diff --git a/app/apis/catalog/brc-analytics-catalog/common/entities.ts b/app/apis/catalog/brc-analytics-catalog/common/entities.ts index 3087c32..28d0b20 100644 --- 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 index 935fde0..0baded0 100644 --- 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 index c364d2c..d960147 100644 --- 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 => { 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 index 3576b9b..ff24ba7 100644 --- a/files/build-catalog.ts +++ b/files/build-catalog.ts @@ -30,10 +30,10 @@ async function buildGenomes(): Promise { 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 index 203502b..771cac1 100644 --- 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 index 7a4519f..92fc0f1 100644 --- 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 index 42d2bf5..208d2a9 100644 --- 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 = { { 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 = { { componentConfig: { component: C.BasicCell, - viewBuilder: V.buildOrganism, + viewBuilder: V.buildTaxon, } as ComponentConfig, - 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 = { ], defaultSort: { desc: SORT_DIRECTION.ASCENDING, - id: BRC_DATA_CATALOG_CATEGORY_KEY.ORGANISM, + id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON, }, } as ListConfig, listView: {