@vitessce/vit-s 2.0.3-beta.0 → 2.0.3
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/index.mjs +84801 -0
- package/{dist → dist-tsc}/index.js +2 -2
- package/package.json +7 -7
- package/src/CallbackPublisher.js +81 -0
- package/src/LoadingIndicator.js +34 -0
- package/src/TitleInfo.js +240 -0
- package/src/VitS.js +180 -0
- package/src/VitessceGrid.js +110 -0
- package/src/VitessceGrid.test.jsx +48 -0
- package/src/Warning.js +62 -0
- package/{dist → src}/classNames.js +0 -0
- package/src/component-registry.js +21 -0
- package/src/data/AbstractLoader.js +46 -0
- package/{dist → src}/data/AbstractTwoStepLoader.js +5 -4
- package/src/data/LoaderResult.js +8 -0
- package/{dist → src}/data/index.js +0 -0
- package/src/data/loader-registry.js +19 -0
- package/src/data-hook-utils.js +197 -0
- package/src/data-hooks.js +354 -0
- package/src/errors/AbstractLoaderError.js +14 -0
- package/src/errors/DataSourceFetchError.js +15 -0
- package/src/errors/DatasetNotFoundError.js +23 -0
- package/src/errors/LoaderNotFoundError.js +24 -0
- package/src/errors/LoaderValidationError.js +23 -0
- package/src/errors/OptionsValidationError.js +25 -0
- package/{dist → src}/errors/index.js +0 -0
- package/src/file-options-schemas-legacy.js +139 -0
- package/src/file-options-schemas-legacy.test.js +138 -0
- package/src/file-options-schemas.js +327 -0
- package/src/file-options-schemas.test.js +26 -0
- package/src/hooks.js +252 -0
- package/src/index.js +101 -0
- package/src/joint-file-types-legacy.js +298 -0
- package/src/joint-file-types-legacy.test.js +412 -0
- package/src/joint-file-types.js +171 -0
- package/src/joint-file-types.test.js +144 -0
- package/{dist/schemas.js → src/json-schemas.js} +6 -1
- package/{dist → src}/plugins.js +102 -70
- package/src/plugins.test.fixtures.js +78 -0
- package/src/plugins.test.js +42 -0
- package/src/schemas/config-0.1.0.schema.json +85 -0
- package/src/schemas/config-1.0.0.schema.json +733 -0
- package/src/schemas/config-1.0.1.schema.json +909 -0
- package/src/schemas/config-1.0.10.schema.json +969 -0
- package/src/schemas/config-1.0.11.schema.json +990 -0
- package/src/schemas/config-1.0.12.schema.json +997 -0
- package/src/schemas/config-1.0.13.schema.json +1013 -0
- package/src/schemas/config-1.0.14.schema.json +1048 -0
- package/src/schemas/config-1.0.15.schema.json +1048 -0
- package/src/schemas/config-1.0.16.schema.json +1069 -0
- package/src/schemas/config-1.0.16.schema.test.js +32 -0
- package/src/schemas/config-1.0.2.schema.json +911 -0
- package/src/schemas/config-1.0.3.schema.json +911 -0
- package/src/schemas/config-1.0.4.schema.json +949 -0
- package/src/schemas/config-1.0.5.schema.json +949 -0
- package/src/schemas/config-1.0.6.schema.json +950 -0
- package/src/schemas/config-1.0.7.schema.json +950 -0
- package/src/schemas/config-1.0.8.schema.json +966 -0
- package/src/schemas/config-1.0.9.schema.json +965 -0
- package/src/schemas/fixtures/cellSets.good.json +16 -0
- package/src/schemas/fixtures/config-1.0.1.bad.json +1 -0
- package/src/schemas/fixtures/config-1.0.1.bad.message.json +11 -0
- package/src/schemas/fixtures/config-1.0.1.good.json +37 -0
- package/src/schemas/fixtures/config-1.0.2.bad.json +1 -0
- package/src/schemas/fixtures/config-1.0.2.bad.message.json +11 -0
- package/src/schemas/fixtures/config-1.0.2.good.json +38 -0
- package/src/schemas/fixtures/config-1.0.3.bad.json +1 -0
- package/src/schemas/fixtures/config-1.0.3.bad.message.json +11 -0
- package/src/schemas/fixtures/config-1.0.3.good.json +38 -0
- package/src/schemas/fixtures/obsSets.bad.json +1 -0
- package/src/schemas/fixtures/obsSets.bad.message.json +11 -0
- package/src/schemas/fixtures/obsSets.good.json +16 -0
- package/src/schemas/fixtures/obsSetsTabular.bad.json +1 -0
- package/src/schemas/fixtures/obsSetsTabular.bad.message.json +11 -0
- package/src/schemas/fixtures/obsSetsTabular.good.json +26 -0
- package/src/schemas/fixtures/raster.bad.json +1 -0
- package/src/schemas/fixtures/raster.bad.message.json +11 -0
- package/src/schemas/fixtures/raster.good.json +39 -0
- package/src/schemas/obsSets.schema.js +195 -0
