feat: add taxonomic levels to assembly list (#312) (#316)

Author: hunterckx

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

@@ -17,9 +17,8 @@ export interface BRCDataCatalogGenome {
   scaffoldCount: number | null;
   scaffoldL50: number | null;
   scaffoldN50: number | null;
-  species: string;
   speciesTaxonomyId: string;
-  strain: string | null;
+  strainName: string | null;
   taxonomicGroup: string[];
   taxonomicLevelClass: string;
   taxonomicLevelFamily: string;

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

@@ -7,7 +7,7 @@ export function getGenomeId(genome: BRCDataCatalogGenome): string {
 
 export function getGenomeTitle(genome?: BRCDataCatalogGenome): string {
   if (!genome) return "";
-  return `${genome.species}`;
+  return `${genome.taxonomicLevelSpecies}`;
 }
 
 export function getOrganismId(organism: BRCDataCatalogOrganism): string {

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

@@ -145,15 +145,28 @@ export const buildGcPercent = (
  * @param genome - Genome entity.
  * @returns Props to be used for the cell.
  */
-export const buildGenomeSpecies = (
+export const buildGenomeTaxonomicLevelSpecies = (
   genome: BRCDataCatalogGenome
 ): ComponentProps<typeof C.Link> => {
   return {
-    label: genome.species,
+    label: genome.taxonomicLevelSpecies,
     url: `${ROUTES.ORGANISMS}/${encodeURIComponent(getGenomeOrganismId(genome))}`,
   };
 };
 
+/**
+ * Build props for the strain cell.
+ * @param genome - Genome entity.
+ * @returns Props to be used for the cell.
+ */
+export const buildGenomeTaxonomicLevelStrain = (
+  genome: BRCDataCatalogGenome
+): ComponentProps<typeof C.BasicCell> => {
+  return {
+    value: getGenomeStrainText(genome),
+  };
+};
+
 /**
  * Build props for the "is ref" cell.
  * @param genome - Genome entity.
@@ -207,6 +220,20 @@ export const buildOrganismAssemblyTaxonomyIds = (
   };
 };
 
+/**
+ * Build props for the species cell.
+ * @param organism - Organism entity.
+ * @returns Props to be used for the cell.
+ */
+export const buildOrganismTaxonomicLevelSpecies = (
+  organism: BRCDataCatalogOrganism
+): ComponentProps<typeof C.Link> => {
+  return {
+    label: organism.taxonomicLevelSpecies,
+    url: `${ROUTES.ORGANISMS}/${encodeURIComponent(getOrganismId(organism))}`,
+  };
+};
+
 /**
  * Build props for the strain cell.
  * @param organism - Organism entity.
@@ -237,106 +264,92 @@ export const buildTaxonomicGroup = (
 
 /**
  * Build props for the class cell.
- * @param organism - Organism entity.
+ * @param entity - Organism or genome entity.
  * @returns Props to be used for the cell.
  */
 export const buildTaxonomicLevelClass = (
-  organism: BRCDataCatalogOrganism
+  entity: BRCDataCatalogOrganism | BRCDataCatalogGenome
 ): ComponentProps<typeof C.BasicCell> => {
   return {
-    value: organism.taxonomicLevelClass,
+    value: entity.taxonomicLevelClass,
   };
 };
 
 /**
  * Build props for the family cell.
- * @param organism - Organism entity.
+ * @param entity - Organism or genome entity.
  * @returns Props to be used for the cell.
  */
 export const buildTaxonomicLevelFamily = (
-  organism: BRCDataCatalogOrganism
+  entity: BRCDataCatalogOrganism | BRCDataCatalogGenome
 ): ComponentProps<typeof C.BasicCell> => {
   return {
-    value: organism.taxonomicLevelFamily,
+    value: entity.taxonomicLevelFamily,
   };
 };
 
 /**
  * Build props for the genus cell.
- * @param organism - Organism entity.
+ * @param entity - Organism or genome entity.
  * @returns Props to be used for the cell.
  */
 export const buildTaxonomicLevelGenus = (
-  organism: BRCDataCatalogOrganism
+  entity: BRCDataCatalogOrganism | BRCDataCatalogGenome
 ): ComponentProps<typeof C.BasicCell> => {
   return {
-    value: organism.taxonomicLevelGenus,
+    value: entity.taxonomicLevelGenus,
   };
 };
 
