@vitessce/vit-s 2.0.1 → 2.0.3-beta.0

package/dist/LoadingIndicator.js

@@ -10,7 +10,7 @@ const useStyles = makeStyles(() => ({
         zIndex: '1040',
         width: '100%',
         height: '100%',
-        borderRadius: '0.25rem',
+        borderRadius: '4px',
         backgroundColor: 'rgba(0, 0, 0, 0.5)',
     },
     loadingIndicatorContainer: {

package/dist/TitleInfo.js

@@ -85,7 +85,7 @@ export const useTitleStyles = makeStyles(theme => ({
         overflow: 'hidden',
         fontSize: '80% !important',
         opacity: '.8',
-        padding: '0 0.25rem',
+        padding: '0 4px',
         justifyContent: 'center',
         lineHeight: '25px !important',
         flexShrink: '1',
@@ -105,16 +105,16 @@ export const useTitleStyles = makeStyles(theme => ({
         border: `1px solid ${theme.palette.cardBorder}`,
         flex: '1 1 auto',
         minHeight: '1px',
-        padding: '0.75rem',
-        marginTop: '0.5rem',
-        marginBottom: '0.5rem',
+        padding: '12px',
+        marginTop: '8px',
+        marginBottom: '8px',
         position: 'relative',
         display: 'flex',
         flexDirection: 'column',
         minWidth: '0',
         wordWrap: 'break-word',
         backgroundClip: 'border-box',
-        borderRadius: '0.25rem',
+        borderRadius: '4px',
     },
     noScrollCard: {
         backgroundColor: theme.palette.secondaryBackground,

package/dist/VitS.js

@@ -11,9 +11,6 @@ import { Warning } from './Warning';
 import CallbackPublisher from './CallbackPublisher';
 import { getComponent } from './component-registry';
 import { checkTypes, initialize, upgradeAndValidate, } from './view-config-utils';
-const generateClassName = createGenerateClassName({
-    disableGlobal: true,
-});
 function logConfig(config, name) {
     console.groupCollapsed(`🚄 Vitessce (${META_VERSION.version}) ${name}`);
     console.info(`data:,${JSON.stringify(config)}`);
@@ -38,9 +35,18 @@ function logConfig(config, name) {
  * @param {boolean} props.validateOnConfigChange Whether to validate
  * against the view config schema when publishing changes. Use for debugging
  * purposes, as this may have a performance impact. By default, false.
+ * @param {undefined|string} props.uid A unique identifier for this Vitessce instance,
+ * for the purpose of avoiding CSS autogenerated class name conflicts. Must be valid as part
+ * of a CSS class name string.
  */
 export function VitS(props) {
-    const { config, rowHeight, height, theme, onWarn, onConfigChange, onLoaderChange, validateOnConfigChange = false, onConfigUpgrade, isBounded = false, } = props;
+    const { config, rowHeight, height, theme, onWarn, onConfigChange, onLoaderChange, validateOnConfigChange = false, onConfigUpgrade, isBounded = false, uid, } = props;
+    const generateClassName = useMemo(() => createGenerateClassName({
+        disableGlobal: false,
+        // Avoid conflicts with portal-ui MUI class names,
+        // and allow setting a UID.
+        productionPrefix: (uid ? `vit${uid}` : 'vit'),
+    }), [uid]);
     // Process the view config and memoize the result:
     // - Validate.
     // - Upgrade, if legacy schema.

