@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 { FileType } from '@vitessce/constants-internal';
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export function expandAnndataZarr(fileDef) {
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const 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 ? (Array.isArray(options.obsEmbedding) ? options.obsEmbedding.map((oe) => ({
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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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// obsLabels
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// eslint-disable-next-line no-nested-ternary
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...(options.obsLabels ? (Array.isArray(options.obsLabels) ? options.obsLabels.map((ol) => ({
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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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// featureLabels
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// eslint-disable-next-line no-nested-ternary
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...(options.featureLabels ? (Array.isArray(options.featureLabels) ? options.featureLabels.map((fl) => ({
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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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{"version":3,"file":"joint-file-types.test.d.ts","sourceRoot":"","sources":["../src/joint-file-types.test.ts"],"names":[],"mappings":""}
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@@ -0,0 +1,128 @@
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import { describe, expect, it } from 'vitest';
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import { expandAnndataZarr, } 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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{"version":3,"file":"latest-config-schema.test.d.ts","sourceRoot":"","sources":["../src/latest-config-schema.test.ts"],"names":[],"mappings":""}
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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 { baseCoordinationTypes, } 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/package.json
CHANGED
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{
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"name": "@vitessce/all",
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"version": "
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"version": "3.0.0",
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"author": "Gehlenborg Lab",
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"homepage": "http://vitessce.io",
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"repository": {
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"url": "git+https://github.com/vitessce/vitessce.git"
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},
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"license": "MIT",
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"type": "module",
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"main": "dist/index.js",
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"files": [
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"
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"src",
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"dist",
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"dist-tsc"
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],
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"dependencies": {
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"@material-ui/core": "~4.12.3",
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"
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"@vitessce/
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"@vitessce/
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"@vitessce/
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"@vitessce/
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"@vitessce/
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"@vitessce/
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"@vitessce/
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"@vitessce/
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"@vitessce/
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"@vitessce/
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"@vitessce/
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"@vitessce/
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"@vitessce/
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"@vitessce/
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"@vitessce/
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"zod": "^3.21.4",
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"@vitessce/constants-internal": "3.0.0",
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"@vitessce/csv": "3.0.0",
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"@vitessce/description": "3.0.0",
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"@vitessce/feature-list": "3.0.0",
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|
+
"@vitessce/genomic-profiles": "3.0.0",
|
26
|
+
"@vitessce/heatmap": "3.0.0",
|
27
|
+
"@vitessce/json": "3.0.0",
|
28
|
+
"@vitessce/layer-controller": "3.0.0",
|
29
|
+
"@vitessce/obs-sets-manager": "3.0.0",
|
30
|
+
"@vitessce/ome-tiff": "3.0.0",
|
31
|
+
"@vitessce/plugins": "3.0.0",
|
32
|
+
"@vitessce/scatterplot-embedding": "3.0.0",
|
33
|
+
"@vitessce/scatterplot-gating": "3.0.0",
|
34
|
+
"@vitessce/schemas": "3.0.0",
|
35
|
+
"@vitessce/spatial": "3.0.0",
|
36
|
+
"@vitessce/statistical-plots": "3.0.0",
|
37
|
+
"@vitessce/status": "3.0.0",
|
38
|
+
"@vitessce/vit-s": "3.0.0",
|
39
|
+
"@vitessce/zarr": "3.0.0"
|
33
40
|
},
|
34
41
|
"devDependencies": {
|
35
|
-
"react": "^18.0.
|
42
|
+
"@types/react": "^18.0.28",
|
43
|
+
"react": "^18.0.0",
|
44
|
+
"vitest": "^0.23.4"
|
36
45
|
},
|
37
46
|
"peerDependencies": {
|
38
47
|
"react": "^16.8.0 || ^17.0.0 || ^18.0.0"
|
39
48
|
},
|
40
49
|
"scripts": {
|
41
|
-
"start": "tsc
|
42
|
-
"build": "tsc"
|
50
|
+
"start": "pnpm -C ../../../ run start-tsc",
|
51
|
+
"build": "pnpm -C ../../../ run build-tsc",
|
52
|
+
"bundle": "pnpm exec vite build -c ../../../scripts/vite.config.js",
|
53
|
+
"test": "pnpm exec vitest --run -r ../../../ --dir ."
