feat: link to organism page from assembly list and detail (#231)

galaxyproject · Jan 24, 2025 · d70d70c · d70d70c
1 parent 09542fc
commit d70d70c
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Showing 3 changed files with 16 additions and 7 deletions.
diff --git a/app/apis/catalog/brc-analytics-catalog/common/utils.ts b/app/apis/catalog/brc-analytics-catalog/common/utils.ts
@@ -13,6 +13,15 @@ export function getOrganismId(organism: BRCDataCatalogOrganism): string {
   return sanitizeEntityId(organism.ncbiTaxonomyId);
 }
 
+/**
+ * Get the ID of the organism entity associated with the given genome.
+ * @param genome - Genome.
+ * @returns organism ID.
+ */
+export function getGenomeOrganismId(genome: BRCDataCatalogGenome): string {
+  return sanitizeEntityId(genome.speciesTaxonomyId);
+}
+
 export function sanitizeEntityId(entityId?: string): string {
   if (!entityId) return "";
   return entityId.replace(/\./g, "_");

diff --git a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
@@ -23,6 +23,7 @@ import {
 } from "site-config/brc-analytics/category";
 import {
   getGenomeId,
+  getGenomeOrganismId,
   getOrganismId,
 } from "../../../../apis/catalog/brc-analytics-catalog/common/utils";
 import { COLUMN_IDENTIFIER } from "@databiosphere/findable-ui/lib/components/Table/common/columnIdentifier";
@@ -145,9 +146,10 @@ export const buildGcPercent = (
  */
 export const buildGenomeSpecies = (
   genome: BRCDataCatalogGenome
-): ComponentProps<typeof C.BasicCell> => {
+): ComponentProps<typeof C.Link> => {
   return {
-    value: genome.species,
+    label: genome.species,
+    url: `${ROUTES.ORGANISMS}/${encodeURIComponent(getGenomeOrganismId(genome))}`,
   };
 };
 
@@ -379,9 +381,7 @@ export const buildGenomeDetails = (
     BRC_DATA_CATALOG_CATEGORY_LABEL.SPECIES,
     C.Link({
       label: genome.species,
-      url: `https://www.ncbi.nlm.nih.gov/datasets/taxonomy/${encodeURIComponent(
-        genome.ncbiTaxonomyId
-      )}/`,
+      url: `${ROUTES.ORGANISMS}/${encodeURIComponent(getGenomeOrganismId(genome))}`,
     })
   );
   keyValuePairs.set(

diff --git a/site-config/brc-analytics/local/index/genomeEntityConfig.ts b/site-config/brc-analytics/local/index/genomeEntityConfig.ts
@@ -107,9 +107,9 @@ export const genomeEntityConfig: BRCEntityConfig<BRCDataCatalogGenome> = {
       },
       {
         componentConfig: {
-          component: C.BasicCell,
+          component: C.Link,
           viewBuilder: V.buildGenomeSpecies,
-        } as ComponentConfig<typeof C.BasicCell, BRCDataCatalogGenome>,
+        } as ComponentConfig<typeof C.Link, BRCDataCatalogGenome>,
         header: BRC_DATA_CATALOG_CATEGORY_LABEL.SPECIES,
         id: BRC_DATA_CATALOG_CATEGORY_KEY.SPECIES,
         width: { max: "1fr", min: "164px" },