feat: build data from ncbi and add organisms with assembly lists (#208)…

… (#209) Co-authored-by: Danielle Callan <[email protected]>
galaxyproject · Jan 16, 2025 · 0947c6d · 0947c6d
1 parent f4bdff4
commit 0947c6d
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Showing 26 changed files with 1,913 additions and 9,958 deletions.
diff --git a/app/apis/catalog/brc-analytics-catalog/common/entities.ts b/app/apis/catalog/brc-analytics-catalog/common/entities.ts
@@ -10,17 +10,31 @@ 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;
+  genomes: BRCDataCatalogGenome[];
+  ncbiTaxonomyId: string;
+  tags: string[];
+  taxon: string;
 }
 
 export interface EntitiesResponse<R> {

diff --git 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
@@ -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/EntityList/components/Organisms/content/index.tsx b/app/components/EntityList/components/Organisms/content/index.tsx
diff --git a/app/components/EntityList/components/Organisms/content/organismsWarning.mdx b/app/components/EntityList/components/Organisms/content/organismsWarning.mdx
diff --git a/...ut/components/Detail/components/DetailViewHero/components/BackButton/backButton.styles.ts b/...ut/components/Detail/components/DetailViewHero/components/BackButton/backButton.styles.ts
diff --git a/...s/Layout/components/Detail/components/DetailViewHero/components/BackButton/backButton.tsx b/...s/Layout/components/Detail/components/DetailViewHero/components/BackButton/backButton.tsx
diff --git a/app/components/Layout/components/Detail/components/DetailViewHero/detailViewHero.tsx b/app/components/Layout/components/Detail/components/DetailViewHero/detailViewHero.tsx
@@ -3,7 +3,6 @@ import { SubTitle } from "@databiosphere/findable-ui/lib/components/Layout/compo
 import { TEXT_HEADING } from "@databiosphere/findable-ui/lib/theme/common/typography";
 import { HeroTitle as Typography } from "@databiosphere/findable-ui/src/components/common/Title/title.styles";
 import { ReactNode } from "react";
-import { BackButton } from "./components/BackButton/backButton";
 import {
   DetailViewHeroHeadline,
   DetailViewHero as DetailViewHeroLayout,
@@ -29,7 +28,6 @@ export const DetailViewHero = ({
     <DetailViewHeroLayout>
       {(breadcrumbs || title) && (
         <DetailViewHeroHeadline>
-          <BackButton />
           <HeroHeader>
             {breadcrumbs}
             <HeroTitle>

diff --git a/app/components/index.ts b/app/components/index.ts
@@ -19,9 +19,11 @@ export {
   BackPageContentSideColumn,
   BackPageContentSingleColumn,
 } from "@databiosphere/findable-ui/lib/components/Layout/components/BackPage/backPageView.styles";
+export { DetailViewTable } from "@databiosphere/findable-ui/lib/components/Detail/components/DetailViewTable/detailViewTable";
 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 { AnalysisMethod } from "./Entity/components/AnalysisMethod/analysisMethod";
 export { AnalysisMethods } from "./Entity/components/AnalysisMethods/analysisMethods";

diff --git 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<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 {