diff --git a/app/apis/catalog/brc-analytics-catalog/common/entities.ts b/app/apis/catalog/brc-analytics-catalog/common/entities.ts index 6ec031a..fb529c2 100644 --- a/app/apis/catalog/brc-analytics-catalog/common/entities.ts +++ b/app/apis/catalog/brc-analytics-catalog/common/entities.ts @@ -10,17 +10,30 @@ export enum ANALYSIS_METHOD { export type BRCCatalog = BRCDataCatalogGenome; export interface BRCDataCatalogGenome { - chromosomes: number; - contigs: number; - geneModelUrl: string; - genomeVersionAssemblyId: string; + accession: string; + annotationStatus: string | null; + chromosomes: number | null; + coverage: string | null; + gcPercent: number; + geneModelUrl: string | null; + isRef: string; + length: number; + level: string; ncbiTaxonomyId: string; - organism: string; - species: string; - strain: string; - supercontigs: number; - ucscBrowserUrl: string; - vEuPathDbProject: string; + scaffoldCount: number; + scaffoldL50: number; + scaffoldN50: number; + strain: string | null; + tags: string[]; + taxon: string; + ucscBrowserUrl: string | null; +} + +export interface BRCDataCatalogOrganism { + assemblyCount: number; + ncbiTaxonomyId: string; + tags: string[]; + taxon: string; } export interface EntitiesResponse { diff --git a/app/apis/catalog/brc-analytics-catalog/common/utils.ts b/app/apis/catalog/brc-analytics-catalog/common/utils.ts index 8146c3b..45fc474 100644 --- a/app/apis/catalog/brc-analytics-catalog/common/utils.ts +++ b/app/apis/catalog/brc-analytics-catalog/common/utils.ts @@ -1,12 +1,16 @@ -import { BRCDataCatalogGenome } from "./entities"; +import { BRCDataCatalogGenome, BRCDataCatalogOrganism } from "./entities"; export function getGenomeId(genome: BRCDataCatalogGenome): string { - return sanitizeEntityId(genome.genomeVersionAssemblyId); + return sanitizeEntityId(genome.accession); } export function getGenomeTitle(genome?: BRCDataCatalogGenome): string { if (!genome) return ""; - return `${genome.species} - ${genome.strain}`; + return `${genome.taxon}`; +} + +export function getOrganismId(organism: BRCDataCatalogOrganism): string { + return sanitizeEntityId(organism.ncbiTaxonomyId); } export function sanitizeEntityId(entityId?: string): string { diff --git a/app/components/Entity/components/AnalysisMethod/types.ts b/app/components/Entity/components/AnalysisMethod/types.ts index 3c8fb1a..852c04a 100644 --- a/app/components/Entity/components/AnalysisMethod/types.ts +++ b/app/components/Entity/components/AnalysisMethod/types.ts @@ -4,6 +4,6 @@ import { ANALYSIS_METHOD } from "../../../../apis/catalog/brc-analytics-catalog/ export interface Props { analysisMethod: ANALYSIS_METHOD; content: ReactNode; - geneModelUrl: string; + geneModelUrl: string | null; genomeVersionAssemblyId: string; } diff --git a/app/components/Home/components/Section/components/SectionHero/sectionHero.tsx b/app/components/Home/components/Section/components/SectionHero/sectionHero.tsx index 0069043..21faa17 100644 --- a/app/components/Home/components/Section/components/SectionHero/sectionHero.tsx +++ b/app/components/Home/components/Section/components/SectionHero/sectionHero.tsx @@ -32,7 +32,7 @@ export const SectionHero = (): JSX.Element => { annotations and functional insights into disease-causing organisms and their carriers - diff --git a/app/components/Home/content/sectionSubHero.mdx b/app/components/Home/content/sectionSubHero.mdx index da94f3a..0512771 100644 --- a/app/components/Home/content/sectionSubHero.mdx +++ b/app/components/Home/content/sectionSubHero.mdx @@ -1,5 +1,5 @@ BRC Analytics is your new destination for analysis of biological data related to pathogens. Building on the foundation of VEuPathDb the platform will provide access and analysis capabilities for -[785 eukaryotic pathogens](/data/organisms), hosts, and vectors. The functionality will +[785 eukaryotic pathogens](/data/genomes), hosts, and vectors. The functionality will be developed and made available incrementally over the [following months](/roadmap). diff --git a/app/components/common/StyledLink/styledLink.styles.tsx b/app/components/common/StyledLink/styledLink.styles.tsx new file mode 100644 index 0000000..c0e74c5 --- /dev/null +++ b/app/components/common/StyledLink/styledLink.styles.tsx @@ -0,0 +1,6 @@ +import { Link } from "@databiosphere/findable-ui/lib/components/Links/components/Link/link"; +import styled from "@emotion/styled"; + +export const StyledLink = styled(Link)` + text-decoration: underline; +`; diff --git a/app/components/index.ts b/app/components/index.ts index 53ec783..88553d9 100644 --- a/app/components/index.ts +++ b/app/components/index.ts @@ -22,7 +22,9 @@ export { export { Logo } from "@databiosphere/findable-ui/lib/components/Layout/components/Header/components/Content/components/Logo/logo"; export { Link } from "@databiosphere/findable-ui/lib/components/Links/components/Link/link"; export { BasicCell } from "@databiosphere/findable-ui/lib/components/Table/components/TableCell/components/BasicCell/basicCell"; +export { NTagCell } from "@databiosphere/findable-ui/lib/components/Table/components/TableCell/components/NTagCell/nTagCell"; export { CopyText } from "./common/CopyText/copyText"; +export { StyledLink } from "./common/StyledLink/styledLink.styles"; export { AnalysisMethod } from "./Entity/components/AnalysisMethod/analysisMethod"; export { AnalysisMethods } from "./Entity/components/AnalysisMethods/analysisMethods"; export { AnalysisMethodsTitle } from "./Entity/components/AnalysisMethodsTitle/analysisMethodsTitle"; diff --git a/app/utils/galaxy-api.ts b/app/utils/galaxy-api.ts index 4063b9d..be3705f 100644 --- a/app/utils/galaxy-api.ts +++ b/app/utils/galaxy-api.ts @@ -32,7 +32,7 @@ const WORKFLOW_LANDING_URL_PREFIX = export async function getWorkflowLandingUrl( workflowId: WORKFLOW_ID, referenceGenome: string, - geneModelUrl: string + geneModelUrl: string | null ): Promise { const body: WorkflowLandingsBody = { public: true, @@ -74,7 +74,7 @@ function buildFastaUrl(identifier: string): string { function getWorkflowLandingsRequestState( workflowId: WORKFLOW_ID, referenceGenome: string, - geneModelUrl: string + geneModelUrl: string | null ): WorkflowLandingsBodyRequestState { if (workflowId === WORKFLOW_ID.VARIANT_CALLING && geneModelUrl) { return { diff --git a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts index 49a7e47..cd0edbf 100644 --- a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts +++ b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts @@ -3,13 +3,30 @@ import { Key, Value, } from "@databiosphere/findable-ui/lib/components/common/KeyValuePairs/keyValuePairs"; +import { LinkProps } from "@databiosphere/findable-ui/lib/components/Links/components/Link/link"; import { ViewContext } from "@databiosphere/findable-ui/lib/config/entities"; import { ComponentProps } from "react"; import { ROUTES } from "../../../../../routes/constants"; -import { BRCDataCatalogGenome } from "../../../../apis/catalog/brc-analytics-catalog/common/entities"; +import { + BRCDataCatalogGenome, + BRCDataCatalogOrganism, +} from "../../../../apis/catalog/brc-analytics-catalog/common/entities"; import * as C from "../../../../components"; import { GENOME_BROWSER, NCBI_DATASETS_URL } from "./constants"; +/** + * Build props for the accession cell. + * @param genome - Genome entity. + * @returns Props to be used for the cell. + */ +export const buildAccession = ( + genome: BRCDataCatalogGenome +): ComponentProps => { + return { + value: genome.accession, + }; +}; + /** * Build props for the genome analysis cell. * @param genome - Genome entity. @@ -20,18 +37,20 @@ export const buildAnalyzeGenome = ( genome: BRCDataCatalogGenome, viewContext: ViewContext ): ComponentProps => { - const { genomeVersionAssemblyId, ncbiTaxonomyId, ucscBrowserUrl } = genome; + const { accession, ncbiTaxonomyId, ucscBrowserUrl } = genome; const rowId = viewContext.cellContext?.row?.id; return { analyze: { label: "Analyze", - url: rowId ? `${ROUTES.ORGANISMS}/${rowId}` : "", + url: rowId ? `${ROUTES.GENOMES}/${rowId}` : "", }, views: [ - { label: "UCSC Genome Browser", url: ucscBrowserUrl }, + ...