diff --git a/package.json b/package.json index c7225cce56b..d7233c97271 100644 --- a/package.json +++ b/package.json @@ -42,10 +42,10 @@ "@oclif/test": "^3.2.1", "@pmmmwh/react-refresh-webpack-plugin": "^0.5.3", "@r2wc/react-to-web-component": "^2.0.3", - "@storybook/addon-essentials": "^7.0.0", - "@storybook/node-logger": "^7.0.0", - "@storybook/react": "^7.0.0", - "@storybook/react-webpack5": "^7.0.0", + "@storybook/addon-essentials": "^8.0.0", + "@storybook/node-logger": "^8.0.0", + "@storybook/react": "^8.0.0", + "@storybook/react-webpack5": "^8.0.0", "@testing-library/dom": "^9.0.0", "@testing-library/jest-dom": "^6.0.0", "@testing-library/react": "^14.0.0", @@ -101,7 +101,7 @@ "dependency-graph": "^0.11.0", "dotenv": "^16.3.1", "dotenv-expand": "^11.0.3", - "electron": "29.1.0", + "electron": "29.1.2", "electron-builder": "^24.9.0", "electron-mock-ipc": "^0.3.8", "eslint": "^8.0.0", @@ -145,7 +145,7 @@ "semver": "^7.3.4", "slugify": "^1.6.5", "source-map-loader": "^5.0.0", - "storybook": "^7.0.0", + "storybook": "^8.0.0", "style-loader": "^3.3.1", "terser-webpack-plugin": "^5.2.5", "ts-node": "^10.4.0", @@ -158,6 +158,5 @@ "webpack-dev-server": "^5.0.0", "webpack-manifest-plugin": "^5.0.0" }, - "version": "0.0.0", - "dependencies": {} + "version": "0.0.0" } diff --git a/packages/core/ui/ErrorMessageStackTraceDialog.tsx b/packages/core/ui/ErrorMessageStackTraceDialog.tsx index 6957c0aabe6..35d9adf99b1 100644 --- a/packages/core/ui/ErrorMessageStackTraceDialog.tsx +++ b/packages/core/ui/ErrorMessageStackTraceDialog.tsx @@ -118,11 +118,15 @@ function stripMessage(trace: string, error: unknown) { } } -function Contents({ text }: { text: string }) { +function Contents({ text, extra }: { text: string; extra?: unknown }) { const err = encodeURIComponent( - 'I got this error from JBrowse, here is the stack trace:\n\n```\n' + - text + - '\n```\n', + [ + 'I got this error from JBrowse, here is the stack trace:\n', + '```', + text, + '```', + extra ? `supporting data: ${extra}` : '', + ].join('\n') + '\n', ) const githubLink = `https://github.com/GMOD/jbrowse-components/issues/new?labels=bug&title=JBrowse+issue&body=${err}` const emailLink = `mailto:jbrowse2dev@gmail.com?subject=JBrowse%202%20error&body=${err}` @@ -143,6 +147,7 @@ function Contents({ text }: { text: string }) { }} > {text} + {extra ? `extra: ${extra}` : ''} ) @@ -151,9 +156,11 @@ function Contents({ text }: { text: string }) { export default function ErrorMessageStackTraceDialog({ error, onClose, + extra, }: { onClose: () => void error: unknown + extra?: unknown }) { const [mappedStackTrace, setMappedStackTrace] = useState() const [secondaryError, setSecondaryError] = useState() @@ -181,7 +188,7 @@ export default function ErrorMessageStackTraceDialog({ ? 'Error loading source map, showing raw stack trace below:' : '', errorText.length > MAX_ERR_LEN - ? errorText.slice(0, MAX_ERR_LEN) + '...' + ? `${errorText.slice(0, MAX_ERR_LEN)}...` : errorText, mappedStackTrace || 'No stack trace available', // @ts-expect-error add version info at bottom if we are in jbrowse-web @@ -194,7 +201,7 @@ export default function ErrorMessageStackTraceDialog({ {mappedStackTrace === undefined ? ( ) : ( - + )} diff --git a/packages/core/ui/SnackbarModel.ts b/packages/core/ui/SnackbarModel.ts deleted file mode 100644 index e6d14380327..00000000000 --- a/packages/core/ui/SnackbarModel.ts +++ /dev/null @@ -1,82 +0,0 @@ -import { IModelType, ModelProperties } from 'mobx-state-tree' -import { IObservableArray, observable } from 'mobx' -import { NotificationLevel, SnackAction } from '../util/types' - -export interface SnackbarMessage { - message: string - level?: NotificationLevel - action?: SnackAction -} - -/** - * #stateModel SnackbarModel - * #category session - */ -function makeExtension(snackbarMessages: IObservableArray) { - return { - views: { - /** - * #getter - */ - get snackbarMessages() { - return snackbarMessages - }, - }, - actions: { - /** - * #action - */ - notify(message: string, level?: NotificationLevel, action?: SnackAction) { - this.pushSnackbarMessage(message, level, action) - if (level === 'info' || level === 'success') { - setTimeout(() => { - this.removeSnackbarMessage(message) - }, 5000) - } - }, - /** - * #action - */ - pushSnackbarMessage( - message: string, - level?: NotificationLevel, - action?: SnackAction, - ) { - return snackbarMessages.push({ message, level, action }) - }, - /** - * #action - */ - popSnackbarMessage() { - return snackbarMessages.pop() - }, - /** - * #action - */ - removeSnackbarMessage(message: string) { - const element = snackbarMessages.find(f => f.message === message) - if (element) { - snackbarMessages.remove(element) - } - }, - }, - } -} - -export default function addSnackbarToModel< - PROPS extends ModelProperties, - OTHERS, ->( - tree: IModelType, -): IModelType< - PROPS, - OTHERS & - ReturnType['actions'] & - ReturnType['views'] -> { - return tree.extend(() => { - const snackbarMessages = observable.array() - - return makeExtension(snackbarMessages) - }) -} diff --git a/packages/core/ui/SnackbarModel.tsx b/packages/core/ui/SnackbarModel.tsx new file mode 100644 index 00000000000..8f3ac2cb456 --- /dev/null +++ b/packages/core/ui/SnackbarModel.tsx @@ -0,0 +1,87 @@ +import React, { lazy } from 'react' +import { types } from 'mobx-state-tree' +import { observable } from 'mobx' + +// locals +import { NotificationLevel, SnackAction } from '../util/types' + +// icons +import Report from '@mui/icons-material/Report' + +// lazies + +const ErrorMessageStackTraceDialog = lazy( + () => import('@jbrowse/core/ui/ErrorMessageStackTraceDialog'), +) + +export interface SnackbarMessage { + message: string + level?: NotificationLevel + action?: SnackAction +} + +/** + * #stateModel SnackbarModel + * #category session + */ +export default function SnackbarModel() { + return types + .model({}) + .volatile(() => ({ + snackbarMessages: observable.array(), + })) + .actions(self => ({ + /** + * #action + */ + notify(message: string, level?: NotificationLevel, action?: SnackAction) { + this.pushSnackbarMessage(message, level, action) + if (level === 'info' || level === 'success') { + setTimeout(() => { + this.removeSnackbarMessage(message) + }, 5000) + } + }, + notifyError(errorMessage: string, error?: unknown, extra?: unknown) { + this.notify(errorMessage, 'error', { + name: , + onClick: () => { + // @ts-expect-error + self.queueDialog((onClose: () => void) => [ + ErrorMessageStackTraceDialog, + { + onClose, + error, + extra, + }, + ]) + }, + }) + }, + /** + * #action + */ + pushSnackbarMessage( + message: string, + level?: NotificationLevel, + action?: SnackAction, + ) { + return self.snackbarMessages.push({ message, level, action }) + }, + /** + * #action + */ + popSnackbarMessage() { + return self.snackbarMessages.pop() + }, + /** + * #action + */ + removeSnackbarMessage(message: string) { + const element = self.snackbarMessages.find(f => f.message === message) + if (element) { + self.snackbarMessages.remove(element) + } + }, + })) +} diff --git a/packages/core/ui/theme.ts b/packages/core/ui/theme.ts index 34b8ca95535..39b169fe0e7 100644 --- a/packages/core/ui/theme.ts +++ b/packages/core/ui/theme.ts @@ -1,6 +1,9 @@ import { blue, green, red, grey, orange } from '@mui/material/colors' import { createTheme, ThemeOptions } from '@mui/material/styles' -import type { PaletteAugmentColorOptions } from '@mui/material/styles/createPalette' +import type { + PaletteAugmentColorOptions, + PaletteColor, +} from '@mui/material/styles/createPalette' import