@vitessce/vit-s 2.0.0-beta.2 → 2.0.1

package/dist/VitS.js

@@ -3,6 +3,7 @@ import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import React, { useEffect, useMemo } from 'react';
 import { ThemeProvider, StylesProvider, createGenerateClassName, } from '@material-ui/core/styles';
 import isEqual from 'lodash/isEqual';
+import { META_VERSION } from '@vitessce/constants-internal';
 import { muiTheme } from './shared-mui/styles';
 import { ViewConfigProvider, createViewConfigStore, AuxiliaryProvider, createAuxiliaryStore, } from './state/hooks';
 import VitessceGrid from './VitessceGrid';
@@ -10,14 +11,11 @@ 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}) ${name}`);
+    console.groupCollapsed(`🚄 Vitessce (${META_VERSION.version}) ${name}`);
     console.info(`data:,${JSON.stringify(config)}`);
     console.info(JSON.stringify(config, null, 2));
     console.groupEnd();

package/dist/VitessceGrid.js

@@ -38,7 +38,11 @@ export default function VitessceGrid(props) {
     const removeComponent = useRemoveComponent();
     const changeLayout = useChangeLayout();
     const layout = useLayout();
-    const changeLayoutPostMount = useCallback(() => (componentWidth > 0 ? changeLayout : () => { }), [changeLayout, componentWidth]);
+    const changeLayoutPostMount = useCallback((newComponentProps) => {
+        if (componentWidth > 0) {
+            changeLayout(newComponentProps);
+        }
+    }, [changeLayout, componentWidth]);
     // Update the view config and loaders in the global state.
     useEffect(() => {
         if (config) {

package/dist/shared-mui/styles.js

@@ -6,6 +6,10 @@ const globalColors = {
     grayMid: '#808080',
     grayDark: '#555555',
     black: '#000000',
+    grayDarkL5: 'rgb(98, 98, 98)',
+    grayDarkD15: 'rgb(47, 47, 47)',
+    grayMidL10: 'rgb(154, 154, 154)',
+    grayLightL10: 'rgb(237, 237, 237)', // lighten(map-get($global-colors, "gray-light"), 10%);
 };
 export const muiTheme = {
     dark: createTheme({
@@ -19,6 +23,9 @@ export const muiTheme = {
             primaryBackgroundDim: '#333333',
             primaryBackgroundLight: '#757575',
             primaryForeground: '#D3D3D3',
+            primaryForegroundL5: 'rgb(224, 224, 224)',
+            primaryForegroundL10: 'rgb(237, 237, 237)',
+            primaryForegroundD15: 'rgb(173, 173, 173)',
             primaryForegroundDim: '#000000',
             primaryForegroundActive: '#9bb7d6',
             secondaryBackground: '#000000',
@@ -45,6 +52,9 @@ export const muiTheme = {
             primaryBackgroundDim: '#8A8A8A',
             primaryBackgroundLight: '#e0e0e0',
             primaryForeground: '#333333',
+            primaryForegroundL5: 'rgb(64, 64, 64)',
+            primaryForegroundL10: 'rgb(77, 77, 77)',
+            primaryForegroundD15: 'rgb(13, 13, 13)',
             primaryForegroundDim: '#808080',
             primaryForegroundActive: '#0074D9',
             secondaryBackground: '#F1F1F1',

package/dist/state/hooks.js

@@ -55,13 +55,12 @@ export const createViewConfigStore = () => create(set => ({
         };
     }),
     changeLayout: newComponentProps => set((state) => {
-        const newLayout = state.viewConfig.layout.slice();
-        newComponentProps.forEach(([i, newProps]) => {
-            newLayout[i] = {
-                ...newLayout[i],
-                ...newProps,
-            };
-        });
+        const newLayout = state.viewConfig.layout
+            .slice()
+            .map(componentProps => ({
+            ...componentProps,
+            ...newComponentProps[componentProps.uid],
+        }));
         return {
             viewConfig: {
                 ...state.viewConfig,