- package/src/schemas/obsSetsTabular.schema.js +39 -0
- package/src/schemas/raster.schema.js +121 -0
- package/src/schemas/schema-schema.sh +34 -0
- package/{dist → src}/schemas/schema.test-old.js +0 -1
- package/src/shared-mui/components.js +79 -0
- package/src/shared-mui/container.js +212 -0
- package/src/shared-mui/styles.js +110 -0
- package/src/shared-plot-options/CellColorEncodingOption.js +43 -0
- package/src/shared-plot-options/OptionSelect.js +19 -0
- package/src/shared-plot-options/OptionsContainer.js +26 -0
- package/{dist → src}/shared-plot-options/index.js +0 -0
- package/src/shared-plot-options/styles.js +49 -0
- package/src/state/hooks.js +633 -0
- package/src/view-config-upgraders.js +628 -0
- package/src/view-config-utils.js +315 -0
- package/src/view-config-utils.test.fixtures.js +893 -0
- package/src/view-config-utils.test.js +95 -0
- package/src/view-config-versions.js +68 -0
- package/src/vitessce-grid-layout/VitessceGridLayout.js +158 -0
- package/src/vitessce-grid-layout/VitessceGridLayout.test.jsx +56 -0
- package/{dist → src}/vitessce-grid-layout/index.js +0 -0
- package/src/vitessce-grid-layout/layout-utils.js +76 -0
- package/src/vitessce-grid-layout/layout-utils.test.js +167 -0
- package/src/vitessce-grid-utils.js +160 -0
- package/dist/CallbackPublisher.js +0 -68
- package/dist/LoadingIndicator.js +0 -27
- package/dist/TitleInfo.js +0 -151
- package/dist/VitS.js +0 -117
- package/dist/Vitessce.integration.test.js +0 -36
- package/dist/Vitessce.js +0 -101
- package/dist/VitessceGrid.js +0 -59
- package/dist/VitessceGrid.test.js +0 -36
- package/dist/Warning.js +0 -45
- package/dist/component-registry.js +0 -16
- package/dist/data/AbstractLoader.js +0 -35
- package/dist/data/LoaderResult.js +0 -7
- package/dist/data/loader-registry.js +0 -15
- package/dist/data-hook-utils.js +0 -175
- package/dist/data-hooks.js +0 -241
- package/dist/errors/AbstractLoaderError.js +0 -13
- package/dist/errors/DataSourceFetchError.js +0 -13
- package/dist/errors/DatasetNotFoundError.js +0 -17
- package/dist/errors/LoaderNotFoundError.js +0 -17
- package/dist/errors/LoaderValidationError.js +0 -15
- package/dist/errors/OptionsValidationError.js +0 -15
- package/dist/export-utils.js +0 -70
- package/dist/export-utils.test.js +0 -66
- package/dist/file-options-schemas-legacy.js +0 -136
- package/dist/file-options-schemas-legacy.test.js +0 -126
- package/dist/file-options-schemas.js +0 -322
- package/dist/file-options-schemas.test.js +0 -23
- package/dist/hooks.js +0 -215
- package/dist/joint-file-types-legacy.js +0 -278
- package/dist/joint-file-types-legacy.test.js +0 -400
- package/dist/joint-file-types.js +0 -148
- package/dist/joint-file-types.test.js +0 -139
- package/dist/loader-registry.js +0 -98
- package/dist/plugins.test.fixtures.js +0 -76
- package/dist/plugins.test.js +0 -30
- package/dist/schemas/PrettyJsonSchema.js +0 -34
- package/dist/schemas/config-0.1.0.schema.json +0 -84
- package/dist/schemas/config-1.0.0.schema.json +0 -733
- package/dist/schemas/config-1.0.1.schema.json +0 -909
- package/dist/schemas/config-1.0.10.schema.json +0 -969
- package/dist/schemas/config-1.0.11.schema.json +0 -990
- package/dist/schemas/config-1.0.12.schema.json +0 -997
- package/dist/schemas/config-1.0.13.schema.json +0 -1013
- package/dist/schemas/config-1.0.14.schema.json +0 -1048
- package/dist/schemas/config-1.0.15.schema.json +0 -1048
- package/dist/schemas/config-1.0.15.schema.test.js +0 -22
- package/dist/schemas/config-1.0.16.schema.json +0 -1109
- package/dist/schemas/config-1.0.16.schema.test.js +0 -22
- package/dist/schemas/config-1.0.2.schema.json +0 -910
- package/dist/schemas/config-1.0.3.schema.json +0 -910
- package/dist/schemas/config-1.0.4.schema.json +0 -949
- package/dist/schemas/config-1.0.5.schema.json +0 -949
- package/dist/schemas/config-1.0.6.schema.json +0 -949
- package/dist/schemas/config-1.0.7.schema.json +0 -949
- package/dist/schemas/config-1.0.8.schema.json +0 -965
- package/dist/schemas/config-1.0.9.schema.json +0 -965
- package/dist/schemas/obs-sets-tabular.schema.js +0 -37
