Austenem/CAT-959 Update epic labels

CHANGELOG-update-epic-labels.md

@@ -0,0 +1,2 @@
+- Use assay_display_name instead of pipeline when labelling EPIC dataset sections.
+- Update language in processed dataset sections from "pipeline" to "analysis".

context/app/static/js/components/detailPage/ProcessedData/HelperPanel/HelperPanel.tsx

@@ -80,7 +80,9 @@ function HelperPanelBody() {
           {currentDataset.description}
         </HelperPanelBodyItem>
       )}
-      <HelperPanelBodyItem label="Pipeline">{currentDataset.pipeline}</HelperPanelBodyItem>
+      <HelperPanelBodyItem label="Analysis Type">
+        {currentDataset.pipeline ?? currentDataset.assay_display_name[0]}
+      </HelperPanelBodyItem>
       <HelperPanelBodyItem label="Group">{currentDataset.group_name}</HelperPanelBodyItem>
       <HelperPanelBodyItem label={dateLabel}>{date && formatDate(date, 'yyyy-MM-dd')}</HelperPanelBodyItem>
     </>

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

@@ -6,14 +6,14 @@ import { sectionIconMap } from 'js/shared-styles/icons/sectionIconMap';
 import ProcessedDataset from './ProcessedDataset';
 import { SectionDescription } from './ProcessedDataset/SectionDescription';
 import HelperPanel from './HelperPanel';
-import { usePipelineCountsInfo, useSortedSearchHits } from './hooks';
+import { useAnalysesCountInfo, useSortedSearchHits } from './hooks';
 import CollapsibleDetailPageSection from '../DetailPageSection/CollapsibleDetailPageSection';
 
 function ProcessedDataSection() {
   const processedDatasets = useProcessedDatasets();
   const sortedSearchHits = useSortedSearchHits(processedDatasets.searchHits);
 
-  const { pipelinesText, pipelineCountsText } = usePipelineCountsInfo(
+  const { analysesText, analysesCountText } = useAnalysesCountInfo(
     processedDatasets.searchHits.map((dataset) => dataset._source),
   );
 
@@ -25,7 +25,7 @@ function ProcessedDataSection() {
       icon={sectionIconMap['processed-data']}
     >
       <SectionDescription
-        addendum={<LabelledSectionText label={pipelinesText}>{pipelineCountsText}</LabelledSectionText>}
+        addendum={<LabelledSectionText label={analysesText}>{analysesCountText}</LabelledSectionText>}
       >
         This section lists analyses generated based on this dataset. These analyses are represented as processed
         datasets and are either generated by HuBMAP using uniform processing pipelines or by an external processing

context/app/static/js/components/detailPage/ProcessedData/ProcessedDataset/ProcessedDatasetAccordion.tsx

@@ -76,7 +76,7 @@ export function ProcessedDatasetAccordion({ children }: PropsWithChildren) {
         <AccordionSummary expandIcon={<ArrowDropDownRounded />}>
           {isLoading ? iconPlaceholder : visualizationIcon}
           <Typography variant="subtitle1" color="inherit" component="h4">
-            {sectionDataset.pipeline}
+            {sectionDataset.pipeline ?? sectionDataset.assay_display_name[0]}
           </Typography>
           <Typography variant="body1" ml="auto" component="div" display="flex" alignItems="center" gap={1}>
             <StatusIcon status={sectionDataset.status} noColor={isExpanded} tooltip />

context/app/static/js/components/detailPage/ProcessedData/hooks.spec.ts

@@ -1,13 +1,13 @@
 import { CreationAction } from 'js/components/types';
 import { renderHook } from 'test-utils/functions';
-import { useSortedSearchHits, createdByCentralProcess, datasetIsPublished, usePipelineCountsInfo } from './hooks';
+import { useSortedSearchHits, createdByCentralProcess, datasetIsPublished, useAnalysesCountInfo } from './hooks';
 
 const testDatasets: {
   _id: string;
   _index: string;
   _score: number;
   _source: {
-    assay_display_name: string[];
+    assay_display_name: string;
     created_timestamp: number;
     creation_action: CreationAction;
     entity_type: string;
@@ -24,7 +24,7 @@ const testDatasets: {
     _index: 'hm_prod_consortium_portal',
     _score: 1,
     _source: {
-      assay_display_name: ['CODEX [Cytokit + SPRM]'],
+      assay_display_name: 'CODEX [Cytokit + SPRM]',
       created_timestamp: 1688952984040,
       creation_action: 'Central Process',
       entity_type: 'Dataset',
@@ -41,7 +41,7 @@ const testDatasets: {
     _index: 'hm_prod_consortium_portal',
     _score: 1,
     _source: {
-      assay_display_name: ['CODEX [Cytokit + SPRM]'],
+      assay_display_name: 'CODEX [Cytokit + SPRM]',
       created_timestamp: 1689198074733,
       creation_action: 'Central Process',
       entity_type: 'Dataset',
@@ -58,7 +58,7 @@ const testDatasets: {
     _index: 'hm_prod_consortium_portal',
     _score: 1,
     _source: {
-      assay_display_name: ['External (Segmentation Mask)'],
+      assay_display_name: 'External (Segmentation Mask)',
       created_timestamp: 1689198074733,
       creation_action: 'External Process',
       entity_type: 'Dataset',
@@ -94,8 +94,8 @@ it('checks if dataset is published', () => {
   expect(datasetIsPublished(testDatasets[2]._source)).toBe(true);
 });
 
