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chore: update findable-ui to latest (#4651) (#4652)
* chore: update findable-ui to latest (#4651) * chore: add explicit JSX imports for React 19 compatibility (#4651) React 19 requires explicit JSX imports as JSX is no longer globally available. Added `import { JSX } from "react"` to all files that use JSX.Element type annotations. Also added next-env.d.ts to .eslintignore as it is auto-generated by Next.js 15. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * chore: remove ky from transpilePackages (#4651) Next.js 15 has native ESM support, so ky no longer needs to be transpiled. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * test: update mock data to use azul_url property name (#4651) Rename url -> azul_url in project matrix test mocks to match the Azul API response format. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * fix: use dynamic NODE_ENV check for MDX development option (#4651) Fixes _jsxDEV is not a function error in CI by matching the pattern used in contentPages.ts instead of hardcoding development: false. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * fix: resolve _jsxDEV error by aligning files/ dependencies (#4651) - Remove duplicate packages from files/package.json that are already in main package.json (unified, remark-parse, remark-rehype, etc.) - Update rehype-stringify from v9 to v10 for unified v11 compatibility - Set NODE_ENV=production in build-anvil-db script to ensure MDX compiles with production JSX runtime instead of development Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * fix: add explicit wait for filter dropdown visibility in E2E test (#4651) Wait for the filter option to be visible before clicking the checkbox to fix flaky test behavior in CI environments with higher latency. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> --------- Co-authored-by: Fran McDade <18710366+frano-m@users.noreply.github.com> Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
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‎.eslintignore‎

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**/node_modules/*
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**/out/*
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**/.next/*
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next-env.d.ts
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build
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‎__tests__/project-matrix-mapper.test.ts‎