- package/dist/schemas/obs-sets.schema.js +0 -194
- package/dist/schemas/obsSets.schema.js +0 -195
- package/dist/schemas/obsSetsTabular.schema.js +0 -38
- package/dist/schemas/raster.schema.js +0 -120
- package/dist/schemas/schema.test.js +0 -46
- package/dist/schemas-extra.js +0 -3
- package/dist/shared-mui/components.js +0 -35
- package/dist/shared-mui/container.js +0 -211
- package/dist/shared-mui/styles.js +0 -107
- package/dist/shared-plot-options/CellColorEncodingOption.js +0 -18
- package/dist/shared-plot-options/OptionSelect.js +0 -12
- package/dist/shared-plot-options/OptionsContainer.js +0 -12
- package/dist/shared-plot-options/styles.js +0 -48
- package/dist/state/hooks.js +0 -549
- package/dist/view-config-upgraders.js +0 -525
- package/dist/view-config-utils.js +0 -286
- package/dist/view-config-utils.test.fixtures.js +0 -765
- package/dist/view-config-utils.test.js +0 -66
- package/dist/view-config-versions.js +0 -47
- package/dist/vitessce-grid-layout/VitessceGridLayout.js +0 -95
- package/dist/vitessce-grid-layout/VitessceGridLayout.test.js +0 -40
- package/dist/vitessce-grid-layout/layout-utils.js +0 -60
- package/dist/vitessce-grid-layout/layout-utils.test.js +0 -146
- package/dist/vitessce-grid-utils.js +0 -140
package/dist/joint-file-types.js
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import { FileType } from '@vitessce/constants-internal';
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import { validateOptions, anndataZarrSchema, } from './file-options-schemas';
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import { expandMoleculesJson, expandExpressionMatrixZarr, expandRasterJson, expandRasterOmeZarr, expandCellSetsJson, expandCellsJson, expandClustersJson, expandGenesJson, expandAnndataCellsZarr, expandAnndataCellSetsZarr, expandAnndataExpressionMatrixZarr, } from './joint-file-types-legacy';
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export function expandAnndataZarr(fileDef) {
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validateOptions(anndataZarrSchema, fileDef.options);
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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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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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...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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coordinationValues: {
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obsType: baseFileDef.coordinationValues.obsType,
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obsLabelsType: ol.obsLabelsType,
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},
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})) : [{
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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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...(options.featureLabels ? (Array.isArray(options.featureLabels) ? options.featureLabels.map(fl => ({
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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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featureType: baseFileDef.coordinationValues.featureType,
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featureLabelsType: fl.featureLabelsType,
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},
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})) : [{
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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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* Built-in joint file type
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* expansion functions.
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*/
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export const JOINT_FILE_TYPES = {
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[FileType.ANNDATA_ZARR]: expandAnndataZarr,
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[FileType.ANNDATA_CELLS_ZARR]: expandAnndataCellsZarr,
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[FileType.ANNDATA_CELL_SETS_ZARR]: expandAnndataCellSetsZarr,
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[FileType.ANNDATA_EXPRESSION_MATRIX_ZARR]: expandAnndataExpressionMatrixZarr,
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[FileType.EXPRESSION_MATRIX_ZARR]: expandExpressionMatrixZarr,
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[FileType.RASTER_JSON]: expandRasterJson,
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[FileType.RASTER_OME_ZARR]: expandRasterOmeZarr,
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[FileType.CELL_SETS_JSON]: expandCellSetsJson,
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[FileType.CLUSTERS_JSON]: expandClustersJson,
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[FileType.GENES_JSON]: expandGenesJson,
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[FileType.CELLS_JSON]: expandCellsJson,
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[FileType.MOLECULES_JSON]: expandMoleculesJson,
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};
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import { FileType, FILE_TYPE_DATA_TYPE_MAPPING } from '@vitessce/constants-internal';
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import { JOINT_FILE_TYPES, expandAnndataZarr, } from './joint-file-types';
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describe('src/app/joint-file-types.js', () => {
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describe('FileType-to-DataType mappings', () => {
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it('every file type is mapped to either a data type or a joint file type expansion function', () => {
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-
const fileTypes = Object.values(FileType).sort();
|
|
7
|
-
const mappedFileTypes = [
|
|
8
|
-
...Object.keys(FILE_TYPE_DATA_TYPE_MAPPING),
|
|
9
|
-
...Object.keys(JOINT_FILE_TYPES),
|
|
10
|
-
].sort();
|
|
11
|
-
expect(fileTypes.length).toEqual(mappedFileTypes.length);
|
|
12
|
-
expect(fileTypes).toEqual(mappedFileTypes);
|
|
13
|
-
});
|
|
14
|
-
});
|
|
15
|
-
describe('expandAnndataZarr', () => {
|
|
16
|
-
it('fails to expand when there are no options', () => {
|
|
17
|
-
expect(() => expandAnndataZarr({
|
|
18
|
-
fileType: 'anndata.zarr',
|
|
19
|
-
url: 'http://localhost:8000/anndata.zarr',
|
|
20
|
-
})).toThrow();
|
|
21
|
-
});
|
|
22
|
-
it('expands when there is an obsEmbedding object', () => {
|
|
23
|
-
expect(expandAnndataZarr({
|
|
24
|
-
fileType: 'anndata.zarr',
|
|
25
|
-
url: 'http://localhost:8000/anndata.zarr',
|
|
26
|
-
options: {
|
|
27
|
-
obsLabels: {
|
|
28
|
-
path: 'obs/spot_name',
|
|
29
|
-
},
|
|
30
|
-
featureLabels: {
|
|
31
|
-
path: 'var/gene_symbol',
|
|
32
|
-
},
|
|
33
|
-
obsEmbedding: {
|
|
34
|
-
path: 'obsm/pca',
|
|
35
|
-
dims: [2, 4],
|
|
36
|
-
},
|
|
37
|
-
},
|
|
38
|
-
coordinationValues: {
|
|
39
|
-
obsType: 'spot',
|
|
40
|
-
featureType: 'transcript',
|
|
41
|
-
obsLabelsType: 'spotName',
|
|
42
|
-
featureLabelsType: 'geneSymbol',
|
|
43
|
-
embeddingType: 'PCA',
|
|
44
|
-
},
|
|
45
|
-
})).toEqual([
|
|
46
|
-
{
|
|
47
|
-
fileType: 'obsEmbedding.anndata.zarr',
|
|
48
|
-
url: 'http://localhost:8000/anndata.zarr',
|
|
49
|
-
options: {
|
|
50
|
-
path: 'obsm/pca',
|
|
51
|
-
dims: [2, 4],
|
|
52
|
-
},
|
|
53
|
-
coordinationValues: {
|
|
54
|
-
obsType: 'spot',
|
|
55
|
-
embeddingType: 'PCA',
|
|
56
|
-
},
|
|
57
|
-
},
|
|
58
|
-
{
|
|
59
|
-
fileType: 'obsLabels.anndata.zarr',
|
|
60
|
-
url: 'http://localhost:8000/anndata.zarr',
|
|
61
|
-
options: {
|
|
62
|
-
path: 'obs/spot_name',
|
|
63
|
-
},
|
|
64
|
-
coordinationValues: {
|
|
65
|
-
obsType: 'spot',
|
|
66
|
-
obsLabelsType: 'spotName',
|
|
67
|
-
},
|
|
68
|
-
},
|
|
69
|
-
{
|
|
70
|
-
fileType: 'featureLabels.anndata.zarr',
|
|
71
|
-
url: 'http://localhost:8000/anndata.zarr',
|
|
72
|
-
options: {
|
|
73
|
-
path: 'var/gene_symbol',
|
|
74
|
-
},
|
|
75
|
-
coordinationValues: {
|
|
76
|
-
featureType: 'transcript',
|
|
77
|
-
featureLabelsType: 'geneSymbol',
|
|
78
|
-
},
|
|
79
|
-
},
|
|
80
|
-
]);
|
|
81
|
-
});
|
|
82
|
-
it('expands when there is an obsEmbedding array of objects', () => {
|
|
83
|
-
expect(expandAnndataZarr({
|
|
84
|
-
fileType: 'anndata.zarr',
|
|
85
|
-
url: 'http://localhost:8000/anndata.zarr',
|
|
86
|
-
options: {
|
|
87
|
-
obsLocations: {
|
|
88
|
-
path: 'obsm/xy',
|
|
89
|
-
},
|
|
90
|
-
obsEmbedding: [
|
|
91
|
-
{
|
|
92
|
-
path: 'obsm/pca',
|
|
93
|
-
dims: [2, 4],
|
|
94
|
-
embeddingType: 'PCA',
|
|
95
|
-
},
|
|
96
|
-
{
|
|
97
|
-
path: 'obsm/umap',
|
|
98
|
-
embeddingType: 'UMAP',
|
|
99
|
-
},
|
|
100
|
-
],
|
|
101
|
-
},
|
|
102
|
-
})).toEqual([
|
|
103
|
-
{
|
|
104
|
-
fileType: 'obsLocations.anndata.zarr',
|
|
105
|
-
url: 'http://localhost:8000/anndata.zarr',
|
|
106
|
-
options: {
|
|
107
|
-
path: 'obsm/xy',
|
|
108
|
-
},
|
|
109
|
-
coordinationValues: {
|
|
110
|
-
obsType: 'cell',
|
|
111
|
-
},
|
|
112
|
-
},
|
|
113
|
-
{
|
|
114
|
-
fileType: 'obsEmbedding.anndata.zarr',
|
|
115
|
-
url: 'http://localhost:8000/anndata.zarr',
|
|
116
|
-
options: {
|
|
117
|
-
path: 'obsm/pca',
|
|
118
|
-
dims: [2, 4],
|
|
119
|
-
},
|
|
120
|
-
coordinationValues: {
|
|
121
|
-
obsType: 'cell',
|
|
122
|
-
embeddingType: 'PCA',
|
|
123
|
-
},
|
|
124
|
-
},
|
|
125
|
-
{
|
|
126
|
-
fileType: 'obsEmbedding.anndata.zarr',
|
|
127
|
-
url: 'http://localhost:8000/anndata.zarr',
|
|
128
|
-
options: {
|
|
129
|
-
path: 'obsm/umap',
|
|
130
|
-
},
|
|
131
|
-
coordinationValues: {
|
|
132
|
-
obsType: 'cell',
|
|
133
|
-
embeddingType: 'UMAP',
|
|
134
|
-
},
|
|
135
|
-
},
|
|
136
|
-
]);
|
|
137
|
-
});
|
|
138
|
-
});
|
|
139
|
-
});
|
package/dist/loader-registry.js
DELETED
|
@@ -1,98 +0,0 @@
|
|
|
1
|
-
import { getLoaderClassesForPluginFileType, } from './plugins';
|
|
2
|
-
// TODO(monorepo)
|
|
3
|
-
/*
|
|
4
|
-
import {
|
|
5
|
-
AnnDataSource,
|
|
6
|
-
ZarrDataSource,
|
|
7
|
-
JsonSource,
|
|
8
|
-
CsvSource,
|
|
9
|
-
} from './data-sources';
|
|
10
|
-
import JsonLoader from './json-loaders/JsonLoader';
|
|
11
|
-
import ObsSetsJsonLoader from './json-loaders/ObsSetsJson';
|
|
12
|
-
import ObsSegmentationsJsonLoader from './json-loaders/ObsSegmentationsJson';
|
|
13
|
-
import OmeZarrLoader from './OmeZarrLoader';
|
|
14
|
-
import AnnDataLoaders from './anndata-loaders';
|
|
15
|
-
import GenomicProfilesZarrLoader from './GenomicProfilesZarrLoader';
|
|
16
|
-
import CellsJsonAsObsLabelsLoader from './legacy-loaders/CellsJsonAsObsLabels';
|
|
17
|
-
import CellsJsonAsObsEmbeddingLoader from './legacy-loaders/CellsJsonAsObsEmbedding';
|
|
18
|
-
import CellsJsonAsObsSegmentationsLoader from './legacy-loaders/CellsJsonAsObsSegmentations';
|
|
19
|
-
import ClustersJsonAsObsFeatureMatrixLoader from './legacy-loaders/ClustersJsonAsObsFeatureMatrix';
|
|
20
|
-
import GenesJsonAsObsFeatureMatrixLoader from './legacy-loaders/GenesJsonAsObsFeatureMatrix';
|
|
21
|
-
import RasterJsonAsImageLoader from './raster-json-loaders/RasterJsonAsImageLoader';
|
|
22
|
-
import RasterJsonAsObsSegmentationsLoader from './raster-json-loaders/RasterJsonAsObsSegmentationsLoader';
|
|
23
|
-
import MatrixZarrAsObsFeatureMatrixLoader from './matrix-loaders/MatrixZarrAsObsFeatureMatrix';
|
|
24
|
-
import MoleculesJsonAsObsLocationsLoader from './legacy-loaders/MoleculesJsonAsObsLocations';
|
|
25
|
-
import MoleculesJsonAsObsLabelsLoader from './legacy-loaders/MoleculesJsonAsObsLabels';
|
|
26
|
-
import CellsJsonAsObsLocationsLoader from './legacy-loaders/CellsJsonAsObsLocations';
|
|
27
|
-
import ObsEmbeddingCsvLoader from './csv-loaders/ObsEmbeddingCsv';
|
|
28
|
-
import ObsLocationsCsvLoader from './csv-loaders/ObsLocationsCsv';
|
|
29
|
-
import ObsLabelsCsvLoader from './csv-loaders/ObsLabelsCsv';
|
|
30
|
-
import FeatureLabelsCsvLoader from './csv-loaders/FeatureLabelsCsv';
|
|
31
|
-
import ObsFeatureMatrixCsvLoader from './csv-loaders/ObsFeatureMatrixCsv';
|
|
32
|
-
import ObsSetsCsvLoader from './csv-loaders/ObsSetsCsv';
|
|
33
|
-
*/
|
|
34
|
-
export const fileTypeToLoaderAndSource = {
|
|
35
|
-
// TODO(monorepo)
|
|
36
|
-
/*
|
|
37
|
-
[FileType.OBS_EMBEDDING_CSV]: [CsvSource, ObsEmbeddingCsvLoader],
|
|
38
|
-
[FileType.OBS_LOCATIONS_CSV]: [CsvSource, ObsLocationsCsvLoader],
|
|
39
|
-
[FileType.OBS_LABELS_CSV]: [CsvSource, ObsLabelsCsvLoader],
|
|
40
|
-
[FileType.FEATURE_LABELS_CSV]: [CsvSource, FeatureLabelsCsvLoader],
|
|
41
|
-
[FileType.OBS_FEATURE_MATRIX_CSV]: [CsvSource, ObsFeatureMatrixCsvLoader],
|
|
42
|
-
[FileType.OBS_SEGMENTATIONS_JSON]: [JsonSource, ObsSegmentationsJsonLoader],
|
|
43
|
-
[FileType.OBS_SETS_CSV]: [CsvSource, ObsSetsCsvLoader],
|
|
44
|
-
[FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR]: [
|
|
45
|
-
AnnDataSource, AnnDataLoaders.ObsFeatureMatrixAnndataLoader,
|
|
46
|
-
],
|
|
47
|
-
[FileType.OBS_SETS_ANNDATA_ZARR]: [
|
|
48
|
-
AnnDataSource, AnnDataLoaders.ObsSetsAnndataLoader,
|
|
49
|
-
],
|
|
50
|
-
[FileType.OBS_EMBEDDING_ANNDATA_ZARR]: [
|
|
51
|
-
AnnDataSource, AnnDataLoaders.ObsEmbeddingAnndataLoader,
|
|
52
|
-
],
|
|
53
|
-
[FileType.OBS_LOCATIONS_ANNDATA_ZARR]: [
|
|
54
|
-
AnnDataSource, AnnDataLoaders.ObsLocationsAnndataLoader,
|
|
55
|
-
],
|
|
56
|
-
[FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR]: [
|
|
57
|
-
AnnDataSource, AnnDataLoaders.ObsSegmentationsAnndataLoader,
|
|
58
|
-
],
|
|
59
|
-
[FileType.OBS_LABELS_ANNDATA_ZARR]: [
|
|
60
|
-
AnnDataSource, AnnDataLoaders.ObsLabelsAnndataLoader,
|
|
61
|
-
],
|
|
62
|
-
[FileType.OBS_FEATURE_MATRIX_EXPRESSION_MATRIX_ZARR]: [
|
|
63
|
-
ZarrDataSource, MatrixZarrAsObsFeatureMatrixLoader,
|
|
64
|
-
],
|
|
65
|
-
[FileType.FEATURE_LABELS_ANNDATA_ZARR]: [
|
|
66
|
-
AnnDataSource, AnnDataLoaders.FeatureLabelsAnndataLoader,
|
|
67
|
-
],
|
|
68
|
-
[FileType.IMAGE_OME_ZARR]: [ZarrDataSource, OmeZarrLoader],
|
|
69
|
-
[FileType.IMAGE_RASTER_JSON]: [JsonSource, RasterJsonAsImageLoader],
|
|
70
|
-
[FileType.OBS_SEGMENTATIONS_RASTER_JSON]: [JsonSource, RasterJsonAsObsSegmentationsLoader],
|
|
71
|
-
[FileType.OBS_SETS_JSON]: [JsonSource, ObsSetsJsonLoader],
|
|
72
|
-
[FileType.OBS_SETS_CELL_SETS_JSON]: [JsonSource, ObsSetsJsonLoader],
|
|
73
|
-
[FileType.OBS_FEATURE_MATRIX_CLUSTERS_JSON]: [JsonSource, ClustersJsonAsObsFeatureMatrixLoader],
|
|
74
|
-
[FileType.OBS_FEATURE_MATRIX_GENES_JSON]: [JsonSource, GenesJsonAsObsFeatureMatrixLoader],
|
|
75
|
-
[FileType.OBS_LABELS_CELLS_JSON]: [JsonSource, CellsJsonAsObsLabelsLoader],
|
|
76
|
-
[FileType.OBS_EMBEDDING_CELLS_JSON]: [JsonSource, CellsJsonAsObsEmbeddingLoader],
|
|
77
|
-
[FileType.OBS_LOCATIONS_CELLS_JSON]: [JsonSource, CellsJsonAsObsLocationsLoader],
|
|
78
|
-
[FileType.OBS_SEGMENTATIONS_CELLS_JSON]: [JsonSource, CellsJsonAsObsSegmentationsLoader],
|
|
79
|
-
[FileType.OBS_LOCATIONS_MOLECULES_JSON]: [JsonSource, MoleculesJsonAsObsLocationsLoader],
|
|
80
|
-
[FileType.OBS_LABELS_MOLECULES_JSON]: [JsonSource, MoleculesJsonAsObsLabelsLoader],
|
|
81
|
-
// Old mappings:
|
|
82
|
-
[FileType.NEIGHBORHOODS_JSON]: [JsonSource, JsonLoader],
|
|
83
|
-
[FileType.GENOMIC_PROFILES_ZARR]: [ZarrDataSource, GenomicProfilesZarrLoader],
|
|
84
|
-
*/
|
|
85
|
-
};
|
|
86
|
-
export function getSourceAndLoaderFromFileType(type) {
|
|
87
|
-
if (fileTypeToLoaderAndSource[type]) {
|
|
88
|
-
return fileTypeToLoaderAndSource[type];
|
|
89
|
-
}
|
|
90
|
-
const pluginFileType = getLoaderClassesForPluginFileType(type);
|
|
91
|
-
if (pluginFileType) {
|
|
92
|
-
return pluginFileType;
|
|
93
|
-
}
|
|
94
|
-
// Fallback to JSON.
|
|
95
|
-
// TODO(monorepo)
|
|
96
|
-
// return [JsonSource, JsonLoader];
|
|
97
|
-
return [null, null];
|
|
98
|
-
}
|
|
@@ -1,76 +0,0 @@
|
|
|
1
|
-
export const convenienceFileDefsCollapsed = {
|
|
2
|
-
version: '1.0.15',
|
|
3
|
-
name: 'My config name',
|
|
4
|
-
description: 'My config description',
|
|
5
|
-
initStrategy: 'auto',
|
|
6
|
-
datasets: [
|
|
7
|
-
{
|
|
8
|
-
files: [
|
|
9
|
-
{
|
|
10
|
-
fileType: 'anndata.convenience.zarr',
|
|
11
|
-
url: 'http://localhost:8000/my_anndata.zarr',
|
|
12
|
-
options: {
|
|
13
|
-
cells: {
|
|
14
|
-
xy: 'obsm/centroids',
|
|
15
|
-
},
|
|
16
|
-
cellSets: [
|
|
17
|
-
{
|
|
18
|
-
groupName: 'Leiden',
|
|
19
|
-
setName: 'obs/leiden',
|
|
20
|
-
},
|
|
21
|
-
],
|
|
22
|
-
},
|
|
23
|
-
},
|
|
24
|
-
],
|
|
25
|
-
name: 'A',
|
|
26
|
-
uid: 'A',
|
|
27
|
-
},
|
|
28
|
-
],
|
|
29
|
-
layout: [],
|
|
30
|
-
};
|
|
31
|
-
export function pluginExpandAnnDataConvenience(fileDef) {
|
|
32
|
-
return [
|
|
33
|
-
{
|
|
34
|
-
fileType: 'anndata-cells.zarr',
|
|
35
|
-
url: fileDef.url,
|
|
36
|
-
options: fileDef.options.cells,
|
|
37
|
-
},
|
|
38
|
-
{
|
|
39
|
-
fileType: 'anndata-cell-sets.zarr',
|
|
40
|
-
url: fileDef.url,
|
|
41
|
-
options: fileDef.options.cellSets,
|
|
42
|
-
},
|
|
43
|
-
];
|
|
44
|
-
}
|
|
45
|
-
export const convenienceFileDefsExpanded = {
|
|
46
|
-
version: '1.0.15',
|
|
47
|
-
name: 'My config name',
|
|
48
|
-
description: 'My config description',
|
|
49
|
-
initStrategy: 'auto',
|
|
50
|
-
datasets: [
|
|
51
|
-
{
|
|
52
|
-
files: [
|
|
53
|
-
{
|
|
54
|
-
fileType: 'anndata-cells.zarr',
|
|
55
|
-
url: 'http://localhost:8000/my_anndata.zarr',
|
|
56
|
-
options: {
|
|
57
|
-
xy: 'obsm/centroids',
|
|
58
|
-
},
|
|
59
|
-
},
|
|
60
|
-
{
|
|
61
|
-
fileType: 'anndata-cell-sets.zarr',
|
|
62
|
-
url: 'http://localhost:8000/my_anndata.zarr',
|
|
63
|
-
options: [
|
|
64
|
-
{
|
|
65
|
-
groupName: 'Leiden',
|
|
66
|
-
setName: 'obs/leiden',
|
|
67
|
-
},
|
|
68
|
-
],
|
|
69
|
-
},
|
|
70
|
-
],
|
|
71
|
-
name: 'A',
|
|
72
|
-
uid: 'A',
|
|
73
|
-
},
|
|
74
|
-
],
|
|
75
|
-
layout: [],
|
|
76
|
-
};
|
package/dist/plugins.test.js
DELETED
|
@@ -1,30 +0,0 @@
|
|
|
1
|
-
/* eslint-disable camelcase */
|
|
2
|
-
import { registerPluginFileType, registerPluginJointFileType, getFileTypeDataTypeMapping, getJointFileTypes, } from './plugins';
|
|
3
|
-
import { convenienceFileDefsCollapsed, convenienceFileDefsExpanded, pluginExpandAnnDataConvenience, } from './plugins.test.fixtures';
|
|
4
|
-
import { initialize, } from './view-config-utils';
|
|
5
|
-
describe('src/app/plugins.js', () => {
|
|
6
|
-
describe('getFileTypeDataTypeMapping', () => {
|
|
7
|
-
it('returns the correct data type for built-in file types', () => {
|
|
8
|
-
const dataType = getFileTypeDataTypeMapping()['image.raster.json'];
|
|
9
|
-
expect(dataType).toEqual('image');
|
|
10
|
-
});
|
|
11
|
-
it('returns the correct data type for plugin file types', () => {
|
|
12
|
-
registerPluginFileType('plugin-cells.json', 'cells', null, null);
|
|
13
|
-
const dataType = getFileTypeDataTypeMapping()['plugin-cells.json'];
|
|
14
|
-
expect(dataType).toEqual('cells');
|
|
15
|
-
});
|
|
16
|
-
});
|
|
17
|
-
describe('convenience file types', () => {
|
|
18
|
-
it('registers plugin convenience file types', () => {
|
|
19
|
-
registerPluginJointFileType('anndata.convenience.zarr', pluginExpandAnnDataConvenience);
|
|
20
|
-
const expansionFuncs = getJointFileTypes();
|
|
21
|
-
expect(Object.keys(expansionFuncs).includes('anndata.convenience.zarr')).toBeTruthy();
|
|
22
|
-
expect(typeof expansionFuncs['anndata.convenience.zarr']).toEqual('function');
|
|
23
|
-
});
|
|
24
|
-
it('uses plugin convenience file types in view config initialization', () => {
|
|
25
|
-
registerPluginJointFileType('anndata.convenience.zarr', pluginExpandAnnDataConvenience);
|
|
26
|
-
expect(initialize(convenienceFileDefsCollapsed).datasets)
|
|
27
|
-
.toEqual(convenienceFileDefsExpanded.datasets);
|
|
28
|
-
});
|
|
29
|
-
});
|
|
30
|
-
});
|
|
@@ -1,34 +0,0 @@
|
|
|
1
|
-
import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
|
|
2
|
-
import React from 'react';
|
|
3
|
-
import yaml from 'js-yaml'; // eslint-disable-line import/no-extraneous-dependencies
|
|
4
|
-
// This should only be used by docz, and should not be part of the app build.
|
|
5
|
-
function abbreviateType(yamlString) {
|
|
6
|
-
return yamlString.replace(/:\s+type: (\w+)/g, ' ($1):');
|
|
7
|
-
}
|
|
8
|
-
function abbreviateRef(yamlString) {
|
|
9
|
-
return yamlString.replace(/:\s+\$ref: '#\/definitions\/(\w+)'/g, ' ($1)');
|
|
10
|
-
}
|
|
11
|
-
function stripAddProps(yamlString) {
|
|
12
|
-
// This should be the default in our schemas, but we don't need it in the docs.
