@vitessce/all 2.0.3-beta.0 → 3.0.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/deflate-f57b3163.js +13 -0
- package/dist/hglib-1422f224.js +138925 -0
- package/dist/index-3f1c1764.js +258272 -0
- package/dist/index.js +12 -2
- package/dist/jpeg-e740c9a5.js +840 -0
- package/dist/lerc-01e6c4d8.js +2006 -0
- package/dist/lzw-865bd058.js +128 -0
- package/dist/packbits-d4191efd.js +30 -0
- package/dist/pako.esm-68f84e2a.js +4022 -0
- package/dist/raw-3c693341.js +12 -0
- package/dist/webimage-83da2258.js +32 -0
- package/dist-tsc/Vitessce.d.ts +2 -0
- package/dist-tsc/Vitessce.d.ts.map +1 -0
- package/dist-tsc/Vitessce.js +41 -0
- package/dist-tsc/base-plugins.d.ts +854 -0
- package/dist-tsc/base-plugins.d.ts.map +1 -0
- package/dist-tsc/base-plugins.js +191 -0
- package/dist-tsc/index.d.ts +4 -0
- package/dist-tsc/index.d.ts.map +1 -0
- package/dist-tsc/index.js +3 -0
- package/dist-tsc/joint-file-types-legacy.d.ts +226 -0
- package/dist-tsc/joint-file-types-legacy.d.ts.map +1 -0
- package/dist-tsc/joint-file-types-legacy.js +266 -0
- package/dist-tsc/joint-file-types-legacy.test.d.ts +2 -0
- package/dist-tsc/joint-file-types-legacy.test.d.ts.map +1 -0
- package/dist-tsc/joint-file-types-legacy.test.js +401 -0
- package/dist-tsc/joint-file-types.d.ts +4 -0
- package/dist-tsc/joint-file-types.d.ts.map +1 -0
- package/dist-tsc/joint-file-types.js +127 -0
- package/dist-tsc/joint-file-types.test.d.ts +2 -0
- package/dist-tsc/joint-file-types.test.d.ts.map +1 -0
- package/dist-tsc/joint-file-types.test.js +128 -0
- package/dist-tsc/latest-config-schema.test.d.ts +2 -0
- package/dist-tsc/latest-config-schema.test.d.ts.map +1 -0
- package/dist-tsc/latest-config-schema.test.js +19 -0
- package/package.json +39 -21
- package/src/Vitessce.tsx +74 -0
- package/src/base-plugins.ts +362 -0
- package/src/index.ts +8 -0
- package/src/joint-file-types-legacy.test.ts +413 -0
- package/src/joint-file-types-legacy.ts +284 -0
- package/src/joint-file-types.test.ts +132 -0
- package/src/joint-file-types.ts +142 -0
- package/src/latest-config-schema.test.ts +26 -0
- package/dist/setup.js +0 -96
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import { describe, expect, it } from 'vitest';
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import {
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expandAnndataZarr,
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} from './joint-file-types.js';
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describe('src/app/joint-file-types.js', () => {
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describe('expandAnndataZarr', () => {
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it('fails to expand when there are no options', () => {
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expect(expandAnndataZarr({
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fileType: 'anndata.zarr',
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url: 'http://localhost:8000/anndata.zarr',
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})).toEqual([]);
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});
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it('expands when there is an obsEmbedding object', () => {
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expect(expandAnndataZarr({
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fileType: 'anndata.zarr',
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url: 'http://localhost:8000/anndata.zarr',
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options: {
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obsLabels: {
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path: 'obs/spot_name',
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},
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featureLabels: {
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path: 'var/gene_symbol',
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},
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obsEmbedding: {
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path: 'obsm/pca',
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dims: [2, 4],
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},
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},
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coordinationValues: {
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obsType: 'spot',
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featureType: 'transcript',
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obsLabelsType: 'spotName',
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featureLabelsType: 'geneSymbol',
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embeddingType: 'PCA',
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},
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})).toEqual([
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{
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fileType: 'obsEmbedding.anndata.zarr',
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url: 'http://localhost:8000/anndata.zarr',
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options: {
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path: 'obsm/pca',
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dims: [2, 4],
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},
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coordinationValues: {
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obsType: 'spot',
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embeddingType: 'PCA',
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},
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},
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{
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fileType: 'obsLabels.anndata.zarr',
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url: 'http://localhost:8000/anndata.zarr',
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options: {
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path: 'obs/spot_name',
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},
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coordinationValues: {
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obsType: 'spot',
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obsLabelsType: 'spotName',
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},
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},
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{
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fileType: 'featureLabels.anndata.zarr',
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url: 'http://localhost:8000/anndata.zarr',
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options: {
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path: 'var/gene_symbol',
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},
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coordinationValues: {
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featureType: 'transcript',
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featureLabelsType: 'geneSymbol',
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},
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},
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]);
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});
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it('expands when there is an obsEmbedding array of objects', () => {
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expect(expandAnndataZarr({
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fileType: 'anndata.zarr',
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url: 'http://localhost:8000/anndata.zarr',
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options: {
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obsLocations: {
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path: 'obsm/xy',
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},
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obsEmbedding: [
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{
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path: 'obsm/pca',
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dims: [2, 4],
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embeddingType: 'PCA',
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},
