fix: FTU Explorer data source updates (#635)

* Data source updates * refactor(ftu-ui): ♻️ Reimplement cell types table data processing logic * style(ftu-ui): 🔥 Remove commented out code * fix(services): Readd ftu data mock service (used by stories) * style(ftu-ui): Fix sonar cloud issues * docs(state): 📝 Increase doc coverage * test(state): ✅ Fix and update tests for data aggregation logic * refactor(state): Update column keys & labels, sort columns alphabetically & update column layout * refactor(ftu-ui): 💄 Style tweak * test(state): ✅ Fix a cell-summary test --------- Co-authored-by: Daniel Bolin <axbolin@iu.edu>
hubmapconsortium · Aug 15, 2024 · 8b2c970 · 8b2c970
1 parent 53f45a8
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diff --git a/apps/ftu-ui/src/assets/TEMP/ftu-cell-summaries.jsonld b/apps/ftu-ui/src/assets/TEMP/ftu-cell-summaries.jsonld
@@ -27,7 +27,7 @@
   "@graph": [
     {
       "@type": "CellSummary",
-      "cell_source": "https://purl.humanatlas.io/2d-ftu/kidney-nephron",
+      "cell_source": "https://doi.org/10.1038/s41467-021-22368-w#CellSummary_kidney-nephron",
       "annotation_method": "Aggregation",
       "biomarker_type": "gene",
       "summary": [
@@ -3746,7 +3746,7 @@
     },
     {
       "@type": "CellSummary",
-      "cell_source": "https://purl.humanatlas.io/2d-ftu/kidney-renal-corpuscle",
+      "cell_source": "https://doi.org/10.1038/s41467-021-22368-w#CellSummary_kidney-renal-corpuscle",
       "annotation_method": "Aggregation",
       "biomarker_type": "gene",
       "summary": [
@@ -6744,7 +6744,7 @@
     },
     {
       "@type": "CellSummary",
-      "cell_source": "https://purl.humanatlas.io/2d-ftu/kidney-cortical-collecting-duct",
+      "cell_source": "https://doi.org/10.1038/s41467-021-22368-w#CellSummary_kidney-cortical-collecting-duct",
       "annotation_method": "Aggregation",
       "biomarker_type": "gene",
       "summary": [
@@ -9756,7 +9756,7 @@
     },
     {
       "@type": "CellSummary",
-      "cell_source": "https://purl.humanatlas.io/2d-ftu/kidney-ascending-thin-loop-of-henle",
+      "cell_source": "https://doi.org/10.1038/s41467-021-22368-w#CellSummary_kidney-ascending-thin-loop-of-henle",
       "annotation_method": "Aggregation",
       "biomarker_type": "gene",
       "summary": [
@@ -11266,7 +11266,7 @@
     },
     {
       "@type": "CellSummary",
-      "cell_source": "https://purl.humanatlas.io/2d-ftu/liver-liver-lobule",
+      "cell_source": "https://doi.org/10.1038/s41467-021-22368-w#CellSummary_liver-liver-lobule",
       "annotation_method": "Aggregation",
       "biomarker_type": "gene",
       "summary": [
@@ -13485,7 +13485,7 @@
     },
     {
       "@type": "CellSummary",
-      "cell_source": "https://purl.humanatlas.io/2d-ftu/lung-pulmonary-alveolus",
+      "cell_source": "https://doi.org/10.1038/s41467-021-22368-w#CellSummary_lung-pulmonary-alveolus",
       "annotation_method": "Aggregation",
       "biomarker_type": "gene",
       "summary": [
@@ -16399,7 +16399,7 @@
     },
     {
       "@type": "CellSummary",
-      "cell_source": "https://purl.humanatlas.io/2d-ftu/lung-bronchial-submucosal-gland",
+      "cell_source": "https://doi.org/10.1038/s41467-021-22368-w#CellSummary_lung-bronchial-submucosal-gland",
       "annotation_method": "Aggregation",
       "biomarker_type": "gene",
       "summary": [