 /**
  * Build props for the kingdom cell.
- * @param organism - Organism entity.
+ * @param entity - Organism or genome entity.
  * @returns Props to be used for the cell.
  */
 export const buildTaxonomicLevelKingdom = (
-  organism: BRCDataCatalogOrganism
+  entity: BRCDataCatalogOrganism | BRCDataCatalogGenome
 ): ComponentProps<typeof C.BasicCell> => {
   return {
-    value: organism.taxonomicLevelKingdom,
+    value: entity.taxonomicLevelKingdom,
   };
 };
 
 /**
  * Build props for the order cell.
- * @param organism - Organism entity.
+ * @param entity - Organism or genome entity.
  * @returns Props to be used for the cell.
  */
 export const buildTaxonomicLevelOrder = (
-  organism: BRCDataCatalogOrganism
+  entity: BRCDataCatalogOrganism | BRCDataCatalogGenome
 ): ComponentProps<typeof C.BasicCell> => {
   return {
-    value: organism.taxonomicLevelOrder,
+    value: entity.taxonomicLevelOrder,
   };
 };
 
 /**
  * Build props for the phylum cell.
- * @param organism - Organism entity.
+ * @param entity - Organism or genome entity.
  * @returns Props to be used for the cell.
  */
 export const buildTaxonomicLevelPhylum = (
-  organism: BRCDataCatalogOrganism
+  entity: BRCDataCatalogOrganism | BRCDataCatalogGenome
 ): 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 buildTaxonomicLevelSpecies = (
-  organism: BRCDataCatalogOrganism
-): ComponentProps<typeof C.Link> => {
-  return {
-    label: organism.taxonomicLevelSpecies,
-    url: `${ROUTES.ORGANISMS}/${encodeURIComponent(getOrganismId(organism))}`,
+    value: entity.taxonomicLevelPhylum,
   };
 };
 
 /**
  * Build props for the superkingdom cell.
- * @param organism - Organism entity.
+ * @param entity - Organism or genome entity.
  * @returns Props to be used for the cell.
  */
 export const buildTaxonomicLevelSuperkingdom = (
-  organism: BRCDataCatalogOrganism
+  entity: BRCDataCatalogOrganism | BRCDataCatalogGenome
 ): ComponentProps<typeof C.BasicCell> => {
   return {
-    value: organism.taxonomicLevelSuperkingdom,
+    value: entity.taxonomicLevelSuperkingdom,
   };
 };
 
@@ -379,19 +392,6 @@ export const buildScaffoldN50 = (
   };
 };
 
-/**
- * Build props for the strain cell.
- * @param genome - Genome entity.
- * @returns Props to be used for the cell.
- */
-export const buildStrain = (
-  genome: BRCDataCatalogGenome
-): ComponentProps<typeof C.BasicCell> => {
-  return {
-    value: genome.strain,
-  };
-};
-
 /**
  * Build props for the taxonomy ID cell.
  * @param genome - Genome entity.
@@ -479,7 +479,7 @@ export const buildGenomeChooseAnalysisMethodDetailViewHero = (
     breadcrumbs: getGenomeEntityChooseAnalysisMethodBreadcrumbs(genome),
     subTitle: C.Link({
       TypographyProps: { color: "ink.light", variant: TEXT_BODY_SMALL_400 },
-      label: `Species: ${genome.species}`,
+      label: `Species: ${genome.taxonomicLevelSpecies}`,
       underline: "hover",
       url: `${ROUTES.ORGANISMS}/${encodeURIComponent(getGenomeOrganismId(genome))}`,
     }),
@@ -497,15 +497,15 @@ export const buildGenomeDetails = (
 ): ComponentProps<typeof C.KeyValuePairs> => {
   const keyValuePairs = new Map<Key, Value>();
   keyValuePairs.set(
-    BRC_DATA_CATALOG_CATEGORY_LABEL.SPECIES,
+    BRC_DATA_CATALOG_CATEGORY_LABEL.TAXONOMIC_LEVEL_SPECIES,
     C.Link({
-      label: genome.species,
+      label: genome.taxonomicLevelSpecies,
       url: `${ROUTES.ORGANISMS}/${encodeURIComponent(getGenomeOrganismId(genome))}`,
     })
   );
   keyValuePairs.set(
-    BRC_DATA_CATALOG_CATEGORY_LABEL.STRAIN,
-    genome.strain ?? LABEL.UNSPECIFIED
+    BRC_DATA_CATALOG_CATEGORY_LABEL.TAXONOMIC_LEVEL_STRAIN,
+    getGenomeStrainText(genome, LABEL.UNSPECIFIED)
   );
   keyValuePairs.set(
     BRC_DATA_CATALOG_CATEGORY_LABEL.TAXONOMY_ID,
@@ -611,9 +611,10 @@ function buildOrganismGenomesTableColumns(): ColumnDef<BRCDataCatalogGenome>[] {
       header: BRC_DATA_CATALOG_CATEGORY_LABEL.ACCESSION,
     },
     {
-      accessorKey: BRC_DATA_CATALOG_CATEGORY_KEY.STRAIN,
-      cell: ({ row }) => C.BasicCell(buildStrain(row.original)),
-      header: BRC_DATA_CATALOG_CATEGORY_LABEL.STRAIN,
+      accessorKey: BRC_DATA_CATALOG_CATEGORY_KEY.TAXONOMIC_LEVEL_STRAIN,
+      cell: ({ row }) =>
+        C.BasicCell(buildGenomeTaxonomicLevelStrain(row.original)),
+      header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXONOMIC_LEVEL_STRAIN,
     },
     {
       accessorKey: BRC_DATA_CATALOG_CATEGORY_KEY.TAXONOMY_ID,
@@ -688,6 +689,22 @@ function getGenomeEntityChooseAnalysisMethodBreadcrumbs(
   ];
 }
 
