feat: rename genome list and update to use data from ncbi (#177)

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<R> {

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 {

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;
 }

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
                 </Subhead>
-                <Button {...BUTTON_PROPS} href={ROUTES.ORGANISMS}>
+                <Button {...BUTTON_PROPS} href={ROUTES.GENOMES}>
                   Get started
                 </Button>
               </SubHeadline>

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).

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;
+`;

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";

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<string> {
   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 {