feat: rename "organism" to "taxon" (#177)

galaxyproject · Nov 17, 2024 · 910ffd2 · 910ffd2
1 parent 2b98f8d
commit 910ffd2
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Showing 7 changed files with 36 additions and 36 deletions.
diff --git a/app/apis/catalog/brc-analytics-catalog/common/entities.ts b/app/apis/catalog/brc-analytics-catalog/common/entities.ts
@@ -20,10 +20,10 @@ export interface BRCDataCatalogGenome {
   length: number;
   level: string;
   ncbiTaxonomyId: string;
-  organism: string;
   scaffoldCount: number;
   scaffoldL50: number;
   scaffoldN50: number;
+  taxon: string;
   ucscBrowserUrl: string | null;
 }
 

diff --git a/app/apis/catalog/brc-analytics-catalog/common/utils.ts b/app/apis/catalog/brc-analytics-catalog/common/utils.ts
@@ -6,7 +6,7 @@ export function getGenomeId(genome: BRCDataCatalogGenome): string {
 
 export function getGenomeTitle(genome?: BRCDataCatalogGenome): string {
   if (!genome) return "";
-  return `${genome.organism}`;
+  return `${genome.taxon}`;
 }
 
 export function sanitizeEntityId(entityId?: string): string {

diff --git a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
@@ -150,15 +150,15 @@ export const buildLevel = (
 };
 
 /**
- * Build props for the organism cell.
+ * Build props for the taxon cell.
  * @param genome - Genome entity.
  * @returns Props to be used for the cell.
  */
-export const buildOrganism = (
+export const buildTaxon = (
   genome: BRCDataCatalogGenome
 ): ComponentProps<typeof C.BasicCell> => {
   return {
-    value: genome.organism,
+    value: genome.taxon,
   };
 };
 
@@ -289,7 +289,7 @@ export const buildGenomeDetails = (
   keyValuePairs.set(
     "Taxon",
     C.Link({
-      label: genome.organism,
+      label: genome.taxon,
       url: `https://www.ncbi.nlm.nih.gov/datasets/taxonomy/${encodeURIComponent(
         genome.ncbiTaxonomyId
       )}/`,
@@ -321,7 +321,7 @@ function getGenomeEntityChooseAnalysisMethodBreadcrumbs(
 ): Breadcrumb[] {
   return [
     { path: ROUTES.GENOMES, text: "Genomes" },
-    { path: "", text: `${genome.organism}` },
+    { path: "", text: `${genome.taxon}` },
     { path: "", text: "Choose Analysis Methods" },
   ];
 }
diff --git a/files/build-catalog.ts b/files/build-catalog.ts
@@ -30,10 +30,10 @@ async function buildGenomes(): Promise<BRCDataCatalogGenome[]> {
       length: parseNumber(row.length),
       level: row.level,
       ncbiTaxonomyId: row.taxonomyId,
-      organism: row.taxon,
       scaffoldCount: parseNumber(row.scaffoldCount),
       scaffoldL50: parseNumber(row.scaffoldL50),
       scaffoldN50: parseNumber(row.scaffoldN50),
+      taxon: row.taxon,
       ucscBrowserUrl: parseStringOrNull(row.ucscBrowser),
     })
   );