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{
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path: 'obsm/umap',
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embeddingType: 'UMAP',
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},
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],
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},
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})).toEqual([
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{
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fileType: 'obsLocations.anndata.zarr',
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url: 'http://localhost:8000/anndata.zarr',
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options: {
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path: 'obsm/xy',
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},
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coordinationValues: {
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obsType: 'cell',
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},
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},
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{
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fileType: 'obsEmbedding.anndata.zarr',
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url: 'http://localhost:8000/anndata.zarr',
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options: {
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path: 'obsm/pca',
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dims: [2, 4],
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},
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coordinationValues: {
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obsType: 'cell',
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embeddingType: 'PCA',
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},
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},
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{
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fileType: 'obsEmbedding.anndata.zarr',
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url: 'http://localhost:8000/anndata.zarr',
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options: {
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path: 'obsm/umap',
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},
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coordinationValues: {
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obsType: 'cell',
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embeddingType: 'UMAP',
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},
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},
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]);
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});
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});
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});
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import type { z } from 'zod';
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import type { latestFileDefSchema } from '@vitessce/schemas';
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import { FileType } from '@vitessce/constants-internal';
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type BaseFileDef = {
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url?: string;
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requestInit?: any;
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coordinationValues: Record<string, string>;
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};
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export function expandAnndataZarr(fileDef: z.infer<typeof latestFileDefSchema>) {
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const baseFileDef: BaseFileDef = {
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url: fileDef.url,
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requestInit: fileDef.requestInit,
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coordinationValues: {
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...fileDef.coordinationValues,
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obsType: fileDef.coordinationValues?.obsType || 'cell',
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featureType: fileDef.coordinationValues?.featureType || 'gene',
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featureValueType: fileDef.coordinationValues?.featureValueType || 'expression',
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},
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};
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const { options = {} } = fileDef;
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return [
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// obsFeatureMatrix
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...(options.obsFeatureMatrix ? [{
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...baseFileDef,
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fileType: FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR,
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options: options.obsFeatureMatrix,
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coordinationValues: {
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obsType: baseFileDef.coordinationValues.obsType,
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featureType: baseFileDef.coordinationValues.featureType,
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featureValueType: baseFileDef.coordinationValues.featureValueType,
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},
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}] : []),
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// obsSets
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...(options.obsSets ? [{
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...baseFileDef,
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fileType: FileType.OBS_SETS_ANNDATA_ZARR,
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options: options.obsSets,
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coordinationValues: {
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obsType: baseFileDef.coordinationValues.obsType,
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},
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}] : []),
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// obsLocations
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...(options.obsLocations ? [{
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...baseFileDef,
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fileType: FileType.OBS_LOCATIONS_ANNDATA_ZARR,
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options: options.obsLocations,
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coordinationValues: {
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obsType: baseFileDef.coordinationValues.obsType,
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},
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}] : []),
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// obsSegmentations
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...(options.obsSegmentations ? [{
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...baseFileDef,
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fileType: FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR,
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options: options.obsSegmentations,
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coordinationValues: {
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obsType: baseFileDef.coordinationValues.obsType,
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},
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}] : []),
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// obsEmbedding
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// eslint-disable-next-line no-nested-ternary
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...(options.obsEmbedding ? (
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Array.isArray(options.obsEmbedding) ? options.obsEmbedding.map((oe: any) => ({
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// obsEmbedding was an array, process each element.
