@databiosphere/findable-ui 30.0.0 → 31.0.0

package/src/components/Table/components/TableCell/components/ChipCell/chipCell.tsx

@@ -1,14 +1,16 @@
 import { Chip, ChipProps } from "@mui/material";
 import { CellContext, RowData } from "@tanstack/react-table";
 import React from "react";
+import { BaseComponentProps } from "../../../../../types";
 
 export const ChipCell = <
   T extends RowData,
   TValue extends ChipProps = ChipProps
 >({
+  className,
   getValue,
-}: CellContext<T, TValue>): JSX.Element | null => {
+}: BaseComponentProps & CellContext<T, TValue>): JSX.Element | null => {
   const props = getValue();
   if (!props) return null;
-  return <Chip {...props} />;
+  return <Chip className={className} {...props} />;
 };

package/src/components/Table/components/TableCell/components/LinkCell/linkCell.tsx

@@ -11,13 +11,13 @@ export const LinkCell = <
   T extends RowData,
   TValue extends LinkProps = LinkProps
 >({
+  className,
   getValue,
 }: BaseComponentProps & CellContext<T, TValue>): JSX.Element | null => {
   const props = getValue();
   if (!props) return null;
   const {
     children,
-    className,
     color,
     href = "",
     rel,

package/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;
+  }
+`;

package/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<T, TValue>): 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 (
+    <StyledMarkdownRenderer
+      className={className}
+      components={{ ...COMPONENTS, ...components }}
+      value={values}
+    />
+  );
+};

package/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<ComponentProps<typeof MarkdownCell>> = {
+  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&nbsp;<br />(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)\\"&nbsp;<br />(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)\\"&nbsp;<br />(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.<br /><br />• *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*).<br />• *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<ComponentProps<typeof MarkdownCell>> = {
+  getValue: (() => ({
+    values:
+      "Hello <br />World <a href='https://www.example.com'>example link</a>",
+  })) as GetValue,
+};

package/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;

package/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<typeof MarkdownCell> = {
+  component: MarkdownCell,
+  decorators: [
+    (Story): JSX.Element => (
+      <Box
+        sx={{
+          backgroundColor: PALETTE.COMMON_WHITE,
+          fontSize: "14px",
+          lineHeight: "20px",
+          padding: 3,
+          width: 480,
+        }}
+      >
+        <Story />
+      </Box>
+    ),
+  ],
+};
+
+export default meta;
+
+type Story = StoryObj<typeof meta>;
+
+export const Default: Story = {
+  args: DEFAULT_ARGS,
+};
+
+export const WithHtml: Story = {
+  args: WITH_HTML_ARGS,
+};

package/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<RowData, MarkdownCellProps>["getValue"];

package/src/components/Table/components/TableCell/components/MarkdownCell/types.ts

@@ -0,0 +1,3 @@
+export type MarkdownCellProps = {
+  values: string;
+};

package/src/styles/common/mui/typography.ts

@@ -6,6 +6,7 @@ type TypographyPropsOptions = {
 };
 
 const COLOR: Record<string, TypographyOwnProps["color"]> = {
+  ERROR: "error",
   INHERIT: "inherit",
   INK_LIGHT: "ink.light",
   INK_MAIN: "ink.main",

package/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(<Default />);
+    expect(await screen.findByText("UBERON:0000955")).toBeInTheDocument();
+  });
+
+  it("renders HTML and anchor elements", async () => {
+    render(<WithHtml />);
+    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(
+      <WithHtml
+        className="css-pygqsj"
+        column={
+          {
+            columnDef: { meta: { components: { a: STYLED_ANCHOR } } },
+          } as unknown as Column<unknown, MarkdownCellProps>
+        }
+      />
+    );
+    const anchorEl = await screen.findByText("example link");
+    expect(anchorEl).toHaveStyleRule("background-color", "green");
+    expect(anchorEl).toHaveStyleRule("color", "white");
+    expect(anchorEl.closest(".css-pygqsj")).toBeInTheDocument();
+  });
+});

package/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<Components>; // For `MarkdownRendererCell` component.
     header?: string;
     width?: GridTrackSize;
   }