(ucscBrowserUrl + ? [{ label: "UCSC Genome Browser", url: ucscBrowserUrl }] + : []), { label: "NCBI Genome Assembly", - url: `${NCBI_DATASETS_URL}/genome/${genomeVersionAssemblyId}`, + url: `${NCBI_DATASETS_URL}/genome/${accession}`, }, { label: "NCBI Taxonomy", @@ -43,6 +62,32 @@ export const buildAnalyzeGenome = ( }; }; +/** + * Build props for the annotation status cell. + * @param genome - Genome entity. + * @returns Props to be used for the cell. + */ +export const buildAnnotationStatus = ( + genome: BRCDataCatalogGenome +): ComponentProps => { + return { + value: genome.annotationStatus, + }; +}; + +/** + * Build props for the assemblies cell. + * @param organism - Genome entity. + * @returns Props to be used for the cell. + */ +export const buildAssemblyCount = ( + organism: BRCDataCatalogOrganism +): ComponentProps => { + return { + value: organism.assemblyCount, + }; +}; + /** * Build props for the chromosomes cell. * @param genome - Genome entity. @@ -57,179 +102,270 @@ export const buildChromosomes = ( }; /** - * Build props for the contigs cell. + * Build props for the coverage cell. * @param genome - Genome entity. * @returns Props to be used for the cell. */ -export const buildContigs = ( +export const buildCoverage = ( genome: BRCDataCatalogGenome ): ComponentProps => { return { - value: genome.contigs, + value: genome.coverage, }; }; /** - * Build props for the genome AnalysisMethod component. + * Build props for the GC% cell. * @param genome - Genome entity. - * @param analysisMethodProps - Analysis Method properties. - * @param analysisMethodProps.analysisMethod - Analysis method. - * @param analysisMethodProps.content - Content to be displayed. - * @returns Props to be used for the AnalysisMethod component. + * @returns Props to be used for the cell. */ -export const buildGenomeAnalysisMethod = ( - genome: BRCDataCatalogGenome, - analysisMethodProps: Pick< - ComponentProps, - "analysisMethod" | "content" - > -): ComponentProps => { +export const buildGcPercent = ( + genome: BRCDataCatalogGenome +): ComponentProps => { return { - ...analysisMethodProps, - geneModelUrl: genome.geneModelUrl, - genomeVersionAssemblyId: genome.genomeVersionAssemblyId, + value: genome.gcPercent, }; }; /** - * Build props for the genome AnalysisPortals component. + * Build props for the taxon cell. * @param genome - Genome entity. - * @returns Props to be used for the AnalysisPortals component. + * @returns Props to be used for the cell. */ -export const buildGenomeAnalysisPortals = ( +export const buildGenomeTaxon = ( genome: BRCDataCatalogGenome -): ComponentProps => { +): ComponentProps => { return { - portals: [ - { - imageProps: { - alt: GENOME_BROWSER, - src: "/analysis-portals/ucsc-genome.png", - width: 20, - }, - label: GENOME_BROWSER, - url: genome.ucscBrowserUrl, - }, - ], + value: genome.taxon, }; }; /** - * Build props for the genome DetailViewHero component. + * Build props for the "is ref" cell. * @param genome - Genome entity. - * @returns Props to be used for the DetailViewHero component. + * @returns Props to be used for the cell. */ -export const buildGenomeChooseAnalysisMethodDetailViewHero = ( +export const buildIsRef = ( genome: BRCDataCatalogGenome -): ComponentProps => { +): ComponentProps => { return { - breadcrumbs: C.Breadcrumbs({ - breadcrumbs: getGenomeEntityChooseAnalysisMethodBreadcrumbs(genome), - }), - title: "Choose Analysis Methods", + value: genome.isRef, }; }; /** - * Build props for the genome detail KeyValuePairs component. + * Build props for the length cell. * @param genome - Genome entity. - * @returns Props to be used for the KeyValuePairs component. + * @returns Props to be used for the cell. */ -export const buildGenomeDetails = ( +export const buildLength = ( genome: BRCDataCatalogGenome -): ComponentProps => { - const keyValuePairs = new Map(); - keyValuePairs.set( - "Species", - C.Link({ - label: genome.species, - url: `https://www.ncbi.nlm.nih.gov/datasets/taxonomy/${encodeURIComponent( - genome.ncbiTaxonomyId - )}/`, - }) - ); - keyValuePairs.set("Strain", genome.strain); - keyValuePairs.set( - "Assembly Version ID", - C.CopyText({ - children: genome.genomeVersionAssemblyId, - value: genome.genomeVersionAssemblyId, - }) - ); - keyValuePairs.set("VeUPathDB Project", genome.vEuPathDbProject); - keyValuePairs.set("Contigs", genome.contigs); - keyValuePairs.set("Super Contigs", genome.supercontigs); - keyValuePairs.set("Chromosomes", genome.chromosomes); +): ComponentProps => { return { - KeyElType: C.KeyElType, - KeyValuesElType: (props) => C.Stack({ gap: 4, ...props }), - ValueElType: C.ValueElType, - keyValuePairs, + value: genome.length, }; }; /** - * Build props for the genome version/assembly ID cell. + * Build props for the level cell. * @param genome - Genome entity. * @returns Props to be used for the cell. */ -export const buildGenomeVersionAssemblyId = ( +export const buildLevel = ( genome: BRCDataCatalogGenome ): ComponentProps => { return { - value: genome.genomeVersionAssemblyId, + value: genome.level, }; }; /** - * Build props for the species cell. + * Build props for the taxon cell. + * @param organism - Organism entity. + * @returns Props to be used for the cell. + */ +export const buildOrganismTaxon = ( + organism: BRCDataCatalogOrganism +): ComponentProps => { + return { + label: organism.taxon, + url: getTaxonGenomesUrlObject(organism.taxon), + }; +}; + +/** + * Build props for the scaffold count cell. * @param genome - Genome entity. * @returns Props to be used for the cell. */ -export const buildSpecies = ( +export const buildScaffoldCount = ( genome: BRCDataCatalogGenome ): ComponentProps => { return { - value: genome.species, + value: genome.scaffoldCount, }; }; /** - * Build props for the strain cell. + * Build props for the scaffold L50 cell. * @param genome - Genome entity. * @returns Props to be used for the cell. */ -export const buildStrain = ( +export const buildScaffoldL50 = ( genome: BRCDataCatalogGenome ): ComponentProps => { return { - value: genome.strain, + value: genome.scaffoldL50, }; }; /** - * Build props for the supercontigs cell. + * Build props for the scaffold N50 cell. * @param genome - Genome entity. * @returns Props to be used for the cell. */ -export const buildSupercontigs = ( +export const buildScaffoldN50 = ( genome: BRCDataCatalogGenome ): ComponentProps => { return { - value: genome.supercontigs, + value: genome.scaffoldN50, }; }; /** - * Build props for the VEuPathDB project cell. + * Build props for the strain cell. * @param genome - Genome entity. * @returns Props to be used for the cell. */ -export const buildVEuPathDbProject = ( +export const buildStrain = ( genome: BRCDataCatalogGenome ): ComponentProps => { return { - value: genome.vEuPathDbProject, + value: genome.strain, + }; +}; + +/** + * Build props for the tags cell. + * @param genome - Genome entity. + * @returns Props to be used for the cell. + */ +export const buildTags = ( + genome: BRCDataCatalogOrganism | BRCDataCatalogGenome +): ComponentProps => { + return { + label: "Tags", + values: genome.tags, + }; +}; + +/** + * Build props for the taxonomy ID cell. + * @param genome - Genome entity. + * @returns Props to be used for the cell. + */ +export const buildTaxonomyId = ( + genome: BRCDataCatalogOrganism | BRCDataCatalogGenome +): ComponentProps => { + return { + value: genome.ncbiTaxonomyId, + }; +}; + +/** + * Build props for the genome AnalysisMethod component. + * @param genome - Genome entity. + * @param analysisMethodProps - Analysis Method properties. + * @param analysisMethodProps.analysisMethod - Analysis method. + * @param analysisMethodProps.content - Content to be displayed. + * @returns Props to be used for the AnalysisMethod component. + */ +export const buildGenomeAnalysisMethod = ( + genome: BRCDataCatalogGenome, + analysisMethodProps: Pick< + ComponentProps, + "analysisMethod" | "content" + > +): ComponentProps => { + return { + ...analysisMethodProps, + geneModelUrl: genome.geneModelUrl, + genomeVersionAssemblyId: genome.accession, + }; +}; + +/** + * Build props for the genome AnalysisPortals component. + * @param genome - Genome entity. + * @returns Props to be used for the AnalysisPortals component. + */ +export const buildGenomeAnalysisPortals = ( + genome: BRCDataCatalogGenome +): ComponentProps => { + return { + portals: genome.ucscBrowserUrl + ? [ + { + imageProps: { + alt: GENOME_BROWSER, + src: "/analysis-portals/ucsc-genome.png", + width: 20, + }, + label: GENOME_BROWSER, + url: genome.ucscBrowserUrl, + }, + ] + : [], + }; +}; + +/** + * Build props for the genome DetailViewHero component. + * @param genome - Genome entity. + * @returns Props to be used for the DetailViewHero component. + */ +export const buildGenomeChooseAnalysisMethodDetailViewHero = ( + genome: BRCDataCatalogGenome +): ComponentProps => { + return { + breadcrumbs: C.Breadcrumbs({ + breadcrumbs: getGenomeEntityChooseAnalysisMethodBreadcrumbs(genome), + }), + title: "Choose Analysis Methods", + }; +}; + +/** + * Build props for the genome detail KeyValuePairs component. + * @param genome - Genome entity. + * @returns Props to be used for the KeyValuePairs component. + */ +export const buildGenomeDetails = ( + genome: BRCDataCatalogGenome +): ComponentProps => { + const keyValuePairs = new Map(); + keyValuePairs.set( + "Taxon", + C.Link({ + label: genome.taxon, + url: `https://www.ncbi.nlm.nih.gov/datasets/taxonomy/${encodeURIComponent( + genome.ncbiTaxonomyId + )}/`, + }) + ); + keyValuePairs.set( + "Accession", + C.CopyText({ + children: genome.accession, + value: genome.accession, + }) + ); + keyValuePairs.set("Chromosomes", genome.chromosomes); + return { + KeyElType: C.KeyElType, + KeyValuesElType: (props) => C.Stack({ gap: 4, ...props }), + ValueElType: C.ValueElType, + keyValuePairs, }; }; @@ -242,8 +378,29 @@ function getGenomeEntityChooseAnalysisMethodBreadcrumbs( genome: BRCDataCatalogGenome ): Breadcrumb[] { return [ - { path: ROUTES.ORGANISMS, text: "Organisms" }, - { path: "", text: `${genome.species} - ${genome.strain}` }, + { path: ROUTES.GENOMES, text: "Genomes" }, + { path: "", text: `${genome.taxon}` }, { path: "", text: "Choose Analysis Methods" }, ]; } + +/** + * Get URL object for genomes filtered by a given taxon. + * @param taxon - Taxon. + * @returns URL object. + */ +function getTaxonGenomesUrlObject(taxon: string): LinkProps["url"] { + return { + href: ROUTES.GENOMES, + query: encodeURIComponent( + JSON.stringify({ + filter: [ + { + categoryKey: "taxon", + value: [taxon], + }, + ], + }) + ), + }; +} diff --git a/files/build-catalog.ts b/files/build-catalog.ts index 8573975..e3f7b88 100644 --- a/files/build-catalog.ts +++ b/files/build-catalog.ts @@ -1,14 +1,27 @@ import { parse as parseCsv } from "csv-parse/sync"; import fsp from "fs/promises"; -import { BRCDataCatalogGenome } from "../app/apis/catalog/brc-analytics-catalog/common/entities"; -import { SourceGenome } from "./entities"; +import { + BRCDataCatalogGenome, + BRCDataCatalogOrganism, +} from "../app/apis/catalog/brc-analytics-catalog/common/entities"; +import { SourceGenome, SourceOrganism } from "./entities"; -const SOURCE_PATH_GENOMES = "files/source/genomes.tsv"; +const SOURCE_PATH_ORGANISMS = "files/source/organisms-from-ncbi.tsv"; +const SOURCE_PATH_GENOMES = "files/source/genomes-from-ncbi.tsv"; buildCatalog(); async function buildCatalog(): Promise { - const genomes = await buildGenomes(); + const organisms = await buildOrganisms(); + + const organismsByTaxon = new Map( + organisms.map((organism) => [organism.taxon, organism]) + ); + + const genomes = await buildGenomes(organismsByTaxon); + + console.log("Organisms:", genomes.length); + await saveJson("files/out/organisms.json", organisms); console.log("Genomes:", genomes.length); await saveJson("files/out/genomes.json", genomes); @@ -16,28 +29,51 @@ async function buildCatalog(): Promise { console.log("Done"); } -async function buildGenomes(): Promise { - const sourceRows = await readValuesFile(SOURCE_PATH_GENOMES); - const mappedRows = sourceRows.map( - (row): BRCDataCatalogGenome => ({ - chromosomes: parseNumber(row.Chromosomes), - contigs: parseNumber(row.Contigs), - geneModelUrl: row.geneModelUrl, - genomeVersionAssemblyId: row["Genome Version/Assembly ID"], - ncbiTaxonomyId: row.taxId, - organism: row.Organism, - species: row.Species, - strain: row.Strain, - supercontigs: parseNumber(row.Supercontigs), - ucscBrowserUrl: row.ucscBrowser, - vEuPathDbProject: row["VEuPathDB Project"], - }) +async function buildOrganisms(): Promise { + const sourceRows = await readValuesFile( + SOURCE_PATH_ORGANISMS ); + const mappedRows = sourceRows.map((row): BRCDataCatalogOrganism => { + return { + assemblyCount: parseNumber(row.assemblyCount), + ncbiTaxonomyId: row.taxonomyId, + tags: row.CustomTags ? [row.CustomTags] : [], + taxon: row.taxon, + }; + }); return mappedRows.sort((a, b) => - a.genomeVersionAssemblyId.localeCompare(b.genomeVersionAssemblyId) + a.ncbiTaxonomyId.localeCompare(b.ncbiTaxonomyId) ); } +async function buildGenomes( + organismsByTaxon: Map +): Promise { + const sourceRows = await readValuesFile(SOURCE_PATH_GENOMES); + const mappedRows = sourceRows.map((row): BRCDataCatalogGenome => { + return { + accession: row.accession, + annotationStatus: parseStringOrNull(row.annotationStatus), + chromosomes: parseNumberOrNull(row.chromosomeCount), + coverage: parseStringOrNull(row.coverage), + gcPercent: parseNumber(row.gcPercent), + geneModelUrl: parseStringOrNull(row.geneModelUrl), + isRef: parseBoolean(row.isRef), + length: parseNumber(row.length), + level: row.level, + ncbiTaxonomyId: row.taxonomyId, + scaffoldCount: parseNumber(row.scaffoldCount), + scaffoldL50: parseNumber(row.scaffoldL50), + scaffoldN50: parseNumber(row.scaffoldN50), + strain: parseStringOrNull(row.strain), + tags: organismsByTaxon.get(row.taxon)?.tags ?? [], + taxon: row.taxon, + ucscBrowserUrl: parseStringOrNull(row.ucscBrowser), + }; + }); + return mappedRows.sort((a, b) => a.accession.localeCompare(b.accession)); +} + async function readValuesFile( filePath: string, delimiter = "\t" @@ -54,6 +90,15 @@ async function saveJson(filePath: string, data: unknown): Promise { await fsp.writeFile(filePath, JSON.stringify(data, undefined, 2) + "\n"); } +function parseStringOrNull(value: string): string | null { + return value || null; +} + +function parseNumberOrNull(value: string): number | null { + if (!value) return null; + return parseNumber(value); +} + function parseNumber(value: string): number { value = value.trim(); const n = Number(value); @@ -61,3 +106,7 @@ function parseNumber(value: string): number { throw new Error(`Invalid number value: ${JSON.stringify(value)}`); return n; } + +function parseBoolean(value: string): string { + return value[0].toLowerCase() === "t" ? "Yes" : "No"; +} diff --git a/files/build-files-from-ncbi.py b/files/build-files-from-ncbi.py index 8a0717b..a882381 100644 --- a/files/build-files-from-ncbi.py +++ b/files/build-files-from-ncbi.py @@ -1,6 +1,7 @@ -from urllib.parse import quote as url_quote import pandas as pd import requests +import urllib.parse +import re TAXA_URL = "https://docs.google.com/spreadsheets/d/1Gg9sw2Qw765tOx2To53XkTAn-RAMiBtqYrfItlLXXrc/gviz/tq?tqx=out:csv&sheet=Sheet1.csv" @@ -14,26 +15,34 @@ def build_taxonomy_request_body(taxa): return {"taxons": taxa, "children": False, "ranks": ["genus"]} -def get_organism_row(organism_taxonomy): +def get_organism_row(organism_info, accession): + if len(organism_info.get("errors", [])) > 0: + raise Exception(organism_info) + + organism_taxonomy = organism_info["taxonomy"] + return { "taxon": organism_taxonomy["current_scientific_name"]["name"], - "taxonomyId": organism_taxonomy["tax_id"], - "assemblyCount": next(count["count"] for count in organism_taxonomy["counts"] if count["type"] == "COUNT_TYPE_ASSEMBLY"), + "taxonomyId": str(organism_taxonomy["tax_id"]), + "assemblyCount": 1, + "accession": accession, } -def get_organisms_df(taxa): - return pd.DataFrame([get_organism_row(organism_info["taxonomy"]) for organism_info in requests.post(TAXONOMY_URL, json=build_taxonomy_request_body(taxa)).json()["reports"]]) +def get_organisms_df(taxa_with_accessions): + organisms_info_with_accessions = [(organism_info, accession) for taxon, accession in taxa_with_accessions for organism_info in requests.post(TAXONOMY_URL, json=build_taxonomy_request_body([taxon])).json()["reports"]] + return pd.DataFrame([get_organism_row(organism_info, accession) for organism_info, accession in organisms_info_with_accessions]) def get_tax_ids(organisms_df): return list(organisms_df["taxonomyId"]) -def build_genomes_url(tax_ids): - return f"https://api.ncbi.nlm.nih.gov/datasets/v2/genome/taxon/{url_quote(",".join([str(id) for id in tax_ids]))}/dataset_report?filters.assembly_source=refseq&filters.has_annotation=true&filters.exclude_paired_reports=true&filters.exclude_atypical=true&filters.assembly_level=scaffold&filters.assembly_level=chromosome&filters.assembly_level=complete_genome" +def build_genomes_url(tax_ids, next_page_token): + return f"https://api.ncbi.nlm.nih.gov/datasets/v2/genome/taxon/{urllib.parse.quote(",".join([str(id) for id in tax_ids]))}/dataset_report?page_size=1000{"&page_token=" + next_page_token if next_page_token else ""}&filters.assembly_source=refseq&filters.has_annotation=true&filters.exclude_paired_reports=true&filters.exclude_atypical=true&filters.assembly_level=scaffold&filters.assembly_level=chromosome&filters.assembly_level=complete_genome" -def get_genome_row(genome_info): +def get_genome_row(genome_info, taxon): refseq_category = genome_info["assembly_info"].get("refseq_category") return { - "taxon": genome_info["organism"]["organism_name"], + "taxon": taxon, + "strain": genome_info["organism"].get("infraspecific_names", {}).get("strain", ""), "taxonomyId": genome_info["organism"]["tax_id"], "accession": genome_info["accession"], "isRef": refseq_category == "reference genome", @@ -49,15 +58,62 @@ def get_genome_row(genome_info): "pairedAccession": genome_info["paired_accession"], } -def get_genomes_df(tax_ids): - return pd.DataFrame(data=[get_genome_row(genome_info) for genome_info in requests.get(build_genomes_url(tax_ids)).json()["reports"]]) +def get_organism_genomes_results(tax_id): + page = 1 + next_page_token = None + results = [] + while next_page_token or page == 1: + print(f"Requesting page {page} of taxon {tax_id}") + page_data = requests.get(build_genomes_url([tax_id], next_page_token)).json() + results += page_data["reports"] + next_page_token = page_data.get("next_page_token") + page += 1 + return results + +def get_organism_genomes(tax_id, accession): + return [genome_info for genome_info in get_organism_genomes_results(tax_id) if genome_info["accession"] == accession] + +def get_genomes_df(organism_ids): + genomes_info_with_organisms = [(genome_info, taxon) for tax_id, taxon, accession in organism_ids for genome_info in get_organism_genomes(tax_id, accession)] + return pd.DataFrame(data=[get_genome_row(*info) for info in genomes_info_with_organisms]) + +def _id_to_gene_model_url(asm_id): + hubs_url = "https://hgdownload.soe.ucsc.edu/hubs/" + components = [asm_id[0:3], asm_id[4:7], asm_id[7:10], asm_id[10:13], asm_id, "genes"] + url = urllib.parse.urljoin(hubs_url, "/".join(components)) + # url looks something like https://hgdownload.soe.ucsc.edu/hubs/GCF/030/504/385/GCF_030504385.1/genes/ + # and contains html content with links to gene models. + # we need to scrape this to get the gtf + print(f"fetching url {url}") + response = requests.get(url) + try: + response.raise_for_status() + except Exception: + # FIXME?: Some accessions don't have a gene folder + return None + # find link to gtf, should ideally be ncbiRefSeq, but augustus will do + html_content = response.text + pattern = rf"{asm_id.replace('.', r'\.')