Unified Datasets (#3464)

* Add changelog * NickAkhmetov/CAT-677 Unified Prov Graph (#3458) Co-authored-by: John Conroy <[email protected]> Co-authored-by: Tabassum Kakar <[email protected]> Co-authored-by: tkakar <[email protected]> Co-authored-by: Austen Money <[email protected]> fix table tabs (#3466) Fix incorrect URL structure in gene search results (#3467) * John conroy/update table of contents CAT-755 (#3473) * Convert table of contents to typescript * Convert route to ts and add boundaries * Fix styling so top works * Add icons map * Fix responsiveness * Handle sub links * Update marker color * Style table of contents * Add icons to table of contents * Add processed datasets for table of contents * Add loading state * Adjust padding per Tiffany feedback * Update style per Tiffany's feedback * Open toc accordions by default * Add visualization to processed data sections in toc * Add processed sections and refactor * Update changelog * Update organ page to use layout * Switch to derived data per tiffany's feedback * Use height props * Pull utils/hooks/types into files * Add a use callback for toc click handler * Pull find active index into hook * Consolidate styles * Use system props --------- Co-authored-by: John Conroy <[email protected]> * NickAkhmetov/CAT-776 Dataset Relationships diagram (#3481) * John conroy/summary bar (#3501) * Remove placeholder for undefined items * Create entity header action buttons * Add workspaces button * Add copy button * Always show entity header * Add basic view select chips * Fix opacity transition * Animation progress * Stash * Add check icon to view select * Add datasets relationship graph to summary bar * Delete unused gene components * Update summary components * Different heights for summary and diagram * Show entity header content when expanded * Use position sticky * Fix divider * Remove version select * Add citation and consortium to summary for datasets * Clamp description in expanded summary * Only show view buttons on large desktops * Show mapped status * Dedupe flask data and entity store assay metadata * Add icons to summary * Split out cases into components * Add icons * Add paper for relationship diagram * Show summary view for more entities * Integrate publication summary * Fix publication summary * Fix undefined * Fix tests * Fix offsets * Remove fit view * Fix comments from review * Fix data-testid propogation --------- Co-authored-by: John Conroy <[email protected]> * NickAkhmetov/CAT-777 Processed Data section (#3495) * make sure sample metadata doesn't get lost * hide empty dataset relationships box on dataset pages without processed descendants --------- Co-authored-by: John Conroy <[email protected]> Co-authored-by: Nikolay Akhmetov <[email protected]>
hubmapconsortium · Aug 21, 2024 · 25b9fea · 25b9fea
1 parent 80dd4af
commit 25b9fea
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Showing 262 changed files with 7,429 additions and 2,858 deletions.
diff --git a/CHANGELOG-cat-831.md b/CHANGELOG-cat-831.md
@@ -0,0 +1,3 @@
+- Extend provenance table logic to handle missing entities.
+- Fix handling of large search requests.
+- Request less data for provenance table tiles.
diff --git a/CHANGELOG-dataset-relationships.md b/CHANGELOG-dataset-relationships.md
@@ -0,0 +1 @@
+- Add dataset relationships diagram.
diff --git a/CHANGELOG-processed-datasets.md b/CHANGELOG-processed-datasets.md
@@ -0,0 +1 @@
+- Added processed datasets section to display all visualizations for a given raw dataset.
diff --git a/CHANGELOG-unified-datasets.md b/CHANGELOG-unified-datasets.md
@@ -0,0 +1,2 @@
+- Update raw dataset detail pages to include processed dataset information.
+- Update table of contents design.
diff --git a/context/.storybook/main.ts b/context/.storybook/main.ts
@@ -16,7 +16,7 @@ const config: StorybookConfig = {
     '@chromatic-com/storybook',
     '@storybook/addon-webpack5-compiler-swc',
   ],
-
+  staticDirs: ['../app/static/assets', '../app/static/storybook-public'],
   webpackFinal: async (config) => {
     // exclude svgs from the default file loader
     config.module?.rules?.forEach((rule) => {

diff --git a/context/.storybook/preview.tsx b/context/.storybook/preview.tsx
@@ -1,24 +1,23 @@
 import React from 'react';
 
 import Providers from '../app/static/js/components/Providers';
-import { initialize, mswDecorator } from 'msw-storybook-addon';
+import { initialize,  mswLoader } from 'msw-storybook-addon';
 import { enableMapSet } from 'immer';
 
