diff --git a/jest.setup.ts b/jest.setup.ts index b5fed2b149..80a3236698 100644 --- a/jest.setup.ts +++ b/jest.setup.ts @@ -22,6 +22,8 @@ jest.mock('interaction-viewer', () => null); jest.mock('/shared/custom-elements/NightingaleMSA', () => jest.fn()); +jest.mock('@nightingale-elements/nightingale-navigation', () => jest.fn()); + jest.mock('swagger-ui-react', () => null); global.beforeEach(() => { @@ -51,3 +53,38 @@ jest.mock('react', () => ({ ...jest.requireActual('react'), useId: mockedUseId, })); + +// eslint-disable-next-line @typescript-eslint/no-explicit-any +(global as any).ResizeObserver = class ResizeObserver { + constructor(callback: ResizeObserverCallback) { + this.callback = callback; + } + + observe(target: Element) { + this.callback([{ target } as ResizeObserverEntry], this); + } + + // eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars + unobserve(target: Element) { + // Mock implementation + } + + // eslint-disable-next-line class-methods-use-this + disconnect() { + // Mock implementation + } + + private callback: ResizeObserverCallback; +}; + +global.ResizeObserver = ResizeObserver; + +/* "Fail on console error" util */ +// Uncomment to have jest stop when a console error is shown in order to fix it +// Recommended to use with Jest's "--bail" option +// const { error } = console; +// // eslint-disable-next-line no-console +// console.error = (message, ...rest) => { +// error.apply(console, [message, ...rest]); // keep default behaviour +// throw message instanceof Error ? message : new Error(message); +// }; diff --git a/package.json b/package.json index 0e22562c04..d16ca63f8b 100644 --- a/package.json +++ b/package.json @@ -56,7 +56,7 @@ "jsx" ], "transformIgnorePatterns": [ - "/node_modules/(?!franklin-sites|p-map|aggregate-error|clean-stack|@nightingale|@lit/react|url-join).+\\.js" + "/node_modules/(?!franklin-sites|p-map|aggregate-error|clean-stack|protvista-uniprot|@nightingale|@lit/react|url-join).+\\.js" ], "testPathIgnorePatterns": [ "/__mocks__/", @@ -98,10 +98,19 @@ "string-width": "4.1.0" }, "dependencies": { + "@floating-ui/dom": "1.6.5", "@hello-pangea/dnd": "17.0.0", "@lit/react": "1.0.5", - "@nightingale-elements/nightingale-msa": "5.0.0", + "@nightingale-elements/nightingale-filter": "5.3.2", + "@nightingale-elements/nightingale-manager": "5.3.2", + "@nightingale-elements/nightingale-msa": "5.3.2", + "@nightingale-elements/nightingale-navigation": "5.3.2", + "@nightingale-elements/nightingale-new-core": "5.3.2", + "@nightingale-elements/nightingale-sequence": "5.3.2", + "@nightingale-elements/nightingale-track": "5.3.2", + "@nightingale-elements/nightingale-variation": "5.3.2", "@sentry/react": "8.31.0", + "@sentry/tracing": "7.27.0", "@sentry/types": "8.31.0", "@swissprot/rhea-reaction-visualizer": "0.0.21", "@swissprot/swissbiopics-visualizer": "0.0.28", @@ -111,7 +120,7 @@ "core-js": "3.38.1", "d3": "5.16.0", "deep-freeze": "0.0.1", - "franklin-sites": "0.0.247", + "franklin-sites": "0.0.249", "front-matter": "4.0.2", "history": "4.10.1", "idb": "8.0.0", @@ -121,21 +130,10 @@ "marked": "14.1.2", "marked-gfm-heading-id": "4.1.0", "p-map": "7.0.2", - "protvista-datatable": "3.8.10", - "protvista-feature-adapter": "3.8.15", - "protvista-filter": "3.8.4", - "protvista-manager": "3.8.4", - "protvista-navigation": "3.8.10", - "protvista-sequence": "3.8.13", - "protvista-tooltip": "3.8.4", - "protvista-track": "3.8.13", - "protvista-uniprot": "2.12.3", - "protvista-variation": "3.8.13", - "protvista-variation-adapter": "3.8.13", - "protvista-zoom-tool": "3.8.4", - "react": "18.3.1", + "protvista-uniprot": "3.0.8", + "react": "18", "react-diff-viewer-continued": "3.4.0", - "react-dom": "18.3.1", + "react-dom": "18", "react-helmet-async": "2.0.5", "react-router-dom": "5.3.4", "sanitize-html": "2.13.0", @@ -173,8 +171,8 @@ "@types/jest": "29.5.13", "@types/lodash-es": "4.17.12", "@types/marked": "6.0.0", - "@types/react": "18.3.8", - "@types/react-dom": "18.3.0", + "@types/react": "18", + "@types/react-dom": "18", "@types/react-router-dom": "5.3.3", "@types/sanitize-html": "2.13.0", "@types/swagger-ui-react": "4.18.3", diff --git a/src/app/components/App.tsx b/src/app/components/App.tsx index ba7ec159d5..731cedf3c4 100755 --- a/src/app/components/App.tsx +++ b/src/app/components/App.tsx @@ -43,6 +43,20 @@ import pkg from '../../../package.json'; import 'franklin-sites/franklin.css'; import './styles/app.scss'; +// This is hackery is to prevent define being repeatedly called for the same +// name. This has been observed in Variant viewer and Feature viewer tabs. +const originalDefine = customElements.define; +function newDefine( + this: typeof customElements.define, + name: string, + constructor: CustomElementConstructor +) { + if (!customElements.get(name)) { + originalDefine.call(this, name, constructor); + } +} +customElements.define = newDefine; + if (process.env.NODE_ENV !== 'development') { SentryInit({ // Key diff --git a/src/app/components/styles/app.scss b/src/app/components/styles/app.scss index e66adcf7e0..6b66875a9e 100644 --- a/src/app/components/styles/app.scss +++ b/src/app/components/styles/app.scss @@ -47,18 +47,6 @@ } } -protvista-datatable:not(:defined) > table { - width: 100%; - overflow-x: auto; - table-layout: fixed; - border-collapse: collapse; - - & td, - & th { - border: 1px solid grey; - } -} - protvista-manager { &:hover, &:focus-within { diff --git a/src/automatic-annotations/shared/entry/styles/conditions-annotations.module.scss b/src/automatic-annotations/shared/entry/styles/conditions-annotations.module.scss index c30310146b..400b591f61 100644 --- a/src/automatic-annotations/shared/entry/styles/conditions-annotations.module.scss +++ b/src/automatic-annotations/shared/entry/styles/conditions-annotations.module.scss @@ -1,6 +1,5 @@ @import 'franklin-sites/src/styles/mixins'; @import 'franklin-sites/src/styles/settings'; -@import 'franklin-sites/src/styles/colours'; .conditions-annotations { margin-bottom: $global-margin; @@ -15,7 +14,7 @@ left: 0; bottom: 0; width: 1ch; - background-color: $colour-sapphire-blue; + background-color: var(--fr--color-sapphire-blue); } } } @@ -56,29 +55,29 @@ margin-bottom: 0; & > li { - border-color: $colour-sapphire-blue; + border-color: var(--fr--color-sapphire-blue); border-style: solid; border-width: 0 0 1em 1ch; .extra & { - border-color: $colour-sea-blue; + border-color: var(--fr--color-sea-blue); } } & .statement { - background-color: $colour-sapphire-blue; + background-color: var(--fr--color-sapphire-blue); &::before { - background-color: $colour-sapphire-blue; + background-color: var(--fr--color-sapphire-blue); } } .extra & { & .statement { - background-color: $colour-sea-blue; + background-color: var(--fr--color-sea-blue); &::before { - background-color: $colour-sea-blue; + background-color: var(--fr--color-sea-blue); } } } @@ -96,10 +95,10 @@ height: 0; border-left: 0.8em solid transparent; border-right: 0.8em solid transparent; - border-top: $global-margin solid $colour-sapphire-blue; + border-top: $global-margin solid var(--fr--color-sapphire-blue); .extra & { - border-top-color: $colour-sea-blue; + border-top-color: var(--fr--color-sea-blue); } @include fs-breakpoints('large') { @@ -123,15 +122,15 @@ } } - border-color: $colour-weldon-blue; + border-color: var(--fr--color-weldon-blue); border-style: solid; border-width: 0 0 1em 1ch; & .statement { - background-color: $colour-weldon-blue; + background-color: var(--fr--color-weldon-blue); &::before { - background-color: $colour-weldon-blue; + background-color: var(--fr--color-weldon-blue); } } } @@ -146,7 +145,7 @@ } .statement { - background-color: $colour-sapphire-blue; + background-color: var(--fr--color-sapphire-blue); color: white; padding: 0 1px; text-transform: uppercase; @@ -193,10 +192,10 @@ height: 0; border-top: 0.8em solid transparent; border-bottom: 0.8em solid transparent; - border-left: $global-margin solid $colour-sapphire-blue; + border-left: $global-margin solid var(--fr--color-sapphire-blue); .extra & { - border-left-color: $colour-sea-blue; + border-left-color: var(--fr--color-sea-blue); } @include fs-breakpoints('large') { @@ -209,7 +208,7 @@ .extra { position: relative; margin-top: $global-margin; - border-bottom: $global-margin solid $colour-sea-blue; + border-bottom: $global-margin solid var(--fr--color-sea-blue); &::before { content: ''; @@ -218,11 +217,11 @@ top: 0; bottom: 0; width: 1ch; - background-color: $colour-sea-blue; + background-color: var(--fr--color-sea-blue); } & > .statement { - background-color: $colour-sea-blue; + background-color: var(--fr--color-sea-blue); padding-left: 1ch; margin-bottom: $global-margin; } diff --git a/src/basket/styles/basket-status.module.scss b/src/basket/styles/basket-status.module.scss index 05eac90139..e109b2df05 100644 --- a/src/basket/styles/basket-status.module.scss +++ b/src/basket/styles/basket-status.module.scss @@ -1,5 +1,3 @@ -@import 'franklin-sites/src/styles/colours'; - :global(.sliding-panel) { .basket-status { display: none; @@ -12,7 +10,7 @@ &:hover, &:focus { svg { - background-color: $colour-sea-blue; + background-color: var(--fr--color-sea-blue); } } @@ -23,7 +21,7 @@ margin: 0 0.5ch; padding: 0.4ch; border-radius: 50%; - background-color: $colour-sapphire-blue; + background-color: var(--fr--color-sapphire-blue); color: white; animation: appear 1 0.5s both ease-out; diff --git a/src/help/components/contextual/ContextualHelp.tsx b/src/help/components/contextual/ContextualHelp.tsx index 0480833d87..77fee3cab7 100644 --- a/src/help/components/contextual/ContextualHelp.tsx +++ b/src/help/components/contextual/ContextualHelp.tsx @@ -40,7 +40,7 @@ const ContextualHelp = () => { useEffect(() => { const eventHandler = (event: MouseEvent) => { const element = event.target as HTMLElement; - const isInTooltip = Boolean(element.closest('[data-tippy-root')); + const isInTooltip = Boolean(element.closest('[role=tooltip]')); // If it's a click within a tooltip, stop the propagation of the event if (isInTooltip) { event.stopPropagation(); diff --git a/src/help/components/contextual/styles/contextual-help.module.scss b/src/help/components/contextual/styles/contextual-help.module.scss index 20ac77f36b..8b4b6961ed 100644 --- a/src/help/components/contextual/styles/contextual-help.module.scss +++ b/src/help/components/contextual/styles/contextual-help.module.scss @@ -10,10 +10,6 @@ cursor: inherit; opacity: 1; } - - [data-tippy-root] &::after { - display: initial; - } } $help-height: 35em; @@ -30,11 +26,11 @@ $help-height: 35em; z-index: 2147483642; :global(.sliding-panel__header) { - background-color: $colour-help-green; + background-color: var(--fr--color-help-green); } :global(.sliding-panel__content) { - @include scroll-shadow($colour-sky-white); + @include scroll-shadow(var(--fr--color-sky-white)); overscroll-behavior: contain; } diff --git a/src/help/components/entry/styles/entry.module.scss b/src/help/components/entry/styles/entry.module.scss index 5a88b16b2b..bf63d93147 100644 --- a/src/help/components/entry/styles/entry.module.scss +++ b/src/help/components/entry/styles/entry.module.scss @@ -1,4 +1,3 @@ -@import 'franklin-sites/src/styles/colours'; @import 'franklin-sites/src/styles/settings'; .in-panel { @@ -22,27 +21,27 @@ } thead { - color: $colour-sky-white; - background: $colour-sea-blue; + color: var(--fr--color-sky-white); + background: var(--fr--color-sea-blue); a { - color: $colour-sky-white; + color: var(--fr--color-sky-white); } } tbody { - border: 1px solid $colour-sea-blue; + border: 1px solid var(--fr--color-sea-blue); } th, td { padding: $global-padding * 0.25 $global-padding * 0.5; - border: 1px solid $colour-sea-blue; + border: 1px solidvar(--fr--color-sea-blue); border-collapse: collapse; } code { - background: $colour-platinum; + background: var(--fr--color-platinum); } p, @@ -53,7 +52,7 @@ /* copied from Franklin's CodeBlock component styles */ pre { display: block; /* except this which is different */ - background: $colour-yankees-blue; + background: var(--fr--color-yankees-blue); color: $white; font-family: $code-font-family; font-weight: $code-font-weight; @@ -69,12 +68,12 @@ } img { - border: 0.5em solid $colour-gainsborough; + border: 0.5em solid var(--fr--color-gainsborough); border-bottom-width: 1em; } figure { - border: 0.5em solid $colour-gainsborough; + border: 0.5em solid var(--fr--color-gainsborough); margin-block: 1em; & img { @@ -83,7 +82,7 @@ } & figcaption { - background: $colour-gainsborough; + background: var(--fr--color-gainsborough); text-align: center; font-style: italic; } diff --git a/src/help/config/featureTypeHelpMappings.ts b/src/help/config/featureTypeHelpMappings.ts index 74f186b36a..950473ef50 100644 --- a/src/help/config/featureTypeHelpMappings.ts +++ b/src/help/config/featureTypeHelpMappings.ts @@ -17,6 +17,7 @@ const FeatureTypeHelpMappings: Omit, 'Other'> = { 'Coiled coil': 'coiled', Motif: 'motif', 'Active site': 'act_site', + BINDING: 'binding', 'Binding site': 'binding', Site: 'site', Intramembrane: 'intramem', diff --git a/src/proteomes/components/entry/__tests__/__snapshots__/Components.spec.tsx.snap b/src/proteomes/components/entry/__tests__/__snapshots__/Components.spec.tsx.snap index fe2e468526..242bf3f604 100644 --- a/src/proteomes/components/entry/__tests__/__snapshots__/Components.spec.tsx.snap +++ b/src/proteomes/components/entry/__tests__/__snapshots__/Components.spec.tsx.snap @@ -58,16 +58,19 @@ exports[`Components view should render 1`] = ` Component name Genome accession(s) Protein count diff --git a/src/proteomes/components/entry/__tests__/__snapshots__/EntryMain.spec.tsx.snap b/src/proteomes/components/entry/__tests__/__snapshots__/EntryMain.spec.tsx.snap index dc143a9e1a..021a29f287 100644 --- a/src/proteomes/components/entry/__tests__/__snapshots__/EntryMain.spec.tsx.snap +++ b/src/proteomes/components/entry/__tests__/__snapshots__/EntryMain.spec.tsx.snap @@ -78,16 +78,19 @@ exports[`EntryMain view should render 1`] = ` Component name Genome accession(s) Protein count diff --git a/src/shared/components/column-select/styles/column-select-drag-drop.scss b/src/shared/components/column-select/styles/column-select-drag-drop.scss index dd2ec2a567..e892876092 100644 --- a/src/shared/components/column-select/styles/column-select-drag-drop.scss +++ b/src/shared/components/column-select/styles/column-select-drag-drop.scss @@ -1,23 +1,20 @@ -@import 'franklin-sites/src/styles/colours'; - .column-select-drag-drop { &__list { - background: $colour-platinum; - display: flex; + background: var(--fr--color-platinum); padding: 0.5rem; overflow: auto; white-space: nowrap; margin: 1rem 0; .chip { - --main-chip-color: #{$colour-sea-blue}; + --main-chip-color: #{var(--fr--color-sea-blue)}; &:hover { - --main-chip-color: #{$colour-vivid-cerulean}; + --main-chip-color: #{var(--fr--color-vivid-cerulean)}; } &--dragging { - --main-chip-color: #{$colour-vivid-cerulean}; + --main-chip-color: #{var(--fr--color-vivid-cerulean)}; } } } diff --git a/src/shared/components/layouts/styles/uniprot-header.module.scss b/src/shared/components/layouts/styles/uniprot-header.module.scss index 22a1eaf67e..1959a35d83 100644 --- a/src/shared/components/layouts/styles/uniprot-header.module.scss +++ b/src/shared/components/layouts/styles/uniprot-header.module.scss @@ -1,5 +1,4 @@ @import 'franklin-sites/src/styles/mixins'; -@import 'franklin-sites/src/styles/colours'; .main-content { margin: 0; @@ -25,14 +24,14 @@ } .logo { - background: $colour-sky-white; + background: var(--fr--color-sky-white); -webkit-mask: url('../../../../images/uniprot-logo.img.svg') no-repeat 0 0; mask: url('../../../../images/uniprot-logo.img.svg') no-repeat 0 0; width: 80px; height: 40px; &.home { - background: $colour-sea-blue; + background: var(--fr--color-sea-blue); } @include fs-breakpoints('large') { diff --git a/src/shared/components/results/ResultsData.tsx b/src/shared/components/results/ResultsData.tsx index 433fe16d24..18844a2bc4 100644 --- a/src/shared/components/results/ResultsData.tsx +++ b/src/shared/components/results/ResultsData.tsx @@ -68,7 +68,7 @@ const ResultsData = ({ const { viewMode } = useViewMode(namespaceOverride, disableCardToggle); const history = useHistory(); const [{ query, direct, groupBy }] = getParamsFromURL(useLocation().search); - const [columns, updateColumnSort] = useColumns( + const [columns, updateColumnSort, tooltipOnHoverRef] = useColumns( namespaceOverride, displayIdMappingColumns, basketSetter, @@ -186,7 +186,7 @@ const ResultsData = ({ } return ( - <> +
{/* Display warning for wildcard searches. It is not related to any warning from ID mapping */} {warnings && !displayIdMappingColumns && ( @@ -212,7 +212,7 @@ const ResultsData = ({ )} {content} - +
); }; diff --git a/src/shared/components/results/__tests__/__snapshots__/ResultsData.spec.tsx.snap b/src/shared/components/results/__tests__/__snapshots__/ResultsData.spec.tsx.snap index 3ea15350c3..931891e263 100644 --- a/src/shared/components/results/__tests__/__snapshots__/ResultsData.spec.tsx.snap +++ b/src/shared/components/results/__tests__/__snapshots__/ResultsData.spec.tsx.snap @@ -2,437 +2,438 @@ exports[`ResultsData component should render the card view with the correct number of cards 1`] = ` - -
-
+ + + +
- Load more data - + +
`; exports[`ResultsData component should render the table view 1`] = ` - - - - + +
-
+ + + + + + + + + + - - - - - - - - - - + + + + - - -
+
+ +
+ 		+ + Entry + +
- -
- - - - + + - P13866 - - -
- - - + P13866 + + +
- + + - P19926 - - -
-
-
+
- Load more data - + +
`; diff --git a/src/shared/components/results/styles/results-data.module.scss b/src/shared/components/results/styles/results-data.module.scss index a0550584d7..74ce379a51 100644 --- a/src/shared/components/results/styles/results-data.module.scss +++ b/src/shared/components/results/styles/results-data.module.scss @@ -13,15 +13,9 @@ top: $action-buttons-height !important; } - // Note: shouldn't use protvista-datatable in results - &:global(.data-table) protvista-datatable thead :global(.pd-group-trigger) { - // override when using it inside a results table - display: none; - } - &:global(.data-table) table thead, &:global(.data-table) table th { - background-color: $colour-independence; + background-color: var(--fr--color-independence); z-index: inherit; } diff --git a/src/shared/components/styles/card-checkbox-cell.scss b/src/shared/components/styles/card-checkbox-cell.scss index 42b8e46059..64800edabb 100644 --- a/src/shared/components/styles/card-checkbox-cell.scss +++ b/src/shared/components/styles/card-checkbox-cell.scss @@ -1,5 +1,3 @@ -@import 'franklin-sites/src/styles/colours'; - // Same classnames as in franklin .data-list .checkbox-cell { height: 100%; @@ -20,7 +18,7 @@ bottom: 0; left: 0; margin: 0; - background: $colour-sea-blue; + background: var(--fr--color-sea-blue); border-radius: 50%; opacity: 0; diff --git a/src/shared/components/table/Table.tsx b/src/shared/components/table/Table.tsx index 6136893e1d..786567e0b9 100644 --- a/src/shared/components/table/Table.tsx +++ b/src/shared/components/table/Table.tsx @@ -11,19 +11,53 @@ import { import { Button, ControlledDropdown } from 'franklin-sites'; import cn from 'classnames'; +import useExpandTable from '../../hooks/useExpandTable'; + import styles from './styles/table.module.scss'; const Table = ({ children, className, + expandable, + id, ...props -}: HTMLAttributes) => ( -
+}: HTMLAttributes & { + expandable?: boolean; + id?: string; +}) => { + const [containerRef, expandTable, setExpandTable, showButton] = + useExpandTable(expandable); + + return expandable ? ( +
+
+ + {children} +
+
+ {(showButton || expandTable) && ( +
+ +
+ )} +
+ ) : ( {children}
-
-); + ); +}; type HeadProps = HTMLAttributes & { toggleAll?: boolean; @@ -41,8 +75,9 @@ const Head = ({ toggleAll, children, className, ...props }: HeadProps) => { const buttons = button .closest('table') ?.querySelectorAll( - // get only the direct children, not the ones within another inner table - `:scope > tbody > tr > td > button[aria-expanded="${!expand}"]` + // get only the direct children, not the ones within another inner table and + // use td:first-child to avoid selecting publication tags if present in the row + `:scope > tbody > tr > td:first-child > button[aria-expanded="${!expand}"]` ); for (const button of buttons || []) { button.click(); @@ -137,6 +172,7 @@ const Row = ({ className, extraContent, isOdd, + onClick, ...props }: HTMLAttributes & { extraContent?: ReactNode; @@ -148,19 +184,17 @@ const Row = ({ const buttonId = useId(); - const handleClick: MouseEventHandler | undefined = - hasExtraContent - ? (event) => { - if ( - (event.target as HTMLElement).closest( - 'a, button:not([aria-controls]), input' - ) - ) { - return; - } - setExpanded((expanded) => !expanded); - } - : undefined; + const handleClick: MouseEventHandler = (event) => { + onClick?.(event); + if ( + hasExtraContent && + !(event.target as HTMLElement).closest( + 'a, button:not([aria-controls]), input' + ) + ) { + setExpanded((expanded) => !expanded); + } + }; return ( diff --git a/src/shared/components/table/TableFromData.tsx b/src/shared/components/table/TableFromData.tsx new file mode 100644 index 0000000000..811fb224e6 --- /dev/null +++ b/src/shared/components/table/TableFromData.tsx @@ -0,0 +1,187 @@ +import { ReactNode, useCallback, useMemo, useState } from 'react'; +import { Message } from 'franklin-sites'; +import cn from 'classnames'; + +import Table from './Table'; + +import styles from './styles/table.module.scss'; + +const UNFILTERED_OPTION = 'All' as const; +const MIN_ROWS_TO_EXPAND = 10 as const; + +type TableHeaderFromDataProps = { + column: TableFromDataColumn; + options?: Set; + onFilterChange: (columnId: string, filterValue: string) => void; +}; +function TableHeaderFromData({ + column, + options, + onFilterChange, +}: TableHeaderFromDataProps) { + return ( + + {column.label} + {options && options.size > 1 && ( + <> +
+ + + )} + + ); +} + +function filterDatum( + datum: T, + columns: TableFromDataColumn[], + filterValues: ColumnsToSelectedFilter +) { + return columns.every((column) => { + const filterValue = filterValues[column.id]; + return typeof filterValue !== 'undefined' && column.filter + ? column.filter(datum, filterValue) + : true; + }); +} + +export type TableFromDataColumn = { + id: string; + label: ReactNode; + render: (datum: T) => ReactNode; + filter?: (datum: T, filterValue: string) => boolean; + getOption?: (datum: T) => string | number; +}; + +const OPTION_TYPES = new Set(['string', 'number']); + +type Props = { + data: T[]; + columns: TableFromDataColumn[]; + rowExtraContent?: (datum: T) => React.ReactNode; + getRowId: (datum: T) => string; + onRowClick?: (datum: T) => void; + markBackground?: (datum: T) => boolean; + markBorder?: (datum: T) => boolean; + noTranslateBody?: boolean; + expandable?: boolean; + id?: string; +}; + +type ColumnsToSelectedFilter = Record; + +function TableFromData({ + data, + columns, + rowExtraContent, + onRowClick, + getRowId, + markBackground, + markBorder, + noTranslateBody, + expandable = true, + ...props +}: Props) { + const [columnsToSelectedOption, setColumnsToSelectedOption] = + useState({}); + const columnIdToFilterOptions = useMemo(() => { + const columnIdToFilterOptions: Record> = {}; + for (const column of columns) { + if (column.filter) { + columnIdToFilterOptions[column.id] = new Set( + data + .map((datum) => { + const r = (column.getOption || column.render)(datum); + return OPTION_TYPES.has(typeof r) ? r : null; + }) + .filter((datum): datum is string => datum !== null) + ); + } + } + return columnIdToFilterOptions; + }, [columns, data]); + + const handleFilterChange = useCallback( + (columnId: string, value: string) => { + setColumnsToSelectedOption((f) => ({ + ...f, + [columnId]: value === UNFILTERED_OPTION ? undefined : value, + })); + }, + [setColumnsToSelectedOption] + ); + + const filteredData = useMemo( + () => + data.filter((datum) => + filterDatum(datum, columns, columnsToSelectedOption) + ), + [columns, data, columnsToSelectedOption] + ); + + return ( + MIN_ROWS_TO_EXPAND} + {...props} + > + + {columns.map((column) => ( + + ))} + + + {filteredData.length ? ( + filteredData.map((datum, index) => ( + {rowExtraContent(datum)} + ) + } + key={getRowId(datum)} + onClick={() => onRowClick?.(datum)} + className={cn({ + [styles['mark-background']]: markBackground?.(datum), + [styles['mark-border']]: markBorder?.(datum), + })} + data-id={getRowId(datum)} + > + {columns.map((column) => ( + + ))} + + )) + ) : ( + + + + )} + +
{column.render(datum)}
+ + No data matches selected filters + +
+ ); +} + +export default TableFromData; diff --git a/src/shared/components/table/__tests__/Table.spec.tsx b/src/shared/components/table/__tests__/Table.spec.tsx new file mode 100644 index 0000000000..196f98ac57 --- /dev/null +++ b/src/shared/components/table/__tests__/Table.spec.tsx @@ -0,0 +1,47 @@ +import { fireEvent, screen } from '@testing-library/react'; + +import customRender from '../../../__test-helpers__/customRender'; + +import Table from '../Table'; + +describe('Table component', () => { + const getTable = (expandable: boolean) => ( + + + + + + + + + + + + + + + + + + + +
NameAgeAlice25Mark30Paul35
+ ); + it('should render with a working toggle button', async () => { + Element.prototype.scrollIntoView = jest.fn(); + const { asFragment } = customRender(getTable(true)); + expect(asFragment()).toMatchSnapshot(); + const button = screen.getByRole('button', { name: /Expand/ }); + expect(button).toBeInTheDocument(); + fireEvent.click(button); + expect( + await screen.findByRole('button', { name: /Collapse/ }) + ).toBeInTheDocument(); + }); + + it('should not render a toggle button if overriden', async () => { + const { asFragment } = customRender(getTable(false)); + expect(asFragment()).toMatchSnapshot(); + expect(screen.queryByRole('button')).not.toBeInTheDocument(); + }); +}); diff --git a/src/shared/components/table/__tests__/__snapshots__/Table.spec.tsx.snap b/src/shared/components/table/__tests__/__snapshots__/Table.spec.tsx.snap new file mode 100644 index 0000000000..980eb6e4af --- /dev/null +++ b/src/shared/components/table/__tests__/__snapshots__/Table.spec.tsx.snap @@ -0,0 +1,139 @@ +// Jest Snapshot v1, https://goo.gl/fbAQLP + +exports[`Table component should not render a toggle button if overriden 1`] = ` + + + + + + + + + + + + + + + + + + + + + + +
+ + Name + + Age +
+ + Alice + + 25 +
+ + Mark + + 30 +
+ + Paul + + 35 +
+ +`; + +exports[`Table component should render with a working toggle button 1`] = ` + +
+ +
+ +
+
+ +`; diff --git a/src/shared/components/table/styles/table.module.scss b/src/shared/components/table/styles/table.module.scss index ee748a41a9..924b7c5ace 100644 --- a/src/shared/components/table/styles/table.module.scss +++ b/src/shared/components/table/styles/table.module.scss @@ -1,7 +1,18 @@ +.expand-button-container { + display: flex; + justify-content: flex-end; + margin-top: 0.5rem; +} + .container { width: calc(100% + 2em); padding-inline: 1em; margin-inline-start: -1em; + overflow: scroll; + + &.collapsed { + height: 25rem; + } } .table { @@ -9,12 +20,29 @@ padding: 0; margin: 1em 0; border-spacing: 0; + border-block-end: 1px solid #c2c4c4; + border-collapse: collapse; border-block-end: 1px solid var(--table_border); + & thead { + position: sticky; + top: 0; + z-index: 1; + box-shadow: + -1em 0 var(--table__header-background), + 1em 0 var(--table__header-background), + 0 -1px var(--table__header-background), + 0 1px var(--table__header-background), + inset -1em 0 var(--table__header-background), + inset 1em 0 var(--table__header-background), + inset 0 -1px var(--table__header-background), + inset 0 1px var(--table__header-background); + } + & th { text-align: left; vertical-align: middle; - background-color: var(--table__header-background,); + background-color: var(--table__header-background); color: var(--table__header-text); text-overflow: ellipsis; text-transform: uppercase; @@ -37,6 +65,23 @@ .row { background-color: var(--table__even); + border-color: transparent; + border-style: solid; + border-width: 0 0.5rem; + + &.mark-background { + &, + & + .extra-content { + background-color: rgba(255, 235, 59, 0.3) !important; + } + } + + &.mark-border { + &, + & + .extra-content { + border-color: rgb(214, 214, 214); + } + } &.odd { background-color: var(--table__odd); @@ -80,3 +125,7 @@ .row:has(+ .extra-content:hover) { background-color: var(--table__hover); } + +.message--no-data { + margin: 0.5rem; +} diff --git a/src/shared/components/views/DatatableWrapper.tsx b/src/shared/components/views/DatatableWrapper.tsx deleted file mode 100644 index 4737a11166..0000000000 --- a/src/shared/components/views/DatatableWrapper.tsx +++ /dev/null @@ -1,121 +0,0 @@ -import { - useState, - useRef, - useEffect, - useLayoutEffect, - HTMLAttributes, -} from 'react'; -import { Button } from 'franklin-sites'; -import { useParams } from 'react-router-dom'; -import cn from 'classnames'; - -import useCustomElement from '../../hooks/useCustomElement'; - -import { sendGtagEventFeatureDataTableViewClick } from '../../utils/gtagEvents'; - -import './styles/datatable-wrapper.scss'; - -type Props = { - alwaysExpanded?: boolean; -} & HTMLAttributes; - -const DatatableWrapper = ({ - alwaysExpanded, - children, - className, - ...props -}: Props) => { - const [showButton, setShowButton] = useState(!alwaysExpanded); - const [expandTable, setExpandTable] = useState(null); - - const tableRef = useRef(null); - const firstRenderRef = useRef(true); - - const params = useParams<{ accession?: string }>(); - - const datatableElement = useCustomElement( - /* istanbul ignore next */ - () => - import( - /* webpackChunkName: "protvista-datatable" */ 'protvista-datatable' - ), - 'protvista-datatable' - ); - - // On expand/collapse change - useEffect(() => { - // except on first render or when always expanded - if (!alwaysExpanded && !firstRenderRef.current) { - // Scroll table back into view when collapsing - if (expandTable === false) { - tableRef.current?.parentElement?.scrollIntoView({ - behavior: 'smooth', - block: 'center', - }); - } - sendGtagEventFeatureDataTableViewClick( - params.accession || '', - expandTable ? 'expanded' : 'collapsed' - ); - } - // If first render was previous render, then it's not the first anymore... - if (firstRenderRef.current) { - firstRenderRef.current = false; - } - }, [alwaysExpanded, expandTable, params.accession]); - - // eslint-disable-next-line consistent-return - useLayoutEffect(() => { - if (!alwaysExpanded && datatableElement.defined && tableRef.current) { - const mo = new MutationObserver(() => { - setShowButton( - tableRef.current?.shadowRoot?.firstElementChild?.scrollHeight !== - tableRef.current?.shadowRoot?.firstElementChild?.clientHeight - ); - }); - mo.observe(tableRef.current, { - childList: true, - // Allows to update when classes are applied to hide some rows - attributes: true, - attributeFilter: ['class'], - subtree: true, - }); - return () => mo.disconnect(); - } - }, [alwaysExpanded, datatableElement.defined]); - - if (datatableElement.defined) { - return ( -
- - {children} - - {(showButton || expandTable) && ( - - )} -
- ); - } - - if (datatableElement.errored) { - return ( -
- {children} -
- ); - } - - return null; -}; - -export default DatatableWrapper; diff --git a/src/shared/components/views/FeaturesView.tsx b/src/shared/components/views/FeaturesView.tsx index 10670a90c4..304f67e02a 100644 --- a/src/shared/components/views/FeaturesView.tsx +++ b/src/shared/components/views/FeaturesView.tsx @@ -1,22 +1,30 @@ -import { Fragment, lazy, ReactNode, useMemo } from 'react'; -import TransformedVariant from 'protvista-variation-adapter'; +import { + Fragment, + lazy, + ReactNode, + useCallback, + useId, + useMemo, + useState, +} from 'react'; +import { Feature } from '@nightingale-elements/nightingale-track'; import LazyComponent from '../LazyComponent'; -import DatatableWrapper from './DatatableWrapper'; +import TableFromData from '../table/TableFromData'; -import useCustomElement from '../../hooks/useCustomElement'; import { useSmallScreen } from '../../hooks/useMatchMedia'; +import useNightingaleFeatureTableScroll from '../../hooks/useNightingaleFeatureTableScroll'; import FeatureTypeHelpMappings from '../../../help/config/featureTypeHelpMappings'; import FeatureType from '../../../uniprotkb/types/featureType'; -import { UniParcProcessedFeature } from '../../../uniparc/components/entry/UniParcFeaturesView'; import { Evidence } from '../../../uniprotkb/types/modelTypes'; import { ConfidenceScore } from '../../../uniprotkb/components/protein-data-views/UniProtKBFeaturesView'; import { Ligand, LigandPart, } from '../../../uniprotkb/components/protein-data-views/LigandDescriptionView'; +import { NightingaleViewRange } from '../../utils/nightingale'; const VisualFeaturesView = lazy( () => @@ -31,9 +39,8 @@ export type Fragment = { export type LocationModifier = 'EXACT' | 'OUTSIDE' | 'UNSURE' | 'UNKNOWN'; -export type ProcessedFeature = { - protvistaFeatureId: string; - featureId?: string; +export type ProcessedFeature = Feature & { + id?: string; // Used for the feature ID eg PRO_0000381966 while Feature.accession used as the UUID start: number; end: number; startModifier?: LocationModifier; @@ -42,8 +49,8 @@ export type ProcessedFeature = { description?: ReactNode; evidences?: Evidence[]; sequence?: string; - locations?: { fragments: Fragment[] }[]; source?: string; + primaryAccession?: string; // PTM specific confidenceScore?: ConfidenceScore; // Binding site @@ -52,47 +59,71 @@ export type ProcessedFeature = { ligandDescription?: string; }; -type FeatureProps = { +export type FeatureColumnConfiguration = { + id: string; + label: ReactNode; + filter?: (data: T, input: string) => boolean; + render: (data: T) => ReactNode; + getOption?: (data: T) => string | number; // Fallback if render fn doesn't return string or number +}; + +type FeatureViewProps = { + sequence?: string; features: T[]; - table: JSX.Element; + rowExtraContent?: (datum: T) => ReactNode; + getRowId: (datum: T) => string; + columns: FeatureColumnConfiguration[]; trackHeight?: number; - sequence?: string; withTitle?: boolean; noLinkToFullView?: boolean; + markBackground?: (markedData: T) => ((data: T) => boolean) | undefined; + markBorder?: ( + nightingaleViewRange: NightingaleViewRange + ) => (datum: T) => boolean; + inResultsTable?: boolean; }; -export type GenericFeature = - | ProcessedFeature - | TransformedVariant - | UniParcProcessedFeature; - -const FeaturesView = ({ +function FeaturesView({ sequence, features, - table, trackHeight, withTitle = true, noLinkToFullView, -}: FeatureProps) => { + rowExtraContent, + getRowId, + markBackground, + markBorder, + columns, + inResultsTable, +}: FeatureViewProps) { const isSmallScreen = useSmallScreen(); - - const managerElement = useCustomElement( - /* istanbul ignore next */ - () => - import(/* webpackChunkName: "protvista-manager" */ 'protvista-manager'), - 'protvista-manager' - ); + const [highlightedFeature, setHighlightedFeature] = useState(); + const [nightingaleViewRange, setNightingaleViewRange] = + useState(); + const tableId = useId(); + const tableScroll = useNightingaleFeatureTableScroll(getRowId, tableId); const featureTypes = useMemo( () => Array.from(new Set(features.map(({ type }) => type))), [features] ); - if (features.length === 0) { - return null; - } + const handleViewRangeChange = useCallback( + (coordinates: NightingaleViewRange) => { + setNightingaleViewRange(coordinates); + }, + [] + ); + + const handleFeatureClick = useCallback( + (feature: T) => { + setHighlightedFeature(feature); + tableScroll(feature); + }, + [tableScroll] + ); - return ( + return !features.length ? null : ( <> {withTitle && ( <> @@ -115,26 +146,41 @@ const FeaturesView = ({