|
54
|
+
},
|
55
|
+
"module": "dist/index.js",
|
56
|
+
"exports": {
|
57
|
+
".": {
|
58
|
+
"types": "./dist-tsc/index.d.ts",
|
59
|
+
"import": "./dist/index.js"
|
60
|
+
}
|
43
61
|
}
|
44
62
|
}
|
package/src/Vitessce.tsx
ADDED
@@ -0,0 +1,74 @@
|
|
1
|
+
/* eslint-disable max-len */
|
2
|
+
import React, { useMemo } from 'react';
|
3
|
+
import {
|
4
|
+
VitS,
|
5
|
+
} from '@vitessce/vit-s';
|
6
|
+
import {
|
7
|
+
upgradeAndParse,
|
8
|
+
} from '@vitessce/schemas';
|
9
|
+
import {
|
10
|
+
baseViewTypes,
|
11
|
+
baseFileTypes,
|
12
|
+
baseJointFileTypes,
|
13
|
+
baseCoordinationTypes,
|
14
|
+
} from './base-plugins.js';
|
15
|
+
|
16
|
+
export function Vitessce(props: any) {
|
17
|
+
const {
|
18
|
+
config,
|
19
|
+
onConfigUpgrade,
|
20
|
+
pluginViewTypes: pluginViewTypesProp,
|
21
|
+
pluginFileTypes: pluginFileTypesProp,
|
22
|
+
pluginCoordinationTypes: pluginCoordinationTypesProp,
|
23
|
+
pluginJointFileTypes: pluginJointFileTypesProp,
|
24
|
+
} = props;
|
25
|
+
|
26
|
+
const configUid = config?.uid;
|
27
|
+
const configVersion = config?.version;
|
28
|
+
|
29
|
+
const [configOrWarning, success] = useMemo(() => {
|
30
|
+
try {
|
31
|
+
const validConfig = upgradeAndParse(config, onConfigUpgrade);
|
32
|
+
return [validConfig, true];
|
33
|
+
} catch (e) {
|
34
|
+
console.error(e);
|
35
|
+
return [
|
36
|
+
{
|
37
|
+
title: 'Config validation or upgrade failed.',
|
38
|
+
unformatted: (e as any).message,
|
39
|
+
},
|
40
|
+
false,
|
41
|
+
];
|
42
|
+
}
|
43
|
+
// eslint-disable-next-line react-hooks/exhaustive-deps
|
44
|
+
}, [configUid, configVersion]);
|
45
|
+
|
46
|
+
const mergedPluginViewTypes = useMemo(() => ([
|
47
|
+
...baseViewTypes, ...(pluginViewTypesProp || []),
|
48
|
+
]), [pluginViewTypesProp]);
|
49
|
+
|
50
|
+
const mergedPluginFileTypes = useMemo(() => ([
|
51
|
+
...baseFileTypes, ...(pluginFileTypesProp || []),
|
52
|
+
]), [pluginFileTypesProp]);
|
53
|
+
|
54
|
+
const mergedPluginJointFileTypes = useMemo(() => ([
|
55
|
+
...baseJointFileTypes, ...(pluginJointFileTypesProp || []),
|
56
|
+
]), [pluginJointFileTypesProp]);
|
57
|
+
|
58
|
+
const mergedPluginCoordinationTypes = useMemo(() => ([
|
59
|
+
...baseCoordinationTypes, ...(pluginCoordinationTypesProp || []),
|
60
|
+
]), [pluginCoordinationTypesProp]);
|
61
|
+
|
62
|
+
|
63
|
+
return (
|
64
|
+
<VitS
|
65
|
+
{...props}
|
66
|
+
config={configOrWarning}
|
67
|
+
viewTypes={mergedPluginViewTypes}
|
68
|
+
fileTypes={mergedPluginFileTypes}
|
69
|
+
jointFileTypes={mergedPluginJointFileTypes}
|
70
|
+
coordinationTypes={mergedPluginCoordinationTypes}
|
71
|
+
warning={(success ? null : configOrWarning)}
|
72
|
+
/>
|
73
|
+
);
|
74
|
+
}
|