+
+import '@fontsource-variable/inter/files/inter-latin-standard-normal.woff2';
+
 enableMapSet();
 
 const allowConditions = [(url) => String(url).endsWith('thumbnail.jpg')];
 initialize({
-  onUnhandledRequest: ({ method, url }) => {
-    if (!allowConditions.some((conditionFn) => conditionFn(url))) {
-      console.error(`Unhandled ${method} request to ${url}.
-
-        This exception has been only logged in the console, however, it's strongly recommended to resolve this error as you don't want unmocked data in Storybook stories.
-
-        If you wish to mock an error response, please refer to this guide: https://mswjs.io/docs/recipes/mocking-error-responses
-      `);
+  serviceWorker: {
+    options: {
+      updateViaCache: 'none'
     }
-  },
+  }
 });
+export const loaders = [mswLoader]
 
 export const parameters = {
   controls: {
@@ -29,15 +28,23 @@ export const parameters = {
   },
 };
 
-export const mockEndpoints = { assetsEndpoint: 'https://assets.hubmapconsortium.org' };
+export const mockEndpoints = { assetsEndpoint: 'https://assets.hubmapconsortium.org', softAssayEndpoint: '/soft-assay-endpoint' };
 export const mockGroupsToken = '';
 
 export const decorators = [
   (Story) => (
-    <Providers endpoints={mockEndpoints} groupsToken={mockGroupsToken} isAuthenticated={false} userEmail={'undefined'} workspacesToken={'undefined'} isWorkspacesUser={false} isHubmapUser={false} flaskData={undefined}>
+    <Providers endpoints={mockEndpoints} groupsToken={mockGroupsToken} isAuthenticated={false} userEmail={'undefined'} workspacesToken={'undefined'} isWorkspacesUser={false} isHubmapUser={false} flaskData={{}}>
       <Story />
     </Providers>
   ),
-  mswDecorator,
 ];
 export const tags = ['autodocs'];
+
+
+const preview = {
+  parameters,
+  loaders,
+  decorators,
+}
+
+export default preview
diff --git a/context/app/routes_browse.py b/context/app/routes_browse.py
@@ -1,5 +1,5 @@
 import json
-from urllib.parse import urlparse
+from urllib.parse import urlparse, quote
 
 from flask import (
     render_template, jsonify,
@@ -47,22 +47,49 @@ def details(type, uuid):
     client = get_client()
     entity = client.get_entity(uuid)
     actual_type = entity['entity_type'].lower()
+
+    # Redirect to primary dataset if this is
+    # - a support entity (e.g. an image pyramid)
+    # - a processed or component dataset
+    is_support = actual_type == 'support'
+    is_processed = entity.get('processing') != 'raw' and actual_type == 'dataset'
+    is_component = entity.get('is_component', False) is True
+    if (is_support or is_processed or is_component):
+        supported_entity = client.get_entities(
+            'datasets',
+            query_override={
+                "bool": {
+                    "must": {
+                        "terms": {
+                            "descendant_ids": [uuid]
+                        }
+                    }
+                }
+            },
+            non_metadata_fields=['hubmap_id', 'uuid']
+        )
+
+        pipeline_anchor = entity.get('pipeline', entity.get('hubmap_id')).replace(' ', '')
+        anchor = quote(f'section-{pipeline_anchor}-{entity.get("status")}').lower()
+
+        if len(supported_entity) > 0:
+            return redirect(
+                url_for('routes_browse.details',
+                        type='dataset',
+                        uuid=supported_entity[0]['uuid'],
+                        _anchor=anchor,
+                        redirected=True))
+
     if type != actual_type:
         return redirect(url_for('routes_browse.details', type=actual_type, uuid=uuid))
 
+    redirected = request.args.get('redirected') == 'True'
+
     flask_data = {
         **get_default_flask_data(),
         'entity': entity,
+        'redirected': redirected,
     }
-    marker = request.args.get('marker')
-
-    if type == 'dataset':
-        conf_cells_uuid = client.get_vitessce_conf_cells_and_lifted_uuid(entity, marker=marker)
-        flask_data.update({
-            'vitessce_conf': conf_cells_uuid.vitessce_conf.conf,
-            'has_notebook': conf_cells_uuid.vitessce_conf.cells is not None,
-            'vis_lifted_uuid': conf_cells_uuid.vis_lifted_uuid
-        })
 