)} - {managerElement.defined ? ( - - {sequence && ( - - - - )} - {table} - - ) : null} + {sequence && ( + + handleFeatureClick(feature as T)} + onViewRangeChange={handleViewRangeChange} + highlightedFeature={highlightedFeature} + /> + + )} + ); -}; +} export default FeaturesView; diff --git a/src/shared/components/views/VisualFeaturesView.tsx b/src/shared/components/views/VisualFeaturesView.tsx index 8dd4ed2033..7667e58a40 100644 --- a/src/shared/components/views/VisualFeaturesView.tsx +++ b/src/shared/components/views/VisualFeaturesView.tsx @@ -1,85 +1,108 @@ -import { useCallback, useState } from 'react'; +import { useEffect, useRef, useState } from 'react'; import { FullViewIcon } from 'franklin-sites'; import { Link, useParams } from 'react-router-dom'; +import NightingaleTrack from '@nightingale-elements/nightingale-track'; +import NightingaleManager from '@nightingale-elements/nightingale-manager'; +import NightingaleNavigation from '@nightingale-elements/nightingale-navigation'; +import NightingaleNavigationComponent from '../../custom-elements/NightingaleNavigation'; +import NightingaleSequenceComponent from '../../custom-elements/NightingaleSequence'; +import NightingalTrackComponent from '../../custom-elements/NightingaleTrack'; +import NightingaleManagerComponent from '../../custom-elements/NightingaleManager'; import NightingaleZoomTool, { iconSize, } from '../../../uniprotkb/components/protein-data-views/NightingaleZoomTool'; import EntryDownloadPanel from '../entry/EntryDownloadPanel'; import EntryDownloadButton from '../entry/EntryDownloadButton'; -import useCustomElement from '../../hooks/useCustomElement'; - import { getEntryPath } from '../../../app/config/urls'; import { sendGtagEventFeatureViewerFullViewClick } from '../../utils/gtagEvents'; import { TabLocation } from '../../../uniprotkb/types/entry'; import { Namespace } from '../../types/namespaces'; import { Dataset } from '../entry/EntryDownload'; -import { GenericFeature } from './FeaturesView'; +import { NightingaleViewRange } from '../../utils/nightingale'; +import { ProcessedFeature } from './FeaturesView'; import styles from './styles/visual-features-view.module.scss'; +function getHighlightedCoordinates(feature?: T) { + return feature?.start && feature?.end + ? `${feature.start}:${feature.end}` + : undefined; +} + type Props = { features: T[]; sequence: string; trackHeight?: number; noLinkToFullView?: boolean; + onFeatureClick: (feature: T) => void; + onViewRangeChange: (range: NightingaleViewRange) => void; + highlightedFeature?: T; }; -function VisualFeaturesView({ +function VisualFeaturesView({ features, sequence, - trackHeight, + trackHeight = 40, noLinkToFullView, + onFeatureClick, + onViewRangeChange, + highlightedFeature, }: Props) { const [displayDownloadPanel, setDisplayDownloadPanel] = useState(false); - const trackElement = useCustomElement( - /* istanbul ignore next */ - () => import(/* webpackChunkName: "protvista-track" */ 'protvista-track'), - 'protvista-track' - ); - const navigationElement = useCustomElement( - /* istanbul ignore next */ - () => - import( - /* webpackChunkName: "protvista-navigation" */ 'protvista-navigation' - ), - 'protvista-navigation' - ); - const sequenceElement = useCustomElement( - /* istanbul ignore next */ - () => - import(/* webpackChunkName: "protvista-sequence" */ 'protvista-sequence'), - 'protvista-sequence' - ); - const params = useParams<{ accession: string }>(); + const trackRef = useRef(null); + const managerRef = useRef(null); + const navigationRef = useRef(null); - const setTrackData = useCallback( - (node: { data: T[] }): void => { - if (node && trackElement.defined) { - // eslint-disable-next-line no-param-reassign - node.data = features; + // NightingaleTrack data loading and feature click event handler + useEffect(() => { + const eventHandler = (e: Event) => { + const { detail } = e as CustomEvent< + NightingaleViewRange & { eventType: 'click'; feature: T } + >; + if (detail?.eventType === 'click' && detail?.feature) { + onFeatureClick(detail.feature as T); } - }, - [trackElement.defined, features] - ); + }; + if (trackRef.current) { + trackRef.current.data = features; + trackRef.current.addEventListener('change', eventHandler); + } + return () => { + document.removeEventListener('change', eventHandler); + }; + }, [trackRef, features, onFeatureClick]); - const ceDefined = - trackElement.defined && - navigationElement.defined && - sequenceElement.defined; + // NightingaleManager view range event handler + useEffect(() => { + const eventHandler = (e: Event) => { + const { detail } = e as CustomEvent< + NightingaleViewRange & { eventType: 'change' } + >; + if (detail?.['display-start'] && detail?.['display-end']) { + onViewRangeChange(detail); + } + }; + if (managerRef.current) { + managerRef.current.addEventListener('change', eventHandler); + } + return () => { + document.removeEventListener('change', eventHandler); + }; + }, [managerRef, onViewRangeChange]); const handleToggleDownload = () => setDisplayDownloadPanel(!displayDownloadPanel); const featureTypes: string[] = Array.from( - new Set(features.flatMap((feature) => feature.type)) + new Set(features.flatMap((feature) => feature.type as string)) ); - return ceDefined ? ( - <> + return ( +
{displayDownloadPanel && ( ({ featureTypes={featureTypes} /> )} - + {!noLinkToFullView && ( ({ )} - - - - - ) : null; + + + + + +
+ ); } export default VisualFeaturesView; diff --git a/src/shared/components/views/__tests__/DatatableWrapper.spec.tsx b/src/shared/components/views/__tests__/DatatableWrapper.spec.tsx deleted file mode 100644 index d821b0b487..0000000000 --- a/src/shared/components/views/__tests__/DatatableWrapper.spec.tsx +++ /dev/null @@ -1,33 +0,0 @@ -import { fireEvent, screen } from '@testing-library/react'; - -import customRender from '../../../__test-helpers__/customRender'; - -import DatatableWrapper from '../DatatableWrapper'; - -describe('DatatableWrapper component', () => { - it('should render with a working toggle button', async () => { - Element.prototype.scrollIntoView = jest.fn(); - const { asFragment } = customRender( - - - - ); - expect(asFragment()).toMatchSnapshot(); - const button = screen.getByRole('button', { name: /Expand/ }); - expect(button).toBeInTheDocument(); - fireEvent.click(button); - expect( - await screen.findByRole('button', { name: /Collapse/ }) - ).toBeInTheDocument(); - }); - - it('should not render a toggle button if overriden', async () => { - const { asFragment } = customRender( - -
- - ); - expect(asFragment()).toMatchSnapshot(); - expect(screen.queryByRole('button')).not.toBeInTheDocument(); - }); -}); diff --git a/src/shared/components/views/__tests__/__snapshots__/DatatableWrapper.spec.tsx.snap b/src/shared/components/views/__tests__/__snapshots__/DatatableWrapper.spec.tsx.snap deleted file mode 100644 index 5f58901df2..0000000000 --- a/src/shared/components/views/__tests__/__snapshots__/DatatableWrapper.spec.tsx.snap +++ /dev/null @@ -1,36 +0,0 @@ -// Jest Snapshot v1, https://goo.gl/fbAQLP - -exports[`DatatableWrapper component should not render a toggle button if overriden 1`] = ` - -
- -
- - - -`; - -exports[`DatatableWrapper component should render with a working toggle button 1`] = ` - -
- -
- - - - -`; diff --git a/src/shared/components/views/styles/datatable-wrapper.scss b/src/shared/components/views/styles/datatable-wrapper.scss deleted file mode 100644 index 098ed5a1ae..0000000000 --- a/src/shared/components/views/styles/datatable-wrapper.scss +++ /dev/null @@ -1,15 +0,0 @@ -protvista-datatable { - margin-bottom: 0.5rem; -} - -protvista-datatable .button { - margin: 0; -} - -.datatable-wrapper { - margin-bottom: 2.5rem; -} - -.toggle-button { - float: right; -} diff --git a/src/shared/components/views/styles/visual-features-view.module.scss b/src/shared/components/views/styles/visual-features-view.module.scss index 00b056c758..c946c22a09 100644 --- a/src/shared/components/views/styles/visual-features-view.module.scss +++ b/src/shared/components/views/styles/visual-features-view.module.scss @@ -1,7 +1,5 @@ -@import 'franklin-sites/src/styles/colours'; - .full-view { float: right; margin-right: 0.5rem; - color: #{$colour-sea-blue}; + color: #{var(--fr--color-sea-blue)}; } diff --git a/src/shared/config/limits.ts b/src/shared/config/limits.ts index 5ebf87d810..73d5fa50e8 100644 --- a/src/shared/config/limits.ts +++ b/src/shared/config/limits.ts @@ -13,3 +13,6 @@ export const MAX_PEPTIDE_FACETS_OR_DOWNLOAD = 1_000; // just because, no actual known limit export const PEPTIDE_SEARCH_SEQ_MINIMUM_LENGTH = 7; export const PEPTIDE_SEARCH_SEQUENCES_COUNT = 100; + +// Feature viewer and variation viewer +export const VARIANT_COUNT_LIMIT = 2_000; diff --git a/src/shared/custom-elements/NightingaleFilter.tsx b/src/shared/custom-elements/NightingaleFilter.tsx new file mode 100644 index 0000000000..1e1a26cb02 --- /dev/null +++ b/src/shared/custom-elements/NightingaleFilter.tsx @@ -0,0 +1,11 @@ +import * as React from 'react'; +import { createComponent } from '@lit/react'; +import NightingaleFilter from '@nightingale-elements/nightingale-filter'; + +export const NightingaleFilterComponent = createComponent({ + tagName: 'nightingale-filter', + elementClass: NightingaleFilter, + react: React, +}); + +export default NightingaleFilterComponent; diff --git a/src/shared/custom-elements/NightingaleManager.tsx b/src/shared/custom-elements/NightingaleManager.tsx new file mode 100644 index 0000000000..49defa360c --- /dev/null +++ b/src/shared/custom-elements/NightingaleManager.tsx @@ -0,0 +1,11 @@ +import * as React from 'react'; +import { createComponent } from '@lit/react'; +import NightingaleManager from '@nightingale-elements/nightingale-manager'; + +export const NightingaleManagerComponent = createComponent({ + tagName: 'nightingale-manager', + elementClass: NightingaleManager, + react: React, +}); + +export default NightingaleManagerComponent; diff --git a/src/shared/custom-elements/NightingaleNavigation.tsx b/src/shared/custom-elements/NightingaleNavigation.tsx new file mode 100644 index 0000000000..708eb908ec --- /dev/null +++ b/src/shared/custom-elements/NightingaleNavigation.tsx @@ -0,0 +1,11 @@ +import * as React from 'react'; +import { createComponent } from '@lit/react'; +import NightingaleNavigation from '@nightingale-elements/nightingale-navigation'; + +export const NightingaleNavigationComponent = createComponent({ + tagName: 'nightingale-navigation', + elementClass: NightingaleNavigation, + react: React, +}); + +export default NightingaleNavigationComponent; diff --git a/src/shared/custom-elements/NightingaleSequence.tsx b/src/shared/custom-elements/NightingaleSequence.tsx new file mode 100644 index 0000000000..58d188ce70 --- /dev/null +++ b/src/shared/custom-elements/NightingaleSequence.tsx @@ -0,0 +1,11 @@ +import * as React from 'react'; +import { createComponent } from '@lit/react'; +import NightingaleSequence from '@nightingale-elements/nightingale-sequence'; + +export const NightingaleSequenceComponent = createComponent({ + tagName: 'nightingale-sequence', + elementClass: NightingaleSequence, + react: React, +}); + +export default NightingaleSequenceComponent; diff --git a/src/shared/custom-elements/NightingaleTrack.tsx b/src/shared/custom-elements/NightingaleTrack.tsx new file mode 100644 index 0000000000..aa7ce51518 --- /dev/null +++ b/src/shared/custom-elements/NightingaleTrack.tsx @@ -0,0 +1,11 @@ +import * as React from 'react'; +import { createComponent } from '@lit/react'; +import NightingaleTrack from '@nightingale-elements/nightingale-track'; + +export const NightingalTrackComponent = createComponent({ + tagName: 'nightingale-track', + elementClass: NightingaleTrack, + react: React, +}); + +export default NightingalTrackComponent; diff --git a/src/shared/custom-elements/NightingaleVariation.tsx b/src/shared/custom-elements/NightingaleVariation.tsx new file mode 100644 index 0000000000..546c2055cd --- /dev/null +++ b/src/shared/custom-elements/NightingaleVariation.tsx @@ -0,0 +1,11 @@ +import * as React from 'react'; +import { createComponent } from '@lit/react'; +import NightingaleVariation from '@nightingale-elements/nightingale-variation'; + +export const NightingaleVariationComponent = createComponent({ + tagName: 'nightingale-variation', + elementClass: NightingaleVariation, + react: React, +}); + +export default NightingaleVariationComponent; diff --git a/src/shared/hooks/useColumns.tsx b/src/shared/hooks/useColumns.tsx index e085475690..ac260417e1 100644 --- a/src/shared/hooks/useColumns.tsx +++ b/src/shared/hooks/useColumns.tsx @@ -4,6 +4,9 @@ import { Dispatch, SetStateAction, useCallback, + useRef, + useEffect, + MutableRefObject, } from 'react'; import { useHistory, useLocation } from 'react-router-dom'; import { BinIcon, Button } from 'franklin-sites'; @@ -20,6 +23,7 @@ import { getSortableColumnToSortColumn, getLocationObjForParams, } from '../../uniprotkb/utils/resultsUtils'; +import { showTooltip } from '../utils/tooltip'; import * as logging from '../utils/logging'; import { mainNamespaces, Namespace } from '../types/namespaces'; @@ -59,6 +63,7 @@ export type ColumnDescriptor = { render: (row: Datum) => ReactNode; sortable?: true; sorted?: SortDirection; + tooltip?: string; }; const convertRow = ( @@ -163,7 +168,11 @@ const useColumns = ( columnsOverride?: ColumnDescriptor[], setSelectedEntries?: Dispatch>, displayPeptideSearchMatchColumns?: boolean -): [ColumnDescriptor[] | undefined, ((columnName: string) => void) | null] => { +): [ + ColumnDescriptor[] | undefined, + ((columnName: string) => void) | null, + MutableRefObject, +] => { const history = useHistory(); const namespace = useNS(namespaceOverride) || Namespace.uniprotkb; const location = useLocation(); @@ -173,6 +182,7 @@ const useColumns = ( displayPeptideSearchMatchColumns, }); const databaseInfoMaps = useDatabaseInfoMaps(); + const tooltipOnHoverRef = useRef(null); const { search: queryParamFromUrl } = location; const [{ query, selectedFacets, sortColumn, sortDirection }] = getParamsFromURL(queryParamFromUrl); @@ -246,6 +256,27 @@ const useColumns = ( setSelectedEntries, ]); + useEffect(() => { + // Detect mouseover events on column header and show tooltip + const onHover = (e: MouseEvent) => { + const eventTarget = e.target as HTMLElement; + const { columnName } = eventTarget.dataset; + if (columns && columnName) { + const info = columns.find(({ name }) => name === columnName); + if (info?.tooltip && eventTarget.firstChild) { + showTooltip( + info.tooltip, + eventTarget, + eventTarget.firstChild as Element + ); + } + } + }; + const wrapper = tooltipOnHoverRef.current; + wrapper?.addEventListener('mouseover', onHover); + return () => wrapper?.removeEventListener('mouseover', onHover); + }); + const updateColumnSort = useCallback( (columnName: string) => { if ( @@ -290,7 +321,7 @@ const useColumns = ( sortableColumnToSortColumn, ] ); - return [columns, updateColumnSort]; + return [columns, updateColumnSort, tooltipOnHoverRef]; }; export default useColumns; diff --git a/src/shared/hooks/useExpandTable.ts b/src/shared/hooks/useExpandTable.ts new file mode 100644 index 0000000000..eb82abbb27 --- /dev/null +++ b/src/shared/hooks/useExpandTable.ts @@ -0,0 +1,67 @@ +import { useState, useRef, useEffect, useLayoutEffect } from 'react'; +import { useParams } from 'react-router-dom'; + +import { sendGtagEventFeatureDataTableViewClick } from '../utils/gtagEvents'; + +const useExpandTable = ( + expandable?: boolean +): [ + containerRef: React.RefObject, + expandTable: boolean | null, + setExpandTable: React.Dispatch>, + showButton: boolean +] => { + const [showButton, setShowButton] = useState(Boolean(expandable)); + const [expandTable, setExpandTable] = useState(null); + const params = useParams<{ accession?: string }>(); + const containerRef = useRef(null); + const firstRenderRef = useRef(true); + // On expand/collapse change + useEffect(() => { + // except on first render or when always expanded + if (expandable && !firstRenderRef.current) { + // Scroll table back into view when collapsing + if (expandTable === false) { + containerRef.current?.parentElement?.scrollIntoView({ + behavior: 'smooth', + block: 'center', + }); + } + sendGtagEventFeatureDataTableViewClick( + params.accession || '', + expandTable ? 'expanded' : 'collapsed' + ); + } + // If first render was previous render, then it's not the first anymore... + if (firstRenderRef.current) { + firstRenderRef.current = false; + } + }, [expandable, expandTable, params.accession]); + + // Only show expand button if expandable=true and there is more content that the container + // eslint-disable-next-line consistent-return + useLayoutEffect(() => { + if (expandable && containerRef.current) { + const mo = new MutationObserver(() => { + setShowButton( + expandTable || + (containerRef.current !== null && + containerRef.current.scrollHeight > + containerRef.current.clientHeight) + ); + }); + mo.observe(containerRef.current, { + childList: true, + // Allows to update when classes are applied to hide some rows + attributes: true, + attributeFilter: ['class'], + subtree: true, + }); + return () => mo.disconnect(); + } + }, [expandTable, expandable]); + + return [containerRef, expandTable, setExpandTable, showButton]; +}; + +export default useExpandTable; diff --git a/src/shared/hooks/useNightingaleFeatureTableScroll.ts b/src/shared/hooks/useNightingaleFeatureTableScroll.ts new file mode 100644 index 0000000000..0e890d7c5e --- /dev/null +++ b/src/shared/hooks/useNightingaleFeatureTableScroll.ts @@ -0,0 +1,38 @@ +import { useCallback } from 'react'; + +function useNightingaleFeatureTableScroll( + getRowId: (feature: T) => string, + tableId: string +) { + return useCallback( + (feature: T) => { + // Select elements based on the feature and tableId + const rowSelector = `tr[data-id="${getRowId(feature)}"]`; + const tableSelector = `table[id="${tableId}"]`; + const row = document.querySelector(rowSelector); + const table = document.querySelector(tableSelector); + + if (!row || !table) { + return; // If we don't have a target row or table, bail early + } + + // Identify table parts and related elements + const thead = table.firstElementChild as HTMLElement | null; + const container = table.parentElement; + + // Determine scroll positioning behavior: use nearest if we can offset + // for the sticky header height, otherwise fallback to center + let block: ScrollLogicalPosition = 'center'; + if (container && thead) { + // Adjust container to account for the sticky header height + container.style.scrollPaddingTop = `${thead.offsetHeight}px`; + block = 'nearest'; + } + + row.scrollIntoView({ behavior: 'smooth', block }); + }, + [getRowId, tableId] + ); +} + +export default useNightingaleFeatureTableScroll; diff --git a/src/shared/types/columnConfiguration.ts b/src/shared/types/columnConfiguration.ts index 719c4937a4..74fe4366ae 100644 --- a/src/shared/types/columnConfiguration.ts +++ b/src/shared/types/columnConfiguration.ts @@ -2,7 +2,7 @@ import { ReactNode } from 'react'; export type ColumRenderer> = { label: ReactNode; - tooltip?: ReactNode; + tooltip?: string; // HTML string which is set with innerHTML // Exclude plain objects as it wouldn't detect an issue when returning // objects to React for rendering render: (data: Schema) => Exclude>; diff --git a/src/shared/utils/getLabelAndTooltip.tsx b/src/shared/utils/getLabelAndTooltip.tsx index 52532fda13..db905bcace 100644 --- a/src/shared/utils/getLabelAndTooltip.tsx +++ b/src/shared/utils/getLabelAndTooltip.tsx @@ -2,20 +2,17 @@ import { ReactNode } from 'react'; const getLabelAndTooltip = ( label: ReactNode, - tooltip: ReactNode, + tooltip: string, articleId?: string ) => ({ label: {label}, - tooltip: ( - <> - {tooltip} - {articleId && ( -
+ tooltip: `${tooltip}${ + articleId + ? `
more -
- )} - - ), +
` + : '' + }`, }); export default getLabelAndTooltip; diff --git a/src/shared/utils/nightingale.ts b/src/shared/utils/nightingale.ts new file mode 100644 index 0000000000..1143aa7bb7 --- /dev/null +++ b/src/shared/utils/nightingale.ts @@ -0,0 +1,34 @@ +import { ProcessedFeature } from '../components/views/FeaturesView'; + +export type NightingaleViewRange = { + 'display-start': number; + 'display-end': number; +}; + +export const withinRange = ( + featureStart: number, + featureEnd: number, + nightingaleViewRange?: NightingaleViewRange +) => + nightingaleViewRange + ? (nightingaleViewRange['display-start'] <= featureStart && + featureStart <= nightingaleViewRange['display-end']) || + (nightingaleViewRange['display-start'] <= featureEnd && + featureEnd <= nightingaleViewRange['display-end']) + : true; + +export const getRowId = (data: ProcessedFeature) => data.accession; + +export const markBackground = (markedData: ProcessedFeature) => { + const markedId = getRowId(markedData); + return typeof markedId === 'undefined' + ? undefined + : (data: ProcessedFeature) => { + const rowId = getRowId(data); + return Boolean(rowId && rowId === markedId); + }; +}; + +export const markBorder = + (nightingaleViewRange: NightingaleViewRange) => (datum: ProcessedFeature) => + withinRange(datum.start, datum.end, nightingaleViewRange); diff --git a/src/shared/utils/styles/tooltip.module.scss b/src/shared/utils/styles/tooltip.module.scss new file mode 100644 index 0000000000..3d522589c7 --- /dev/null +++ b/src/shared/utils/styles/tooltip.module.scss @@ -0,0 +1,51 @@ +@import 'franklin-sites/src/styles/common/z-index'; + +.tooltip { + max-width: 350px; + position: absolute; + background: #333; + background-color: #333; + color: #fff; + border-radius: 4px; + font-size: 14px; + top: 0; + left: 0; + z-index: $z-index-high; + + .tooltip-content { + max-height: 400px; + padding: 5px 9px; + line-height: 1.4; + white-space: normal; + overflow-y: auto; + } + + * { + color: #fff !important; + } + + a { + text-decoration: underline; + } + + p { + margin-bottom: 1rem; + } + + ul { + line-height: 1.4; + } + + hr { + margin-bottom: 0.5rem; + } +} + +.arrow { + position: absolute; + background: #333; + width: 8px; + height: 8px; + transform: rotate(45deg); + z-index: $z-index-high; +} diff --git a/src/shared/utils/tooltip.ts b/src/shared/utils/tooltip.ts new file mode 100644 index 0000000000..e5e09e7b87 --- /dev/null +++ b/src/shared/utils/tooltip.ts @@ -0,0 +1,182 @@ +import { + computePosition, + flip, + shift, + offset, + arrow, + autoUpdate, +} from '@floating-ui/dom'; + +import styles from './styles/tooltip.module.scss'; + +type StaticSide = 'bottom' | 'left' | 'top' | 'right'; + +const getTooltip = (content: string) => { + const tooltip = document.createElement('div'); + tooltip.setAttribute('role', 'tooltip'); + tooltip.className = styles.tooltip; + const tooltipContent = document.createElement('div'); + tooltipContent.className = styles['tooltip-content']; + tooltipContent.innerHTML = content; + tooltip.appendChild(tooltipContent); + const arrowElement = document.createElement('div'); + arrowElement.className = styles.arrow; + tooltip.appendChild(arrowElement); + return [tooltip, arrowElement]; +}; + +const getUpdate = + (reference: Element, tooltip: HTMLElement, arrowElement: HTMLElement) => + () => { + computePosition(reference, tooltip, { + placement: 'top', + middleware: [ + offset(10), + flip(), + shift({ padding: 10 }), + arrow({ element: arrowElement }), + ], + }).then(({ x: tooltipX, y: tooltipY, placement, middlewareData }) => { + Object.assign(tooltip.style, { + left: `${tooltipX}px`, + top: `${tooltipY}px`, + }); + const { x: arrowX, y: arrowY } = middlewareData.arrow || {}; + const staticSide = { + top: 'bottom', + right: 'left', + bottom: 'top', + left: 'right', + }[placement.split('-')[0]] as StaticSide; + + Object.assign(arrowElement.style, { + left: arrowX != null ? `${arrowX}px` : '', + top: arrowY != null ? `${arrowY}px` : '', + right: '', + bottom: '', + [staticSide]: '-4px', + }); + }); + }; + +export const addTooltip = ( + target: Element, + content: string, + triggers?: Element[] +) => { + const [tooltip, arrowElement] = getTooltip(content); + const update = getUpdate(target, tooltip, arrowElement); + let cleanup: ReturnType | undefined; + function showTooltip() { + document.body.append(tooltip); + cleanup = autoUpdate(target, tooltip, update); + } + function hideTooltip() { + tooltip.remove(); + cleanup?.(); + } + const eventsAndListeners: [string, () => void][] = [ + ['mouseenter', showTooltip], + ['focus', showTooltip], + ['mouseleave', hideTooltip], + ['blur', hideTooltip], + ]; + const allTriggers = [target, ...(triggers || [])]; + eventsAndListeners.forEach(([event, listener]) => { + allTriggers.forEach((trigger) => { + trigger.addEventListener(event, listener); + }); + }); + + // Return cleanup function to remove tooltip and remove event listeners + return () => { + hideTooltip(); + eventsAndListeners.forEach(([event, listener]) => { + allTriggers.forEach((trigger) => { + trigger.removeEventListener(event, listener); + }); + }); + }; +}; + +export const showTooltip = ( + content: string, + target: Element, + displayTarget: Element +) => { + const [tooltip, arrowElement] = getTooltip(content); + const update = getUpdate(displayTarget, tooltip, arrowElement); + const cleanup = autoUpdate(displayTarget, tooltip, update); + document.body.append(tooltip); + let timeoutId: ReturnType | null = null; + + function onLeave() { + // Start a timer when the mouse has left either the target or the tooltip + timeoutId = setTimeout(() => { + hideTooltip(); + }, 50); + } + + function onEnterTooltip() { + // Cancel the timer if user enters the tooltip to keep it visible + if (timeoutId) { + clearTimeout(timeoutId); + } + } + + function hideTooltip() { + cleanup?.(); + tooltip.remove(); + target.removeEventListener('mouseleave', onLeave); + tooltip.removeEventListener('mouseleave', onLeave); + tooltip.removeEventListener('mouseenter', onEnterTooltip); + } + + target.addEventListener('mouseleave', onLeave); + tooltip.addEventListener('mouseleave', onLeave); + tooltip.addEventListener('mouseenter', onEnterTooltip); +}; + +export const showTooltipAtCoordinates = ( + x: number, + y: number, + content: string +) => { + const [tooltip, arrowElement] = getTooltip(content); + const reference = { + getBoundingClientRect() { + return { + x: 0, + y: 0, + top: y, + left: x, + bottom: 0, + right: 0, + width: 0, + height: 0, + }; + }, + } as Element; + + const update = getUpdate(reference, tooltip, arrowElement); + const cleanup = autoUpdate(reference, tooltip, update); + + document.body.append(tooltip); + document.body.addEventListener('click', interactionHandler, true); + document.body.addEventListener('scroll', interactionHandler, true); + document.body.addEventListener('wheel', interactionHandler, true); + + function interactionHandler(e?: Event) { + const target = e?.target as Node | null; + // if scroll/wheel is within the tooltip element, do not remove the tooltip + if (target && !tooltip.contains(target)) { + tooltip?.remove(); + cleanup?.(); + document.body.removeEventListener('click', interactionHandler, true); + document.body.removeEventListener('scroll', interactionHandler, true); + document.body.removeEventListener('wheel', interactionHandler, true); + } + } + + return interactionHandler; +}; diff --git a/src/tools/align/utils/useSequenceInfo.ts b/src/tools/align/utils/useSequenceInfo.ts index 21ab8078cc..48ff4e73cd 100644 --- a/src/tools/align/utils/useSequenceInfo.ts +++ b/src/tools/align/utils/useSequenceInfo.ts @@ -110,7 +110,9 @@ const useSequenceInfo = (rawSequences?: string): SequenceInfo => { const sequencedAndFeatures = { sequence: sequence.value, features: processUniProtKBFeaturesData( - removeFeaturesWithUnknownModifier(features) + removeFeaturesWithUnknownModifier(features), + primaryAccession, + sequence.value ), }; idToSequenceAndFeatures.set(primaryAccession, sequencedAndFeatures); diff --git a/src/tools/blast/components/results/BlastResultTable.tsx b/src/tools/blast/components/results/BlastResultTable.tsx index cb2e4f9346..9f25b786e0 100644 --- a/src/tools/blast/components/results/BlastResultTable.tsx +++ b/src/tools/blast/components/results/BlastResultTable.tsx @@ -9,12 +9,13 @@ import { } from 'react'; import { DataTable, Chip, Loader, Button } from 'franklin-sites'; import cn from 'classnames'; +import { v1 } from 'uuid'; import { Except } from 'type-fest'; +import NightingaleTrack from '@nightingale-elements/nightingale-track'; import { HSPDetailPanelProps } from './HSPDetailPanel'; import useStaggeredRenderingHelper from '../../../../shared/hooks/useStaggeredRenderingHelper'; -import useCustomElement from '../../../../shared/hooks/useCustomElement'; import useColumns, { ColumnDescriptor, } from '../../../../shared/hooks/useColumns'; @@ -28,6 +29,8 @@ import { UniProtkbAPIModel } from '../../../../uniprotkb/adapters/uniProtkbConve import { UniRefLiteAPIModel } from '../../../../uniref/adapters/uniRefConverter'; import { UniParcAPIModel } from '../../../../uniparc/adapters/uniParcConverter'; import NoResultsPage from '../../../../shared/components/error-pages/full-pages/NoResultsPage'; +import NightingalTrackComponent from '../../../../shared/custom-elements/NightingaleTrack'; +import NightingaleNavigationComponent from '../../../../shared/custom-elements/NightingaleNavigation'; const scoringDict: Partial> = { hsp_identity: 'Identity', @@ -41,14 +44,6 @@ const scoringColorDict: Partial> = { hsp_expect: 'var(--fr--color-outer-space)', }; -type TrackNodeData = { - start: number; - end: number; - color: string | undefined; - shape?: string; - opacity?: number; -}; - type BlastSummaryTrackProps = { hsp: BlastHsp; queryLength: number; @@ -72,15 +67,9 @@ const BlastSummaryTrack = ({ }: BlastSummaryTrackProps) => { const { hsp_query_from, hsp_query_to } = hsp; - const trackElement = useCustomElement( - /* istanbul ignore next */ - () => import(/* webpackChunkName: "protvista-track" */ 'protvista-track'), - 'protvista-track' - ); - const setTrackData = useCallback( - (node: { data: TrackNodeData[] }): void => { - if (node && trackElement.defined) { + (node: NightingaleTrack | null): void => { + if (node) { /** * TODO - would be nice to add gaps * at some point @@ -108,18 +97,21 @@ const BlastSummaryTrack = ({ // eslint-disable-next-line no-param-reassign node.data = [ { + accession: v1().toString(), start: 1, end: hsp.hsp_query_from, shape: 'line', color, }, { + accession: v1().toString(), start: hsp.hsp_query_from, end: hsp.hsp_query_to, color, opacity, }, { + accession: v1().toString(), start: hsp.hsp_query_to, end: hitLength > hsp.hsp_query_to ? hitLength : hsp.hsp_query_to, shape: 'line', @@ -128,13 +120,13 @@ const BlastSummaryTrack = ({ ]; } }, - [trackElement.defined, hsp, selectedScoring, hitLength, maxScorings] + [hsp, selectedScoring, hitLength, maxScorings] ); return (
- void; @@ -281,32 +271,6 @@ const BlastResultTable = ({ : undefined ); - const navigationElement = useCustomElement( - /* istanbul ignore next */ - () => - import( - /* webpackChunkName: "protvista-navigation" */ 'protvista-navigation' - ), - 'protvista-navigation' - ); - - // The "query" column header - const queryColumnHeaderRef = useCallback( - (node: { data: QueryNodeData[] }) => { - if (node && navigationElement.defined && data) { - const { query_len } = data; - // eslint-disable-next-line no-param-reassign - node.data = [ - { - start: 1, - end: query_len, - }, - ]; - } - }, - [data, navigationElement.defined] - ); - const maxScorings = useMemo>>(() => { if (!data?.hits) { return { hsp_identity: 100, hsp_score: 1, hsp_expect: 1 }; @@ -333,7 +297,6 @@ const BlastResultTable = ({ }, [data]); const queryLen = data?.query_len; - const NavigationElementName = navigationElement.name; const [columns] = useColumns(namespace); // Disable sorting, as we want to keep the BLAST sorting (for now...); @@ -343,10 +306,12 @@ const BlastResultTable = ({ const trackColumn = { label: (
-
), diff --git a/src/tools/blast/components/results/HSPDetailPanel.tsx b/src/tools/blast/components/results/HSPDetailPanel.tsx index 981c9ab802..11439203d6 100644 --- a/src/tools/blast/components/results/HSPDetailPanel.tsx +++ b/src/tools/blast/components/results/HSPDetailPanel.tsx @@ -64,7 +64,9 @@ const convertHSPtoMSAInputs = ( features: extra && 'features' in extra ? processFeaturesData( - removeFeaturesWithUnknownModifier(extra.features) + removeFeaturesWithUnknownModifier(extra.features), + hitAccession, + hsp_hseq ) : [], }, diff --git a/src/tools/blast/components/results/__tests__/__snapshots__/BlastResultTable.spec.tsx.snap b/src/tools/blast/components/results/__tests__/__snapshots__/BlastResultTable.spec.tsx.snap index 58eb849c43..285b56030f 100644 --- a/src/tools/blast/components/results/__tests__/__snapshots__/BlastResultTable.spec.tsx.snap +++ b/src/tools/blast/components/results/__tests__/__snapshots__/BlastResultTable.spec.tsx.snap @@ -67,90 +67,77 @@ exports[`BlastResultTable tests should render, and toggle the extra HSPs 1`] = `
diff --git a/src/uniparc/components/entry/styles/Timeline.module.scss b/src/uniparc/components/entry/styles/Timeline.module.scss index 7251d4e5aa..5c55b26e2b 100644 --- a/src/uniparc/components/entry/styles/Timeline.module.scss +++ b/src/uniparc/components/entry/styles/Timeline.module.scss @@ -1,16 +1,14 @@ -@import 'franklin-sites/src/styles/colours'; - .container { position: relative; height: 1em; min-width: 5em; - background: $colour-sea-blue; + background: var(--fr--color-sea-blue); } .xref { height: inherit; position: absolute; - background: $colour-uniparc; + background: var(--fr--color-uniparc); width: 50%; left: 25%; } diff --git a/src/uniprotkb/adapters/functionConverter.ts b/src/uniprotkb/adapters/functionConverter.ts index a5a84f54cb..ed45ad2801 100644 --- a/src/uniprotkb/adapters/functionConverter.ts +++ b/src/uniprotkb/adapters/functionConverter.ts @@ -138,6 +138,7 @@ export const functionFeaturesToColumns: Readonly< 'DNA binding': UniProtKBColumn.ftDnaBind, 'Active site': UniProtKBColumn.ftActSite, 'Binding site': UniProtKBColumn.ftBinding, + BINDING: UniProtKBColumn.ftBinding, Site: UniProtKBColumn.ftSite, }; diff --git a/src/uniprotkb/components/entry/GoRibbon.tsx b/src/uniprotkb/components/entry/GoRibbon.tsx index 6df20aeaff..a43831396d 100644 --- a/src/uniprotkb/components/entry/GoRibbon.tsx +++ b/src/uniprotkb/components/entry/GoRibbon.tsx @@ -6,7 +6,6 @@ import ExternalLink from '../../../shared/components/ExternalLink'; import UniProtKBEvidenceTag from '../protein-data-views/UniProtKBEvidenceTag'; import GOTermEvidenceTag from '../protein-data-views/GOTermEvidenceTag'; import LazyComponent from '../../../shared/components/LazyComponent'; -import DatatableWrapper from '../../../shared/components/views/DatatableWrapper'; import useSafeState from '../../../shared/hooks/useSafeState'; import { useSmallScreen } from '../../../shared/hooks/useMatchMedia'; @@ -15,7 +14,11 @@ import useDatabaseInfoMaps from '../../../shared/hooks/useDatabaseInfoMaps'; import { getUrlFromDatabaseInfo } from '../../../shared/utils/xrefs'; import externalUrls from '../../../shared/config/externalUrls'; -import { GOTermID, GroupedGoTerms } from '../../adapters/functionConverter'; +import { + GoTerm, + GOTermID, + GroupedGoTerms, +} from '../../adapters/functionConverter'; import { AGRRibbonGroup, AGRRibbonSubject, @@ -28,6 +31,42 @@ import { TaxonomyDatum } from '../../../supporting-data/taxonomy/adapters/taxono import { UniProtKBSimplifiedTaxonomy } from '../../adapters/uniProtkbConverter'; import styles from './styles/go-ribbon.module.scss'; +import TableFromData, { + TableFromDataColumn, +} from '../../../shared/components/table/TableFromData'; + +const useColumns = () => { + const databaseInfoMaps = useDatabaseInfoMaps(); + + const columns: TableFromDataColumn[] = [ + { + id: 'aspect', + label: 'Aspect', + render: (data) => data.aspect, + }, + { + id: 'term', + label: 'Term', + render: (data) => ( + <> + + {data.termDescription || data.id} + + + + + ), + }, + ]; + + return columns; +}; + +const getRowId = (data: GoTerm) => data.id; type CellClick = { detail: { @@ -44,7 +83,7 @@ type GroupClick = { }; }; -type GoRibbonType = { +type GoRibbonProps = { primaryAccession: string; goTerms?: GroupedGoTerms; geneNamesData?: GeneNamesData; @@ -56,9 +95,9 @@ const GoRibbon = ({ goTerms, geneNamesData, organismData, -}: GoRibbonType) => { +}: GoRibbonProps) => { const isSmallScreen = useSmallScreen(); - const databaseInfoMaps = useDatabaseInfoMaps(); + const columns = useColumns(); const nodeRef = useRef(); @@ -217,43 +256,6 @@ const GoRibbon = ({ ); } - const table = ( -
- -
-
@@ -210,10 +197,9 @@ exports[`BlastResultTable tests should render, and toggle the extra HSPs 1`] = `
-
-
-
- - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + min-height="10" + min-width="10" + style="display: inline-block; line-height: 0; width: 100%; height: 100%;" + > + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
- + min-height="10" + min-width="10" + style="display: inline-block; line-height: 0; width: 100%; height: 100%;" + > + + + + + + + + + + + + + + + +
- - - + +
{ - const trackElement = useCustomElement( - /* istanbul ignore next */ - () => import(/* webpackChunkName: "protvista-track" */ 'protvista-track'), - 'protvista-track' - ); - const setTrackData = useCallback( - (node: { data: SegmentTrackData[] }): void => { - if (node && trackElement.defined) { + (node: { data: Feature[] } | null): void => { + if (node) { // eslint-disable-next-line no-param-reassign node.data = data; } }, - [data, trackElement.defined] + [data] ); return ( - ); }; const AlignmentOverview = memo( - ({ height, data, length, highlight }: AlignmentOverviewProps) => { - if (!data?.length) { - return null; - } - - const singleTrackHeight = Math.floor(parseInt(height, 10) / data.length); - - return ( + ({ trackHeight, data, length, highlight }: AlignmentOverviewProps) => + !data?.length ? null : (
{data.map((trackData, index) => ( ))}
- ); - } + ) ); export default AlignmentOverview; diff --git a/src/tools/components/AlignmentView.tsx b/src/tools/components/AlignmentView.tsx index da029b4d6b..faaf4213ad 100644 --- a/src/tools/components/AlignmentView.tsx +++ b/src/tools/components/AlignmentView.tsx @@ -1,6 +1,6 @@ import { useState, useEffect, useMemo, useRef, useCallback } from 'react'; -import { TreeSelect, Loader } from 'franklin-sites'; -import { formatTooltip } from 'protvista-feature-adapter'; +import { TreeSelect } from 'franklin-sites'; +import { getFeatureTooltip } from 'protvista-uniprot'; import Wrapped from './Wrapped'; import Overview from './Overview'; @@ -11,7 +11,6 @@ import { msaColorSchemeToString, } from '../config/msaColorSchemes'; -import useCustomElement from '../../shared/hooks/useCustomElement'; import { findSequenceFeature, getFullAlignmentLength, @@ -19,6 +18,7 @@ import { MSAFeature, } from '../utils/sequences'; import { prepareFeatureForTooltip } from '../utils/feature'; +import { showTooltipAtCoordinates } from '../../shared/utils/tooltip'; import FeatureType from '../../uniprotkb/types/featureType'; import { @@ -79,18 +79,9 @@ const AlignmentView = ({ handleEntrySelection, containerSelector, }: AlignmentViewProps) => { - const [tooltipContent, setTooltipContent] = useState<{ - __html: string; - } | null>(); - const tooltipRef = useRef(); - - const tooltipElement = useCustomElement( - /* istanbul ignore next */ - () => - import(/* webpackChunkName: "protvista-tooltip" */ 'protvista-tooltip'), - 'protvista-tooltip' - ); - + const hideTooltip = useRef | null>(null); const annotationChoices = useMemo(() => { const features = alignment .map(({ features }) => features) @@ -159,6 +150,13 @@ const AlignmentView = ({ } }, [annotation, annotationChoices]); + useEffect( + () => () => { + hideTooltip.current?.(); + }, + [] + ); + const selectedMSAFeatures = useMemo( // This gets the features to display on all of the MSA sequences (ie not // just the active. Notice the final filter(Boolean), this is to remove @@ -218,30 +216,12 @@ const AlignmentView = ({ setActiveId(accession); }, []); - const tooltipCloseCallback = useCallback( - (e: Event) => { - // If click is inside of the tooltip, don't do anything - if (tooltipRef.current.contains(e.target)) { - return; - } - - setTooltipContent(null); - }, - [setTooltipContent] - ); - - if (tooltipRef?.current) { - tooltipRef.current.container = containerSelector; - } - const updateTooltip: UpdateTooltip = useCallback( ({ id, x, y }) => { const sequenceFeature = findSequenceFeature(id, alignment); - if (!sequenceFeature) { return; } - const preparedFeature = prepareFeatureForTooltip(sequenceFeature); let yOffset = 0; if (containerSelector) { @@ -251,10 +231,15 @@ const AlignmentView = ({ yOffset = rect.y; } } - tooltipRef.current.title = `${preparedFeature.type} ${preparedFeature.start}-${preparedFeature.end}`; - setTooltipContent({ __html: formatTooltip(preparedFeature) }); - tooltipRef.current.x = x; - tooltipRef.current.y = y - yOffset; + const title = + preparedFeature.type && preparedFeature.start && preparedFeature.end + ? `

