Merge branch 'main' into john-conroy/replace-searchkit

context/app/markdown/CHANGELOG.md

@@ -1,3 +1,36 @@
+# Changelog
+
+## v1.12.2 - 2024-10-17
+
+- Add access levels to processed dataset helper panels.
+- Use relevant access levels when determining whether or not to show workspace buttons on dataset detail pages.
+- Add title to changelog page.
+- Ensure visualizations for image pyramids use parent UUID to fetch notebooks.
+- Restore missing columns to derived entities section.
+- Remove Provenance section from donor page in favor of using derived data tables.
+- Fix Webkit-specific bugs that caused the entity header to become misaligned.
+- Resolve issues of header cutting off the top of detail pages and header shifting off-screen when scrolling.
+- Switch to using metadata table with tabs component in the Sample and Donor pages.
+- In the metadata sections of Dataset, Sample, and Donor pages, add tabs for any entities in the Provenance section with metadata.
+- Update the metadata table component to show unique labels for each tab and to be scrollable when many tabs are present.
+- Fix issue of Workspaces button being available for protected datasets in the Visualization section.
+
+
+
+## v1.12.1 - 2024-10-10
+
+- Prevent collections without a DOI from being counted on the homepage.
+- Avoid page scrolling from using arrow keys on vitessce visualization.
+- Prevent malformed provenance graph data from crashing the entire page.
+- Improve readability of pipeline list in processed dataset sections.
+- Append HuBMAP ID to errored datasets' URL anchors to avoid anchor duplication on dataset pages with multiple failed processing attempts.
+- Improve entity header state handling of page resizes.
+- Fix push script to correctly check latest minor version date.
+- Sort publications by their date of publication.
+- Update Unified View redirect toast to be more informative.
+- Update group for HIVE-processed datasets to be 'HIVE'.
+
+
 ## v1.12.0 - 2024-10-07
 
 - Fix bug on dataset detail page for workspace dialogs opened in succession for different processed datasets. 

context/app/routes_browse.py

@@ -78,7 +78,9 @@ def details(type, uuid):
                         type='dataset',
                         uuid=supported_entity[0]['uuid'],
                         _anchor=anchor,
-                        redirected=True))
+                        redirected=True,
+                        redirectedFromId=entity.get('hubmap_id'),
+                        redirectedFromPipeline=entity.get('pipeline')))
 
     if type != actual_type:
         return redirect(url_for('routes_browse.details', type=actual_type, uuid=uuid))
@@ -89,6 +91,8 @@ def details(type, uuid):
         **get_default_flask_data(),
         'entity': entity,
         'redirected': redirected,
+        'redirectedFromId': request.args.get('redirectedFromId'),
+        'redirectedFromPipeline': request.args.get('redirectedFromPipeline')
     }
 
     if type == 'publication':

context/app/static/js/components/Contexts.tsx

@@ -10,6 +10,8 @@ export interface FlaskDataContextType {
   title: string; // preview page title
   vis_lifted_uuid?: string;
   redirected?: boolean;
+  redirectedFromId?: string | null;
+  redirectedFromPipeline?: string | null;
 }
 
 export const FlaskDataContext = createContext<FlaskDataContextType>('FlaskDataContext');

context/app/static/js/components/detailPage/DetailPageSection/DetailPageSection.tsx

@@ -15,12 +15,19 @@ function DetailPageSection({ children, ...rest }: PropsWithChildren<React.HTMLAt
       const strippedHash = initialHash.slice(1);
       if (strippedHash === rest.id) {
         setTimeout(() => {
-          sectionRef.current?.scrollIntoView({
+          // Manually scroll to section and account for header offset
+          const sectionTop = sectionRef.current?.getBoundingClientRect().top ?? 0;
+          const scrollPosition = window.scrollY + sectionTop - offset;
+
+          window.scrollTo({
+            top: Math.max(scrollPosition, 0),
             behavior: 'smooth',
           });
         }, 1000);
       }
     }
+    // We do not want to re-scroll down to the section if the header view changes (aka offset changes)
+    // eslint-disable-next-line react-hooks/exhaustive-deps
   }, [initialHash, rest.id]);
 
