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"https://registry.npmjs.org/relateurl/-/relateurl-0.2.7.tgz", @@ -33261,6 +34158,19 @@ "unified": "^11.0.0" } }, + "remark-rehype": { + "version": "11.1.2", + "resolved": "https://registry.npmjs.org/remark-rehype/-/remark-rehype-11.1.2.tgz", + "integrity": "sha512-Dh7l57ianaEoIpzbp0PC9UKAdCSVklD8E5Rpw7ETfbTl3FqcOOgq5q2LVDhgGCkaBv7p24JXikPdvhhmHvKMsw==", + "dev": true, + "requires": { + "@types/hast": "^3.0.0", + "@types/mdast": "^4.0.0", + "mdast-util-to-hast": "^13.0.0", + "unified": "^11.0.0", + "vfile": "^6.0.0" + } + }, "remark-stringify": { "version": "11.0.0", "resolved": "https://registry.npmjs.org/remark-stringify/-/remark-stringify-11.0.0.tgz", @@ -33765,6 +34675,12 @@ } } }, + "space-separated-tokens": { + "version": "2.0.2", + "resolved": "https://registry.npmjs.org/space-separated-tokens/-/space-separated-tokens-2.0.2.tgz", + "integrity": "sha512-PEGlAwrG8yXGXRjW32fGbg66JAlOAwbObuqVoJpv/mRgoWDQfgH1wDPvtzWyUSNAXBGSk8h755YDbbcEy3SH2Q==", + "dev": true + }, "spdx-correct": { "version": "3.2.0", "resolved": "https://registry.npmjs.org/spdx-correct/-/spdx-correct-3.2.0.tgz", @@ -34018,6 +34934,16 @@ "es-object-atoms": "^1.0.0" } }, + "stringify-entities": { + "version": "4.0.4", + "resolved": "https://registry.npmjs.org/stringify-entities/-/stringify-entities-4.0.4.tgz", + "integrity": "sha512-IwfBptatlO+QCJUo19AqvrPNqlVMpW9YEL2LIVY+Rpv2qsjCGxaDLNRgeGsQWJhfItebuJhsGSLjaBbNSQ+ieg==", + "dev": true, + "requires": { + "character-entities-html4": "^2.0.0", + "character-entities-legacy": "^3.0.0" + } + }, "strip-ansi": { "version": "6.0.1", "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-6.0.1.tgz", @@ -34070,6 +34996,24 @@ "dev": true, "requires": {} }, + "style-to-js": { + "version": "1.1.16", + "resolved": "https://registry.npmjs.org/style-to-js/-/style-to-js-1.1.16.tgz", + "integrity": "sha512-/Q6ld50hKYPH3d/r6nr117TZkHR0w0kGGIVfpG9N6D8NymRPM9RqCUv4pRpJ62E5DqOYx2AFpbZMyCPnjQCnOw==", + "dev": true, + "requires": { + "style-to-object": "1.0.8" + } + }, + "style-to-object": { + "version": "1.0.8", + "resolved": "https://registry.npmjs.org/style-to-object/-/style-to-object-1.0.8.tgz", + "integrity": "sha512-xT47I/Eo0rwJmaXC4oilDGDWLohVhR6o/xAQcPQN8q6QBuZVL8qMYL85kLmST5cPjAorwvqIA4qXTRQoYHaL6g==", + "dev": true, + "requires": { + "inline-style-parser": "0.2.4" + } + }, "styled-jsx": { "version": "5.1.1", "resolved": "https://registry.npmjs.org/styled-jsx/-/styled-jsx-5.1.1.tgz", @@ -34297,6 +35241,12 @@ "punycode": "^2.1.1" } }, + "trim-lines": { + "version": "3.0.1", + "resolved": "https://registry.npmjs.org/trim-lines/-/trim-lines-3.0.1.tgz", + "integrity": "sha512-kRj8B+YHZCc9kQYdWfJB2/oUl9rA99qbowYYBtr4ui4mZyAQ2JpvVBd/6U2YloATfqBhBTSMhTpgBHtU0Mf3Rg==", + "dev": true + }, "trim-newlines": { "version": "3.0.1", "resolved": "https://registry.npmjs.org/trim-newlines/-/trim-newlines-3.0.1.tgz", @@ -34625,6 +35575,15 @@ "@types/unist": "^3.0.0" } }, + "unist-util-position": { + "version": "5.0.0", + "resolved": "https://registry.npmjs.org/unist-util-position/-/unist-util-position-5.0.0.tgz", + "integrity": "sha512-fucsC7HjXvkB5R3kTCO7kUjRdrS0BJt3M/FPxmHMBOm8JQi2BsHAHFsy27E0EolP8rp0NzXsJ+jNPyDWvOJZPA==", + "dev": true, + "requires": { + "@types/unist": "^3.0.0" + } + }, "unist-util-stringify-position": { "version": "4.0.0", "resolved": "https://registry.npmjs.org/unist-util-stringify-position/-/unist-util-stringify-position-4.0.0.tgz", @@ -34786,6 +35745,16 @@ "vfile-message": "^4.0.0" } }, + "vfile-location": { + "version": "5.0.3", + "resolved": "https://registry.npmjs.org/vfile-location/-/vfile-location-5.0.3.tgz", + "integrity": "sha512-5yXvWDEgqeiYiBe1lbxYF7UMAIm/IcopxMHrMQDq3nvKcjPKIhZklUKL+AE7J7uApI4kwe2snsK+eI6UTj9EHg==", + "dev": true, + "requires": { + "@types/unist": "^3.0.0", + "vfile": "^6.0.0" + } + }, "vfile-message": { "version": "4.0.2", "resolved": "https://registry.npmjs.org/vfile-message/-/vfile-message-4.0.2.tgz", @@ -34830,6 +35799,12 @@ "graceful-fs": "^4.1.2" } }, + "web-namespaces": { + "version": "2.0.1", + "resolved": "https://registry.npmjs.org/web-namespaces/-/web-namespaces-2.0.1.tgz", + "integrity": "sha512-bKr1DkiNa2krS7qxNtdrtHAmzuYGFQLiQ13TsorsdT6ULTkPLKuu5+GsFpDlg6JFjUTwX2DyhMPG2be8uPrqsQ==", + "dev": true + }, "webidl-conversions": { "version": "7.0.0", "resolved": "https://registry.npmjs.org/webidl-conversions/-/webidl-conversions-7.0.0.tgz", diff --git a/package.json b/package.json index 8f774e50..4477d9d6 100644 --- a/package.json +++ b/package.json @@ -62,6 +62,11 @@ "jest-fetch-mock": "^3.0.3", "prettier": "^2.8.3", "prettier-plugin-organize-imports": "^3.2.2", + "rehype-raw": "^7.0.0", + "rehype-react": "^8.0.0", + "rehype-sanitize": "^6.0.0", + "remark-gfm": "^4.0.1", + "remark-rehype": "^11.1.2", "storybook": "^8.6.4", "ts-jest": "^29.2.5", "typescript": "^5.5.4" diff --git a/src/components/MarkdownRenderer/components/Anchor/anchor.tsx b/src/components/MarkdownRenderer/components/Anchor/anchor.tsx new file mode 100644 index 00000000..bf96b372 --- /dev/null +++ b/src/components/MarkdownRenderer/components/Anchor/anchor.tsx @@ -0,0 +1,34 @@ +import React, { AnchorHTMLAttributes, ClassAttributes } from "react"; +import { Link } from "../../../Links/components/Link/link"; +import { BaseComponentProps } from "../../../types"; + +/** + * rehype-sanitize's default schema allows only a limited set of attributes on elements: + * - aria-* + * - className + * - data-footnote-backref + * - data-footnote-ref + * - href + * + * By default, attributes such as: + * - download + * - rel + * - target + * are not permitted and will be stripped from anchor tags during sanitization. + * + * Note: This component currently does not support these excluded attributes. + */ + +export const Anchor = ( + props: BaseComponentProps & + ClassAttributes & + AnchorHTMLAttributes +): JSX.Element => { + return ( + + ); +}; diff --git a/src/components/MarkdownRenderer/components/Table/table.styles.ts b/src/components/MarkdownRenderer/components/Table/table.styles.ts new file mode 100644 index 00000000..68784322 --- /dev/null +++ b/src/components/MarkdownRenderer/components/Table/table.styles.ts @@ -0,0 +1,41 @@ +import styled from "@emotion/styled"; +import { PALETTE } from "../../../../styles/common/constants/palette"; +import { textBody500 } from "../../../../styles/common/mixins/fonts"; + +export const StyledTable = styled("table")` + border-collapse: collapse; + margin: 16px 0; + table-layout: fixed; + width: 100%; + + thead { + all: unset; + display: table-header-group; + } + + tbody { + all: unset; + display: table-row-group; + } + + tr { + all: unset; + display: table-row; + } + + td, + th { + display: table-cell; + padding: 2px 4px; + } + + th { + ${textBody500} + border-bottom: 1px solid ${PALETTE.SMOKE_MAIN}; + } + + td { + font: inherit; + overflow-wrap: break-word; + } +`; diff --git a/src/components/MarkdownRenderer/components/Table/table.tsx b/src/components/MarkdownRenderer/components/Table/table.tsx new file mode 100644 index 00000000..8d61cade --- /dev/null +++ b/src/components/MarkdownRenderer/components/Table/table.tsx @@ -0,0 +1,13 @@ +import { BaseComponentProps } from "components/types"; +import React, { ClassAttributes, TableHTMLAttributes } from "react"; +import { StyledTable } from "./table.styles"; + +export const Table = ( + props: BaseComponentProps & + ClassAttributes & + TableHTMLAttributes +): JSX.Element => { + return ( + {props.children} + ); +}; diff --git a/src/components/MarkdownRenderer/constants.ts b/src/components/MarkdownRenderer/constants.ts new file mode 100644 index 00000000..308e81b1 --- /dev/null +++ b/src/components/MarkdownRenderer/constants.ts @@ -0,0 +1,8 @@ +import { Components } from "rehype-react"; +import { Anchor } from "./components/Anchor/anchor"; +import { Table } from "./components/Table/table"; + +export const COMPONENTS: Partial = { + a: Anchor, + table: Table, +}; diff --git a/src/components/MarkdownRenderer/markdownRenderer.styles.ts b/src/components/MarkdownRenderer/markdownRenderer.styles.ts new file mode 100644 index 00000000..83763415 --- /dev/null +++ b/src/components/MarkdownRenderer/markdownRenderer.styles.ts @@ -0,0 +1,16 @@ +import styled from "@emotion/styled"; + +// See https://github.com/emotion-js/emotion/issues/1105. +// See https://github.com/emotion-js/emotion/releases/tag/%40emotion%2Fcache%4011.10.2. +const ignoreSsrWarning = + "/* emotion-disable-server-rendering-unsafe-selector-warning-please-do-not-use-this-the-warning-exists-for-a-reason */"; + +export const StyledContainer = styled("div")` + > *:first-child:not(style)${ignoreSsrWarning} { + margin-top: 0; + } + + > *:last-child:not(style)${ignoreSsrWarning} { + margin-bottom: 0; + } +`; diff --git a/src/components/MarkdownRenderer/markdownRenderer.tsx b/src/components/MarkdownRenderer/markdownRenderer.tsx new file mode 100644 index 00000000..b4aa0108 --- /dev/null +++ b/src/components/MarkdownRenderer/markdownRenderer.tsx @@ -0,0 +1,62 @@ +import { Typography } from "@mui/material"; +import React, { useEffect, useState } from "react"; +import * as production from "react/jsx-runtime"; +import rehypeRaw from "rehype-raw"; +import rehypeReact, { Components } from "rehype-react"; +import rehypeSanitize, { defaultSchema } from "rehype-sanitize"; +import remarkGfm from "remark-gfm"; +import remarkParse from "remark-parse"; +import remarkRehype from "remark-rehype"; +import { unified } from "unified"; +import { TYPOGRAPHY_PROPS } from "../../styles/common/mui/typography"; +import { COMPONENTS } from "./constants"; +import { StyledContainer } from "./markdownRenderer.styles"; +import { MarkdownRendererProps } from "./types"; + +export const MarkdownRenderer = ({ + className, + components = COMPONENTS, + value, +}: MarkdownRendererProps): JSX.Element => { + const [element, setElement] = useState(null); + const [error, setError] = useState(null); + const [componentOptions] = useState>(components); + + useEffect(() => { + let cancelled = false; + setError(null); + + const processor = unified() + .use(remarkParse) + .use(remarkGfm) + .use(remarkRehype, { allowDangerousHtml: true }) + .use(rehypeRaw) + .use(rehypeSanitize, defaultSchema) + .use(rehypeReact, { ...production, components: componentOptions }); + + processor + .process(value) + .then((file) => { + if (!cancelled) setElement(file?.result); + }) + .catch((err) => { + if (!cancelled) setError(err.message); + }); + + return (): void => { + cancelled = true; + }; + }, [componentOptions, value]); + + if (error) + return ( + + {error} + + ); + + return {element}; +}; diff --git a/src/components/MarkdownRenderer/types.ts b/src/components/MarkdownRenderer/types.ts new file mode 100644 index 00000000..af0e22fe --- /dev/null +++ b/src/components/MarkdownRenderer/types.ts @@ -0,0 +1,7 @@ +import { Components } from "rehype-react"; +import { BaseComponentProps } from "../types"; + +export interface MarkdownRendererProps extends