${preparedFeature.type} ${preparedFeature.start}-${preparedFeature.end}

` + : ''; + hideTooltip.current = showTooltipAtCoordinates( + x, + y - yOffset, + `${title}${getFeatureTooltip(preparedFeature)}` + ); }, [alignment, containerSelector] ); @@ -271,53 +256,8 @@ const AlignmentView = ({ [updateTooltip] ); - useEffect(() => { - if (tooltipContent) { - window.addEventListener('click', tooltipCloseCallback, true); - } else { - window.removeEventListener('click', tooltipCloseCallback, true); - } - - return () => - window.removeEventListener('click', tooltipCloseCallback, true); - }, [tooltipCloseCallback, tooltipContent]); - - // Need to listen for scroll events to close the tooltip to prevent - // it from persisting and giving the appearance of floating, unanchored. - // Can see this in the Wrapped view specifically when the number of rows - // causes the page to scroll. - const mainContentAndFooter = useMemo(() => { - const className = '.main-content-and-footer'; - const el = document.querySelector(className); - // tooltip is here but main-content-and-footer isn't - if (tooltipRef.current && !el) { - throw Error(`Cannot find :${className}`); - } - return el; - }, [tooltipRef]); - - useEffect(() => { - if (!(mainContentAndFooter && 'addEventListener' in mainContentAndFooter)) { - return; - } - const handler = () => { - setTooltipContent(null); - }; - mainContentAndFooter.addEventListener('scroll', handler, { passive: true }); - // eslint-disable-next-line consistent-return - return () => { - mainContentAndFooter.removeEventListener('scroll', handler); - }; - }, [mainContentAndFooter]); - - const tooltipVisibility = tooltipContent ? { visible: true } : {}; - const defaultActiveNodes = useMemo(() => [MsaColorScheme.CONSERVATION], []); - if (!tooltipElement.defined) { - return ; - } - return ( <>
@@ -376,12 +316,6 @@ const AlignmentView = ({
- { const containerRef = useRef(null); - const navigationRef = useRef(null); const [highlightPosition, setHighlightPosition] = useState(''); const [initialDisplayEnd, setInitialDisplayEnd] = useState< number | undefined @@ -58,7 +64,10 @@ const AlignOverview = ({ >([undefined, undefined]); const tracksOffset = Math.max(...alignment.map(({ from }) => from)); const findHighlightPositions = useCallback( - ({ displaystart, displayend }: EventDetail) => { + ({ + 'display-start': displaystart, + 'display-end': displayend, + }: EventDetail) => { if ( typeof displaystart === 'undefined' || typeof displayend === 'undefined' @@ -98,23 +107,21 @@ const AlignOverview = ({ }, [alignment, initialDisplayEnd] ); + const navigationRef = useCallback( + (node: NightingaleNavigation) => { + if (node && initialDisplayEnd) { + node['display-start'] = 1; + node['display-end'] = initialDisplayEnd; + } + }, + [initialDisplayEnd] + ); const managerRef = useCallback( - (node: { - addEventListener: ( - name: 'change', - event: ({ detail }: { detail: EventDetail }) => void - ) => void; - setAttribute: ( - attributre: 'displaystart' | 'displayend' | 'height', - value: number - ) => void; - }): void => { + (node: NightingaleManager | null): void => { if (node && initialDisplayEnd) { - node.addEventListener('change', ({ detail }: { detail: EventDetail }) => - findHighlightPositions(detail) + node.addEventListener('change', (event) => + findHighlightPositions((event as CustomEvent).detail) ); - node.setAttribute('displaystart', 1); - node.setAttribute('displayend', initialDisplayEnd); setHighlightPosition( (highlight) => highlight || `${tracksOffset}:${tracksOffset + initialDisplayEnd}` @@ -124,9 +131,6 @@ const AlignOverview = ({ [initialDisplayEnd, findHighlightPositions, tracksOffset] ); - const navigationHeight = - navigationRef.current?.getClientRects()?.[0]?.height || 0; - useEffect(() => { const handler = handleEvent(updateTooltip) as (e: Event) => void; const element = containerRef?.current; @@ -136,50 +140,28 @@ const AlignOverview = ({ }; }, [updateTooltip]); - const trackElement = useCustomElement( - /* istanbul ignore next */ - () => import(/* webpackChunkName: "protvista-track" */ 'protvista-track'), - 'protvista-track' - ); - const navigationElement = useCustomElement( - /* istanbul ignore next */ - () => - import( - /* webpackChunkName: "protvista-navigation" */ 'protvista-navigation' - ), - 'protvista-navigation' - ); - const managerElement = useCustomElement( - /* istanbul ignore next */ - () => - import(/* webpackChunkName: "protvista-manager" */ 'protvista-manager'), - 'protvista-manager' - ); - const ceDefined = - trackElement.defined && navigationElement.defined && managerElement.defined; - const setFeatureTrackData = useCallback( - (node: { data: ReturnType[] }): void => { - if (node && ceDefined && activeAnnotation && activeAlignment?.sequence) { + (node: NightingaleTrack | null): void => { + if (node && activeAnnotation && activeAlignment?.sequence) { node.data = activeAnnotation // The Overview feature track always starts from the start of the protein // hence the need to have `from` := 1 .map((f) => createGappedFeature(f, activeAlignment?.sequence, 1)) - .filter(Boolean); + .filter((f): f is Feature => Boolean(f)); } }, - [activeAlignment?.sequence, activeAnnotation, ceDefined] + [activeAlignment?.sequence, activeAnnotation] ); - const overviewHeight = ( - alignment && alignment.length > 10 ? alignment.length * 3 : 30 - ).toString(); - const alignmentOverviewData = useMemo( () => (alignment ? getFullAlignmentSegments(alignment) : []), [alignment] ); + const overviewHeight = + alignment && alignment.length > 10 ? alignment.length * 3 : 30; + const trackHeight = Math.floor(overviewHeight / alignmentOverviewData.length); + useEffect(() => { const displayEndValue = Math.round(alignmentLength / widthOfAA); const maxSequenceLength = Math.max( @@ -190,10 +172,6 @@ const AlignOverview = ({ } }, [alignmentLength, alignment, displayPosition]); - if (!ceDefined) { - return ; - } - return (
Overview
{annotation && ( - )}
@@ -244,23 +224,15 @@ const AlignOverview = ({ ))}
-
- + - - +
{alignment.map((s) => ( @@ -287,7 +257,7 @@ const AlignOverview = ({ s.sequence, displayPosition[1] ?? initialDisplayEnd ?? 0 ) - : displayPosition[1] ?? initialDisplayEnd ?? 0 + : (displayPosition[1] ?? initialDisplayEnd ?? 0) )}
))} diff --git a/src/tools/components/Wrapped.tsx b/src/tools/components/Wrapped.tsx index a4df69e1d5..7ee35dc719 100644 --- a/src/tools/components/Wrapped.tsx +++ b/src/tools/components/Wrapped.tsx @@ -9,13 +9,16 @@ import { lazy, } from 'react'; import { debounce } from 'lodash-es'; -import { Loader } from 'franklin-sites'; - import { Region } from '@nightingale-elements/nightingale-msa'; +import NightingaleTrack, { + Feature, +} from '@nightingale-elements/nightingale-track'; + +import NightingalTrackComponent from '../../shared/custom-elements/NightingaleTrack'; + import useSize from '../../shared/hooks/useSize'; import useSafeState from '../../shared/hooks/useSafeState'; import useStaggeredRenderingHelper from '../../shared/hooks/useStaggeredRenderingHelper'; -import useCustomElement from '../../shared/hooks/useCustomElement'; import { MsaColorScheme } from '../config/msaColorSchemes'; @@ -90,9 +93,9 @@ export const handleEvent = (updateTooltip: UpdateTooltip) => (event: CustomEvent) => { event.stopPropagation(); - if (event?.detail?.eventtype === 'click') { + if (event?.detail?.eventType === 'click') { updateTooltip({ - id: event.detail.feature.protvistaFeatureId, + id: event.detail.feature.accession, x: event.detail.coords[0], y: event.detail.coords[1], }); @@ -117,15 +120,9 @@ export const WrappedRow = ({ onMSAFeatureClick, lastRow, }: WrappedRowProps) => { - const trackElement = useCustomElement( - /* istanbul ignore next */ - () => import(/* webpackChunkName: "protvista-track" */ 'protvista-track'), - 'protvista-track' - ); - const setFeatureTrackData = useCallback( - (node: { data: ReturnType[] }): void => { - if (node && trackElement.defined && activeAlignment?.sequence) { + (node: NightingaleTrack | null): void => { + if (node && activeAlignment?.sequence) { node.data = activeAnnotation .map((f) => createGappedFeature( @@ -136,12 +133,12 @@ export const WrappedRow = ({ activeAlignment?.from ) ) - .filter(Boolean); + .filter((f): f is Feature => Boolean(f)); } }, // TODO: replace this with fragments to have one big grid // -> to keep the right column of the right size to fit all possible values - [activeAlignment, activeAnnotation, trackElement.defined] + [activeAlignment, activeAnnotation] ); // Using just the sequences resulted in occassional off by one errors so do this only for @@ -183,10 +180,6 @@ export const WrappedRow = ({ [length, selectedMSAFeatures, sequences, trackStart, width] ); - if (!trackElement.defined) { - return ; - } - return ( <>
{annotation && !delayRender && ( - )}
diff --git a/src/tools/components/__mocks__/featureShapesMocks.json b/src/tools/components/__mocks__/featureShapesMocks.json deleted file mode 100644 index 68f8489a8f..0000000000 --- a/src/tools/components/__mocks__/featureShapesMocks.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "BLAST": { - "length": 751, - "highlight": "41:125", - "data": [ - [ - { - "start": 40, - "end": 40, - "shape": "line", - "color": "#014371", - "locations": [ - { - "fragments": [ - { - "start": 40, - "end": 40 - } - ] - } - ] - }, - { - "start": 41, - "end": 267, - "color": "#014371", - "locations": [ - { - "fragments": [ - { - "start": 41, - "end": 267 - } - ] - } - ] - }, - { - "start": 268, - "end": 582, - "shape": "line", - "color": "#014371", - "locations": [ - { - "fragments": [ - { - "start": 268, - "end": 582 - } - ] - } - ] - } - ], - [ - { - "start": 0, - "end": 40, - "shape": "line", - "color": "#014371" - }, - { - "start": 41, - "end": 267, - "color": "#014371" - }, - { - "start": 268, - "end": 751, - "shape": "line", - "color": "#014371" - } - ] - ] - } -} diff --git a/src/tools/components/__mocks__/featureShapesMocks.ts b/src/tools/components/__mocks__/featureShapesMocks.ts new file mode 100644 index 0000000000..5d8dcda219 --- /dev/null +++ b/src/tools/components/__mocks__/featureShapesMocks.ts @@ -0,0 +1,89 @@ +import { Feature } from '@nightingale-elements/nightingale-track'; + +type T = { + length: number; + highlight: string; + data: Feature[][]; +}; +const mock: T = { + length: 751, + highlight: '41:125', + data: [ + [ + { + accession: '1', + start: 40, + end: 40, + shape: 'line', + color: '#014371', + locations: [ + { + fragments: [ + { + start: 40, + end: 40, + }, + ], + }, + ], + }, + { + accession: '2', + start: 41, + end: 267, + color: '#014371', + locations: [ + { + fragments: [ + { + start: 41, + end: 267, + }, + ], + }, + ], + }, + { + accession: '3', + start: 268, + end: 582, + shape: 'line', + color: '#014371', + locations: [ + { + fragments: [ + { + start: 268, + end: 582, + }, + ], + }, + ], + }, + ], + [ + { + accession: '4', + start: 0, + end: 40, + shape: 'line', + color: '#014371', + }, + { + accession: '5', + start: 41, + end: 267, + color: '#014371', + }, + { + accession: '6', + start: 268, + end: 751, + shape: 'line', + color: '#014371', + }, + ], + ], +}; + +export default mock; diff --git a/src/tools/components/__mocks__/msaMocks.json b/src/tools/components/__mocks__/msaMocks.json index 2d9fe951cd..3f3dea4b85 100644 --- a/src/tools/components/__mocks__/msaMocks.json +++ b/src/tools/components/__mocks__/msaMocks.json @@ -16,7 +16,7 @@ "accession": "P05066", "features": [ { - "protvistaFeatureId": "cb1e3e80-227f-11eb-8c7f-bd249b5a2490", + "accession": "cb1e3e80-227f-11eb-8c7f-bd249b5a2490", "start": 75, "end": 226, "startModifier": "EXACT", @@ -25,7 +25,7 @@ "description": "Photolyase/cryptochrome alpha/beta" }, { - "protvistaFeatureId": "cb1e3e81-227f-11eb-8c7f-bd249b5a2490", + "accession": "cb1e3e81-227f-11eb-8c7f-bd249b5a2490", "start": 338, "end": 342, "startModifier": "EXACT", @@ -39,7 +39,7 @@ ] }, { - "protvistaFeatureId": "cb1e3e82-227f-11eb-8c7f-bd249b5a2490", + "accession": "cb1e3e82-227f-11eb-8c7f-bd249b5a2490", "start": 482, "end": 484, "startModifier": "EXACT", @@ -53,7 +53,7 @@ ] }, { - "protvistaFeatureId": "cb1e3e83-227f-11eb-8c7f-bd249b5a2490", + "accession": "cb1e3e83-227f-11eb-8c7f-bd249b5a2490", "start": 384, "end": 391, "startModifier": "EXACT", @@ -67,7 +67,7 @@ ] }, { - "protvistaFeatureId": "cb1e3e84-227f-11eb-8c7f-bd249b5a2490", + "accession": "cb1e3e84-227f-11eb-8c7f-bd249b5a2490", "start": 451, "end": 452, "startModifier": "EXACT", @@ -81,7 +81,7 @@ ] }, { - "protvistaFeatureId": "cb1e3e85-227f-11eb-8c7f-bd249b5a2490", + "accession": "cb1e3e85-227f-11eb-8c7f-bd249b5a2490", "start": 326, "end": 326, "startModifier": "EXACT", @@ -95,7 +95,7 @@ ] }, { - "protvistaFeatureId": "cb1e3e86-227f-11eb-8c7f-bd249b5a2490", + "accession": "cb1e3e86-227f-11eb-8c7f-bd249b5a2490", "start": 514, "end": 514, "startModifier": "EXACT", @@ -109,7 +109,7 @@ ] }, { - "protvistaFeatureId": "cb1e3e87-227f-11eb-8c7f-bd249b5a2490", + "accession": "cb1e3e87-227f-11eb-8c7f-bd249b5a2490", "start": 416, "end": 416, "startModifier": "EXACT", @@ -123,7 +123,7 @@ ] }, { - "protvistaFeatureId": "cb1e3e88-227f-11eb-8c7f-bd249b5a2490", + "accession": "cb1e3e88-227f-11eb-8c7f-bd249b5a2490", "start": 469, "end": 469, "startModifier": "EXACT", @@ -137,7 +137,7 @@ ] }, { - "protvistaFeatureId": "cb1e3e89-227f-11eb-8c7f-bd249b5a2490", + "accession": "cb1e3e89-227f-11eb-8c7f-bd249b5a2490", "start": 492, "end": 492, "startModifier": "EXACT", @@ -151,7 +151,7 @@ ] }, { - "protvistaFeatureId": "cb1e3e8a-227f-11eb-8c7f-bd249b5a2490", + "accession": "cb1e3e8a-227f-11eb-8c7f-bd249b5a2490", "start": 387, "end": 387, "startModifier": "EXACT", @@ -167,7 +167,7 @@ ] }, { - "protvistaFeatureId": "cb1e3e8b-227f-11eb-8c7f-bd249b5a2490", + "accession": "cb1e3e8b-227f-11eb-8c7f-bd249b5a2490", "start": 463, "end": 463, "startModifier": "EXACT", @@ -183,7 +183,7 @@ ] }, { - "protvistaFeatureId": "cb1e3e8c-227f-11eb-8c7f-bd249b5a2490", + "accession": "cb1e3e8c-227f-11eb-8c7f-bd249b5a2490", "start": 507, "end": 507, "startModifier": "EXACT", @@ -199,7 +199,7 @@ ] }, { - "protvistaFeatureId": "cb1e3e8d-227f-11eb-8c7f-bd249b5a2490", + "accession": "cb1e3e8d-227f-11eb-8c7f-bd249b5a2490", "start": 517, "end": 517, "startModifier": "EXACT", @@ -208,7 +208,7 @@ "description": "Reduces substrate binding 10-fold." }, { - "protvistaFeatureId": "cb1e3e8e-227f-11eb-8c7f-bd249b5a2490", + "accession": "cb1e3e8e-227f-11eb-8c7f-bd249b5a2490", "start": 77, "end": 77, "startModifier": "EXACT", @@ -222,7 +222,7 @@ ] }, { - "protvistaFeatureId": "cb1e3e8f-227f-11eb-8c7f-bd249b5a2490", + "accession": "cb1e3e8f-227f-11eb-8c7f-bd249b5a2490", "start": 165, "end": 165, "startModifier": "EXACT", @@ -236,7 +236,7 @@ ] }, { - "protvistaFeatureId": "cb1e3e90-227f-11eb-8c7f-bd249b5a2490", + "accession": "cb1e3e90-227f-11eb-8c7f-bd249b5a2490", "start": 169, "end": 169, "startModifier": "EXACT", @@ -250,7 +250,7 @@ ] }, { - "protvistaFeatureId": "cb1e3e91-227f-11eb-8c7f-bd249b5a2490", + "accession": "cb1e3e91-227f-11eb-8c7f-bd249b5a2490", "start": 200, "end": 200, "startModifier": "EXACT", @@ -264,7 +264,7 @@ ] }, { - "protvistaFeatureId": "cb1e3e92-227f-11eb-8c7f-bd249b5a2490", + "accession": "cb1e3e92-227f-11eb-8c7f-bd249b5a2490", "start": 351, "end": 351, "startModifier": "EXACT", @@ -278,7 +278,7 @@ ] }, { - "protvistaFeatureId": "cb1e3e93-227f-11eb-8c7f-bd249b5a2490", + "accession": "cb1e3e93-227f-11eb-8c7f-bd249b5a2490", "start": 365, "end": 365, "startModifier": "EXACT", @@ -292,7 +292,7 @@ ] }, { - "protvistaFeatureId": "cb1e3e94-227f-11eb-8c7f-bd249b5a2490", + "accession": "cb1e3e94-227f-11eb-8c7f-bd249b5a2490", "start": 473, "end": 473, "startModifier": "EXACT", @@ -320,7 +320,7 @@ "accession": "P05066", "features": [ { - "protvistaFeatureId": "id1", + "accession": "id1", "start": 75, "end": 226, "startModifier": "EXACT", @@ -329,7 +329,7 @@ "description": "Photolyase/cryptochrome alpha/beta" }, { - "protvistaFeatureId": "id2", + "accession": "id2", "start": 338, "end": 342, "startModifier": "EXACT", @@ -358,7 +358,7 @@ "accession": "P05067", "features": [ { - "protvistaFeatureId": "8751c02f-2336-11eb-92aa-bfb3fff0c9c0", + "accession": "8751c02f-2336-11eb-92aa-bfb3fff0c9c0", "start": 1, "end": 17, "startModifier": "EXACT", @@ -384,7 +384,7 @@ ] }, { - "protvistaFeatureId": "PRO_0000000088", + "accession": "PRO_0000000088", "featureId": "PRO_0000000088", "start": 18, "end": 770, @@ -409,7 +409,7 @@ "accession": "P05062", "features": [ { - "protvistaFeatureId": "8751c0da-2336-11eb-92aa-bfb3fff0c9c0", + "accession": "8751c0da-2336-11eb-92aa-bfb3fff0c9c0", "start": 1, "end": 1, "startModifier": "EXACT", @@ -430,7 +430,7 @@ ] }, { - "protvistaFeatureId": "PRO_0000216940", + "accession": "PRO_0000216940", "featureId": "PRO_0000216940", "start": 2, "end": 364, @@ -455,7 +455,7 @@ "accession": "P05064", "features": [ { - "protvistaFeatureId": "PRO_0000216937", + "accession": "PRO_0000216937", "featureId": "PRO_0000216937", "start": 2, "end": 364, @@ -465,7 +465,7 @@ "description": "Fructose-bisphosphate aldolase A" }, { - "protvistaFeatureId": "8751e737-2336-11eb-92aa-bfb3fff0c9c0", + "accession": "8751e737-2336-11eb-92aa-bfb3fff0c9c0", "start": 188, "end": 188, "startModifier": "EXACT", diff --git a/src/tools/components/__mocks__/wrappedRowMocks.json b/src/tools/components/__mocks__/wrappedRowMocks.json index 4897d1e707..0c4aae267a 100644 --- a/src/tools/components/__mocks__/wrappedRowMocks.json +++ b/src/tools/components/__mocks__/wrappedRowMocks.json @@ -15,7 +15,7 @@ "end": 4, "features": [ { - "protvistaFeatureId": "a1bdae00-235f-11eb-9899-4330e39f65ae", + "accession": "a1bdae00-235f-11eb-9899-4330e39f65ae", "start": 75, "end": 226, "startModifier": "EXACT", @@ -24,7 +24,7 @@ "description": "Photolyase/cryptochrome alpha/beta" }, { - "protvistaFeatureId": "a1bdae01-235f-11eb-9899-4330e39f65ae", + "accession": "a1bdae01-235f-11eb-9899-4330e39f65ae", "start": 338, "end": 342, "startModifier": "EXACT", @@ -48,7 +48,7 @@ "end": 46, "features": [ { - "protvistaFeatureId": "a1bdae15-235f-11eb-9899-4330e39f65ae", + "accession": "a1bdae15-235f-11eb-9899-4330e39f65ae", "start": 1, "end": 17, "startModifier": "EXACT", @@ -74,7 +74,7 @@ ] }, { - "protvistaFeatureId": "PRO_0000000088", + "accession": "PRO_0000000088", "featureId": "PRO_0000000088", "start": 18, "end": 770, @@ -94,7 +94,7 @@ "end": 0, "features": [ { - "protvistaFeatureId": "a1bdd55a-235f-11eb-9899-4330e39f65ae", + "accession": "a1bdd55a-235f-11eb-9899-4330e39f65ae", "start": 1, "end": 1, "startModifier": "EXACT", @@ -115,7 +115,7 @@ ] }, { - "protvistaFeatureId": "PRO_0000216940", + "accession": "PRO_0000216940", "featureId": "PRO_0000216940", "start": 2, "end": 364, @@ -135,7 +135,7 @@ "end": 0, "features": [ { - "protvistaFeatureId": "a1be716a-235f-11eb-9899-4330e39f65ae", + "accession": "a1be716a-235f-11eb-9899-4330e39f65ae", "start": 1, "end": 1, "startModifier": "EXACT", @@ -151,7 +151,7 @@ ] }, { - "protvistaFeatureId": "PRO_0000216937", + "accession": "PRO_0000216937", "featureId": "PRO_0000216937", "start": 2, "end": 364, @@ -171,7 +171,7 @@ "delayRender": false, "activeAnnotation": [ { - "protvistaFeatureId": "a1bdae00-235f-11eb-9899-4330e39f65ae", + "accession": "a1bdae00-235f-11eb-9899-4330e39f65ae", "start": 75, "end": 226, "startModifier": "EXACT", @@ -191,7 +191,7 @@ "accession": "P05066", "features": [ { - "protvistaFeatureId": "a1bdae00-235f-11eb-9899-4330e39f65ae", + "accession": "a1bdae00-235f-11eb-9899-4330e39f65ae", "start": 75, "end": 226, "startModifier": "EXACT", @@ -200,7 +200,7 @@ "description": "Photolyase/cryptochrome alpha/beta" }, { - "protvistaFeatureId": "a1bdae01-235f-11eb-9899-4330e39f65ae", + "accession": "a1bdae01-235f-11eb-9899-4330e39f65ae", "start": 338, "end": 342, "startModifier": "EXACT", diff --git a/src/tools/components/__tests__/AlignmentOverview.spec.tsx b/src/tools/components/__tests__/AlignmentOverview.spec.tsx index 46e35692ac..b4ca526710 100644 --- a/src/tools/components/__tests__/AlignmentOverview.spec.tsx +++ b/src/tools/components/__tests__/AlignmentOverview.spec.tsx @@ -2,7 +2,7 @@ import customRender from '../../../shared/__test-helpers__/customRender'; import AlignmentOverview from '../AlignmentOverview'; -import { BLAST as mockData } from '../__mocks__/featureShapesMocks.json'; +import mockData from '../__mocks__/featureShapesMocks'; describe('AlignmentOverview', () => { describe('BLAST', () => { @@ -11,7 +11,7 @@ describe('AlignmentOverview', () => { rendered = customRender( @@ -27,7 +27,7 @@ describe('AlignmentOverview', () => { const { asFragment } = customRender( diff --git a/src/tools/components/__tests__/__snapshots__/AlignmentOverview.spec.tsx.snap b/src/tools/components/__tests__/__snapshots__/AlignmentOverview.spec.tsx.snap index c7b664a5a1..46de3e48f0 100644 --- a/src/tools/components/__tests__/__snapshots__/AlignmentOverview.spec.tsx.snap +++ b/src/tools/components/__tests__/__snapshots__/AlignmentOverview.spec.tsx.snap @@ -3,18 +3,230 @@ exports[`AlignmentOverview BLAST should render 1`] = `
- - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + min-height="10" + min-width="10" + style="display: inline-block; line-height: 0; width: 100%; height: 100%;" + > + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
`; diff --git a/src/tools/components/__tests__/__snapshots__/AlignmentView.spec.tsx.snap b/src/tools/components/__tests__/__snapshots__/AlignmentView.spec.tsx.snap index 3525beba25..23da34affe 100644 --- a/src/tools/components/__tests__/__snapshots__/AlignmentView.spec.tsx.snap +++ b/src/tools/components/__tests__/__snapshots__/AlignmentView.spec.tsx.snap @@ -56,7 +56,6 @@ exports[`AlignmentView Align should render 1`] = `
-
- - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + min-height="10" + min-width="10" + style="display: inline-block; line-height: 0; width: 100%; height: 100%;" + > + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
- + min-height="10" + min-width="10" + style="display: inline-block; line-height: 0; width: 100%; height: 100%;" + > + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
- - - + +
-
- - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + min-height="10" + min-width="10" + style="display: inline-block; line-height: 0; width: 100%; height: 100%;" + > + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
- + min-height="10" + min-width="10" + style="display: inline-block; line-height: 0; width: 100%; height: 100%;" + > + + + + + + + + + + + + + + + +
- - - + +
- + min-height="10" + min-width="10" + style="display: inline-block; line-height: 0; width: 100%; height: 100%;" + > + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
`; diff --git a/src/tools/config/tooltipEvidences.ts b/src/tools/config/tooltipEvidences.ts new file mode 100644 index 0000000000..6de078efef --- /dev/null +++ b/src/tools/config/tooltipEvidences.ts @@ -0,0 +1,105 @@ +const ecoMap = [ + { + name: 'ECO:0000269', + description: 'Manual assertion based on experiment', + shortDescription: 'Publication', + acronym: 'EXP', + isManual: true, + }, + { + name: 'ECO:0000303', + description: 'Manual assertion based on opinion', + shortDescription: 'Publication', + acronym: 'NAS', + isManual: true, + }, + { + name: 'ECO:0000305', + description: 'Manual assertion inferred by curator', + shortDescription: 'Curated', + acronym: 'IC', + isManual: true, + }, + { + name: 'ECO:0000250', + description: 'Manual assertion inferred from sequence similarity', + shortDescription: 'By similarity', + acronym: 'ISS', + isManual: true, + }, + { + name: 'ECO:0000255', + description: 'Manual assertion according to rules', + shortDescription: 'Sequence Analysis', + acronym: 'ISM', + isManual: true, + }, + { + name: 'ECO:0007744', + description: + 'Manual assertion inferred from combination of experimental and computational evidence', + shortDescription: 'Combined sources', + acronym: 'MIXM', + isManual: true, + }, + { + name: 'ECO:0000312', + description: 'Manual assertion inferred from database entries', + shortDescription: 'Imported', + acronym: 'MI', + isManual: true, + }, + { + name: 'ECO:0000256', + description: 'Automatic assertion according to rules', + shortDescription: 'Automatic annotation', + acronym: 'AA', + }, + { + name: 'ECO:0000259', + description: 'Automatic assertion inferred from signature match', + shortDescription: 'Automatic annotation', + acronym: 'AA', + }, + { + name: 'ECO:0007829', + description: + 'Automatic assertion inferred from combination of experimental and computational evidence', + shortDescription: 'Combined sources', + acronym: 'MIXA', + }, + /* ECO:0007829 replaced ECO:0000213 from release 2022_02. + Some evidences still have the obsolete code. eg: https://www.ebi.ac.uk/proteins/api/antigen/P49841 + It is better to show the evidence rather than being it empty */ + { + name: 'ECO:0000213', + description: + 'Automatic assertion inferred from combination of experimental and computational evidence', + shortDescription: 'Combined sources', + acronym: 'MIXA', + }, + // ECO:0007744 replaced ECO:0000244 from release 2022_02. Same as above + { + name: 'ECO:0000244', + description: + 'Manual assertion inferred from combination of experimental and computational evidence', + shortDescription: 'Combined sources', + acronym: 'MIXM', + isManual: true, + }, + { + name: 'ECO:0000313', + description: 'Automatic assertion inferred from database entries', + shortDescription: 'Imported', + acronym: 'AI', + }, + { + name: 'ECO:0000260', + description: 'Manual assertion inferred from signature match', + shortDescription: 'InterPro annotation', + acronym: 'SGNM', + isManual: true, + }, +]; + +export default ecoMap; diff --git a/src/tools/peptide-search/components/results/__tests__/__snapshots__/PeptideSearchResult.spec.tsx.snap b/src/tools/peptide-search/components/results/__tests__/__snapshots__/PeptideSearchResult.spec.tsx.snap index 88d29dd56a..b562fca7b9 100644 --- a/src/tools/peptide-search/components/results/__tests__/__snapshots__/PeptideSearchResult.spec.tsx.snap +++ b/src/tools/peptide-search/components/results/__tests__/__snapshots__/PeptideSearchResult.spec.tsx.snap @@ -145,283 +145,265 @@ exports[`PeptideSearchResult should render with the correct number of results in Resubmit - - - - + + + + + + +
-
+ + + + - + - - - - - - - - - - - - + + + + + - - - + + - - - - - - - + + - - - + + + + - - - - - -
- - - Entry - - - Match - - - - + Entry Name - - - Protein Names - - - Gene Names - - - Organism - - - Length - -
- - - +
- + + - P13866 - - - - - - - - - SC5A1_HUMAN - - + + P13866 + + + + - Sodium/glucose cotransporter 1 + - + SC5A1_HUMAN + + - [...] - - - - - SLC5A1 - - , NAGT, SGLT1 - - - Homo sapiens (Human) - - - 664 AA -
- - - + + Sodium/glucose cotransporter 1 + + + + + + SLC5A1 + + , NAGT, SGLT1 + - P19926 + Homo sapiens (Human) - - - - - - - - AGP_ECOLI - - + + 664 AA +
+ + - Glucose-1-phosphatase + + P19926 + - + + - [...] - - - - - agp - - , b1002, JW0987 - - - Escherichia coli (strain K12) - - - 413 AA -
-
+ + + +
+ AGP_ECOLI + + + + Glucose-1-phosphatase + + + + + + agp + + , b1002, JW0987 + + + Escherichia coli (strain K12) + + + 413 AA +
+
+
{{ SideBarLayout end }} @@ -573,283 +555,265 @@ exports[`PeptideSearchResult should render with the correct number of results in Resubmit - - - - + + + + + + +
-
+ + + + - + - - - - - - - - - - - - + + + + + - - - + + - - - - - - - + + - - - + + + + - - - - - -
- - - Entry - - - Match - - - - + Entry Name - - - Protein Names - - - Gene Names - - - Organism - - - Length - -
- - - +
- + + - P13866 - - - - - - - - - SC5A1_HUMAN - - + + P13866 + + + + - Sodium/glucose cotransporter 1 + - + SC5A1_HUMAN + + - [...] - - - - - SLC5A1 - - , NAGT, SGLT1 - - - Homo sapiens (Human) - - - 664 AA -
- - - + + Sodium/glucose cotransporter 1 + + + + + + SLC5A1 + + , NAGT, SGLT1 + - P19926 + Homo sapiens (Human) - - - - - - - - AGP_ECOLI - - + + 664 AA +
+ + - Glucose-1-phosphatase + + P19926 + - + + - [...] - - - - - agp - - , b1002, JW0987 - - - Escherichia coli (strain K12) - - - 413 AA -
-
+ + + +
+ AGP_ECOLI + + + + Glucose-1-phosphatase + + + + + + agp + + , b1002, JW0987 + + + Escherichia coli (strain K12) + + + 413 AA +
+
+
{{ SideBarLayout end }} diff --git a/src/tools/types/alignment.ts b/src/tools/types/alignment.ts index 1a3b0bdbfb..e39548fd49 100644 --- a/src/tools/types/alignment.ts +++ b/src/tools/types/alignment.ts @@ -21,8 +21,8 @@ export type ConservationOptions = { }; export type NightingaleChangeEvent = { - eventtype: string; - feature: { protvistaFeatureId: string }; + eventType: string; + feature: { accession: string }; coords: number[]; }; diff --git a/src/tools/utils/__mocks__/toolTipFeatureTestData.json b/src/tools/utils/__mocks__/toolTipFeatureTestData.json index 9c6cff3a14..e20de14625 100644 --- a/src/tools/utils/__mocks__/toolTipFeatureTestData.json +++ b/src/tools/utils/__mocks__/toolTipFeatureTestData.json @@ -2,7 +2,7 @@ { "description": "Should return correctly formed feature with evidence", "feature": { - "protvistaFeatureId": "251179d6-225c-11eb-8a47-55ba8956ec3b", + "accession": "251179d6-225c-11eb-8a47-55ba8956ec3b", "start": 28, "end": 189, "startModifier": "EXACT", @@ -18,6 +18,7 @@ ] }, "tooltipFeature": { + "ftId": "251179d6-225c-11eb-8a47-55ba8956ec3b", "type": "Domain", "start": 28, "end": 189, @@ -37,7 +38,7 @@ { "description": "Should return correctly formed feature without evidence", "feature": { - "protvistaFeatureId": "72f1d160-225f-11eb-b210-87bf075e497c", + "accession": "72f1d160-225f-11eb-b210-87bf075e497c", "start": 75, "end": 226, "startModifier": "EXACT", @@ -46,6 +47,7 @@ "description": "Photolyase/cryptochrome alpha/beta" }, "tooltipFeature": { + "ftId": "72f1d160-225f-11eb-b210-87bf075e497c", "type": "Domain", "start": 75, "end": 226, @@ -55,7 +57,7 @@ { "description": "Should return feature with featureId as ftId", "feature": { - "protvistaFeatureId": "PRO_0000381966", + "accession": "PRO_0000381966", "featureId": "PRO_0000381966", "start": 18, "end": 286, @@ -75,7 +77,7 @@ { "description": "Should return feature without description", "feature": { - "protvistaFeatureId": "PRO_0000381966", + "accession": "PRO_0000381966", "featureId": "PRO_0000381966", "start": 18, "end": 286, @@ -93,7 +95,7 @@ { "description": "Should return correctly formed feature with evidence but without id or source", "feature": { - "protvistaFeatureId": "251179d6-225c-11eb-8a47-55ba8956ec3b", + "accession": "251179d6-225c-11eb-8a47-55ba8956ec3b", "start": 28, "end": 189, "startModifier": "EXACT", @@ -107,6 +109,7 @@ ] }, "tooltipFeature": { + "ftId": "251179d6-225c-11eb-8a47-55ba8956ec3b", "type": "Domain", "start": 28, "end": 189, @@ -121,7 +124,7 @@ { "description": "Should return correctly formed feature with evidence but with unknown source", "feature": { - "protvistaFeatureId": "251179d6-225c-11eb-8a47-55ba8956ec3b", + "accession": "251179d6-225c-11eb-8a47-55ba8956ec3b", "start": 28, "end": 189, "startModifier": "EXACT", @@ -137,6 +140,7 @@ ] }, "tooltipFeature": { + "ftId": "251179d6-225c-11eb-8a47-55ba8956ec3b", "type": "Domain", "start": 28, "end": 189, @@ -155,7 +159,7 @@ { "description": "Should return correctly formed feature with evidence and with alternate url when source is PubMed", "feature": { - "protvistaFeatureId": "251179d6-225c-11eb-8a47-55ba8956ec3b", + "accession": "251179d6-225c-11eb-8a47-55ba8956ec3b", "start": 28, "end": 189, "startModifier": "EXACT", @@ -171,6 +175,7 @@ ] }, "tooltipFeature": { + "ftId": "251179d6-225c-11eb-8a47-55ba8956ec3b", "type": "Domain", "start": 28, "end": 189, diff --git a/src/tools/utils/feature.ts b/src/tools/utils/feature.ts index 739ae6f398..6ed61bc5d7 100644 --- a/src/tools/utils/feature.ts +++ b/src/tools/utils/feature.ts @@ -8,19 +8,19 @@ import { import { getEvidenceLink } from '../../uniprotkb/config/evidenceUrls'; import FeatureType from '../../uniprotkb/types/featureType'; -type Source = { +export type Source = { id: string; name: string; url?: string; alternativeUrl?: string; }; -type Evidence = { +export type Evidence = { code: string; source?: Source; }; -type TooltipFeature = { +export type TooltipFeature = { type: FeatureType; start: number; end: number; @@ -50,8 +50,8 @@ export const prepareFeatureForTooltip = ( } } - if (feature.featureId) { - tooltipFeature.ftId = feature.featureId; + if (feature.accession) { + tooltipFeature.ftId = feature.accession; } if (!feature.evidences) { diff --git a/src/tools/utils/sequences.ts b/src/tools/utils/sequences.ts index ad0fbc8127..38b1c301a0 100644 --- a/src/tools/utils/sequences.ts +++ b/src/tools/utils/sequences.ts @@ -1,5 +1,9 @@ -/* eslint-disable camelcase */ -import { getColorByType } from 'protvista-track'; +import { + Feature, + getColorByType, +} from '@nightingale-elements/nightingale-track'; +import { v1 } from 'uuid'; + import { MSAInput } from '../types/alignment'; import { FeatureDatum } from '../../uniprotkb/components/protein-data-views/UniProtKBFeaturesView'; import { ProcessedFeature } from '../../shared/components/views/FeaturesView'; @@ -53,14 +57,9 @@ export const getFullAlignmentLength = ( return prefix - 1 + alignmentLength + suffix; }; -export type SegmentTrackData = { - start: number; - end: number; - shape?: string; - color: string; -}; - -export const getFullAlignmentSegments = (alignment: MSAInput[]) => { +export const getFullAlignmentSegments = ( + alignment: MSAInput[] +): Feature[][] => { // franklin $colour-sapphire-blue const colour = '#014371'; @@ -75,17 +74,20 @@ export const getFullAlignmentSegments = (alignment: MSAInput[]) => { const offset = maxFrom - al.from > 0 ? maxFrom - al.from : 0; return [ { + accession: v1(), start: offset, end: offset + al.from - 1, shape: 'line', color: colour, }, ...findSequenceSegments(al.sequence).map(([start, end]) => ({ + accession: v1(), start: offset + (al.from - 1) + start, end: offset + (al.from - 1) + end, color: colour, })), { + accession: v1(), start: offset + al.to + countGaps(al.sequence) + 1, end: offset + al.length + countGaps(al.sequence), shape: 'line', @@ -117,7 +119,7 @@ export const createGappedFeature = ( feature: ProcessedFeature, sequence: string, from: number -) => { +): Feature | null => { /* input: feature and sequence are both 1-based */ @@ -152,7 +154,7 @@ export const createGappedFeature = ( } if (!fragments.length) { // At this point the feature start & end must be before the BLAST match's from. - return; + return null; } const gappedFeature = { @@ -169,13 +171,13 @@ export const createGappedFeature = ( }; export const findSequenceFeature = ( - protvistaFeatureId: string, + accession: string, alignment: MSAInput[] ) => { for (const sequence of alignment) { if (sequence?.features) { const foundFeature = sequence.features.find( - (feature) => feature.protvistaFeatureId === protvistaFeatureId + (feature) => feature.accession === accession ); if (foundFeature) { return foundFeature; @@ -202,14 +204,20 @@ export const getMSAFeature = ( from: number ): MSAFeature | null => { const gappedFeature = createGappedFeature(feature, sequence, from); - if (!gappedFeature) { + if ( + !gappedFeature || + typeof gappedFeature.start === 'undefined' || + typeof gappedFeature.end === 'undefined' + ) { return null; } - const borderColor = getColorByType(gappedFeature.type); + const borderColor = gappedFeature.type + ? getColorByType(gappedFeature.type) + : 'black'; return { residues: { from: gappedFeature.start, to: gappedFeature.end }, sequences: { from: sequenceIndex, to: sequenceIndex }, - id: feature.protvistaFeatureId, + id: feature.accession, borderColor, fillColor: 'transparent', mouseOverFillColor: 'transparent', diff --git a/src/types/protvista-datatable.d.ts b/src/types/protvista-datatable.d.ts deleted file mode 100644 index 0bfd156b05..0000000000 --- a/src/types/protvista-datatable.d.ts +++ /dev/null @@ -1,8 +0,0 @@ -/* eslint-disable @typescript-eslint/no-explicit-any */ -declare module 'protvista-datatable'; - -declare namespace JSX { - interface IntrinsicElements { - 'protvista-datatable': any; - } -} diff --git a/src/types/protvista-manager.d.ts b/src/types/protvista-manager.d.ts deleted file mode 100644 index cb50d794ba..0000000000 --- a/src/types/protvista-manager.d.ts +++ /dev/null @@ -1,8 +0,0 @@ -/* eslint-disable @typescript-eslint/no-explicit-any */ -declare module 'protvista-manager'; - -declare namespace JSX { - interface IntrinsicElements { - 'protvista-manager': any; - } -} diff --git a/src/types/protvista-navigation.d.ts b/src/types/protvista-navigation.d.ts deleted file mode 100644 index 7cbd3485f0..0000000000 --- a/src/types/protvista-navigation.d.ts +++ /dev/null @@ -1,8 +0,0 @@ -/* eslint-disable @typescript-eslint/no-explicit-any */ -declare module 'protvista-navigation'; - -declare namespace JSX { - interface IntrinsicElements { - 'protvista-navigation': any; - } -} diff --git a/src/types/protvista-sequence.d.ts b/src/types/protvista-sequence.d.ts deleted file mode 100644 index 8f3e7f2b60..0000000000 --- a/src/types/protvista-sequence.d.ts +++ /dev/null @@ -1,8 +0,0 @@ -/* eslint-disable @typescript-eslint/no-explicit-any */ -declare module 'protvista-sequence'; - -declare namespace JSX { - interface IntrinsicElements { - 'protvista-sequence': any; - } -} diff --git a/src/types/protvista-tooltip.d.ts b/src/types/protvista-tooltip.d.ts deleted file mode 100644 index a12c9c94cb..0000000000 --- a/src/types/protvista-tooltip.d.ts +++ /dev/null @@ -1,8 +0,0 @@ -/* eslint-disable @typescript-eslint/no-explicit-any */ -declare module 'protvista-tooltip'; - -declare namespace JSX { - interface IntrinsicElements { - 'protvista-tooltip': any; - } -} diff --git a/src/types/protvista-track.d.ts b/src/types/protvista-track.d.ts deleted file mode 100644 index efbcac8a06..0000000000 --- a/src/types/protvista-track.d.ts +++ /dev/null @@ -1,8 +0,0 @@ -/* eslint-disable @typescript-eslint/no-explicit-any */ -declare module 'protvista-track'; - -declare namespace JSX { - interface IntrinsicElements { - 'protvista-track': any; - } -} diff --git a/src/types/protvista-uniprot.d.ts b/src/types/protvista-uniprot.d.ts index 85c6b06a5a..e1d6da66ee 100644 --- a/src/types/protvista-uniprot.d.ts +++ b/src/types/protvista-uniprot.d.ts @@ -1,9 +1,13 @@ -/* eslint-disable @typescript-eslint/no-explicit-any */ -declare module 'protvista-uniprot'; +type ProtvistaUniprotElement = React.DetailedHTMLProps< + React.HTMLAttributes, + HTMLElement +> & { + accession?: string; +}; declare namespace JSX { interface IntrinsicElements { - 'protvista-uniprot': any; - 'protvista-uniprot-structure': any; + 'protvista-uniprot': ProtvistaUniprotElement; + 'protvista-uniprot-structure': ProtvistaUniprotElement; } } diff --git a/src/types/protvista-variation.d.ts b/src/types/protvista-variation.d.ts deleted file mode 100644 index b8ba727b73..0000000000 --- a/src/types/protvista-variation.d.ts +++ /dev/null @@ -1,7 +0,0 @@ -/* eslint-disable @typescript-eslint/no-explicit-any */ - -declare namespace JSX { - interface IntrinsicElements { - 'protvista-variation': any; - } -} diff --git a/src/types/protvista-zoom-tool.d.ts b/src/types/protvista-zoom-tool.d.ts deleted file mode 100644 index 875dc5922a..0000000000 --- a/src/types/protvista-zoom-tool.d.ts +++ /dev/null @@ -1,8 +0,0 @@ -/* eslint-disable @typescript-eslint/no-explicit-any */ -declare module 'protvista-zoom-tool'; - -declare namespace JSX { - interface IntrinsicElements { - 'protvista-zoom-tool': any; - } -} diff --git a/src/uniparc/components/entry/UniParcFeaturesView.tsx b/src/uniparc/components/entry/UniParcFeaturesView.tsx index b3f609f908..777c36d815 100644 --- a/src/uniparc/components/entry/UniParcFeaturesView.tsx +++ b/src/uniparc/components/entry/UniParcFeaturesView.tsx @@ -1,4 +1,5 @@ import { useMemo } from 'react'; +import { v1 } from 'uuid'; import ExternalLink from '../../../shared/components/ExternalLink'; import FeaturesView, { @@ -11,8 +12,10 @@ import externalUrls from '../../../shared/config/externalUrls'; import { stringToColour } from '../../../shared/utils/color'; import { processUrlTemplate } from '../../../shared/utils/xrefs'; import { sortByLocation } from '../../../uniprotkb/utils'; +import { markBorder, markBackground } from '../../../shared/utils/nightingale'; import { SequenceFeature } from '../../adapters/uniParcConverter'; +import { TableFromDataColumn } from '../../../shared/components/table/TableFromData'; export type UniParcProcessedFeature = ProcessedFeature & { database: string; @@ -28,8 +31,8 @@ export const convertData = ( data .flatMap((feature) => feature.locations.map((locationFeature) => ({ + accession: v1(), // Can't rely on feature.databaseId being unique type: 'Other' as const, - protvistaFeatureId: feature.databaseId, start: locationFeature.start, end: locationFeature.end, database: feature.database, @@ -41,6 +44,8 @@ export const convertData = ( ) .sort(sortByLocation); +const getRowId = (data: UniParcProcessedFeature) => data.accession; + type UniParcFeaturesViewProps = { data: SequenceFeature[]; sequence: string; @@ -50,27 +55,40 @@ const UniParcFeaturesView = ({ data, sequence }: UniParcFeaturesViewProps) => { const processedData = useMemo(() => convertData(data), [data]); const databaseInfoMaps = useDatabaseInfoMaps(); - // Define table contents - const table = ( - - - - - - - - - - - {processedData.map((feature) => { - const { database, databaseId } = feature; - const databaseInfo = - databaseInfoMaps?.databaseToDatabaseInfo[database]; + const columns: TableFromDataColumn[] = useMemo( + () => [ + { + label: 'InterPro Group', + id: 'interpro-group', + render: (feature) => + feature.interproGroupId ? ( + + {feature.interproGroupName} + + ) : ( + 'N/A' + ), + }, + { + label: 'Position(s)', + id: 'position', + render: (feature) => { let position = `${feature.start}`; if (feature.start !== feature.end) { position += `-${feature.end}`; } - + return position; + }, + }, + { + label: 'Database identifier', + id: 'database-identifier', + render: (feature) => { + const { database, databaseId } = feature; + const databaseInfo = + databaseInfoMaps?.databaseToDatabaseInfo[database]; // Additional prefix 'G3DSA:' in UniParc will be removed in https://www.ebi.ac.uk/panda/jira/browse/TRM-32164. // Adjust the below logic accordingly let revisedDatabaseId; @@ -92,52 +110,42 @@ const UniParcFeaturesView = ({ data, sequence }: UniParcFeaturesViewProps) => { } return ( - - - - - - + <> + {databaseInfo?.uriLink && databaseId && ( + + {databaseId} + + )} + {/* Need to be removed when FUNFAM is added in 2024_06 */} + {database === 'FUNFAM' && funFamURL && ( + {databaseId} + )} + ); - })} - -
InterPro GroupPosition(s)Database identifierDatabase
- {feature.interproGroupId ? ( - - {feature.interproGroupName} - - ) : ( - 'N/A' - )} - {position} - {databaseInfo?.uriLink && databaseId && ( - - {databaseId} - - )} - {/* Need to be removed when FUNFAM is added in 2024_06 */} - {database === 'FUNFAM' && funFamURL && ( - {databaseId} - )} - {feature.database}
+ }, + }, + { + label: 'Database', + id: 'database', + render: (feature) => feature.database, + }, + ], + [databaseInfoMaps?.databaseToDatabaseInfo] ); return ( ); }; diff --git a/src/uniparc/components/entry/__tests__/__snapshots__/XRefsSection.spec.tsx.snap b/src/uniparc/components/entry/__tests__/__snapshots__/XRefsSection.spec.tsx.snap index 4be95528e3..973f241bdf 100644 --- a/src/uniparc/components/entry/__tests__/__snapshots__/XRefsSection.spec.tsx.snap +++ b/src/uniparc/components/entry/__tests__/__snapshots__/XRefsSection.spec.tsx.snap @@ -39,36 +39,43 @@ exports[`XrefSection component should render the xref table properly and match s
Database Identifier Version Organism First seen Last seen Active
- - - - - - - - {filteredGoTerms.map( - (goTerm) => - goTerm.id && ( - - - - - ) - )} - -
AspectTerm
{goTerm.aspect} - - {goTerm.termDescription || goTerm.id} - - - -
- ); - return (

