vitessce/src/loaders/anndata-loaders/MatrixZarrLoader.test.js

Vitessce app and React component library

/* eslint-disable func-names */
import expect from 'expect';
import MatrixZarrLoader from './MatrixZarrLoader';
import { AnnDataSource } from '../data-sources';

const createMatrixLoader = (config) => {
  const source = new AnnDataSource(config);
  return new MatrixZarrLoader(source, config);
};

describe('loaders/MatrixZarrLoader', () => {
  describe('AnnData v0.7', () => {
    it('loadFilteredGeneNames returns gene names', async function () {
      this.timeout(15000);
      const loader = createMatrixLoader({
        url: 'http://127.0.0.1:8080/anndata-0.7/anndata-dense.zarr', options: { matrix: 'X' },
      });
      const names = await loader.loadFilteredGeneNames();
      expect(names).toEqual(Array.from({ length: 15 }).map((_, i) => `gene_${i}`));
    });

    it('loadGeneSelection matches across storage methods', async () => {
      const selection = { selection: ['gene_1', 'gene_5'] };
      const loaderCsr = createMatrixLoader({
        url: 'http://127.0.0.1:8080/anndata-0.7/anndata-csr.zarr', options: { matrix: 'X' },
      });
      const csrSelection = await loaderCsr.loadGeneSelection(selection);
      const loaderDense = createMatrixLoader({
        url: 'http://127.0.0.1:8080/anndata-0.7/anndata-dense.zarr', options: { matrix: 'X' },
      });
      const denseSelection = await loaderDense.loadGeneSelection(selection);
      const loaderCsc = createMatrixLoader({
        url: 'http://127.0.0.1:8080/anndata-0.7/anndata-csc.zarr', options: { matrix: 'X' },
      });
      const cscSelection = await loaderCsc.loadGeneSelection(selection);
      expect(cscSelection).toEqual(denseSelection);
      expect(csrSelection).toEqual(denseSelection);
    });

    it('loadCellXGene matches across storage methods', async () => {
      const loaderCsr = createMatrixLoader({
        url: 'http://127.0.0.1:8080/anndata-0.7/anndata-csr.zarr', options: { matrix: 'X' },
      });
      const csrMatrix = await loaderCsr.loadCellXGene();
      const loaderDense = createMatrixLoader({
        url: 'http://127.0.0.1:8080/anndata-0.7/anndata-dense.zarr', options: { matrix: 'X' },
      });
      const denseMatrix = await loaderDense.loadCellXGene();
      const loaderCsc = createMatrixLoader({
        url: 'http://127.0.0.1:8080/anndata-0.7/anndata-csc.zarr', options: { matrix: 'X' },
      });
      const cscMatrix = await loaderCsc.loadCellXGene();
      expect(cscMatrix).toEqual(denseMatrix);
      expect(csrMatrix).toEqual(denseMatrix);
    });
  });

  describe('AnnData v0.8', () => {
    it('loadFilteredGeneNames returns gene names', async function () {
      this.timeout(15000);
      const loader = createMatrixLoader({
        url: 'http://127.0.0.1:8080/anndata-0.8/anndata-dense.zarr', options: { matrix: 'X' },
      });
      const names = await loader.loadFilteredGeneNames();
      expect(names).toEqual(Array.from({ length: 15 }).map((_, i) => `gene_${i}`));
    });

    it('loadGeneSelection matches across storage methods', async () => {
      const selection = { selection: ['gene_1', 'gene_5'] };
      const loaderCsr = createMatrixLoader({
        url: 'http://127.0.0.1:8080/anndata-0.8/anndata-csr.zarr', options: { matrix: 'X' },
      });
      const csrSelection = await loaderCsr.loadGeneSelection(selection);
      const loaderDense = createMatrixLoader({
        url: 'http://127.0.0.1:8080/anndata-0.8/anndata-dense.zarr', options: { matrix: 'X' },
      });
      const denseSelection = await loaderDense.loadGeneSelection(selection);
      const loaderCsc = createMatrixLoader({
        url: 'http://127.0.0.1:8080/anndata-0.8/anndata-csc.zarr', options: { matrix: 'X' },
      });
      const cscSelection = await loaderCsc.loadGeneSelection(selection);
      expect(cscSelection).toEqual(denseSelection);
      expect(csrSelection).toEqual(denseSelection);
    });

    it('loadCellXGene matches across storage methods', async () => {
      const loaderCsr = createMatrixLoader({
        url: 'http://127.0.0.1:8080/anndata-0.8/anndata-csr.zarr', options: { matrix: 'X' },
      });
      const csrMatrix = await loaderCsr.loadCellXGene();
      const loaderDense = createMatrixLoader({
        url: 'http://127.0.0.1:8080/anndata-0.8/anndata-dense.zarr', options: { matrix: 'X' },
      });
      const denseMatrix = await loaderDense.loadCellXGene();
      const loaderCsc = createMatrixLoader({
        url: 'http://127.0.0.1:8080/anndata-0.8/anndata-csc.zarr', options: { matrix: 'X' },
      });
      const cscMatrix = await loaderCsc.loadCellXGene();
      expect(cscMatrix).toEqual(denseMatrix);
      expect(csrMatrix).toEqual(denseMatrix);
    });
  });
});