feat: add ucsc browser column (#5)

data-catalog/app/apis/catalog/brc-analytics-catalog/common/entities.ts

@@ -6,5 +6,6 @@ export interface BRCDataCatalogGenome {
   species: string;
   strain: string;
   supercontigs: number;
+  ucscBrowserUrl: string | null;
   vEuPathDbProject: string;
 }

data-catalog/app/components/index.ts

@@ -1 +1,2 @@
+export { Link } from "@databiosphere/findable-ui/lib/components/Links/components/Link/link";
 export { BasicCell } from "@databiosphere/findable-ui/lib/components/Table/components/TableCell/components/BasicCell/basicCell";

data-catalog/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts

@@ -79,6 +79,25 @@ export const buildSupercontigs = (
   };
 };
 
+/**
+ * Build props for the UCSC browser URL cell.
+ * @param genome - Genome entity.
+ * @returns Props to be used for the cell.
+ */
+export const buildUcscBrowserUrl = (
+  genome: BRCDataCatalogGenome
+): React.ComponentProps<typeof C.Link> => {
+  return genome.ucscBrowserUrl
+    ? {
+        label: "UCSC Browser",
+        url: genome.ucscBrowserUrl,
+      }
+    : {
+        label: "Unspecified",
+        url: "",
+      };
+};
+
 /**
  * Build props for the VEuPathDB project cell.
  * @param genome - Genome entity.

data-catalog/files/build-catalog.ts

@@ -27,6 +27,7 @@ async function buildGenomes(): Promise<BRCDataCatalogGenome[]> {
       species: row.Species,
       strain: row.Strain,
       supercontigs: parseNumber(row.Supercontigs),
+      ucscBrowserUrl: parseStringOrNull(row.ucscBrowser),
       vEuPathDbProject: row["VEuPathDB Project"],
     })
   );
@@ -51,6 +52,10 @@ async function saveJson(filePath: string, data: unknown): Promise<void> {
   await fsp.writeFile(filePath, JSON.stringify(data, undefined, 2) + "\n");
 }
 
+function parseStringOrNull(value: string): string | null {
+  return value || null;
+}
+
 function parseNumber(value: string): number {
   value = value.trim();
   const n = Number(value);

data-catalog/files/entities.ts

@@ -1,12 +1,20 @@
 export interface SourceGenome {
+  asmId: string;
   Chromosomes: string;
+  comName: string;
   Contigs: string;
+  genBank: string;
   "Genome Source": string;
   "Genome Version/Assembly ID": string;
+  identical: string;
   "Is Reference Strain": string;
   Organism: string;
+  refSeq: string;
+  sciName: string;
   Species: string;
   Strain: string;
   Supercontigs: string;
+  taxId: string;
+  ucscBrowser: string;
   "VEuPathDB Project": string;
 }