     if type == 'publication':
         publication_ancillary_data = client.get_publication_ancillary_json(entity)
@@ -93,7 +120,11 @@ def details_vitessce(type, uuid):
         abort(404)
     client = get_client()
     entity = client.get_entity(uuid)
-    vitessce_conf = client.get_vitessce_conf_cells_and_lifted_uuid(entity).vitessce_conf
+    parent_uuid = request.args.get('parent') or None
+    marker = request.args.get('marker') or None
+    parent = client.get_entity(parent_uuid) if parent_uuid else None
+    vitessce_conf = client.get_vitessce_conf_cells_and_lifted_uuid(
+        entity, marker=marker, parent=parent).vitessce_conf
     # Returns a JSON null if there is no visualization.
     response = jsonify(vitessce_conf.conf)
     response.headers.add("Access-Control-Allow-Origin", "*")

diff --git a/context/app/static/js/components/Contexts.tsx b/context/app/static/js/components/Contexts.tsx
@@ -1,14 +1,15 @@
 import { useContext, createContext } from 'js/helpers/context';
-import { Entity } from './types';
+import { AllEntities } from './types';
 
 // TODO: Continue populating these types as we find more of the uses of the flask data and app contexts
 
 export interface FlaskDataContextType {
   redirected_from: string;
-  entity: Entity; // Update to handle different entities.
+  entity: AllEntities; // Update to handle different entities.
   [key: string]: unknown;
   title: string; // preview page title
   vis_lifted_uuid?: string;
+  redirected?: boolean;
 }
 
 export const FlaskDataContext = createContext<FlaskDataContextType>('FlaskDataContext');
@@ -27,6 +28,7 @@ interface AppContextType {
   assetsEndpoint: string;
   entityEndpoint: string;
   elasticsearchEndpoint: string;
+  softAssayEndpoint: string;
   groupsToken: string;
   workspacesToken: string;
   workspacesEndpoint: string;

diff --git a/context/app/static/js/components/Providers.jsx b/context/app/static/js/components/Providers.jsx
@@ -8,8 +8,11 @@ import CssBaseline from '@mui/material/CssBaseline';
 import { FlaskDataContext, AppContext } from 'js/components/Contexts';
 import GlobalStyles from 'js/components/globalStyles';
 import { ProtocolAPIContext } from 'js/components/detailPage/Protocol/ProtocolAPIContext';
+import { EntityStoreProvider } from 'js/stores/useEntityStore';
+import { InitialHashContextProvider } from 'js/hooks/useInitialHash';
 import theme from '../theme';
 import GlobalFonts from '../fonts';
+import { useEntityHeaderSprings } from './detailPage/entityHeader/EntityHeader/hooks';
 
 const swrConfig = {
   revalidateOnFocus: false,
@@ -55,22 +58,30 @@ export default function Providers({
     [flaskData],
   );
 