package/dist/vitessce-grid-layout/VitessceGridLayout.js

@@ -2,7 +2,7 @@ import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-run
 import React, { useState } from 'react';
 import { Responsive, WidthProvider } from 'react-grid-layout-with-lodash';
 import isEqual from 'lodash/isEqual';
-import { getMaxRows, resolveLayout, COMPONENT_ID_PREFIX } from './layout-utils';
+import { getMaxRows, resolveLayout } from './layout-utils';
 const ResponsiveGridLayout = WidthProvider(Responsive);
 class ResponsiveHeightGridLayout extends ResponsiveGridLayout {
     componentDidUpdate(prevProps) {
@@ -44,12 +44,11 @@ export function VitessceGridLayout(props) {
     const [lastValidGridLayouts, setLastValidGridLayouts] = useState(gridLayouts);
     const onValidLayoutChange = (newLayout) => {
         if (newLayout.length === Object.entries(gridComponents).length) {
-            const newComponentProps = [];
+            const newComponentProps = {};
             newLayout.forEach((nextC) => {
                 const id = nextC.i;
                 const prevC = gridComponents[id];
                 if (prevC) {
-                    const i = parseInt(id.substring(id.indexOf(COMPONENT_ID_PREFIX) + 1), 10);
                     const nextProps = {
                         x: nextC.x, y: nextC.y, w: nextC.w, h: nextC.h,
                     };
@@ -57,11 +56,11 @@ export function VitessceGridLayout(props) {
                         x: prevC.x, y: prevC.y, w: prevC.w, h: prevC.h,
                     };
                     if (!isEqual(nextProps, prevProps)) {
-                        newComponentProps.push([i, nextProps]);
+                        newComponentProps[id] = nextProps;
                     }
                 }
             });
-            if (newComponentProps.length > 0) {
+            if (Object.keys(newComponentProps).length > 0) {
                 onLayoutChangeProp(newComponentProps);
             }
         }

package/dist/vitessce-grid-layout/layout-utils.js

@@ -1,5 +1,4 @@
 import range from 'lodash/range';
-export const COMPONENT_ID_PREFIX = 'i';
 function sum(a) {
     return a.reduce((x, y) => x + y, 0);
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/vit-s",
-  "version": "2.0.0-beta.2",
+  "version": "2.0.1",
   "author": "Gehlenborg Lab",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -15,8 +15,6 @@
   "dependencies": {
     "@material-ui/core": "~4.12.3",
     "@material-ui/icons": "~4.11.2",
-    "@vitessce/constants-internal": "2.0.0-beta.2",
-    "@vitessce/utils": "2.0.0-beta.2",
     "ajv": "^6.10.0",
     "clsx": "^1.1.1",
     "fast-deep-equal": "^3.1.3",
@@ -25,7 +23,9 @@
     "lodash": "^4.17.21",
     "react-grid-layout-with-lodash": "^1.3.5",
     "uuid": "^3.3.2",
-    "zustand": "^3.5.10"
+    "zustand": "^3.5.10",
+    "@vitessce/constants-internal": "2.0.1",
+    "@vitessce/utils": "2.0.1"
   },
   "devDependencies": {
     "react": "^18.0.0",

package/dist/Vitessce.integration.test.js

@@ -1,36 +0,0 @@
-"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

@@ -1,101 +0,0 @@
-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/export-utils.js

@@ -1,70 +0,0 @@
-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

@@ -1,66 +0,0 @@
-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/loader-registry.js

@@ -1,98 +0,0 @@
-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

@@ -1,34 +0,0 @@
-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)] }));
-}

