feat: add filters for taxonomic levels to organisms list (#301) (#306)

Author: hunterckx

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

@@ -21,6 +21,15 @@ export interface BRCDataCatalogGenome {
   speciesTaxonomyId: string;
   strain: string | null;
   taxonomicGroup: string[];
+  taxonomicLevelClass: string;
+  taxonomicLevelFamily: string;
+  taxonomicLevelGenus: string;
+  taxonomicLevelKingdom: string;
+  taxonomicLevelOrder: string;
+  taxonomicLevelPhylum: string;
+  taxonomicLevelSpecies: string;
+  taxonomicLevelStrain: string;
+  taxonomicLevelSuperkingdom: string;
   ucscBrowserUrl: string | null;
 }
 
@@ -29,8 +38,16 @@ export interface BRCDataCatalogOrganism {
   assemblyTaxonomyIds: string[];
   genomes: BRCDataCatalogGenome[];
   ncbiTaxonomyId: string;
-  species: string;
   taxonomicGroup: string[];
+  taxonomicLevelClass: string;
+  taxonomicLevelFamily: string;
+  taxonomicLevelGenus: string;
+  taxonomicLevelKingdom: string;
+  taxonomicLevelOrder: string;
+  taxonomicLevelPhylum: string;
+  taxonomicLevelSpecies: string;
+  taxonomicLevelStrain: string[];
+  taxonomicLevelSuperkingdom: string;
 }
 
 export interface EntitiesResponse<R> {

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

@@ -207,6 +207,20 @@ export const buildOrganismAssemblyTaxonomyIds = (
   };
 };
 
+/**
+ * Build props for the strain cell.
+ * @param organism - Organism entity.
+ * @returns Props to be used for the cell.
+ */
+export const buildOrganismTaxonomicLevelStrain = (
+  organism: BRCDataCatalogOrganism
+): ComponentProps<typeof C.NTagCell> => {
+  return {
+    label: "strains",
+    values: organism.taxonomicLevelStrain,
+  };
+};
+
 /**
  * Build props for the taxonomic group cell.
  * @param entity - Organism or genome entity.
@@ -221,20 +235,111 @@ export const buildTaxonomicGroup = (
   };
 };
 
+/**
+ * Build props for the class cell.
+ * @param organism - Organism entity.
+ * @returns Props to be used for the cell.
+ */
+export const buildTaxonomicLevelClass = (
+  organism: BRCDataCatalogOrganism
+): ComponentProps<typeof C.BasicCell> => {
+  return {
+    value: organism.taxonomicLevelClass,
+  };
+};
+
+/**
+ * Build props for the family cell.
+ * @param organism - Organism entity.
+ * @returns Props to be used for the cell.
+ */
+export const buildTaxonomicLevelFamily = (
+  organism: BRCDataCatalogOrganism
+): ComponentProps<typeof C.BasicCell> => {
+  return {
+    value: organism.taxonomicLevelFamily,
+  };
+};
+
+/**
+ * Build props for the genus cell.
+ * @param organism - Organism entity.
+ * @returns Props to be used for the cell.
+ */
+export const buildTaxonomicLevelGenus = (
+  organism: BRCDataCatalogOrganism
+): ComponentProps<typeof C.BasicCell> => {
+  return {
+    value: organism.taxonomicLevelGenus,
+  };
+};
+
+/**
+ * Build props for the kingdom cell.
+ * @param organism - Organism entity.
+ * @returns Props to be used for the cell.
+ */
+export const buildTaxonomicLevelKingdom = (
+  organism: BRCDataCatalogOrganism
+): ComponentProps<typeof C.BasicCell> => {
+  return {
+    value: organism.taxonomicLevelKingdom,
+  };
+};
+
+/**
+ * Build props for the order cell.
+ * @param organism - Organism entity.
+ * @returns Props to be used for the cell.
+ */
+export const buildTaxonomicLevelOrder = (
+  organism: BRCDataCatalogOrganism
+): ComponentProps<typeof C.BasicCell> => {
+  return {
+    value: organism.taxonomicLevelOrder,
+  };
+};
+
+/**
+ * Build props for the phylum cell.
+ * @param organism - Organism entity.
+ * @returns Props to be used for the cell.
+ */
+export const buildTaxonomicLevelPhylum = (
+  organism: BRCDataCatalogOrganism
+): ComponentProps<typeof C.BasicCell> => {
+  return {
+    value: organism.taxonomicLevelPhylum,
+  };
+};
+
 /**
  * Build props for the species cell.
  * @param organism - Organism entity.
  * @returns Props to be used for the cell.
  */
-export const buildOrganismSpecies = (
+export const buildTaxonomicLevelSpecies = (
   organism: BRCDataCatalogOrganism
 ): ComponentProps<typeof C.Link> => {
   return {
-    label: organism.species,
+    label: organism.taxonomicLevelSpecies,
     url: `${ROUTES.ORGANISMS}/${encodeURIComponent(getOrganismId(organism))}`,
   };
 };
 
+/**
+ * Build props for the superkingdom cell.
+ * @param organism - Organism entity.
+ * @returns Props to be used for the cell.
+ */
+export const buildTaxonomicLevelSuperkingdom = (
+  organism: BRCDataCatalogOrganism
+): ComponentProps<typeof C.BasicCell> => {
+  return {
+    value: organism.taxonomicLevelSuperkingdom,
+  };
+};
+
 /**
  * Build props for the scaffold count cell.
  * @param genome - Genome entity.
@@ -462,7 +567,7 @@ export const buildOrganismAssembliesHero = (
 ): ComponentProps<typeof C.BackPageHero> => {
   return {
     breadcrumbs: getOrganismEntityAssembliesBreadcrumbs(organism),
-    title: organism.species,
+    title: organism.taxonomicLevelSpecies,
   };
 };
 
@@ -593,7 +698,7 @@ function getOrganismEntityAssembliesBreadcrumbs(
 ): Breadcrumb[] {
   return [
     { path: ROUTES.ORGANISMS, text: "Organisms" },
-    { path: "", text: `${organism.species}` },
+    { path: "", text: `${organism.taxonomicLevelSpecies}` },
     { path: "", text: "Assemblies" },
   ];
 }