+/**
+ * Get text for genome strain, consisting of, from highest to lowest priority, either: strain-only name; strain name including species; or the specified default value.
+ * @param genome - Genome entity.
+ * @param defaultValue - Default value to use if there's no strain.
+ * @returns strain text.
+ */
+function getGenomeStrainText(
+  genome: BRCDataCatalogGenome,
+  defaultValue = ""
+): string {
+  if (genome.strainName) return genome.strainName;
+  if (genome.taxonomicLevelStrain !== "None")
+    return genome.taxonomicLevelStrain;
+  return defaultValue;
+}
+
 /**
  * Get the organism entity breadcrumbs.
  * @param organism - Organism entity.

catalog/build/ts/build-catalog.ts

@@ -51,6 +51,7 @@ async function buildGenomes(): Promise<BRCDataCatalogGenome[]> {
       console.log(`Skipping assembly ${row.accession} - ploidy not found`);
       continue;
     }
+    const taxonomicLevelStrain = row.taxonomicLevelStrain || (row.strain ? `${row.taxonomicLevelSpecies} strain ${row.strain}` : "None");
     mappedRows.push({
       accession: row.accession,
       annotationStatus: parseStringOrNull(row.annotationStatus),
@@ -66,9 +67,8 @@ async function buildGenomes(): Promise<BRCDataCatalogGenome[]> {
       scaffoldCount: parseNumberOrNull(row.scaffoldCount),
       scaffoldL50: parseNumberOrNull(row.scaffoldL50),
       scaffoldN50: parseNumberOrNull(row.scaffoldN50),
-      species: row.species,
       speciesTaxonomyId: row.speciesTaxonomyId,
-      strain: parseStringOrNull(row.strain),
+      strainName: parseStringOrNull(row.strain),
       taxonomicGroup: row.taxonomicGroup ? row.taxonomicGroup.split(",") : [],
       taxonomicLevelClass: defaultStringToNone(row.taxonomicLevelClass),
       taxonomicLevelFamily: defaultStringToNone(row.taxonomicLevelFamily),
@@ -77,7 +77,7 @@ async function buildGenomes(): Promise<BRCDataCatalogGenome[]> {
       taxonomicLevelOrder: defaultStringToNone(row.taxonomicLevelOrder),
       taxonomicLevelPhylum: defaultStringToNone(row.taxonomicLevelPhylum),
       taxonomicLevelSpecies: defaultStringToNone(row.taxonomicLevelSpecies),
-      taxonomicLevelStrain: defaultStringToNone(row.taxonomicLevelStrain),
+      taxonomicLevelStrain,
       taxonomicLevelSuperkingdom: defaultStringToNone(row.taxonomicLevelSuperkingdom),
       ucscBrowserUrl: parseStringOrNull(row.ucscBrowser),
     });