package/dist/schemas/obsSets.schema.json

@@ -1,194 +0,0 @@
-{
-    "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "https://github.com/vitessce/vitessce/#cell-sets",
-    "title": "Vitessce obs sets data",
-    "type": "object",
-    "definitions": {
-        "stringArray": {
-            "type": "array",
-            "items": {
-                "type": "string"
-            }
-        },
-        "stringProbabilityTupleArray": {
-            "type": "array",
-            "items": {
-                "type": "array",
-                "additionalItems": false,
-                "items": [
-                    {
-                        "type": "string"
-                    },
-                    {
-                        "oneOf": [
-                            {
-                                "type": "number",
-                                "minimum": 0.0,
-                                "maximum": 1.0
-                            },
-                            {
-                                "type": "null"
-                            }
-                        ]
-                    }
-                ]
-            }
-        },
-        "colorArray": {
-            "type": "array",
-            "items": {
-                "type": "integer",
-                "minimum": 0,
-                "maximum": 255
-            },
-            "minItems": 3,
-            "maxItems": 3
-        },
-        "treeNodeLeaf": {
-            "type": "object",
-            "additionalProperties": false,
-            "required": ["name"],
-            "properties": {
-                "name": {
-                    "type": "string"
-                },
-                "color": {
-                    "$ref": "#/definitions/colorArray"
-                },
-                "set": {
-                    "$ref": "#/definitions/stringArray"
-                }
-            }
-        },
-        "treeNodeNonLeaf": {
-            "type": "object",
-            "additionalProperties": false,
-            "required": ["name"],
-            "properties": {
-                "name": {
-                    "type": "string"
-                },
-                "color": {
-                    "$ref": "#/definitions/colorArray"
-                },
-                "children": {
-                    "type": "array",
-                    "items": {
-                        "$ref": "#/definitions/treeNode"
-                    }
-                }
-            }
-        },
-        "treeNode": {
-            "oneOf": [
-                {
-                    "$ref": "#/definitions/treeNodeNonLeaf"
-                },
-                {
-                    "$ref": "#/definitions/treeNodeLeaf"
-                }
-            ]
-        },
-        "version0.1.2": {
-            "type": "object",
-            "additionalProperties": false,
-            "required": ["version", "datatype", "tree"],
-            "properties": {
-                "dataset": {
-                    "type": "string"
-                },
-                "version": {
-                    "type": "string",
-                    "enum": ["0.1.2"]
-                },
-                "datatype": {
-                    "type": "string",
-                    "enum": ["cell", "obs"]
-                },
-                "tree": {
-                    "type": "array",
-                    "items": {
-                        "$ref": "#/definitions/treeNodeNonLeaf"
-                    }
-                }
-            }
-        },
-        "treeNodeLeafProbabilistic": {
-            "type": "object",
-            "additionalProperties": false,
-            "required": ["name"],
-            "properties": {
-                "name": {
-                    "type": "string"
-                },
-                "color": {
-                    "$ref": "#/definitions/colorArray"
-                },
-                "set": {
-                    "$ref": "#/definitions/stringProbabilityTupleArray"
-                }
-            }
-        },
-        "treeNodeNonLeafProbabilistic": {
-            "type": "object",
-            "additionalProperties": false,
-            "required": ["name"],
-            "properties": {
-                "name": {
-                    "type": "string"
-                },
-                "color": {
-                    "$ref": "#/definitions/colorArray"
-                },
-                "children": {
-                    "type": "array",
-                    "items": {
-                        "$ref": "#/definitions/treeNodeProbabilistic"
-                    }
-                }
-            }
-        },
-        "treeNodeProbabilistic": {
-            "oneOf": [
-                {
-                    "$ref": "#/definitions/treeNodeNonLeafProbabilistic"
-                },
-                {
-                    "$ref": "#/definitions/treeNodeLeafProbabilistic"
-                }
-            ]
-        },
-        "version0.1.3": {
-            "type": "object",
-            "additionalProperties": false,
-            "required": ["version", "datatype", "tree"],
-            "properties": {
-                "dataset": {
-                    "type": "string"
-                },
-                "version": {
-                    "type": "string",
-                    "enum": ["0.1.3"]
-                },
-                "datatype": {
-                    "type": "string",
-                    "enum": ["cell", "obs"]
-                },
-                "tree": {
-                    "type": "array",
-                    "items": {
-                        "$ref": "#/definitions/treeNodeNonLeafProbabilistic"
-                    }
-                }
-            }
-        }
-    },
-    "oneOf": [
-        {
-            "$ref": "#/definitions/version0.1.2"
-        },
-        {
-            "$ref": "#/definitions/version0.1.3"
-        }
-    ]
-}

package/dist/schemas/obsSetsTabular.schema.json

@@ -1,37 +0,0 @@
-{
-    "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "https://github.com/vitessce/vitessce/#obsSetsTabular",
-    "title": "Vitessce obs sets data, tabular format",
-    "definitions": {
-        "colorArray": {
-            "type": "array",
-            "items": { "type": "integer", "minimum": 0, "maximum": 255 },
-            "minItems": 3,
-            "maxItems": 3
-        }
-    },
-    "type": "array",
-    "items": {
-        "type": "object",
-        "additionalProperties": false,
-        "required": ["groupName", "setName", "obsId"],
-        "properties": {
-            "groupName": { "type": "string" },
-            "setName": { "type": "string" },
-            "setColor": { "$ref": "#/definitions/colorArray" },
-            "obsId": { "type": "string" },
-            "predictionScore": {
-                "oneOf": [
-                    {
-                        "type": "number",
-                        "minimum": 0.0,
-                        "maximum": 1.0
-                    },
-                    {
-                        "type": "null"
-                    }
-                ]
-            }
-        }
-    }
-}