diff --git a/apps/ftu-ui/src/assets/TEMP/ftu-datasets.jsonld b/apps/ftu-ui/src/assets/TEMP/ftu-datasets.jsonld
@@ -30,7 +30,7 @@
       "@type": "FtuIllustration",
       "data_sources": [
         {
-          "@id": "https://cns-iu.github.io/hra-cell-type-populations-supporting-information/data/enriched_rui_locations.jsonld#36e76662-60b8-4193-8a70-1bfd4f6938d0_D088_Lung",
+          "@id": "https://doi.org/10.1038/s41467-021-22368-w#CellSummary_kidney-nephron",
           "@type": "Dataset",
           "label": "snRNA-seq of Three Healthy Human Kidney Tissue",
           "link": "https://doi.org/10.1038/s41467-021-22368-w",
@@ -53,7 +53,7 @@
       "@type": "FtuIllustration",
       "data_sources": [
         {
-          "@id": "https://cns-iu.github.io/hra-cell-type-populations-supporting-information/data/enriched_rui_locations.jsonld#36e76662-60b8-4193-8a70-1bfd4f6938d0_D088_Lung",
+          "@id": "https://doi.org/10.1038/s41467-021-22368-w#CellSummary_kidney-renal-corpuscle",
           "@type": "Dataset",
           "label": "snRNA-seq of Three Healthy Human Kidney Tissue",
           "link": "https://doi.org/10.1038/s41467-021-22368-w",
@@ -76,7 +76,7 @@
       "@type": "FtuIllustration",
       "data_sources": [
         {
-          "@id": "https://cns-iu.github.io/hra-cell-type-populations-supporting-information/data/enriched_rui_locations.jsonld#36e76662-60b8-4193-8a70-1bfd4f6938d0_D088_Lung",
+          "@id": "https://doi.org/10.1038/s41467-021-22368-w#CellSummary_kidney-cortical-collecting-duct",
           "@type": "Dataset",
           "label": "snRNA-seq of Three Healthy Human Kidney Tissue",
           "link": "https://doi.org/10.1038/s41467-021-22368-w",
@@ -99,7 +99,7 @@
       "@type": "FtuIllustration",
       "data_sources": [
         {
-          "@id": "https://cns-iu.github.io/hra-cell-type-populations-supporting-information/data/enriched_rui_locations.jsonld#36e76662-60b8-4193-8a70-1bfd4f6938d0_D088_Lung",
+          "@id": "https://doi.org/10.1038/s41467-021-22368-w#CellSummary_kidney-ascending-thin-loop-of-henle",
           "@type": "Dataset",
           "label": "snRNA-seq of Three Healthy Human Kidney Tissue",
           "link": "https://doi.org/10.1038/s41467-021-22368-w",
@@ -122,7 +122,7 @@
       "@type": "FtuIllustration",
       "data_sources": [
         {
-          "@id": "https://cns-iu.github.io/hra-cell-type-populations-supporting-information/data/enriched_rui_locations.jsonld#36e76662-60b8-4193-8a70-1bfd4f6938d0_D088_Lung",
+          "@id": "https://doi.org/10.1038/s41467-021-22368-w#CellSummary_lung-bronchial-submucosal-gland",
           "@type": "Dataset",
           "label": "scRNA Seq of Resected Human Lung Tissue",
           "link": "https://doi.org/10.1038/s41591-019-0468-5",
@@ -149,7 +149,7 @@
       "@type": "FtuIllustration",
       "data_sources": [
         {
-          "@id": "https://cns-iu.github.io/hra-cell-type-populations-supporting-information/data/enriched_rui_locations.jsonld#36e76662-60b8-4193-8a70-1bfd4f6938d0_D088_Lung",
+          "@id": "https://doi.org/10.1038/s41467-021-22368-w#CellSummary_lung-pulmonary-alveolus",
           "@type": "Dataset",
           "label": "scRNA Seq of Resected Human Lung Tissue",
           "link": "https://doi.org/10.1038/s41591-019-0468-5",
@@ -176,7 +176,7 @@
       "@type": "FtuIllustration",
       "data_sources": [
         {
-          "@id": "https://cns-iu.github.io/hra-cell-type-populations-supporting-information/data/enriched_rui_locations.jsonld#36e76662-60b8-4193-8a70-1bfd4f6938d0_D088_Lung",
+          "@id": "https://doi.org/10.1038/s41467-021-22368-w#CellSummary_liver-liver-lobule",
           "@type": "Dataset",
           "label": "sc Bulk Transcriptomics of Liver Data",
           "link": "https://doi.org/10.1038/s41598-021-98806-y",

diff --git a/libs/components/behavioral/src/lib/biomarker-details/biomarker-details.component.scss b/libs/components/behavioral/src/lib/biomarker-details/biomarker-details.component.scss
@@ -128,7 +128,6 @@
     height: 100%;
 
     &.small {
-      height: fit-content;
       min-height: fit-content;
     }
   }

diff --git a/libs/components/organisms/src/lib/biomarker-table/biomarker-table.component.scss b/libs/components/organisms/src/lib/biomarker-table/biomarker-table.component.scss
@@ -4,10 +4,9 @@
 :host {
   display: block;
 