package/dist/Vitessce.integration.test.js

@@ -0,0 +1,36 @@
+"use strict";
+/* eslint-disable max-len */
+// import React from 'react';
+// import Adapter from 'enzyme-adapter-react-16';
+// import { mount, configure } from 'enzyme';
+// import Ajv from 'ajv';
+// import expect from 'expect';
+// import Vitessce from './Vitessce';
+// import { configs } from './api';
+// import configSchema from '../schemas/config.schema.json';
+// configure({ adapter: new Adapter() });
+// describe('Vitessce.js', () => {
+//   describe('<Vitessce />', () => {
+//     it('Produces valid view config', (done) => {
+//       const config = configs['linnarsson-2018'];
+//       let updatedConfig = {};
+//       // eslint-disable-next-line no-return-assign
+//       const wrapper = mount(<Vitessce config={config} onConfigChange={c => updatedConfig = c} />);
+//       setTimeout(() => {
+//         // Simulate usage of some of the app
+//         wrapper.find('[id^="deckgl-overlay-"]').at(0).simulate('wheel', { deltaY: 1000, deltaX: 1000 });
+//         wrapper.find('[id^="deckgl-overlay-"]').at(1).simulate('wheel', { deltaY: 1000, deltaX: 1000 });
+//         wrapper.find('[id^="deckgl-overlay-"]').at(2).simulate('wheel', { deltaY: 1000, deltaX: 1000 });
+//         const validate = new Ajv().compile(configSchema);
+//         const valid = validate(updatedConfig);
+//         if (!valid) {
+//           const failureReason = JSON.stringify(validate.errors, null, 2);
+//           console.error(failureReason);
+//         }
+//         expect(valid).toEqual(true);
+//         wrapper.unmount();
+//         done();
+//       }, 20000);
+//     }).timeout(30000);
+//   });
+// });

package/dist/Vitessce.js

@@ -0,0 +1,101 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+/* eslint-disable camelcase */
+import React, { useEffect, useMemo } from 'react';
+import { ThemeProvider, StylesProvider, createGenerateClassName, } from '@material-ui/core/styles';
+import isEqual from 'lodash/isEqual';
+import { muiTheme } from './shared-mui/styles';
+import { ViewConfigProvider, createViewConfigStore, AuxiliaryProvider, createAuxiliaryStore, } from './state/hooks';
+import VitessceGrid from './VitessceGrid';
+import { Warning } from './Warning';
+import CallbackPublisher from './CallbackPublisher';
+import { getComponent } from './component-registry';
+import { checkTypes, initialize, upgradeAndValidate } from './view-config-utils';
+// TODO(monorepo): figure out how to get the current package version from package.json
+// import packageJson from '../package.json';
+const packageJson = { version: 'unk' };
+const generateClassName = createGenerateClassName({
+    disableGlobal: true,
+});
+function logConfig(config, name) {
+    console.groupCollapsed(`🚄 Vitessce (${packageJson.version}) ${name}`);
+    console.info(`data:,${JSON.stringify(config)}`);
+    console.info(JSON.stringify(config, null, 2));
+    console.groupEnd();
+}
+/**
+ * The Vitessce component.
+ * @param {object} props
+ * @param {object} props.config A Vitessce view config.
+ * If the config is valid, the VitessceGrid will be rendered as a child.
+ * If the config is invalid, a Warning will be rendered instead.
+ * @param {number} props.rowHeight Row height for grid layout. Optional.
+ * @param {number} props.height Total height for grid layout. Optional.
+ * @param {string} props.theme The theme, used for styling as
+ * light or dark. Optional. By default, "dark"
+ * @param {function} props.onWarn A callback for warning messages. Optional.
+ * @param {function} props.onConfigChange A callback for view config
+ * updates. Optional.
+ * @param {function} props.onLoaderChange A callback for loader
+ * updates. Optional.
+ * @param {boolean} props.validateOnConfigChange Whether to validate
+ * against the view config schema when publishing changes. Use for debugging
+ * purposes, as this may have a performance impact. By default, false.
+ */
+export function Vitessce(props) {
+    const { config, rowHeight, height, theme, onWarn, onConfigChange, onLoaderChange, validateOnConfigChange = false, onConfigUpgrade, isBounded = false, } = props;
+    // Process the view config and memoize the result:
+    // - Validate.
+    // - Upgrade, if legacy schema.
+    // - Validate after upgrade, if legacy schema.
+    // - Initialize (based on initStrategy).
+    const [configOrWarning, success] = useMemo(() => {
+        // If the config value is undefined, show a warning message.
+        if (!config) {
+            return [{
+                    title: 'No such dataset',
+                    unformatted: 'The dataset configuration could not be found.',
+                }, false];
+        }
+        // If the view config is missing a version, show a warning message.
+        if (!config.version) {
+            return [{
+                    title: 'Missing version',
+                    unformatted: 'The dataset configuration is missing a version, preventing validation.',
+                }, false];
+        }
+        logConfig(config, 'input view config');
+        // Check if this is a "legacy" view config.
+        const [upgradedConfig, upgradeSuccess] = upgradeAndValidate(config, onConfigUpgrade);
+        if (upgradeSuccess) {
+            logConfig(upgradedConfig, 'upgraded view config');
+            // Initialize the view config according to the initStrategy.
+            const [typeCheckSuccess, typeCheckMessage] = checkTypes(upgradedConfig);
+            if (typeCheckSuccess) {
+                try {
+                    const initializedConfig = initialize(upgradedConfig);
+                    logConfig(initializedConfig, 'initialized view config');
+                    return [initializedConfig, true];
+                }
+                catch (e) {
+                    return [{
+                            title: 'View config initialization failed.',
+                            unformatted: e.message,
+                        }, false];
+                }
+            }
+            return [{
+                    title: 'View config checks failed.',
+                    unformatted: typeCheckMessage,
+                }, false];
+        }
+        return [upgradedConfig, false];
+    }, [config, onConfigUpgrade]);
+    // Emit the upgraded/initialized view config
+    // to onConfigChange if necessary.
+    useEffect(() => {
+        if (success && !isEqual(configOrWarning, config) && onConfigChange) {
+            onConfigChange(configOrWarning);
+        }
+    }, [success, config, configOrWarning, onConfigChange]);
+    return success ? (_jsx(StylesProvider, { generateClassName: generateClassName, children: _jsx(ThemeProvider, { theme: muiTheme[theme], children: _jsx(ViewConfigProvider, { createStore: createViewConfigStore, children: _jsxs(AuxiliaryProvider, { createStore: createAuxiliaryStore, children: [_jsx(VitessceGrid, { config: configOrWarning, getComponent: getComponent, rowHeight: rowHeight, height: height, theme: theme, isBounded: isBounded }), _jsx(CallbackPublisher, { onWarn: onWarn, onConfigChange: onConfigChange, onLoaderChange: onLoaderChange, validateOnConfigChange: validateOnConfigChange })] }) }) }) })) : (_jsx(StylesProvider, { generateClassName: generateClassName, children: _jsx(ThemeProvider, { theme: muiTheme[theme], children: _jsx(Warning, { ...configOrWarning }) }) }));
+}