-it('counts pipelines and their occurrences', () => {
-  const { pipelinesText, pipelineCountsText } = usePipelineCountsInfo(testDatasets.map((dataset) => dataset._source));
-  expect(pipelinesText).toBe('Pipelines (2)');
-  expect(pipelineCountsText).toBe('Cytokit + SPRM (2) and Segmentation Mask');
+it('counts analyses and their occurrences', () => {
+  const { analysesText, analysesCountText } = useAnalysesCountInfo(testDatasets.map((dataset) => dataset._source));
+  expect(analysesText).toBe('Analyses (2)');
+  expect(analysesCountText).toBe('Cytokit + SPRM (2) and Segmentation Mask');
 });

context/app/static/js/components/detailPage/ProcessedData/hooks.ts

@@ -40,26 +40,26 @@ export function useSortedSearchHits(datasets: ReturnType<typeof useProcessedData
 }
 
 /**
- * Formats the processed datasets' pipelines and their counts for presentation.
- * @param datasets The processed datasets to count the pipelines of.
- * @returns Text for the pipelines label, and additional text for each pipeline and its count.
+ * Formats the processed datasets' analyses and their counts for presentation.
+ * @param datasets The processed datasets to count the analyses of.
+ * @returns Text for the analyses label, and additional text for each analysis and its count.
  */
-export function usePipelineCountsInfo(datasets: Pick<ProcessedDatasetInfo, 'pipeline'>[]) {
-  const pipelines = datasets.map((dataset) => dataset.pipeline);
-  const pipelineCounts = pipelines.reduce(
-    (acc, pipeline) => {
-      acc[pipeline] = (acc[pipeline] || 0) + 1;
+export function useAnalysesCountInfo(datasets: Pick<ProcessedDatasetInfo, 'pipeline' | 'assay_display_name'>[]) {
+  const analyses = datasets.map((dataset) => dataset.pipeline ?? dataset.assay_display_name[0]);
+  const analysesCount = analyses.reduce(
+    (acc, analysis) => {
+      acc[analysis] = (acc[analysis] || 0) + 1;
       return acc;
     },
     {} as Record<string, number>,
   );
-  const pipelinesText = `Pipelines (${Object.keys(pipelineCounts).length})`;
-  const pipelineCountsText = generateCommaList(
-    Object.entries(pipelineCounts).map(([pipeline, count]) => (count > 1 ? `${pipeline} (${count})` : pipeline)),
+  const analysesText = `Analyses (${Object.keys(analysesCount).length})`;
+  const analysesCountText = generateCommaList(
+    Object.entries(analysesCount).map(([analysis, count]) => (count > 1 ? `${analysis} (${count})` : analysis)),
   );
 
   return {
-    pipelinesText,
-    pipelineCountsText,
+    analysesText,
+    analysesCountText,
   };
 }

context/app/static/js/pages/Dataset/hooks.ts

@@ -135,7 +135,8 @@ function getProcessedDatasetSection({
   hit: Required<SearchHit<ProcessedDatasetInfo>>;
   conf?: VitessceConf;
 }) {
-  const { pipeline, hubmap_id, files, metadata, visualization, creation_action, contributors } = hit._source;
+  const { pipeline, assay_display_name, hubmap_id, files, metadata, visualization, creation_action, contributors } =
+    hit._source;
 
   const shouldDisplaySection = {
     summary: true,
@@ -146,10 +147,11 @@ function getProcessedDatasetSection({
   };
 
   const sectionsToDisplay = Object.entries(shouldDisplaySection).filter(([_k, v]) => v === true);
+  const sectionTitle = pipeline ?? assay_display_name[0] ?? hubmap_id;
 
   return {
     // TODO: Improve the lookup for descendants to exclude anything with a missing pipeline name
-    ...getSectionFromString(pipeline ?? hubmap_id, datasetSectionId(hit._source, 'section')),
+    ...getSectionFromString(sectionTitle, datasetSectionId(hit._source, 'section')),
     items: sectionsToDisplay.map(([s]) => ({
       ...getSectionFromString(s, datasetSectionId(hit._source, s)),
       hash: datasetSectionId(hit._source, s),