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@@ -23,14 +23,14 @@ const COUNT_MATRIX = "Count Matrix";
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const LARGE_INTESTINE = "large intestine";
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const LYMPH_NODE = "lymph node";
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const MOCK_PROJECT_MATRIX_FILE_0 = {
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azul_url: "https://path/to/file0?version=0&catalog=dcp2ebi",
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name: "123.loom",
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size: 254147853,
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url: "https://path/to/file0?version=0&catalog=dcp2ebi",
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};
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const MOCK_PROJECT_MATRIX_FILE_1 = {
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azul_url: "https://path/to/file1?version=0&catalog=dcp2ebi",
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name: "456.loom",
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size: 254147854,
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url: "https://path/to/file1?version=0&catalog=dcp2ebi",
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};
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const CONTRIBUTED_ANALYSES = {
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genusSpecies: {
@@ -42,16 +42,16 @@ const CONTRIBUTED_ANALYSES = {
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libraryConstructionApproach: {
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[LibraryConstructionApproach.TENX_V2]: [
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{
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azul_url: MOCK_PROJECT_MATRIX_FILE_0.azul_url,
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name: MOCK_PROJECT_MATRIX_FILE_0.name,
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size: MOCK_PROJECT_MATRIX_FILE_0.size,
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url: MOCK_PROJECT_MATRIX_FILE_0.url,
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},
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],
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[LibraryConstructionApproach.SMART_SEQ2]: [
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{
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azul_url: MOCK_PROJECT_MATRIX_FILE_1.azul_url,
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name: MOCK_PROJECT_MATRIX_FILE_1.name,
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size: MOCK_PROJECT_MATRIX_FILE_1.size,
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url: MOCK_PROJECT_MATRIX_FILE_1.url,
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},
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],
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},
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libraryConstructionApproach: {
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[LibraryConstructionApproach.TENX_V2]: [
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{
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azul_url: MOCK_PROJECT_MATRIX_FILE_0.azul_url,
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name: MOCK_PROJECT_MATRIX_FILE_0.name,
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size: MOCK_PROJECT_MATRIX_FILE_0.size,
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url: MOCK_PROJECT_MATRIX_FILE_0.url,
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},
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{
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azul_url: MOCK_PROJECT_MATRIX_FILE_1.azul_url,
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name: MOCK_PROJECT_MATRIX_FILE_1.name,
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size: MOCK_PROJECT_MATRIX_FILE_1.size,
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url: MOCK_PROJECT_MATRIX_FILE_1.url,
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},
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],
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},
@@ -99,7 +99,7 @@ describe("MatrixMapper", () => {
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expect(matrixView0.stage[0]).toEqual("adult");
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expect(matrixView0.fileName).toEqual(MOCK_PROJECT_MATRIX_FILE_0.name);
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expect(matrixView0.size).toEqual(MOCK_PROJECT_MATRIX_FILE_0.size);
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expect(matrixView0.url).toEqual(MOCK_PROJECT_MATRIX_FILE_0.url);
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expect(matrixView0.url).toEqual(MOCK_PROJECT_MATRIX_FILE_0.azul_url);
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const matrixView1 = matrixViews[1];
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expect(matrixView0.libraryConstructionApproach.length).toEqual(1);
@@ -112,7 +112,7 @@ describe("MatrixMapper", () => {
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expect(matrixView1.stage[0]).toEqual("adult");
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expect(matrixView1.fileName).toEqual(MOCK_PROJECT_MATRIX_FILE_1.name);
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expect(matrixView1.size).toEqual(MOCK_PROJECT_MATRIX_FILE_1.size);
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expect(matrixView1.url).toEqual(MOCK_PROJECT_MATRIX_FILE_1.url);
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expect(matrixView1.url).toEqual(MOCK_PROJECT_MATRIX_FILE_1.azul_url);
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const matrixView2 = matrixViews[2];
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expect(matrixView0.libraryConstructionApproach.length).toEqual(1);
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expect(matrixView2.stage[0]).toEqual("adult");
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expect(matrixView2.fileName).toEqual(MOCK_PROJECT_MATRIX_FILE_0.name);
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expect(matrixView2.size).toEqual(MOCK_PROJECT_MATRIX_FILE_0.size);
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expect(matrixView2.url).toEqual(MOCK_PROJECT_MATRIX_FILE_0.url);
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expect(matrixView2.url).toEqual(MOCK_PROJECT_MATRIX_FILE_0.azul_url);
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const matrixView3 = matrixViews[3];
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expect(matrixView0.libraryConstructionApproach.length).toEqual(1);
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expect(matrixView3.stage[0]).toEqual("adult");
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expect(matrixView3.fileName).toEqual(MOCK_PROJECT_MATRIX_FILE_1.name);
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expect(matrixView3.size).toEqual(MOCK_PROJECT_MATRIX_FILE_1.size);
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expect(matrixView3.url).toEqual(MOCK_PROJECT_MATRIX_FILE_1.url);
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expect(matrixView3.url).toEqual(MOCK_PROJECT_MATRIX_FILE_1.azul_url);
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});
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/**
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const matrixView0 = matrixViews[0];
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expect(matrixView0.fileName).toEqual(MOCK_PROJECT_MATRIX_FILE_0.name);
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expect(matrixView0.size).toEqual(MOCK_PROJECT_MATRIX_FILE_0.size);
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expect(matrixView0.url).toEqual(MOCK_PROJECT_MATRIX_FILE_0.url);
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expect(matrixView0.url).toEqual(MOCK_PROJECT_MATRIX_FILE_0.azul_url);
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expect(matrixView0.organ.length).toEqual(2);
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expect(matrixView0.organ.indexOf(LARGE_INTESTINE)).not.toEqual(-1);
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expect(matrixView0.organ.indexOf(LYMPH_NODE)).not.toEqual(-1);
@@ -166,7 +166,7 @@ describe("MatrixMapper", () => {
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const matrixView1 = matrixViews[1];
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expect(matrixView1.fileName).toEqual(MOCK_PROJECT_MATRIX_FILE_1.name);
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expect(matrixView1.size).toEqual(MOCK_PROJECT_MATRIX_FILE_1.size);
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expect(matrixView1.url).toEqual(MOCK_PROJECT_MATRIX_FILE_1.url);
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expect(matrixView1.url).toEqual(MOCK_PROJECT_MATRIX_FILE_1.azul_url);
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expect(matrixView1.organ.length).toEqual(2);
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expect(matrixView1.organ.indexOf(LARGE_INTESTINE)).not.toEqual(-1);
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expect(matrixView1.organ.indexOf(LYMPH_NODE)).not.toEqual(-1);
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],
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organ: [LYMPH_NODE, LARGE_INTESTINE],
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size: MOCK_PROJECT_MATRIX_FILE_0.size,
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url: MOCK_PROJECT_MATRIX_FILE_0.url,
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url: MOCK_PROJECT_MATRIX_FILE_0.azul_url,
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version: "1",
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},
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];
@@ -223,8 +223,8 @@ describe("MatrixMapper", () => {
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genusSpecies: {
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"Homo sapiens,Mus musculus": [
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{
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azul_url: MOCK_PROJECT_MATRIX_FILE_0.azul_url,
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name: MOCK_PROJECT_MATRIX_FILE_0.name,
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url: MOCK_PROJECT_MATRIX_FILE_0.url,
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},
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],
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},
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genusSpecies: {
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"Mus musculus,Homo sapiens": [
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{
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azul_url: MOCK_PROJECT_MATRIX_FILE_0.azul_url,
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name: MOCK_PROJECT_MATRIX_FILE_0.name,
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url: MOCK_PROJECT_MATRIX_FILE_0.url,
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},
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],
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},
@@ -273,7 +273,7 @@ describe("MatrixMapper", () => {
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libraryConstructionApproach: [LibraryConstructionApproach.TENX_V2],
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organ: [LYMPH_NODE, LARGE_INTESTINE],
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size: MOCK_PROJECT_MATRIX_FILE_0.size,
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url: MOCK_PROJECT_MATRIX_FILE_0.url,
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url: MOCK_PROJECT_MATRIX_FILE_0.azul_url,
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version: "1",
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},
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{
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libraryConstructionApproach: [LibraryConstructionApproach.TENX_V2],
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organ: [LYMPH_NODE, LARGE_INTESTINE],
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size: MOCK_PROJECT_MATRIX_FILE_1.size,
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url: MOCK_PROJECT_MATRIX_FILE_1.url,
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url: MOCK_PROJECT_MATRIX_FILE_1.azul_url,
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version: "1",
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},
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];
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libraryConstructionApproach: [LibraryConstructionApproach.TENX_V2],
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organ: [LYMPH_NODE],
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size: MOCK_PROJECT_MATRIX_FILE_0.size,
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url: MOCK_PROJECT_MATRIX_FILE_0.url,
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url: MOCK_PROJECT_MATRIX_FILE_0.azul_url,
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version: "1",
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},
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{
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libraryConstructionApproach: [LibraryConstructionApproach.TENX_V2],
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organ: [LARGE_INTESTINE],
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size: MOCK_PROJECT_MATRIX_FILE_1.size,
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url: MOCK_PROJECT_MATRIX_FILE_1.url,
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url: MOCK_PROJECT_MATRIX_FILE_1.azul_url,
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version: "1",
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},
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];
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libraryConstructionApproach: [LibraryConstructionApproach.SMART_SEQ2],
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organ: [LYMPH_NODE],
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size: MOCK_PROJECT_MATRIX_FILE_0.size,
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url: MOCK_PROJECT_MATRIX_FILE_0.url,
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url: MOCK_PROJECT_MATRIX_FILE_0.azul_url,
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version: "1",
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},
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{
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libraryConstructionApproach: [LibraryConstructionApproach.TENX_V2], // "10x .."
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organ: [LYMPH_NODE],
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size: MOCK_PROJECT_MATRIX_FILE_1.size,
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url: MOCK_PROJECT_MATRIX_FILE_1.url,
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url: MOCK_PROJECT_MATRIX_FILE_1.azul_url,
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version: "1",
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},
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];
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genusSpecies: {
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"Homo sapiens": [
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{
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azul_url: MOCK_PROJECT_MATRIX_FILE_0.azul_url,
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name: MOCK_PROJECT_MATRIX_FILE_0.name,
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size: MOCK_PROJECT_MATRIX_FILE_0.size,
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url: MOCK_PROJECT_MATRIX_FILE_0.url,
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},
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{
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azul_url: MOCK_PROJECT_MATRIX_FILE_1.azul_url,
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name: MOCK_PROJECT_MATRIX_FILE_1.name,
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size: MOCK_PROJECT_MATRIX_FILE_1.size,
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url: MOCK_PROJECT_MATRIX_FILE_1.url,
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},
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],
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},