package/dist/Warning.js

@@ -24,16 +24,16 @@ const useStyles = makeStyles(theme => ({
         border: `1px solid ${theme.palette.cardBorder}`,
         flex: '1 1 auto',
         minHeight: '1px',
-        padding: '0.75rem',
-        marginTop: '0.5rem',
-        marginBottom: '0.5rem',
+        padding: '12px',
+        marginTop: '8px',
+        marginBottom: '8px',
         position: 'relative',
         display: 'flex',
         flexDirection: 'column',
         minWidth: '0',
         wordWrap: 'break-word',
         backgroundClip: 'border-box',
-        borderRadius: '0.25rem',
+        borderRadius: '4px',
         backgroundColor: theme.palette.primaryBackground,
         color: theme.palette.primaryForeground,
     },

package/dist/export-utils.js

@@ -0,0 +1,70 @@
+import Bowser from 'bowser';
+import { compressToEncodedURIComponent, decompressFromEncodedURIComponent } from 'lz-string';
+const CURRENT_VERSION = '0.0.1';
+const VITESSCE_CONF_QUERY_STRING = 'vitessce_conf';
+const VERSION_QUERY_STRING = 'vitessce_conf_version';
+const LENGTH_QUERY_STRING = 'vitessce_conf_length';
+function sniffBrowser() {
+    const { browser } = Bowser.parse(window.navigator.userAgent);
+    return browser.name;
+}
+// https://stackoverflow.com/questions/417142/what-is-the-maximum-length-of-a-url-in-different-browsers
+const MAX_BROWSER_URL_LENGTHS = {
+    Chrome: 32779,
+    'Internet Explorer': 2047,
+    Edge: 2047,
+    Safari: 65000,
+    Firefox: 65000,
+};
+export default class CompressedConfLengthError {
+    constructor(message) {
+        this.message = message;
+    }
+}
+/**
+ * Encode a configuration as url params with a version and an lz-compressed conf.
+ * @param {Object} params
+ * @param {Object} params.conf Previous scope names.
+ * @param {function} params.onOverMaximumUrlLength Callback for when new url
+ * is over max length for your browser - takes two arguments: { message, willWorkOn }
+ * for the error message and the browsers for which the url will work (optional).
+ * @returns {string} The new params like
+ * vitessce_conf_length=10&vitessce_conf_version=0.0.1&vitessce_conf=fksdfasdfjkl
+ */
+export function encodeConfInUrl({ conf, onOverMaximumUrlLength = () => { }, }) {
+    const compressedConf = compressToEncodedURIComponent(JSON.stringify(conf));
+    const newParams = `${LENGTH_QUERY_STRING}=${compressedConf.length}&${VERSION_QUERY_STRING}=${CURRENT_VERSION}&${VITESSCE_CONF_QUERY_STRING}=${compressedConf}`;
+    const browser = sniffBrowser();
+    const maxLength = MAX_BROWSER_URL_LENGTHS[browser];
+    if (newParams.length > maxLength) {
+        const willWorkOn = Object.entries(MAX_BROWSER_URL_LENGTHS)
+            .filter(entry => entry[1] > newParams.length)
+            .map(entry => entry[0]);
+        const message = `Configuration is ${compressedConf.length} characters; max URL for ${browser} is ${maxLength}: it will work on ${willWorkOn.join(', ') || 'no browser'}.`;
+        console.error(message);
+        onOverMaximumUrlLength({ message, willWorkOn });
+    }
+    return newParams;
+}
+/**
+ * Decode URL params to a Vitessce configuration.
+ * The URL params must have version and vitessce_conf params,
+ * like vitessce_conf_length=10&vitessce_conf_version=0.0.1&vitessce_conf=fksdfasdfjkl.
+ * @param {Object} queryString The URL params,
+ * like vitessce_conf_length=10&vitessce_conf_version=0.0.1&vitessce_conf=fksdfasdfjkl.
+ * @returns {string} A vitessce configuration.
+ */
+export function decodeURLParamsToConf(queryString) {
+    const params = new URLSearchParams(queryString.replace('#', '&'));
+    const compressedConfString = params.get(VITESSCE_CONF_QUERY_STRING);
+    const expectedConfLength = Number(params.get(LENGTH_QUERY_STRING));
+    if (expectedConfLength !== compressedConfString.length) {
+        throw new CompressedConfLengthError(`Compressed conf length (${compressedConfString.length}) != expected (${expectedConfLength}). URL truncated?`);
+    }
+    const version = params.get(VERSION_QUERY_STRING);
+    if (version === CURRENT_VERSION) {
+        const conf = JSON.parse(decompressFromEncodedURIComponent(compressedConfString));
+        return conf;
+    }
+    throw new Error('Unrecognized URL Param Version');
+}

