Merge branch 'nickakhmetov/hmp-194-lint-config' into nickakhmetov/hmp…

…-194-lint-fixes
hubmapconsortium · Jul 5, 2023 · f7f6779 · f7f6779
2 parents 639673a + 74b7316
commit f7f6779
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diff --git a/CHANGELOG-fair-data-messaging.md b/CHANGELOG-fair-data-messaging.md
@@ -0,0 +1 @@
+- Add messaging for fair data principles to homepage, vitessce, and the dataset file browser.
diff --git a/CHANGELOG-fix-homepage-vitessce-link.md b/CHANGELOG-fix-homepage-vitessce-link.md
@@ -0,0 +1 @@
+- Fixed homepage Vitessce demonstration link.
diff --git a/CHANGELOG-fix-provenance.md b/CHANGELOG-fix-provenance.md
@@ -0,0 +1 @@
+- Fix flask data context destructuring to restore provenance features.
diff --git a/CHANGELOG-hmp-103-add-tests.md b/CHANGELOG-hmp-103-add-tests.md
diff --git a/CHANGELOG-hmp-154.md b/CHANGELOG-hmp-154.md
diff --git a/CHANGELOG-hmp-156-update-text-for-access-permissions-for-workspaces.md b/CHANGELOG-hmp-156-update-text-for-access-permissions-for-workspaces.md
@@ -0,0 +1 @@
+- Update workspaces landing page messaging to instruct users without membership in the workspaces Globus group to request access.
diff --git a/CHANGELOG-hmp-181-remove-search-feature.md b/CHANGELOG-hmp-181-remove-search-feature.md
diff --git a/CHANGELOG-hmp-182-lineup.md b/CHANGELOG-hmp-182-lineup.md
diff --git a/CHANGELOG-hmp-20-trim-sub-header.md b/CHANGELOG-hmp-20-trim-sub-header.md
diff --git a/CHANGELOG-hmp-207-fix-line-break.md b/CHANGELOG-hmp-207-fix-line-break.md
@@ -0,0 +1 @@
+- Adjusted publication header to appear on one line only.
diff --git a/CHANGELOG-hotfix.md b/CHANGELOG-hotfix.md
@@ -0,0 +1 @@
+- Fixed changelog file format.
diff --git a/CHANGELOG-lint-updates.md b/CHANGELOG-lint-updates.md
@@ -1,3 +1,3 @@
-- Updated project ESLint configuration and dependencies
-- Removed Babel
-- Introduced TypeScript
+- Update project ESLint configuration and dependencies.
+- Remove Babel.
+- Introduce TypeScript.
diff --git a/CHANGELOG-remove-non-datasets-from-datasets-charts.md b/CHANGELOG-remove-non-datasets-from-datasets-charts.md
diff --git a/CHANGELOG-remove-support-files-from-publications.md b/CHANGELOG-remove-support-files-from-publications.md
diff --git a/context/app/markdown/CHANGELOG.md b/context/app/markdown/CHANGELOG.md
@@ -1,3 +1,24 @@
+## v0.73.1 - 2023-06-28
+
+- Adjust page-wide error boundary to prevent error messages from overflowing
+- Add error boundary around Vitessce visualization to keep Vitessce errors from crashing full page
+- Update Cypress testing suite.
+- Add end-to-end tests for publication pages.
+- Upgrade from Webpack 4 -> 5
+- Upgrade from Storybook 6 -> 7
+- Migrate from babel-loader -> swc-loader
+- Migrate to @swc/jest test runner
+- Removed search feature from home page.
+- Added vertical padding to the count section.
+- Formatted 10k+ homepage entity counts to nearest thousands place. (10,500 -> 10.5k)
+- Added tooltip hover feature on count entities.  
+ - Ensure that lineup pages' data all have necessary keys and report any incomplete metadata in console
+- Trim publication sub header characters to 100 max with trailing ellisis.
+- Bump `portal-visualization` to 0.0.12.
+- Remove publications and other dataset subtypes from dataset charts.
+- Remove globus link for lifted publication ancillary entities on publication pages.
+
+
 ## v0.73.0 - 2023-06-20
 
 - Fix donor metadata table display.

diff --git a/context/app/markdown/dependencies.md b/context/app/markdown/dependencies.md
@@ -7,7 +7,7 @@ The services the portal relies on are [listed separately](/services).
 ## Git submodules
 
 ```
- 79cab515ee56184a824c6755ff25fc6e2d1a3a65 context/ingest-validation-tools (v0.0.13-23-g79cab51)
+ 79cab515ee56184a824c6755ff25fc6e2d1a3a65 context/ingest-validation-tools (v0.0.13-23-g79cab515)
 ```
 
