@databiosphere/findable-ui 29.0.2 → 31.0.0

package/src/components/Table/common/utils.ts

@@ -9,7 +9,7 @@ import {
   sortingFns,
   Table,
 } from "@tanstack/react-table";
-import { SelectCategory } from "../../../common/entities";
+import { Category } from "../../../common/categories/models/types";
 import { EXPLORE_MODE, ExploreMode } from "../../../hooks/useExploreMode/types";
 import { COLUMN_IDENTIFIER } from "./columnIdentifier";
 
@@ -38,26 +38,47 @@ type TableData = number | string | string[];
 export function buildCategoryViews<T extends RowData>(
   columns: Column<T>[],
   columnFilters: ColumnFiltersState
-): SelectCategory[] {
-  const categoryViews: SelectCategory[] = [];
+): Category[] {
+  const categoryViews: Category[] = [];
   for (const column of columns) {
-    const { columnDef, getCanFilter, getFacetedUniqueValues, id } = column;
+    const {
+      columnDef,
+      getCanFilter,
+      getFacetedMinMaxValues,
+      getFacetedUniqueValues,
+      id,
+    } = column;
     const { header: columnHeader } = columnDef;
     if (getCanFilter()) {
-      updateFacetedUniqueValues(getFacetedUniqueValues(), columnFilters, id);
       const key = id;
       const label = columnHeader as string;
-      const values = [...getFacetedUniqueValues()].map(([value, count]) => ({
-        count,
-        key: value,
-        label: String(value ?? ""),
-        selected: false, // Selected state updated in reducer.
-      }));
-      categoryViews.push({
-        key,
-        label,
-        values: values,
-      });
+      // Handle range categories.
+      if (columnDef.filterFn === "inNumberRange") {
+        const minMax = getFacetedMinMaxValues();
+        categoryViews.push({
+          key,
+          label,
+          max: minMax?.[1] || Infinity,
+          min: minMax?.[0] || -Infinity,
+          selectedMax: null, // Selected state updated in reducer.
+          selectedMin: null, // Selected state updated in reducer.
+        });
+      }
+      // Handle select categories.
+      if (columnDef.filterFn === "arrIncludesSome") {
+        updateFacetedUniqueValues(getFacetedUniqueValues(), columnFilters, id);
+        const values = [...getFacetedUniqueValues()].map(([value, count]) => ({
+          count,
+          key: value,
+          label: String(value ?? ""),
+          selected: false, // Selected state updated in reducer.
+        }));
+        categoryViews.push({
+          key,
+          label,
+          values: values,
+        });
+      }
     }
   }
   return categoryViews;

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

@@ -0,0 +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,
+}: BaseComponentProps & CellContext<T, TValue>): JSX.Element | null => {
+  const props = getValue();
+  if (!props) return null;
+  return <Chip className={className} {...props} />;
+};

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

@@ -0,0 +1,64 @@
+import { LinkProps, Link as MLink, Typography } from "@mui/material";
+import { CellContext, RowData } from "@tanstack/react-table";
+import { BaseComponentProps } from "components/types";
+import React from "react";
+import { isValidUrl } from "../../../../../../common/utils";
+import { TYPOGRAPHY_PROPS } from "../../../../../../styles/common/mui/typography";
+import { isClientSideNavigation } from "../../../../../Links/common/utils";
+import { getComponent, getRelAttribute, getTargetAttribute } from "./utils";
+
+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,
+    color,
+    href = "",
+    rel,
+    target,
+    underline,
+    ...linkProps
+  } = props;
+
+  // Determine if the href should use client-side navigation.
+  const isClientSide = isClientSideNavigation(href);
+
+  // Determine if the href is valid.
+  const isValid = isClientSide || isValidUrl(href);
+
+  // If the href is invalid, return a Typography component.
+  if (!isValid)
+    return (
+      <Typography
+        className={className}
+        color={TYPOGRAPHY_PROPS.COLOR.INHERIT}
+        component="span"
+        variant={TYPOGRAPHY_PROPS.VARIANT.INHERIT}
+        {...linkProps}
+      >
+        {children}
+      </Typography>
+    );
+
+  // If the href is valid, return a Link component.
+  return (
+    <MLink
+      className={className}
+      color={color}
+      component={getComponent(href, isClientSide)}
+      href={href}
+      rel={getRelAttribute(rel, isClientSide)}
+      target={getTargetAttribute(target, isClientSide)}
+      underline={underline}
+      {...linkProps}
+    >
+      {children}
+    </MLink>
+  );
+};

package/src/components/Table/components/TableCell/components/LinkCell/stories/args.ts