diff --git a/files/out/genomes.json b/files/out/genomes.json
@@ -10,10 +10,10 @@
     "length": 27007701,
     "level": "Chromosome",
     "ncbiTaxonomyId": "5855",
-    "organism": "Plasmodium vivax",
     "scaffoldCount": 2747,
     "scaffoldL50": 6,
     "scaffoldN50": 1678596,
+    "taxon": "Plasmodium vivax",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002415.2"
   },
   {
@@ -27,10 +27,10 @@
     "length": 26075494,
     "level": "Chromosome",
     "ncbiTaxonomyId": "185431",
-    "organism": "Trypanosoma brucei brucei TREU927",
     "scaffoldCount": 12,
     "scaffoldL50": 4,
     "scaffoldN50": 2481190,
+    "taxon": "Trypanosoma brucei brucei TREU927",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002445.2"
   },
   {
@@ -44,10 +44,10 @@
     "length": 32855089,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "347515",
-    "organism": "Leishmania major strain Friedlin",
     "scaffoldCount": 36,
     "scaffoldL50": 11,
     "scaffoldN50": 1091540,
+    "taxon": "Leishmania major strain Friedlin",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002725.2"
   },
   {
@@ -61,10 +61,10 @@
     "length": 23292622,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "36329",
-    "organism": "Plasmodium falciparum 3D7",
     "scaffoldCount": 14,
     "scaffoldL50": 5,
     "scaffoldN50": 1687656,
+    "taxon": "Plasmodium falciparum 3D7",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002765.5"
   },
   {
@@ -78,10 +78,10 @@
     "length": 32068771,
     "level": "Chromosome",
     "ncbiTaxonomyId": "420245",
-    "organism": "Leishmania braziliensis MHOM/BR/75/M2904",
     "scaffoldCount": 138,
     "scaffoldL50": 11,
     "scaffoldN50": 992961,
+    "taxon": "Leishmania braziliensis MHOM/BR/75/M2904",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002845.2"
   },
   {
@@ -95,10 +95,10 @@
     "length": 65633124,
     "level": "Chromosome",
     "ncbiTaxonomyId": "508771",
-    "organism": "Toxoplasma gondii ME49",
     "scaffoldCount": 2276,
     "scaffoldL50": 6,
     "scaffoldN50": 4973582,
+    "taxon": "Toxoplasma gondii ME49",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000006565.2"
   },
   {
@@ -112,10 +112,10 @@
     "length": 28947925,
     "level": "Scaffold",
     "ncbiTaxonomyId": "246410",
-    "organism": "Coccidioides immitis RS",
     "scaffoldCount": 6,
     "scaffoldL50": 3,
     "scaffoldN50": 4323945,
+    "taxon": "Coccidioides immitis RS",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000149335.2"
   },
   {
@@ -129,10 +129,10 @@
     "length": 4411532,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "83332",
-    "organism": "Mycobacterium tuberculosis H37Rv",
     "scaffoldCount": 1,
     "scaffoldL50": 1,
     "scaffoldN50": 4411532,
+    "taxon": "Mycobacterium tuberculosis H37Rv",
     "ucscBrowserUrl": null
   },
   {
@@ -146,10 +146,10 @@
     "length": 89937456,
     "level": "Scaffold",
     "ncbiTaxonomyId": "5693",
-    "organism": "Trypanosoma cruzi",
     "scaffoldCount": 29495,
     "scaffoldL50": 212,
     "scaffoldN50": 88624,
+    "taxon": "Trypanosoma cruzi",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000209065.1"
   },
   {
@@ -163,10 +163,10 @@
     "length": 32444968,
     "level": "Chromosome",
     "ncbiTaxonomyId": "5661",
-    "organism": "Leishmania donovani",
     "scaffoldCount": 36,
     "scaffoldL50": 11,
     "scaffoldN50": 1024085,
+    "taxon": "Leishmania donovani",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000227135.1"
   },
   {
@@ -180,10 +180,10 @@
     "length": 4411709,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "83332",
-    "organism": "Mycobacterium tuberculosis H37Rv",
     "scaffoldCount": 1,
     "scaffoldL50": 1,
     "scaffoldN50": 4411709,
+    "taxon": "Mycobacterium tuberculosis H37Rv",
     "ucscBrowserUrl": null
   },
   {
@@ -197,10 +197,10 @@
     "length": 196858,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "10244",
-    "organism": "Monkeypox virus",
     "scaffoldCount": 1,
     "scaffoldL50": 1,
     "scaffoldN50": 196858,
+    "taxon": "Monkeypox virus",
     "ucscBrowserUrl": null
   },
   {
@@ -214,10 +214,10 @@
     "length": 29903,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "2697049",
-    "organism": "Severe acute respiratory syndrome coronavirus 2",
     "scaffoldCount": 1,
     "scaffoldL50": 1,
     "scaffoldN50": 29903,
+    "taxon": "Severe acute respiratory syndrome coronavirus 2",
     "ucscBrowserUrl": null
   },
   {
@@ -231,10 +231,10 @@
     "length": 566339288,
     "level": "Chromosome",
     "ncbiTaxonomyId": "42434",