}.*?\.gtf\.gz" + augustus_file = None + for match in re.findall(pattern, html_content): + if "ncbiRefSeq" in match: + return urllib.parse.urljoin(f"{url}/", match) + elif "augustus" in match: + augustus_file = match + if augustus_file: + return urllib.parse.urljoin(f"{url}/", augustus_file) + # No match, I guess that's OK ? + return None + +def add_gene_model_url(genomes_df: pd.DataFrame): + return pd.concat([genomes_df, genomes_df["accession"].apply(_id_to_gene_model_url).rename("geneModelUrl")], axis="columns") def build_files(): print("Building files") taxa_df = pd.read_csv(TAXA_URL, keep_default_na=False) - organisms_source_df = get_organisms_df(list(taxa_df["Name"])) + organisms_source_df = get_organisms_df([(taxon.strip(), accession.strip()) for taxon, accession in zip(taxa_df["Name"], taxa_df["RefSeq Accession"]) if taxon]) organisms_df = organisms_source_df.merge(taxa_df[["TaxId", "CustomTags"]], how="left", left_on="taxonomyId", right_on="TaxId").drop(columns=["TaxId"]) @@ -65,13 +121,17 @@ def build_files(): print(f"Wrote to {ORGANISMS_OUTPUT_PATH}") - genomes_source_df = get_genomes_df(get_tax_ids(organisms_df)) + genomes_source_df = get_genomes_df(zip(organisms_df["taxonomyId"], organisms_df["taxon"], organisms_df["accession"])) assemblies_df = pd.DataFrame(requests.get(ASSEMBLIES_URL).json()["data"])[["ucscBrowser", "genBank", "refSeq"]] - gen_bank_merge_df = genomes_source_df.merge(assemblies_df, how="left", left_on="pairedAccession", right_on="genBank") + gen_bank_merge_df = genomes_source_df.merge(assemblies_df, how="left", left_on="accession", right_on="genBank") ref_seq_merge_df = genomes_source_df.merge(assemblies_df, how="left", left_on="accession", right_on="refSeq") - genomes_df = gen_bank_merge_df.combine_first(ref_seq_merge_df) + unmatched_accessions = genomes_source_df["accession"][~(genomes_source_df["accession"].isin(assemblies_df["genBank"]) | genomes_source_df["accession"].isin(assemblies_df["refSeq"]))] + if len(unmatched_accessions) > 0: + print(f"{len(unmatched_accessions)} accessions had no match in assembly list: {", ".join(unmatched_accessions)}") + + genomes_df = add_gene_model_url(gen_bank_merge_df.combine_first(ref_seq_merge_df)) genomes_df.to_csv(GENOMES_OUTPUT_PATH, index=False, sep="\t") diff --git a/files/entities.ts b/files/entities.ts index dad7cc1..a96f44f 100644 --- a/files/entities.ts +++ b/files/entities.ts @@ -1,21 +1,25 @@ export interface SourceGenome { - asmId: string; - Chromosomes: string; - comName: string; - Contigs: string; - genBank: string; + accession: string; + annotationStatus: string; + chromosomeCount: string; + coverage: string; + gcPercent: string; geneModelUrl: string; - "Genome Source": string; - "Genome Version/Assembly ID": string; - identical: string; - "Is Reference Strain": string; - Organism: string; - refSeq: string; - sciName: string; - Species: string; - Strain: string; - Supercontigs: string; - taxId: string; + isRef: string; + length: string; + level: string; + scaffoldCount: string; + scaffoldL50: string; + scaffoldN50: string; + strain: string; + taxon: string; + taxonomyId: string; ucscBrowser: string; - "VEuPathDB Project": string; +} + +export interface SourceOrganism { + assemblyCount: string; + CustomTags: string; + taxon: string; + taxonomyId: string; } diff --git a/files/out/genomes.json b/files/out/genomes.json index 14bb70e..7fe173d 100644 --- a/files/out/genomes.json +++ b/files/out/genomes.json @@ -1,9674 +1,433 @@ [ { - "chromosomes": 7, - "contigs": 0, - "genomeVersionAssemblyId": "GCA_000001215.4", - "ncbiTaxonomyId": "7227", - "organism": "Drosophila melanogaster iso-1", - "species": "Drosophila melanogaster", - "strain": "iso-1", - "supercontigs": 1862, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000001215.4", - "vEuPathDbProject": "VectorBase", - "geneModelUrl": "" - }, - { - "chromosomes": 0, - "contigs": 0, - "genomeVersionAssemblyId": "GCA_000001985.1", - "ncbiTaxonomyId": "441960", - "organism": "Talaromyces marneffei ATCC 18224", - "species": "Talaromyces marneffei", - "strain": "ATCC 18224", - "supercontigs": 452, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000001985.1", - "vEuPathDbProject": "FungiDB", - "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCA/000/001/985/GCA_000001985.1/genes/GCA_000001985.1_JCVI-PMFA1-2.0.augustus.gtf.gz" - }, - { - "chromosomes": 14, - "contigs": 2733, - "genomeVersionAssemblyId": "GCA_000002415.2", + "accession": "GCF_000002415.2", + "annotationStatus": "Full annotation", + "chromosomes": 14, + "coverage": null, + "gcPercent": 42.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/415/GCF_000002415.2/genes/GCF_000002415.2_ASM241v2.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 27007701, + "level": "Chromosome", "ncbiTaxonomyId": "5855", - "organism": "Plasmodium vivax Sal-1", - "species": "Plasmodium vivax", - "strain": "Sal-1", - "supercontigs": 0, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002415.2", - "vEuPathDbProject": "PlasmoDB", - "geneModelUrl": "" - }, - { - "chromosomes": 5, - "contigs": 0, - "genomeVersionAssemblyId": "GCA_000002435.2", - "ncbiTaxonomyId": "5741", - "organism": "Giardia Assemblage A isolate WB 2019", - "species": "Giardia Assemblage A", - "strain": "isolate WB 2019", - "supercontigs": 30, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002435.2", - "vEuPathDbProject": "GiardiaDB", - "geneModelUrl": "" - }, - { - "chromosomes": 16, - "contigs": 115, - "genomeVersionAssemblyId": "GCA_000002445.1", + "scaffoldCount": 2747, + "scaffoldL50": 6, + "scaffoldN50": 1678596, + "strain": "Salvador I", + "tags": [ + "VEuPathDB" + ], + "taxon": "Plasmodium vivax", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002415.2" + }, + { + "accession": "GCF_000002445.2", + "annotationStatus": "Full annotation", + "chromosomes": 11, + "coverage": null, + "gcPercent": 46.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/445/GCF_000002445.2/genes/GCF_000002445.2_ASM244v1.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 26075494, + "level": "Chromosome", "ncbiTaxonomyId": "185431", - "organism": "Trypanosoma brucei brucei TREU927", - "species": "Trypanosoma brucei", - "strain": "brucei TREU927", - "supercontigs": 0, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002445.2", - "vEuPathDbProject": "TriTrypDB", - "geneModelUrl": "" - }, - { - "chromosomes": 7, - "contigs": 0, - "genomeVersionAssemblyId": "GCA_000002495.2", - "ncbiTaxonomyId": "242507", - "organism": "Pyricularia oryzae 70-15", - "species": "Pyricularia oryzae", - "strain": "70-15", - "supercontigs": 46, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002495.2", - "vEuPathDbProject": "FungiDB", - "geneModelUrl": "" - }, - { - "chromosomes": 6, - "contigs": 0, - "genomeVersionAssemblyId": "GCA_000002515.1", - "ncbiTaxonomyId": "28985", - "organism": "Kluyveromyces lactis NRRL Y-1140", - "species": "Kluyveromyces lactis", - "strain": "NRRL Y-1140", - "supercontigs": 0, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002515.2", - "vEuPathDbProject": "FungiDB", - "geneModelUrl": "" - }, - { - "chromosomes": 6, - "contigs": 0, - "genomeVersionAssemblyId": "GCA_000002525.1", - "ncbiTaxonomyId": "284591", - "organism": "Yarrowia lipolytica CLIB122", - "species": "Yarrowia lipolytica", - "strain": "CLIB122", - "supercontigs": 0, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002525.2", - "vEuPathDbProject": "FungiDB", - "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCA/000/002/525/GCA_000002525.1/genes/GCA_000002525.1_ASM252v1.augustus.gtf.gz" - }, - { - "chromosomes": 13, - "contigs": 0, - "genomeVersionAssemblyId": "GCA_000002545.2", - "ncbiTaxonomyId": "5478", - "organism": "Nakaseomyces glabratus CBS 138", - "species": "Nakaseomyces glabratus", - "strain": "CBS 138", - "supercontigs": 0, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002545.3", - "vEuPathDbProject": "FungiDB", - "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCA/000/002/545/GCA_000002545.2/genes/GCA_000002545.2_ASM254v2.augustus.gtf.gz" - }, - { + "scaffoldCount": 12, + "scaffoldL50": 4, + "scaffoldN50": 2481190, + "strain": null, + "tags": [ + "VEuPathDB" + ], + "taxon": "Trypanosoma brucei", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002445.2" + }, + { + "accession": "GCF_000002655.1", + "annotationStatus": "Full annotation", "chromosomes": 8, - "contigs": 0, - "genomeVersionAssemblyId": "GCA_000002655.1", + "coverage": null, + "gcPercent": 50, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/655/GCF_000002655.1/genes/GCF_000002655.1_ASM265v1.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 29384958, + "level": "Chromosome", "ncbiTaxonomyId": "330879", - "organism": "Aspergillus fumigatus Af293", - "species": "Aspergillus fumigatus", + "scaffoldCount": 8, + "scaffoldL50": 4, + "scaffoldN50": 3948441, "strain": "Af293", - "supercontigs": 0, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002655.1", - "vEuPathDbProject": "FungiDB", - "geneModelUrl": "" - }, - { - "chromosomes": 0, - "contigs": 0, - "genomeVersionAssemblyId": "GCA_000002715.1", - "ncbiTaxonomyId": "344612", - "organism": "Aspergillus clavatus NRRL 1", - "species": "Aspergillus clavatus", - "strain": "NRRL 1", - "supercontigs": 143, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002715.2", - "vEuPathDbProject": "FungiDB", - "geneModelUrl": "" + "tags": [], + "taxon": "Aspergillus fumigatus", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002655.1" }, { + "accession": "GCF_000002725.2", + "annotationStatus": "Full annotation", "chromosomes": 36, - "contigs": 0, - "genomeVersionAssemblyId": "GCA_000002725.2", + "coverage": null, + "gcPercent": 59.