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...baseFileDef,
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fileType: FileType.OBS_EMBEDDING_ANNDATA_ZARR,
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options: {
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path: oe.path,
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dims: oe.dims,
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},
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coordinationValues: {
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obsType: baseFileDef.coordinationValues.obsType,
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// Move embedding type property out of options and into coordinationValues.
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embeddingType: oe.embeddingType,
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},
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})) : [{
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// obsEmbedding was an object.
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...baseFileDef,
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fileType: FileType.OBS_EMBEDDING_ANNDATA_ZARR,
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options: options.obsEmbedding,
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coordinationValues: {
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obsType: baseFileDef.coordinationValues.obsType,
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embeddingType: baseFileDef.coordinationValues.embeddingType,
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},
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}]
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) : []),
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// obsLabels
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// eslint-disable-next-line no-nested-ternary
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...(options.obsLabels ? (
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Array.isArray(options.obsLabels) ? options.obsLabels.map((ol: any) => ({
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// obsLabels was an array, process each element.
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...baseFileDef,
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fileType: FileType.OBS_LABELS_ANNDATA_ZARR,
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options: {
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path: ol.path,
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},
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coordinationValues: {
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obsType: baseFileDef.coordinationValues.obsType,
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// Move obsLabels type property out of options and into coordinationValues.
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obsLabelsType: ol.obsLabelsType,
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},
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})) : [{
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// obsLabels was an object.
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...baseFileDef,
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fileType: FileType.OBS_LABELS_ANNDATA_ZARR,
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options: options.obsLabels,
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coordinationValues: {
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obsType: baseFileDef.coordinationValues.obsType,
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obsLabelsType: baseFileDef.coordinationValues.obsLabelsType,
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},
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}]
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) : []),
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// featureLabels
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// eslint-disable-next-line no-nested-ternary
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...(options.featureLabels ? (
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Array.isArray(options.featureLabels) ? options.featureLabels.map((fl: any) => ({
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// featureLabels was an array, process each element.
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...baseFileDef,
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fileType: FileType.FEATURE_LABELS_ANNDATA_ZARR,
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options: {
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path: fl.path,
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},
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coordinationValues: {
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featureType: baseFileDef.coordinationValues.featureType,
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// Move featureLabels type property out of options and into coordinationValues.
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featureLabelsType: fl.featureLabelsType,
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},
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})) : [{
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// featureLabels was an object.
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...baseFileDef,
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fileType: FileType.FEATURE_LABELS_ANNDATA_ZARR,
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options: options.featureLabels,
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coordinationValues: {
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featureType: baseFileDef.coordinationValues.featureType,
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featureLabelsType: baseFileDef.coordinationValues.featureLabelsType,
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},
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}]
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) : []),
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];
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}
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@@ -0,0 +1,26 @@
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import { describe, expect, it } from 'vitest';
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import { CoordinationType } from '@vitessce/constants-internal';
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import {
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baseCoordinationTypes,
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} from './base-plugins.js';
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describe('view config schema', () => {
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describe('coordination types', () => {
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it('defines schema for all valid coordination types', () => {