 ## Python packages
@@ -27,7 +27,7 @@ hubmap-api-py-client>=0.0.9
 hubmap-commons>=2.0.12
 
 # Plain "git+https://github.com/..." references can't be hashed, so we point to a release zip instead.
-https://github.com/hubmapconsortium/portal-visualization/archive/refs/tags/0.0.11.zip
+https://github.com/hubmapconsortium/portal-visualization/archive/refs/tags/0.0.12.zip
 
 # Security warning for older versions;
 # Can be removed when commons drops prov dependency.
@@ -69,7 +69,7 @@ lxml>=4.9.1
 "date-fns": "^2.27.0",
 "fast-deep-equal": "^3.1.3",
 "fromentries": "^1.2.0",
-"html-webpack-plugin": "^4.3.0",
+"html-webpack-plugin": "^5.5.3",
 "immer": "^9.0.6",
 "intersection-observer": "^0.11.0",
 "lineupjsx": "^4.0.0",
@@ -93,8 +93,11 @@ lxml>=4.9.1
 "react-vega": "^7.3.0",
 "sass": "^1.53.0",
 "searchkit": "^2.4.1-alpha.4",
+"stream-browserify": "^3.0.0",
 "styled-components": "^5.1.0",
+"swc-loader": "^0.2.3",
 "swr": "^2.1.5",
+"timers-browserify": "^2.0.12",
 "typeface-inter": "^3.12.0",
 "universal-cookie": "^4.0.3",
 "use-debounce": "^8.0.1",

diff --git a/context/app/static/js/components/App.jsx b/context/app/static/js/components/App.jsx
@@ -31,7 +31,7 @@ function App(props) {
   const { endpoints, globalAlertMd } = flaskData;
   delete flaskData.endpoints;
   delete flaskData.globalAlertMd;
-  const isWorkspacesUser = userGroups.includes('Workspaces') || workspacesUsers.includes(userEmail);
+  const isWorkspacesUser = userGroups?.includes('Workspaces') || workspacesUsers.includes(userEmail);
 
   return (
     <Providers

diff --git a/context/app/static/js/components/Header/Dropdown/Dropdown.jsx b/context/app/static/js/components/Header/Dropdown/Dropdown.jsx
@@ -9,13 +9,13 @@ import MenuList from '@material-ui/core/MenuList';
 
 import { OffsetPopper } from './style';
 
-function Dropdown({ title, children, menuListId }) {
+function Dropdown({ title, children, menuListId, ...rest }) {
   const [open, toggle] = useReducer((v) => !v, false);
   const anchorRef = useRef(null);
 
   return (
     <>
-      <Button ref={anchorRef} onClick={toggle} style={{ color: 'white' }}>
+      <Button ref={anchorRef} onClick={toggle} style={{ color: 'white' }} {...rest}>
         {title}
         {open ? <ArrowDropUpIcon /> : <ArrowDropDownIcon />}
       </Button>

diff --git a/context/app/static/js/components/Header/UserLinks/UserLinks.jsx b/context/app/static/js/components/Header/UserLinks/UserLinks.jsx
@@ -11,14 +11,19 @@ function UserLinks({ isAuthenticated, userEmail }) {
   const { isWorkspacesUser } = useAppContext();
 
   return (
-    <Dropdown title={<TruncatedSpan>{isAuthenticated ? userEmail || 'User' : 'User Profile'}</TruncatedSpan>}>
+    <Dropdown
+      title={<TruncatedSpan>{isAuthenticated ? userEmail || 'User' : 'User Profile'}</TruncatedSpan>}
+      data-testid="user-profile-dropdown"
+    >
       <DropdownLink href="/my-lists">My Lists</DropdownLink>
       {isWorkspacesUser && <DropdownLink href="/workspaces">My Workspaces</DropdownLink>}
       <StyledDivider />
       {isAuthenticated ? (
         <WarningDropdownLink href="/logout">Log Out</WarningDropdownLink>
       ) : (
-        <DropdownLink href="/login">Log In</DropdownLink>
+        <DropdownLink href="/login" data-testid="login-link">
+          Log In
+        </DropdownLink>
       )}
     </Dropdown>
   );

diff --git a/context/app/static/js/components/detailPage/files/FileBrowser/FileBrowser.jsx b/context/app/static/js/components/detailPage/files/FileBrowser/FileBrowser.jsx
@@ -7,6 +7,8 @@ import TableRow from '@material-ui/core/TableRow';
 import TableBody from '@material-ui/core/TableBody';
 import Chip from '@material-ui/core/Chip';
 