-  @media (min-height: 60.75rem) {
-    .table th {
-      height: 4.5rem !important;
-    }
+  .table th,
+  .table th div {
+    height: 6.5rem !important;
   }
 
   cdk-virtual-scroll-viewport {
@@ -104,10 +103,13 @@
 
   .icon-header {
     .header-column-text {
-      transform: rotate(-45deg);
+      // transform: rotate(-90deg);
+      writing-mode: vertical-rl;
+      transform: rotate(180deg);
       white-space: nowrap;
       overflow: hidden;
       text-overflow: ellipsis;
+      margin: 0.5rem auto;
     }
   }
 

diff --git a/libs/components/organisms/src/lib/biomarker-table/biomarker-table.component.ts b/libs/components/organisms/src/lib/biomarker-table/biomarker-table.component.ts
@@ -170,7 +170,7 @@ export class BiomarkerTableComponent<T extends DataCell> implements OnInit, OnCh
    * @param changes object consisting of change in the Input
    */
   ngOnChanges(changes: SimpleChanges): void {
-    this.checkDisplayedColumns();
+    this.checkDisplayedColumns('columns' in changes);
     if ('data' in changes || 'illustrationIds' in changes) {
       this.dataSource.data = this.sortTableData(this.data);
     }
@@ -194,11 +194,11 @@ export class BiomarkerTableComponent<T extends DataCell> implements OnInit, OnCh
   /**
    * Checks to see if columns should be updated
    */
-  checkDisplayedColumns(): void {
+  checkDisplayedColumns(forceUpdate = false): void {
     const scrollable = this.vscroll.scrollable;
     const size = scrollable.measureViewportSize('horizontal');
     const offset = scrollable.measureScrollOffset('start');
-    let shouldUpdate = false;
+    let shouldUpdate = forceUpdate;
 
     if (size !== this.horizontalViewportSize) {
       this.updateHorizontalViewportSize(size);

diff --git a/libs/services/src/lib/ftu-data/ftu-data.impl.ts b/libs/services/src/lib/ftu-data/ftu-data.impl.ts
@@ -11,7 +11,6 @@ import {
   RAW_CELL_SUMMARIES,
   RAW_DATASETS,
   RAW_ILLUSTRATIONS_JSONLD,
-  RawCellSummary,
   RawDatasets,
   RawIllustrationFile,
   RawIllustrationsJsonld,
@@ -59,11 +58,6 @@ const EMPTY_TISSUE_LIBRARY: TissueLibrary = {
   nodes: {},
 };
 
-/** Capitalizes the first character */
-function capitalize(str: string): string {
-  return str.slice(0, 1).toUpperCase() + str.slice(1);
-}
-
 /** Converts case to title case for organ name */
 function titleCase(name: string) {
   return name
@@ -139,10 +133,7 @@ export class FtuDataImplService extends FtuDataService {
   @returns An Observable that emits an CellSummary array.
   */
   override getCellSummaries(iri: Iri): Observable<CellSummary[]> {
-    return this.fetchData(iri, 'summaries', RAW_CELL_SUMMARIES).pipe(
-      map((data) => data?.['@graph']),
-      map((data) => (data ? this.constructCellSummaries(data) : [])),
-    );
+    return this.fetchData(iri, 'summaries', RAW_CELL_SUMMARIES).pipe(map((data) => data?.['@graph'] ?? []));
   }
 
   /**
@@ -289,68 +280,6 @@ export class FtuDataImplService extends FtuDataService {
     return results;
   }
 
-  /**
-   * constructCellSummaries : Formates Cell Summary after fetching the data
-   * @param data
-   * @returns
-   */
-  private constructCellSummaries(data: RawCellSummary['@graph']): CellSummary[] {
-    type SummaryItem = RawCellSummary['@graph'][number]['summary'][number];
-    const cellSummaries: CellSummary[] = [];
-    const defaultBiomarkerLables = ['gene', 'protein', 'lipid'];
-    const biomarkersPresent = new Set(data.map((summary) => summary.biomarker_type.toLowerCase()));
-    const expandGenes = (summary: SummaryItem) =>
-      summary.genes.map((gene) => ({
-        ...summary,
-        ...gene,
-      }));
-
-    data.forEach((summaryGroup) => {
-      const nestedSummaries = summaryGroup.summary.map(expandGenes);
-      const summary = nestedSummaries.reduce((acc, items) => acc.concat(items), [] as (typeof nestedSummaries)[number]);
-
-      const cells = summary.map((entry) => ({
-        id: entry.cell_id as Iri,
-        label: entry.cell_label,
-      }));
-
-      const biomarkers = summary.map((entry) => ({
-        id: entry.gene_id as Iri,
-        label: entry.gene_label,
-      }));
-
-      const summaries = summary.map((entry) => ({
-        cell: entry.cell_id as Iri,
-        biomarker: entry.gene_id as Iri,
-        count: entry.count,
-        percentage: entry.percentage,
-        meanExpression: entry.mean_expression,
-      }));
-
-      cellSummaries.push({
-        label: `${capitalize(summaryGroup.biomarker_type)} Biomarkers`,
-        cellSource: summaryGroup.cell_source,
-        cells,
-        biomarkers,
-        summaries,
-      });
-    });
-
-    defaultBiomarkerLables.forEach((defaultLabel) => {
-      if (!biomarkersPresent.has(defaultLabel)) {
-        cellSummaries.push({
-          label: `${capitalize(defaultLabel)} Biomarkers`,
-          cellSource: '',
-          cells: [],
-          biomarkers: [],
-          summaries: [],
-        });
-      }
-    });
-
-    return cellSummaries;
-  }
-
   /**
    * Constructs tissue library ,forming parent and child nodes
    * @param items