-    "organism": "Culex pipiens pallens",
     "scaffoldCount": 289,
     "scaffoldL50": 2,
     "scaffoldN50": 186194774,
+    "taxon": "Culex pipiens pallens",
     "ucscBrowserUrl": null
   },
   {
@@ -248,10 +248,10 @@
     "length": 28193268,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "443226",
-    "organism": "Coccidioides posadasii str. Silveira",
     "scaffoldCount": 9,
     "scaffoldL50": 2,
     "scaffoldN50": 8079863,
+    "taxon": "Coccidioides posadasii str. Silveira",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_018416015.2"
   },
   {
@@ -265,10 +265,10 @@
     "length": 4516435,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "1773",
-    "organism": "Mycobacterium tuberculosis",
     "scaffoldCount": 1,
     "scaffoldL50": 1,
     "scaffoldN50": 4516435,
+    "taxon": "Mycobacterium tuberculosis",
     "ucscBrowserUrl": null
   },
   {
@@ -282,10 +282,10 @@
     "length": 23043114,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "5861",
-    "organism": "Plasmodium yoelii",
     "scaffoldCount": 14,
     "scaffoldL50": 5,
     "scaffoldN50": 2046250,
+    "taxon": "Plasmodium yoelii",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_900002385.2"
   },
   {
@@ -299,10 +299,10 @@
     "length": 18338688,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "54757",
-    "organism": "Plasmodium vinckei vinckei",
     "scaffoldCount": 14,
     "scaffoldL50": 5,
     "scaffoldN50": 1692345,
+    "taxon": "Plasmodium vinckei vinckei",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_900681995.1"
   },
   {
@@ -316,10 +316,10 @@
     "length": 264451381,
     "level": "Chromosome",
     "ncbiTaxonomyId": "7165",
-    "organism": "Anopheles gambiae",
     "scaffoldCount": 190,
     "scaffoldL50": 2,
     "scaffoldN50": 99149756,
+    "taxon": "Anopheles gambiae",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943734735.2"
   },
   {
@@ -333,10 +333,10 @@
     "length": 4469156,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "1773",
-    "organism": "Mycobacterium tuberculosis",
     "scaffoldCount": 1,
     "scaffoldL50": 1,
     "scaffoldN50": 4469156,
+    "taxon": "Mycobacterium tuberculosis",
     "ucscBrowserUrl": null
   }
 ]
diff --git a/site-config/brc-analytics/category.ts b/site-config/brc-analytics/category.ts
@@ -8,10 +8,10 @@ export const BRC_DATA_CATALOG_CATEGORY_KEY = {
   IS_REF: "isRef",
   LENGTH: "length",
   LEVEL: "level",
-  ORGANISM: "organism",
   SCAFFOLD_COUNT: "scaffoldCount",
   SCAFFOLD_L50: "scaffoldL50",
   SCAFFOLD_N50: "scaffoldN50",
+  TAXON: "taxon",
   TAXONOMY_ID: "ncbiTaxonomyId",
   UCSC_BROWSER_URL: "ucscBrowserUrl",
 };
@@ -26,10 +26,10 @@ export const BRC_DATA_CATALOG_CATEGORY_LABEL = {
   IS_REF: "Is Reference",
   LENGTH: "Length",
   LEVEL: "Level",
-  ORGANISM: "Organism",
   SCAFFOLD_COUNT: "Scaffolds",
   SCAFFOLD_L50: "Scaffold L50",
   SCAFFOLD_N50: "Scaffold N50",
+  TAXON: "Taxon",
   TAXONOMY_ID: "Taxonomy ID",
   UCSC_BROWSER_URL: "UCSC Browser",
 };
diff --git a/site-config/brc-analytics/local/index/genomeEntityConfig.ts b/site-config/brc-analytics/local/index/genomeEntityConfig.ts
@@ -30,8 +30,8 @@ export const genomeEntityConfig: BRCEntityConfig<BRCDataCatalogGenome> = {
       {
         categoryConfigs: [
           {
-            key: BRC_DATA_CATALOG_CATEGORY_KEY.ORGANISM,
-            label: BRC_DATA_CATALOG_CATEGORY_LABEL.ORGANISM,
+            key: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON,
+            label: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXON,
           },
           {
             key: BRC_DATA_CATALOG_CATEGORY_KEY.TAXONOMY_ID,
@@ -99,10 +99,10 @@ export const genomeEntityConfig: BRCEntityConfig<BRCDataCatalogGenome> = {
       {
         componentConfig: {
           component: C.BasicCell,
-          viewBuilder: V.buildOrganism,
+          viewBuilder: V.buildTaxon,
         } as ComponentConfig<typeof C.BasicCell, BRCDataCatalogGenome>,
-        header: BRC_DATA_CATALOG_CATEGORY_LABEL.ORGANISM,
-        id: BRC_DATA_CATALOG_CATEGORY_KEY.ORGANISM,
+        header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXON,
+        id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON,
         width: { max: "1fr", min: "284px" },
       },
       {
@@ -217,7 +217,7 @@ export const genomeEntityConfig: BRCEntityConfig<BRCDataCatalogGenome> = {
     ],
     defaultSort: {
       desc: SORT_DIRECTION.ASCENDING,
-      id: BRC_DATA_CATALOG_CATEGORY_KEY.ORGANISM,
+      id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON,
     },
   } as ListConfig<BRCDataCatalogGenome>,
   listView: {