@@ -0,0 +1,35 @@
+import { ComponentProps } from "react";
+import { TYPOGRAPHY_PROPS } from "../../../../../../../styles/common/mui/typography";
+import { LinkCell } from "../linkCell";
+import { GetValue } from "./types";
+
+export const CLIENT_SIDE_ARGS: Partial<ComponentProps<typeof LinkCell>> = {
+  getValue: (() => ({
+    children: "Explore",
+    href: "/",
+  })) as GetValue,
+};
+
+export const EXTERNAL_ARGS: Partial<ComponentProps<typeof LinkCell>> = {
+  getValue: (() => ({
+    children: "Explore",
+    href: "https://www.example.com",
+  })) as GetValue,
+};
+
+export const INVALID_ARGS: Partial<ComponentProps<typeof LinkCell>> = {
+  getValue: (() => ({
+    children: "Explore",
+  })) as GetValue,
+};
+
+export const WITH_CUSTOM_STYLE_ARGS: Partial<ComponentProps<typeof LinkCell>> =
+  {
+    getValue: (() => ({
+      children: "Explore",
+      color: "success",
+      href: "/",
+      underline: "none",
+      variant: TYPOGRAPHY_PROPS.VARIANT.TEXT_BODY_SMALL_400,
+    })) as GetValue,
+  };

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

@@ -0,0 +1,32 @@
+import { Meta, StoryObj } from "@storybook/react";
+import { LinkCell } from "../linkCell";
+import {
+  CLIENT_SIDE_ARGS,
+  EXTERNAL_ARGS,
+  INVALID_ARGS,
+  WITH_CUSTOM_STYLE_ARGS,
+} from "./args";
+
+const meta: Meta<typeof LinkCell> = {
+  component: LinkCell,
+};
+
+export default meta;
+
+type Story = StoryObj<typeof meta>;
+
+export const ClientSide: Story = {
+  args: CLIENT_SIDE_ARGS,
+};
+
+export const External: Story = {
+  args: EXTERNAL_ARGS,
+};
+
+export const Invalid: Story = {
+  args: INVALID_ARGS,
+};
+
+export const WithCustomStyle: Story = {
+  args: WITH_CUSTOM_STYLE_ARGS,
+};

package/src/components/Table/components/TableCell/components/LinkCell/stories/types.ts

@@ -0,0 +1,4 @@
+import { LinkProps } from "@mui/material";
+import { CellContext, RowData } from "@tanstack/react-table";
+
+export type GetValue = CellContext<RowData, LinkProps>["getValue"];

package/src/components/Table/components/TableCell/components/LinkCell/utils.ts

@@ -0,0 +1,59 @@
+import Link from "next/link";
+import { ElementType } from "react";
+import { isValidUrl } from "../../../../../../common/utils";
+import {
+  ANCHOR_TARGET,
+  REL_ATTRIBUTE,
+} from "../../../../../Links/common/entities";
+import {
+  assertAnchorRelAttribute,
+  assertAnchorTargetAttribute,
+} from "../../../../../common/Link/typeGuards";
+
+/**
+ * Returns the component to use for a link based on the given href and client-side navigation flag.
+ * @param href - The href attribute to use.
+ * @param isClientSide - Whether the link is a client-side navigation.
+ * @returns The component to use for the link.
+ */
+export function getComponent(href: string, isClientSide: boolean): ElementType {
+  if (isClientSide) return Link; // Use Next/Link for client-side navigation.
+  if (isValidUrl(href)) return "a"; // Use anchor tag for external links.
+  return "span"; // Use span for invalid links.
+}
+
+/**
+ * Returns the rel attribute for a link based on the given rel and client-side navigation flag.
+ * @param rel - The rel attribute to use.
+ * @param isClientSideNavigation - Whether the link is a client-side navigation.
+ * @returns The rel attribute for the link.
+ */
+export function getRelAttribute(
+  rel: string | undefined,
+  isClientSideNavigation: boolean
+): string {
+  if (rel) {
+    assertAnchorRelAttribute(rel);
+    return rel;
+  }
+  return isClientSideNavigation
+    ? REL_ATTRIBUTE.NO_OPENER
+    : REL_ATTRIBUTE.NO_OPENER_NO_REFERRER;
+}
+
+/**
+ * Returns the target attribute for a link based on the given target and client-side navigation flag.
+ * @param target - The target attribute to use.
+ * @param isClientSideNavigation - Whether the link is a client-side navigation.
+ * @returns The target attribute for the link.
+ */
+export function getTargetAttribute(
+  target: string | undefined,
+  isClientSideNavigation: boolean
+): string {
+  if (target) {
+    assertAnchorTargetAttribute(target);
+    return target;
+  }
+  return isClientSideNavigation ? ANCHOR_TARGET.SELF : ANCHOR_TARGET.BLANK;
+}

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/components/Table/featureOptions/facetedColumn/getFacetedMinMaxValues.ts