   return (

context/app/static/js/components/detailPage/MetadataSection/MetadataSection.tsx

@@ -6,66 +6,14 @@ import { CollapsibleDetailPageSection } from 'js/components/detailPage/DetailPag
 import { useTrackEntityPageEvent } from 'js/components/detailPage/useTrackEntityPageEvent';
 import { tableToDelimitedString, createDownloadUrl } from 'js/helpers/functions';
 import { useMetadataFieldDescriptions } from 'js/hooks/useUBKG';
-import { getMetadata, hasMetadata } from 'js/helpers/metadata';
-import { ESEntityType, isDataset } from 'js/components/types';
-import { useProcessedDatasets } from 'js/pages/Dataset/hooks';
-import { entityIconMap } from 'js/shared-styles/icons/entityIconMap';
+import { Dataset, Donor, Sample, isDataset } from 'js/components/types';
 import withShouldDisplay from 'js/helpers/withShouldDisplay';
 import { sectionIconMap } from 'js/shared-styles/icons/sectionIconMap';
+import { getTableEntities } from 'js/components/detailPage/MetadataSection/utils';
 import { DownloadIcon, StyledWhiteBackgroundIconButton } from '../MetadataTable/style';
 import MetadataTabs from '../multi-assay/MultiAssayMetadataTabs';
-import { Columns, defaultTSVColumns } from './columns';
 import { SectionDescription } from '../ProcessedData/ProcessedDataset/SectionDescription';
-import MetadataTable from '../MetadataTable';
-import { nodeIcons } from '../DatasetRelationships/nodeTypes';
-
-export function getDescription(
-  field: string,
-  metadataFieldDescriptions: Record<string, string> | Record<string, never>,
-) {
-  const [prefix, stem] = field.split('.');
-  if (!stem) {
-    return metadataFieldDescriptions?.[field];
-  }
-  const description = metadataFieldDescriptions?.[stem];
-  if (!description) {
-    return undefined;
-  }
-  if (prefix === 'donor') {
-    return `For the original donor: ${metadataFieldDescriptions?.[stem]}`;
-  }
-  if (prefix === 'sample') {
-    return `For the original sample: ${metadataFieldDescriptions?.[stem]}`;
-  }
-  throw new Error(`Unrecognized metadata field prefix: ${prefix}`);
-}
-
-export function buildTableData(
-  tableData: Record<string, string | object | unknown[]>,
-  metadataFieldDescriptions: Record<string, string> | Record<string, never>,
-  extraValues: Record<string, string> = {},
-) {
-  return (
-    Object.entries(tableData)
-      // Filter out nested objects, like nested "metadata" for Samples...
-      // but allow arrays. Remember, in JS: typeof [] === 'object'
-      .filter((entry) => typeof entry[1] !== 'object' || Array.isArray(entry[1]))
-      // Filter out fields from TSV that aren't really metadata:
-      .filter((entry) => !['contributors_path', 'antibodies_path', 'version'].includes(entry[0]))
-      .map((entry) => ({
-        ...extraValues,
-        key: entry[0],
-        // eslint-disable-next-line @typescript-eslint/no-base-to-string
-        value: Array.isArray(entry[1]) ? entry[1].join(', ') : entry[1].toString(),
-        description: getDescription(entry[0], metadataFieldDescriptions),
-      }))
-  );
-}
-
-function useTableData(tableData: Record<string, string>) {
-  const { data: fieldDescriptions } = useMetadataFieldDescriptions();
-  return buildTableData(tableData, fieldDescriptions);
-}
+import { Columns, defaultTSVColumns } from './columns';
 
 interface TableRow {
   key: string;
@@ -124,76 +72,25 @@ function MetadataWrapper({ allTableRows, tsvColumns = defaultTSVColumns, childre
   );
 }
 
-function SingleMetadata({ metadata }: { metadata: Record<string, string> }) {
-  const tableRows = useTableData(metadata);
-
-  return (
-    <MetadataWrapper allTableRows={tableRows}>
-      <MetadataTable tableRows={tableRows} />
-    </MetadataWrapper>
-  );
-}
-
-function getEntityIcon(entity: { entity_type: ESEntityType; is_component?: boolean; processing?: string }) {
-  if (isDataset(entity)) {
-    if (entity.is_component) {
-      return nodeIcons.componentDataset;
-    }
-    if (entity.processing === 'processed') {
-      return nodeIcons.processedDataset;
-    }
-    return nodeIcons.primaryDataset;
-  }
-  return entityIconMap[entity.entity_type];
-}
-
 interface MetadataProps {
-  metadata?: Record<string, string>;
+  entities: (Donor | Dataset | Sample)[];
 }
 
-function Metadata({ metadata }: MetadataProps) {
-  const { searchHits: datasetsWithMetadata, isLoading } = useProcessedDatasets(true);
+function Metadata({ entities }: MetadataProps) {
   const { data: fieldDescriptions } = useMetadataFieldDescriptions();
+  const {
+    entity: { uuid },
+  } = useFlaskDataContext();
 
-  const { entity } = useFlaskDataContext();
-
-  if (!isDataset(entity)) {
-    return <SingleMetadata metadata={metadata!} />;
-  }
-
-  if (isLoading || !datasetsWithMetadata) {
-    return null;
-  }
-
-  const { donor, source_samples } = entity;
-
-  const entities = [entity, ...datasetsWithMetadata.map((d) => d._source), ...source_samples, donor]
-    .filter((e) => hasMetadata({ targetEntityType: e.entity_type, currentEntity: e }))
-    .map((e) => {
-      const label = isDataset(e) ? e.assay_display_name : e.entity_type;
-      return {
-        uuid: e.uuid,
-        label,
-        icon: getEntityIcon(e),
-        tableRows: buildTableData(
-          getMetadata({
-            targetEntityType: e.entity_type,
-            currentEntity: e,
-          }),
-          fieldDescriptions,
-          { hubmap_id: e.hubmap_id, label },
-        ),
-      };
-    });
-
-  const allTableRows = entities.map((d) => d.tableRows).flat();
+  const tableEntities = getTableEntities({ entities, uuid, fieldDescriptions });
+  const allTableRows = tableEntities.map((d) => d.tableRows).flat();
 
   return (
     <MetadataWrapper
       allTableRows={allTableRows}
       tsvColumns={[{ id: 'hubmap_id', label: 'HuBMAP ID' }, { id: 'label', label: 'Entity' }, ...defaultTSVColumns]}
     >
-      <MetadataTabs entities={entities} />
+      <MetadataTabs entities={tableEntities} />
     </MetadataWrapper>
   );
 }