BaseComponentProps { + components?: Partial; + value: string; +} diff --git a/src/components/Table/components/TableCell/components/MarkdownCell/markdownCell.styles.ts b/src/components/Table/components/TableCell/components/MarkdownCell/markdownCell.styles.ts new file mode 100644 index 00000000..44930c75 --- /dev/null +++ b/src/components/Table/components/TableCell/components/MarkdownCell/markdownCell.styles.ts @@ -0,0 +1,31 @@ +import styled from "@emotion/styled"; +import { PALETTE } from "../../../../../../styles/common/constants/palette"; +import { MarkdownRenderer } from "../../../../../MarkdownRenderer/markdownRenderer"; + +export const StyledMarkdownRenderer = styled(MarkdownRenderer)` + align-self: flex-start; + + code { + all: unset; + font: inherit; + font-family: Roboto Mono, monospace; + } + + h2, + h3, + h4, + h5, + h6 { + margin: 8px 0; + } + + hr { + border: none; + border-bottom: 1px solid ${PALETTE.SMOKE_MAIN}; + margin: 16px 0; + } + + p { + font: inherit; + } +`; diff --git a/src/components/Table/components/TableCell/components/MarkdownCell/markdownCell.tsx b/src/components/Table/components/TableCell/components/MarkdownCell/markdownCell.tsx new file mode 100644 index 00000000..d5c59ae3 --- /dev/null +++ b/src/components/Table/components/TableCell/components/MarkdownCell/markdownCell.tsx @@ -0,0 +1,29 @@ +import { CellContext, RowData } from "@tanstack/react-table"; +import { BaseComponentProps } from "components/types"; +import React from "react"; +import { COMPONENTS } from "../../../../../MarkdownRenderer/constants"; +import { StyledMarkdownRenderer } from "./markdownCell.styles"; +import { MarkdownCellProps } from "./types"; + +export const MarkdownCell = < + T extends RowData, + TValue extends MarkdownCellProps = MarkdownCellProps +>({ + className, + column, + getValue, +}: BaseComponentProps & CellContext): JSX.Element | null => { + const props = getValue(); + if (!props) return null; + const { values } = props; + const columnDef = column?.columnDef; + const columnMeta = columnDef?.meta; + const components = columnMeta?.components; + return ( + + ); +}; diff --git a/src/components/Table/components/TableCell/components/MarkdownCell/stories/args.ts b/src/components/Table/components/TableCell/components/MarkdownCell/stories/args.ts new file mode 100644 index 00000000..fb875e6a --- /dev/null +++ b/src/components/Table/components/TableCell/components/MarkdownCell/stories/args.ts @@ -0,0 +1,17 @@ +import { ComponentProps } from "react"; +import { MarkdownCell } from "../markdownCell"; +import { GetValue } from "./types"; + +export const DEFAULT_ARGS: Partial> = { + getValue: (() => ({ + values: + '| Key | Annotator | Value |\n| --- | --- | --- |\n| `tissue_ontology_term_id` | Curator | categorical with `str` categories. This **MUST** be the UBERON or CL term that best describes the tissue the cell was derived from, depending on the sample type. |\n\n**Mapping guidance**\n\n| For | Use |\n| --- | --- |\n| Tissue | STRONGLY RECOMMENDED to be an UBERON term 
(e.g. [`UBERON:0008930`](http://purl.obolibrary.org/obo/UBERON_0008930) for a *somatosensory cortex* tissue sample) |\n| Cell culture | MUST be a CL term appended with \\" (cell culture)\\" 
(e.g. [`CL:0000057`](http://purl.obolibrary.org/obo/CL_0000057) **(cell culture)** for the *WTC-11* cell line) |\n| Organoid | MUST be an UBERON term appended with \\" (organoid)\\" 
(e.g. [`UBERON:0000955`](http://purl.obolibrary.org/obo/UBERON_0000955) **(organoid)** for a *brain organoid*) |\n| Enriched / sorted / isolated cells from a tissue | MUST be an UBERON or CL term and **SHOULD NOT** use terms that do not capture the tissue of origin.