GO annotations

@@ -289,7 +291,13 @@ const GoRibbon = ({ )} {elementLoaded && ribbon} - {!!filteredGoTerms.length && {table}} + {!!filteredGoTerms.length && ( + + )}
); }; diff --git a/src/uniprotkb/components/entry/InteractionSection.tsx b/src/uniprotkb/components/entry/InteractionSection.tsx index 343bfc1443..53ec0589b6 100644 --- a/src/uniprotkb/components/entry/InteractionSection.tsx +++ b/src/uniprotkb/components/entry/InteractionSection.tsx @@ -8,7 +8,9 @@ import EntrySection from '../../types/entrySection'; import FreeTextView from '../protein-data-views/FreeTextView'; import XRefView from '../protein-data-views/XRefView'; import LazyComponent from '../../../shared/components/LazyComponent'; -import DatatableWrapper from '../../../shared/components/views/DatatableWrapper'; +import TableFromData, { + TableFromDataColumn, +} from '../../../shared/components/table/TableFromData'; import { useSmallScreen } from '../../../shared/hooks/useMatchMedia'; @@ -104,6 +106,82 @@ const interactionSorter = (a: Interaction, b: Interaction) => { return 0; }; +const getRowId = (data: Interaction) => + `${data.interactantOne.intActId}${data.interactantTwo.intActId}`; + +const columns: TableFromDataColumn[] = [ + { + id: 'type', + label: 'Type', + render: (data) => (data.organismDiffer ? 'XENO' : 'BINARY'), // NOTE: Add 'SELF' + filter: (data, input) => + (data.organismDiffer ? 'XENO' : 'BINARY') === input, + }, + { + id: 'entry-1', + label: 'Entry 1', + render: (data) => + data.interactantOne.uniProtKBAccession ? ( + + {data.interactantOne.geneName} {data.interactantOne.chainId}{' '} + {data.interactantOne.uniProtKBAccession} + + ) : ( + <> + {data.interactantOne.geneName} {data.interactantOne.chainId} + + ), + getOption: (data) => data.interactantOne.uniProtKBAccession || 'Other', + filter: (data, input) => + (data.interactantOne.uniProtKBAccession || 'Other') === input, + }, + { + id: 'entry-2', + label: 'Entry 2', + render: (data) => + data.interactantTwo.uniProtKBAccession ? ( + + {data.interactantTwo.geneName} {data.interactantTwo.chainId}{' '} + {data.interactantTwo.uniProtKBAccession} + + ) : ( + <> + {data.interactantTwo.geneName} {data.interactantTwo.chainId} + + ), + }, + { + id: 'number-of-experiments', + label: 'Number of experiments', + render: (data) => data.numberOfExperiments, + }, + { + id: 'intact', + label: IntAct, + render: (data) => ( + + {data.interactantOne.intActId}, {data.interactantTwo.intActId} + + ), + }, +]; + type Props = { data: UIModel; primaryAccession: string; @@ -164,91 +242,6 @@ const InteractionSection = ({ data, primaryAccession }: Props) => { | FreeTextComment[] | undefined; - const table = ( - - - - - - - - - - - - {tableData.map((interaction) => ( - - - - - - - - ))} - -
TypeEntry 1Entry 2Number of experimentsIntact
- {/* NOTE: Add 'SELF' */} - {interaction.organismDiffer ? 'XENO' : 'BINARY'} - - {interaction.interactantOne.uniProtKBAccession ? ( - - {interaction.interactantOne.geneName}{' '} - {interaction.interactantOne.chainId}{' '} - {interaction.interactantOne.uniProtKBAccession} - - ) : ( - <> - {interaction.interactantOne.geneName}{' '} - {interaction.interactantOne.chainId} - - )} - - {interaction.interactantTwo.uniProtKBAccession ? ( - - {interaction.interactantTwo.geneName}{' '} - {interaction.interactantTwo.chainId}{' '} - {interaction.interactantTwo.uniProtKBAccession} - - ) : ( - <> - {interaction.interactantTwo.geneName}{' '} - {interaction.interactantTwo.chainId} - - )} - {interaction.numberOfExperiments} - - {interaction.interactantOne.intActId},{' '} - {interaction.interactantTwo.intActId} - -
- ); - const complexId = viewerID || Array.from(complexPortalXrefs.keys())[0]; const complexName = complexPortalXrefs.get(complexId)?.properties?.EntryName || ''; @@ -278,7 +271,12 @@ const InteractionSection = ({ data, primaryAccession }: Props) => { - {table} + ) : null} diff --git a/src/uniprotkb/components/entry/KineticsTableView.tsx b/src/uniprotkb/components/entry/KineticsTableView.tsx index 9cb08adc7b..b01df6371d 100644 --- a/src/uniprotkb/components/entry/KineticsTableView.tsx +++ b/src/uniprotkb/components/entry/KineticsTableView.tsx @@ -1,5 +1,3 @@ -import useCustomElement from '../../../shared/hooks/useCustomElement'; - import { RichText, TextView } from '../protein-data-views/FreeTextView'; import UniProtKBEvidenceTag from '../protein-data-views/UniProtKBEvidenceTag'; @@ -8,6 +6,7 @@ import { Evidence } from '../../types/modelTypes'; import helper from '../../../shared/styles/helper.module.scss'; import styles from './styles/kinetics-table.module.scss'; +import Table from '../../../shared/components/table/Table'; const pHRegEx = /pH\s(([0-9]*[.])?[0-9]+-?(([0-9]*[.])?[0-9]+)?)/; const tempRegEx = /(([0-9]*[.])?[0-9]+)\sdegrees\scelsius/i; @@ -38,53 +37,41 @@ const KineticsTable = ({ columns: string[]; data: KinecticsTableRow[]; }) => { - const protvistaDataTableElement = useCustomElement( - () => - import( - /* webpackChunkName: "protvista-datatable" */ 'protvista-datatable' - ), - 'protvista-datatable' - ); - const hasSubstrate = columns.includes('SUBSTRATE'); if (data && data.length) { return ( - - - - - {columns.map((name) => ( - - ))} - - - - {data.map((value) => ( - - - {hasSubstrate && ( - - )} - - - +
- {` ${name} `} -
- {value.constant} - - {value.substrate} - {value.ph}{value.temp} - {value.notes} -
+ + {columns.map((name) => ( + + ))} + + + {data.map((value, i) => ( + + + {hasSubstrate && ( - - ))} - -
+ {` ${name} `} + + {value.constant} + - + {value.substrate}
- + )} + {value.ph} + {value.temp} + + {value.notes} + + + + + + ))} + + ); } return null; diff --git a/src/uniprotkb/components/entry/__tests__/ProteinProcessingSection.spec.tsx b/src/uniprotkb/components/entry/__tests__/ProteinProcessingSection.spec.tsx index a290594322..396d77fee1 100644 --- a/src/uniprotkb/components/entry/__tests__/ProteinProcessingSection.spec.tsx +++ b/src/uniprotkb/components/entry/__tests__/ProteinProcessingSection.spec.tsx @@ -25,6 +25,11 @@ axiosMock .reply(404); describe('ProteinProcessingSection', () => { + beforeAll(() => { + jest.mock('@nightingale-elements/nightingale-sequence', () => jest.fn()); + jest.mock('@nightingale-elements/nightingale-track', () => jest.fn()); + }); + it('should render when PTMeXchange is available', async () => { const transformedData = uniProtKbConverter(mockHumanData, databaseInfoMaps); const { asFragment } = customRender( diff --git a/src/uniprotkb/components/entry/__tests__/__snapshots__/ComputationallyMappedSequences.spec.tsx.snap b/src/uniprotkb/components/entry/__tests__/__snapshots__/ComputationallyMappedSequences.spec.tsx.snap index 6b946b882f..8ce2a7a26a 100644 --- a/src/uniprotkb/components/entry/__tests__/__snapshots__/ComputationallyMappedSequences.spec.tsx.snap +++ b/src/uniprotkb/components/entry/__tests__/__snapshots__/ComputationallyMappedSequences.spec.tsx.snap @@ -69,24 +69,29 @@ exports[`Computationally mapped isoforms should render correctly 1`] = ` Entry Entry name Gene name Length diff --git a/src/uniprotkb/components/entry/__tests__/__snapshots__/EntryMain.spec.tsx.snap b/src/uniprotkb/components/entry/__tests__/__snapshots__/EntryMain.spec.tsx.snap index 057519af1b..80b6edb622 100644 --- a/src/uniprotkb/components/entry/__tests__/__snapshots__/EntryMain.spec.tsx.snap +++ b/src/uniprotkb/components/entry/__tests__/__snapshots__/EntryMain.spec.tsx.snap @@ -366,164 +366,180 @@ exports[`Entry view should render 1`] = ` Isoform 3 - - + - - - - - - - - - - - - - + + + + + + + + + + + + - - - - -
- KM - - SUBSTRATE - - pH - - TEMPERATURE[C] - - NOTES - - EVIDENCE -
+ + + KM + + SUBSTRATE + + pH + + TEMPERATURE[C] + + NOTES + + EVIDENCE +
+ + 2.0999999046325684 μM + + sub1 + + + + + - sub1 - - - - - -
-
- - - + PROSITE-ProRule annotation + + +
+ + + +
+ + - - - - - - - - - - - - + + + + + + + + + + + - - - - -
- Vmax - - pH - - TEMPERATURE[C] - - NOTES - - EVIDENCE -
+ + + Vmax + + pH + + TEMPERATURE[C] + + NOTES + + EVIDENCE +
+ + 1 μnit1 + + + + 1 + + - - - 1 - - -
-
- + + PROSITE-ProRule annotation + + +
+ + + +
value1.

value1.

value1. - + + + + XENO + + + + gen PROC_12345 P12345 + + + + + gene1 PROC_123454 P21802 + + + + 6 + + + + EBI-00011, EBI-00012 + + + + + + + + XENO + + + + gen PROC_12344 P21802 + + + + + gene1 PROC_12347 P12345-1 + + + + 3 + + + + EBI-0001, EBI-0002 + + + + + + @@ -3143,7 +3165,7 @@ exports[`Entry view should render 1`] = ` #keyword value

- - + - - - - - - - - - - - - - + + + + + + + + + + + + - - - - -
- KM - - SUBSTRATE - - pH - - TEMPERATURE[C] - - NOTES - - EVIDENCE -
+ + + KM + + SUBSTRATE + + pH + + TEMPERATURE[C] + + NOTES + + EVIDENCE +
+ + 340 μM + + A antigen type 1 penta-MU + + + + + - A antigen type 1 penta-MU - - - - - -
-
- + + 1 publication + + +
+ + + +

@@ -4060,7 +4090,7 @@ exports[`Entry view should render for non-human entry 1`] = ` > Optimum pH is 8.0.

@@ -4094,475 +4124,467 @@ exports[`Entry view should render for non-human entry 1`] = ` .

- -
- - - - - - - - - - - - - - - - - - - - + - - - - + + + + + + + + + + + + + + - - + +
+
- - - - + +
+ +
+ + + + + + + - - + +
+
- - - - + +
+ +
+ + + + + + + - - + +
+
- - - - + +
+ +
+ + + + + + + + + + + + + + + - - -
- Type - - ID - - Position(s) - - Description - -
- Binding site - - - 87 - - substrate - -
- -
-
-
- - Sequence: - - S -
+ - Binding site - - - 123 - - substrate - -
- -
-
-
+ Type + + ID + + Position(s) + + Description + +
+ + + Binding site + + + 87 + + substrate + - - Sequence: - - H -
- Binding site - - - 126 - - a divalent metal cation ( - - UniProtKB - - | - - ChEBI - - - ) - -
- -
-
-
+
+ + + Binding site + + + 123 + + substrate + - - Sequence: - - D -
- Binding site - - - 236 - - substrate - -
- -
-
-
+
+ + + Binding site + + + 126 + + a divalent metal cation ( + + UniProtKB + + | + + ChEBI + + + ) + - - Sequence: - - Y -
- Binding site - - - 278 - - a divalent metal cation ( - - UniProtKB - - | - - ChEBI - - - ) - -
- -
-
-
+
+ + + Binding site + + + 236 + + substrate + +
+ +
+
+
+ + + Binding site + + + 278 + + a divalent metal cation ( + + UniProtKB + + | + + ChEBI + + + ) + - - Sequence: - - H -
- - +
+ +
+ + + + - Expand table - -
- + + + +
@@ -4587,116 +4609,119 @@ exports[`Entry view should render for non-human entry 1`] = ` />
-
- - - - - - - - - - - - - - - - - - -
- Aspect - - Term -
- Molecular Function - - - hydrolase activity, acting on glycosyl bonds - - - -
-
- Molecular Function - - - metal ion binding - - - -
-
- - -
+ + + + Aspect + + + Term + + + + + + + + Molecular Function + + + + hydrolase activity, acting on glycosyl bonds + + + +
+ + + + + + Molecular Function + + + + metal ion binding + + + +
+ + + +

A type blood N-acetyl-alpha-D-galactosamine deacetylase

@@ -4937,7 +4962,7 @@ exports[`Entry view should render for non-human entry 1`] = ` ) +
+ + + + - Expand table - -
- + + + +
@@ -5735,383 +5752,395 @@ exports[`Entry view should render for non-human entry 1`] = ` .

- -
- - - - - - - - - - - - + + + + + + + + + + + + + + - - - - - + + + + + + + + + + + + - - + +
+ +
- - - - - + + + + + + + + + + + + - - + +
+ +
- - - - - + + + + + + + + + + + + - - + +
+ +
- - - - - + + - - -
- Type - - ID - - Position(s) - - Description - -
+ + + Type +
+ + 		+ ID + + Position(s) + + Description + +
+ + + Region + + + 180-402 + + Deacetylase activity + +
+
+
+
- Region - - - 180-402 - - Deacetylase activity - -
-
-
- - -
-
+ + + Domain + + + 494-605 + + F5/8 type C + - - Sequence: - - WSKPTSDAERQVADGEDDFITAIASPDRYDMLSPTIVYDDFRDVFILWANNTGDVGYQNGQANFVEMRYSDDGITWGEPVRVNGFLGLDENGQQLAPWHQDVQYVPDLKEFVCISQCFAGRNPDGSVLHLTTSKDGVNWEQVGTKPLLSPGPDGSWDDFQIYRSSFYYEPGSSAGDGTMRVWYSALQKDTNNKMVADSSGNLTIQAKSEDDRIWRIGYAENSF -
+
+
- Domain - - - 494-605 - - F5/8 type C - -
-
-
- - -
-
+ + + Region + + + 502-765 + + CBM32 carbohydrate-binding domain + - - Sequence: - - SDDLEIAVVENPYTLIPQSNMTATATSVYGGTTEGPASNVLDGNVRTIWHTNYAPKDELPQSITVSFDQPYTVGRFVYTPRQNGTNGIISEYELYAIHQDGSKDLVASGSDW -
+
+
- Region - - - 502-765 - - CBM32 carbohydrate-binding domain - -
-
-
- - -
-
+ + + Region + + + 515-772 + + Not required for activity on soluble substrates + - - Sequence: - - VENPYTLIPQSNMTATATSVYGGTTEGPASNVLDGNVRTIWHTNYAPKDELPQSITVSFDQPYTVGRFVYTPRQNGTNGIISEYELYAIHQDGSKDLVASGSDWALDAKDKTVSFAPVEAVGLELKAIAGAGGFGTAAELNVYAYGPIEPAPVYVPVDDRDASLVFTGAWNSDSNGSFYEGTARYTNEIGASVEFTFVGTAIRWYGQNDVNFGAAEVYVDGVLAGEVNVYGPAAAQQLLFEADGLAYGKHTIRIVCVSPVVDFD -
+
+
- Region - - - 515-772 - - Not required for activity on soluble substrates - -
-
-
- - -
-
- - Sequence: - - TATATSVYGGTTEGPASNVLDGNVRTIWHTNYAPKDELPQSITVSFDQPYTVGRFVYTPRQNGTNGIISEYELYAIHQDGSKDLVASGSDWALDAKDKTVSFAPVEAVGLELKAIAGAGGFGTAAELNVYAYGPIEPAPVYVPVDDRDASLVFTGAWNSDSNGSFYEGTARYTNEIGASVEFTFVGTAIRWYGQNDVNFGAAEVYVDGVLAGEVNVYGPAAAQQLLFEADGLAYGKHTIRIVCVSPVVDFDYFSYVGE -
- - +
+ + + - Expand table - - - + + + +

@@ -6122,7 +6151,7 @@ exports[`Entry view should render for non-human entry 1`] = ` > The deacetylase domain is in the N-terminus, while the C-terminus has a CBM32-type carbohydrate-binding domain that is not required for activity on soluble substrates. The CBM32 domain binds preferentially to repeating N-acetyl lactosamine structures. + + + + - Expand table - - - + + + + + + + + Modified residue (large scale data) + + + + 215 + + + PTMeXchange + + + Phosphoserine + + + + +
+ + + + + + + +
@@ -393,16 +437,13 @@ exports[`ProteinProcessingSection should render when no PTMeXchange is available .

- - +
- +
+ + + + - Expand table - - - + + + + diff --git a/src/uniprotkb/components/entry/similar-proteins/__tests__/__snapshots__/SimilarProteins.spec.tsx.snap b/src/uniprotkb/components/entry/similar-proteins/__tests__/__snapshots__/SimilarProteins.spec.tsx.snap index ae72e125d6..c21f08706e 100644 --- a/src/uniprotkb/components/entry/similar-proteins/__tests__/__snapshots__/SimilarProteins.spec.tsx.snap +++ b/src/uniprotkb/components/entry/similar-proteins/__tests__/__snapshots__/SimilarProteins.spec.tsx.snap @@ -69,19 +69,23 @@ exports[`SimilarProteins tests should fetch data and render 1`] = ` Protein name Organism Length @@ -183,19 +187,23 @@ exports[`SimilarProteins tests should fetch data and render 1`] = ` Protein name Organism Length diff --git a/src/uniprotkb/components/entry/styles/kinetics-table.module.scss b/src/uniprotkb/components/entry/styles/kinetics-table.module.scss index 3fb67cd72e..321e3013f9 100644 --- a/src/uniprotkb/components/entry/styles/kinetics-table.module.scss +++ b/src/uniprotkb/components/entry/styles/kinetics-table.module.scss @@ -1,3 +1,3 @@ .kinetics-table { - margin-bottom: 1em; + margin-bottom: 2em; } diff --git a/src/uniprotkb/components/entry/tabs/FeatureViewer.tsx b/src/uniprotkb/components/entry/tabs/FeatureViewer.tsx index b214e3f3aa..080c882ce6 100644 --- a/src/uniprotkb/components/entry/tabs/FeatureViewer.tsx +++ b/src/uniprotkb/components/entry/tabs/FeatureViewer.tsx @@ -1,31 +1,28 @@ -import { useCallback, useRef, useState } from 'react'; +import { useCallback, useEffect, useRef, useState } from 'react'; import { Link, useLocation } from 'react-router-dom'; import { Loader, Message } from 'franklin-sites'; import EntryDownloadPanel from '../../../../shared/components/entry/EntryDownloadPanel'; import EntryDownloadButton from '../../../../shared/components/entry/EntryDownloadButton'; -import NightingaleZoomTool, { - ZoomOperations, -} from '../../protein-data-views/NightingaleZoomTool'; +import NightingaleZoomTool from '../../protein-data-views/NightingaleZoomTool'; import useDataApi from '../../../../shared/hooks/useDataApi'; import useCustomElement from '../../../../shared/hooks/useCustomElement'; -import { UniProtkbAPIModel } from '../../../adapters/uniProtkbConverter'; import apiUrls from '../../../../shared/config/apiUrls/apiUrls'; import { Dataset } from '../../../../shared/components/entry/EntryDownload'; -import { VARIANT_COUNT_LIMIT } from './variation-viewer/VariationViewer'; import { getEntryPath } from '../../../../app/config/urls'; +import { showTooltipAtCoordinates } from '../../../../shared/utils/tooltip'; + +import { VARIANT_COUNT_LIMIT } from '../../../../shared/config/limits'; import { Namespace } from '../../../../shared/types/namespaces'; import { TabLocation } from '../../../types/entry'; +import { UniProtkbAPIModel } from '../../../adapters/uniProtkbConverter'; import tabsStyles from './styles/tabs-styles.module.scss'; -interface ProtvistaManager extends HTMLElement { - displaystart: number; - displayend: number; -} +const hideTooltipEvents = new Set([undefined, 'reset', 'click']); const FeatureViewer = ({ accession, @@ -38,54 +35,56 @@ const FeatureViewer = ({ }) => { const [displayDownloadPanel, setDisplayDownloadPanel] = useState(false); const protvistaUniprotRef = useRef(null); + const hideTooltip = useRef | null>(null); // just to make sure not to render protvista-uniprot if we won't get any data const { loading, data } = useDataApi( apiUrls.proteinsApi.proteins(accession) ); - const protvistaElement = useCustomElement( + const protvistaUniprotElement = useCustomElement( /* istanbul ignore next */ () => import(/* webpackChunkName: "protvista-uniprot" */ 'protvista-uniprot'), 'protvista-uniprot' ); - const handleZoom = useCallback( - (operation: ZoomOperations) => { - if (!protvistaElement.defined || !protvistaUniprotRef.current) { - return; - } - const manager: ProtvistaManager | null = - protvistaUniprotRef.current.querySelector('protvista-manager'); - if (!manager) { - return; - } - // Following logic is lifted from ProtvistaZoomTool - const scaleFactor = sequence.length / 5; - const { displayend, displaystart } = manager; - let k = 0; - if (operation === 'zoom-in') { - k = scaleFactor; - } else if (operation === 'zoom-out') { - k = -scaleFactor; - } else if (operation === 'zoom-in-seq') { - k = displayend - displaystart - 29; - } - const newEnd = displayend - k; - let newStart = displaystart; - // if we've reached the end when zooming out, remove from start - if (newEnd > sequence.length) { - newStart -= newEnd - sequence.length; - } - if (displaystart < newEnd) { - manager.setAttribute('displaystart', Math.max(1, newStart).toString()); - manager.setAttribute( - 'displayend', - Math.min(newEnd, sequence.length).toString() - ); - } + const onProtvistaUniprotChange = useCallback((e: Event) => { + const { detail } = e as CustomEvent; + if (hideTooltipEvents.has(detail?.eventType)) { + hideTooltip.current?.(); + } + if ( + detail?.eventType === 'click' && + detail?.feature?.tooltipContent && + e.target + ) { + const [x, y] = detail.coords; + const { feature } = detail; + const title = + feature.type && feature.start && feature.end + ? `

${feature.type} ${feature.start}-${feature.end}

` + : ''; + const content = `${title}${detail.feature.tooltipContent}`; + hideTooltip.current = showTooltipAtCoordinates(x, y, content); + } + }, []); + + useEffect(() => { + const ref = protvistaUniprotRef.current; + ref?.addEventListener('change', onProtvistaUniprotChange); + }, [onProtvistaUniprotChange, protvistaUniprotElement]); + + useEffect( + () => () => { + hideTooltip.current?.(); + protvistaUniprotRef.current?.removeEventListener( + 'change', + onProtvistaUniprotChange + ); }, - [protvistaElement.defined, sequence] + [onProtvistaUniprotChange] ); const searchParams = new URLSearchParams(useLocation().search); @@ -120,13 +119,20 @@ const FeatureViewer = ({ {data?.features && ( <> {shouldRender && ( - + + protvistaUniprotRef.current?.querySelector( + 'nightingale-navigation' + ) || null + } + /> )} )} {shouldRender ? ( - diff --git a/src/uniprotkb/components/entry/tabs/genomic-coordinates/__tests__/__snapshots__/GenomicCoordinates.spec.tsx.snap b/src/uniprotkb/components/entry/tabs/genomic-coordinates/__tests__/__snapshots__/GenomicCoordinates.spec.tsx.snap index e1505800bb..b4c4860f48 100644 --- a/src/uniprotkb/components/entry/tabs/genomic-coordinates/__tests__/__snapshots__/GenomicCoordinates.spec.tsx.snap +++ b/src/uniprotkb/components/entry/tabs/genomic-coordinates/__tests__/__snapshots__/GenomicCoordinates.spec.tsx.snap @@ -255,469 +255,465 @@ exports[`GenomicCoordinates component renders on data 1`] = ` -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + - + + + + + + + + + - - - - - - - + + + + + + + + + - + + + + + + + + + - + + + + + + + + + - - - - - - - + + + + + + + + + - + + + + + + + + + - + + + + + + + + + - - - - -
- - - Exon coordinates - - - O00560 - -
- - - - 8:58,565,034 - 58,565,084 - - - - 1 - - - - - 17 - -
- - - - 8:58,570,887 - 58,570,965 - - - - 18 - - - - - 44 - -
- - - - 8:58,572,205 - 58,572,314 - - - - 44 - - - - - 80 - -
- - - - 8:58,575,900 - 58,576,061 - - - - 81 - - - - - 134 - -
- - - - 8:58,578,033 - 58,578,208 - - - - 135 - - - - + -
- - - 8:58,579,623 - 58,579,794 - - - + + + Exon coordinates + + - 193 - - + +
+ + + - - - + + + 1 + + - + + 17 + +
+ + + - 250 - -
- - - - 8:58,580,517 - 58,580,608 - - - + + + 18 + + - + + 44 + +
+ + + - 251 - + + + 44 + + - + + 80 + +
+ + + - - - + + + 81 + + - + + 134 + +
+ + + - 281 - -
- - - - 8:58,581,686 - 58,581,737 - - - + + + 135 + + - + + 193 + +
+ + + - 281 - + + + 193 + + - + + 250 + +
+ + + - - - + + + 251 + + - + + 281 + +
+ + + - 298 - -
-
+ 8:58,581,686 - 58,581,737 + + + + + 281 + + + - + + + 298 + + + + + + + + diff --git a/src/uniprotkb/components/entry/tabs/variation-viewer/VariationViewer.tsx b/src/uniprotkb/components/entry/tabs/variation-viewer/VariationViewer.tsx index e1245c3d26..afbf60632e 100644 --- a/src/uniprotkb/components/entry/tabs/variation-viewer/VariationViewer.tsx +++ b/src/uniprotkb/components/entry/tabs/variation-viewer/VariationViewer.tsx @@ -7,36 +7,50 @@ import { lazy, ReactNode, Suspense, + useId, } from 'react'; import { Link, useLocation } from 'react-router-dom'; import { EllipsisReveal, Loader, LongNumber, Message } from 'franklin-sites'; -import { groupBy, intersection, union } from 'lodash-es'; import cn from 'classnames'; import { PartialDeep, SetRequired } from 'type-fest'; - -import { ProteinsAPIVariation } from 'protvista-variation-adapter/dist/es/variants'; -import { transformData, TransformedVariant } from 'protvista-variation-adapter'; +import { + ProteinsAPIVariation, + transformData, +} from '@nightingale-elements/nightingale-variation'; +import NightingaleManager from '@nightingale-elements/nightingale-manager'; +import { filterConfig } from 'protvista-uniprot'; import ExternalLink from '../../../../../shared/components/ExternalLink'; import UniProtKBEvidenceTag from '../../../protein-data-views/UniProtKBEvidenceTag'; -import DatatableWrapper from '../../../../../shared/components/views/DatatableWrapper'; import ErrorHandler from '../../../../../shared/components/error-pages/ErrorHandler'; import EntryDownloadPanel from '../../../../../shared/components/entry/EntryDownloadPanel'; import EntryDownloadButton from '../../../../../shared/components/entry/EntryDownloadButton'; +import NightingaleManagerComponent from '../../../../../shared/custom-elements/NightingaleManager'; +import TableFromData, { + TableFromDataColumn, +} from '../../../../../shared/components/table/TableFromData'; import useDataApi from '../../../../../shared/hooks/useDataApi'; -import useCustomElement from '../../../../../shared/hooks/useCustomElement'; import { useSmallScreen } from '../../../../../shared/hooks/useMatchMedia'; +import useNightingaleFeatureTableScroll from '../../../../../shared/hooks/useNightingaleFeatureTableScroll'; import apiUrls from '../../../../../shared/config/apiUrls/apiUrls'; import externalUrls from '../../../../../shared/config/externalUrls'; + import { sortByLocation } from '../../../../utils'; import { getEntryPath } from '../../../../../app/config/urls'; +import { + NightingaleViewRange, + withinRange, +} from '../../../../../shared/utils/nightingale'; + +import { VARIANT_COUNT_LIMIT } from '../../../../../shared/config/limits'; import { Evidence } from '../../../../types/modelTypes'; import { Namespace } from '../../../../../shared/types/namespaces'; import { TabLocation } from '../../../../types/entry'; import { Dataset } from '../../../../../shared/components/entry/EntryDownload'; +import { TransformedVariant } from '../../../../types/variation'; import styles from './styles/variation-viewer.module.scss'; import tabsStyles from '../styles/tabs-styles.module.scss'; @@ -49,9 +63,6 @@ const VisualVariationView = lazy( ) ); -// hardcoded threshold -export const VARIANT_COUNT_LIMIT = 2_000; - type ProteinsAPIEvidence = SetRequired< PartialDeep[number]>, 'code' @@ -75,54 +86,321 @@ const isUniProt = (string: string) => string === 'UniProt'; const sortProvenanceByUniProtFirst = (a: string, b: string) => +isUniProt(b) - +isUniProt(a); -type ObjWithVariants = { variants: TransformedVariant[] }; +const groupByCategory = (filters: FilterConfig, category: string) => + filters.filter((f) => f.type.name === category); -type Filter = { - category: string; - filterFn: (obj: ObjWithVariants[]) => ObjWithVariants[]; -}; +type FilterConfig = typeof filterConfig; +type FilterConfigItem = FilterConfig[0]; -// copied/adapted logic from protvista-variation -const deepArrayOperation = ( - arrays: ObjWithVariants[][], - operation: typeof union | typeof intersection -) => { - if (!arrays || arrays.length <= 0) { - return null; - } - const firstArray = arrays[0]; - // Iterate over positions - firstArray.forEach((position, i) => { - const filteredVariants = arrays.map((array) => array[i].variants); - /* eslint-disable no-param-reassign */ - position.variants = operation(...filteredVariants); - }); - return firstArray; -}; +const getFilter = (haystack: FilterConfig, needle: FilterConfigItem) => + haystack?.find((f) => f.name === needle.name); -// copied/adapted logic from protvista-variation -const applyFilters = (variants: TransformedVariant[], filters: Filter[]) => { +// copied/adapted logic from protvista-uniprot +const applyFilters = (variants: TransformedVariant[], filters: string[]) => { if (!filters.length) { return variants; } - const originalData: ObjWithVariants[] = [{ variants }]; - - const groupedFilters = groupBy(filters, 'category'); - const filteredGroups = Object.values(groupedFilters).map((filterGroup) => { - const filteredData = filterGroup.map((filterItem) => - filterItem.filterFn(originalData) + const activeFilters = filterConfig.filter((f) => filters.includes(f.name)); + const consequenceFilters = groupByCategory(activeFilters, 'consequence'); + const provenanceFilters = groupByCategory(activeFilters, 'provenance'); + + const selectedConsequenceFilters = activeFilters + .map((f) => getFilter(consequenceFilters, f)) + .filter(Boolean); + const selectedProvenanceFilters = activeFilters + .map((f) => getFilter(provenanceFilters, f)) + .filter(Boolean); + + const filteredVariants = variants + ?.filter((variant) => + selectedConsequenceFilters.some((filter) => + filter?.filterPredicate(variant) + ) + ) + .filter((variant) => + selectedProvenanceFilters.some((filter) => + filter?.filterPredicate(variant) + ) ); - // Basically, *within* groups, logical OR... - return deepArrayOperation(filteredData, union) || []; - }); - - const transformedData = - // ... and, *across* groups, logical AND - deepArrayOperation(filteredGroups, intersection) || []; - return transformedData[0]?.variants; + return filteredVariants; }; +const getHighlightedCoordinates = (feature?: TransformedVariant) => + feature?.begin && feature?.end + ? `${feature.begin}:${feature.end}` + : undefined; + +const getRowId = (data: TransformedVariant) => data.accession; + +const getColumns = ( + primaryAccession: string +): TableFromDataColumn[] => [ + { + id: 'variant-id', + label: ( + <> + Variant +
+ ID(s) + + ), + render: (data) => ( + <> + { + // note that the type needs to be updated, xrefs is optional on association object + Array.from(new Set(data.xrefs?.map((xref) => xref.id))) + .sort(sortIDByUniProtFirst) + .map((id, i) => ( + + {i !== 0 &&
} + + {id} + + + )) + } + + ), + }, + { + id: 'position', + label: 'Position(s)', + render: (data) => + `${data.start}${+data.end === data.start ? '' : `-${data.end}`}`, + }, + { + id: 'change', + label: 'Change', + render: (data) => { + let from: ReactNode = data.wildType; + if (!data.wildType) { + from = missing; + } else if (data.wildType.length > 3) { + from = ( + <> + {data.wildType.slice(0, 2)} + {data.wildType.slice(2)} + + ); + } + + let to: ReactNode = data.alternativeSequence; + if (!data.alternativeSequence) { + to = missing; + } else if (data.alternativeSequence.length > 3) { + to = ( + <> + {data.alternativeSequence.slice(0, 2)} + {data.alternativeSequence.slice(2)} + + ); + } + + const change = ( + <> + {from} + {'>'} + {to} + + ); + + return ( + + {data.consequenceType !== '-' && + data.wildType?.length === 1 && + data.alternativeSequence?.length === 1 ? ( + + {change} + + ) : ( + change + )} + + ); + }, + }, + { + id: 'description', + label: 'Description', + render: (data) => { + const uniProtEvidences = data.evidences?.map( + (evidence: ProteinsAPIEvidence) => + ({ + evidenceCode: evidence.code, + id: evidence?.source?.id, + source: evidence?.source?.name, + url: evidence?.source?.url, + }) as Evidence + ); + + return data.descriptions?.length ? ( + Array.from(data.descriptions) + .sort(sortDescriptionByUniProtFirst) + .map((description) => ( +
+ {`${description.value} (${description.sources.join(', ')})`} + +
+ )) + ) : ( + + ); + }, + }, + { + id: 'clinical-significance', + label: ( + <> + Clinical +
+ significance + + ), + render: (data) => + data.clinicalSignificances?.map((clinicalSignificance, i) => ( + // eslint-disable-next-line react/no-array-index-key + + {i !== 0 &&
} + + {`${clinicalSignificance.type} (${clinicalSignificance.sources.join( + ', ' + )})`} + + + )), + }, + { + id: 'provenance', + label: 'Provenance', + render: (data) => + Array.from( + new Set( + data.xrefNames.map((name) => (name === 'uniprot' ? 'UniProt' : name)) + ) + ) + .sort(sortProvenanceByUniProtFirst) + .map((name, i) => ( + + {i !== 0 &&
} + + {name} + + + )), + }, +]; + +const RowExtraContent = (data: TransformedVariant) => ( + +
+ Consequence: + {data.consequenceType} +
+ {data.predictions?.length ? ( +
+ Predictions: + {data.predictions?.map((pred) => ( +
+ {`- ${pred.predAlgorithmNameType}: ${pred.predictionValType} (${pred.score})`} +
+ ))} +
+ ) : null} +
+ Somatic: {data.somaticStatus === 1 ? 'Yes' : 'No'} +
+ {data.populationFrequencies?.length ? ( +
+ Population frequencies: + {data.populationFrequencies?.map((populationFrequency) => ( +
+ {`- ${populationFrequency.populationName}: ${populationFrequency.frequency} (${populationFrequency.source})`} +
+ ))} +
+ ) : null} +
+ Accession: {data.accession} +
+ {data.codon && ( +
+ Codon: {data.codon} +
+ )} +
+ Consequence type: {data.consequenceType} +
+
+ Cytogenetic band: {data.cytogeneticBand} +
+
+ Genomic location: {data.genomicLocation?.join(', ')} +
+ {data.locations?.length ? ( +
+ Locations: + {data.locations?.map((location) => ( +
+ {`- ${location.loc} (${location.source}:${location.seqId})`} +
+ ))} +
+ ) : null} + {data.association?.length ? ( +
+ Disease association: + {data.association?.map((association) => ( +
+ {'- '} + {association.name} +
+ ))} +
+ ) : null} +
+ Source type: {data.sourceType?.replace(/_/g, ' ')} +
+ {/* note that the type needs to be updated, xrefs is optional on association object */} + {/* Also, some xrefs don't have URLs... type should be optional */} + {data.xrefs?.length ? ( +
+ Cross-references: + {data.xrefs?.map((xref) => ( +
+ {'- '} + + {xref.name}: {xref.id} + +
+ ))} +
+ ) : null} + +); + type VariationViewProps = { importedVariants: number | 'loading'; primaryAccession: string; @@ -135,6 +413,13 @@ const VariationViewer = ({ title, }: VariationViewProps) => { const isSmallScreen = useSmallScreen(); + const [highlightedVariant, setHighlightedVariant] = + useState(); + const [nightingaleViewRange, setNightingaleViewRange] = + useState(); + const tableId = useId(); + const tableScroll = useNightingaleFeatureTableScroll(getRowId, tableId); + const searchParams = new URLSearchParams(useLocation().search); const loadAllVariants = searchParams.get('loadVariants'); @@ -150,8 +435,8 @@ const VariationViewer = ({ shouldRender ? apiUrls.proteinsApi.variation(primaryAccession) : undefined ); - const [filters, setFilters] = useState([]); - const managerRef = useRef(null); + const [filters, setFilters] = useState([]); + const managerRef = useRef(null); useEffect(() => { const { current: element } = managerRef; @@ -163,13 +448,18 @@ const VariationViewer = ({ const { detail } = event as CustomEvent; if (detail?.type === 'filters') { setFilters(detail.value); + } else if (detail?.eventType === 'click' && detail?.feature) { + setHighlightedVariant(detail.feature); + tableScroll(detail.feature); + } else if (detail?.['display-start'] && detail?.['display-end']) { + setNightingaleViewRange(detail); } }; element.addEventListener('change', listener); // eslint-disable-next-line consistent-return return () => element.removeEventListener('change', listener); - }, [data]); + }, [data, tableScroll]); // 'data' is not directly used in the effect, but we know it's when we're // ready to attach the event listener and avoid re-calling this on each render @@ -192,15 +482,10 @@ const VariationViewer = ({ // Filter data on every filter interaction out of the memoised sorted data const filteredVariants = useMemo( - () => sortedVariants && applyFilters(sortedVariants, filters), - [sortedVariants, filters] - ); - - const managerElement = useCustomElement( - /* istanbul ignore next */ () => - import(/* webpackChunkName: "protvista-manager" */ 'protvista-manager'), - 'protvista-manager' + sortedVariants && + applyFilters(sortedVariants as TransformedVariant[], filters), + [sortedVariants, filters] ); if (loading || importedVariants === 'loading') { @@ -278,307 +563,15 @@ const VariationViewer = ({ ); } - const table = ( - - - - - - - - - - - - - {filteredVariants.map((variantFeature) => { - let position = variantFeature.start; - if (variantFeature.start !== variantFeature.end) { - position += `-${variantFeature.end}`; - } - - const uniProtEvidences = variantFeature.evidences?.map( - (evidence: ProteinsAPIEvidence) => - ({ - evidenceCode: evidence.code, - id: evidence?.source?.id, - source: evidence?.source?.name, - url: evidence?.source?.url, - } as Evidence) - ); - - let from: ReactNode = variantFeature.wildType; - if (!variantFeature.wildType) { - from = missing; - } else if (variantFeature.wildType.length > 3) { - from = ( - <> - {variantFeature.wildType.slice(0, 2)} - - {variantFeature.wildType.slice(2)} - - - ); - } - - let to: ReactNode = variantFeature.alternativeSequence; - if (!variantFeature.alternativeSequence) { - to = missing; - } else if (variantFeature.alternativeSequence.length > 3) { - to = ( - <> - {variantFeature.alternativeSequence.slice(0, 2)} - - {variantFeature.alternativeSequence.slice(2)} - - - ); - } - - const change = ( - <> - {from} - {'>'} - {to} - - ); - - return ( - - - - - - - - - - - - - - ); - })} - -
- Variant -
- ID(s) - 		Position(s)ChangeDescription - Clinical -
- significance - 		Provenance
- {Array.from( - // note that the type needs to be updated, xrefs is optional on association object - new Set(variantFeature.xrefs?.map((xref) => xref.id)) - ) - .sort(sortIDByUniProtFirst) - .map((id, i) => ( - - {i !== 0 &&
} - - {id} - - - ))} - 		{position} - {variantFeature.consequenceType !== '-' && - variantFeature.wildType?.length === 1 && - variantFeature.alternativeSequence?.length === 1 ? ( - - {change} - - ) : ( - change - )} - {!variantFeature.wildType && - !variantFeature.alternativeSequence && missing} - - {variantFeature.descriptions?.length ? ( - Array.from(variantFeature.descriptions) - .sort(sortDescriptionByUniProtFirst) - .map((description) => ( -
- {`${description.value} (${description.sources.join( - ', ' - )})`} - -
- )) - ) : ( - - )} - 		- {variantFeature.clinicalSignificances?.map( - (clinicalSignificance, i) => ( - // eslint-disable-next-line react/no-array-index-key - - {i !== 0 &&
} - - {`${ - clinicalSignificance.type - } (${clinicalSignificance.sources.join(', ')})`} - - - ) - )} - 		- {Array.from( - new Set( - // 'uniprot' gets injected somehow in - // 'protvista-variation-adapter' transformData, remove it - variantFeature.xrefNames.map((name) => - name === 'uniprot' ? 'UniProt' : name - ) - ) - ) - .sort(sortProvenanceByUniProtFirst) - .map((name, i) => ( - - {i !== 0 &&
} - - {name} - - - ))} -
-
- Consequence: - {variantFeature.consequenceType} -
- {variantFeature.predictions?.length ? ( -
- Predictions: - {variantFeature.predictions?.map((pred) => ( -
- {`- ${pred.predAlgorithmNameType}: ${pred.predictionValType} (${pred.score})`} -
- ))} -
- ) : null} -
- Somatic: {' '} - {variantFeature.somaticStatus === 1 ? 'Yes' : 'No'} -
- {variantFeature.populationFrequencies?.length ? ( -
- Population frequencies: - {variantFeature.populationFrequencies?.map( - (populationFrequency) => ( -
- {`- ${populationFrequency.populationName}: ${populationFrequency.frequency} (${populationFrequency.source})`} -
- ) - )} -
- ) : null} -
- Accession: {variantFeature.accession} -
- {variantFeature.codon && ( -
- Codon: {variantFeature.codon} -
- )} -
- Consequence type: {' '} - {variantFeature.consequenceType} -
-
- Cytogenetic band: {' '} - {variantFeature.cytogeneticBand} -
-
- Genomic location: {' '} - {variantFeature.genomicLocation?.join(', ')} -
- {variantFeature.locations?.length ? ( -
- Locations: - {variantFeature.locations?.map((location) => ( -
- {`- ${location.loc} (${location.source}:${location.seqId})`} -
- ))} -
- ) : null} - {variantFeature.association?.length ? ( -
- Disease association: - {variantFeature.association?.map((association) => ( -
- {'- '} - {association.name} -
- ))} -
- ) : null} -
- Source type: {' '} - {variantFeature.sourceType.replace(/_/g, ' ')} -
- {/* note that the type needs to be updated, xrefs is optional on association object */} - {/* Also, some xrefs don't have URLs... type should be optional */} - {variantFeature.xrefs?.length ? ( -
- Cross-references: - {variantFeature.xrefs?.map((xref) => ( -
- {'- '} - - {xref.name}: {xref.id} - -
- ))} -
- ) : null} -
- ); - if (isSmallScreen) { return (
{title &&