package/dist/export-utils.test.js

@@ -0,0 +1,66 @@
+import expect from 'expect';
+import { encodeConfInUrl, decodeURLParamsToConf, } from './export-utils';
+const fakeConfig = {
+    version: '0.1.0',
+    public: false,
+    layers: [
+        {
+            name: 'cells',
+            type: 'CELLS',
+            fileType: 'cells.json',
+            url: 'http://example.com/cells.json',
+        },
+    ],
+    name: 'Just scatterplot',
+    staticLayout: [
+        {
+            component: 'scatterplot',
+            props: {
+                mapping: 't-SNE',
+                view: {
+                    zoom: 0.75,
+                    target: [0, 0, 0],
+                },
+            },
+            x: 0,
+            y: 0,
+            w: 12,
+            h: 2,
+        },
+    ],
+};
+function makeLongString(length) {
+    let result = '';
+    const characters = 'ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789';
+    const charactersLength = characters.length;
+    // eslint-disable-next-line no-plusplus
+    for (let i = 0; i < length; i++) {
+        result += characters.charAt(Math.floor(Math.random() * charactersLength));
+    }
+    return result;
+}
+describe('src/app/export-utils.js', () => {
+    describe('encodeConfInUrl', () => {
+        it('encodes a view config for a URL', () => {
+            const urlParams1 = encodeConfInUrl({ conf: {} });
+            expect(urlParams1).toEqual('vitessce_conf_length=5&vitessce_conf_version=0.0.1&vitessce_conf=N4XyA');
+            const urlParams2 = encodeConfInUrl({ conf: fakeConfig });
+            expect(urlParams2).toEqual('vitessce_conf_length=327&vitessce_conf_version=0.0.1&vitessce_conf=N4IgbgpgTgzglgewHYgFwgAwDoCMWMgA0IADgK4BGANnAMZoBmAhlTBMVUwJ7QxoDaoJEwC2ENCFoQqrIiAAuXEuPQBhAKIAZTQGU5DOFQgAVJSsnTWWAFYxkcslCoSAFvPklUAei8QAHqIkRli0CCJeUjIwNnYoAL4AusTCYhIAUmQw8gAEMLRM7tBBCPJyWQV0mtwIZKWogpJhJMgQSHUgeQXyRVQlciRQCCR8qKAiTCQkcEgA5hLyALQ6AHLqcmBwEADuaKAAXghhaNgA7ACsxPJMUDMQdfwYhI8YCXFxxH7HxFxfIDuoOAATMQXGhAYk4kA');
+        });
+        it('Calls onOverMaximumUrlLength for conf too long', () => {
+            let browsers;
+            // eslint-disable-next-line no-return-assign
+            const onOverMaximumUrlLength = ({ willWorkOn }) => browsers = willWorkOn;
+            encodeConfInUrl({ conf: { foo: makeLongString(69000) }, onOverMaximumUrlLength });
+            expect(browsers).toEqual([]);
+            encodeConfInUrl({ conf: { foo: makeLongString(37000) }, onOverMaximumUrlLength });
+            expect(browsers).toEqual(['Safari', 'Firefox']);
+        });
+        it('decodes a view config for a URL', () => {
+            const viewConfig1 = decodeURLParamsToConf('vitessce_conf_length=5&vitessce_conf_version=0.0.1&vitessce_conf=N4XyA');
+            expect(viewConfig1).toEqual({});
+            const viewConfig2 = decodeURLParamsToConf('vitessce_conf_length=327&vitessce_conf_version=0.0.1&vitessce_conf=N4IgbgpgTgzglgewHYgFwgAwDoCMWMgA0IADgK4BGANnAMZoBmAhlTBMVUwJ7QxoDaoJEwC2ENCFoQqrIiAAuXEuPQBhAKIAZTQGU5DOFQgAVJSsnTWWAFYxkcslCoSAFvPklUAei8QAHqIkRli0CCJeUjIwNnYoAL4AusTCYhIAUmQw8gAEMLRM7tBBCPJyWQV0mtwIZKWogpJhJMgQSHUgeQXyRVQlciRQCCR8qKAiTCQkcEgA5hLyALQ6AHLqcmBwEADuaKAAXghhaNgA7ACsxPJMUDMQdfwYhI8YCXFxxH7HxFxfIDuoOAATMQXGhAYk4kA');
+            expect(viewConfig2).toEqual(fakeConfig);
+        });
+    });
+});

package/dist/index.js

@@ -1,7 +1,7 @@
 export { VitS } from './VitS';
 export { TitleInfo } from './TitleInfo';
 export { PopperMenu } from './shared-mui/components';
-export { registerPluginViewType, registerPluginCoordinationType, registerPluginFileType, } from './plugins';
+export { registerPluginViewType, registerPluginCoordinationType, registerPluginFileType, registerPluginJointFileType, } from './plugins';
 // For plugin view types:
 export { useReady, useUrls, useVitessceContainer, useDeckCanvasSize, useExpressionValueGetter, useGetObsInfo, useClosestVitessceContainerSize, useWindowDimensions, useGridItemSize, } from './hooks';
 export { useCoordination, useMultiDatasetCoordination, useDatasetUids, useLoaders, useMatchingLoader, useViewConfigStore, useViewConfigStoreApi, useComponentHover, useSetComponentHover, useComponentViewInfo, useSetComponentViewInfo, useWarning, useSetWarning, useAuxiliaryCoordination, useComponentLayout, } from './state/hooks';