• *CD3+ kidney cells* → [`UBERON:0002113`](https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http://purl.obolibrary.org/obo/UBERON_0002113) (*kidney*) instead of [`CL:000084`](https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http://purl.obolibrary.org/obo/CL_0000084) (*T cell*).
• *EPCAM+ cervical cells* → [`CL:0000066`](https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http://purl.obolibrary.org/obo/CL_0000066) (*epithelial cell* of the cervix). |\n\n---\n\nWhen a dataset is uploaded, the **cellxgene Data Portal** MUST automatically add the matching human-readable name for the corresponding ontology term to the `obs` dataframe. Curators **MUST NOT** annotate the following columns.\n\n### `assay`\n\n| Key | Annotator | Value |\n| --- | --- | --- |\n| `assay` | Data Portal | categorical with `str` categories. This **MUST** be the human-readable name assigned to the value of `assay_ontology_term_id`. |', + })) as GetValue, +}; + +export const WITH_HTML_ARGS: Partial> = { + getValue: (() => ({ + values: + "Hello
World example link", + })) as GetValue, +}; diff --git a/src/components/Table/components/TableCell/components/MarkdownCell/stories/constants.ts b/src/components/Table/components/TableCell/components/MarkdownCell/stories/constants.ts new file mode 100644 index 00000000..f258096f --- /dev/null +++ b/src/components/Table/components/TableCell/components/MarkdownCell/stories/constants.ts @@ -0,0 +1,11 @@ +import styled from "@emotion/styled"; +import { Anchor } from "../../../../../../MarkdownRenderer/components/Anchor/anchor"; + +/** + * Styled anchor component for testing purposes. + */ + +export const STYLED_ANCHOR = styled(Anchor)` + background-color: green; + color: white; +` as typeof Anchor; diff --git a/src/components/Table/components/TableCell/components/MarkdownCell/stories/markdownCell.stories.tsx b/src/components/Table/components/TableCell/components/MarkdownCell/stories/markdownCell.stories.tsx new file mode 100644 index 00000000..9cc3dd66 --- /dev/null +++ b/src/components/Table/components/TableCell/components/MarkdownCell/stories/markdownCell.stories.tsx @@ -0,0 +1,37 @@ +import { Box } from "@mui/material"; +import { Meta, StoryObj } from "@storybook/react"; +import React from "react"; +import { PALETTE } from "../../../../../../../styles/common/constants/palette"; +import { MarkdownCell } from "../markdownCell"; +import { DEFAULT_ARGS, WITH_HTML_ARGS } from "./args"; + +const meta: Meta = { + component: MarkdownCell, + decorators: [ + (Story): JSX.Element => ( + + + + ), + ], +}; + +export default meta; + +type Story = StoryObj; + +export const Default: Story = { + args: DEFAULT_ARGS, +}; + +export const WithHtml: Story = { + args: WITH_HTML_ARGS, +}; diff --git a/src/components/Table/components/TableCell/components/MarkdownCell/stories/types.ts b/src/components/Table/components/TableCell/components/MarkdownCell/stories/types.ts new file mode 100644 index 00000000..605de638 --- /dev/null +++ b/src/components/Table/components/TableCell/components/MarkdownCell/stories/types.ts @@ -0,0 +1,4 @@ +import { CellContext, RowData } from "@tanstack/react-table"; +import { MarkdownCellProps } from "../types"; + +export type GetValue = CellContext["getValue"]; diff --git a/src/components/Table/components/TableCell/components/MarkdownCell/types.ts b/src/components/Table/components/TableCell/components/MarkdownCell/types.ts