+import HubmapDataFooter from 'js/components/detailPage/files/HubmapDataFooter';
+import { useFlaskDataContext } from 'js/components/Contexts';
 import useFilesStore from 'js/stores/useFilesStore';
 import { relativeFilePathsToTree } from './utils';
 import FileBrowserNode from '../FileBrowserNode';
@@ -19,6 +21,9 @@ const filesStoreSelector = (state) => ({
 
 function FileBrowser({ files }) {
   const { displayOnlyQaQc, toggleDisplayOnlyQaQc } = useFilesStore(filesStoreSelector);
+  const {
+    entity: { entity_type },
+  } = useFlaskDataContext();
 
   const fileTrees = useMemo(
     () => ({
@@ -29,31 +34,34 @@ function FileBrowser({ files }) {
   );
 
   return (
-    <StyledTableContainer component={Paper}>
-      <ChipWrapper>
-        <Chip
-          label="Show QA Files Only"
-          clickable
-          onClick={toggleDisplayOnlyQaQc}
-          color={displayOnlyQaQc ? 'primary' : undefined}
-          icon={displayOnlyQaQc ? <DoneIcon /> : undefined}
-          component="button"
-          disabled={Object.keys(fileTrees.qa).length === 0}
-        />
-      </ChipWrapper>
-      <Table data-testid="file-browser">
-        <HiddenTableHead>
-          <TableRow>
-            <td>Name</td>
-            <td>Type</td>
-            <td>Size</td>
-          </TableRow>
-        </HiddenTableHead>
-        <TableBody>
-          <FileBrowserNode fileSubTree={displayOnlyQaQc ? fileTrees.qa : fileTrees.all} depth={0} />
-        </TableBody>
-      </Table>
-    </StyledTableContainer>
+    <>
+      <StyledTableContainer component={Paper}>
+        <ChipWrapper>
+          <Chip
+            label="Show QA Files Only"
+            clickable
+            onClick={toggleDisplayOnlyQaQc}
+            color={displayOnlyQaQc ? 'primary' : undefined}
+            icon={displayOnlyQaQc ? <DoneIcon /> : undefined}
+            component="button"
+            disabled={Object.keys(fileTrees.qa).length === 0}
+          />
+        </ChipWrapper>
+        <Table data-testid="file-browser">
+          <HiddenTableHead>
+            <TableRow>
+              <td>Name</td>
+              <td>Type</td>
+              <td>Size</td>
+            </TableRow>
+          </HiddenTableHead>
+          <TableBody>
+            <FileBrowserNode fileSubTree={displayOnlyQaQc ? fileTrees.qa : fileTrees.all} depth={0} />
+          </TableBody>
+        </Table>
+      </StyledTableContainer>
+      {['Dataset', 'Support'].includes(entity_type) && <HubmapDataFooter />}
+    </>
   );
 }
 

diff --git a/context/app/static/js/components/detailPage/files/FileBrowser/FileBrowser.spec.js b/context/app/static/js/components/detailPage/files/FileBrowser/FileBrowser.spec.js
@@ -2,6 +2,7 @@ import React from 'react';
 import userEvent from '@testing-library/user-event';
 import { render, screen } from 'test-utils/functions';
 
+import { FlaskDataContext } from 'js/components/Contexts';
 import DetailContext from 'js/components/detailPage/context';
 import FileBrowser from './FileBrowser';
 import FilesContext from '../Files/context';
@@ -12,12 +13,15 @@ const uuid = 'fakeuuid';
 
 const detailContext = { uuid };
 const filesContext = { openDUA: fakeOpenDUA, hasAgreedToDUA: 'fakedua' };
+const flaskDataContext = { entity: { entity_type: 'Dataset' } };
 
 function FilesProviders({ children }) {
   return (
-    <DetailContext.Provider value={detailContext}>
-      <FilesContext.Provider value={filesContext}>{children}</FilesContext.Provider>
-    </DetailContext.Provider>
+    <FlaskDataContext.Provider value={flaskDataContext}>
+      <DetailContext.Provider value={detailContext}>
+        <FilesContext.Provider value={filesContext}>{children}</FilesContext.Provider>
+      </DetailContext.Provider>
+    </FlaskDataContext.Provider>
   );
 }
 

diff --git a/context/app/static/js/components/detailPage/files/Files/Files.spec.js b/context/app/static/js/components/detailPage/files/Files/Files.spec.js
@@ -4,6 +4,7 @@ import { render, screen, waitForElementToBeRemoved, appProviderEndpoints } from
 import { rest } from 'msw';
 import { setupServer } from 'msw/node';
 