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const coordinationTypeNamesFromConstants = Object.values(CoordinationType).sort();
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const coordinationTypeNamesFromBasePlugins = baseCoordinationTypes.map(ct => ct.name).sort();
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expect(coordinationTypeNamesFromConstants)
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.toEqual(expect.arrayContaining(coordinationTypeNamesFromBasePlugins));
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});
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it('defines schema for only valid coordination types (does not have extra)', () => {
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const coordinationTypeNamesFromConstants = Object.values(CoordinationType).sort();
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const coordinationTypeNamesFromBasePlugins = baseCoordinationTypes.map(ct => ct.name).sort();
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expect(coordinationTypeNamesFromBasePlugins)
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.toEqual(expect.arrayContaining(coordinationTypeNamesFromConstants));
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});
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});
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});
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package/dist/setup.js
DELETED
@@ -1,96 +0,0 @@
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import { jsx as _jsx } from "react/jsx-runtime";
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/* eslint-disable max-len */
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import { useState, useLayoutEffect } from 'react';
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import { VitS, registerPluginFileType } from '@vitessce/vit-s';
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// Register view type plugins
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import { register as registerDescription } from '@vitessce/description';
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import { register as registerObsSetsManager } from '@vitessce/obs-sets-manager';
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import { register as registerScatterplotEmbedding } from '@vitessce/scatterplot-embedding';
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import { register as registerScatterplotGating } from '@vitessce/scatterplot-gating';
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import { register as registerSpatial } from '@vitessce/spatial';
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import { register as registerHeatmap } from '@vitessce/heatmap';
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import { register as registerFeatureList } from '@vitessce/feature-list';
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import { register as registerLayerController } from '@vitessce/layer-controller';
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import { register as registerStatus } from '@vitessce/status';
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import { registerCellSetExpression, registerCellSetSizes, registerExpressionHistogram } from '@vitessce/statistical-plots';
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import { registerHiglass, registerGenomicProfiles } from '@vitessce/genomic-profiles';
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// Register file type plugins
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import {
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// CSV
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CsvSource, ObsSetsCsvLoader, ObsEmbeddingCsvLoader, ObsLocationsCsvLoader, ObsLabelsCsvLoader, ObsFeatureMatrixCsvLoader, FeatureLabelsCsvLoader, } from '@vitessce/csv';
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import {
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// JSON
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JsonSource, JsonLoader, ObsSegmentationsJsonLoader, ObsSetsJsonLoader,
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// Legacy
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RasterJsonAsImageLoader, RasterJsonAsObsSegmentationsLoader, ClustersJsonAsObsFeatureMatrixLoader, GenesJsonAsObsFeatureMatrixLoader, CellsJsonAsObsLabelsLoader, CellsJsonAsObsEmbeddingLoader, CellsJsonAsObsLocationsLoader, CellsJsonAsObsSegmentationsLoader, MoleculesJsonAsObsLocationsLoader, MoleculesJsonAsObsLabelsLoader, } from '@vitessce/json';
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import {
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// AnnData
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AnnDataSource, ObsFeatureMatrixAnndataLoader, ObsEmbeddingAnndataLoader, ObsLocationsAnndataLoader, ObsSegmentationsAnndataLoader, ObsSetsAnndataLoader, ObsLabelsAnndataLoader, FeatureLabelsAnndataLoader,
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// OME
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OmeZarrLoader,
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// Legacy
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ZarrDataSource, MatrixZarrAsObsFeatureMatrixLoader, GenomicProfilesZarrLoader, } from '@vitessce/zarr';
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import { FileType, DataType } from '@vitessce/constants-internal';
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function setup() {
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// View types
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registerDescription();
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registerObsSetsManager();
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registerScatterplotEmbedding();
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registerScatterplotGating();
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registerSpatial();
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registerHeatmap();
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registerFeatureList();
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registerLayerController();
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registerStatus();
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// Statistical plots
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registerCellSetExpression();
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registerCellSetSizes();
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registerExpressionHistogram();
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// Higlass
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registerHiglass();
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registerGenomicProfiles();
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// File types
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// All CSV file types
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registerPluginFileType(FileType.OBS_SETS_CSV, DataType.OBS_SETS, ObsSetsCsvLoader, CsvSource);
