feat: add realm to taxonomic lineage filters (#389) (#390)

Author: hunterckx

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

@@ -28,6 +28,7 @@ export interface BRCDataCatalogGenome {
   taxonomicLevelKingdom: string;
   taxonomicLevelOrder: string;
   taxonomicLevelPhylum: string;
+  taxonomicLevelRealm: string;
   taxonomicLevelSpecies: string;
   taxonomicLevelStrain: string;
   ucscBrowserUrl: string | null;
@@ -46,6 +47,7 @@ export interface BRCDataCatalogOrganism {
   taxonomicLevelKingdom: string;
   taxonomicLevelOrder: string;
   taxonomicLevelPhylum: string;
+  taxonomicLevelRealm: string;
   taxonomicLevelSpecies: string;
   taxonomicLevelStrain: string[];
 }

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

@@ -353,6 +353,19 @@ export const buildTaxonomicLevelPhylum = (
   };
 };
 
+/**
+ * Build props for the realm cell.
+ * @param entity - Organism or genome entity.
+ * @returns Props to be used for the cell.
+ */
+export const buildTaxonomicLevelRealm = (
+  entity: BRCDataCatalogOrganism | BRCDataCatalogGenome
+): ComponentProps<typeof C.BasicCell> => {
+  return {
+    value: entity.taxonomicLevelRealm,
+  };
+};
+
 /**
  * Build props for the scaffold count cell.
  * @param genome - Genome entity.

catalog/build/intermediate/genomes-from-ncbi.tsv

@@ -26,13 +26,14 @@
 }
 
 TAXANOMIC_LEVELS_FOR_TREE = [
-  "domain", 
-  "kingdom", 
-  "phylum", 
-  "class", 
-  "order", 
-  "family", 
-  "genus", 
+  "domain",
+  "realm",
+  "kingdom",
+  "phylum",
+  "class",
+  "order",
+  "family",
+  "genus",
   "species",
   "strain"
 ]

catalog/build/py/build-files-from-ncbi.py

@@ -104,6 +104,7 @@ async function buildGenomes(): Promise<BRCDataCatalogGenome[]> {
       taxonomicLevelKingdom: defaultStringToNone(row.taxonomicLevelKingdom),
       taxonomicLevelOrder: defaultStringToNone(row.taxonomicLevelOrder),
       taxonomicLevelPhylum: defaultStringToNone(row.taxonomicLevelPhylum),
+      taxonomicLevelRealm: defaultStringToNone(row.taxonomicLevelRealm),
       taxonomicLevelSpecies: defaultStringToNone(row.taxonomicLevelSpecies),
       taxonomicLevelStrain,
       ucscBrowserUrl: parseStringOrNull(row.ucscBrowser),
@@ -147,6 +148,7 @@ function buildOrganism(
     taxonomicLevelKingdom: genome.taxonomicLevelKingdom,
     taxonomicLevelOrder: genome.taxonomicLevelOrder,
     taxonomicLevelPhylum: genome.taxonomicLevelPhylum,
+    taxonomicLevelRealm: genome.taxonomicLevelRealm,
     taxonomicLevelSpecies: genome.taxonomicLevelSpecies,
     taxonomicLevelStrain: accumulateArrayValue(
       organism?.taxonomicLevelStrain,

catalog/build/ts/build-catalog.ts

@@ -22,6 +22,7 @@ export const SOURCE_GENOME_KEYS = [
   "taxonomicLevelKingdom",
   "taxonomicLevelOrder",
   "taxonomicLevelPhylum",
+  "taxonomicLevelRealm",
   "taxonomicLevelSpecies",
   "taxonomicLevelStrain",
   "taxonomicLevelDomain",