package/dist/loader-registry.js

@@ -0,0 +1,98 @@
+import { getLoaderClassesForPluginFileType, } from './plugins';
+// TODO(monorepo)
+/*
+import {
+  AnnDataSource,
+  ZarrDataSource,
+  JsonSource,
+  CsvSource,
+} from './data-sources';
+import JsonLoader from './json-loaders/JsonLoader';
+import ObsSetsJsonLoader from './json-loaders/ObsSetsJson';
+import ObsSegmentationsJsonLoader from './json-loaders/ObsSegmentationsJson';
+import OmeZarrLoader from './OmeZarrLoader';
+import AnnDataLoaders from './anndata-loaders';
+import GenomicProfilesZarrLoader from './GenomicProfilesZarrLoader';
+import CellsJsonAsObsLabelsLoader from './legacy-loaders/CellsJsonAsObsLabels';
+import CellsJsonAsObsEmbeddingLoader from './legacy-loaders/CellsJsonAsObsEmbedding';
+import CellsJsonAsObsSegmentationsLoader from './legacy-loaders/CellsJsonAsObsSegmentations';
+import ClustersJsonAsObsFeatureMatrixLoader from './legacy-loaders/ClustersJsonAsObsFeatureMatrix';
+import GenesJsonAsObsFeatureMatrixLoader from './legacy-loaders/GenesJsonAsObsFeatureMatrix';
+import RasterJsonAsImageLoader from './raster-json-loaders/RasterJsonAsImageLoader';
+import RasterJsonAsObsSegmentationsLoader from './raster-json-loaders/RasterJsonAsObsSegmentationsLoader';
+import MatrixZarrAsObsFeatureMatrixLoader from './matrix-loaders/MatrixZarrAsObsFeatureMatrix';
+import MoleculesJsonAsObsLocationsLoader from './legacy-loaders/MoleculesJsonAsObsLocations';
+import MoleculesJsonAsObsLabelsLoader from './legacy-loaders/MoleculesJsonAsObsLabels';
+import CellsJsonAsObsLocationsLoader from './legacy-loaders/CellsJsonAsObsLocations';
+import ObsEmbeddingCsvLoader from './csv-loaders/ObsEmbeddingCsv';
+import ObsLocationsCsvLoader from './csv-loaders/ObsLocationsCsv';
+import ObsLabelsCsvLoader from './csv-loaders/ObsLabelsCsv';
+import FeatureLabelsCsvLoader from './csv-loaders/FeatureLabelsCsv';
+import ObsFeatureMatrixCsvLoader from './csv-loaders/ObsFeatureMatrixCsv';
+import ObsSetsCsvLoader from './csv-loaders/ObsSetsCsv';
+*/
+export const fileTypeToLoaderAndSource = {
+// TODO(monorepo)
+/*
+[FileType.OBS_EMBEDDING_CSV]: [CsvSource, ObsEmbeddingCsvLoader],
+[FileType.OBS_LOCATIONS_CSV]: [CsvSource, ObsLocationsCsvLoader],
+[FileType.OBS_LABELS_CSV]: [CsvSource, ObsLabelsCsvLoader],
+[FileType.FEATURE_LABELS_CSV]: [CsvSource, FeatureLabelsCsvLoader],
+[FileType.OBS_FEATURE_MATRIX_CSV]: [CsvSource, ObsFeatureMatrixCsvLoader],
+[FileType.OBS_SEGMENTATIONS_JSON]: [JsonSource, ObsSegmentationsJsonLoader],
+[FileType.OBS_SETS_CSV]: [CsvSource, ObsSetsCsvLoader],