{title}

} - {table} +
); } @@ -593,15 +586,34 @@ const VariationViewer = ({ /> )} - - + - {table} - + + + typeof highlightedVariant?.accession !== 'undefined' && + datum.accession === highlightedVariant.accession + } + markBorder={(datum) => + Boolean(nightingaleViewRange) && + withinRange(+datum.begin, +datum.end, nightingaleViewRange) + } + /> ); }; diff --git a/src/uniprotkb/components/entry/tabs/variation-viewer/__tests__/VariationViewer.spec.tsx b/src/uniprotkb/components/entry/tabs/variation-viewer/__tests__/VariationViewer.spec.tsx index fd2a9c50cc..fffb2f4584 100644 --- a/src/uniprotkb/components/entry/tabs/variation-viewer/__tests__/VariationViewer.spec.tsx +++ b/src/uniprotkb/components/entry/tabs/variation-viewer/__tests__/VariationViewer.spec.tsx @@ -16,6 +16,19 @@ jest.mock('../../../../protein-data-views/VisualVariationView', () => ({ })); describe('VariationViewer component', () => { + beforeEach(() => { + let counter = 0; + const step = 0.01; + jest.spyOn(global.Math, 'random').mockImplementation(() => { + counter += 1; + return counter * step; + }); + }); + + afterEach(() => { + jest.spyOn(global.Math, 'random').mockRestore(); + }); + it('renders on loading', () => { (useDataApi as jest.Mock).mockReturnValue({ loading: true }); const { asFragment } = customRender( @@ -61,11 +74,13 @@ describe('VariationViewer component', () => { ); expect(asFragment()).toMatchSnapshot(); + // Add 1 for thead row + expect(screen.getAllByRole('row')).toHaveLength(P0DPR0.features.length + 1); // TODO: see if this can be changed after the big Nightingale upgrade // At the moment it's taking the variants from this mock: // __mocks__/protvista-variation-adapter.js // See if this mock can be removed altogether - expect(screen.getAllByRole('row')).toHaveLength(5); + // expect(screen.getAllByRole('row')).toHaveLength(5); // expect(screen.getAllByRole('row')).toHaveLength(P0DPR0.features.length); }); }); diff --git a/src/uniprotkb/components/entry/tabs/variation-viewer/__tests__/__mocks__/P0DPR0.ts b/src/uniprotkb/components/entry/tabs/variation-viewer/__tests__/__mocks__/P0DPR0.ts index cf0c8e5632..cd2bec0a32 100644 --- a/src/uniprotkb/components/entry/tabs/variation-viewer/__tests__/__mocks__/P0DPR0.ts +++ b/src/uniprotkb/components/entry/tabs/variation-viewer/__tests__/__mocks__/P0DPR0.ts @@ -1,4 +1,4 @@ -import { ProteinsAPIVariation } from 'protvista-variation-adapter/dist/es/variants'; +import { ProteinsAPIVariation } from '@nightingale-elements/nightingale-variation'; // Source: https://www.ebi.ac.uk/proteins/api/variation/P0DPR0 // Retrieved: 2024-12-10 diff --git a/src/uniprotkb/components/entry/tabs/variation-viewer/__tests__/__snapshots__/VariationViewer.spec.tsx.snap b/src/uniprotkb/components/entry/tabs/variation-viewer/__tests__/__snapshots__/VariationViewer.spec.tsx.snap index 2baadc21bc..4c3dca7d6f 100644 --- a/src/uniprotkb/components/entry/tabs/variation-viewer/__tests__/__snapshots__/VariationViewer.spec.tsx.snap +++ b/src/uniprotkb/components/entry/tabs/variation-viewer/__tests__/__snapshots__/VariationViewer.spec.tsx.snap @@ -12,292 +12,613 @@ exports[`VariationViewer component renders on data 1`] = ` Download - + -
- -
- - - - - - - - - - - - + - - - - + + + + + + + + + + + + + + + - - + + + + + + + + + + + - - - - - + >SK + - - -
- Variant -
- ID(s) - 		- Position(s) - - Change - - Description - - Clinical -
- significance - 		- Provenance -
- - 8-10 - - B> - - missing - - -
- a description (uniprot) -
- 		- -
+ Variant +
+ ID(s) + 		+ Position(s) + + Change + + Description + + Clinical +
+ significance + 		+ Provenance +
+ + + + 22 + + + - -
- - Consequence: - -
-
- - Somatic: - - Yes -
-
- - Accession: - - NC_000021.9:g.26170608A>C -
-
- - Consequence type: - - -
-
- - Cytogenetic band: - - -
-
- - Genomic location: - - -
-
- - Source type: - - large scale study -
-
+
+ strain: Type C / C-6814 (UniProt) +
+ 		+ + + UniProt + +
+ + + + 39-44 + + + NK + - - rs1446208112 - - - 10 - - - L>A - - - - - - TOPMed - -
- - gnomAD - -
-
- - Consequence: - - missense -
-
- - Predictions: - -
- - PolyPhen: benign (0.001) -
-
- - SIFT: tolerated (0.26) -
-
-
- - Somatic: - - No -
-
- - Accession: - - NC_000021.9:g.26170608A>C -
-
- - Codon: - - TTG/GTG -
-
- - Consequence type: - - missense -
-
- - Cytogenetic band: - - 21q21.3 -
-
- - Genomic location: - - NC_000021.9:g.26170608A>C -
-
- - Locations: - -
- - p.Leu5Val (Ensembl:ENST00000346798) -
-
- - c.13T>G (Ensembl:ENST00000346798) -
-
-
- - Source type: - - large scale study -
-
- - Cross-references: - - - -
-
- - - + [...] + + + + +
+ strain: Type C / C-6814 (UniProt) +
+ + + + + UniProt + + + + + + + + + + + + + 74 + + + + + N>D + + + + +
+ strain: Type C / C-6814 (UniProt) +
+ + + + + UniProt + + + + + + + + + + + + + 88-89 + + + + GD>TN + + + +
+ strain: Type C / C-6814 (UniProt) +
+ + + + + UniProt + + + + + + + + + + + + + 98 + + + + + N>D + + + + +
+ strain: Type C / C-6814 (UniProt) +
+ + + + + UniProt + + + + + + + + + + + + + 106 + + + + + I>L + + + + +
+ strain: Type C / C-6814 (UniProt) +
+ + + + + UniProt + + + + + + + + + + + + + 120 + + + + + I>T + + + + +
+ strain: Type C / C-6814 (UniProt) +
+ + + + + UniProt + + + + + + + + + + + + + 125 + + + + + M>I + + + + +
+ strain: Type C / C-6814 (UniProt) +
+ + + + + UniProt + + + + + + + + + + + + + 133 + + + + + S>N + + + + +
+ strain: Type C / C-6814 (UniProt) +
+ + + + + UniProt + + + + + + + + + + + + + 267 + + + + + H>N + + + + +
+ strain: Type C / C-6814 (UniProt) +
+ + + + + UniProt + + + + + + + + `; diff --git a/src/uniprotkb/components/protein-data-views/DiseaseInvolvementView.tsx b/src/uniprotkb/components/protein-data-views/DiseaseInvolvementView.tsx index 09aa62ea42..9ee0df269e 100644 --- a/src/uniprotkb/components/protein-data-views/DiseaseInvolvementView.tsx +++ b/src/uniprotkb/components/protein-data-views/DiseaseInvolvementView.tsx @@ -5,9 +5,9 @@ import { escapeRegExp } from 'lodash-es'; import UniProtKBEvidenceTag from './UniProtKBEvidenceTag'; import { XRef } from './XRefView'; -import DatatableWrapper from '../../../shared/components/views/DatatableWrapper'; import ExternalLink from '../../../shared/components/ExternalLink'; import { RichText } from './FreeTextView'; +import Table from '../../../shared/components/table/Table'; import useDatabaseInfoMaps from '../../../shared/hooks/useDatabaseInfoMaps'; @@ -79,69 +79,60 @@ const DiseaseVariants = ({ }: { variants: FeatureDatum[]; accession: string; -}) => { - const table = ( - - - - - - - - - - - {variants.map((variant, i) => { - let position = `${variant.location.start.value}`; - if (variant.location.start.value !== variant.location.end.value) { - position += `-${variant.location.end.value}`; - } - - let { description } = variant; +}) => ( +
Variant IDPosition(s)ChangeDescription
+ + + + + + + + {variants.map((variant, i) => { + let position = `${variant.location.start.value}`; + if (variant.location.start.value !== variant.location.end.value) { + position += `-${variant.location.end.value}`; + } - if (variant.location.sequence) { - description = `In isoform ${variant.location.sequence}; ${description}`; - } + let { description } = variant; - return ( - // eslint-disable-next-line react/no-array-index-key - - - - - - - - - ); - })} - -
Variant IDPosition(s)ChangeDescription
- {variant.alternativeSequence?.originalSequence?.length === - 1 && - variant.alternativeSequence?.alternativeSequences?.[0] - .length === 1 && - variant.featureId ? ( - - {variant.featureId} - - ) : ( - variant.featureId - )} - {position} - {protvarVariantLink(variant, accession)} - - {description} - -
- ); + if (variant.location.sequence) { + description = `In isoform ${variant.location.sequence}; ${description}`; + } - return {table}; -}; + return ( + // eslint-disable-next-line react/no-array-index-key + + + {variant.alternativeSequence?.originalSequence?.length === 1 && + variant.alternativeSequence?.alternativeSequences?.[0].length === + 1 && + variant.featureId ? ( + + {variant.featureId} + + ) : ( + variant.featureId + )} + + {position} + + {protvarVariantLink(variant, accession)} + + + {description} + + + + ); + })} + + +); const reDiseaseAcronymSentence = /^in [^;]+(;|$)/i; diff --git a/src/uniprotkb/components/protein-data-views/EMBLView.tsx b/src/uniprotkb/components/protein-data-views/EMBLView.tsx index ba72773a6e..fc2e8af66e 100644 --- a/src/uniprotkb/components/protein-data-views/EMBLView.tsx +++ b/src/uniprotkb/components/protein-data-views/EMBLView.tsx @@ -1,5 +1,6 @@ import ExternalLink from '../../../shared/components/ExternalLink'; -import DatatableWrapper from '../../../shared/components/views/DatatableWrapper'; + +import Table from '../../../shared/components/table/Table'; import useDatabaseInfoMaps from '../../../shared/hooks/useDatabaseInfoMaps'; @@ -74,22 +75,23 @@ const EMBLView = ({ xrefs }: { xrefs: Xref[] }) => { PropertyKey.ProteinId )?.uriLink; - const table = ( - - - - - - - - - - + return ( +
Nucleotide SequenceProtein SequenceMolecule TypeStatus
10}> + + + + + + + {data.map( - (d) => + (d, i) => d && (d.proteinId || d.sequenceId) && ( - + - + ) )} - -
Nucleotide SequenceProtein SequenceMolecule TypeStatus
{d.sequenceId ? ( <> @@ -162,13 +164,12 @@ const EMBLView = ({ xrefs }: { xrefs: Xref[] }) => { : '-'} {d.status}
+ + ); - return {table}; }; export default EMBLView; diff --git a/src/uniprotkb/components/protein-data-views/NightingaleZoomTool.tsx b/src/uniprotkb/components/protein-data-views/NightingaleZoomTool.tsx index dd78fcf17b..30258f673f 100644 --- a/src/uniprotkb/components/protein-data-views/NightingaleZoomTool.tsx +++ b/src/uniprotkb/components/protein-data-views/NightingaleZoomTool.tsx @@ -1,56 +1,95 @@ +import { RefObject, useCallback } from 'react'; import { ZoomIn, ZoomOut, ZoomToSequence } from 'franklin-sites'; -import useCustomElement from '../../../shared/hooks/useCustomElement'; +import NightingaleNavigation from '@nightingale-elements/nightingale-navigation'; -import './styles/nightingale-zoom-tool.scss'; +import styles from './styles/nightingale-zoom-tool.module.scss'; export type ZoomOperations = 'zoom-in' | 'zoom-out' | 'zoom-in-seq'; // Icons and icon size TBD once designed. export const iconSize = 19; +type Props = { + length: number; + nightingaleNavigationRef?: RefObject | null; + nightingaleNavigationGetter?: () => NightingaleNavigation | null; +}; + const NightingaleZoomTool = ({ length, - onZoom, -}: { - length: number; - onZoom?: (x: ZoomOperations) => void; -}) => { - const protvistaZoomToolElement = useCustomElement( - /* istanbul ignore next */ - () => - import( - /* webpackChunkName: "protvista-zoom-tool" */ 'protvista-zoom-tool' - ), - 'protvista-zoom-tool' + nightingaleNavigationRef, + nightingaleNavigationGetter, +}: Props) => { + const handleZoom = useCallback( + (operation: ZoomOperations) => { + const nightingaleNavigation = + nightingaleNavigationRef?.current || nightingaleNavigationGetter?.(); + if (!nightingaleNavigation) { + return; + } + // Following logic is lifted from ProtvistaZoomTool + const scaleFactor = length / 5; + const { 'display-end': displayEnd, 'display-start': displayStart } = + nightingaleNavigation; + if ( + typeof displayEnd === 'undefined' || + typeof displayStart === 'undefined' + ) { + return; + } + let k = 0; + if (operation === 'zoom-in') { + k = scaleFactor; + } else if (operation === 'zoom-out') { + k = -scaleFactor; + } else if (operation === 'zoom-in-seq') { + k = displayEnd - displayStart - 29; + } + const newEnd = displayEnd - k; + let newStart = displayStart; + // if we've reached the end when zooming out, remove from start + if (newEnd > length) { + newStart -= newEnd - length; + } + if (displayStart < newEnd) { + nightingaleNavigation.dispatchEvent( + new CustomEvent('change', { + detail: { + 'display-start': Math.max(1, newStart).toString(), + 'display-end': Math.min(newEnd, length).toString(), + }, + bubbles: true, + cancelable: true, + }) + ); + } + }, + [length, nightingaleNavigationGetter, nightingaleNavigationRef] ); - return ( - +
onZoom?.('zoom-in')} + className={styles['nightingale-button-content']} + onClick={() => handleZoom?.('zoom-out')} aria-hidden="true" > - + onZoom?.('zoom-out')} + className={styles['nightingale-button-content']} + onClick={() => handleZoom?.('zoom-in')} aria-hidden="true" > - + onZoom?.('zoom-in-seq')} + className={styles['nightingale-button-content']} + onClick={() => handleZoom?.('zoom-in-seq')} aria-hidden="true" > - +
); }; diff --git a/src/uniprotkb/components/protein-data-views/PDBView.tsx b/src/uniprotkb/components/protein-data-views/PDBView.tsx index 2aac658bfd..6001abe85e 100644 --- a/src/uniprotkb/components/protein-data-views/PDBView.tsx +++ b/src/uniprotkb/components/protein-data-views/PDBView.tsx @@ -1,7 +1,7 @@ import { Fragment } from 'react'; import ExternalLink from '../../../shared/components/ExternalLink'; -import DatatableWrapper from '../../../shared/components/views/DatatableWrapper'; +import Table from '../../../shared/components/table/Table'; import useDatabaseInfoMaps from '../../../shared/hooks/useDatabaseInfoMaps'; @@ -30,7 +30,7 @@ const processData = (xrefs: Xref[]) => resolution: !Resolution || Resolution === '-' ? null : Resolution, chain, positions, - protvistaFeatureId: id, + accession: id, }; }); @@ -47,60 +47,56 @@ const PDBView = ({ xrefs }: { xrefs: Xref[] }) => { * Note: this view is duplicated in protvista-uniprot-structure * This is because the AF data is not currently available as part of the entry * Eventually it might make sense to just use protvista-structure and - * protvista-datatable. + * a Table. */ const data = processData(xrefs); const databaseInfoMaps = useDatabaseInfoMaps(); return ( - - - - - - - - - - - - - - {data.map( - (d) => - d && ( - - - - - - - - - ) - )} - -
PDB EntryMethodResolutionChainPositionsLinks
{d.id}{d.method}{d.resolution?.replace('A', 'Å')}{d.chain}{d.positions} - {databaseInfoMaps && - getPDBMirrorsInfo( - databaseInfoMaps.databaseToDatabaseInfo - ).map(({ displayName, uriLink }, index) => ( - - {index ? ' · ' : null} - - {displayName} - - - ))} -
- + 10}> + + + + + + + + + + {data.map( + (d, i) => + d && ( + + + + + + + + + ) + )} + +
PDB EntryMethodResolutionChainPositionsLinks{d.id}{d.method}{d.resolution?.replace('A', 'Å')}{d.chain}{d.positions} + {databaseInfoMaps && + getPDBMirrorsInfo( + databaseInfoMaps.databaseToDatabaseInfo + ).map(({ displayName, uriLink }, index) => ( + + {index ? ' · ' : null} + + {displayName} + + + ))} +
); }; diff --git a/src/uniprotkb/components/protein-data-views/SubCellViz.tsx b/src/uniprotkb/components/protein-data-views/SubCellViz.tsx index 36eeb0af42..a16c47b26c 100644 --- a/src/uniprotkb/components/protein-data-views/SubCellViz.tsx +++ b/src/uniprotkb/components/protein-data-views/SubCellViz.tsx @@ -1,13 +1,13 @@ /* eslint-disable react/no-this-in-sfc */ import { FC, memo, useEffect, useRef } from 'react'; -import tippy from 'tippy.js'; import '@swissprot/swissbiopics-visualizer'; import { groupBy } from 'lodash-es'; import { RequireExactlyOne } from 'type-fest'; import { VizTab, SubCellularLocation } from './SubcellularLocationWithVizView'; -import 'tippy.js/dist/tippy.css'; +import { addTooltip } from '../../../shared/utils/tooltip'; + import './styles/sub-cell-viz.scss'; /* @@ -95,7 +95,7 @@ const attachTooltips = ( partOfShown: boolean ) => { if (!triggerTargetSvgs?.length) { - return; + return null; } const name = locationGroup.querySelector('.subcell_name')?.textContent; let description = locationGroup.querySelector( @@ -116,7 +116,7 @@ const attachTooltips = ( const locationTextQueryResult = instance?.querySelectorAll(locationTextSelector); if (!locationTextQueryResult) { - return; + return null; } const locationTextElements = Array.from(locationTextQueryResult); @@ -130,11 +130,12 @@ const attachTooltips = ( ...locationTextElements, ...triggerTargetSvgs, ].filter(Boolean); - tippy(tooltipTarget, { - allowHTML: true, - content: `${name}
${description}`, - triggerTarget: tooltipTriggerTargets, - }); + + return addTooltip( + tooltipTarget, + `${name}
${description}`, + tooltipTriggerTargets + ); }; type Props = RequireExactlyOne< @@ -277,6 +278,7 @@ const SubCellViz: FC> = memo( instanceName.current ); const shadowRoot = instance?.shadowRoot; + const cleanupTooltips: ReturnType[] = []; const onSvgLoaded = () => { const tabsHeaderHeight = @@ -377,11 +379,13 @@ const SubCellViz: FC> = memo( scopedShapesSelector ); } - attachTooltips( - subcellularPresentSVG, - instance, - triggerTargetSvgs, - false + cleanupTooltips.push( + attachTooltips( + subcellularPresentSVG, + instance, + triggerTargetSvgs, + false + ) ); } } @@ -389,6 +393,7 @@ const SubCellViz: FC> = memo( }; shadowRoot?.addEventListener('svgloaded', onSvgLoaded); return () => { + cleanupTooltips.forEach((cleanup) => cleanup?.()); shadowRoot?.removeEventListener('svgloaded', onSvgLoaded); }; }, [uniProtLocationIds, uniProtLocations, goLocationIds, goLocations]); diff --git a/src/uniprotkb/components/protein-data-views/UniProtKBFeaturesView.tsx b/src/uniprotkb/components/protein-data-views/UniProtKBFeaturesView.tsx index 57c46c0c92..958a8c7c28 100644 --- a/src/uniprotkb/components/protein-data-views/UniProtKBFeaturesView.tsx +++ b/src/uniprotkb/components/protein-data-views/UniProtKBFeaturesView.tsx @@ -1,34 +1,33 @@ -import { useMemo, Fragment, ReactNode } from 'react'; +import { useMemo, ReactNode } from 'react'; import { v1 } from 'uuid'; -import { Chip } from 'franklin-sites'; -import UniProtKBEvidenceTag from './UniProtKBEvidenceTag'; import FeaturesView, { + FeatureColumnConfiguration, LocationModifier, ProcessedFeature, } from '../../../shared/components/views/FeaturesView'; -import { RichText } from './FreeTextView'; -import ToolsDropdown from '../../../shared/components/action-buttons/ToolsDropdown'; -import CopyButton from '../../../shared/components/action-buttons/Copy'; -import AddToBasketButton from '../../../shared/components/action-buttons/AddToBasket'; import LigandDescriptionView, { Ligand, LigandPart, } from './LigandDescriptionView'; -import ExternalLink from '../../../shared/components/ExternalLink'; import { useSmallScreen } from '../../../shared/hooks/useMatchMedia'; import listFormat from '../../../shared/utils/listFormat'; -import { stringToID } from '../../utils'; -import externalUrls from '../../../shared/config/externalUrls'; +import { + getRowId, + markBackground, + markBorder, +} from '../../../shared/utils/nightingale'; import { Evidence } from '../../types/modelTypes'; import FeatureType from '../../types/featureType'; import { Xref } from '../../../shared/types/apiModel'; -import PtmExchangeEvidenceTag from './PtmExchangeEvidenceTag'; -import styles from './styles/uniprotkb-features-view.module.scss'; +import { + UniProtKBFeatureExtraContent, + columnConfiguration, +} from '../../config/UniProtKBFeatureColumnConfiguration'; type FeatureLocation = { value: number; @@ -59,17 +58,7 @@ export type FeatureDatum = { confidenceScore?: ConfidenceScore; }; -export type ProtvistaFeature = { - type: string; - description: ReactNode; - evidences: Evidence[]; - start: number; - end: number; - startModifier: LocationModifier; - endModifier: LocationModifier; -}; - -type FeatureProps = { +type UniProtKBFeaturesViewProps = { primaryAccession: string; sequence?: string; features: FeatureDatum[]; @@ -79,8 +68,8 @@ type FeatureProps = { export const processFeaturesData = ( data: FeatureDatum[], - sequence?: string, - includeSource?: boolean + primaryAccession: string, + sequence?: string ): ProcessedFeature[] => data.map((feature): ProcessedFeature => { let s: string | undefined; @@ -123,8 +112,9 @@ export const processFeaturesData = ( } return { - protvistaFeatureId: feature.featureId || v1(), - featureId: feature.featureId, + accession: v1().toString(), + id: feature.featureId, + primaryAccession, start: feature.location.start.value, end: feature.location.end.value, startModifier: feature.location.start.modifier, @@ -133,7 +123,7 @@ export const processFeaturesData = ( description, evidences: feature.evidences, sequence: s, - source: includeSource ? feature.source || 'UniProt' : undefined, + source: feature.source || 'UniProt', confidenceScore: feature.confidenceScore, ligand: feature.ligand, ligandPart: feature.ligandPart, @@ -147,14 +137,30 @@ const UniProtKBFeaturesView = ({ features, inResultsTable, showSourceColumn = false, -}: FeatureProps) => { +}: UniProtKBFeaturesViewProps) => { const processedData = useMemo( - () => processFeaturesData(features, sequence, showSourceColumn), - [features, sequence, showSourceColumn] + () => processFeaturesData(features, primaryAccession, sequence), + [features, primaryAccession, sequence] ); const smallScreen = useSmallScreen(); + const columns: FeatureColumnConfiguration[] = useMemo< + FeatureColumnConfiguration[] + >( + () => + columnConfiguration.filter((column) => { + if (column.id === 'source') { + return showSourceColumn; + } + if (column.id === 'tools') { + return !smallScreen; + } + return true; + }), + [showSourceColumn, smallScreen] + ); + if (processedData.length === 0) { return null; } @@ -163,170 +169,19 @@ const UniProtKBFeaturesView = ({ a.start === b.start ? a.end - b.end : a.start - b.start ); - const table = ( - - - - {inResultsTable ? : } - - - {showSourceColumn && } - - {smallScreen ? null : ( - - )} - - - - {processedData.map((feature: ProcessedFeature) => { - const start = - feature.startModifier === 'UNKNOWN' ? '?' : feature.start; - const end = feature.endModifier === 'UNKNOWN' ? '?' : feature.end; - const positionStart = `${ - feature.startModifier === 'UNSURE' ? '?' : '' - }${start}`; - const positionEnd = `${ - feature.endModifier === 'UNSURE' ? '?' : '' - }${end}`; - // feature of type Disulfide bonds and Cross-links describe links, not subsequences. - const isLink = - feature.type === 'Disulfide bond' || feature.type === 'Cross-link'; - - const position = - positionStart === positionEnd - ? positionStart - : `${positionStart}${isLink ? '↔' : '-'}${positionEnd}`; - - let { description } = feature; - if (typeof feature.description === 'string') { - description = {feature.description}; - } - return ( - - - {inResultsTable ? ( - - ) : ( - - )} - - - {showSourceColumn && ( - - )} - - {smallScreen ? null : ( - - )} - - {feature.sequence && ( - - - - )} - - ); - })} - -
TypeTypeIDPosition(s)SourceDescription - {/* Intentionally left blank, corresponds to tools/basket */} -
{feature.type} - {feature.type} - - {feature.type === 'Natural variant' && - position === positionStart && - // Expasy links are only valid for SNPs (e.g. "R → G":) - feature.sequence?.length === 5 && - feature.featureId ? ( - - {feature.featureId} - - ) : ( - feature.featureId - )} - {position} - {feature.source} - - {description} - {!!feature.confidenceScore && ( - - - {feature.confidenceScore} - - - )} - {feature.source === 'PTMeXchange' ? ( - - ) : ( - - )} - - {/* Not using React Router link as this is copied into the table DOM */} - {feature.end - feature.start >= 2 && - feature.type !== 'Disulfide bond' && - feature.type !== 'Cross-link' && ( -
- - {(closeDropdown: () => unknown) => ( -
  • - - Copy sequence - -
    • - )} -     - -
    - )} -
    - Sequence: - {feature.sequence} -
    - ); - return ( ); }; diff --git a/src/uniprotkb/components/protein-data-views/VisualVariationView.tsx b/src/uniprotkb/components/protein-data-views/VisualVariationView.tsx index 7637133d89..1ed607bd52 100644 --- a/src/uniprotkb/components/protein-data-views/VisualVariationView.tsx +++ b/src/uniprotkb/components/protein-data-views/VisualVariationView.tsx @@ -1,16 +1,16 @@ -import { useCallback } from 'react'; - -// We have to import this specific file otherwise it gets everything in at the -// same time (including molstar...). But this path causes issues with Jest -// because it doesn't support es modules natively yet. So, not testable atm -import filterConfig, { - colorConfig, -} from 'protvista-uniprot/dist/es/filterConfig'; -import { TransformedVariant } from 'protvista-variation-adapter'; +import { useCallback, useRef } from 'react'; +import NightingaleVariation from '@nightingale-elements/nightingale-variation'; +import NightingaleNavigation from '@nightingale-elements/nightingale-navigation'; +import { Filter } from '@nightingale-elements/nightingale-filter'; +import { filterConfig, colorConfig } from 'protvista-uniprot'; +import NightingaleNavigationComponent from '../../../shared/custom-elements/NightingaleNavigation'; +import NightingaleSequenceComponent from '../../../shared/custom-elements/NightingaleSequence'; +import NightingaleVariationComponent from '../../../shared/custom-elements/NightingaleVariation'; +import NightingaleFilterComponent from '../../../shared/custom-elements/NightingaleFilter'; import NightingaleZoomTool from './NightingaleZoomTool'; -import useCustomElement from '../../../shared/hooks/useCustomElement'; +import { TransformedVariant } from '../../types/variation'; import styles from './styles/visual-variation-view.module.scss'; @@ -20,96 +20,49 @@ type VariationViewProps = { }; const VisualVariationView = ({ sequence, variants }: VariationViewProps) => { - const filterElement = useCustomElement( - /* istanbul ignore next */ - () => import(/* webpackChunkName: "protvista-filter" */ 'protvista-filter'), - 'protvista-filter' - ); - - const protvistaFilterRef = useCallback( - (node: { filters: typeof filterConfig }) => { - if (node && filterElement.defined) { - // eslint-disable-next-line no-param-reassign - node.filters = filterConfig; - } - }, - [filterElement.defined] - ); - - const variationElement = useCustomElement( - /* istanbul ignore next */ - () => - import( - /* webpackChunkName: "protvista-variation" */ 'protvista-variation' - ), - 'protvista-variation' - ); - - const protvistaVariationRef = useCallback( - (node: { - colorConfig: typeof colorConfig; - data: VariationViewProps; - length: number; - }) => { - if (node && variationElement.defined && variants) { + const navigationRef = useRef(null); + const setNightingaleVariation = useCallback( + (node: NightingaleVariation) => { + if (node && sequence && variants) { // eslint-disable-next-line no-param-reassign node.colorConfig = colorConfig; // eslint-disable-next-line no-param-reassign node.data = { sequence, variants }; - // eslint-disable-next-line no-param-reassign - node.length = sequence.length; } }, - [variationElement.defined, sequence, variants] - ); - - const navigationElement = useCustomElement( - /* istanbul ignore next */ - () => - import( - /* webpackChunkName: "protvista-navigation" */ 'protvista-navigation' - ), - 'protvista-navigation' - ); - const sequenceElement = useCustomElement( - /* istanbul ignore next */ - () => - import(/* webpackChunkName: "protvista-sequence" */ 'protvista-sequence'), - 'protvista-sequence' + [sequence, variants] ); - const ceDefined = - filterElement.defined && - variationElement.defined && - navigationElement.defined && - sequenceElement.defined; - return ( - <> - {ceDefined && ( -
    - - - - - -
    - )} - +
    + + + + + + +
    ); }; diff --git a/src/uniprotkb/components/protein-data-views/__tests__/UniProtKBFeaturesView.tsx b/src/uniprotkb/components/protein-data-views/__tests__/UniProtKBFeaturesView.spec.tsx similarity index 100% rename from src/uniprotkb/components/protein-data-views/__tests__/UniProtKBFeaturesView.tsx rename to src/uniprotkb/components/protein-data-views/__tests__/UniProtKBFeaturesView.spec.tsx diff --git a/src/uniprotkb/components/protein-data-views/__tests__/__snapshots__/DiseaseInvolvementView.spec.tsx.snap b/src/uniprotkb/components/protein-data-views/__tests__/__snapshots__/DiseaseInvolvementView.spec.tsx.snap index 13858cc806..ae06c0e44e 100644 --- a/src/uniprotkb/components/protein-data-views/__tests__/__snapshots__/DiseaseInvolvementView.spec.tsx.snap +++ b/src/uniprotkb/components/protein-data-views/__tests__/__snapshots__/DiseaseInvolvementView.spec.tsx.snap @@ -97,15 +97,20 @@ exports[`DiseaseInvolvement should render DiseaseInvolvement 1`] = `
    Natural variants in AD
    -
    - +
    `; diff --git a/src/uniprotkb/components/protein-data-views/__tests__/__snapshots__/UniProtKBFeaturesView.spec.tsx.snap b/src/uniprotkb/components/protein-data-views/__tests__/__snapshots__/UniProtKBFeaturesView.spec.tsx.snap new file mode 100644 index 0000000000..cf7a699ae9 --- /dev/null +++ b/src/uniprotkb/components/protein-data-views/__tests__/__snapshots__/UniProtKBFeaturesView.spec.tsx.snap @@ -0,0 +1,3 @@ +// Jest Snapshot v1, https://goo.gl/fbAQLP + +exports[`UniProtKBFeaturesView component should render without crashing 1`] = ``; diff --git a/src/uniprotkb/components/protein-data-views/__tests__/__snapshots__/UniProtKBFeaturesView.tsx.snap b/src/uniprotkb/components/protein-data-views/__tests__/__snapshots__/UniProtKBFeaturesView.tsx.snap deleted file mode 100644 index 5c50039485..0000000000 --- a/src/uniprotkb/components/protein-data-views/__tests__/__snapshots__/UniProtKBFeaturesView.tsx.snap +++ /dev/null @@ -1,89 +0,0 @@ -// Jest Snapshot v1, https://goo.gl/fbAQLP - -exports[`UniProtKBFeaturesView component should render without crashing 1`] = ` - - - - - - - - - - - - - - - - - - - - -
    - Type - - ID - - Position(s) - - Description - -
    - Signal - - - 1-17 - - -
    - - -
    -
    - - Sequence: - - ASDASDASASDASDASD -
    -     -`; diff --git a/src/uniprotkb/components/protein-data-views/__tests__/__snapshots__/XrefView.spec.tsx.snap b/src/uniprotkb/components/protein-data-views/__tests__/__snapshots__/XrefView.spec.tsx.snap index ba86a32cbe..4ee47dd1d2 100644 --- a/src/uniprotkb/components/protein-data-views/__tests__/__snapshots__/XrefView.spec.tsx.snap +++ b/src/uniprotkb/components/protein-data-views/__tests__/__snapshots__/XrefView.spec.tsx.snap @@ -5,96 +5,93 @@ exports[`XRefView should render section 1`] = `