diff --git a/libs/services/src/lib/ftu-data/ftu-data.mock.ts b/libs/services/src/lib/ftu-data/ftu-data.mock.ts
@@ -324,25 +324,7 @@ const sourceReferences: SourceReference[] = [
 /**
  * Dummy data extract om Mock Data of tissue mock
  */
-const CELL_SUMMARY_DATA: CellSummary[] = Object.values(MOCK_SUMMARIES).map((summary) => ({
-  label: summary.label,
-  cellSource: summary.cellSource,
-  cells: summary.entries.map((entry) => ({
-    id: entry.cell.id as Iri,
-    label: entry.cell.label,
-  })),
-  biomarkers: summary.entries.map((entry) => ({
-    id: entry.biomarker.id as Iri,
-    label: entry.biomarker.label,
-  })),
-  summaries: summary.entries.map((entry) => ({
-    cell: entry.cell.id as Iri,
-    biomarker: entry.biomarker.id as Iri,
-    count: entry.count,
-    percentage: entry.percentage,
-    meanExpression: entry.meanExpression,
-  })),
-}));
+const CELL_SUMMARY_DATA: CellSummary[] = [];
 
 /**
 This class represents a mock implementation of the FtuDataService class.

diff --git a/libs/services/src/lib/ftu-data/ftu-data.model.ts b/libs/services/src/lib/ftu-data/ftu-data.model.ts
@@ -52,14 +52,14 @@ export const CELL = z.object({
 
 /** Zod Schema for a BIOMARKER */
 export const BIOMARKER = z.object({
-  id: IRI,
+  id: z.string(),
   label: z.string(),
 });
 
 /** Zod Schema for a CELL_SUMMARY_ROW */
 export const CELL_SUMMARY_ROW = z.object({
   cell: IRI,
-  biomarker: IRI,
+  biomarker: z.string(),
   count: COUNT,
   percentage: PERCENTAGE,
   meanExpression: PERCENTAGE,
@@ -68,11 +68,25 @@ export const CELL_SUMMARY_ROW = z.object({
 
 /** Zod Schema for a CELL_SUMMARY */
 export const CELL_SUMMARY = z.object({
-  label: z.string(),
-  cellSource: z.string(),
-  cells: CELL.array(),
-  biomarkers: BIOMARKER.array(),
-  summaries: CELL_SUMMARY_ROW.array(),
+  cell_source: IRI,
+  biomarker_type: z.string(),
+  summary: z
+    .object({
+      cell_id: IRI,
+      cell_label: z.string(),
+      genes: z
+        .object({
+          gene_id: z.string(),
+          gene_label: z.string(),
+          ensemble_id: z.string(),
+          mean_expression: z.number(),
+        })
+        .array(),
+      count: z.number(),
+      percentage: z.number(),
+      dataset_count: z.number().optional(),
+    })
+    .array(),
 });
 
 /** Zod Schema for a DATA_FILE_REFERENCE */
@@ -155,29 +169,7 @@ export const RAW_DATASETS = z.object({
 
 /** CELL_SUMMARIES zod object reflecting the format in the file*/
 export const RAW_CELL_SUMMARIES = z.object({
-  '@graph': z
-    .object({
-      cell_source: IRI,
-      biomarker_type: z.string(),
-      summary: z
-        .object({
-          cell_id: z.string(),
-          cell_label: z.string(),
-          genes: z
-            .object({
-              '@type': z.string(),
-              gene_id: z.string(),
-              gene_label: z.string(),
-              mean_expression: z.number(),
-            })
-            .array(),
-          count: z.number(),
-          percentage: z.number(),
-          dataset_count: z.number().optional(),
-        })
-        .array(),
-    })
-    .array(),
+  '@graph': CELL_SUMMARY.array(),
 });
 
 // ---------------------------------------