+[FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR]: [
+  AnnDataSource, AnnDataLoaders.ObsFeatureMatrixAnndataLoader,
+],
+[FileType.OBS_SETS_ANNDATA_ZARR]: [
+  AnnDataSource, AnnDataLoaders.ObsSetsAnndataLoader,
+],
+[FileType.OBS_EMBEDDING_ANNDATA_ZARR]: [
+  AnnDataSource, AnnDataLoaders.ObsEmbeddingAnndataLoader,
+],
+[FileType.OBS_LOCATIONS_ANNDATA_ZARR]: [
+  AnnDataSource, AnnDataLoaders.ObsLocationsAnndataLoader,
+],
+[FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR]: [
+  AnnDataSource, AnnDataLoaders.ObsSegmentationsAnndataLoader,
+],
+[FileType.OBS_LABELS_ANNDATA_ZARR]: [
+  AnnDataSource, AnnDataLoaders.ObsLabelsAnndataLoader,
+],
+[FileType.OBS_FEATURE_MATRIX_EXPRESSION_MATRIX_ZARR]: [
+  ZarrDataSource, MatrixZarrAsObsFeatureMatrixLoader,
+],
+[FileType.FEATURE_LABELS_ANNDATA_ZARR]: [
+  AnnDataSource, AnnDataLoaders.FeatureLabelsAnndataLoader,
+],
+[FileType.IMAGE_OME_ZARR]: [ZarrDataSource, OmeZarrLoader],
+[FileType.IMAGE_RASTER_JSON]: [JsonSource, RasterJsonAsImageLoader],
+[FileType.OBS_SEGMENTATIONS_RASTER_JSON]: [JsonSource, RasterJsonAsObsSegmentationsLoader],
+[FileType.OBS_SETS_JSON]: [JsonSource, ObsSetsJsonLoader],
+[FileType.OBS_SETS_CELL_SETS_JSON]: [JsonSource, ObsSetsJsonLoader],
+[FileType.OBS_FEATURE_MATRIX_CLUSTERS_JSON]: [JsonSource, ClustersJsonAsObsFeatureMatrixLoader],
+[FileType.OBS_FEATURE_MATRIX_GENES_JSON]: [JsonSource, GenesJsonAsObsFeatureMatrixLoader],
+[FileType.OBS_LABELS_CELLS_JSON]: [JsonSource, CellsJsonAsObsLabelsLoader],
+[FileType.OBS_EMBEDDING_CELLS_JSON]: [JsonSource, CellsJsonAsObsEmbeddingLoader],
+[FileType.OBS_LOCATIONS_CELLS_JSON]: [JsonSource, CellsJsonAsObsLocationsLoader],
+[FileType.OBS_SEGMENTATIONS_CELLS_JSON]: [JsonSource, CellsJsonAsObsSegmentationsLoader],
+[FileType.OBS_LOCATIONS_MOLECULES_JSON]: [JsonSource, MoleculesJsonAsObsLocationsLoader],
+[FileType.OBS_LABELS_MOLECULES_JSON]: [JsonSource, MoleculesJsonAsObsLabelsLoader],
+// Old mappings:
+[FileType.NEIGHBORHOODS_JSON]: [JsonSource, JsonLoader],
+[FileType.GENOMIC_PROFILES_ZARR]: [ZarrDataSource, GenomicProfilesZarrLoader],
+*/
+};
+export function getSourceAndLoaderFromFileType(type) {
+    if (fileTypeToLoaderAndSource[type]) {
+        return fileTypeToLoaderAndSource[type];
+    }
+    const pluginFileType = getLoaderClassesForPluginFileType(type);
+    if (pluginFileType) {
+        return pluginFileType;
+    }
+    // Fallback to JSON.
+    // TODO(monorepo)
+    // return [JsonSource, JsonLoader];
+    return [null, null];
+}

