@vitessce/vit-s 2.0.3-beta.0 → 2.0.3

package/dist/schemas/obs-sets-tabular.schema.js

@@ -1,37 +0,0 @@
-export const obsSetsTabularSchema = {
-    $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/obs-sets.schema.js

@@ -1,194 +0,0 @@
-export const obsSetsSchema = {
-    $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/obsSets.schema.js

@@ -1,195 +0,0 @@
-const schema = {
-    $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',
-        },
-    ],
-};
-export default schema;

package/dist/schemas/obsSetsTabular.schema.js

@@ -1,38 +0,0 @@
-const schema = {
-    $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',
-                    },
-                ],
-            },
-        },
-    },
-};
-export default schema;

package/dist/schemas/raster.schema.js

@@ -1,120 +0,0 @@
-const schema = {
-    $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' },
-        },
-    },
-};
-export default schema;

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);
-            });
-        });
-    });
-});

package/dist/schemas-extra.js

@@ -1,3 +0,0 @@
-export { schema as rasterSchema } from './schemas/raster.schema';
-export { schema as obsSetsSchema } from './schemas/obs-sets.schema';
-export { schema as obsSetsTabularSchema } from './schemas/obs-sets-tabular.schema';

package/dist/shared-mui/components.js

@@ -1,35 +0,0 @@
-import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
-import React, { useRef } from 'react';
-import { makeStyles } from '@material-ui/core/styles';
-import Paper from '@material-ui/core/Paper';
-import Popper from '@material-ui/core/Popper';
-import IconButton from '@material-ui/core/IconButton';
-import MenuList from '@material-ui/core/MenuList';
-import ClickAwayListener from '@material-ui/core/ClickAwayListener';
-import Fade from '@material-ui/core/Fade';
-import { useVitessceContainer } from '../hooks';
-const useStyles = makeStyles(() => ({
-    paper: {
-        maxHeight: 200,
-        overflow: 'auto',
-    },
-    container: {
-        position: 'relative',
-        left: 0,
-        top: 0,
-    },
-}));
-export function PopperMenu(props) {
-    const { buttonIcon, open, setOpen, children, buttonClassName, placement = 'bottom-end', } = props;
-    const classes = useStyles();
-    const anchorRef = useRef();
-    const handleClick = () => {
-        setOpen(prev => !prev);
-    };
-    const handleClose = () => {
-        setOpen(false);
-    };
-    const id = open ? 'v-popover-menu' : undefined;
-    const getTooltipContainer = useVitessceContainer(anchorRef);
-    return (_jsxs("div", { ref: anchorRef, className: classes.container, children: [_jsx(IconButton, { "aria-describedby": id, onClick: handleClick, size: "small", className: buttonClassName, children: buttonIcon }), _jsx(Popper, { id: id, open: open, anchorEl: anchorRef && anchorRef.current, container: getTooltipContainer, onClose: handleClose, placement: placement, transition: true, children: ({ TransitionProps }) => (_jsx(ClickAwayListener, { onClickAway: handleClose, children: _jsx(Fade, { ...TransitionProps, timeout: 100, children: _jsx(Paper, { elevation: 4, className: classes.paper, children: _jsx(MenuList, { children: children }) }) }) })) })] }));
-}