    Chemistry

    -
    - - - - - - - - - - - - - - - - - -
    - Nucleotide Sequence - - Protein Sequence - - Molecule Type - - Status -
    - 1234 -
    - - EMBL - - - · - - GenBank - - - · - - DDBJ - - -     		- - - - - - -
    -     - -
    + + + + 1234 +
    + + EMBL + + + · + + GenBank + + + · + + DDBJ + + + + + - + + + - + + + + +     `; diff --git a/src/uniprotkb/components/protein-data-views/styles/nightingale-zoom-tool.module.scss b/src/uniprotkb/components/protein-data-views/styles/nightingale-zoom-tool.module.scss new file mode 100644 index 0000000000..3b4422ff19 --- /dev/null +++ b/src/uniprotkb/components/protein-data-views/styles/nightingale-zoom-tool.module.scss @@ -0,0 +1,15 @@ +@import 'franklin-sites/src/styles/colours'; + +.nightingale-zoom-tool { + float: left; + margin-left: 0.1667rem; + margin-right: 0.75rem; + margin-top: 0.1667rem; + + .nightingale-button-content { + background: none; + padding-left: 0.75rem; + font-size: 0.9rem; + color: var(--fr--color-sea-blue); + } +} diff --git a/src/uniprotkb/components/protein-data-views/styles/nightingale-zoom-tool.scss b/src/uniprotkb/components/protein-data-views/styles/nightingale-zoom-tool.scss deleted file mode 100644 index fea5e2c9c1..0000000000 --- a/src/uniprotkb/components/protein-data-views/styles/nightingale-zoom-tool.scss +++ /dev/null @@ -1,10 +0,0 @@ -@import 'franklin-sites/src/styles/colours'; - -protvista-zoom-tool { - --button-background: none; - --button-padding-h: 0.5rem; - --button-margin-h: 0; - --button-font-size: 0.9rem; - --button-text-color: #{$colour-sea-blue}; - --button-border-radius: 0; -} diff --git a/src/uniprotkb/components/protein-data-views/styles/sub-cell-viz.scss b/src/uniprotkb/components/protein-data-views/styles/sub-cell-viz.scss index 43acfdb83d..6cf08082a4 100644 --- a/src/uniprotkb/components/protein-data-views/styles/sub-cell-viz.scss +++ b/src/uniprotkb/components/protein-data-views/styles/sub-cell-viz.scss @@ -1,5 +1,3 @@ -@import 'franklin-sites/src/styles/colours'; - .sub-cell-viz__in-view-pin { display: none; } @@ -14,7 +12,7 @@ &.lookedAt, &:hover { - background-color: $colour-sea-blue; + background-color: var(--fr--color-sea-blue); color: white; & article { diff --git a/src/uniprotkb/components/protein-data-views/styles/uniprotkb-features-view.module.scss b/src/uniprotkb/components/protein-data-views/styles/uniprotkb-features-view.module.scss deleted file mode 100644 index f1d2009516..0000000000 --- a/src/uniprotkb/components/protein-data-views/styles/uniprotkb-features-view.module.scss +++ /dev/null @@ -1,13 +0,0 @@ -@import 'franklin-sites/src/styles/colours'; - -.Gold { - --main-chip-color: #{$colour-reviewed}; -} - -.Silver { - --main-chip-color: #{$colour-weldon-blue}; -} - -.Bronze { - --main-chip-color: #{$colour-bronze}; -} diff --git a/src/uniprotkb/components/protein-data-views/styles/visual-variation-view.module.scss b/src/uniprotkb/components/protein-data-views/styles/visual-variation-view.module.scss index c28468e833..80fe693afc 100644 --- a/src/uniprotkb/components/protein-data-views/styles/visual-variation-view.module.scss +++ b/src/uniprotkb/components/protein-data-views/styles/visual-variation-view.module.scss @@ -3,8 +3,8 @@ grid-template-columns: 12vw 1fr; gap: 0.2rem 0.7rem; - protvista-navigation, - protvista-sequence { + nightingale-navigation, + nightingale-sequence { grid-column-start: 2; } } diff --git a/src/uniprotkb/components/results/styles/group-by.module.scss b/src/uniprotkb/components/results/styles/group-by.module.scss index 8ad3681712..a77f4da67c 100644 --- a/src/uniprotkb/components/results/styles/group-by.module.scss +++ b/src/uniprotkb/components/results/styles/group-by.module.scss @@ -1,5 +1,3 @@ -@import 'franklin-sites/src/styles/colours'; - .groupby-container { .autocomplete { width: 50ch; @@ -11,15 +9,13 @@ } ul.groupby { - border-left: 1px solid $colour-gainsborough; - margin-left: 1rem; + border-left: 1px solid var(--fr--color-gainsborough); margin-bottom: 0; &__header { border-left: 0; margin-left: 0; - border-bottom: 1px solid $colour-gainsborough; - padding-bottom: 0.5rem; + border-bottom: 1px solid var(--fr--color-gainsborough); li.header { h3 { @@ -57,7 +53,7 @@ .warning { margin-left: 0.75rem; - color: $colour-warning; + color: var(--fr--color-warning); } .spinner { @@ -79,7 +75,7 @@ left: -0.75ch; right: -0.75ch; opacity: 0.4; - background-color: $colour-warning; + background-color: var(--fr--color-warning); } } @@ -96,7 +92,7 @@ margin-left: 0.725rem; transition: transform 0.25s ease-out; background-color: transparent; - color: $colour-sea-blue; + color: var(--fr--color-sea-blue); &[aria-expanded='true'] { transform: rotateZ(90deg); @@ -117,7 +113,7 @@ .bar { display: inline-block; - background-color: $colour-sea-blue; + background-color: var(--fr--color-sea-blue); top: 2px; height: 1.5ch; position: relative; diff --git a/src/uniprotkb/components/statistics/styles/statistics-page.module.scss b/src/uniprotkb/components/statistics/styles/statistics-page.module.scss index baedbe7b83..ed49cc890d 100644 --- a/src/uniprotkb/components/statistics/styles/statistics-page.module.scss +++ b/src/uniprotkb/components/statistics/styles/statistics-page.module.scss @@ -1,4 +1,3 @@ -@import 'franklin-sites/src/styles/colours'; @import 'franklin-sites/src/styles/settings'; .statistics-page { @@ -20,22 +19,22 @@ } thead { - color: $colour-sky-white; - background: $colour-sea-blue; + color: var(--fr--color-sky-white); + background: var(--fr--color-sea-blue); a { - color: $colour-sky-white; + color: var(--fr--color-sky-white); } } tbody { - border: 1px solid $colour-sea-blue; + border: 1px solid var(--fr--color-sea-blue); } th, td { padding: $global-padding * 0.25 $global-padding * 0.5; - border: 1px solid $colour-sea-blue; + border: 1px solid var(--fr--color-sea-blue); border-collapse: collapse; &.indent { diff --git a/src/uniprotkb/config/UniProtKBFeatureColumnConfiguration.tsx b/src/uniprotkb/config/UniProtKBFeatureColumnConfiguration.tsx new file mode 100644 index 0000000000..88674a0644 --- /dev/null +++ b/src/uniprotkb/config/UniProtKBFeatureColumnConfiguration.tsx @@ -0,0 +1,153 @@ +import { Card, Chip, ExternalLink } from 'franklin-sites'; + +import PtmExchangeEvidenceTag from '../components/protein-data-views/PtmExchangeEvidenceTag'; +import UniProtKBEvidenceTag from '../components/protein-data-views/UniProtKBEvidenceTag'; +import AddToBasketButton from '../../shared/components/action-buttons/AddToBasket'; +import { RichText } from '../components/protein-data-views/FreeTextView'; +import CopyButton from '../../shared/components/action-buttons/Copy'; +import ToolsDropdown from '../../shared/components/action-buttons/ToolsDropdown'; + +import externalUrls from '../../shared/config/externalUrls'; + +import { + FeatureColumnConfiguration, + ProcessedFeature, +} from '../../shared/components/views/FeaturesView'; + +import styles from './styles/uniprotkb-feature-column-configuration.module.scss'; + +// TODO: use getLabelAndTooltip? + +export const UniProtKBFeatureExtraContent = (data: ProcessedFeature) => ( + + Sequence: + {data.sequence} + +); + +export const columnConfiguration: FeatureColumnConfiguration[] = + [ + { + id: 'type', + label: 'Type', + filter: (data, input) => data.type === input, + render: (data) => data.type, + }, + { + id: 'id', + label: 'ID', + render: (data) => + data.type === 'Natural variant' && + data.startModifier !== 'UNSURE' && + data.startModifier !== 'UNKNOWN' && + // Expasy links are only valid for SNPs (e.g. "R → G":) + data.sequence?.length === 5 && + data.id ? ( + + {data.id} + + ) : ( + data.id + ), + }, + { + id: 'position', + label: 'Position(s)', + render: (data) => { + const positionStart = `${data.startModifier === 'UNSURE' ? '?' : ''}${ + data.startModifier === 'UNKNOWN' ? '?' : data.start + }`; + const positionEnd = `${data.endModifier === 'UNSURE' ? '?' : ''}${ + data.endModifier === 'UNKNOWN' ? '?' : data.end + }`; + return positionStart === positionEnd + ? positionStart + : `${positionStart}${ + data.type === 'Disulfide bond' || data.type === 'Cross-link' + ? // The reason for the ↔: This is for links or bounds, it's basically because the + // important parts for these are really the areas at the start and at the end, + // not the bit in between. For a domain the whole sequence is important, but here's + // that's not the case thinking in 3d, it would be for example a bit of the + // structure when the sequence folds on itself and touches/binds, start and end + // would be the coordinates of the 2 parts of the sequence that touch + '↔' + : '-' + }${positionEnd}`; + }, + }, + { + id: 'source', + label: 'Source', + filter: (data, input) => data.source === input, + render: (data) => data.source, + }, + { + id: 'description', + label: 'Description', + render: (data) => ( + <> + {typeof data.description === 'string' ? ( + {data.description} + ) : ( + data.description + )} + {!!data.confidenceScore && ( + + + {data.confidenceScore} + + + )} + {data.source === 'PTMeXchange' ? ( + + ) : ( + + )} + + ), + }, + { + id: 'tools', + // Intentionally left blank, corresponds to tools/basket + label: '', + render: (data) => + data.primaryAccession && + data.end - data.start >= 2 && + data.type !== 'Disulfide bond' && + data.type !== 'Cross-link' && ( +
    + + {(closeDropdown: () => unknown) => ( +
  • + + Copy sequence + +
    • + )} +     + + +
    + ), + }, + ]; diff --git a/src/uniprotkb/config/__tests__/__snapshots__/UniProtKBColumnConfiguration.spec.tsx.snap b/src/uniprotkb/config/__tests__/__snapshots__/UniProtKBColumnConfiguration.spec.tsx.snap index 73f0ed4ee1..13a886ffc7 100644 --- a/src/uniprotkb/config/__tests__/__snapshots__/UniProtKBColumnConfiguration.spec.tsx.snap +++ b/src/uniprotkb/config/__tests__/__snapshots__/UniProtKBColumnConfiguration.spec.tsx.snap @@ -1266,154 +1266,129 @@ exports[`UniProtKBColumnConfiguration component should render column "ft_carbohy exports[`UniProtKBColumnConfiguration component should render column "ft_chain": ft_chain 1`] = ` - -
    + + + + Type + + + ID + + + Position(s) + + + Description + + + + + - - - - - - - - - - - - + + + + + - - - - - - + Tools + + + - - -
    - Type - - ID - - Position(s) - - Description - -
    + + Chain + + id value CHAIN + + 2-8 + + Cu + + 2+ + + A2 ( + + UniProtKB + + | + + ChEBI + + + ); Some note of Ca + + 2+ + + A1 ( + + UniProtKB + + | + + ChEBI + + + ); Some note; In isoform sequence 1; description value 123 + +
    +
    		- Chain - - id value CHAIN - - 2-8 - - Cu - - 2+ - - A2 ( - - UniProtKB - - | - - ChEBI - - - ); Some note of Ca - - 2+ - - A1 ( - - UniProtKB - - | - - ChEBI - - - ); Some note; In isoform sequence 1; description value 123 - -
    - - -
    -
    - - Sequence: - - original value → alternative value -
    -     - -
    -     + + Add + + + + + +     `; diff --git a/src/uniprotkb/config/styles/uniprotkb-feature-column-configuration.module.scss b/src/uniprotkb/config/styles/uniprotkb-feature-column-configuration.module.scss new file mode 100644 index 0000000000..a06e0d4492 --- /dev/null +++ b/src/uniprotkb/config/styles/uniprotkb-feature-column-configuration.module.scss @@ -0,0 +1,18 @@ +@import 'franklin-sites/src/styles/colours'; + +.Gold { + --main-chip-color: #{var(--fr--color-reviewed)}; +} + +.Silver { + --main-chip-color: #{var(--fr--color-weldon-blue)}; +} + +.Bronze { + --main-chip-color: #{var(--fr--color-bronze)}; +} + +.sequence { + max-width: 60vw; + overflow-wrap: break-word; +} diff --git a/src/uniprotkb/types/featureType.ts b/src/uniprotkb/types/featureType.ts index 9445cae0f5..da22df18d9 100644 --- a/src/uniprotkb/types/featureType.ts +++ b/src/uniprotkb/types/featureType.ts @@ -13,6 +13,7 @@ export type FunctionFeatures = | 'DNA binding' | 'Active site' | 'Binding site' + | 'BINDING' | 'Site'; export type SubcellularLocationFeatures = diff --git a/src/uniprotkb/types/variation.ts b/src/uniprotkb/types/variation.ts new file mode 100644 index 0000000000..43eb8a9821 --- /dev/null +++ b/src/uniprotkb/types/variation.ts @@ -0,0 +1,4 @@ +import { VariationDatum } from '@nightingale-elements/nightingale-variation/dist/nightingale-variation'; +import { Variant } from '@nightingale-elements/nightingale-variation/dist/proteinAPI'; + +export type TransformedVariant = Variant & VariationDatum; diff --git a/src/uniprotkb/utils/index.ts b/src/uniprotkb/utils/index.ts index d614220835..173f136a0d 100644 --- a/src/uniprotkb/utils/index.ts +++ b/src/uniprotkb/utils/index.ts @@ -44,7 +44,7 @@ export const getPropertyValue = ( return found ? found.value : null; }; -type Sortable = { start: number | string; end: number | string }; +type Sortable = { start: number | string; end?: number | string }; export const sortByLocation = (a: Sortable, b: Sortable) => { const aStart = +a.start; const aEnd = a.end ? +a.end : -Infinity; diff --git a/tsconfig.json b/tsconfig.json index 232fcb7680..0dec3b68a3 100644 --- a/tsconfig.json +++ b/tsconfig.json @@ -27,7 +27,10 @@ { "name": "typescript-plugin-css-modules" } - ] + ], + "paths": { + "react": ["./node_modules/@types/react"] + } }, "include": ["src"], "exclude": ["node_modules"] diff --git a/webpack.config.js b/webpack.config.js index 41fe8fea64..9119ba1118 100644 --- a/webpack.config.js +++ b/webpack.config.js @@ -138,9 +138,6 @@ const getConfigFor = ({ // We use realpathSync otherwise doesn't work with symlinks fs.realpathSync(`${__dirname}/node_modules/franklin-sites`), fs.realpathSync(`${__dirname}/node_modules/molstar/build`), - fs.realpathSync( - `${__dirname}/node_modules/tippy.js/dist/tippy.css` - ), fs.realpathSync(`${__dirname}/node_modules/lite-youtube-embed`), fs.realpathSync(`${__dirname}/node_modules/swagger-ui-react`), fs.realpathSync( @@ -195,9 +192,8 @@ const getConfigFor = ({ }, // SVGs from nightingale and protvista packages { - test: /\.svg$/, + test: /\.svg$/i, include: [ - fs.realpathSync(`${__dirname}/node_modules/protvista-datatable`), fs.realpathSync(`${__dirname}/node_modules/protvista-uniprot`), ], loader: 'svg-inline-loader', diff --git a/yarn.lock b/yarn.lock index f57e907ea4..7917b8bde8 100644 --- a/yarn.lock +++ b/yarn.lock @@ -3,9 +3,9 @@ "@adobe/css-tools@^4.4.0": - version "4.4.0" - resolved "https://registry.yarnpkg.com/@adobe/css-tools/-/css-tools-4.4.0.tgz#728c484f4e10df03d5a3acd0d8adcbbebff8ad63" - integrity sha512-Ff9+ksdQQB3rMncgqDK78uLznstjyfIf2Arnh22pW8kBpLs6rpKDwgnZT46hin5Hl1WzazzK64DOrhSwYpS7bQ== + version "4.4.1" + resolved "https://registry.yarnpkg.com/@adobe/css-tools/-/css-tools-4.4.1.tgz#2447a230bfe072c1659e6815129c03cf170710e3" + integrity sha512-12WGKBQzjUAI4ayyF4IAtfw2QR/IDoqk6jTddXDhtYTJF9ASmoE1zst7cVtP0aL/F1jUJL5r+JxKXKEgHNbEUQ== "@adobe/css-tools@~4.3.1": version "4.3.3" @@ -29,20 +29,21 @@ jsonpointer "^5.0.0" leven "^3.1.0" 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version "1.5.8" @@ -2844,9 +3300,9 @@ integrity sha512-hroOstUScF6zhIi+5+x0dzqrHA1EJi+Irri6b1fxolMTqqHIV/Cg77EtnQcZqZCu8hR3mX2BzIxN4/GzI68Kfw== "@types/qs@*": - version "6.9.16" - resolved "https://registry.yarnpkg.com/@types/qs/-/qs-6.9.16.tgz#52bba125a07c0482d26747d5d4947a64daf8f794" - integrity sha512-7i+zxXdPD0T4cKDuxCUXJ4wHcsJLwENa6Z3dCu8cfCK743OGy5Nu1RmAGqDPsoTDINVEcdXKRvR/zre+P2Ku1A== + version "6.9.17" + resolved "https://registry.yarnpkg.com/@types/qs/-/qs-6.9.17.tgz#fc560f60946d0aeff2f914eb41679659d3310e1a" + integrity sha512-rX4/bPcfmvxHDv0XjfJELTTr+iB+tn032nPILqHm5wbthUUUuVtNGGqzhya9XUxjTP8Fpr0qYgSZZKxGY++svQ== "@types/ramda@~0.30.0": version "0.30.2" @@ -2860,19 +3316,10 @@ resolved "https://registry.yarnpkg.com/@types/range-parser/-/range-parser-1.2.7.tgz#50ae4353eaaddc04044279812f52c8c65857dbcb" integrity sha512-hKormJbkJqzQGhziax5PItDUTMAM9uE2XXQmM37dyd4hVM+5aVl7oVxMVUiVQn2oCQFN/LKCZdvSM0pFRqbSmQ== -"@types/react-dom@18.3.0": - version "18.3.0" - resolved 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-"@types/unist@^2": +"@types/unist@*", "@types/unist@^3.0.0": + version "3.0.3" + resolved "https://registry.yarnpkg.com/@types/unist/-/unist-3.0.3.tgz#acaab0f919ce69cce629c2d4ed2eb4adc1b6c20c" + integrity sha512-ko/gIFJRv177XgZsZcBwnqJN5x/Gien8qNOn0D5bQU/zAzVf9Zt3BlcUiLqhV9y4ARk0GbT3tnUiPNgnTXzc/Q== + +"@types/unist@^2", "@types/unist@^2.0.0": version "2.0.11" resolved "https://registry.yarnpkg.com/@types/unist/-/unist-2.0.11.tgz#11af57b127e32487774841f7a4e54eab166d03c4" integrity sha512-CmBKiL6NNo/OqgmMn95Fk9Whlp2mtvIv+KNpQKN2F4SjvrEesubTRWGYSg+BnWZOnlCaSTU1sMpsBOzgbYhnsA== -"@types/use-sync-external-store@^0.0.3": - version "0.0.3" - resolved "https://registry.yarnpkg.com/@types/use-sync-external-store/-/use-sync-external-store-0.0.3.tgz#b6725d5f4af24ace33b36fafd295136e75509f43" - integrity sha512-EwmlvuaxPNej9+T4v5AuBPJa2x2UOJVdjCtDHgcDqitUeOtjnJKJ+apYjVcAoBEMjKW1VVFGZLUb5+qqa09XFA== +"@types/use-sync-external-store@^0.0.6": + version "0.0.6" + resolved 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"https://registry.yarnpkg.com/argparse/-/argparse-1.0.10.tgz#bcd6791ea5ae09725e17e5ad988134cd40b3d911" @@ -3489,24 +3975,24 @@ array-includes@^3.1.4, array-includes@^3.1.5, array-includes@^3.1.6: is-string "^1.0.7" array.prototype.flat@^1.2.5, array.prototype.flat@^1.3.1: - version "1.3.2" - resolved "https://registry.yarnpkg.com/array.prototype.flat/-/array.prototype.flat-1.3.2.tgz#1476217df8cff17d72ee8f3ba06738db5b387d18" - integrity sha512-djYB+Zx2vLewY8RWlNCUdHjDXs2XOgm602S9E7P/UpHgfeHL00cRiIF+IN/G/aUJ7kGPb6yO/ErDI5V2s8iycA== + version "1.3.3" + resolved "https://registry.yarnpkg.com/array.prototype.flat/-/array.prototype.flat-1.3.3.tgz#534aaf9e6e8dd79fb6b9a9917f839ef1ec63afe5" + integrity sha512-rwG/ja1neyLqCuGZ5YYrznA62D4mZXg0i1cIskIUKSiqF3Cje9/wXAls9B9s1Wa2fomMsIv8czB8jZcPmxCXFg== dependencies: - call-bind "^1.0.2" - define-properties "^1.2.0" - es-abstract "^1.22.1" - es-shim-unscopables "^1.0.0" + call-bind "^1.0.8" + define-properties "^1.2.1" + es-abstract "^1.23.5" + 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-arraybuffer.prototype.slice@^1.0.3: - version "1.0.3" - resolved "https://registry.yarnpkg.com/arraybuffer.prototype.slice/-/arraybuffer.prototype.slice-1.0.3.tgz#097972f4255e41bc3425e37dc3f6421cf9aefde6" - integrity sha512-bMxMKAjg13EBSVscxTaYA4mRc5t1UAXa2kXiGTNfZ079HIWXEkKmkgFrh/nJqamaLSrXO5H4WFFkPEaLJWbs3A== +arraybuffer.prototype.slice@^1.0.4: + version "1.0.4" + resolved "https://registry.yarnpkg.com/arraybuffer.prototype.slice/-/arraybuffer.prototype.slice-1.0.4.tgz#9d760d84dbdd06d0cbf92c8849615a1a7ab3183c" + integrity sha512-BNoCY6SXXPQ7gF2opIP4GBE+Xw7U+pHMYKuzjgCN3GwiaIR09UUeKfheyIry77QtrCBlC0KK0q5/TER/tYh3PQ== dependencies: array-buffer-byte-length "^1.0.1" - call-bind "^1.0.5" + call-bind "^1.0.8" define-properties "^1.2.1" - es-abstract "^1.22.3" - es-errors "^1.2.1" - get-intrinsic "^1.2.3" + es-abstract "^1.23.5" + es-errors "^1.3.0" + get-intrinsic "^1.2.6" is-array-buffer "^3.0.4" - is-shared-array-buffer "^1.0.2" assert@2.1.0: version "2.1.0" @@ -3588,9 +4073,9 @@ available-typed-arrays@^1.0.7: possible-typed-array-names "^1.0.0" axe-core@^4.4.3: - version "4.10.0" - resolved "https://registry.yarnpkg.com/axe-core/-/axe-core-4.10.0.tgz#d9e56ab0147278272739a000880196cdfe113b59" - integrity sha512-Mr2ZakwQ7XUAjp7pAwQWRhhK8mQQ6JAaNWSjmjxil0R8BPioMtQsTLOolGYkji1rcL++3dCqZA3zWqpT+9Ew6g== + version "4.10.2" + resolved "https://registry.yarnpkg.com/axe-core/-/axe-core-4.10.2.tgz#85228e3e1d8b8532a27659b332e39b7fa0e022df" + integrity sha512-RE3mdQ7P3FRSe7eqCWoeQ/Z9QXrtniSjp1wUjt5nRC3WIpz5rSCve6o3fsZ2aCpJtrZjSZgjwXAoTO5k4tEI0w== axios-mock-adapter@2.0.0: version "2.0.0" @@ -3600,7 +4085,7 @@ axios-mock-adapter@2.0.0: fast-deep-equal "^3.1.3" is-buffer "^2.0.5" -axios@1.7.7, axios@^1.4.0: +axios@1.7.7: version "1.7.7" resolved "https://registry.yarnpkg.com/axios/-/axios-1.7.7.tgz#2f554296f9892a72ac8d8e4c5b79c14a91d0a47f" integrity sha512-S4kL7XrjgBmvdGut0sN3yJxqYzrDOnivkBiN0OFs6hLiUam3UPvswUo0kqGyhqUZGEOytHyumEdXsAkgCOUf3Q== @@ -3609,6 +4094,15 @@ axios@1.7.7, axios@^1.4.0: form-data "^4.0.0" proxy-from-env "^1.1.0" +axios@^1.7.4: + version "1.7.9" + resolved "https://registry.yarnpkg.com/axios/-/axios-1.7.9.tgz#d7d071380c132a24accda1b2cfc1535b79ec650a" + integrity sha512-LhLcE7Hbiryz8oMDdDptSrWowmB4Bl6RCt6sIJKpRB4XtVf0iEgewX3au/pJqm+Py1kCASkb/FFKjxQaLtxJvw== + dependencies: + follow-redirects "^1.15.6" + form-data "^4.0.0" + proxy-from-env "^1.1.0" + axobject-query@^2.2.0: version "2.2.0" resolved "https://registry.yarnpkg.com/axobject-query/-/axobject-query-2.2.0.tgz#943d47e10c0b704aa42275e20edf3722648989be" @@ -3673,12 +4167,12 @@ babel-plugin-macros@^3.1.0: resolve "^1.19.0" babel-plugin-polyfill-corejs2@^0.4.10: - version "0.4.11" - resolved "https://registry.yarnpkg.com/babel-plugin-polyfill-corejs2/-/babel-plugin-polyfill-corejs2-0.4.11.tgz#30320dfe3ffe1a336c15afdcdafd6fd615b25e33" - integrity sha512-sMEJ27L0gRHShOh5G54uAAPaiCOygY/5ratXuiyb2G46FmlSpc9eFCzYVyDiPxfNbwzA7mYahmjQc5q+CZQ09Q== + version "0.4.12" + resolved "https://registry.yarnpkg.com/babel-plugin-polyfill-corejs2/-/babel-plugin-polyfill-corejs2-0.4.12.tgz#ca55bbec8ab0edeeef3d7b8ffd75322e210879a9" + integrity sha512-CPWT6BwvhrTO2d8QVorhTCQw9Y43zOu7G9HigcfxvepOU6b8o3tcWad6oVgZIsZCTt42FFv97aA7ZJsbM4+8og== dependencies: "@babel/compat-data" "^7.22.6" - "@babel/helper-define-polyfill-provider" "^0.6.2" + "@babel/helper-define-polyfill-provider" "^0.6.3" semver "^6.3.1" babel-plugin-polyfill-corejs3@^0.10.6: @@ -3690,11 +4184,11 @@ babel-plugin-polyfill-corejs3@^0.10.6: core-js-compat "^3.38.0" babel-plugin-polyfill-regenerator@^0.6.1: - version "0.6.2" - resolved "https://registry.yarnpkg.com/babel-plugin-polyfill-regenerator/-/babel-plugin-polyfill-regenerator-0.6.2.tgz#addc47e240edd1da1058ebda03021f382bba785e" - integrity sha512-2R25rQZWP63nGwaAswvDazbPXfrM3HwVoBXK6HcqeKrSrL/JqcC/rDcf95l4r7LXLyxDXc8uQDa064GubtCABg== + version "0.6.3" + resolved "https://registry.yarnpkg.com/babel-plugin-polyfill-regenerator/-/babel-plugin-polyfill-regenerator-0.6.3.tgz#abeb1f3f1c762eace37587f42548b08b57789bc8" + integrity sha512-LiWSbl4CRSIa5x/JAU6jZiG9eit9w6mz+yVMFwDE83LAWvt0AfGBoZ7HS/mkhrKuh2ZlzfVZYKoLjXdqw6Yt7Q== dependencies: - "@babel/helper-define-polyfill-provider" "^0.6.2" + "@babel/helper-define-polyfill-provider" "^0.6.3" babel-preset-current-node-syntax@^1.0.0: version "1.1.0" @@ -3725,6 +4219,11 @@ babel-preset-jest@^29.6.3: babel-plugin-jest-hoist "^29.6.3" babel-preset-current-node-syntax "^1.0.0" +bail@^2.0.0: + version "2.0.2" + resolved "https://registry.yarnpkg.com/bail/-/bail-2.0.2.tgz#d26f5cd8fe5d6f832a31517b9f7c356040ba6d5d" + integrity sha512-0xO6mYd7JB2YesxDKplafRpsiOzPt9V02ddPCLbY1xYGPOX24NTyN50qnUxgCPcSoYMhKpAuBTjQoRZCAkUDRw== + balanced-match@^1.0.0: version "1.0.2" resolved "https://registry.yarnpkg.com/balanced-match/-/balanced-match-1.0.2.tgz#e83e3a7e3f300b34cb9d87f615fa0cbf357690ee" @@ -3750,6 +4249,18 @@ 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"^2.0.4" readable-stream "^3.4.0" -body-parser@1.20.3, body-parser@^1.19.0: +body-parser@1.20.3, body-parser@^1.20.2: version "1.20.3" resolved "https://registry.yarnpkg.com/body-parser/-/body-parser-1.20.3.tgz#1953431221c6fb5cd63c4b36d53fab0928e548c6" integrity sha512-7rAxByjUMqQ3/bHJy7D6OGXvx/MMc4IqBn/X0fcM1QUcAItpZrBEYhWGem+tzXH90c+G01ypMcYJBO9Y30203g== @@ -3778,9 +4289,9 @@ body-parser@1.20.3, body-parser@^1.19.0: unpipe "1.0.0" bonjour-service@^1.2.1: - version "1.2.1" - resolved "https://registry.yarnpkg.com/bonjour-service/-/bonjour-service-1.2.1.tgz#eb41b3085183df3321da1264719fbada12478d02" - integrity sha512-oSzCS2zV14bh2kji6vNe7vrpJYCHGvcZnlffFQ1MEoX/WOeQ/teD8SYWKR942OI3INjq8OMNJlbPK5LLLUxFDw== + version "1.3.0" + resolved "https://registry.yarnpkg.com/bonjour-service/-/bonjour-service-1.3.0.tgz#80d867430b5a0da64e82a8047fc1e355bdb71722" + integrity sha512-3YuAUiSkWykd+2Azjgyxei8OWf8thdn8AITIog2M4UICzoqfjlqr64WIjEXZllf/W6vK1goqleSR6brGomxQqA== dependencies: fast-deep-equal "^3.1.3" multicast-dns "^7.2.5" @@ -3812,15 +4323,15 @@ braces@^3.0.3, braces@~3.0.2: dependencies: fill-range "^7.1.1" -browserslist@^4.21.10, browserslist@^4.23.1, browserslist@^4.23.3: - version "4.23.3" - resolved "https://registry.yarnpkg.com/browserslist/-/browserslist-4.23.3.tgz#debb029d3c93ebc97ffbc8d9cbb03403e227c800" - integrity sha512-btwCFJVjI4YWDNfau8RhZ+B1Q/VLoUITrm3RlP6y1tYGWIOa+InuYiRGXUBXo8nA1qKmHMyLB/iVQg5TT4eFoA== +browserslist@^4.21.10, browserslist@^4.24.0, browserslist@^4.24.2: + version "4.24.3" + resolved "https://registry.yarnpkg.com/browserslist/-/browserslist-4.24.3.tgz#5fc2725ca8fb3c1432e13dac278c7cc103e026d2" + integrity sha512-1CPmv8iobE2fyRMV97dAcMVegvvWKxmq94hkLiAkUGwKVTyDLw33K+ZxiFrREKmmps4rIw6grcCFCnTMSZ/YiA== dependencies: - caniuse-lite "^1.0.30001646" - electron-to-chromium "^1.5.4" - node-releases "^2.0.18" - update-browserslist-db "^1.1.0" + caniuse-lite "^1.0.30001688" + electron-to-chromium "^1.5.73" + node-releases "^2.0.19" + update-browserslist-db "^1.1.1" bser@2.1.1: version "2.1.1" @@ -3857,26 +4368,60 @@ bundle-name@^4.1.0: dependencies: run-applescript "^7.0.0" -bytes@3.0.0: - version "3.0.0" - resolved "https://registry.yarnpkg.com/bytes/-/bytes-3.0.0.tgz#d32815404d689699f85a4ea4fa8755dd13a96048" - integrity sha512-pMhOfFDPiv9t5jjIXkHosWmkSyQbvsgEVNkz0ERHbuLh2T/7j4Mqqpz523Fe8MVY89KC6Sh/QfS2sM+SjgFDcw== - bytes@3.1.2: version "3.1.2" resolved "https://registry.yarnpkg.com/bytes/-/bytes-3.1.2.tgz#8b0beeb98605adf1b128fa4386403c009e0221a5" integrity sha512-/Nf7TyzTx6S3yRJObOAV7956r8cr2+Oj8AC5dt8wSP3BQAoeX58NoHyCU8P8zGkNXStjTSi6fzO6F0pBdcYbEg== -call-bind@^1.0.0, call-bind@^1.0.2, call-bind@^1.0.5, call-bind@^1.0.6, call-bind@^1.0.7: - version "1.0.7" - resolved "https://registry.yarnpkg.com/call-bind/-/call-bind-1.0.7.tgz#06016599c40c56498c18769d2730be242b6fa3b9" - integrity sha512-GHTSNSYICQ7scH7sZ+M2rFopRoLh8t2bLSW6BbgrtLsahOIB5iyAVJf9GjWK3cYTDaMj4XdBpM1cA6pIS0Kv2w== +cacache@^16.1.0: + version "16.1.3" 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es-define-property "^1.0.0" es-errors "^1.3.0" function-bind "^1.1.2" + +call-bind@^1.0.0, call-bind@^1.0.2, call-bind@^1.0.5, call-bind@^1.0.6, call-bind@^1.0.7, call-bind@^1.0.8: + version "1.0.8" + resolved "https://registry.yarnpkg.com/call-bind/-/call-bind-1.0.8.tgz#0736a9660f537e3388826f440d5ec45f744eaa4c" + integrity sha512-oKlSFMcMwpUg2ednkhQ454wfWiU/ul3CkJe/PEHcTKuiX6RpbehUiFMXu13HalGZxfUwCQzZG747YXBn1im9ww== + dependencies: + call-bind-apply-helpers "^1.0.0" + es-define-property "^1.0.0" get-intrinsic "^1.2.4" - set-function-length "^1.2.1" + set-function-length "^1.2.2" + +call-bound@^1.0.2, call-bound@^1.0.3: + version "1.0.3" + resolved "https://registry.yarnpkg.com/call-bound/-/call-bound-1.0.3.tgz#41cfd032b593e39176a71533ab4f384aa04fd681" + integrity sha512-YTd+6wGlNlPxSuri7Y6X8tY2dmm12UMH66RpKMhiX6rsk5wXXnYgbUcOt8kiS31/AjfoTOvCsE+w8nZQLQnzHA== + dependencies: + call-bind-apply-helpers "^1.0.1" + get-intrinsic "^1.2.6" callsites@^3.0.0: version "3.1.0" @@ -3906,10 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+character-reference-invalid@^2.0.0: + version "2.0.1" + resolved "https://registry.yarnpkg.com/character-reference-invalid/-/character-reference-invalid-2.0.1.tgz#85c66b041e43b47210faf401278abf808ac45cb9" + integrity sha512-iBZ4F4wRbyORVsu0jPV7gXkOsGYjGHPmAyv+HiHG8gi5PtC9KI2j1+v8/tlibRvjoWX027ypmG/n0HtO5t7unw== + "chokidar@>=3.0.0 <4.0.0", chokidar@^3.6.0: version "3.6.0" resolved "https://registry.yarnpkg.com/chokidar/-/chokidar-3.6.0.tgz#197c6cc669ef2a8dc5e7b4d97ee4e092c3eb0d5b" @@ -3999,6 +4578,11 @@ chownr@^1.1.1: resolved "https://registry.yarnpkg.com/chownr/-/chownr-1.1.4.tgz#6fc9d7b42d32a583596337666e7d08084da2cc6b" integrity sha512-jJ0bqzaylmJtVnNgzTeSOs8DPavpbYgEr/b0YL8/2GO3xJEhInFmhKMUnEJQjZumK7KXGFhUy89PrsJWlakBVg== +chownr@^2.0.0: + version "2.0.0" + resolved "https://registry.yarnpkg.com/chownr/-/chownr-2.0.0.tgz#15bfbe53d2eab4cf70f18a8cd68ebe5b3cb1dece" + integrity sha512-bIomtDF5KGpdogkLd9VspvFzk9KfpyyGlS8YFVZl7TGPBHL5snIOnxeshwVgPteQ9b4Eydl+pVbIyE1DcvCWgQ== + chrome-trace-event@^1.0.2: version "1.0.4" resolved "https://registry.yarnpkg.com/chrome-trace-event/-/chrome-trace-event-1.0.4.tgz#05bffd7ff928465093314708c93bdfa9bd1f0f5b" @@ -4036,6 +4620,11 @@ clean-css@^5.2.2, clean-css@~5.3.2: dependencies: source-map "~0.6.0" +clean-stack@^2.0.0: + version "2.2.0" + resolved "https://registry.yarnpkg.com/clean-stack/-/clean-stack-2.2.0.tgz#ee8472dbb129e727b31e8a10a427dee9dfe4008b" + integrity sha512-4diC9HaTE+KRAMWhDhrGOECgWZxoevMc5TlkObMqNSsVU62PYzXZ/SMTjzyGAFF1YusgxGcSWTEXBhp0CPwQ1A== + cli-cursor@^5.0.0: version "5.0.0" resolved "https://registry.yarnpkg.com/cli-cursor/-/cli-cursor-5.0.0.tgz#24a4831ecf5a6b01ddeb32fb71a4b2088b0dce38" @@ -4126,6 +4715,11 @@ color-name@~1.1.4: resolved "https://registry.yarnpkg.com/color-name/-/color-name-1.1.4.tgz#c2a09a87acbde69543de6f63fa3995c826c536a2" integrity sha512-dOy+3AuW3a2wNbZHIuMZpTcgjGuLU/uBL/ubcZF9OXbDo8ff4O8yVp5Bf0efS8uEoYo5q4Fx7dY9OgQGXgAsQA== +color-support@^1.1.2, color-support@^1.1.3: + version "1.1.3" + resolved "https://registry.yarnpkg.com/color-support/-/color-support-1.1.3.tgz#93834379a1cc9a0c61f82f52f0d04322251bd5a2" + integrity sha512-qiBjkpbMLO/HL68y+lh4q0/O1MZFj2RX6X/KmMa3+gJD3z+WwI1ZzDHysvqHGS3mP6mznPckpXmw1nI9cJjyRg== + colorbrewer@1.3.0: version "1.3.0" resolved "https://registry.yarnpkg.com/colorbrewer/-/colorbrewer-1.3.0.tgz#1d7e92a6277e42dc56377911bbd867bdbcb2ff7d" @@ -4148,6 +4742,11 @@ comma-separated-tokens@^1.0.0: resolved "https://registry.yarnpkg.com/comma-separated-tokens/-/comma-separated-tokens-1.0.8.tgz#632b80b6117867a158f1080ad498b2fbe7e3f5ea" integrity sha512-GHuDRO12Sypu2cV70d1dkA2EUmXHgntrzbpvOB+Qy+49ypNfGgFQIC2fhhXbnyrJRynDCAARsT7Ou0M6hirpfw== +comma-separated-tokens@^2.0.0: + version "2.0.3" + resolved "https://registry.yarnpkg.com/comma-separated-tokens/-/comma-separated-tokens-2.0.3.tgz#4e89c9458acb61bc8fef19f4529973b2392839ee" + integrity sha512-Fu4hJdvzeylCfQPp9SGWidpzrMs7tTrlu6Vb8XGaRGck8QSNZJJp538Wrb60Lax4fPwR64ViY468OIUTbRlGZg== + commander@2, commander@^2.20.0: version "2.20.3" resolved "https://registry.yarnpkg.com/commander/-/commander-2.20.3.tgz#fd485e84c03eb4881c20722ba48035e8531aeb33" @@ -4203,7 +4802,7 @@ complexviewer@2.2.2: point2d "0.0.1" rgb-color "2.1.2" -compressible@~2.0.16: +compressible@~2.0.18: version "2.0.18" resolved "https://registry.yarnpkg.com/compressible/-/compressible-2.0.18.tgz#af53cca6b070d4c3c0750fbd77286a6d7cc46fba" integrity sha512-AF3r7P5dWxL8MxyITRMlORQNaOA2IkAFaTr4k7BUumjPtRpGDTZpl0Pb1XCO6JeDCBdp126Cgs9sMxqSjgYyRg== @@ -4211,16 +4810,16 @@ compressible@~2.0.16: mime-db ">= 1.43.0 < 2" compression@^1.7.4: - version "1.7.4" - resolved "https://registry.yarnpkg.com/compression/-/compression-1.7.4.tgz#95523eff170ca57c29a0ca41e6fe131f41e5bb8f" - integrity sha512-jaSIDzP9pZVS4ZfQ+TzvtiWhdpFhE2RDHz8QJkpX9SIpLq88VueF5jJw6t+6CUQcAoA6t+x89MLrWAqpfDE8iQ== + version "1.7.5" + resolved "https://registry.yarnpkg.com/compression/-/compression-1.7.5.tgz#fdd256c0a642e39e314c478f6c2cd654edd74c93" + integrity sha512-bQJ0YRck5ak3LgtnpKkiabX5pNF7tMUh1BSy2ZBOTh0Dim0BUu6aPPwByIns6/A5Prh8PufSPerMDUklpzes2Q== dependencies: - accepts "~1.3.5" - bytes "3.0.0" - compressible "~2.0.16" + bytes "3.1.2" + compressible "~2.0.18" debug "2.6.9" + negotiator "~0.6.4" on-headers "~1.0.2" - safe-buffer "5.1.2" + safe-buffer "5.2.1" vary "~1.1.2" concat-map@0.0.1: @@ -4246,6 +4845,11 @@ connect-history-api-fallback@^2.0.0: resolved "https://registry.yarnpkg.com/connect-history-api-fallback/-/connect-history-api-fallback-2.0.0.tgz#647264845251a0daf25b97ce87834cace0f5f1c8" integrity sha512-U73+6lQFmfiNPrYbXqr6kZ1i1wiRqXnp2nhMsINseWXO8lDau0LGEffJ8kQi4EjLZympVgRdvqjAgiZ1tgzDDA== +console-control-strings@^1.0.0, console-control-strings@^1.1.0: + version "1.1.0" + resolved "https://registry.yarnpkg.com/console-control-strings/-/console-control-strings-1.1.0.tgz#3d7cf4464db6446ea644bf4b39507f9851008e8e" + integrity 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"https://registry.yarnpkg.com/cross-spawn/-/cross-spawn-6.0.5.tgz#4a5ec7c64dfae22c3a14124dbacdee846d80cbc4" - integrity sha512-eTVLrBSt7fjbDygz805pMnstIs2VTBNkRm0qxZd+M7A5XDdxVRWO5MxGBXZhjY4cqLYLdtrGqRf8mBPmzwSpWQ== + version "6.0.6" + resolved "https://registry.yarnpkg.com/cross-spawn/-/cross-spawn-6.0.6.tgz#30d0efa0712ddb7eb5a76e1e8721bffafa6b5d57" + integrity sha512-VqCUuhcd1iB+dsv8gxPttb5iZh/D0iubSP21g36KXdEuf6I5JiioesUVjpCdHV9MZRUfVFlvwtIUyPfxo5trtw== dependencies: nice-try "^1.0.4" path-key "^2.0.1" @@ -4386,9 +5005,9 @@ cross-spawn@^6.0.5: which "^1.2.9" cross-spawn@^7.0.0, cross-spawn@^7.0.2, cross-spawn@^7.0.3: - version "7.0.3" - resolved "https://registry.yarnpkg.com/cross-spawn/-/cross-spawn-7.0.3.tgz#f73a85b9d5d41d045551c177e2882d4ac85728a6" - integrity sha512-iRDPJKUPVEND7dHPO8rkbOnPpyDygcDFtWjpeWNCgy8WP2rXcxXL8TskReQl6OrB2G7+UJrags1q15Fudc7G6w== + version "7.0.6" + resolved "https://registry.yarnpkg.com/cross-spawn/-/cross-spawn-7.0.6.tgz#8a58fe78f00dcd70c370451759dfbfaf03e8ee9f" + integrity sha512-uV2QOWP2nWzsy2aMp8aRibhi9dlzF5Hgh5SHaB9OiTGEyDTiJJyx0uy51QXdyWbtAHNua4XJzUKca3OzKUd3vA== dependencies: path-key "^3.1.0" shebang-command "^2.0.0" @@ -4516,13 +5135,6 @@ d3-array@1, d3-array@^1.1.1, d3-array@^1.2.0: resolved "https://registry.yarnpkg.com/d3-array/-/d3-array-1.2.4.tgz#635ce4d5eea759f6f605863dbcfc30edc737f71f" integrity sha512-KHW6M86R+FUPYGb3R5XiYjXPq7VzwxZ22buHhAEVG5ztoEcZZMLov530mmccaqA1GghZArjQV46fuc8kUqhhHw== -d3-array@2, d3-array@^2.3.0: - version "2.12.1" - resolved "https://registry.yarnpkg.com/d3-array/-/d3-array-2.12.1.tgz#e20b41aafcdffdf5d50928004ececf815a465e81" - integrity sha512-B0ErZK/66mHtEsR1TkPEEkwdy+WDesimkM5gpZr5Dsg54BiTA5RXtYW5qTLIAcekaS9xfZrzBLF/OAkB3Qn1YQ== - dependencies: - internmap "^1.0.0" - "d3-array@2 - 3", "d3-array@2.10.0 - 3", "d3-array@2.5.0 - 3", d3-array@3, d3-array@^3.2.0: version "3.2.4" resolved "https://registry.yarnpkg.com/d3-array/-/d3-array-3.2.4.tgz#15fec33b237f97ac5d7c986dc77da273a8ed0bb5" @@ -4587,11 +5199,6 @@ d3-color@1: resolved "https://registry.yarnpkg.com/d3-color/-/d3-color-1.4.1.tgz#c52002bf8846ada4424d55d97982fef26eb3bc8a" integrity sha512-p2sTHSLCJI2QKunbGb7ocOh7DgTAn8IrLx21QRc/BSnodXM4sv6aLQlnfpvehFMLZEfBc6g9pH9SWQccFYfJ9Q== -"d3-color@1 - 2": - version "2.0.0" - resolved "https://registry.yarnpkg.com/d3-color/-/d3-color-2.0.0.tgz#8d625cab42ed9b8f601a1760a389f7ea9189d62e" - integrity sha512-SPXi0TSKPD4g9tw0NMZFnR95XVgUZiBH+uUTqQuDu1OsE2zomHU7ho0FISciaPvosimixwHFl3WHLGabv6dDgQ== - "d3-color@1 - 3", d3-color@3: version "3.1.0" resolved "https://registry.yarnpkg.com/d3-color/-/d3-color-3.1.0.tgz#395b2833dfac71507f12ac2f7af23bf819de24e2" @@ -4717,11 +5324,6 @@ d3-format@1: resolved "https://registry.yarnpkg.com/d3-format/-/d3-format-1.4.5.tgz#374f2ba1320e3717eb74a9356c67daee17a7edb4" integrity sha512-J0piedu6Z8iB6TbIGfZgDzfXxUFN3qQRMofy2oPdXzQibYGqPB/9iMcxr/TGalU+2RsyDO+U4f33id8tbnSRMQ== -"d3-format@1 - 2": - version "2.0.0" - resolved "https://registry.yarnpkg.com/d3-format/-/d3-format-2.0.0.tgz#a10bcc0f986c372b729ba447382413aabf5b0767" - integrity sha512-Ab3S6XuE/Q+flY96HXT0jOXcM4EAClYFnRGY5zsjRGNy6qCYrQsMffs7cV5Q9xejb35zxW5hf/guKw34kvIKsA== - "d3-format@1 - 3", d3-format@3: version "3.1.0" resolved "https://registry.yarnpkg.com/d3-format/-/d3-format-3.1.0.tgz#9260e23a28ea5cb109e93b21a06e24e2ebd55641" @@ -4765,13 +5367,6 @@ d3-interpolate@1: dependencies: d3-color "1 - 3" -"d3-interpolate@1.2.0 - 2": - version "2.0.1" - resolved "https://registry.yarnpkg.com/d3-interpolate/-/d3-interpolate-2.0.1.tgz#98be499cfb8a3b94d4ff616900501a64abc91163" - integrity sha512-c5UhwwTs/yybcmTpAVqwSFl6vrQ8JZJoT5F7xNFK9pymv5C0Ymcc9/LIJHtYIggg/yS9YHw8i8O8tgb9pupjeQ== - dependencies: - d3-color "1 - 2" - d3-path@1: version "1.0.9" resolved "https://registry.yarnpkg.com/d3-path/-/d3-path-1.0.9.tgz#48c050bb1fe8c262493a8caf5524e3e9591701cf" @@ -4851,17 +5446,6 @@ d3-scale@4, d3-scale@~4.0.2: d3-time "2.1.1 - 3" d3-time-format "2 - 4" -d3-scale@^3.2.3: - version "3.3.0" - resolved "https://registry.yarnpkg.com/d3-scale/-/d3-scale-3.3.0.tgz#28c600b29f47e5b9cd2df9749c206727966203f3" - integrity sha512-1JGp44NQCt5d1g+Yy+GeOnZP7xHo0ii8zsQp6PGzd+C1/dl0KGsp9A7Mxwp+1D1o4unbTTxVdU/ZOIEBoeZPbQ== - dependencies: - d3-array "^2.3.0" - d3-format "1 - 2" - d3-interpolate "1.2.0 - 2" - d3-time "^2.1.1" - d3-time-format "2 - 3" - d3-selection@1, d3-selection@^1.1.0: version "1.4.2" resolved "https://registry.yarnpkg.com/d3-selection/-/d3-selection-1.4.2.tgz#dcaa49522c0dbf32d6c1858afc26b6094555bc5c" @@ -4893,13 +5477,6 @@ d3-time-format@2: dependencies: d3-time "1" -"d3-time-format@2 - 3": - version "3.0.0" - resolved "https://registry.yarnpkg.com/d3-time-format/-/d3-time-format-3.0.0.tgz#df8056c83659e01f20ac5da5fdeae7c08d5f1bb6" - integrity sha512-UXJh6EKsHBTjopVqZBhFysQcoXSv/5yLONZvkQ5Kk3qbwiUYkdX17Xa1PT6U1ZWXGGfB1ey5L8dKMlFq2DO0Ag== - dependencies: - d3-time "1 - 2" - "d3-time-format@2 - 4", d3-time-format@4: version "4.1.0" resolved "https://registry.yarnpkg.com/d3-time-format/-/d3-time-format-4.1.0.tgz#7ab5257a5041d11ecb4fe70a5c7d16a195bb408a" @@ -4912,13 +5489,6 @@ d3-time@1: resolved "https://registry.yarnpkg.com/d3-time/-/d3-time-1.1.0.tgz#b1e19d307dae9c900b7e5b25ffc5dcc249a8a0f1" integrity sha512-Xh0isrZ5rPYYdqhAVk8VLnMEidhz5aP7htAADH6MfzgmmicPkTo8LhkLxci61/lCB7n7UmE3bN0leRt+qvkLxA== -"d3-time@1 - 2", d3-time@^2.1.1: - version "2.1.1" - resolved "https://registry.yarnpkg.com/d3-time/-/d3-time-2.1.1.tgz#e9d8a8a88691f4548e68ca085e5ff956724a6682" - integrity sha512-/eIQe/eR4kCQwq7yxi7z4c6qEXf2IYGcjoWB5OOQy4Tq9Uv39/947qlDcN2TLkiTzQWzvnsuYPB9TrWaNfipKQ== - dependencies: - d3-array "2" - "d3-time@1 - 3", "d3-time@2.1.1 - 3", d3-time@3: version "3.1.0" resolved "https://registry.yarnpkg.com/d3-time/-/d3-time-3.1.0.tgz#9310db56e992e3c0175e1ef385e545e48a9bb5c7" @@ -5023,7 +5593,43 @@ d3@5.16.0: d3-voronoi "1" d3-zoom "1" -d3@7.9.0: +d3@7.8.5: + version "7.8.5" + resolved "https://registry.yarnpkg.com/d3/-/d3-7.8.5.tgz#fde4b760d4486cdb6f0cc8e2cbff318af844635c" + integrity sha512-JgoahDG51ncUfJu6wX/1vWQEqOflgXyl4MaHqlcSruTez7yhaRKR9i8VjjcQGeS2en/jnFivXuaIMnseMMt0XA== + dependencies: + d3-array "3" + d3-axis "3" + d3-brush "3" + d3-chord "3" + d3-color "3" + d3-contour "4" + d3-delaunay "6" + d3-dispatch "3" + d3-drag "3" + d3-dsv "3" + d3-ease "3" + d3-fetch "3" + d3-force "3" + d3-format "3" + d3-geo "3" + d3-hierarchy "3" + d3-interpolate "3" + d3-path "3" + d3-polygon "3" + d3-quadtree "3" + d3-random "3" + d3-scale "4" + d3-scale-chromatic "3" + d3-selection "3" + d3-shape "3" + d3-time "3" + d3-time-format "4" + d3-timer "3" + d3-transition "3" + d3-zoom "3" + +d3@7.9.0, d3@^7.9.0: version "7.9.0" resolved "https://registry.yarnpkg.com/d3/-/d3-7.9.0.tgz#579e7acb3d749caf8860bd1741ae8d371070cd5d" integrity sha512-e1U46jVP+w7Iut8Jt8ri1YsPOvFpg46k+K8TpCb0P+zjCkjkPnV7WzfDJzMHy1LnA+wj5pLT1wjO901gLXeEhA== @@ -5100,15 +5706,7 @@ damerau-levenshtein@^1.0.8: resolved "https://registry.yarnpkg.com/damerau-levenshtein/-/damerau-levenshtein-1.0.8.tgz#b43d286ccbd36bc5b2f7ed41caf2d0aba1f8a6e7" integrity sha512-sdQSFB7+llfUcQHUQO3+B8ERRj0Oa4w9POWMI/puGtuf7gFywGmkaLCElnudfTiKZV+NvHqL0ifzdrI8Ro7ESA== -data-loader@^2.9.1: - version "2.12.0" - resolved "https://registry.yarnpkg.com/data-loader/-/data-loader-2.12.0.tgz#e14158ed1c6ffa5314590871a7b8758da9617add" - integrity sha512-HhFGutLwfMIfz96ctq4FZ03WMQ9W8zdMBHkEKJGaaTaChKhczVIoRtldWd4MkERHNIFWJJkTgi+pjNAZjzwfeA== - dependencies: - "@types/lodash-es" "4.17.3" - lodash-es "^4.17.11" - -data-loader@^3.8.22: +data-loader@^3.8.4: version "3.8.22" resolved "https://registry.yarnpkg.com/data-loader/-/data-loader-3.8.22.tgz#2b73a9ddf7d12b267d5775a7a29f08899191026d" integrity sha512-x62gXAb7kW1wLo+laGrLRJ4yVLsIr+WQ23Jebe89EnzuvpUFf0ckmxtK2lvllBJ9U1ZEwCeSfX9xGc3kwI3Otg== @@ -5116,14 +5714,6 @@ data-loader@^3.8.22: "@types/lodash-es" "4.17.3" lodash-es "^4.17.11" -data-loader@^3.8.4: - version "3.8.4" - resolved "https://registry.yarnpkg.com/data-loader/-/data-loader-3.8.4.tgz#e9d33e0a8ccb626ff3098e1f53074e252c4b048d" - integrity sha512-0SeXJ7oVktX3lYoWfsOj1u4b2vsDcZfAWIApBjCoDflfh1h1Xmh7QABzi3Tl24OI/5InSot0VF91Bwm++ictVA== - dependencies: - "@types/lodash-es" "4.17.3" - lodash-es "^4.17.11" - data-urls@^3.0.2: version "3.0.2" resolved "https://registry.yarnpkg.com/data-urls/-/data-urls-3.0.2.tgz#9cf24a477ae22bcef5cd5f6f0bfbc1d2d3be9143" @@ -5172,10 +5762,10 @@ debug@2.6.9, debug@^2.6.9: dependencies: ms "2.0.0" -debug@4, debug@^4.1.0, debug@^4.1.1, debug@^4.3.1, debug@^4.3.2, debug@^4.3.4, debug@~4.3.6: - version "4.3.7" - resolved "https://registry.yarnpkg.com/debug/-/debug-4.3.7.tgz#87945b4151a011d76d95a198d7111c865c360a52" - integrity sha512-Er2nc/H7RrMXZBFCEim6TCmMk02Z8vLC2Rbi1KEBggpo0fS6l0S1nnapwmIi3yW/+GOJap1Krg4w0Hg80oCqgQ== +debug@4, debug@^4.0.0, debug@^4.1.0, debug@^4.1.1, debug@^4.3.1, debug@^4.3.2, debug@^4.3.3, debug@^4.3.4: + version "4.4.0" + resolved "https://registry.yarnpkg.com/debug/-/debug-4.4.0.tgz#2b3f2aea2ffeb776477460267377dc8710faba8a" + integrity sha512-6WTZ/IxCY/T6BALoZHaE4ctp9xm+Z5kY/pzYaCHRFeyVhojxlrm+46y68HA6hr0TcwEssoxNiDEUJQjfPZ/RYA== dependencies: ms "^2.1.3" @@ -5186,6 +5776,13 @@ debug@^3.2.7: dependencies: ms "^2.1.1" +debug@~4.3.6: + version "4.3.7" + resolved "https://registry.yarnpkg.com/debug/-/debug-4.3.7.tgz#87945b4151a011d76d95a198d7111c865c360a52" + integrity sha512-Er2nc/H7RrMXZBFCEim6TCmMk02Z8vLC2Rbi1KEBggpo0fS6l0S1nnapwmIi3yW/+GOJap1Krg4w0Hg80oCqgQ== + dependencies: + ms "^2.1.3" + decamelize@^1.1.1: version "1.2.0" resolved "https://registry.yarnpkg.com/decamelize/-/decamelize-1.2.0.tgz#f6534d15148269b20352e7bee26f501f9a191290" @@ -5196,6 +5793,20 @@ decimal.js@^10.4.2: resolved "https://registry.yarnpkg.com/decimal.js/-/decimal.js-10.4.3.tgz#1044092884d245d1b7f65725fa4ad4c6f781cc23" integrity sha512-VBBaLc1MgL5XpzgIP7ny5Z6Nx3UrRkIViUkPUdtl9aya5amy3De1gsUUSB1g3+3sExYNjCAsAznmukyxCb1GRA== +decode-named-character-reference@^1.0.0: + version "1.0.2" + resolved "https://registry.yarnpkg.com/decode-named-character-reference/-/decode-named-character-reference-1.0.2.tgz#daabac9690874c394c81e4162a0304b35d824f0e" + integrity sha512-O8x12RzrUF8xyVcY0KJowWsmaJxQbmy0/EtnNtHRpsOcT7dFk5W598coHqBVpmWo1oQQfsCqfCmkZN5DJrZVdg== + dependencies: + character-entities "^2.0.0" + +decompress-response@^4.2.0: + version "4.2.1" + resolved "https://registry.yarnpkg.com/decompress-response/-/decompress-response-4.2.1.tgz#414023cc7a302da25ce2ec82d0d5238ccafd8986" + integrity sha512-jOSne2qbyE+/r8G1VU+G/82LBs2Fs4LAsTiLSHOCOMZQl2OKZ6i8i4IyHemTe+/yIXOtTcRQMzPcgyhoFlqPkw== + dependencies: + mimic-response "^2.0.0" + decompress-response@^6.0.0: version "6.0.0" resolved "https://registry.yarnpkg.com/decompress-response/-/decompress-response-6.0.0.tgz#ca387612ddb7e104bd16d85aab00d5ecf09c66fc" @@ -5276,6 +5887,11 @@ delayed-stream@~1.0.0: resolved "https://registry.yarnpkg.com/delayed-stream/-/delayed-stream-1.0.0.tgz#df3ae199acadfb7d440aaae0b29e2272b24ec619" integrity sha512-ZySD7Nf91aLB0RxL4KGrKHBXl7Eds1DAmEdcoVawXnLD7SDhpNgtuII2aAkg7a7QS41jxPSZ17p4VdGnMHk3MQ== +delegates@^1.0.0: + version "1.0.0" + resolved "https://registry.yarnpkg.com/delegates/-/delegates-1.0.0.tgz#84c6e159b81904fdca59a0ef44cd870d31250f9a" + integrity sha512-bd2L678uiWATM6m5Z1VzNCErI3jiGzt6HGY8OVICs40JQq/HALfbyNJmp0UDakEY4pMMaN0Ly5om/B1VI/+xfQ== + denque@^1.1.1: version "1.5.1" resolved "https://registry.yarnpkg.com/denque/-/denque-1.5.1.tgz#07f670e29c9a78f8faecb2566a1e2c11929c5cbf" @@ -5291,7 +5907,7 @@ depd@~1.1.2: resolved "https://registry.yarnpkg.com/depd/-/depd-1.1.2.tgz#9bcd52e14c097763e749b274c4346ed2e560b5a9" integrity sha512-7emPTl6Dpo6JRXOXjLRxck+FlLRX5847cLKEn00PLAgc3g2hTZZgr+e4c2v6QpSmLeFP3n5yUo7ft6avBK/5jQ== -dequal@^2.0.3: +dequal@^2.0.0, dequal@^2.0.3: version "2.0.3" resolved "https://registry.yarnpkg.com/dequal/-/dequal-2.0.3.tgz#2644214f1997d39ed0ee0ece72335490a7ac67be" integrity sha512-0je+qPKHEMohvfRTCEo3CrPG6cAzAYgmzKyxRiYSSDkS6eGJdyVJm7WaYA5ECaAD9wLB2T4EEeymA5aFVcYXCA== @@ -5301,6 +5917,11 @@ destroy@1.2.0: resolved "https://registry.yarnpkg.com/destroy/-/destroy-1.2.0.tgz#4803735509ad8be552934c67df614f94e66fa015" integrity sha512-2sJGJTaXIIaR1w4iJSNoN0hnMY7Gpc/n8D4qSCJw8QqFWXf7cuAgnEHxBpweaVcPevC2l3KpjYCx3NypQQgaJg== +detect-libc@^1.0.3: + version "1.0.3" + resolved "https://registry.yarnpkg.com/detect-libc/-/detect-libc-1.0.3.tgz#fa137c4bd698edf55cd5cd02ac559f91a4c4ba9b" + integrity 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+ resolved "https://registry.yarnpkg.com/dunder-proto/-/dunder-proto-1.0.0.tgz#c2fce098b3c8f8899554905f4377b6d85dabaa80" + integrity sha512-9+Sj30DIu+4KvHqMfLUGLFYL2PkURSYMVXJyXe92nFRvlYq5hBjLEhblKB+vkd/WVlUYMWigiY07T91Fkk0+4A== + dependencies: + call-bind-apply-helpers "^1.0.0" + es-errors "^1.3.0" + gopd "^1.2.0" + duplexer@^0.1.2: version "0.1.2" resolved "https://registry.yarnpkg.com/duplexer/-/duplexer-0.1.2.tgz#3abe43aef3835f8ae077d136ddce0f276b0400e6" @@ -5492,10 +6124,10 @@ ejs@^3.1.6: dependencies: jake "^10.8.5" -electron-to-chromium@^1.5.4: - version "1.5.27" - resolved "https://registry.yarnpkg.com/electron-to-chromium/-/electron-to-chromium-1.5.27.tgz#5203ce5d6054857d84ba84d3681cbe59132ade78" - integrity sha512-o37j1vZqCoEgBuWWXLHQgTN/KDKe7zwpiY5CPeq2RvUqOyJw9xnrULzZAEVQ5p4h+zjMk7hgtOoPdnLxr7m/jw== +electron-to-chromium@^1.5.73: + version "1.5.73" + resolved 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"https://registry.yarnpkg.com/end-of-stream/-/end-of-stream-1.4.4.tgz#5ae64a5f45057baf3626ec14da0ca5e4b2431eb0" @@ -5547,11 +6186,16 @@ entities@^2.0.0: resolved "https://registry.yarnpkg.com/entities/-/entities-2.2.0.tgz#098dc90ebb83d8dffa089d55256b351d34c4da55" integrity sha512-p92if5Nz619I0w+akJrLZH0MX0Pb5DX39XOwQTtXSdQQOaYH03S1uIQp4mhOZtAXrxq4ViO67YTiLBo2638o9A== -entities@^4.2.0, entities@^4.4.0: +entities@^4.2.0, entities@^4.4.0, entities@^4.5.0: version "4.5.0" resolved "https://registry.yarnpkg.com/entities/-/entities-4.5.0.tgz#5d268ea5e7113ec74c4d033b79ea5a35a488fb48" integrity sha512-V0hjH4dGPh9Ao5p0MoRY6BVqtwCjhz6vI5LT8AJ55H+4g9/4vbHx1I54fS0XuclLhDHArPQCiMjDxjaL8fPxhw== +env-paths@^2.2.0: + version "2.2.1" + resolved "https://registry.yarnpkg.com/env-paths/-/env-paths-2.2.1.tgz#420399d416ce1fbe9bc0a07c62fa68d67fd0f8f2" + integrity sha512-+h1lkLKhZMTYjog1VEpJNG7NZJWcuc2DDk/qsqSTRRCOXiLjeQ1d1/udrUGhqMxUgAlwKNZ0cf2uqan5GLuS2A== + envinfo@^7.7.3: version "7.14.0" resolved "https://registry.yarnpkg.com/envinfo/-/envinfo-7.14.0.tgz#26dac5db54418f2a4c1159153a0b2ae980838aae" @@ -5562,6 +6206,11 @@ environment@^1.0.0: resolved "https://registry.yarnpkg.com/environment/-/environment-1.1.0.tgz#8e86c66b180f363c7ab311787e0259665f45a9f1" integrity sha512-xUtoPkMggbz0MPyPiIWr1Kp4aeWJjDZ6SMvURhimjdZgsRuDplF5/s9hcgGhyXMhs+6vpnuoiZ2kFiu3FMnS8Q== +err-code@^2.0.2: + version "2.0.3" + resolved "https://registry.yarnpkg.com/err-code/-/err-code-2.0.3.tgz#23c2f3b756ffdfc608d30e27c9a941024807e7f9" + integrity sha512-2bmlRpNKBxT/CRmPOlyISQpNj+qSeYvcym/uT0Jx2bMOlKLtSy1ZmLuVxSEKKyor/N5yhvp/ZiG1oE3DEYMSFA== + errno@^0.1.1: version "0.1.8" resolved "https://registry.yarnpkg.com/errno/-/errno-0.1.8.tgz#8bb3e9c7d463be4976ff888f76b4809ebc2e811f" @@ -5576,71 +6225,71 @@ error-ex@^1.2.0, error-ex@^1.3.1: dependencies: is-arrayish "^0.2.1" -es-abstract@^1.17.2, es-abstract@^1.22.1, es-abstract@^1.22.3, es-abstract@^1.23.0, es-abstract@^1.23.2: - version "1.23.3" - resolved 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function.prototype.name "^1.1.6" - get-intrinsic "^1.2.4" + es-to-primitive "^1.3.0" + function.prototype.name "^1.1.7" + get-intrinsic "^1.2.6" get-symbol-description "^1.0.2" - globalthis "^1.0.3" - gopd "^1.0.1" + globalthis "^1.0.4" + gopd "^1.2.0" has-property-descriptors "^1.0.2" - has-proto "^1.0.3" - has-symbols "^1.0.3" + has-proto "^1.2.0" + has-symbols "^1.1.0" hasown "^2.0.2" - internal-slot "^1.0.7" + internal-slot "^1.1.0" is-array-buffer "^3.0.4" is-callable "^1.2.7" - is-data-view "^1.0.1" + is-data-view "^1.0.2" is-negative-zero "^2.0.3" - is-regex "^1.1.4" + is-regex "^1.2.1" is-shared-array-buffer "^1.0.3" - is-string "^1.0.7" + is-string "^1.1.1" is-typed-array "^1.1.13" - is-weakref "^1.0.2" - object-inspect "^1.13.1" + is-weakref "^1.1.0" + math-intrinsics "^1.0.0" + object-inspect "^1.13.3" object-keys "^1.1.1" object.assign "^4.1.5" - regexp.prototype.flags "^1.5.2" - safe-array-concat "^1.1.2" - safe-regex-test "^1.0.3" - string.prototype.trim "^1.2.9" - string.prototype.trimend "^1.0.8" + regexp.prototype.flags "^1.5.3" + safe-array-concat "^1.1.3" + safe-regex-test "^1.1.0" + string.prototype.trim "^1.2.10" + string.prototype.trimend "^1.0.9" string.prototype.trimstart "^1.0.8" typed-array-buffer "^1.0.2" typed-array-byte-length "^1.0.1" - typed-array-byte-offset "^1.0.2" - typed-array-length "^1.0.6" + typed-array-byte-offset "^1.0.3" + typed-array-length "^1.0.7" unbox-primitive "^1.0.2" - which-typed-array "^1.1.15" + which-typed-array "^1.1.16" es-array-method-boxes-properly@^1.0.0: version "1.0.0" resolved "https://registry.yarnpkg.com/es-array-method-boxes-properly/-/es-array-method-boxes-properly-1.0.0.tgz#873f3e84418de4ee19c5be752990b2e44718d09e" integrity sha512-wd6JXUmyHmt8T5a2xreUwKcGPq6f1f+WwIJkijUqiGcJz1qqnZgP6XIK+QyIWU5lT7imeNxUll48bziG+TSYcA== -es-define-property@^1.0.0: - version "1.0.0" - resolved "https://registry.yarnpkg.com/es-define-property/-/es-define-property-1.0.0.tgz#c7faefbdff8b2696cf5f46921edfb77cc4ba3845" - integrity sha512-jxayLKShrEqqzJ0eumQbVhTYQM27CfT1T35+gCgDFoL82JLsXqTJ76zv6A0YLOgEnLUMvLzsDsGIrl8NFpT2gQ== - dependencies: - get-intrinsic "^1.2.4" +es-define-property@^1.0.0, es-define-property@^1.0.1: + version "1.0.1" + resolved "https://registry.yarnpkg.com/es-define-property/-/es-define-property-1.0.1.tgz#983eb2f9a6724e9303f61addf011c72e09e0b0fa" + integrity sha512-e3nRfgfUZ4rNGL232gUgX06QNyyez04KdjFrF+LTRoOXmrOgFKDg4BCdsjW8EnT69eqdYGmRpJwiPVYNrCaW3g== -es-errors@^1.2.1, es-errors@^1.3.0: +es-errors@^1.3.0: version "1.3.0" resolved "https://registry.yarnpkg.com/es-errors/-/es-errors-1.3.0.tgz#05f75a25dab98e4fb1dcd5e1472c0546d5057c8f" integrity sha512-Zf5H2Kxt2xjTvbJvP2ZWLEICxA6j+hAmMzIlypy4xcBg1vKVnx89Wy0GbS+kf5cwCVFFzdCFh2XSCFNULS6csw== @@ -5666,23 +6315,23 @@ es-set-tostringtag@^2.0.3: has-tostringtag "^1.0.2" hasown "^2.0.1" -es-shim-unscopables@^1.0.0: +es-shim-unscopables@^1.0.2: version "1.0.2" resolved "https://registry.yarnpkg.com/es-shim-unscopables/-/es-shim-unscopables-1.0.2.tgz#1f6942e71ecc7835ed1c8a83006d8771a63a3763" integrity sha512-J3yBRXCzDu4ULnQwxyToo/OjdMx6akgVC7K6few0a7F/0wLtmKKN7I73AH5T2836UuXRqN7Qg+IIUw/+YJksRw== dependencies: hasown "^2.0.0" -es-to-primitive@^1.2.1: - version "1.2.1" - resolved "https://registry.yarnpkg.com/es-to-primitive/-/es-to-primitive-1.2.1.tgz#e55cd4c9cdc188bcefb03b366c736323fc5c898a" - integrity sha512-QCOllgZJtaUo9miYBcLChTUaHNjJF3PYs1VidD7AwiEj1kYxKeQTctLAezAOH5ZKRH0g2IgPn6KwB4IT8iRpvA== +es-to-primitive@^1.3.0: + version "1.3.0" + resolved "https://registry.yarnpkg.com/es-to-primitive/-/es-to-primitive-1.3.0.tgz#96c89c82cc49fd8794a24835ba3e1ff87f214e18" + integrity sha512-w+5mJ3GuFL+NjVtJlvydShqE1eN3h3PbI7/5LAsYJP/2qtuMXjfL2LpHSRqo4b4eSF5K/DH1JXKUAHSB2UW50g== dependencies: - is-callable "^1.1.4" - is-date-object "^1.0.1" - is-symbol "^1.0.2" + is-callable "^1.2.7" + is-date-object "^1.0.5" + is-symbol "^1.0.4" -escalade@^3.1.1, escalade@^3.1.2: +escalade@^3.1.1, escalade@^3.2.0: version "3.2.0" resolved "https://registry.yarnpkg.com/escalade/-/escalade-3.2.0.tgz#011a3f69856ba189dffa7dc8fcce99d2a87903e5" integrity sha512-WUj2qlxaQtO4g6Pq5c29GTcWGDyd8itL8zTlipgECz3JesAiiOKotd8JU6otB3PACgG6xkJUyVhboMS+bje/jA== @@ -5752,9 +6401,9 @@ eslint-import-resolver-node@^0.3.6: resolve "^1.22.4" eslint-module-utils@^2.7.3: - version "2.11.0" - resolved "https://registry.yarnpkg.com/eslint-module-utils/-/eslint-module-utils-2.11.0.tgz#b99b211ca4318243f09661fae088f373ad5243c4" - integrity sha512-gbBE5Hitek/oG6MUVj6sFuzEjA/ClzNflVrLovHi/JgLdC7fiN5gLAY1WIPW1a0V5I999MnsrvVrCOGmmVqDBQ== + version "2.12.0" + resolved "https://registry.yarnpkg.com/eslint-module-utils/-/eslint-module-utils-2.12.0.tgz#fe4cfb948d61f49203d7b08871982b65b9af0b0b" + integrity sha512-wALZ0HFoytlyh/1+4wuZ9FJCD/leWHQzzrxJ8+rebyReSLk7LApMyd3WJaLVoN+D5+WIdJyDK1c6JnE65V4Zyg== dependencies: debug "^3.2.7" @@ -5840,7 +6489,7 @@ eslint-scope@^7.2.2: esrecurse "^4.3.0" estraverse "^5.2.0" -eslint-visitor-keys@^3.3.0, eslint-visitor-keys@^3.4.1, eslint-visitor-keys@^3.4.3: +eslint-visitor-keys@^3.4.1, eslint-visitor-keys@^3.4.3: version "3.4.3" resolved "https://registry.yarnpkg.com/eslint-visitor-keys/-/eslint-visitor-keys-3.4.3.tgz#0cd72fe8550e3c2eae156a96a4dddcd1c8ac5800" integrity sha512-wpc+LXeiyiisxPlEkUzU6svyS1frIO3Mgxj1fdy7Pm8Ygzguax2N3Fa/D/ag1WqbOprdI+uY6wMUl8/a2G+iag== @@ -5927,6 +6576,11 @@ estraverse@^5.1.0, estraverse@^5.2.0, estraverse@^5.3.0: resolved "https://registry.yarnpkg.com/estraverse/-/estraverse-5.3.0.tgz#2eea5290702f26ab8fe5370370ff86c965d21123" integrity sha512-MMdARuVEQziNTeJD8DgMqmhwR11BRQ/cBP+pLtYdSTnf3MIO8fFeiINEbX36ZdNlfU/7A9f3gUw49B3oQsvwBA== +estree-util-is-identifier-name@^3.0.0: + version "3.0.0" + resolved "https://registry.yarnpkg.com/estree-util-is-identifier-name/-/estree-util-is-identifier-name-3.0.0.tgz#0b5ef4c4ff13508b34dcd01ecfa945f61fce5dbd" + integrity 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fake-indexeddb@6.0.0: version "6.0.0" resolved "https://registry.yarnpkg.com/fake-indexeddb/-/fake-indexeddb-6.0.0.tgz#3173d5ad141436dace95f8de6e9ecdc3d9787d5d" @@ -6100,9 +6764,9 @@ fast-levenshtein@^2.0.6: integrity sha512-DCXu6Ifhqcks7TZKY3Hxp3y6qphY5SJZmrWMDrKcERSOXWQdMhU9Ig/PYrzyw/ul9jOIyh0N4M0tbC5hodg8dw== fast-uri@^3.0.1: - version "3.0.1" - resolved "https://registry.yarnpkg.com/fast-uri/-/fast-uri-3.0.1.tgz#cddd2eecfc83a71c1be2cc2ef2061331be8a7134" - integrity sha512-MWipKbbYiYI0UC7cl8m/i/IWTqfC8YXsqjzybjddLsFjStroQzsHXkc73JutMvBiXmOvapk+axIl79ig5t55Bw== + version "3.0.3" + resolved "https://registry.yarnpkg.com/fast-uri/-/fast-uri-3.0.3.tgz#892a1c91802d5d7860de728f18608a0573142241" + integrity sha512-aLrHthzCjH5He4Z2H9YZ+v6Ujb9ocRuW6ZzkJQOrTxleEijANq4v1TsaPaVG1PZcuurEzrLcWRyYBYXD5cEiaw== fastest-levenshtein@^1.0.12: version "1.0.16" @@ -6144,10 +6808,10 @@ file-entry-cache@^6.0.1: dependencies: flat-cache "^3.0.4" -file-saver@^2.0.2: - version "2.0.5" - resolved 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-6345,6 +7007,13 @@ fs-extra@^9.0.1: jsonfile "^6.0.1" universalify "^2.0.0" +fs-minipass@^2.0.0, fs-minipass@^2.1.0: + version "2.1.0" + resolved "https://registry.yarnpkg.com/fs-minipass/-/fs-minipass-2.1.0.tgz#7f5036fdbf12c63c169190cbe4199c852271f9fb" + integrity sha512-V/JgOLFCS+R6Vcq0slCuaeWEdNC3ouDlJMNIsacH2VtALiu9mV4LPrHc5cDl8k5aw6J8jwgWWpiTo5RYhmIzvg== + dependencies: + minipass "^3.0.0" + fs.realpath@^1.0.0: version "1.0.0" resolved "https://registry.yarnpkg.com/fs.realpath/-/fs.realpath-1.0.0.tgz#1504ad2523158caa40db4a2787cb01411994ea4f" @@ -6360,21 +7029,51 @@ function-bind@^1.1.2: resolved "https://registry.yarnpkg.com/function-bind/-/function-bind-1.1.2.tgz#2c02d864d97f3ea6c8830c464cbd11ab6eab7a1c" integrity sha512-7XHNxH7qX9xG5mIwxkhumTox/MIRNcOgDrxWsMt2pAr23WHp6MrRlN7FBSFpCpr+oVO0F744iUgR82nJMfG2SA== -function.prototype.name@^1.1.6: - version "1.1.6" - resolved 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string-width "^4.2.3" + strip-ansi "^6.0.1" + wide-align "^1.1.5" + gensync@^1.0.0-beta.2: version "1.0.0-beta.2" resolved "https://registry.yarnpkg.com/gensync/-/gensync-1.0.0-beta.2.tgz#32a6ee76c3d7f52d46b2b1ae5d93fea8580a25e0" @@ -6391,20 +7090,25 @@ get-caller-file@^2.0.5: integrity sha512-DyFP3BM/3YHTQOCUL/w0OZHR0lpKeGrxotcHWcqNEdnltqFwXVfhEBQ94eIo34AfQpo0rGki4cyIiftY06h2Fg== get-east-asian-width@^1.0.0: - version "1.2.0" - resolved "https://registry.yarnpkg.com/get-east-asian-width/-/get-east-asian-width-1.2.0.tgz#5e6ebd9baee6fb8b7b6bd505221065f0cd91f64e" - integrity sha512-2nk+7SIVb14QrgXFHcm84tD4bKQz0RxPuMT8Ag5KPOq7J5fEmAg0UbXdTOSHqNuHSU28k55qnceesxXRZGzKWA== + version "1.3.0" + resolved "https://registry.yarnpkg.com/get-east-asian-width/-/get-east-asian-width-1.3.0.tgz#21b4071ee58ed04ee0db653371b55b4299875389" + integrity sha512-vpeMIQKxczTD/0s2CdEWHcb0eeJe6TFjxb+J5xgX7hScxqrGuyjmv4c1D4A/gelKfyox0gJJwIHF+fLjeaM8kQ== -get-intrinsic@^1.1.3, get-intrinsic@^1.2.1, get-intrinsic@^1.2.3, get-intrinsic@^1.2.4: - version "1.2.4" - resolved "https://registry.yarnpkg.com/get-intrinsic/-/get-intrinsic-1.2.4.tgz#e385f5a4b5227d449c3eabbad05494ef0abbeadd" - integrity sha512-5uYhsJH8VJBTv7oslg4BznJYhDoRI6waYCxMmCdnTrcCrHA/fCFKoTFz2JKKE0HdDFUF7/oQuhzumXJK7paBRQ== +get-intrinsic@^1.2.1, get-intrinsic@^1.2.4, get-intrinsic@^1.2.5, get-intrinsic@^1.2.6: + version "1.2.6" + resolved "https://registry.yarnpkg.com/get-intrinsic/-/get-intrinsic-1.2.6.tgz#43dd3dd0e7b49b82b2dfcad10dc824bf7fc265d5" + integrity sha512-qxsEs+9A+u85HhllWJJFicJfPDhRmjzoYdl64aMWW9yRIJmSyxdn8IEkuIM530/7T+lv0TIHd8L6Q/ra0tEoeA== dependencies: + call-bind-apply-helpers "^1.0.1" + dunder-proto "^1.0.0" + es-define-property "^1.0.1" es-errors "^1.3.0" + es-object-atoms "^1.0.0" function-bind "^1.1.2" - has-proto "^1.0.1" - has-symbols "^1.0.3" - hasown "^2.0.0" + gopd "^1.2.0" + has-symbols "^1.1.0" + hasown "^2.0.2" + math-intrinsics "^1.0.0" get-own-enumerable-property-symbols@^3.0.0: version "3.0.2" @@ -6450,6 +7154,19 @@ github-slugger@^2.0.0: resolved "https://registry.yarnpkg.com/github-slugger/-/github-slugger-2.0.0.tgz#52cf2f9279a21eb6c59dd385b410f0c0adda8f1a" integrity sha512-IaOQ9puYtjrkq7Y0Ygl9KDZnrf/aiUJYUpVf89y8kyaxbRG7Y1SrX/jaumrv81vc61+kiMempujsM3Yw7w5qcw== +gl@^6.0.2: + version "6.0.2" + resolved "https://registry.yarnpkg.com/gl/-/gl-6.0.2.tgz#685579732a19075e3acf4684edb1270278e551c7" + integrity sha512-yBbfpChOtFvg5D+KtMaBFvj6yt3vUnheNAH+UrQH2TfDB8kr0tERdL0Tjhe0W7xJ6jR6ftQBluTZR9jXUnKe8g== + dependencies: + bindings "^1.5.0" + bit-twiddle "^1.0.2" + glsl-tokenizer "^2.1.5" + nan "^2.17.0" + node-abi "^3.26.0" + node-gyp "^9.2.0" + prebuild-install "^7.1.1" + glob-parent@^5.1.2, glob-parent@~5.1.2: version "5.1.2" resolved "https://registry.yarnpkg.com/glob-parent/-/glob-parent-5.1.2.tgz#869832c58034fe68a4093c17dc15e8340d8401c4" @@ -6493,6 +7210,17 @@ glob@^7.1.3, glob@^7.1.4, glob@^7.1.6: once "^1.3.0" path-is-absolute "^1.0.0" +glob@^8.0.1: + version "8.1.0" + resolved "https://registry.yarnpkg.com/glob/-/glob-8.1.0.tgz#d388f656593ef708ee3e34640fdfb99a9fd1c33e" + integrity sha512-r8hpEjiQEYlF2QU0df3dS+nxxSIreXQS1qRhMJM0Q5NDdR386C7jb7Hwwod8Fgiuex+k0GFjgft18yvxm5XoCQ== + dependencies: + fs.realpath "^1.0.0" + inflight "^1.0.4" + inherits "2" + minimatch "^5.0.1" + once "^1.3.0" + globals@^11.1.0: version "11.12.0" resolved "https://registry.yarnpkg.com/globals/-/globals-11.12.0.tgz#ab8795338868a0babd8525758018c2a7eb95c42e" @@ -6505,7 +7233,7 @@ globals@^13.19.0: dependencies: type-fest "^0.20.2" -globalthis@^1.0.3: +globalthis@^1.0.4: version "1.0.4" resolved "https://registry.yarnpkg.com/globalthis/-/globalthis-1.0.4.tgz#7430ed3a975d97bfb59bcce41f5cabbafa651236" integrity sha512-DpLKbNU4WylpxJykQujfCcwYWiV/Jhm50Goo0wrVILAv5jOr9d+H+UR3PhSCD2rCCEIg0uc+G+muBTwD54JhDQ== @@ -6525,12 +7253,17 @@ globby@^14.0.0: slash "^5.1.0" unicorn-magic "^0.1.0" -gopd@^1.0.1: - version "1.0.1" - resolved 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dependencies: ansi-regex "^2.0.0" -has-bigints@^1.0.1, has-bigints@^1.0.2: +has-bigints@^1.0.2: version "1.0.2" resolved "https://registry.yarnpkg.com/has-bigints/-/has-bigints-1.0.2.tgz#0871bd3e3d51626f6ca0966668ba35d5602d6eaa" integrity sha512-tSvCKtBr9lkF0Ex0aQiP9N+OpV4zi2r/Nee5VkRDbaqv35RLYMzbwQfFSZZH0kR+Rd6302UJZ2p/bJCEoR3VoQ== @@ -6593,15 +7326,17 @@ has-property-descriptors@^1.0.0, has-property-descriptors@^1.0.2: dependencies: es-define-property "^1.0.0" -has-proto@^1.0.1, has-proto@^1.0.3: - version "1.0.3" - resolved "https://registry.yarnpkg.com/has-proto/-/has-proto-1.0.3.tgz#b31ddfe9b0e6e9914536a6ab286426d0214f77fd" - integrity sha512-SJ1amZAJUiZS+PhsVLf5tGydlaVB8EdFpaSO4gmiUKUOxk8qzn5AIy4ZeJUmh22znIdk/uMAUT2pl3FxzVUH+Q== +has-proto@^1.0.1, has-proto@^1.0.3, has-proto@^1.2.0: + version "1.2.0" + resolved "https://registry.yarnpkg.com/has-proto/-/has-proto-1.2.0.tgz#5de5a6eabd95fdffd9818b43055e8065e39fe9d5" + integrity 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"https://registry.yarnpkg.com/has-unicode/-/has-unicode-2.0.1.tgz#e0e6fe6a28cf51138855e086d1691e771de2a8b9" + integrity sha512-8Rf9Y83NBReMnx0gFzA8JImQACstCYWUplepDa9xprwwtmgEZUF0h/i5xSA625zB/I37EtrswSST6OXxwaaIJQ== + has@^1.0.3: version "1.0.4" resolved "https://registry.yarnpkg.com/has/-/has-1.0.4.tgz#2eb2860e000011dae4f1406a86fe80e530fb2ec6" @@ -6627,6 +7367,34 @@ hast-util-parse-selector@^2.0.0: resolved "https://registry.yarnpkg.com/hast-util-parse-selector/-/hast-util-parse-selector-2.2.5.tgz#d57c23f4da16ae3c63b3b6ca4616683313499c3a" integrity sha512-7j6mrk/qqkSehsM92wQjdIgWM2/BW61u/53G6xmC8i1OmEdKLHbk419QKQUjz6LglWsfqoiHmyMRkP1BGjecNQ== +hast-util-to-jsx-runtime@^2.0.0: + version "2.3.2" + resolved "https://registry.yarnpkg.com/hast-util-to-jsx-runtime/-/hast-util-to-jsx-runtime-2.3.2.tgz#6d11b027473e69adeaa00ca4cfb5bb68e3d282fa" + integrity sha512-1ngXYb+V9UT5h+PxNRa1O1FYguZK/XL+gkeqvp7EdHlB9oHUG0eYRo/vY5inBdcqo3RkPMC58/H94HvkbfGdyg== + dependencies: + "@types/estree" "^1.0.0" + "@types/hast" "^3.0.0" + "@types/unist" "^3.0.0" + comma-separated-tokens "^2.0.0" + devlop "^1.0.0" + estree-util-is-identifier-name "^3.0.0" + hast-util-whitespace "^3.0.0" + mdast-util-mdx-expression "^2.0.0" + mdast-util-mdx-jsx "^3.0.0" + mdast-util-mdxjs-esm "^2.0.0" + property-information "^6.0.0" + space-separated-tokens "^2.0.0" + style-to-object "^1.0.0" + unist-util-position "^5.0.0" + vfile-message "^4.0.0" + +hast-util-whitespace@^3.0.0: + version "3.0.0" + resolved "https://registry.yarnpkg.com/hast-util-whitespace/-/hast-util-whitespace-3.0.0.tgz#7778ed9d3c92dd9e8c5c8f648a49c21fc51cb621" + integrity sha512-88JUN06ipLwsnv+dVn+OIYOvAuvBMy/Qoi6O7mQHxdPXpjy+Cd6xRkWwux7DKO+4sYILtLBRIKgsdpS2gQc7qw== + dependencies: + "@types/hast" "^3.0.0" + hastscript@^6.0.0: version "6.0.0" resolved "https://registry.yarnpkg.com/hastscript/-/hastscript-6.0.0.tgz#e8768d7eac56c3fdeac8a92830d58e811e5bf640" @@ -6643,11 +7411,27 @@ he@^1.2.0: resolved "https://registry.yarnpkg.com/he/-/he-1.2.0.tgz#84ae65fa7eafb165fddb61566ae14baf05664f0f" integrity sha512-F/1DnUGPopORZi0ni+CvrCgHQ5FyEAHRLSApuYWMmrbSwoN2Mn/7k+Gl38gJnR7yyDZk6WLXwiGod1JOWNDKGw== +heatmap-component@1.0.1: + version "1.0.1" + resolved "https://registry.yarnpkg.com/heatmap-component/-/heatmap-component-1.0.1.tgz#1bec0546b8f85912d59bffb297172372e4c87256" + integrity sha512-FftYefBTv6Dbw4f5gMj6OqtpZrzDVWLQvxti9VjbPJhoP2VGkTWYvSO/kiBORrFelR8HA22UjRtm0kLxVx+k7w== + dependencies: + d3 "^7.9.0" + lodash "^4.17.21" + rxjs "^7.8.1" + tslib "^2.6.2" + typescript "^5.3.3" + highlight.js@^10.4.1, highlight.js@~10.7.0: version "10.7.3" resolved "https://registry.yarnpkg.com/highlight.js/-/highlight.js-10.7.3.tgz#697272e3991356e40c3cac566a74eef681756531" integrity sha512-tzcUFauisWKNHaRkN4Wjl/ZA07gENAjFl3J/c480dprkGTg5EQstgaNFqBfUqCq54kZRIEcreTsAgF/m2quD7A== +highlightjs-vue@^1.0.0: + version "1.0.0" + resolved "https://registry.yarnpkg.com/highlightjs-vue/-/highlightjs-vue-1.0.0.tgz#fdfe97fbea6354e70ee44e3a955875e114db086d" + integrity sha512-PDEfEF102G23vHmPhLyPboFCD+BkMGu+GuJe2d9/eH4FsCwvgBpnc9n0pGE+ffKdph38s6foEZiEjdgHdzp+IA== + history@4.10.1, history@^4.9.0: version "4.10.1" resolved "https://registry.yarnpkg.com/history/-/history-4.10.1.tgz#33371a65e3a83b267434e2b3f3b1b4c58aad4cf3" @@ -6740,6 +7524,11 @@ html-minifier-terser@^7.2.0: relateurl "^0.2.7" terser "^5.15.1" +html-url-attributes@^3.0.0: + version "3.0.1" + resolved "https://registry.yarnpkg.com/html-url-attributes/-/html-url-attributes-3.0.1.tgz#83b052cd5e437071b756cd74ae70f708870c2d87" + integrity sha512-ol6UPyBWqsrO6EJySPz2O7ZSr856WDrEzM5zMqp+FJJLGMW35cLYmmZnl0vztAZxRUoNZJFTCohfjuIJ8I4QBQ== + html-webpack-plugin@5.6.0: version "5.6.0" resolved "https://registry.yarnpkg.com/html-webpack-plugin/-/html-webpack-plugin-5.6.0.tgz#50a8fa6709245608cb00e811eacecb8e0d7b7ea0" @@ -6771,6 +7560,11 @@ htmlparser2@^8.0.0: domutils "^3.0.1" entities "^4.4.0" +http-cache-semantics@^4.1.0: + version "4.1.1" + resolved "https://registry.yarnpkg.com/http-cache-semantics/-/http-cache-semantics-4.1.1.tgz#abe02fcb2985460bf0323be664436ec3476a6d5a" + integrity sha512-er295DKPVsV82j5kw1Gjt+ADA/XYHsajl82cGNQG2eyoPkvgUhX+nDIyelzhIWbbsXP39EHcI6l5tYs2FYqYXQ== + http-deceiver@^1.2.7: version "1.2.7" resolved "https://registry.yarnpkg.com/http-deceiver/-/http-deceiver-1.2.7.tgz#fa7168944ab9a519d337cb0bec7284dc3e723d87" @@ -6812,9 +7606,9 @@ http-proxy-agent@^5.0.0: debug "4" http-proxy-middleware@^2.0.3: - version "2.0.6" - resolved "https://registry.yarnpkg.com/http-proxy-middleware/-/http-proxy-middleware-2.0.6.tgz#e1a4dd6979572c7ab5a4e4b55095d1f32a74963f" - integrity sha512-ya/UeJ6HVBYxrgYotAZo1KvPWlgB48kUJLDePFeneHsVujFaW5WNj2NgWCAE//B1Dl02BIfYlpNgBy8Kf8Rjmw== + version "2.0.7" + resolved "https://registry.yarnpkg.com/http-proxy-middleware/-/http-proxy-middleware-2.0.7.tgz#915f236d92ae98ef48278a95dedf17e991936ec6" + integrity sha512-fgVY8AV7qU7z/MmXJ/rxwbrtQH4jBQ9m7kp3llF0liB7glmFeVZFBepQb32T3y8n8k2+AEYuMPCpinYW+/CuRA== dependencies: "@types/http-proxy" "^1.17.8" http-proxy "^1.18.1" @@ -6831,7 +7625,7 @@ http-proxy@^1.18.1: follow-redirects "^1.0.0" requires-port "^1.0.0" -https-proxy-agent@^5.0.1: +https-proxy-agent@^5.0.0, https-proxy-agent@^5.0.1: version "5.0.1" resolved "https://registry.yarnpkg.com/https-proxy-agent/-/https-proxy-agent-5.0.1.tgz#c59ef224a04fe8b754f3db0063a25ea30d0005d6" integrity sha512-dFcAjpTQFgoLMzC2VwU+C/CbS7uRL0lWmxDITmqm7C+7F0Odmj6s9l6alZc6AELXhrnggM2CeWSXHGOdX2YtwA== @@ -6849,6 +7643,13 @@ human-signals@^5.0.0: resolved "https://registry.yarnpkg.com/human-signals/-/human-signals-5.0.0.tgz#42665a284f9ae0dade3ba41ebc37eb4b852f3a28" integrity sha512-AXcZb6vzzrFAUE61HnN4mpLqd/cSIwNQjtNWR0euPm6y0iqx3G4gOXaIDdtdDwZmhwe82LA6+zinmW4UBWVePQ== +humanize-ms@^1.2.1: + version "1.2.1" + resolved "https://registry.yarnpkg.com/humanize-ms/-/humanize-ms-1.2.1.tgz#c46e3159a293f6b896da29316d8b6fe8bb79bbed" + integrity sha512-Fl70vYtsAFb/C06PTS9dZBo7ihau+Tu/DNCk/OyHhea07S+aeMWpFFkUaXRa8fI+ScZbEI8dfSxwY7gxZ9SAVQ== + dependencies: + ms "^2.0.0" + husky@9.1.6: version "9.1.6" resolved "https://registry.yarnpkg.com/husky/-/husky-9.1.6.tgz#e23aa996b6203ab33534bdc82306b0cf2cb07d6c" @@ -6866,7 +7667,7 @@ iconv-lite@0.4, iconv-lite@0.4.24: dependencies: safer-buffer ">= 2.1.2 < 3" -iconv-lite@0.6, iconv-lite@0.6.3, iconv-lite@^0.6.3: +iconv-lite@0.6, iconv-lite@0.6.3, iconv-lite@^0.6.2, iconv-lite@^0.6.3: version "0.6.3" resolved "https://registry.yarnpkg.com/iconv-lite/-/iconv-lite-0.6.3.tgz#a52f80bf38da1952eb5c681790719871a1a72501" integrity sha512-4fCk79wshMdzMp2rH06qWrJE4iolqLhCUH+OiuIgU++RB0+94NlDL81atO7GX55uUKueo0txHNtvEyI6D7WdMw== @@ -6910,21 +7711,26 @@ image-size@~0.5.0: resolved 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sha512-15gZoQ38eYjEjxkorfbcgBKBL6R7T459OuK+CpcWt7O3KF4uPCx2tD0uFETlUDIyo+1789crbMhTvQBSR5yBMg== -immutable@^4.0.0: +immutable@^4.0.0, immutable@^4.3.4: version "4.3.7" resolved "https://registry.yarnpkg.com/immutable/-/immutable-4.3.7.tgz#c70145fc90d89fb02021e65c84eb0226e4e5a381" integrity sha512-1hqclzwYwjRDFLjcFxOM5AYkkG0rpFPpr1RLPMEuGczoS7YA8gLhy8SWXYRAA/XwfEHpfo3cw5JGioS32fnMRw== +immutable@^5.0.2: + version "5.0.3" + resolved "https://registry.yarnpkg.com/immutable/-/immutable-5.0.3.tgz#aa037e2313ea7b5d400cd9298fa14e404c933db1" + integrity sha512-P8IdPQHq3lA1xVeBRi5VPqUm5HDgKnx0Ru51wZz5mjxHr5n3RWhjIpOFU7ybkUxfB+5IToy+OLaHYDBIWsv+uw== + import-fresh@^3.2.1: version "3.3.0" resolved "https://registry.yarnpkg.com/import-fresh/-/import-fresh-3.3.0.tgz#37162c25fcb9ebaa2e6e53d5b4d88ce17d9e0c2b" @@ -6951,6 +7757,11 @@ indent-string@^4.0.0: resolved "https://registry.yarnpkg.com/indent-string/-/indent-string-4.0.0.tgz#624f8f4497d619b2d9768531d58f4122854d7251" integrity 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version "10.9.2" @@ -7538,16 +8439,6 @@ jest-css-modules-transform@4.4.2: postcss "^7.0.30 || ^8.0.0" postcss-nested "^4.2.1 || ^5.0.0" -jest-diff@^26.0.0: - version "26.6.2" - resolved "https://registry.yarnpkg.com/jest-diff/-/jest-diff-26.6.2.tgz#1aa7468b52c3a68d7d5c5fdcdfcd5e49bd164394" - integrity sha512-6m+9Z3Gv9wN0WFVasqjCL/06+EFCMTqDEUl/b87HYK2rAPTyfz4ZIuSlPhY51PIQRWx5TaxeF1qmXKe9gfN3sA== - dependencies: - chalk "^4.0.0" - diff-sequences "^26.6.2" - jest-get-type "^26.3.0" - pretty-format "^26.6.2" - jest-diff@^29.7.0: version "29.7.0" resolved "https://registry.yarnpkg.com/jest-diff/-/jest-diff-29.7.0.tgz#017934a66ebb7ecf6f205e84699be10afd70458a" @@ -7610,11 +8501,6 @@ jest-fetch-mock@3.0.3: cross-fetch "^3.0.4" promise-polyfill "^8.1.3" -jest-get-type@^26.3.0: - version "26.3.0" - resolved "https://registry.yarnpkg.com/jest-get-type/-/jest-get-type-26.3.0.tgz#e97dc3c3f53c2b406ca7afaed4493b1d099199e0" - integrity 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locate-path@^7.1.0: dependencies: p-locate "^6.0.0" +lodash-es@4.17.11: + version "4.17.11" + resolved "https://registry.yarnpkg.com/lodash-es/-/lodash-es-4.17.11.tgz#145ab4a7ac5c5e52a3531fb4f310255a152b4be0" + integrity sha512-DHb1ub+rMjjrxqlB3H56/6MXtm1lSksDp2rA2cNWjG8mlDUYFhUj3Di2Zn5IwSU87xLv8tNIQ7sSwE/YOX/D/Q== + +lodash-es@4.17.15: + version "4.17.15" + resolved "https://registry.yarnpkg.com/lodash-es/-/lodash-es-4.17.15.tgz#21bd96839354412f23d7a10340e5eac6ee455d78" + integrity sha512-rlrc3yU3+JNOpZ9zj5pQtxnx2THmvRykwL4Xlxoa8I9lHBlVbbyPhgyPMioxVZ4NqyxaVVtaJnzsyOidQIhyyQ== + lodash-es@4.17.21, lodash-es@^4.17.11: version "4.17.21" resolved "https://registry.yarnpkg.com/lodash-es/-/lodash-es-4.17.21.tgz#43e626c46e6591b7750beb2b50117390c609e3ee" @@ -8334,6 +9249,11 @@ log-update@^6.1.0: strip-ansi "^7.1.0" wrap-ansi "^9.0.0" +longest-streak@^3.0.0: + version "3.1.0" + resolved 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param-case@^3.0.4: version "3.0.4" @@ -9149,6 +10561,19 @@ parse-entities@^2.0.0: is-decimal "^1.0.0" is-hexadecimal "^1.0.0" +parse-entities@^4.0.0: + version "4.0.2" + resolved "https://registry.yarnpkg.com/parse-entities/-/parse-entities-4.0.2.tgz#61d46f5ed28e4ee62e9ddc43d6b010188443f159" + integrity sha512-GG2AQYWoLgL877gQIKeRPGO1xF9+eG1ujIb5soS5gPvLQ1y2o8FL90w2QWNdf9I361Mpp7726c+lj3U0qK1uGw== + dependencies: + "@types/unist" "^2.0.0" + character-entities-legacy "^3.0.0" + character-reference-invalid "^2.0.0" + decode-named-character-reference "^1.0.0" + is-alphanumerical "^2.0.0" + is-decimal "^2.0.0" + is-hexadecimal "^2.0.0" + parse-json@^2.2.0: version "2.2.0" resolved "https://registry.yarnpkg.com/parse-json/-/parse-json-2.2.0.tgz#f480f40434ef80741f8469099f8dea18f55a4dc9" @@ -9185,11 +10610,11 @@ parse-srcset@^1.0.2: integrity sha512-/2qh0lav6CmI15FzA3i/2Bzk2zCgQhGMkvhOhKNcBVQ1ldgpbfiNTVslmooUmWJcADi1f1kIeynbDRVzNlfR6Q== parse5@^7.0.0, parse5@^7.1.1, parse5@^7.1.2: - version 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find-up "^6.3.0" +pngjs@^6.0.0: + version "6.0.0" + resolved "https://registry.yarnpkg.com/pngjs/-/pngjs-6.0.0.tgz#ca9e5d2aa48db0228a52c419c3308e87720da821" + integrity sha512-TRzzuFRRmEoSW/p1KVAmiOgPco2Irlah+bGFCeNfJXxxYGwSw7YwAOAcd7X28K/m5bjBWKsC29KyoMfHbypayg== + point2d@0.0.1: version "0.0.1" resolved "https://registry.yarnpkg.com/point2d/-/point2d-0.0.1.tgz#2d64c4add98e6a81e15ae6b8dcb9b89348387d08" @@ -9366,20 +10801,20 @@ postcss-modules-extract-imports@^3.0.0, postcss-modules-extract-imports@^3.1.0: integrity sha512-k3kNe0aNFQDAZGbin48pL2VNidTF0w4/eASDsxlyspobzU3wZQLOGj7L9gfRe0Jo9/4uud09DsjFNH7winGv8Q== postcss-modules-local-by-default@^4.0.4, postcss-modules-local-by-default@^4.0.5: - version "4.0.5" - resolved "https://registry.yarnpkg.com/postcss-modules-local-by-default/-/postcss-modules-local-by-default-4.0.5.tgz#f1b9bd757a8edf4d8556e8d0f4f894260e3df78f" - integrity sha512-6MieY7sIfTK0hYfafw1OMEG+2bg8Q1ocHCpoWLqOKj3JXlKu4G7btkmM/B7lFubYkYWmRSPLZi5chid63ZaZYw== + version 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dependencies: - postcss-selector-parser "^6.0.4" + postcss-selector-parser "^7.0.0" postcss-modules-values@^4.0.0: version "4.0.0" @@ -9395,7 +10830,7 @@ postcss-modules-values@^4.0.0: dependencies: postcss-selector-parser "^6.0.6" -postcss-selector-parser@^6.0.2, postcss-selector-parser@^6.0.4, postcss-selector-parser@^6.0.6: +postcss-selector-parser@^6.0.6: version "6.1.2" resolved "https://registry.yarnpkg.com/postcss-selector-parser/-/postcss-selector-parser-6.1.2.tgz#27ecb41fb0e3b6ba7a1ec84fff347f734c7929de" integrity sha512-Q8qQfPiZ+THO/3ZrOrO0cJJKfpYCagtMUkXbnEfmgUjwXg6z/WBeOyS9APBBPCTSiDV+s4SwQGu8yFsiMRIudg== @@ -9403,18 +10838,26 @@ postcss-selector-parser@^6.0.2, postcss-selector-parser@^6.0.4, postcss-selector cssesc "^3.0.0" util-deprecate "^1.0.2" +postcss-selector-parser@^7.0.0: + version "7.0.0" + resolved "https://registry.yarnpkg.com/postcss-selector-parser/-/postcss-selector-parser-7.0.0.tgz#41bd8b56f177c093ca49435f65731befe25d6b9c" + integrity 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"https://registry.yarnpkg.com/scheduler/-/scheduler-0.23.2.tgz#414ba64a3b282892e944cf2108ecc078d115cdc3" @@ -10619,7 +11847,7 @@ schema-dts@1.1.2: resolved "https://registry.yarnpkg.com/schema-dts/-/schema-dts-1.1.2.tgz#82ccf71b5dcb80065a1cc5941888507a4ce1e44b" integrity sha512-MpNwH0dZJHinVxk9bT8XUdjKTxMYrA5bLtrrGmFA6PTLwlOKnhi67XoRd6/ty+Djt6ZC0slR57qFhZDNMI6DhQ== -schema-utils@^3.0.0, schema-utils@^3.1.1, schema-utils@^3.2.0: +schema-utils@^3.0.0, schema-utils@^3.2.0: version "3.3.0" resolved "https://registry.yarnpkg.com/schema-utils/-/schema-utils-3.3.0.tgz#f50a88877c3c01652a15b622ae9e9795df7a60fe" integrity sha512-pN/yOAvcC+5rQ5nERGuwrjLlYvLTbCibnZ1I7B1LaiAz9BRBlE9GMgE/eqV30P7aJQUf7Ddimy/RsbYO/GrVGg== @@ -10628,10 +11856,10 @@ schema-utils@^3.0.0, schema-utils@^3.1.1, schema-utils@^3.2.0: ajv "^6.12.5" ajv-keywords "^3.5.2" -schema-utils@^4.0.0, schema-utils@^4.2.0: - version "4.2.0" - resolved 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"https://registry.yarnpkg.com/simple-get/-/simple-get-4.0.1.tgz#4a39db549287c979d352112fa03fd99fd6bc3543" @@ -10892,6 +12159,11 @@ slice-ansi@^7.1.0: ansi-styles "^6.2.1" is-fullwidth-code-point "^5.0.0" +smart-buffer@^4.2.0: + version "4.2.0" + resolved "https://registry.yarnpkg.com/smart-buffer/-/smart-buffer-4.2.0.tgz#6e1d71fa4f18c05f7d0ff216dd16a481d0e8d9ae" + integrity sha512-94hK0Hh8rPqQl2xXc3HsaBoOXKV20MToPkcXvwbISWLEs+64sBq5kFgn2kJDHb1Pry9yrP0dxrCI9RRci7RXKg== + smob@^1.0.0: version "1.5.0" resolved "https://registry.yarnpkg.com/smob/-/smob-1.5.0.tgz#85d79a1403abf128d24d3ebc1cdc5e1a9548d3ab" @@ -10906,6 +12178,23 @@ sockjs@^0.3.24: uuid "^8.3.2" websocket-driver "^0.7.4" +socks-proxy-agent@^7.0.0: + version "7.0.0" + resolved "https://registry.yarnpkg.com/socks-proxy-agent/-/socks-proxy-agent-7.0.0.tgz#dc069ecf34436621acb41e3efa66ca1b5fed15b6" + integrity sha512-Fgl0YPZ902wEsAyiQ+idGd1A7rSFx/ayC1CQVMw5P+EQx2V0SgpGtf6OKFhVjPflPUl9YMmEOnmfjCdMUsygww== + dependencies: + agent-base "^6.0.2" + debug "^4.3.3" + socks "^2.6.2" + +socks@^2.6.2: + version "2.8.3" + resolved "https://registry.yarnpkg.com/socks/-/socks-2.8.3.tgz#1ebd0f09c52ba95a09750afe3f3f9f724a800cb5" + integrity sha512-l5x7VUUWbjVFbafGLxPWkYsHIhEvmF85tbIeFZWc8ZPtoMyybuEhL7Jye/ooC4/d48FgOjSJXgsF/AJPYCW8Zw== + dependencies: + ip-address "^9.0.5" + smart-buffer "^4.2.0" + source-list-map@^2.0.0: version "2.0.1" resolved "https://registry.yarnpkg.com/source-list-map/-/source-list-map-2.0.1.tgz#3993bd873bfc48479cca9ea3a547835c7c154b34" @@ -10964,6 +12253,11 @@ space-separated-tokens@^1.0.0: resolved "https://registry.yarnpkg.com/space-separated-tokens/-/space-separated-tokens-1.1.5.tgz#85f32c3d10d9682007e917414ddc5c26d1aa6899" integrity sha512-q/JSVd1Lptzhf5bkYm4ob4iWPjx0KiRe3sRFBNrVqbJkFaBm5vbbowy1mymoPNLRa52+oadOhJ+K49wsSeSjTA== +space-separated-tokens@^2.0.0: + version "2.0.2" + resolved "https://registry.yarnpkg.com/space-separated-tokens/-/space-separated-tokens-2.0.2.tgz#1ecd9d2350a3844572c3f4a312bceb018348859f" + integrity sha512-PEGlAwrG8yXGXRjW32fGbg66JAlOAwbObuqVoJpv/mRgoWDQfgH1wDPvtzWyUSNAXBGSk8h755YDbbcEy3SH2Q== + spdx-correct@^3.0.0: version "3.2.0" resolved "https://registry.yarnpkg.com/spdx-correct/-/spdx-correct-3.2.0.tgz#4f5ab0668f0059e34f9c00dce331784a12de4e9c" @@ -11013,11 +12307,23 @@ spdy@^4.0.2: select-hose "^2.0.0" spdy-transport "^3.0.0" +sprintf-js@^1.1.3: + version "1.1.3" + resolved "https://registry.yarnpkg.com/sprintf-js/-/sprintf-js-1.1.3.tgz#4914b903a2f8b685d17fdf78a70e917e872e444a" + integrity sha512-Oo+0REFV59/rz3gfJNKQiBlwfHaSESl1pcGyABQsnnIfWOFt6JNj5gCog2U6MLZ//IGYD+nA8nI+mTShREReaA== + sprintf-js@~1.0.2: version "1.0.3" resolved "https://registry.yarnpkg.com/sprintf-js/-/sprintf-js-1.0.3.tgz#04e6926f662895354f3dd015203633b857297e2c" integrity sha512-D9cPgkvLlV3t3IzL0D0YLvGA9Ahk4PcvVwUbN0dSGr1aP0Nrt4AEnTUbuGvquEC0mA64Gqt1fzirlRs5ibXx8g== +ssri@^9.0.0: + version "9.0.1" + resolved "https://registry.yarnpkg.com/ssri/-/ssri-9.0.1.tgz#544d4c357a8d7b71a19700074b6883fcb4eae057" + integrity sha512-o57Wcn66jMQvfHG1FlYbWeZWW/dHZhJXjpIcTfXldXEk5nz5lStPo3mK0OJQfGR3RbZUlbISexbljkJzuEj/8Q== + dependencies: + minipass "^3.1.1" + stable@^0.1.8: version "0.1.8" resolved "https://registry.yarnpkg.com/stable/-/stable-0.1.8.tgz#836eb3c8382fe2936feaf544631017ce7d47a3cf" @@ -11062,7 +12368,7 @@ string-length@^4.0.1: is-fullwidth-code-point "^3.0.0" strip-ansi "^6.0.1" -string-width@4.1.0, string-width@^1.0.1, string-width@^2.0.0, string-width@^4.1.0, string-width@^4.2.0, string-width@^4.2.3, string-width@^5.1.2, string-width@^7.0.0: +string-width@4.1.0, string-width@^1.0.1, "string-width@^1.0.2 || 2 || 3 || 4", string-width@^2.0.0, string-width@^4.1.0, string-width@^4.2.0, string-width@^4.2.3, string-width@^5.1.2, string-width@^7.0.0: version "4.1.0" resolved 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define-data-property "^1.1.4" define-properties "^1.2.1" - es-abstract "^1.23.0" + es-abstract "^1.23.5" es-object-atoms "^1.0.0" + has-property-descriptors "^1.0.2" -string.prototype.trimend@^1.0.8: - version "1.0.8" - resolved "https://registry.yarnpkg.com/string.prototype.trimend/-/string.prototype.trimend-1.0.8.tgz#3651b8513719e8a9f48de7f2f77640b26652b229" - integrity sha512-p73uL5VCHCO2BZZ6krwwQE3kCzM7NKmis8S//xEC6fQonchbum4eP6kR4DLEjQFO3Wnj3Fuo8NM0kOSjVdHjZQ== +string.prototype.trimend@^1.0.9: + version "1.0.9" + resolved "https://registry.yarnpkg.com/string.prototype.trimend/-/string.prototype.trimend-1.0.9.tgz#62e2731272cd285041b36596054e9f66569b6942" + integrity sha512-G7Ok5C6E/j4SGfyLCloXTrngQIQU3PWtXGst3yM7Bea9FRURf1S42ZHlZZtsNque2FN2PoUhfZXYLNWwEr4dLQ== dependencies: - call-bind "^1.0.7" + call-bind "^1.0.8" + call-bound "^1.0.2" define-properties "^1.2.1" es-object-atoms "^1.0.0" @@ -11134,6 +12444,11 @@ string_decoder@^1.1.1: dependencies: safe-buffer "~5.2.0" +string_decoder@~0.10.x: + version "0.10.31" + resolved "https://registry.yarnpkg.com/string_decoder/-/string_decoder-0.10.31.tgz#62e203bc41766c6c28c9fc84301dab1c5310fa94" + integrity sha512-ev2QzSzWPYmy9GuqfIVildA4OdcGLeFZQrq5ys6RtiuF+RQQiZWr8TZNyAcuVXyQRYfEO+MsoB/1BuQVhOJuoQ== + string_decoder@~1.1.1: version "1.1.1" resolved "https://registry.yarnpkg.com/string_decoder/-/string_decoder-1.1.1.tgz#9cf1611ba62685d7030ae9e4ba34149c3af03fc8" @@ -11141,6 +12456,14 @@ string_decoder@~1.1.1: dependencies: safe-buffer "~5.1.0" +stringify-entities@^4.0.0: + version "4.0.4" + resolved "https://registry.yarnpkg.com/stringify-entities/-/stringify-entities-4.0.4.tgz#b3b79ef5f277cc4ac73caeb0236c5ba939b3a4f3" + integrity sha512-IwfBptatlO+QCJUo19AqvrPNqlVMpW9YEL2LIVY+Rpv2qsjCGxaDLNRgeGsQWJhfItebuJhsGSLjaBbNSQ+ieg== + dependencies: + character-entities-html4 "^2.0.0" + character-entities-legacy "^3.0.0" + stringify-object@^3.3.0: version "3.3.0" resolved "https://registry.yarnpkg.com/stringify-object/-/stringify-object-3.3.0.tgz#703065aefca19300d3ce88af4f5b3956d7556629" @@ -11150,7 +12473,7 @@ stringify-object@^3.3.0: is-obj "^1.0.1" is-regexp "^1.0.0" -"strip-ansi-cjs@npm:strip-ansi@^6.0.1", strip-ansi@^6.0.0, strip-ansi@^6.0.1: +"strip-ansi-cjs@npm:strip-ansi@^6.0.1": version "6.0.1" resolved "https://registry.yarnpkg.com/strip-ansi/-/strip-ansi-6.0.1.tgz#9e26c63d30f53443e9489495b2105d37b67a85d9" integrity sha512-Y38VPSHcqkFrCpFnQ9vuSXmquuv5oXOKpGeT6aGrr3o3Gc9AlVa6JBfUSOCnbxGGZF+/0ooI7KrPuUSztUdU5A== @@ -11171,6 +12494,13 @@ strip-ansi@^5.2.0: dependencies: ansi-regex "^4.1.0" +strip-ansi@^6.0.0, strip-ansi@^6.0.1: + version "6.0.1" + resolved "https://registry.yarnpkg.com/strip-ansi/-/strip-ansi-6.0.1.tgz#9e26c63d30f53443e9489495b2105d37b67a85d9" + integrity sha512-Y38VPSHcqkFrCpFnQ9vuSXmquuv5oXOKpGeT6aGrr3o3Gc9AlVa6JBfUSOCnbxGGZF+/0ooI7KrPuUSztUdU5A== + dependencies: + ansi-regex "^5.0.1" + strip-ansi@^7.0.1, strip-ansi@^7.1.0: version "7.1.0" resolved "https://registry.yarnpkg.com/strip-ansi/-/strip-ansi-7.1.0.tgz#d5b6568ca689d8561370b0707685d22434faff45" @@ -11230,6 +12560,13 @@ style-loader@4.0.0: resolved "https://registry.yarnpkg.com/style-loader/-/style-loader-4.0.0.tgz#0ea96e468f43c69600011e0589cb05c44f3b17a5" integrity sha512-1V4WqhhZZgjVAVJyt7TdDPZoPBPNHbekX4fWnCJL1yQukhCeZhJySUL+gL9y6sNdN95uEOS83Y55SqHcP7MzLA== +style-to-object@^1.0.0: + version "1.0.8" + resolved "https://registry.yarnpkg.com/style-to-object/-/style-to-object-1.0.8.tgz#67a29bca47eaa587db18118d68f9d95955e81292" + integrity sha512-xT47I/Eo0rwJmaXC4oilDGDWLohVhR6o/xAQcPQN8q6QBuZVL8qMYL85kLmST5cPjAorwvqIA4qXTRQoYHaL6g== + dependencies: + inline-style-parser "0.2.4" + stylis@4.2.0: version "4.2.0" resolved "https://registry.yarnpkg.com/stylis/-/stylis-4.2.0.tgz#79daee0208964c8fe695a42fcffcac633a211a51" @@ -11311,17 +12648,18 @@ svgo@^1.2.2: util.promisify "~1.0.0" swagger-client@^3.28.1: - version "3.29.2" - resolved 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+which-boxed-primitive@^1.1.0, which-boxed-primitive@^1.1.1: + version "1.1.1" + resolved "https://registry.yarnpkg.com/which-boxed-primitive/-/which-boxed-primitive-1.1.1.tgz#d76ec27df7fa165f18d5808374a5fe23c29b176e" + integrity sha512-TbX3mj8n0odCBFVlY8AxkqcHASw3L60jIuF8jFP78az3C2YhmGvqbHBpAjTRH2/xqYunrJ9g1jSyjCjpoWzIAA== + dependencies: + is-bigint "^1.1.0" + is-boolean-object "^1.2.1" + is-number-object "^1.1.1" + is-string "^1.1.1" + is-symbol "^1.1.1" + +which-builtin-type@^1.2.0: + version "1.2.1" + resolved "https://registry.yarnpkg.com/which-builtin-type/-/which-builtin-type-1.2.1.tgz#89183da1b4907ab089a6b02029cc5d8d6574270e" + integrity sha512-6iBczoX+kDQ7a3+YJBnh3T+KZRxM/iYNPXicqk66/Qfm1b93iu+yOImkg0zHbj5LNOcNv1TEADiZ0xa34B4q6Q== + dependencies: + call-bound "^1.0.2" + function.prototype.name "^1.1.6" + has-tostringtag "^1.0.2" + is-async-function "^2.0.0" + is-date-object "^1.1.0" + is-finalizationregistry "^1.1.0" + is-generator-function "^1.0.10" + is-regex "^1.2.1" + is-weakref "^1.0.2" + isarray "^2.0.5" + which-boxed-primitive "^1.1.0" + which-collection "^1.0.2" + which-typed-array "^1.1.16" + +which-collection@^1.0.2: version "1.0.2" - resolved "https://registry.yarnpkg.com/which-boxed-primitive/-/which-boxed-primitive-1.0.2.tgz#13757bc89b209b049fe5d86430e21cf40a89a8e6" - integrity sha512-bwZdv0AKLpplFY2KZRX6TvyuN7ojjr7lwkg6ml0roIy9YeuSr7JS372qlNW18UQYzgYK9ziGcerWqZOmEn9VNg== + resolved "https://registry.yarnpkg.com/which-collection/-/which-collection-1.0.2.tgz#627ef76243920a107e7ce8e96191debe4b16c2a0" + integrity sha512-K4jVyjnBdgvc86Y6BkaLZEN933SwYOuBFkdmBu9ZfkcAbdVbpITnDmjvZ/aQjRXQrv5EPkTnD1s39GiiqbngCw== dependencies: - is-bigint "^1.0.1" - is-boolean-object "^1.1.0" - is-number-object "^1.0.4" - is-string "^1.0.5" - is-symbol "^1.0.3" + is-map "^2.0.3" + is-set "^2.0.3" + is-weakmap "^2.0.2" + is-weakset "^2.0.3" which-module@^2.0.0: version "2.0.1" resolved 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dependencies: isexe "^2.0.0" -which@^2.0.1: +which@^2.0.1, which@^2.0.2: version "2.0.2" resolved "https://registry.yarnpkg.com/which/-/which-2.0.2.tgz#7c6a8dd0a636a0327e10b59c9286eee93f3f51b1" integrity sha512-BLI3Tl1TW3Pvl70l3yq3Y64i+awpwXqsGBYWkkqMtnbXgrMD+yj7rhW0kuEDxzJaYXGjEW5ogapKNMEKNMjibA== dependencies: isexe "^2.0.0" +wide-align@^1.1.2, wide-align@^1.1.5: + version "1.1.5" + resolved "https://registry.yarnpkg.com/wide-align/-/wide-align-1.1.5.tgz#df1d4c206854369ecf3c9a4898f1b23fbd9d15d3" + integrity sha512-eDMORYaPNZ4sQIuuYPDHdQvf4gyCF9rEEV/yPxGfwPkRodwEgiMUUXTx/dex+Me0wxx53S+NgUHaP7y3MGlDmg== + dependencies: + string-width "^1.0.2 || 2 || 3 || 4" + wildcard@^2.0.0: version "2.0.1" resolved "https://registry.yarnpkg.com/wildcard/-/wildcard-2.0.1.tgz#5ab10d02487198954836b6349f74fff961e10f67" @@ -12437,7 +13920,16 @@ worker-loader@3.0.8: loader-utils "^2.0.0" schema-utils "^3.0.0" -"wrap-ansi-cjs@npm:wrap-ansi@^7.0.0", wrap-ansi@7.0.0, wrap-ansi@^2.0.0, wrap-ansi@^7.0.0, wrap-ansi@^8.1.0, wrap-ansi@^9.0.0: +"wrap-ansi-cjs@npm:wrap-ansi@^7.0.0": + version "7.0.0" + resolved "https://registry.yarnpkg.com/wrap-ansi/-/wrap-ansi-7.0.0.tgz#67e145cff510a6a6984bdf1152911d69d2eb9e43" + integrity sha512-YVGIj2kamLSTxw6NsZjoBxfSwsn0ycdesmc4p+Q21c5zPuZ1pl+NfxVdxPtdHvmNVOQ6XSYG4AUtyt/Fi7D16Q== + dependencies: + ansi-styles "^4.0.0" + string-width "^4.1.0" + strip-ansi "^6.0.0" + +wrap-ansi@7.0.0, wrap-ansi@^2.0.0, wrap-ansi@^7.0.0, wrap-ansi@^8.1.0, wrap-ansi@^9.0.0: version "7.0.0" resolved "https://registry.yarnpkg.com/wrap-ansi/-/wrap-ansi-7.0.0.tgz#67e145cff510a6a6984bdf1152911d69d2eb9e43" integrity sha512-YVGIj2kamLSTxw6NsZjoBxfSwsn0ycdesmc4p+Q21c5zPuZ1pl+NfxVdxPtdHvmNVOQ6XSYG4AUtyt/Fi7D16Q== @@ -12469,7 +13961,7 @@ ws@^8.11.0, ws@^8.18.0: resolved "https://registry.yarnpkg.com/ws/-/ws-8.18.0.tgz#0d7505a6eafe2b0e712d232b42279f53bc289bbc" integrity sha512-8VbfWfHLbbwu3+N6OKsOMpBdT4kXPDDB9cJk2bJ6mh9ucxdlnNvH1e+roYkKmN9Nxw2yjz7VzeO9oOz2zJ04Pw== -xhr2@^0.2.0: +xhr2@^0.2.1: version "0.2.1" resolved "https://registry.yarnpkg.com/xhr2/-/xhr2-0.2.1.tgz#4e73adc4f9cfec9cbd2157f73efdce3a5f108a93" integrity sha512-sID0rrVCqkVNUn8t6xuv9+6FViXjUVXq8H5rWOH2rz9fDNQEd4g0EA2XlcEdJXRz5BMEn4O1pJFdT+z4YHhoWw== @@ -12496,7 +13988,7 @@ xmlchars@^2.2.0: resolved "https://registry.yarnpkg.com/xmlchars/-/xmlchars-2.2.0.tgz#060fe1bcb7f9c76fe2a17db86a9bc3ab894210cb" integrity sha512-JZnDKK8B0RCDw84FNdDAIpZK+JuJw+s7Lz8nksI7SIuU3UXJJslUthsi+uWBUYOwPFwW7W7PRLRfUKpxjtjFCw== -xtend@^4.0.0: +"xtend@>=4.0.0 <4.1.0-0", xtend@^4.0.0: version "4.0.2" resolved "https://registry.yarnpkg.com/xtend/-/xtend-4.0.2.tgz#bb72779f5fa465186b1f438f674fa347fdb5db54" integrity sha512-LKYU1iAXJXUgAXn9URjiu+MWhyUXHsvfp7mcuYm9dSUKK0/CjtrUwFAxD82/mCWbtLsGjFIad0wIsod4zrTAEQ== @@ -12521,6 +14013,11 @@ yallist@^3.0.2: resolved "https://registry.yarnpkg.com/yallist/-/yallist-3.1.1.tgz#dbb7daf9bfd8bac9ab45ebf602b8cbad0d5d08fd" integrity sha512-a4UGQaWPH59mOXUYnAG2ewncQS4i4F43Tv3JoAM+s2VDAmS9NsK8GpDMLrCHPksFT7h3K6TOoUNn2pb7RoXx4g== +yallist@^4.0.0: + version "4.0.0" + resolved "https://registry.yarnpkg.com/yallist/-/yallist-4.0.0.tgz#9bb92790d9c0effec63be73519e11a35019a3a72" + integrity sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A== + yaml@^1.10.0, yaml@^1.10.2: version "1.10.2" resolved "https://registry.yarnpkg.com/yaml/-/yaml-1.10.2.tgz#2301c5ffbf12b467de8da2333a459e29e7920e4b" @@ -12589,3 +14086,8 @@ zenscroll@^4.0.2: version "4.0.2" resolved "https://registry.yarnpkg.com/zenscroll/-/zenscroll-4.0.2.tgz#e8d5774d1c0738a47bcfa8729f3712e2deddeb25" integrity sha512-jEA1znR7b4C/NnaycInCU6h/d15ZzCd1jmsruqOKnZP6WXQSMH3W2GL+OXbkruslU4h+Tzuos0HdswzRUk/Vgg== + +zwitch@^2.0.0: + version "2.0.4" + resolved "https://registry.yarnpkg.com/zwitch/-/zwitch-2.0.4.tgz#c827d4b0acb76fc3e685a4c6ec2902d51070e9d7" + integrity 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