@@ -0,0 +1,64 @@
+import { getMemoOptions, memo, RowData, Table } from "@tanstack/react-table";
+
+/**
+ * Returns an array of two numbers, the minimum and maximum values for the column, or undefined if the column does not exist or has no values.
+ * Customized version of the default getFacetedMinMaxValues function from tanstack table handling mixed null and possible NaN values.
+ * See https://tanstack.com/table/v8/docs/api/features/column-faceting#getfacetedminmaxvalues.
+ * @returns An array of two numbers, the minimum and maximum values for the column, or undefined if the column does not exist or has no values.
+ */
+export function getFacetedMinMaxValues<TData extends RowData>(): (
+  table: Table<TData>,
+  columnId: string
+) => () => undefined | [number, number] {
+  // eslint-disable-next-line sonarjs/cognitive-complexity -- Customized copy of tanstack table function.
+  return (table, columnId) =>
+    memo(
+      () => [table.getColumn(columnId)?.getFacetedRowModel()],
+      (facetedRowModel) => {
+        if (!facetedRowModel) return undefined;
+
+        // Initialize with the smallest and largest possible numbers.
+        const facetedMinMaxValues: [number, number] = [Infinity, -Infinity];
+
+        for (let i = 0; i < facetedRowModel.flatRows.length; i++) {
+          const values =
+            facetedRowModel.flatRows[i]!.getUniqueValues<number>(columnId);
+
+          for (let j = 0; j < values.length; j++) {
+            const value = values[j]!;
+            // Convert value to a number.
+            const numericValue = Number(value);
+
+            // Skip null and NaN values.
+            if (value === null || isNaN(numericValue)) continue;
+
+            if (numericValue < facetedMinMaxValues[0]) {
+              facetedMinMaxValues[0] = numericValue;
+            }
+            if (numericValue > facetedMinMaxValues[1]) {
+              facetedMinMaxValues[1] = numericValue;
+            }
+          }
+        }
+
+        // Return undefined if all values are null or NaN.
+        if (
+          facetedMinMaxValues[0] === Infinity &&
+          facetedMinMaxValues[1] === -Infinity
+        ) {
+          return undefined;
+        }
+
+        // Normalize -0 to 0.
+        if (Object.is(facetedMinMaxValues[0], -0)) {
+          facetedMinMaxValues[0] = 0;
+        }
+        if (Object.is(facetedMinMaxValues[1], -0)) {
+          facetedMinMaxValues[1] = 0;
+        }
+
+        return facetedMinMaxValues;
+      },
+      getMemoOptions(table.options, "debugTable", "getFacetedMinMaxValues")
+    );
+}

package/src/components/common/Link/typeGuards.ts

@@ -0,0 +1,35 @@
+import { ANCHOR_TARGET, REL_ATTRIBUTE } from "../../Links/common/entities";
+
+/**
+ * Asserts that the given value is a valid REL_ATTRIBUTE.
+ * @param value - Value to assert.
+ * @throws Error if the value is not a valid REL_ATTRIBUTE.
+ */
+export function assertAnchorRelAttribute(
+  value: string
+): asserts value is REL_ATTRIBUTE {
+  if (!Object.values(REL_ATTRIBUTE).includes(value as REL_ATTRIBUTE)) {
+    throw new Error(
+      `Expecting rel attribute: ${value} to be one of ${Object.values(
+        REL_ATTRIBUTE
+      )}`
+    );
+  }
+}
+
+/**
+ * Asserts that the given value is a valid ANCHOR_TARGET.
+ * @param value - Value to assert.
+ * @throws Error if the value is not a valid ANCHOR_TARGET.
+ */
+export function assertAnchorTargetAttribute(
+  value: string
+): asserts value is ANCHOR_TARGET {
+  if (!Object.values(ANCHOR_TARGET).includes(value as ANCHOR_TARGET)) {
+    throw new Error(
+      `Expecting anchor target: ${value} to be one of ${Object.values(
+        ANCHOR_TARGET
+      )}`
+    );
+  }
+}

package/src/config/entities.ts

@@ -10,10 +10,10 @@ import {
   TableOptions,
 } from "@tanstack/react-table";
 import { JSXElementConstructor, ReactNode } from "react";
+import { CategoryConfig } from "../common/categories/config/types";
 import {
   DataDictionaryAnnotation,
   DataDictionaryConfig,
-  SelectCategoryValueView,
   SelectedFilter,
 } from "../common/entities";
 import { HeroTitle } from "../components/common/Title/title";
@@ -88,19 +88,6 @@ export interface CategoryGroup {
   label?: string;
 }
 
-/**
- * Model of category configured in site config.
- */
-export interface CategoryConfig {
-  annotation?: DataDictionaryAnnotation;
-  enableChartView?: boolean;
-  key: string;
-  label: string;
-  mapSelectCategoryValue?: (
-    selectCategoryValue: SelectCategoryValueView
-  ) => SelectCategoryValueView;
-}
-
 /**
  * Column configuration.
  * TanStack ColumnDef properties not currently supported include: