@vitessce/all 2.0.3 → 3.0.0

package/dist-tsc/base-plugins.d.ts.map

@@ -0,0 +1 @@
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package/dist-tsc/base-plugins.js

@@ -0,0 +1,191 @@
+import { FileType, DataType, ViewType, CoordinationType, COMPONENT_COORDINATION_TYPES, } from '@vitessce/constants-internal';
+import { PluginFileType, PluginJointFileType, PluginViewType, PluginCoordinationType, } from '@vitessce/plugins';
+import { z, obsEmbeddingCsvSchema, obsSetsCsvSchema, obsLocationsCsvSchema, obsLabelsCsvSchema, featureLabelsCsvSchema, obsSetsAnndataSchema, obsEmbeddingAnndataSchema, obsLocationsAnndataSchema, obsLabelsAnndataSchema, obsFeatureMatrixAnndataSchema, obsSegmentationsAnndataSchema, featureLabelsAnndataSchema, rasterJsonSchema, anndataZarrSchema, anndataCellsZarrSchema, anndataCellSetsZarrSchema, anndataExpressionMatrixZarrSchema, cellsJsonSchema, imageOmeZarrSchema, imageOmeTiffSchema, obsSetPath, rgbArray, obsSetsSchema, imageLayerObj, cellsLayerObj, neighborhoodsLayerObj, moleculesLayerObj, } from '@vitessce/schemas';
+// Register view type plugins
+import { DescriptionSubscriber } from '@vitessce/description';
+import { ObsSetsManagerSubscriber } from '@vitessce/obs-sets-manager';
+import { EmbeddingScatterplotSubscriber } from '@vitessce/scatterplot-embedding';
+import { GatingSubscriber } from '@vitessce/scatterplot-gating';
+import { SpatialSubscriber } from '@vitessce/spatial';
+import { HeatmapSubscriber } from '@vitessce/heatmap';
+import { FeatureListSubscriber } from '@vitessce/feature-list';
+import { LayerControllerSubscriber } from '@vitessce/layer-controller';
+import { StatusSubscriber } from '@vitessce/status';
+import { HiGlassSubscriber, GenomicProfilesSubscriber } from '@vitessce/genomic-profiles';
+import { CellSetExpressionPlotSubscriber, CellSetSizesPlotSubscriber, ExpressionHistogramSubscriber, } from '@vitessce/statistical-plots';
+// Register file type plugins
+import { 
+// CSV
+CsvSource, ObsSetsCsvLoader, ObsEmbeddingCsvLoader, ObsLocationsCsvLoader, ObsLabelsCsvLoader, ObsFeatureMatrixCsvLoader, FeatureLabelsCsvLoader, } from '@vitessce/csv';
+import { 
+// JSON
+JsonSource, JsonLoader, ObsSegmentationsJsonLoader, ObsSetsJsonLoader, 
+// Legacy
+RasterJsonAsImageLoader, RasterJsonAsObsSegmentationsLoader, ClustersJsonAsObsFeatureMatrixLoader, GenesJsonAsObsFeatureMatrixLoader, CellsJsonAsObsLabelsLoader, CellsJsonAsObsEmbeddingLoader, CellsJsonAsObsLocationsLoader, CellsJsonAsObsSegmentationsLoader, MoleculesJsonAsObsLocationsLoader, MoleculesJsonAsObsLabelsLoader, } from '@vitessce/json';
+import { 
+// AnnData
+AnnDataSource, ObsFeatureMatrixAnndataLoader, ObsEmbeddingAnndataLoader, ObsLocationsAnndataLoader, ObsSegmentationsAnndataLoader, ObsSetsAnndataLoader, ObsLabelsAnndataLoader, FeatureLabelsAnndataLoader, 
+// MuData
+MuDataSource, 
+// OME
+OmeZarrLoader, 
+// Legacy
+ZarrDataSource, MatrixZarrAsObsFeatureMatrixLoader, GenomicProfilesZarrLoader, } from '@vitessce/zarr';
+import { OmeTiffAsObsSegmentationsLoader, OmeTiffLoader, OmeTiffSource, } from '@vitessce/ome-tiff';
+// Joint file types
+import { expandAnndataZarr, } from './joint-file-types.js';
+import { expandAnndataCellSetsZarr, expandAnndataCellsZarr, expandAnndataExpressionMatrixZarr, expandCellSetsJson, expandCellsJson, expandClustersJson, expandExpressionMatrixZarr, expandGenesJson, expandMoleculesJson, expandRasterJson, expandRasterOmeZarr, } from './joint-file-types-legacy.js';
+// Helper function to use COMPONENT_COORDINATION_TYPES.
+function makeViewType(name, component) {
+    return new PluginViewType(name, component, COMPONENT_COORDINATION_TYPES[name]);
+}
+function makeFileType(name, dataType, dataLoaderClass, dataSourceClass, optionsSchema) {
+    return new PluginFileType(name, dataType, dataLoaderClass, dataSourceClass, optionsSchema);
+}
+export const baseViewTypes = [
+    makeViewType(ViewType.DESCRIPTION, DescriptionSubscriber),
+    makeViewType(ViewType.OBS_SETS, ObsSetsManagerSubscriber),
+    makeViewType(ViewType.SCATTERPLOT, EmbeddingScatterplotSubscriber),
+    makeViewType(ViewType.GATING, GatingSubscriber),
+    makeViewType(ViewType.SPATIAL, SpatialSubscriber),
+    makeViewType(ViewType.HEATMAP, HeatmapSubscriber),
+    makeViewType(ViewType.FEATURE_LIST, FeatureListSubscriber),
+    makeViewType(ViewType.LAYER_CONTROLLER, LayerControllerSubscriber),
+    makeViewType(ViewType.STATUS, StatusSubscriber),
+    makeViewType(ViewType.OBS_SET_FEATURE_VALUE_DISTRIBUTION, CellSetExpressionPlotSubscriber),
+    makeViewType(ViewType.OBS_SET_SIZES, CellSetSizesPlotSubscriber),
+    makeViewType(ViewType.FEATURE_VALUE_HISTOGRAM, ExpressionHistogramSubscriber),
+    makeViewType('higlass', HiGlassSubscriber),
+    makeViewType(ViewType.GENOMIC_PROFILES, GenomicProfilesSubscriber),
+];
+export const baseFileTypes = [
+    // All CSV file types
+    makeFileType(FileType.OBS_SETS_CSV, DataType.OBS_SETS, ObsSetsCsvLoader, CsvSource, obsSetsCsvSchema),
+    makeFileType(FileType.OBS_EMBEDDING_CSV, DataType.OBS_EMBEDDING, ObsEmbeddingCsvLoader, CsvSource, obsEmbeddingCsvSchema),
+    makeFileType(FileType.OBS_LOCATIONS_CSV, DataType.OBS_LOCATIONS, ObsLocationsCsvLoader, CsvSource, obsLocationsCsvSchema),
+    makeFileType(FileType.OBS_LABELS_CSV, DataType.OBS_LABELS, ObsLabelsCsvLoader, CsvSource, obsLabelsCsvSchema),
+    makeFileType(FileType.OBS_FEATURE_MATRIX_CSV, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixCsvLoader, CsvSource, z.null()),
+    makeFileType(FileType.FEATURE_LABELS_CSV, DataType.FEATURE_LABELS, FeatureLabelsCsvLoader, CsvSource, featureLabelsCsvSchema),
+    // All JSON file types
+    makeFileType(FileType.OBS_SEGMENTATIONS_JSON, DataType.OBS_SEGMENTATIONS, ObsSegmentationsJsonLoader, JsonSource, z.null()),
+    makeFileType(FileType.OBS_SETS_JSON, DataType.OBS_SETS, ObsSetsJsonLoader, JsonSource, z.null()),
+    // All AnnData file types
+    makeFileType(FileType.OBS_SETS_ANNDATA_ZARR, DataType.OBS_SETS, ObsSetsAnndataLoader, AnnDataSource, obsSetsAnndataSchema),
+    makeFileType(FileType.OBS_EMBEDDING_ANNDATA_ZARR, DataType.OBS_EMBEDDING, ObsEmbeddingAnndataLoader, AnnDataSource, obsEmbeddingAnndataSchema),
+    makeFileType(FileType.OBS_LOCATIONS_ANNDATA_ZARR, DataType.OBS_LOCATIONS, ObsLocationsAnndataLoader, AnnDataSource, obsLocationsAnndataSchema),
+    makeFileType(FileType.OBS_LABELS_ANNDATA_ZARR, DataType.OBS_LABELS, ObsLabelsAnndataLoader, AnnDataSource, obsLabelsAnndataSchema),
+    makeFileType(FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixAnndataLoader, AnnDataSource, obsFeatureMatrixAnndataSchema),
+    makeFileType(FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR, DataType.OBS_SEGMENTATIONS, ObsSegmentationsAnndataLoader, AnnDataSource, obsSegmentationsAnndataSchema),
+    makeFileType(FileType.FEATURE_LABELS_ANNDATA_ZARR, DataType.FEATURE_LABELS, FeatureLabelsAnndataLoader, AnnDataSource, featureLabelsAnndataSchema),
+    // All MuData file types
+    makeFileType(FileType.OBS_SETS_MUDATA_ZARR, DataType.OBS_SETS, ObsSetsAnndataLoader, MuDataSource, obsSetsAnndataSchema),
+    makeFileType(FileType.OBS_EMBEDDING_MUDATA_ZARR, DataType.OBS_EMBEDDING, ObsEmbeddingAnndataLoader, MuDataSource, obsEmbeddingAnndataSchema),
+    makeFileType(FileType.OBS_LOCATIONS_MUDATA_ZARR, DataType.OBS_LOCATIONS, ObsLocationsAnndataLoader, MuDataSource, obsLocationsAnndataSchema),
+    makeFileType(FileType.OBS_LABELS_MUDATA_ZARR, DataType.OBS_LABELS, ObsLabelsAnndataLoader, MuDataSource, obsLabelsAnndataSchema),
+    makeFileType(FileType.OBS_FEATURE_MATRIX_MUDATA_ZARR, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixAnndataLoader, MuDataSource, obsFeatureMatrixAnndataSchema),
+    makeFileType(FileType.OBS_SEGMENTATIONS_MUDATA_ZARR, DataType.OBS_SEGMENTATIONS, ObsSegmentationsAnndataLoader, MuDataSource, obsSegmentationsAnndataSchema),
+    makeFileType(FileType.FEATURE_LABELS_MUDATA_ZARR, DataType.FEATURE_LABELS, FeatureLabelsAnndataLoader, MuDataSource, featureLabelsAnndataSchema),
+    // All OME file types
+    makeFileType(FileType.IMAGE_OME_ZARR, DataType.IMAGE, OmeZarrLoader, ZarrDataSource, imageOmeZarrSchema),
+    makeFileType(FileType.IMAGE_OME_TIFF, DataType.IMAGE, OmeTiffLoader, OmeTiffSource, imageOmeTiffSchema),
+    makeFileType(FileType.OBS_SEGMENTATIONS_OME_TIFF, DataType.OBS_SEGMENTATIONS, OmeTiffAsObsSegmentationsLoader, OmeTiffSource, imageOmeZarrSchema),
+    // All legacy file types
+    makeFileType(FileType.OBS_FEATURE_MATRIX_EXPRESSION_MATRIX_ZARR, DataType.OBS_FEATURE_MATRIX, MatrixZarrAsObsFeatureMatrixLoader, ZarrDataSource, z.null()),
+    makeFileType(FileType.IMAGE_RASTER_JSON, DataType.IMAGE, RasterJsonAsImageLoader, JsonSource, rasterJsonSchema),
+    makeFileType(FileType.OBS_SEGMENTATIONS_RASTER_JSON, DataType.OBS_SEGMENTATIONS, RasterJsonAsObsSegmentationsLoader, JsonSource, rasterJsonSchema),
+    makeFileType(FileType.OBS_SETS_CELL_SETS_JSON, DataType.OBS_SETS, ObsSetsJsonLoader, JsonSource, z.null()),
+    makeFileType(FileType.OBS_FEATURE_MATRIX_CLUSTERS_JSON, DataType.OBS_FEATURE_MATRIX, ClustersJsonAsObsFeatureMatrixLoader, JsonSource, z.null()),
+    makeFileType(FileType.OBS_FEATURE_MATRIX_GENES_JSON, DataType.OBS_FEATURE_MATRIX, GenesJsonAsObsFeatureMatrixLoader, JsonSource, z.null()),
+    makeFileType(FileType.OBS_LABELS_CELLS_JSON, DataType.OBS_LABELS, CellsJsonAsObsLabelsLoader, JsonSource, z.null()),
+    makeFileType(FileType.OBS_EMBEDDING_CELLS_JSON, DataType.OBS_EMBEDDING, CellsJsonAsObsEmbeddingLoader, JsonSource, z.null()),
+    makeFileType(FileType.OBS_LOCATIONS_CELLS_JSON, DataType.OBS_LOCATIONS, CellsJsonAsObsLocationsLoader, JsonSource, z.null()),
+    makeFileType(FileType.OBS_SEGMENTATIONS_CELLS_JSON, DataType.OBS_SEGMENTATIONS, CellsJsonAsObsSegmentationsLoader, JsonSource, z.null()),
+    makeFileType(FileType.OBS_LOCATIONS_MOLECULES_JSON, DataType.OBS_LOCATIONS, MoleculesJsonAsObsLocationsLoader, JsonSource, z.null()),
+    makeFileType(FileType.OBS_LABELS_MOLECULES_JSON, DataType.OBS_LABELS, MoleculesJsonAsObsLabelsLoader, JsonSource, z.null()),
+    makeFileType(FileType.NEIGHBORHOODS_JSON, DataType.NEIGHBORHOODS, JsonLoader, JsonSource, z.null()),
+    makeFileType(FileType.GENOMIC_PROFILES_ZARR, DataType.GENOMIC_PROFILES, GenomicProfilesZarrLoader, ZarrDataSource, z.null()),
+];
+export const baseJointFileTypes = [
+    new PluginJointFileType(FileType.ANNDATA_ZARR, expandAnndataZarr, anndataZarrSchema),
+    // For legacy file types:
+    new PluginJointFileType(FileType.ANNDATA_CELLS_ZARR, expandAnndataCellsZarr, anndataCellsZarrSchema),
+    new PluginJointFileType(FileType.ANNDATA_CELL_SETS_ZARR, expandAnndataCellSetsZarr, anndataCellSetsZarrSchema),
+    new PluginJointFileType(FileType.ANNDATA_EXPRESSION_MATRIX_ZARR, expandAnndataExpressionMatrixZarr, anndataExpressionMatrixZarrSchema),
+    new PluginJointFileType(FileType.EXPRESSION_MATRIX_ZARR, expandExpressionMatrixZarr, z.null()),
+    new PluginJointFileType(FileType.RASTER_JSON, expandRasterJson, rasterJsonSchema),
+    new PluginJointFileType(FileType.RASTER_OME_ZARR, expandRasterOmeZarr, z.null()),
+    new PluginJointFileType(FileType.CELL_SETS_JSON, expandCellSetsJson, z.null()),
+    new PluginJointFileType(FileType.CLUSTERS_JSON, expandClustersJson, z.null()),
+    new PluginJointFileType(FileType.GENES_JSON, expandGenesJson, z.null()),
+    new PluginJointFileType(FileType.CELLS_JSON, expandCellsJson, cellsJsonSchema),
+    new PluginJointFileType(FileType.MOLECULES_JSON, expandMoleculesJson, z.null()),
+];
+// TODO: should these schemas be imported from a common location in package/ rather than here in packages/main/?
+// That would allow view implementations to depend on them for type checking and their default values.
+export const baseCoordinationTypes = [
+    new PluginCoordinationType(CoordinationType.DATASET, null, z.string().nullable()),
+    new PluginCoordinationType(CoordinationType.OBS_TYPE, 'cell', z.string()),
+    new PluginCoordinationType(CoordinationType.FEATURE_TYPE, 'gene', z.string()),
+    new PluginCoordinationType(CoordinationType.FEATURE_VALUE_TYPE, 'expression', z.string()),
+    new PluginCoordinationType(CoordinationType.OBS_LABELS_TYPE, null, z.string().nullable()),
+    new PluginCoordinationType(CoordinationType.EMBEDDING_ZOOM, null, z.number().nullable()),
+    new PluginCoordinationType(CoordinationType.EMBEDDING_ROTATION, 0, z.number().nullable()),
+    new PluginCoordinationType(CoordinationType.EMBEDDING_TARGET_X, null, z.number().nullable()),
+    new PluginCoordinationType(CoordinationType.EMBEDDING_TARGET_Y, null, z.number().nullable()),
+    new PluginCoordinationType(CoordinationType.EMBEDDING_TARGET_Z, 0, z.number().nullable()),
+    new PluginCoordinationType(CoordinationType.EMBEDDING_TYPE, null, z.string().nullable()),
+    new PluginCoordinationType(CoordinationType.EMBEDDING_OBS_SET_POLYGONS_VISIBLE, false, z.boolean()),
+    new PluginCoordinationType(CoordinationType.EMBEDDING_OBS_SET_LABELS_VISIBLE, false, z.boolean()),
+    new PluginCoordinationType(CoordinationType.EMBEDDING_OBS_SET_LABEL_SIZE, 14, z.number()),
+    new PluginCoordinationType(CoordinationType.EMBEDDING_OBS_RADIUS, 1, z.number()),
+    new PluginCoordinationType(CoordinationType.EMBEDDING_OBS_OPACITY, 1, z.number()),
+    new PluginCoordinationType(CoordinationType.EMBEDDING_OBS_RADIUS_MODE, 'auto', z.enum(['manual', 'auto'])),
+    new PluginCoordinationType(CoordinationType.EMBEDDING_OBS_OPACITY_MODE, 'auto', z.enum(['manual', 'auto'])),
+    new PluginCoordinationType(CoordinationType.SPATIAL_ZOOM, null, z.number().nullable()),
+    new PluginCoordinationType(CoordinationType.SPATIAL_ROTATION, 0, z.number().nullable()),
+    new PluginCoordinationType(CoordinationType.SPATIAL_TARGET_X, null, z.number().nullable()),
+    new PluginCoordinationType(CoordinationType.SPATIAL_TARGET_Y, null, z.number().nullable()),
+    new PluginCoordinationType(CoordinationType.SPATIAL_TARGET_Z, null, z.number().nullable()),
+    new PluginCoordinationType(CoordinationType.SPATIAL_ROTATION_X, null, z.number().nullable()),
+    new PluginCoordinationType(CoordinationType.SPATIAL_ROTATION_Y, null, z.number().nullable()),
+    new PluginCoordinationType(CoordinationType.SPATIAL_ROTATION_Z, null, z.number().nullable()),
+    new PluginCoordinationType(CoordinationType.SPATIAL_ROTATION_ORBIT, 0, z.number().nullable()),
+    new PluginCoordinationType(CoordinationType.SPATIAL_ORBIT_AXIS, 'Y', z.string().nullable()),
+    new PluginCoordinationType(CoordinationType.SPATIAL_AXIS_FIXED, false, z.boolean().nullable()),
+    new PluginCoordinationType(CoordinationType.SPATIAL_IMAGE_LAYER, null, imageLayerObj.nullable()),
+    new PluginCoordinationType(CoordinationType.SPATIAL_SEGMENTATION_LAYER, null, z.union([
+        cellsLayerObj, imageLayerObj,
+    ]).nullable()),
+    new PluginCoordinationType(CoordinationType.SPATIAL_NEIGHBORHOOD_LAYER, null, neighborhoodsLayerObj.nullable()),
+    new PluginCoordinationType(CoordinationType.SPATIAL_POINT_LAYER, null, moleculesLayerObj.nullable()),
+    new PluginCoordinationType(CoordinationType.HEATMAP_ZOOM_X, 0, z.number()),
+    new PluginCoordinationType(CoordinationType.HEATMAP_ZOOM_Y, 0, z.number()),
+    new PluginCoordinationType(CoordinationType.HEATMAP_TARGET_X, 0, z.number()),
+    new PluginCoordinationType(CoordinationType.HEATMAP_TARGET_Y, 0, z.number()),
+    new PluginCoordinationType(CoordinationType.OBS_FILTER, null, z.array(z.string()).nullable()),
+    new PluginCoordinationType(CoordinationType.OBS_HIGHLIGHT, null, z.string().nullable()),
+    new PluginCoordinationType(CoordinationType.OBS_SET_SELECTION, null, z.array(obsSetPath).nullable()),
+    new PluginCoordinationType(CoordinationType.OBS_SET_EXPANSION, null, z.array(obsSetPath).nullable()),
+    new PluginCoordinationType(CoordinationType.OBS_SET_HIGHLIGHT, null, obsSetPath.nullable()),
+    new PluginCoordinationType(CoordinationType.OBS_SET_COLOR, null, z.array(z.object({
+        path: obsSetPath,
+        color: rgbArray,
+    })).nullable()),
+    new PluginCoordinationType(CoordinationType.OBS_COLOR_ENCODING, 'cellSetSelection', z.enum(['geneSelection', 'cellSetSelection'])),
+    new PluginCoordinationType(CoordinationType.FEATURE_FILTER, null, z.array(z.string()).nullable()),
+    new PluginCoordinationType(CoordinationType.FEATURE_HIGHLIGHT, null, z.string().nullable()),
+    new PluginCoordinationType(CoordinationType.FEATURE_SELECTION, null, z.array(z.string()).nullable()),
+    new PluginCoordinationType(CoordinationType.FEATURE_VALUE_TRANSFORM, null, z.enum(['log1p', 'arcsinh']).nullable()),
+    new PluginCoordinationType(CoordinationType.FEATURE_VALUE_TRANSFORM_COEFFICIENT, 1, z.number()),
+    new PluginCoordinationType(CoordinationType.TOOLTIPS_VISIBLE, true, z.boolean()),
+    new PluginCoordinationType(CoordinationType.FEATURE_VALUE_COLORMAP, 'plasma', z.string().nullable()),
+    new PluginCoordinationType(CoordinationType.FEATURE_VALUE_COLORMAP_RANGE, [0.0, 1.0], z.array(z.number()).length(2)),
+    new PluginCoordinationType(CoordinationType.GATING_FEATURE_SELECTION_X, null, z.string().nullable()),
+    new PluginCoordinationType(CoordinationType.GATING_FEATURE_SELECTION_Y, null, z.string().nullable()),
+    new PluginCoordinationType(CoordinationType.GENOMIC_ZOOM_X, 0, z.number()),
+    new PluginCoordinationType(CoordinationType.GENOMIC_ZOOM_Y, 0, z.number()),
+    new PluginCoordinationType(CoordinationType.GENOMIC_TARGET_X, 1549999999.5, z.number()),
+    new PluginCoordinationType(CoordinationType.GENOMIC_TARGET_Y, 1549999999.5, z.number()),
+    new PluginCoordinationType(CoordinationType.ADDITIONAL_OBS_SETS, null, obsSetsSchema.nullable()),
+    new PluginCoordinationType(CoordinationType.MOLECULE_HIGHLIGHT, null, z.string().nullable()),
+];

package/dist-tsc/index.d.ts

@@ -0,0 +1,4 @@
+export { Vitessce } from './Vitessce.js';
+export { PluginFileType, PluginViewType, PluginCoordinationType, PluginJointFileType, } from '@vitessce/plugins';
+export { z } from '@vitessce/schemas';
+//# sourceMappingURL=index.d.ts.map

package/dist-tsc/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAC;AACzC,OAAO,EACL,cAAc,EACd,cAAc,EACd,sBAAsB,EACtB,mBAAmB,GACpB,MAAM,mBAAmB,CAAC;AAC3B,OAAO,EAAE,CAAC,EAAE,MAAM,mBAAmB,CAAC"}

package/dist-tsc/index.js

@@ -1,2 +1,3 @@
-export { Vitessce } from './setup';
-export { registerPluginFileType, registerPluginViewType, registerPluginCoordinationType, registerPluginJointFileType, } from '@vitessce/vit-s';
+export { Vitessce } from './Vitessce.js';
+export { PluginFileType, PluginViewType, PluginCoordinationType, PluginJointFileType, } from '@vitessce/plugins';
+export { z } from '@vitessce/schemas';

package/dist-tsc/joint-file-types-legacy.d.ts

@@ -0,0 +1,226 @@
+import type { z } from 'zod';
+import type { latestFileDefSchema } from '@vitessce/schemas';
+declare type legacyFileDefSchema = z.infer<typeof latestFileDefSchema> & {
+    type?: string;
+};
+export declare function expandMoleculesJson(fileDef: legacyFileDefSchema): {
+    fileType: string;
+    coordinationValues: {
+        obsType: string;
+    };
+    name?: string | undefined;
+    url?: string | undefined;
+    options?: any;
+    requestInit?: {
+        method?: string | undefined;
+        headers?: Record<string, any> | undefined;
+        body?: string | undefined;
+        mode?: string | undefined;
+        credentials?: string | undefined;
+        cache?: string | undefined;
+        redirect?: string | undefined;
+        referrer?: string | undefined;
+        integrity?: string | undefined;
+    } | undefined;
+    type?: string | undefined;
+}[];
+export declare function expandExpressionMatrixZarr(fileDef: legacyFileDefSchema): {
+    fileType: string;
+    coordinationValues: {
+        obsType: string;
+        featureType: string;
+        featureValueType: string;
+    };
+    name?: string | undefined;
+    url?: string | undefined;
+    options?: any;
+    requestInit?: {
+        method?: string | undefined;
+        headers?: Record<string, any> | undefined;
+        body?: string | undefined;
+        mode?: string | undefined;
+        credentials?: string | undefined;
+        cache?: string | undefined;
+        redirect?: string | undefined;
+        referrer?: string | undefined;
+        integrity?: string | undefined;
+    } | undefined;
+    type?: string | undefined;
+}[];
+export declare function expandRasterJson(fileDef: legacyFileDefSchema): {
+    fileType: string;
+    name?: string | undefined;
+    url?: string | undefined;
+    options?: any;
+    requestInit?: {
+        method?: string | undefined;
+        headers?: Record<string, any> | undefined;
+        body?: string | undefined;
+        mode?: string | undefined;
+        credentials?: string | undefined;
+        cache?: string | undefined;
+        redirect?: string | undefined;
+        referrer?: string | undefined;
+        integrity?: string | undefined;
+    } | undefined;
+    coordinationValues?: Record<string, string> | undefined;
+    type?: string | undefined;
+}[];
+export declare function expandRasterOmeZarr(fileDef: legacyFileDefSchema): {
+    fileType: string;
+    name?: string | undefined;
+    url?: string | undefined;
+    options?: any;
+    requestInit?: {
+        method?: string | undefined;
+        headers?: Record<string, any> | undefined;
+        body?: string | undefined;
+        mode?: string | undefined;
+        credentials?: string | undefined;
+        cache?: string | undefined;
+        redirect?: string | undefined;
+        referrer?: string | undefined;
+        integrity?: string | undefined;
+    } | undefined;
+    coordinationValues?: Record<string, string> | undefined;
+    type?: string | undefined;
+}[];
+export declare function expandCellSetsJson(fileDef: legacyFileDefSchema): {
+    fileType: string;
+    coordinationValues: {
+        obsType: string;
+    };
+    name?: string | undefined;
+    url?: string | undefined;
+    options?: any;
+    requestInit?: {
+        method?: string | undefined;
+        headers?: Record<string, any> | undefined;
+        body?: string | undefined;
+        mode?: string | undefined;
+        credentials?: string | undefined;
+        cache?: string | undefined;
+        redirect?: string | undefined;
+        referrer?: string | undefined;
+        integrity?: string | undefined;
+    } | undefined;
+    type?: string | undefined;
+}[];
+export declare function expandCellsJson(fileDef: legacyFileDefSchema): any[];
+export declare function expandClustersJson(fileDef: legacyFileDefSchema): {
+    fileType: string;
+    coordinationValues: {
+        obsType: string;
+        featureType: string;
+        featureValueType: string;
+    };
+    name?: string | undefined;
+    url?: string | undefined;
+    options?: any;
+    requestInit?: {
+        method?: string | undefined;
+        headers?: Record<string, any> | undefined;
+        body?: string | undefined;
+        mode?: string | undefined;
+        credentials?: string | undefined;
+        cache?: string | undefined;
+        redirect?: string | undefined;
+        referrer?: string | undefined;
+        integrity?: string | undefined;
+    } | undefined;
+    type?: string | undefined;
+}[];
+export declare function expandGenesJson(fileDef: legacyFileDefSchema): {
+    fileType: string;
+    coordinationValues: {
+        obsType: string;
+        featureType: string;
+        featureValueType: string;
+    };
+    name?: string | undefined;
+    url?: string | undefined;
+    options?: any;
+    requestInit?: {
+        method?: string | undefined;
+        headers?: Record<string, any> | undefined;
+        body?: string | undefined;
+        mode?: string | undefined;
+        credentials?: string | undefined;
+        cache?: string | undefined;
+        redirect?: string | undefined;
+        referrer?: string | undefined;
+        integrity?: string | undefined;
+    } | undefined;
+    type?: string | undefined;
+}[];
+export declare function expandAnndataCellsZarr(fileDef: legacyFileDefSchema): any[];
+export declare function expandAnndataCellSetsZarr(fileDef: legacyFileDefSchema): {
+    fileType: string;
+    options: any;
+    coordinationValues: {
+        obsType: string;
+    };
+    url: string | undefined;
+    requestInit: {
+        method?: string | undefined;
+        headers?: Record<string, any> | undefined;
+        body?: string | undefined;
+        mode?: string | undefined;
+        credentials?: string | undefined;
+        cache?: string | undefined;
+        redirect?: string | undefined;
+        referrer?: string | undefined;
+        integrity?: string | undefined;
+    } | undefined;
+}[];
+export declare function expandAnndataExpressionMatrixZarr(fileDef: legacyFileDefSchema): ({
+    fileType: string;
+    options: {
+        path: any;
+        featureFilterPath?: undefined;
+        initialFeatureFilterPath?: undefined;
+    };
+    coordinationValues: {
+        featureType: string;
+        obsType?: undefined;
+        featureValueType?: undefined;
+    };
+    url: string | undefined;
+    requestInit: {
+        method?: string | undefined;
+        headers?: Record<string, any> | undefined;
+        body?: string | undefined;
+        mode?: string | undefined;
+        credentials?: string | undefined;
+        cache?: string | undefined;
+        redirect?: string | undefined;
+        referrer?: string | undefined;
+        integrity?: string | undefined;
+    } | undefined;
+} | {
+    fileType: string;
+    options: {
+        path: any;
+        featureFilterPath: any;
+        initialFeatureFilterPath: any;
+    };
+    coordinationValues: {
+        obsType: string;
+        featureType: string;
+        featureValueType: string;
+    };
+    url: string | undefined;
+    requestInit: {
+        method?: string | undefined;
+        headers?: Record<string, any> | undefined;
+        body?: string | undefined;
+        mode?: string | undefined;
+        credentials?: string | undefined;
+        cache?: string | undefined;
+        redirect?: string | undefined;
+        referrer?: string | undefined;
+        integrity?: string | undefined;
+    } | undefined;
+})[];
+export {};
+//# sourceMappingURL=joint-file-types-legacy.d.ts.map

package/dist-tsc/joint-file-types-legacy.d.ts.map

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