‎app/components/Detail/components/AccessibilityBadge/accessibilityBadge.tsx‎

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import { JSX } from "react";
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import { AccessibilityBadgeProps } from "@databiosphere/findable-ui/lib/components/Detail/components/AccessibilityBadge/accessibilityBadge";
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import { AccessibilityBadge as Badge } from "./accessibilityBadge.styles";
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‎app/components/Detail/components/AccessibilityBadge/components/Stack/stack.tsx‎

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import { Stack as MStack } from "@mui/material";
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import { ReactNode } from "react";
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import { JSX, ReactNode } from "react";
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interface StackProps {
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children: ReactNode | ReactNode[];

‎app/components/Detail/components/AnVILCMG/components/RequestAccess/requestAccess.tsx‎

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import { JSX } from "react";
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import { Props } from "./types";
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import { ListItemText, MenuItem } from "@mui/material";
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import { Actions } from "@databiosphere/findable-ui/lib/components/Layout/components/BackPage/components/BackPageHero/components/Actions/actions";

‎app/components/Detail/components/ConsentCodeList/consentCodeList.tsx‎

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import { JSX } from "react";
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import { ConsentTooltip } from "../ConsentTooltip/consentTooltip";
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interface ConsentCodeListProps {

‎app/components/Detail/components/ConsentTooltip/consentTooltip.tsx‎

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import { JSX } from "react";
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import { Tooltip } from "@mui/material";
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interface ConsentTooltipProps {

‎app/components/Detail/components/Consortium/components/ConsortiumDescription/consortiumDescription.tsx‎

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import { JSX } from "react";
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import {
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MdxMarkdown,
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MDXSerializeResult,

‎app/components/Detail/components/EntityGuard/components/EntityDeprecated/entityDeprecated.tsx‎

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import { JSX } from "react";
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import { ButtonPrimary } from "@databiosphere/findable-ui/lib/components/common/Button/components/ButtonPrimary/buttonPrimary";
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import { AlertIcon } from "@databiosphere/findable-ui/lib/components/common/CustomIcon/components/AlertIcon/alertIcon";
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import { SectionActions } from "@databiosphere/findable-ui/lib/components/common/Section/section.styles";

‎app/components/Detail/components/EntityGuard/components/EntityWithdrawn/entityWithdrawn.tsx‎

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import { JSX } from "react";
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import { ButtonPrimary } from "@databiosphere/findable-ui/lib/components/common/Button/components/ButtonPrimary/buttonPrimary";
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import { AlertIcon } from "@databiosphere/findable-ui/lib/components/common/CustomIcon/components/AlertIcon/alertIcon";
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import { SectionActions } from "@databiosphere/findable-ui/lib/components/common/Section/section.styles";

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