+import { FlaskDataContext } from 'js/components/Contexts';
 import DetailContext from 'js/components/detailPage/context';
 import Files from './Files';
 
@@ -65,9 +66,11 @@ test('handles DUA flow', async () => {
   ];
 
   render(
-    <DetailProvider>
-      <Files files={testFiles} uuid={uuid} hubmap_id="fakedoi" />
-    </DetailProvider>,
+    <FlaskDataContext.Provider value={{ entity: { entity_type: 'Dataset' } }}>
+      <DetailProvider>
+        <Files files={testFiles} uuid={uuid} hubmap_id="fakedoi" />
+      </DetailProvider>
+    </FlaskDataContext.Provider>,
   );
 
   userEvent.click(screen.getByRole('button', { name: 'fake5.txt' }));

diff --git a/context/app/static/js/components/detailPage/files/HubmapDataFooter/HubmapDataFooter.jsx b/context/app/static/js/components/detailPage/files/HubmapDataFooter/HubmapDataFooter.jsx
@@ -0,0 +1,35 @@
+import React from 'react';
+
+import SectionFooter from 'js/shared-styles/sections/SectionFooter';
+import { SecondaryBackgroundTooltip } from 'js/shared-styles/tooltips';
+import { StyledInfoIcon } from './style';
+
+const tooltipText =
+  'HuBMAP data is managed and published in the Data Portal and Human Reference Atlas according to FAIR Principles, including standardized processing with reproducible pipelines. HuBMAP data may also be processed by other methods in scientific results published by HuBMAP consortium collaborations.';
+
+function DataCaptionWithTooltip() {
+  return (
+    <>
+      About this Data
+      <SecondaryBackgroundTooltip title={tooltipText}>
+        <StyledInfoIcon color="primary" />
+      </SecondaryBackgroundTooltip>
+    </>
+  );
+}
+
+function HubmapDataFooter({ items = [] }) {
+  return (
+    <SectionFooter
+      items={[
+        ...items,
+        {
+          key: 'hubmap-data-tooltip',
+          component: <DataCaptionWithTooltip />,
+        },
+      ]}
+    />
+  );
+}
+
+export default HubmapDataFooter;
diff --git a/context/app/static/js/components/detailPage/files/HubmapDataFooter/index.js b/context/app/static/js/components/detailPage/files/HubmapDataFooter/index.js
@@ -0,0 +1,3 @@
+import HubmapDataFooter from './HubmapDataFooter';
+
+export default HubmapDataFooter;
diff --git a/context/app/static/js/components/detailPage/files/HubmapDataFooter/style.js b/context/app/static/js/components/detailPage/files/HubmapDataFooter/style.js
@@ -0,0 +1,8 @@
+import styled from 'styled-components';
+import { InfoIcon } from 'js/shared-styles/icons';
+
+const StyledInfoIcon = styled(InfoIcon)`
+  margin-left: ${(props) => props.theme.spacing(0.5)}px;
+`;
+
+export { StyledInfoIcon };
diff --git a/context/app/static/js/components/detailPage/provenance/ProvTabs/ProvTabs.jsx b/context/app/static/js/components/detailPage/provenance/ProvTabs/ProvTabs.jsx
@@ -8,7 +8,9 @@ import ProvAnalysisDetails from '../ProvAnalysisDetails';
 import { hasDataTypes } from './utils';
 
 function ProvTabs({ provData }) {
-  const { uuid, metadata, entity_type, ancestors, data_types } = useFlaskDataContext();
+  const {
+    entity: { uuid, metadata, entity_type, ancestors, data_types },
+  } = useFlaskDataContext();
 
   const [open, setOpen] = React.useState(0);
   const handleChange = (event, newValue) => {

diff --git a/context/app/static/js/components/detailPage/summary/SummaryData/SummaryData.jsx b/context/app/static/js/components/detailPage/summary/SummaryData/SummaryData.jsx
@@ -24,17 +24,19 @@ function SummaryData({
   children,
   mapped_external_group_name,
 }) {
+  const isPublication = entity_type === 'Publication';
+  const LeftTextContainer = isPublication ? React.Fragment : 'div';
   return (
     <>
       <SummaryTitle data-testid="entity-type">{entity_type}</SummaryTitle>
       <SpacedSectionButtonRow
         leftText={
-          <div>
+          <LeftTextContainer>
             <StyledTypography variant="h2" data-testid="entity-title">
               {title}
             </StyledTypography>
             {children && <FlexEnd data-testid="summary-data-parent">{children}</FlexEnd>}
-          </div>
+          </LeftTextContainer>
         }
         buttons={
           <FlexEnd>