new file mode 100644 index 00000000..44105868 --- /dev/null +++ b/src/components/Table/components/TableCell/components/MarkdownCell/types.ts @@ -0,0 +1,3 @@ +export type MarkdownCellProps = { + values: string; +}; diff --git a/src/styles/common/mui/typography.ts b/src/styles/common/mui/typography.ts index 88bd8814..aaede8a7 100644 --- a/src/styles/common/mui/typography.ts +++ b/src/styles/common/mui/typography.ts @@ -6,6 +6,7 @@ type TypographyPropsOptions = { }; const COLOR: Record = { + ERROR: "error", INHERIT: "inherit", INK_LIGHT: "ink.light", INK_MAIN: "ink.main", diff --git a/tests/markdownCell.test.tsx b/tests/markdownCell.test.tsx new file mode 100644 index 00000000..3d703f97 --- /dev/null +++ b/tests/markdownCell.test.tsx @@ -0,0 +1,53 @@ +import { matchers } from "@emotion/jest"; +import { composeStories } from "@storybook/react"; +import { Column } from "@tanstack/react-table"; +import "@testing-library/jest-dom"; +import { render, screen } from "@testing-library/react"; +import React from "react"; +import { + ANCHOR_TARGET, + REL_ATTRIBUTE, +} from "../src/components/Links/common/entities"; +import { STYLED_ANCHOR } from "../src/components/Table/components/TableCell/components/MarkdownCell/stories/constants"; +import * as stories from "../src/components/Table/components/TableCell/components/MarkdownCell/stories/markdownCell.stories"; +import { MarkdownCellProps } from "../src/components/Table/components/TableCell/components/MarkdownCell/types"; + +expect.extend(matchers); + +const { Default, WithHtml } = composeStories(stories); + +describe("MarkdownCell", () => { + it("renders the markdown content", async () => { + render(); + expect(await screen.findByText("UBERON:0000955")).toBeInTheDocument(); + }); + + it("renders HTML and anchor elements", async () => { + render(); + const anchorEl = await screen.findByText("example link"); + expect(anchorEl).toBeInTheDocument(); + expect(anchorEl.getAttribute("href")).toBe("https://www.example.com"); + expect(anchorEl.getAttribute("target")).toBe(ANCHOR_TARGET.BLANK); + expect(anchorEl.getAttribute("rel")).toBe( + REL_ATTRIBUTE.NO_OPENER_NO_REFERRER + ); + expect(anchorEl).toHaveClass("MuiLink-root"); + }); + + it("applies the correct className and component", async () => { + render( + + } + /> + ); + const anchorEl = await screen.findByText("example link"); + expect(anchorEl).toHaveStyleRule("background-color", "green"); + expect(anchorEl).toHaveStyleRule("color", "white"); + expect(anchorEl.closest(".css-pygqsj")).toBeInTheDocument(); + }); +}); diff --git a/types/data-explorer-ui.d.ts b/types/data-explorer-ui.d.ts index 5c90d7e6..5ec579fc 100644 --- a/types/data-explorer-ui.d.ts +++ b/types/data-explorer-ui.d.ts @@ -19,6 +19,7 @@ import type {} from "@mui/material/Toolbar"; import type {} from "@mui/material/Typography"; import type {} from "@tanstack/react-table"; import { RowData } from "@tanstack/react-table"; +import { Components } from "rehype-react"; import { DataLayer } from "../src/common/analytics/entities"; import { DataDictionaryAnnotation } from "../src/common/entities"; import { @@ -230,6 +231,7 @@ declare module "@tanstack/react-table" { align?: TableCellProps["align"]; annotation?: DataDictionaryAnnotation; columnPinned?: boolean; + components?: Partial; // For `MarkdownRendererCell` component. header?: string; width?: GridTrackSize; }