front-page'
 import Admin from './pages/admin/admin'
-import SearchRoutes from './refactor_2021/search/search-routes'
-import APIKey from './refactor_2021/user/api'
+import SearchRoutes from './search/search-routes'
+import APIKey from './pages/api'
 import ErrorRoute from './errors/errorRoute'
 import { PETRedirect } from './pages/pet-redirect'
 import Citation from './pages/citation-page'