|
|
13
|
-
return yamlString.replace(/\s+additionalProperties: false/g, '');
|
|
14
|
-
}
|
|
15
|
-
function valuesAre(yamlString) {
|
|
16
|
-
return yamlString.replace(/patternProperties:\s+\./g, 'Object values are');
|
|
17
|
-
}
|
|
18
|
-
function hasProperties(yamlString) {
|
|
19
|
-
return yamlString.replace(/\.:\s+properties:/g, 'Each value has these properties:');
|
|
20
|
-
}
|
|
21
|
-
function pretty(title, obj) {
|
|
22
|
-
// This is entirely ad-hoc:
|
|
23
|
-
// It woks well for our schema, but no assertion that it should work for anyone else.
|
|
24
|
-
if (!obj)
|
|
25
|
-
return '';
|
|
26
|
-
return (_jsxs(_Fragment, { children: [_jsx("h3", { children: title }), _jsx("pre", { children: hasProperties(valuesAre(stripAddProps(abbreviateRef(abbreviateType(yaml.safeDump(obj)))))) })] }));
|
|
27
|
-
}
|
|
28
|
-
export default function PrettyJsonSchema(props) {
|
|
29
|
-
const { children } = props;
|
|
30
|
-
const { definitions, patternProperties, properties } = children;
|
|
31
|
-
// We could grab the title as well, but when we output an <h2> it is not anchored;
|
|
32
|
-
// better to put the section headers in MD.
|
|
33
|
-
return (_jsxs("blockquote", { children: [pretty('Definitions', definitions), pretty('Properties', patternProperties), pretty('Properties', properties)] }));
|
|
34
|
-
}
|
|
@@ -1,84 +0,0 @@
|
|
|
1
|
-
{
|
|
2
|
-
"$schema": "http://json-schema.org/draft-07/schema#",
|
|
3
|
-
"$id": "https://github.com/vitessce/vitessce/#dataset",
|
|
4
|
-
"title": "Vitessce data set",
|
|
5
|
-
"type": "object",
|
|
6
|
-
"definitions": {
|
|
7
|
-
"components": {
|
|
8
|
-
"type": "array",
|
|
9
|
-
"items": {
|
|
10
|
-
"type": "object",
|
|
11
|
-
"additionalProperties": false,
|
|
12
|
-
"required": ["component", "x", "y"],
|
|
13
|
-
"properties": {
|
|
14
|
-
"component": { "type": "string" },
|
|
15
|
-
"props": { "type": "object" },
|
|
16
|
-
"x": { "type": "integer" },
|
|
17
|
-
"y": { "type": "integer" },
|
|
18
|
-
"w": { "type": "integer" },
|
|
19
|
-
"h": { "type": "integer" }
|
|
20
|
-
}
|
|
21
|
-
}
|
|
22
|
-
},
|
|
23
|
-
"requestInit": {
|
|
24
|
-
"type": "object",
|
|
25
|
-
"additionalProperties": false,
|
|
26
|
-
"required": [],
|
|
27
|
-
"properties": {
|
|
28
|
-
"method": {
|
|
29
|
-
"type": "string"
|
|
30
|
-
},
|
|
31
|
-
"headers": {
|
|
32
|
-
"type": "object"
|
|
33
|
-
},
|
|
34
|
-
"body": {
|
|
35
|
-
"type": "string"
|
|
36
|
-
},
|
|
37
|
-
"mode": {
|
|
38
|
-
"type": "string"
|
|
39
|
-
},
|
|
40
|
-
"credentials": {
|
|
41
|
-
"type": "string"
|
|
42
|
-
},
|
|
43
|
-
"cache": {
|
|
44
|
-
"type": "string"
|
|
45
|
-
},
|
|
46
|
-
"redirect": {
|
|
47
|
-
"type": "string"
|
|
48
|
-
},
|
|
49
|
-
"referrer": {
|
|
50
|
-
"type": "string"
|
|
51
|
-
},
|
|
52
|
-
"integrity": {
|
|
53
|
-
"type": "string"
|
|
54
|
-
}
|
|
55
|
-
}
|
|
56
|
-
}
|
|
57
|
-
},
|
|
58
|
-
"additionalProperties": false,
|
|
59
|
-
"required": ["version", "name", "layers"],
|
|
60
|
-
"properties": {
|
|
61
|
-
"name": { "type": "string" },
|
|
62
|
-
"public": { "type": "boolean" },
|
|
63
|
-
"description": { "type": "string" },
|
|
64
|
-
"layers": {
|
|
65
|
-
"type": "array",
|
|
66
|
-
"items": {
|
|
67
|
-
"type": "object",
|
|
68
|
-
"additionalProperties": false,
|
|
69
|
-
"required": ["name", "type", "fileType", "url"],
|
|
70
|
-
"properties": {
|
|
71
|
-
"name": { "type": "string" },
|
|
72
|
-
"type": { "type": "string" },
|
|
73
|
-
"fileType": { "type": "string" },
|
|
74
|
-
"url": { "type": "string" },
|
|
75
|
-
"requestInit": { "$ref": "#/definitions/requestInit" }
|
|
76
|
-
}
|
|
77
|
-
}
|
|
78
|
-
},
|
|
79
|
-
"staticLayout": { "$ref": "#/definitions/components" },
|
|
80
|
-
"version": {
|
|
81
|
-
"type": "string", "enum": ["0.1.0"]
|
|
82
|
-
}
|
|
83
|
-
}
|
|
84
|
-
}
|