+  const flaskDataWithDefaults = useMemo(() => ({ entity: {}, ...flaskData }), [flaskData]);
+
+  const { springs } = useEntityHeaderSprings();
+
   return (
     <SWRConfig value={swrConfig}>
-      <GlobalFonts />
-      <MuiThemeProvider theme={theme}>
-        <SCThemeProvider theme={theme}>
-          <AppContext.Provider value={appContext}>
-            <FlaskDataContext.Provider value={flaskData}>
-              <ProtocolAPIContext.Provider value={protocolsContext}>
-                <CssBaseline />
-                <GlobalStyles />
-                {children}
-              </ProtocolAPIContext.Provider>
-            </FlaskDataContext.Provider>
-          </AppContext.Provider>
-        </SCThemeProvider>
-      </MuiThemeProvider>
+      <InitialHashContextProvider>
+        <GlobalFonts />
+        <MuiThemeProvider theme={theme}>
+          <SCThemeProvider theme={theme}>
+            <AppContext.Provider value={appContext}>
+              <FlaskDataContext.Provider value={flaskDataWithDefaults}>
+                <EntityStoreProvider springs={springs} assayMetadata={flaskData?.entity ?? {}}>
+                  <ProtocolAPIContext.Provider value={protocolsContext}>
+                    <CssBaseline />
+                    <GlobalStyles />
+                    {children}
+                  </ProtocolAPIContext.Provider>
+                </EntityStoreProvider>
+              </FlaskDataContext.Provider>
+            </AppContext.Provider>
+          </SCThemeProvider>
+        </MuiThemeProvider>
+      </InitialHashContextProvider>
     </SWRConfig>
   );
 }
diff --git a/context/app/static/js/components/Routes/Route/Route.jsx b/context/app/static/js/components/Routes/Route/Route.jsx
diff --git a/context/app/static/js/components/Routes/Route/Route.tsx b/context/app/static/js/components/Routes/Route/Route.tsx
@@ -0,0 +1,44 @@
+import React, { PropsWithChildren, Suspense } from 'react';
+import Stack from '@mui/material/Stack';
+import Box from '@mui/material/Box';
+import { ContainerProps } from '@mui/material/Container';
+
+import { useIsDesktop } from 'js/hooks/media-queries';
+import RouteLoader from '../RouteLoader';
+import { StyledContainer } from './style';
+
+export const leftRouteBoundaryID = 'left-route-boundary';
+export const rightRouteBoundaryID = 'right-route-boundary';
+
+function RouteBoundary({
+  id,
+  showBoundary,
+}: {
+  id: typeof leftRouteBoundaryID | typeof rightRouteBoundaryID;
+  showBoundary: boolean;
+}) {
+  return <Box id={id} flex="1 0" padding={2} display={!showBoundary ? 'none' : 'block'} />;
+}
+
+function Route({ children, disableWidthConstraint = false }: PropsWithChildren<{ disableWidthConstraint: boolean }>) {
+  const constrainWidthProps: Partial<ContainerProps> = disableWidthConstraint
+    ? { maxWidth: false, disableGutters: true }
+    : { maxWidth: 'lg' };
+
+  const isDesktop = useIsDesktop();
+  const shouldShowBoundaries = !disableWidthConstraint && isDesktop;
+
+  return (
+    <Suspense fallback={<RouteLoader />}>
+      <Stack direction="row" width="100%">
+        <RouteBoundary id={leftRouteBoundaryID} showBoundary={shouldShowBoundaries} />
+        <StyledContainer {...constrainWidthProps} component="div">
+          {children}
+        </StyledContainer>
+        <RouteBoundary id={rightRouteBoundaryID} showBoundary={shouldShowBoundaries} />
+      </Stack>
+    </Suspense>
+  );
+}
+
+export default Route;
diff --git a/context/app/static/js/components/Routes/Route/style.js b/context/app/static/js/components/Routes/Route/style.js
diff --git a/context/app/static/js/components/Routes/Route/style.ts b/context/app/static/js/components/Routes/Route/style.ts
@@ -0,0 +1,17 @@
+import { styled } from '@mui/material/styles';
+import Container from '@mui/material/Container';
+
+const StyledContainer = styled(Container)(({ theme }) => ({
+  marginTop: theme.spacing(2),
+  backgroundColor: theme.palette.background.default,
+  flexGrow: 1,
+  flexShrink: 1,
+  flexDirection: 'column',
+  display: 'flex',
+})) as typeof Container;
+
+// max width for a lg container
+const routeContainerMaxWidth = 1232;
+const routeContainerPadding = 32;
+
+export { StyledContainer, routeContainerMaxWidth, routeContainerPadding };
diff --git a/context/app/static/js/components/Routes/Routes.jsx b/context/app/static/js/components/Routes/Routes.jsx
@@ -45,8 +45,6 @@ function Routes({ flaskData }) {
     markdown,
     errorCode,
     list_uuid,
-    has_notebook,
-    vis_lifted_uuid,
     entities,
     organs,
     organs_count,
@@ -86,12 +84,7 @@ function Routes({ flaskData }) {
   if (urlPath.startsWith('/browse/dataset/') || urlPath.startsWith('/browse/support/')) {
     return (
       <Route>
-        <Dataset
-          assayMetadata={entity}
-          vitData={vitessce_conf}
-          hasNotebook={has_notebook}
-          visLiftedUUID={vis_lifted_uuid}
-        />
+        <Dataset assayMetadata={entity} />
       </Route>
     );
   }
@@ -341,6 +334,7 @@ Routes.propTypes = {
     redirected_from: PropTypes.string,
     cell_type: PropTypes.string,
     globusGroups: PropTypes.object,
+    redirected: PropTypes.bool,
   }),
 };
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		- Added processed datasets section to display all visualizations for a given raw dataset.
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		- Update raw dataset detail pages to include processed dataset information.
		- Update table of contents design.