package/dist/schemas/PrettyJsonSchema.js

@@ -0,0 +1,34 @@
+import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
+import React from 'react';
+import yaml from 'js-yaml'; // eslint-disable-line import/no-extraneous-dependencies
+// This should only be used by docz, and should not be part of the app build.
+function abbreviateType(yamlString) {
+    return yamlString.replace(/:\s+type: (\w+)/g, ' ($1):');
+}
+function abbreviateRef(yamlString) {
+    return yamlString.replace(/:\s+\$ref: '#\/definitions\/(\w+)'/g, ' ($1)');
+}
+function stripAddProps(yamlString) {
+    // This should be the default in our schemas, but we don't need it in the docs.
+    return yamlString.replace(/\s+additionalProperties: false/g, '');
+}
+function valuesAre(yamlString) {
+    return yamlString.replace(/patternProperties:\s+\./g, 'Object values are');
+}
+function hasProperties(yamlString) {
+    return yamlString.replace(/\.:\s+properties:/g, 'Each value has these properties:');
+}
+function pretty(title, obj) {
+    // This is entirely ad-hoc:
+    // It woks well for our schema, but no assertion that it should work for anyone else.
+    if (!obj)
+        return '';
+    return (_jsxs(_Fragment, { children: [_jsx("h3", { children: title }), _jsx("pre", { children: hasProperties(valuesAre(stripAddProps(abbreviateRef(abbreviateType(yaml.safeDump(obj)))))) })] }));
+}
+export default function PrettyJsonSchema(props) {
+    const { children } = props;
+    const { definitions, patternProperties, properties } = children;
+    // We could grab the title as well, but when we output an <h2> it is not anchored;
+    // better to put the section headers in MD.
+    return (_jsxs("blockquote", { children: [pretty('Definitions', definitions), pretty('Properties', patternProperties), pretty('Properties', properties)] }));
+}