package/dist/schemas/raster.schema.json

@@ -1,119 +0,0 @@
-{
-    "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "https://github.com/vitessce/vitessce/#raster",
-    "title": "Vitessce image data",
-    "type": "object",
-    "definitions": {
-        "transform": {
-            "type": "object",
-            "additionalProperties": false,
-            "oneOf": [{ "required": ["scale", "translate"] }, { "required": ["matrix"] }],
-            "properties": {
-                "scale": { "type": "number" },
-                "translate": {
-                    "type": "object",
-                    "additionalProperties": false,
-                    "required": ["y", "x"],
-                    "properties": {
-                        "y": { "type": "number" },
-                        "x": { "type": "number" }
-                    }
-                },
-                "matrix": {
-                    "type": "array",
-                    "items": { "type": "number" },
-                    "minItems": 16,
-                    "maxItems": 16
-                }
-            }
-        },
-        "dimensions": {
-            "type": "array",
-            "items": {
-                "type": "object",
-                "additionalProperties": false,
-                "required": ["field", "type", "values"],
-                "properties": {
-                    "field": { "type": "string" },
-                    "type": {
-                        "type": "string",
-                        "enum": ["quantitative", "nominal", "ordinal", "temporal"]
-                    },
-                    "values": {
-                        "type": ["array", "null"],
-                        "items": { "type": "string" }
-                    }
-                }
-            }
-        },
-        "metadata": {
-            "type": "object",
-            "additionalProperties": false,
-            "anyOf": [{ "required": ["dimensions", "isPyramid"] }, { "required": ["transform"] }, { "required": ["omeTiffOffsetsUrl"] }, { "required": ["isBitmask"] }],
-            "properties": {
-                "dimensions": { "$ref": "#/definitions/dimensions" },
-                "isPyramid": { "type": "boolean" },
-                "transform": { "$ref": "#/definitions/transform" },
-                "isBitmask": { "type": "boolean" },
-                "omeTiffOffsetsUrl": { "type": "string", "format": "uri" }
-            }
-        },
-        "requestInit": {
-            "type": "object",
-            "additionalProperties": false,
-            "required": [],
-            "properties": {
-                "method": {
-                    "type": "string"
-                },
-                "headers": {
-                    "type": "object"
-                },
-                "body": {
-                    "type": "string"
-                },
-                "mode": {
-                    "type": "string"
-                },
-                "credentials": {
-                    "type": "string"
-                },
-                "cache": {
-                    "type": "string"
-                },
-                "redirect": {
-                    "type": "string"
-                },
-                "referrer": {
-                    "type": "string"
-                },
-                "integrity": {
-                    "type": "string"
-                }
-            }
-        },
-        "image": {
-            "type": "object",
-            "additionalProperties": false,
-            "required": ["name", "url", "type"],
-            "properties": {
-                "name": { "type": "string" },
-                "url": { "type": "string", "format": "uri" },
-                "type": { "type": "string" },
-                "metadata": { "$ref": "#/definitions/metadata" },
-                "requestInit": { "$ref": "#/definitions/requestInit" }
-            }
-        }
-    },
-    "additionalProperties": false,
-    "required": ["schemaVersion", "images"],
-    "properties": {
-        "schemaVersion": { "type": "string" },
-        "usePhysicalSizeScaling": { "type": "boolean", "description": "Default is false: passing true in will infer scaling from the reported physcial size" },
-        "renderLayers": { "type": "array", "items": { "type": "string" } },
-        "images": {
-            "type": "array",
-            "items": { "$ref": "#/definitions/image" }
-        }
-    }
-}

package/dist/schemas/schema.test.js

@@ -1,46 +0,0 @@
-import Ajv from 'ajv';
-/* eslint-disable import/no-dynamic-require */
-/* eslint-disable global-require */
-describe('schemas', () => {
-    [
-        'config-1.0.1',
-        'obsSets',
-        'obsSetsTabular',
-        'raster',
-    ].forEach((type) => {
-        const schemaFile = `${type}.schema.json`;
-        describe(schemaFile, () => {
-            const schema = require(`./${schemaFile}`);
-            let validate;
-            if (type === 'config-1.0.1') {
-                const obsSets = require('./obsSets.schema.json');
-                const raster = require('./raster.schema.json');
-                validate = new Ajv()
-                    .addSchema(obsSets)
-                    .addSchema(raster)
-                    .compile(schema);
-            }
-            else {
-                validate = new Ajv().compile(schema);
-            }
-            const [goodFixture, badFixture, badMessage] = [
-                'good', 'bad', 'bad.message',
-            ].map(stem => `${type}.${stem}.json`);
-            it(`passes ${goodFixture}`, () => {
-                const data = require(`./fixtures/${goodFixture}`);
-                const valid = validate(data);
-                if (!valid) {
-                    console.warn(validate.errors);
-                }
-                expect(valid).toEqual(true);
-            });
-            it(`fails ${badFixture}`, () => {
-                const data = require(`./fixtures/${badFixture}`);
-                const message = require(`./fixtures/${badMessage}`);
-                const valid = validate(data);
-                expect(valid).toEqual(false);
-                expect(validate.errors).toEqual(message);
-            });
-        });
-    });
-});