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/725/GCF_000002725.2/genes/GCF_000002725.2_ASM272v2.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 32855089, + "level": "Complete Genome", "ncbiTaxonomyId": "347515", - "organism": "Leishmania major strain Friedlin", - "species": "Leishmania major", - "strain": "strain Friedlin", - "supercontigs": 0, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002725.2", - "vEuPathDbProject": "TriTrypDB", - "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCA/000/002/725/GCA_000002725.2/genes/GCA_000002725.2_ASM272v2.augustus.gtf.gz" - }, - { - "chromosomes": 14, - "contigs": 0, - "genomeVersionAssemblyId": "GCA_000002765.3", + "scaffoldCount": 36, + "scaffoldL50": 11, + "scaffoldN50": 1091540, + "strain": "Friedlin", + "tags": [ + "VEuPathDB" + ], + "taxon": "Leishmania major", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002725.2" + }, + { + "accession": "GCF_000002765.6", + "annotationStatus": "Full annotation", + "chromosomes": 14, + "coverage": "100.0x", + "gcPercent": 19.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/765/GCF_000002765.6/genes/GCF_000002765.6_GCA_000002765.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 23292622, + "level": "Complete Genome", "ncbiTaxonomyId": "36329", - "organism": "Plasmodium falciparum 3D7", - "species": "Plasmodium falciparum", - "strain": "3D7", - "supercontigs": 0, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002765.5", - "vEuPathDbProject": "PlasmoDB", - "geneModelUrl": "" - }, - { - "chromosomes": 0, - "contigs": 0, - "genomeVersionAssemblyId": "GCA_000002825.1", - "ncbiTaxonomyId": "412133", - "organism": "Trichomonas vaginalis G3", - "species": "Trichomonas vaginalis", - "strain": "G3", - "supercontigs": 64764, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002825.2", - "vEuPathDbProject": "TrichDB", - "geneModelUrl": "" - }, - { - "chromosomes": 36, - "contigs": 103, - "genomeVersionAssemblyId": "GCA_000002845.2", + "scaffoldCount": 14, + "scaffoldL50": 5, + "scaffoldN50": 1687656, + "strain": null, + "tags": [ + "VEuPathDB" + ], + "taxon": "Plasmodium falciparum", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002765.6" + }, + { + "accession": "GCF_000002845.2", + "annotationStatus": null, + "chromosomes": 35, + "coverage": null, + "gcPercent": 58, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/845/GCF_000002845.2/genes/GCF_000002845.2_ASM284v2.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 32068771, + "level": "Chromosome", "ncbiTaxonomyId": "420245", - "organism": "Leishmania braziliensis MHOM/BR/75/M2904", - "species": "Leishmania braziliensis", + "scaffoldCount": 138, + "scaffoldL50": 11, + "scaffoldN50": 992961, "strain": "MHOM/BR/75/M2904", - "supercontigs": 0, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002845.2", - "vEuPathDbProject": "TriTrypDB", - "geneModelUrl": "" - }, - { - "chromosomes": 0, - "contigs": 0, - "genomeVersionAssemblyId": "GCA_000002855.2", - "ncbiTaxonomyId": "5061", - "organism": "Aspergillus niger CBS 513.88", - "species": "Aspergillus niger", - "strain": "CBS 513.88", - "supercontigs": 19, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002855.4", - "vEuPathDbProject": "FungiDB", - "geneModelUrl": "" - }, - { - "chromosomes": 0, - "contigs": 5617, - "genomeVersionAssemblyId": "GCA_000003085.2", - "ncbiTaxonomyId": "73239", - "organism": "Plasmodium yoelii yoelii 17XNL", - "species": "Plasmodium yoelii", - "strain": "yoelii 17XNL", - "supercontigs": 0, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000003085.2", - "vEuPathDbProject": "PlasmoDB", - "geneModelUrl": "" - }, - { - "chromosomes": 0, - "contigs": 0, - "genomeVersionAssemblyId": "GCA_000003125.1", - "ncbiTaxonomyId": "441959", - "organism": "Talaromyces stipitatus ATCC 10500", - "species": "Talaromyces stipitatus", - "strain": "ATCC 10500", - "supercontigs": 820, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000003125.1", - "vEuPathDbProject": "FungiDB", - "geneModelUrl": "" - }, - { - "chromosomes": 4, - "contigs": 0, - "genomeVersionAssemblyId": "GCA_000003225.1", - "ncbiTaxonomyId": "5874", - "organism": "Theileria annulata strain Ankara", - "species": "Theileria annulata", - "strain": "strain Ankara", - "supercontigs": 0, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000003225.1", - "vEuPathDbProject": "PiroplasmaDB", - "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCA/000/003/225/GCA_000003225.1/genes/GCA_000003225.1_ASM322v1.augustus.gtf.gz" - }, - { - "chromosomes": 0, - "contigs": 0, - "genomeVersionAssemblyId": "GCA_000003515.2", - 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}, - { - "chromosomes": 18, - "contigs": 0, - "genomeVersionAssemblyId": "GCF_947242115.1", - "ncbiTaxonomyId": "6526", - "organism": "Biomphalaria glabrata XG47", - "species": "Biomphalaria glabrata", - "strain": "XG47", - "supercontigs": 25, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_947242115.1", - "vEuPathDbProject": "VectorBase", - "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/947/242/115/GCF_947242115.1/genes/GCF_947242115.1_xgBioGlab47.1.ncbiRefSeq.gtf.gz" + "scaffoldCount": 190, + "scaffoldL50": 2, + "scaffoldN50": 99149756, + "strain": null, + "tags": [ + "VEuPathDB" + ], + "taxon": "Anopheles gambiae", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943734735.2" } ] diff --git a/files/out/organisms.json b/files/out/organisms.json new file mode 100644 index 0000000..6d29b69 --- /dev/null +++ b/files/out/organisms.json @@ -0,0 +1,160 @@ +[ + { + "assemblyCount": 1, + "ncbiTaxonomyId": "10244", + "tags": [ + "Virus" + ], + "taxon": "Monkeypox virus" + }, + { + "assemblyCount": 1, + "ncbiTaxonomyId": "1773", + "tags": [ + "Bact" + ], + "taxon": "Mycobacterium tuberculosis" + }, + { + "assemblyCount": 1, + "ncbiTaxonomyId": "199306", + "tags": [ + "VEuPathDB" + ], + "taxon": "Coccidioides posadasii" + }, + { + "assemblyCount": 1, + "ncbiTaxonomyId": "2697049", + "tags": [ + "Virus" + ], + "taxon": "Severe acute respiratory syndrome coronavirus 2" + }, + { + "assemblyCount": 1, + "ncbiTaxonomyId": "42434", + "tags": [], + "taxon": "Culex pipiens pallens" + }, + { + "assemblyCount": 1, + "ncbiTaxonomyId": "5207", + "tags": [], + "taxon": "Cryptococcus neoformans" + }, + { + "assemblyCount": 1, + "ncbiTaxonomyId": "5476", + "tags": [], + "taxon": "Candida albicans" + }, + { + "assemblyCount": 1, + "ncbiTaxonomyId": "5501", + "tags": [], + "taxon": "Coccidioides immitis" + }, + { + "assemblyCount": 1, + "ncbiTaxonomyId": "5660", + "tags": [ + "VEuPathDB" + ], + "taxon": "Leishmania braziliensis" + }, + { + "assemblyCount": 1, + "ncbiTaxonomyId": "5661", + "tags": [ + "VEuPathDB" + ], + "taxon": "Leishmania donovani" + }, + { + "assemblyCount": 1, + "ncbiTaxonomyId": "5664", + "tags": [ + "VEuPathDB" + ], + "taxon": "Leishmania major" + }, + { + "assemblyCount": 1, + "ncbiTaxonomyId": "5691", + "tags": [ + "VEuPathDB" + ], + "taxon": "Trypanosoma brucei" + }, + { + "assemblyCount": 1, + "ncbiTaxonomyId": "5693", + "tags": [ + "VEuPathDB" + ], + "taxon": "Trypanosoma cruzi" + }, + { + "assemblyCount": 1, + "ncbiTaxonomyId": "5811", + "tags": [ + "VEuPathDB" + ], + "taxon": "Toxoplasma gondii" + }, + { + "assemblyCount": 1, + "ncbiTaxonomyId": "5833", + "tags": [ + "VEuPathDB" + ], + "taxon": "Plasmodium falciparum" + }, + { + "assemblyCount": 1, + "ncbiTaxonomyId": "5855", + "tags": [ + "VEuPathDB" + ], + "taxon": "Plasmodium vivax" + }, + { + "assemblyCount": 1, + "ncbiTaxonomyId": "5860", + "tags": [ + "VEuPathDB" + ], + "taxon": "Plasmodium vinckei" + }, + { + "assemblyCount": 1, + "ncbiTaxonomyId": "5861", + "tags": [ + "VEuPathDB" + ], + "taxon": "Plasmodium yoelii" + }, + { + "assemblyCount": 1, + "ncbiTaxonomyId": "7165", + "tags": [ + "VEuPathDB" + ], + "taxon": "Anopheles gambiae" + }, + { + "assemblyCount": 1, + "ncbiTaxonomyId": "7176", + "tags": [ + "VEuPathDB" + ], + "taxon": "Culex quinquefasciatus" + }, + { + "assemblyCount": 1, + "ncbiTaxonomyId": "746128", + "tags": [], + "taxon": "Aspergillus fumigatus" + } +] diff --git a/files/source/genomes-from-ncbi.tsv b/files/source/genomes-from-ncbi.tsv index 8876bf3..5b137dc 100644 --- a/files/source/genomes-from-ncbi.tsv +++ b/files/source/genomes-from-ncbi.tsv @@ -1,21 +1,22 @@ -taxon taxonomyId accession isRef level chromosomeCount length scaffoldCount scaffoldN50 scaffoldL50 coverage gcPercent annotationStatus pairedAccession ucscBrowser genBank refSeq -Mycobacterium tuberculosis H37Rv 83332 GCF_000195955.2 True Complete Genome 1.0 4411532 1 4411532 1 65.5 GCA_000195955.2 -Plasmodium falciparum 3D7 36329 GCF_000002765.6 True Complete Genome 14.0 23292622 14 1687656 5 100.0x 19.5 Full annotation GCA_000002765.3 https://genome.ucsc.edu/h/GCF_000002765.5 GCA_000002765.3 GCF_000002765.5 -Leishmania major strain Friedlin 347515 GCF_000002725.2 True Complete Genome 36.0 32855089 36 1091540 11 59.5 Full annotation GCA_000002725.2 