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registerPluginFileType(FileType.OBS_EMBEDDING_CSV, DataType.OBS_EMBEDDING, ObsEmbeddingCsvLoader, CsvSource);
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registerPluginFileType(FileType.OBS_LOCATIONS_CSV, DataType.OBS_LOCATIONS, ObsLocationsCsvLoader, CsvSource);
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registerPluginFileType(FileType.OBS_LABELS_CSV, DataType.OBS_LABELS, ObsLabelsCsvLoader, CsvSource);
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registerPluginFileType(FileType.OBS_FEATURE_MATRIX_CSV, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixCsvLoader, CsvSource);
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registerPluginFileType(FileType.FEATURE_LABELS_CSV, DataType.FEATURE_LABELS, FeatureLabelsCsvLoader, CsvSource);
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// All JSON file types
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registerPluginFileType(FileType.OBS_SEGMENTATIONS_JSON, DataType.OBS_SEGMENTATIONS, ObsSegmentationsJsonLoader, JsonSource);
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registerPluginFileType(FileType.OBS_SETS_JSON, DataType.OBS_SETS, ObsSetsJsonLoader, JsonSource);
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63
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// All AnnData file types
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registerPluginFileType(FileType.OBS_SETS_ANNDATA_ZARR, DataType.OBS_SETS, ObsSetsAnndataLoader, AnnDataSource);
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registerPluginFileType(FileType.OBS_EMBEDDING_ANNDATA_ZARR, DataType.OBS_EMBEDDING, ObsEmbeddingAnndataLoader, AnnDataSource);
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registerPluginFileType(FileType.OBS_LOCATIONS_ANNDATA_ZARR, DataType.OBS_LOCATIONS, ObsLocationsAnndataLoader, AnnDataSource);
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registerPluginFileType(FileType.OBS_LABELS_ANNDATA_ZARR, DataType.OBS_LABELS, ObsLabelsAnndataLoader, AnnDataSource);
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registerPluginFileType(FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixAnndataLoader, AnnDataSource);
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registerPluginFileType(FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR, DataType.OBS_SEGMENTATIONS, ObsSegmentationsAnndataLoader, AnnDataSource);
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registerPluginFileType(FileType.FEATURE_LABELS_ANNDATA_ZARR, DataType.FEATURE_LABELS, FeatureLabelsAnndataLoader, AnnDataSource);
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// All OME file types
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registerPluginFileType(FileType.IMAGE_OME_ZARR, DataType.IMAGE, OmeZarrLoader, ZarrDataSource);
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// All legacy file types
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registerPluginFileType(FileType.OBS_FEATURE_MATRIX_EXPRESSION_MATRIX_ZARR, DataType.OBS_FEATURE_MATRIX, MatrixZarrAsObsFeatureMatrixLoader, ZarrDataSource);
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registerPluginFileType(FileType.IMAGE_RASTER_JSON, DataType.IMAGE, RasterJsonAsImageLoader, JsonSource);
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registerPluginFileType(FileType.OBS_SEGMENTATIONS_RASTER_JSON, DataType.OBS_SEGMENTATIONS, RasterJsonAsObsSegmentationsLoader, JsonSource);
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registerPluginFileType(FileType.OBS_SETS_CELL_SETS_JSON, DataType.OBS_SETS, ObsSetsJsonLoader, JsonSource);
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registerPluginFileType(FileType.OBS_FEATURE_MATRIX_CLUSTERS_JSON, DataType.OBS_FEATURE_MATRIX, ClustersJsonAsObsFeatureMatrixLoader, JsonSource);
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79
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registerPluginFileType(FileType.OBS_FEATURE_MATRIX_GENES_JSON, DataType.OBS_FEATURE_MATRIX, GenesJsonAsObsFeatureMatrixLoader, JsonSource);
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80
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registerPluginFileType(FileType.OBS_LABELS_CELLS_JSON, DataType.OBS_LABELS, CellsJsonAsObsLabelsLoader, JsonSource);
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81
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registerPluginFileType(FileType.OBS_EMBEDDING_CELLS_JSON, DataType.OBS_EMBEDDING, CellsJsonAsObsEmbeddingLoader, JsonSource);
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82
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registerPluginFileType(FileType.OBS_LOCATIONS_CELLS_JSON, DataType.OBS_LOCATIONS, CellsJsonAsObsLocationsLoader, JsonSource);
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83
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registerPluginFileType(FileType.OBS_SEGMENTATIONS_CELLS_JSON, DataType.OBS_SEGMENTATIONS, CellsJsonAsObsSegmentationsLoader, JsonSource);
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registerPluginFileType(FileType.OBS_LOCATIONS_MOLECULES_JSON, DataType.OBS_LOCATIONS, MoleculesJsonAsObsLocationsLoader, JsonSource);
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registerPluginFileType(FileType.OBS_LABELS_MOLECULES_JSON, DataType.OBS_LABELS, MoleculesJsonAsObsLabelsLoader, JsonSource);
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registerPluginFileType(FileType.NEIGHBORHOODS_JSON, DataType.NEIGHBORHOODS, JsonLoader, JsonSource);
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registerPluginFileType(FileType.GENOMIC_PROFILES_ZARR, DataType.GENOMIC_PROFILES, GenomicProfilesZarrLoader, ZarrDataSource);
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88
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}
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89
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export function Vitessce(props) {
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90
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const [ready, setReady] = useState(false);
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91
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useLayoutEffect(() => {
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92
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setup();
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93
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setReady(true);
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94
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}, []);
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95
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return (ready ? (_jsx(VitS, { ...props })) : null);
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96
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}
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