https://genome.ucsc.edu/h/GCF_000002725.2 GCA_000002725.2 GCF_000002725.2 -Plasmodium yoelii 5861 GCF_900002385.2 True Complete Genome 14.0 23043114 14 2046250 5 100.0x 21.5 Full annotation GCA_900002385.2 https://genome.ucsc.edu/h/GCF_900002385.2 GCA_900002385.2 GCF_900002385.2 -Coccidioides posadasii str. Silveira 443226 GCF_018416015.2 True Complete Genome 9.0 28193268 9 8079863 2 475.0x 46.5 Full annotation GCA_018416015.2 https://genome.ucsc.edu/h/GCA_018416015.2 GCA_018416015.2 GCF_018416015.1 -Plasmodium vinckei vinckei 54757 GCF_900681995.1 True Complete Genome 14.0 18338688 14 1692345 5 155.0x 23.0 Full annotation GCA_900681995.1 https://genome.ucsc.edu/h/GCF_900681995.1 GCA_900681995.1 GCF_900681995.1 -Leishmania donovani 5661 GCF_000227135.1 True Chromosome 36.0 32444968 36 1024085 11 59.5 Full annotation GCA_000227135.2 https://genome.ucsc.edu/h/GCF_000227135.1 GCA_000227135.2 GCF_000227135.1 -Toxoplasma gondii ME49 508771 GCF_000006565.2 True Chromosome 14.0 65633124 2276 4973582 6 26.5x 52.5 GCA_000006565.2 https://genome.ucsc.edu/h/GCF_000006565.2 GCA_000006565.2 GCF_000006565.2 -Trypanosoma brucei brucei TREU927 185431 GCF_000002445.2 True Chromosome 11.0 26075494 12 2481190 4 46.5 Full annotation GCA_000002445.1 https://genome.ucsc.edu/h/GCF_000002445.2 GCA_000002445.1 GCF_000002445.2 -Anopheles gambiae 7165 GCF_943734735.2 True Chromosome 3.0 264451381 190 99149756 2 54.0x 44.5 Full annotation GCA_943734735.2 https://genome.ucsc.edu/h/GCF_943734735.2 GCA_943734735.2 GCF_943734735.2 -Plasmodium vivax 5855 GCF_000002415.2 True Chromosome 14.0 27007701 2747 1678596 6 42.5 Full annotation GCA_000002415.2 https://genome.ucsc.edu/h/GCF_000002415.2 GCA_000002415.2 GCF_000002415.2 -Culex pipiens pallens 42434 GCF_016801865.2 True Chromosome 3.0 566339288 289 186194774 2 250.0x 37.0 Full annotation GCA_016801865.2 -Leishmania braziliensis MHOM/BR/75/M2904 420245 GCF_000002845.2 True Chromosome 35.0 32068771 138 992961 11 58.0 GCA_000002845.2 https://genome.ucsc.edu/h/GCF_000002845.2 GCA_000002845.2 GCF_000002845.2 -Trypanosoma cruzi 5693 GCF_000209065.1 True Scaffold 89937456 29495 88624 212 51.5 Full annotation GCA_000209065.1 https://genome.ucsc.edu/h/GCF_000209065.1 GCA_000209065.1 GCF_000209065.1 -Coccidioides immitis RS 246410 GCF_000149335.2 True Scaffold 28947925 6 4323945 3 46.0 Full annotation GCA_000149335.2 https://genome.ucsc.edu/h/GCF_000149335.2 GCA_000149335.2 GCF_000149335.2 -Mycobacterium tuberculosis H37Rv 83332 GCF_000277735.2 False Complete Genome 1.0 4411709 1 4411709 1 65.5 GCA_000277735.2 -Severe acute respiratory syndrome coronavirus 2 2697049 GCF_009858895.2 False Complete Genome 1.0 29903 1 29903 1 38.0 GCA_009858895.3 -Monkeypox virus 10244 GCF_000857045.1 False Complete Genome 1.0 196858 1 196858 1 33.0 GCA_000857045.1 -Mycobacterium tuberculosis 1773 GCF_030566675.1 False Complete Genome 1.0 4516435 1 4516435 1 20.0x 65.5 GCA_030566675.1 -Mycobacterium tuberculosis 1773 GCF_963525475.1 False Complete Genome 1.0 4469156 1 4469156 1 100.0x 65.5 GCA_963525475.1 +taxon strain taxonomyId accession isRef level chromosomeCount length scaffoldCount scaffoldN50 scaffoldL50 coverage gcPercent annotationStatus pairedAccession ucscBrowser genBank refSeq geneModelUrl +Plasmodium falciparum 36329 GCF_000002765.6 True Complete Genome 14.0 23292622 14 1687656 5 100.0x 19.5 Full annotation GCA_000002765.3 https://genome.ucsc.edu/h/GCF_000002765.6 GCA_000002765.3 GCF_000002765.6 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/765/GCF_000002765.6/genes/GCF_000002765.6_GCA_000002765.ncbiRefSeq.gtf.gz +Plasmodium vivax Salvador I 5855 GCF_000002415.2 True Chromosome 14.0 27007701 2747 1678596 6 42.5 Full annotation GCA_000002415.2 https://genome.ucsc.edu/h/GCF_000002415.2 GCA_000002415.2 GCF_000002415.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/415/GCF_000002415.2/genes/GCF_000002415.2_ASM241v2.ncbiRefSeq.gtf.gz +Plasmodium yoelii 17X 5861 GCF_900002385.2 True Complete Genome 14.0 23043114 14 2046250 5 100.0x 21.5 Full annotation GCA_900002385.2 https://genome.ucsc.edu/h/GCF_900002385.2 GCA_900002385.2 GCF_900002385.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/900/002/385/GCF_900002385.2/genes/GCF_900002385.2_GCA_900002385.ncbiRefSeq.gtf.gz +Plasmodium vinckei 54757 GCF_900681995.1 True Chromosome 14.0 18338688 14 1692345 5 155.0x 23.0 Full annotation GCA_900681995.1 https://genome.ucsc.edu/h/GCF_900681995.1 GCA_900681995.1 GCF_900681995.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/900/681/995/GCF_900681995.1/genes/GCF_900681995.1_PVVCY_v1.ncbiRefSeq.gtf.gz +Culex pipiens pallens 42434 GCF_016801865.2 True Chromosome 3.0 566339288 289 186194774 2 250.0x 37.0 Full annotation GCA_016801865.2 https://genome.ucsc.edu/h/GCF_016801865.2 GCA_016801865.2 GCF_016801865.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/016/801/865/GCF_016801865.2/genes/GCF_016801865.2_TS_CPP_V2.ncbiRefSeq.gtf.gz +Culex quinquefasciatus JHB 7176 GCF_015732765.1 True Chromosome 3.0 573214445 56 201550677 2 76.0x 37.0 Full annotation GCA_015732765.1 https://genome.ucsc.edu/h/GCF_015732765.1 GCA_015732765.1 GCF_015732765.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/015/732/765/GCF_015732765.1/genes/GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal.ncbiRefSeq.gtf.gz +Anopheles gambiae 7165 GCF_943734735.2 True Chromosome 3.0 264451381 190 99149756 2 54.0x 44.5 Full annotation GCA_943734735.2 https://genome.ucsc.edu/h/GCF_943734735.2 GCA_943734735.2 GCF_943734735.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/943/734/735/GCF_943734735.2/genes/GCF_943734735.2_idAnoGambNW_F1_1.ncbiRefSeq.gtf.gz +Toxoplasma gondii ME49 508771 GCF_000006565.2 True Chromosome 14.0 65633124 2276 4973582 6 26.5x 52.5 GCA_000006565.2 https://genome.ucsc.edu/h/GCF_000006565.2 GCA_000006565.2 GCF_000006565.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/006/565/GCF_000006565.2/genes/GCF_000006565.2_TGA4.ncbiRefSeq.gtf.gz +Mycobacterium tuberculosis H37Rv 83332 GCF_000195955.2 True Complete Genome 1.0 4411532 1 4411532 1 65.5 GCA_000195955.2 https://genome.ucsc.edu/h/GCF_000195955.2 GCA_000195955.2 GCF_000195955.2 +Coccidioides posadasii Silveira 443226 GCF_018416015.2 True Complete Genome 9.0 28193268 9 8079863 2 475.0x 46.5 Full annotation GCA_018416015.2 https://genome.ucsc.edu/h/GCF_018416015.2 GCA_018416015.2 GCF_018416015.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/018/416/015/GCF_018416015.2/genes/GCF_018416015.2_ASM1841601v2.ncbiRefSeq.gtf.gz +Coccidioides immitis RS 246410 GCF_000149335.2 True Scaffold 28947925 6 4323945 3 46.0 Full annotation GCA_000149335.2 https://genome.ucsc.edu/h/GCF_000149335.2 GCA_000149335.2 GCF_000149335.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/149/335/GCF_000149335.2/genes/GCF_000149335.2_ASM14933v2.ncbiRefSeq.gtf.gz +Trypanosoma cruzi CL Brener 5693 GCF_000209065.1 True Scaffold 89937456 29495 88624 212 51.5 Full annotation GCA_000209065.1 https://genome.ucsc.edu/h/GCF_000209065.1 GCA_000209065.1 GCF_000209065.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/209/065/GCF_000209065.1/genes/GCF_000209065.1_ASM20906v1.ncbiRefSeq.gtf.gz +Trypanosoma brucei 185431 GCF_000002445.2 True Chromosome 11.0 26075494 12 2481190 4 46.5 Full annotation GCA_000002445.1 https://genome.ucsc.edu/h/GCF_000002445.2 GCA_000002445.1 GCF_000002445.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/445/GCF_000002445.2/genes/GCF_000002445.2_ASM244v1.ncbiRefSeq.gtf.gz +Leishmania major Friedlin 347515 GCF_000002725.2 True Complete Genome 36.0 32855089 36 1091540 11 59.5 Full annotation GCA_000002725.2 https://genome.ucsc.edu/h/GCF_000002725.2 GCA_000002725.2 GCF_000002725.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/725/GCF_000002725.2/genes/GCF_000002725.2_ASM272v2.ncbiRefSeq.gtf.gz +Leishmania donovani BPK282A1 5661 GCF_000227135.1 True Chromosome 36.0 32444968 36 1024085 11 59.5 Full annotation GCA_000227135.2 https://genome.ucsc.edu/h/GCF_000227135.1 GCA_000227135.2 GCF_000227135.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/227/135/GCF_000227135.1/genes/GCF_000227135.1_ASM22713v2.ncbiRefSeq.gtf.gz +Leishmania braziliensis MHOM/BR/75/M2904 420245 GCF_000002845.2 True Chromosome 35.0 32068771 138 992961 11 58.0 GCA_000002845.2 https://genome.ucsc.edu/h/GCF_000002845.2 GCA_000002845.2 GCF_000002845.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/845/GCF_000002845.2/genes/GCF_000002845.2_ASM284v2.ncbiRefSeq.gtf.gz +Severe acute respiratory syndrome coronavirus 2 2697049 GCF_009858895.2 False Complete Genome 1.0 29903 1 29903 1 38.0 GCA_009858895.3 https://genome.ucsc.edu/h/GCF_009858895.2 GCA_009858895.3 GCF_009858895.2 +Monkeypox virus Zaire-96-I-16 10244 GCF_000857045.1 False Complete Genome 1.0 196858 1 196858 1 33.0 GCA_000857045.1 https://genome.ucsc.edu/h/GCF_000857045.1 GCA_000857045.1 GCF_000857045.1 +Aspergillus fumigatus Af293 330879 GCF_000002655.1 True Chromosome 8.0 29384958 8 3948441 4 50.0 Full annotation GCA_000002655.1 https://genome.ucsc.edu/h/GCF_000002655.1 GCA_000002655.1 GCF_000002655.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/655/GCF_000002655.1/genes/GCF_000002655.1_ASM265v1.ncbiRefSeq.gtf.gz +Candida albicans SC5314 237561 GCF_000182965.3 True Chromosome 8.0 14282666 8 2231883 3 700.0x 33.5 Full annotation GCA_000182965.3 https://genome.ucsc.edu/h/GCF_000182965.3 GCA_000182965.3 GCF_000182965.3 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/182/965/GCF_000182965.3/genes/GCF_000182965.3_ASM18296v3.ncbiRefSeq.gtf.gz +Cryptococcus neoformans JEC21 214684 GCF_000091045.1 True Chromosome 14.0 19051922 14 1438950 6 48.5 Full annotation GCA_000091045.1 https://genome.ucsc.edu/h/GCF_000091045.1 GCA_000091045.1 GCF_000091045.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/091/045/GCF_000091045.1/genes/GCF_000091045.1_ASM9104v1.ncbiRefSeq.gtf.gz diff --git a/files/source/organisms-from-ncbi.tsv b/files/source/organisms-from-ncbi.tsv index 83237cd..0615f1a 100644 --- a/files/source/organisms-from-ncbi.tsv +++ b/files/source/organisms-from-ncbi.tsv @@ -1,18 +1,22 @@ -taxon taxonomyId assemblyCount CustomTags -Anopheles gambiae 7165 7 VEuPathDb -Coccidioides immitis 5501 5 -Coccidioides posadasii 199306 13 -Culex pipiens 7175 5 VEuPathDb -Leishmania braziliensis 5660 11 VEuPathDb -Leishmania donovani 5661 12 VEuPathDb -Leishmania major 5664 7 VEuPathDb -Monkeypox virus 10244 6911 Virus -Mycobacterium tuberculosis 1773 7823 Bact -Plasmodium falciparum 5833 67 VEuPathDb -Plasmodium vinckei 5860 10 VEuPathDb -Plasmodium vivax 5855 19 VEuPathDb -Plasmodium yoelii 5861 15 VEuPathDb -Severe acute respiratory syndrome coronavirus 2 2697049 92 Virus -Toxoplasma gondii 5811 29 VEuPathDb -Trypanosoma brucei 5691 5 VEuPathDb -Trypanosoma cruzi 5693 45 VEuPathDb +taxon taxonomyId assemblyCount accession CustomTags +Plasmodium falciparum 5833 1 GCF_000002765.6 VEuPathDB +Plasmodium vivax 5855 1 GCF_000002415.2 VEuPathDB +Plasmodium yoelii 5861 1 GCF_900002385.2 VEuPathDB +Plasmodium vinckei 5860 1 GCF_900681995.1 VEuPathDB +Culex pipiens pallens 42434 1 GCF_016801865.2 +Culex quinquefasciatus 7176 1 GCF_015732765.1 VEuPathDB +Anopheles gambiae 7165 1 GCF_943734735.2 VEuPathDB +Toxoplasma gondii 5811 1 GCF_000006565.2 VEuPathDB +Mycobacterium tuberculosis 1773 1 GCF_000195955.2 Bact +Coccidioides posadasii 199306 1 GCF_018416015.2 VEuPathDB +Coccidioides immitis 5501 1 GCF_000149335.2 +Trypanosoma cruzi 5693 1 GCF_000209065.1 VEuPathDB +Trypanosoma brucei 5691 1 GCF_000002445.2 VEuPathDB +Leishmania major 5664 1 GCF_000002725.2 VEuPathDB +Leishmania donovani 5661 1 GCF_000227135.1 VEuPathDB +Leishmania braziliensis 5660 1 GCF_000002845.2 VEuPathDB +Severe acute respiratory syndrome coronavirus 2 2697049 1 GCF_009858895.2 Virus +Monkeypox virus 10244 1 GCF_000857045.1 Virus +Aspergillus fumigatus 746128 1 GCF_000002655.1 +Candida albicans 5476 1 GCF_000182965.3 +Cryptococcus neoformans 5207 1 GCF_000091045.1 diff --git a/package-lock.json b/package-lock.json index c62da75..f276898 100644 --- a/package-lock.json +++ b/package-lock.json @@ -8,7 +8,7 @@ "name": "brc-analytics", "version": "0.0.0", "dependencies": { - "@databiosphere/findable-ui": "15.0.2", + "@databiosphere/findable-ui": "^16.1.0", "@emotion/react": "^11.13.3", "@emotion/styled": "^11.13.0", "@mdx-js/loader": "^3.0.1", @@ -1383,9 +1383,9 @@ } }, "node_modules/@databiosphere/findable-ui": { - "version": "15.0.2", - "resolved": "https://registry.npmjs.org/@databiosphere/findable-ui/-/findable-ui-15.0.2.tgz", - "integrity": "sha512-q6ANGEVeYmF8XjCAAiXadIva6tYZ4sO29grgQYAdcewgw1B7BxbiP7OXlQ9jAhSVGILZelWH8jqgFIR09lCrBw==", + "version": "16.1.0", + "resolved": "https://registry.npmjs.org/@databiosphere/findable-ui/-/findable-ui-16.1.0.tgz", + "integrity": "sha512-qoU0mVsbqJz+Dl8kfJPiRP/vniESbDNeNz1rGLsi0vaC2z1TdRT3SQfmE0b8KYzMd2aOw3UiRBPQIKQvHrVVCg==", "engines": { "node": "20.10.0" }, diff --git a/package.json b/package.json index 28ee298..779fb3c 100644 --- a/package.json +++ b/package.json @@ -14,7 +14,7 @@ "build-brc-db": "esrun files/build-catalog.ts" }, "dependencies": { - "@databiosphere/findable-ui": "15.0.2", + "@databiosphere/findable-ui": "^16.1.0", "@emotion/react": "^11.13.3", "@emotion/styled": "^11.13.0", "@mdx-js/loader": "^3.0.1", diff --git a/pages/_app.tsx b/pages/_app.tsx index 3e99414..3844bc2 100644 --- a/pages/_app.tsx +++ b/pages/_app.tsx @@ -20,7 +20,7 @@ import { StyledFooter } from "../app/components/Layout/components/Footer/footer. import { config } from "../app/config/config"; import { mergeAppTheme } from "../app/theme/theme"; -const DEFAULT_ENTITY_LIST_TYPE = "organisms"; +const DEFAULT_ENTITY_LIST_TYPE = "genomes"; export interface PageProps extends AzulEntitiesStaticResponse { pageTitle?: string; diff --git a/routes/constants.ts b/routes/constants.ts index c44740a..b1f6088 100644 --- a/routes/constants.ts +++ b/routes/constants.ts @@ -1,5 +1,6 @@ export const ROUTES = { ABOUT: "/about", + GENOMES: "/data/genomes", ORGANISMS: "/data/organisms", ROADMAP: "/roadmap", }; diff --git a/site-config/brc-analytics/category.ts b/site-config/brc-analytics/category.ts index 825f5d8..6b11043 100644 --- a/site-config/brc-analytics/category.ts +++ b/site-config/brc-analytics/category.ts @@ -1,23 +1,41 @@ export const BRC_DATA_CATALOG_CATEGORY_KEY = { + ACCESSION: "accession", ANALYZE_GENOME: "analyzeGenome", + ANNOTATION_STATUS: "annotationStatus", + ASSEMBLY_COUNT: "assemblyCount", CHROMOSOMES: "chromosomes", - CONTIGS: "contigs", - GENOME_VERSION_ASSEMBLY_ID: "genomeVersionAssemblyId", - SPECIES: "species", + COVERAGE: "coverage", + GC_PERCENT: "gcPercent", + IS_REF: "isRef", + LENGTH: "length", + LEVEL: "level", + SCAFFOLD_COUNT: "scaffoldCount", + SCAFFOLD_L50: "scaffoldL50", + SCAFFOLD_N50: "scaffoldN50", STRAIN: "strain", - SUPERCONTIGS: "supercontigs", + TAGS: "tags", + TAXON: "taxon", + TAXONOMY_ID: "ncbiTaxonomyId", UCSC_BROWSER_URL: "ucscBrowserUrl", - VEUPATHDB_PROJECT: "vEuPathDbProject", }; export const BRC_DATA_CATALOG_CATEGORY_LABEL = { + ACCESSION: "Accession", ANALYZE_GENOME: "Action", + ANNOTATION_STATUS: "Annotation Status", + ASSEMBLY_COUNT: "Assemblies", CHROMOSOMES: "Chromosomes", - CONTIGS: "Contigs", - GENOME_VERSION_ASSEMBLY_ID: "Assembly Version ID", - SPECIES: "Species", + COVERAGE: "Coverage", + GC_PERCENT: "GC%", + IS_REF: "Is Reference", + LENGTH: "Length", + LEVEL: "Level", + SCAFFOLD_COUNT: "Scaffolds", + SCAFFOLD_L50: "Scaffold L50", + SCAFFOLD_N50: "Scaffold N50", STRAIN: "Strain", - SUPERCONTIGS: "Supercontigs", + TAGS: "Tags", + TAXON: "Taxon", + TAXONOMY_ID: "Taxonomy ID", UCSC_BROWSER_URL: "UCSC Browser", - VEUPATHDB_PROJECT: "VEuPathDB Project", }; diff --git a/site-config/brc-analytics/local/config.ts b/site-config/brc-analytics/local/config.ts index 5d6e907..627af71 100644 --- a/site-config/brc-analytics/local/config.ts +++ b/site-config/brc-analytics/local/config.ts @@ -1,11 +1,15 @@ import { ANCHOR_TARGET } from "@databiosphere/findable-ui/lib/components/Links/common/entities"; import { SiteConfig } from "@databiosphere/findable-ui/lib/config/entities"; import { EntityConfig } from "@databiosphere/findable-ui/src/config/entities"; -import { BRCDataCatalogGenome } from "../../../app/apis/catalog/brc-analytics-catalog/common/entities"; +import { + BRCDataCatalogGenome, + BRCDataCatalogOrganism, +} from "../../../app/apis/catalog/brc-analytics-catalog/common/entities"; import * as C from "../../../app/components"; import { ROUTES } from "../../../routes/constants"; import { floating } from "./floating/floating"; import { genomeEntityConfig } from "./index/genomeEntityConfig"; +import { organismEntityConfig } from "./index/organismEntityConfig"; import { socialMedia } from "./socialMedia"; const LOCALHOST = "http://localhost:3000"; @@ -35,7 +39,10 @@ export function makeConfig(browserUrl: string, gitHubUrl: string): SiteConfig { dataSource: { url: "", }, - entities: [genomeEntityConfig as EntityConfig], + entities: [ + organismEntityConfig as EntityConfig, + genomeEntityConfig as EntityConfig, + ], explorerTitle: APP_TITLE, gitHubUrl, layout: { @@ -68,7 +75,8 @@ export function makeConfig(browserUrl: string, gitHubUrl: string): SiteConfig { undefined, [ { label: "About", url: ROUTES.ABOUT }, - { label: "Datasets", url: ROUTES.ORGANISMS }, + { label: "Organisms", url: ROUTES.ORGANISMS }, + { label: "Genomes", url: ROUTES.GENOMES }, { label: "Roadmap", url: ROUTES.ROADMAP }, ], undefined, diff --git a/site-config/brc-analytics/local/index/genomeEntityConfig.ts b/site-config/brc-analytics/local/index/genomeEntityConfig.ts index 63f37fa..1544144 100644 --- a/site-config/brc-analytics/local/index/genomeEntityConfig.ts +++ b/site-config/brc-analytics/local/index/genomeEntityConfig.ts @@ -30,20 +30,40 @@ export const genomeEntityConfig: BRCEntityConfig = { { categoryConfigs: [ { - key: BRC_DATA_CATALOG_CATEGORY_KEY.SPECIES, - label: BRC_DATA_CATALOG_CATEGORY_LABEL.SPECIES, + key: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON, + label: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXON, }, { key: BRC_DATA_CATALOG_CATEGORY_KEY.STRAIN, label: BRC_DATA_CATALOG_CATEGORY_LABEL.STRAIN, }, { - key: BRC_DATA_CATALOG_CATEGORY_KEY.GENOME_VERSION_ASSEMBLY_ID, - label: BRC_DATA_CATALOG_CATEGORY_LABEL.GENOME_VERSION_ASSEMBLY_ID, + key: BRC_DATA_CATALOG_CATEGORY_KEY.TAXONOMY_ID, + label: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXONOMY_ID, }, { - key: BRC_DATA_CATALOG_CATEGORY_KEY.VEUPATHDB_PROJECT, - label: BRC_DATA_CATALOG_CATEGORY_LABEL.VEUPATHDB_PROJECT, + key: BRC_DATA_CATALOG_CATEGORY_KEY.ACCESSION, + label: BRC_DATA_CATALOG_CATEGORY_LABEL.ACCESSION, + }, + { + key: BRC_DATA_CATALOG_CATEGORY_KEY.IS_REF, + label: BRC_DATA_CATALOG_CATEGORY_LABEL.IS_REF, + }, + { + key: BRC_DATA_CATALOG_CATEGORY_KEY.LEVEL, + label: BRC_DATA_CATALOG_CATEGORY_LABEL.LEVEL, + }, + { + key: BRC_DATA_CATALOG_CATEGORY_KEY.COVERAGE, + label: BRC_DATA_CATALOG_CATEGORY_LABEL.COVERAGE, + }, + { + key: BRC_DATA_CATALOG_CATEGORY_KEY.ANNOTATION_STATUS, + label: BRC_DATA_CATALOG_CATEGORY_LABEL.ANNOTATION_STATUS, + }, + { + key: BRC_DATA_CATALOG_CATEGORY_KEY.TAGS, + label: BRC_DATA_CATALOG_CATEGORY_LABEL.TAGS, }, ], }, @@ -64,10 +84,10 @@ export const genomeEntityConfig: BRCEntityConfig = { ], }, exploreMode: EXPLORE_MODE.CS_FETCH_CS_FILTERING, - explorerTitle: "Organisms", + explorerTitle: "Genomes", getId: getGenomeId, getTitle: getGenomeTitle, - label: "Organisms", + label: "Genomes", list: { columns: [ { @@ -83,11 +103,11 @@ export const genomeEntityConfig: BRCEntityConfig = { { componentConfig: { component: C.BasicCell, - viewBuilder: V.buildSpecies, + viewBuilder: V.buildGenomeTaxon, } as ComponentConfig, - header: BRC_DATA_CATALOG_CATEGORY_LABEL.SPECIES, - id: BRC_DATA_CATALOG_CATEGORY_KEY.SPECIES, - width: { max: "1fr", min: "284px" }, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXON, + id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON, + width: { max: "1fr", min: "240px" }, }, { componentConfig: { @@ -96,44 +116,44 @@ export const genomeEntityConfig: BRCEntityConfig = { } as ComponentConfig, header: BRC_DATA_CATALOG_CATEGORY_LABEL.STRAIN, id: BRC_DATA_CATALOG_CATEGORY_KEY.STRAIN, - width: { max: "1fr", min: "124px" }, + width: { max: "0.5fr", min: "180px" }, }, { - columnPinned: true, componentConfig: { component: C.BasicCell, - viewBuilder: V.buildGenomeVersionAssemblyId, + viewBuilder: V.buildTaxonomyId, } as ComponentConfig, - header: BRC_DATA_CATALOG_CATEGORY_LABEL.GENOME_VERSION_ASSEMBLY_ID, - id: BRC_DATA_CATALOG_CATEGORY_KEY.GENOME_VERSION_ASSEMBLY_ID, - width: { max: "1fr", min: "164px" }, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXONOMY_ID, + id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXONOMY_ID, + width: { max: "0.5fr", min: "100px" }, }, { + columnPinned: true, componentConfig: { component: C.BasicCell, - viewBuilder: V.buildVEuPathDbProject, + viewBuilder: V.buildAccession, } as ComponentConfig, - header: BRC_DATA_CATALOG_CATEGORY_LABEL.VEUPATHDB_PROJECT, - id: BRC_DATA_CATALOG_CATEGORY_KEY.VEUPATHDB_PROJECT, - width: { max: "1fr", min: "140px" }, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.ACCESSION, + id: BRC_DATA_CATALOG_CATEGORY_KEY.ACCESSION, + width: { max: "1fr", min: "164px" }, }, { componentConfig: { component: C.BasicCell, - viewBuilder: V.buildContigs, + viewBuilder: V.buildIsRef, } as ComponentConfig, - header: BRC_DATA_CATALOG_CATEGORY_LABEL.CONTIGS, - id: BRC_DATA_CATALOG_CATEGORY_KEY.CONTIGS, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.IS_REF, + id: BRC_DATA_CATALOG_CATEGORY_KEY.IS_REF, width: { max: "0.5fr", min: "100px" }, }, { componentConfig: { component: C.BasicCell, - viewBuilder: V.buildSupercontigs, + viewBuilder: V.buildLevel, } as ComponentConfig, - header: BRC_DATA_CATALOG_CATEGORY_LABEL.SUPERCONTIGS, - id: BRC_DATA_CATALOG_CATEGORY_KEY.SUPERCONTIGS, - width: { max: "0.5fr", min: "140px" }, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.LEVEL, + id: BRC_DATA_CATALOG_CATEGORY_KEY.LEVEL, + width: { max: "0.5fr", min: "142px" }, }, { componentConfig: { @@ -144,10 +164,82 @@ export const genomeEntityConfig: BRCEntityConfig = { id: BRC_DATA_CATALOG_CATEGORY_KEY.CHROMOSOMES, width: { max: "0.5fr", min: "142px" }, }, + { + componentConfig: { + component: C.BasicCell, + viewBuilder: V.buildLength, + } as ComponentConfig, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.LENGTH, + id: BRC_DATA_CATALOG_CATEGORY_KEY.LENGTH, + width: { max: "0.5fr", min: "120px" }, + }, + { + componentConfig: { + component: C.BasicCell, + viewBuilder: V.buildScaffoldCount, + } as ComponentConfig, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.SCAFFOLD_COUNT, + id: BRC_DATA_CATALOG_CATEGORY_KEY.SCAFFOLD_COUNT, + width: { max: "0.5fr", min: "80px" }, + }, + { + componentConfig: { + component: C.BasicCell, + viewBuilder: V.buildScaffoldN50, + } as ComponentConfig, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.SCAFFOLD_N50, + id: BRC_DATA_CATALOG_CATEGORY_KEY.SCAFFOLD_N50, + width: { max: "0.5fr", min: "142px" }, + }, + { + componentConfig: { + component: C.BasicCell, + viewBuilder: V.buildScaffoldL50, + } as ComponentConfig, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.SCAFFOLD_L50, + id: BRC_DATA_CATALOG_CATEGORY_KEY.SCAFFOLD_L50, + width: { max: "0.5fr", min: "80px" }, + }, + { + componentConfig: { + component: C.BasicCell, + viewBuilder: V.buildCoverage, + } as ComponentConfig, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.COVERAGE, + id: BRC_DATA_CATALOG_CATEGORY_KEY.COVERAGE, + width: { max: "0.5fr", min: "80px" }, + }, + { + componentConfig: { + component: C.BasicCell, + viewBuilder: V.buildGcPercent, + } as ComponentConfig, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.GC_PERCENT, + id: BRC_DATA_CATALOG_CATEGORY_KEY.GC_PERCENT, + width: { max: "0.5fr", min: "80px" }, + }, + { + componentConfig: { + component: C.BasicCell, + viewBuilder: V.buildAnnotationStatus, + } as ComponentConfig, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.ANNOTATION_STATUS, + id: BRC_DATA_CATALOG_CATEGORY_KEY.ANNOTATION_STATUS, + width: { max: "0.5fr", min: "142px" }, + }, + { + componentConfig: { + component: C.NTagCell, + viewBuilder: V.buildTags, + } as ComponentConfig, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAGS, + id: BRC_DATA_CATALOG_CATEGORY_KEY.TAGS, + width: { max: "0.5fr", min: "142px" }, + }, ], defaultSort: { desc: SORT_DIRECTION.ASCENDING, - id: BRC_DATA_CATALOG_CATEGORY_KEY.SPECIES, + id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON, }, } as ListConfig, listView: { @@ -156,6 +248,6 @@ export const genomeEntityConfig: BRCEntityConfig = { enableTab: false, listHero, }, - route: "organisms", + route: "genomes", staticLoadFile: "files/out/genomes.json", }; diff --git a/site-config/brc-analytics/local/index/organismEntityConfig.ts b/site-config/brc-analytics/local/index/organismEntityConfig.ts new file mode 100644 index 0000000..6c007c0 --- /dev/null +++ b/site-config/brc-analytics/local/index/organismEntityConfig.ts @@ -0,0 +1,102 @@ +import { + ComponentConfig, + ListConfig, + SORT_DIRECTION, +} from "@databiosphere/findable-ui/lib/config/entities"; +import { EXPLORE_MODE } from "@databiosphere/findable-ui/lib/hooks/useExploreMode"; +import { BRCDataCatalogOrganism } from "../../../../app/apis/catalog/brc-analytics-catalog/common/entities"; +import { getOrganismId } from "../../../../app/apis/catalog/brc-analytics-catalog/common/utils"; +import * as C from "../../../../app/components"; +import * as V from "../../../../app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders"; +import { BRCEntityConfig } from "../../../common/entities"; +import { + BRC_DATA_CATALOG_CATEGORY_KEY, + BRC_DATA_CATALOG_CATEGORY_LABEL, +} from "../../category"; + +/** + * Entity config object responsible to config anything related to the /genomes route. + */ +export const organismEntityConfig: BRCEntityConfig = { + categoryGroupConfig: { + categoryGroups: [ + { + categoryConfigs: [ + { + key: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON, + label: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXON, + }, + { + key: BRC_DATA_CATALOG_CATEGORY_KEY.TAXONOMY_ID, + label: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXONOMY_ID, + }, + { + key: BRC_DATA_CATALOG_CATEGORY_KEY.TAGS, + label: BRC_DATA_CATALOG_CATEGORY_LABEL.TAGS, + }, + ], + }, + ], + key: "organisms", + }, + detail: { + detailOverviews: [], + staticLoad: true, + tabs: [], + }, + exploreMode: EXPLORE_MODE.CS_FETCH_CS_FILTERING, + explorerTitle: "Organisms", + getId: getOrganismId, + label: "Organisms", + list: { + columns: [ + { + componentConfig: { + component: C.StyledLink, + viewBuilder: V.buildOrganismTaxon, + } as ComponentConfig, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXON, + id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON, + width: "auto", + }, + { + componentConfig: { + component: C.BasicCell, + viewBuilder: V.buildTaxonomyId, + } as ComponentConfig, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXONOMY_ID, + id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXONOMY_ID, + width: { max: "0.5fr", min: "164px" }, + }, + { + componentConfig: { + component: C.BasicCell, + viewBuilder: V.buildAssemblyCount, + } as ComponentConfig, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.ASSEMBLY_COUNT, + id: BRC_DATA_CATALOG_CATEGORY_KEY.ASSEMBLY_COUNT, + width: { max: "0.5fr", min: "164px" }, + }, + { + componentConfig: { + component: C.NTagCell, + viewBuilder: V.buildTags, + } as ComponentConfig, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAGS, + id: BRC_DATA_CATALOG_CATEGORY_KEY.TAGS, + width: { max: "0.5fr", min: "142px" }, + }, + ], + defaultSort: { + desc: SORT_DIRECTION.ASCENDING, + id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON, + }, + } as ListConfig, + listView: { + disablePagination: true, + enableDownload: true, + enableTab: false, + }, + route: "organisms", + staticLoadFile: "files/out/organisms.json", +};