deepmerge from 'deepmerge' declare module '@mui/material/styles/createPalette' { @@ -16,6 +19,24 @@ declare module '@mui/material/styles/createPalette' { G: Palette['primary'] T: Palette['primary'] } + frames: [ + null, + Palette['primary'] | undefined, + Palette['primary'] | undefined, + Palette['primary'] | undefined, + Palette['primary'] | undefined, + Palette['primary'] | undefined, + Palette['primary'] | undefined, + ] + framesCDS: [ + null, + Palette['primary'] | undefined, + Palette['primary'] | undefined, + Palette['primary'] | undefined, + Palette['primary'] | undefined, + Palette['primary'] | undefined, + Palette['primary'] | undefined, + ] } interface PaletteOptions { tertiary?: PaletteOptions['primary'] @@ -29,15 +50,68 @@ declare module '@mui/material/styles/createPalette' { G?: PaletteOptions['primary'] T?: PaletteOptions['primary'] } + framesCDS?: [ + null, + Palette['primary'] | undefined, + Palette['primary'] | undefined, + Palette['primary'] | undefined, + Palette['primary'] | undefined, + Palette['primary'] | undefined, + Palette['primary'] | undefined, + ] + frames?: [ + null, + Palette['primary'] | undefined, + Palette['primary'] | undefined, + Palette['primary'] | undefined, + Palette['primary'] | undefined, + Palette['primary'] | undefined, + Palette['primary'] | undefined, + ] } } +type Frames = [ + null, + PaletteColor, + PaletteColor, + PaletteColor, + PaletteColor, + PaletteColor, + PaletteColor, +] + const midnight = '#0D233F' const grape = '#721E63' const forest = '#135560' const mandarin = '#FFB11D' - const refTheme = createTheme() +const bases = { + A: refTheme.palette.augmentColor({ color: green }), + C: refTheme.palette.augmentColor({ color: blue }), + G: refTheme.palette.augmentColor({ color: orange }), + T: refTheme.palette.augmentColor({ color: red }), +} +const framesCDS = [ + null, + refTheme.palette.augmentColor({ color: { main: '#FF8080' } }), + refTheme.palette.augmentColor({ color: { main: '#80FF80' } }), + refTheme.palette.augmentColor({ color: { main: '#8080FF' } }), + refTheme.palette.augmentColor({ color: { main: '#8080FF' } }), + refTheme.palette.augmentColor({ color: { main: '#80FF80' } }), + refTheme.palette.augmentColor({ color: { main: '#FF8080' } }), +] as Frames +const frames = [ + null, + refTheme.palette.augmentColor({ color: { main: '#8f8f8f' } }), + refTheme.palette.augmentColor({ color: { main: '#adadad' } }), + refTheme.palette.augmentColor({ color: { main: '#d8d8d8' } }), + refTheme.palette.augmentColor({ color: { main: '#d8d8d8' } }), + refTheme.palette.augmentColor({ color: { main: '#adadad' } }), + refTheme.palette.augmentColor({ color: { main: '#8f8f8f' } }), +] as Frames +const stopCodon = '#e22' +const startCodon = '#3e3' function stockTheme() { return { @@ -48,14 +122,11 @@ function stockTheme() { tertiary: refTheme.palette.augmentColor({ color: { main: forest } }), quaternary: refTheme.palette.augmentColor({ color: { main: mandarin } }), highlight: refTheme.palette.augmentColor({ color: { main: mandarin } }), - stopCodon: '#e22', - startCodon: '#3e3', - bases: { - A: refTheme.palette.augmentColor({ color: green }), - C: refTheme.palette.augmentColor({ color: blue }), - G: refTheme.palette.augmentColor({ color: orange }), - T: refTheme.palette.augmentColor({ color: red }), - }, + stopCodon, + startCodon, + bases, + frames, + framesCDS, }, components: { MuiLink: { @@ -97,14 +168,11 @@ function getDarkStockTheme() { tertiary: refTheme.palette.augmentColor({ color: { main: forest } }), quaternary: refTheme.palette.augmentColor({ color: { main: mandarin } }), highlight: refTheme.palette.augmentColor({ color: { main: mandarin } }), - stopCodon: '#e22', - startCodon: '#3e3', - bases: { - A: refTheme.palette.augmentColor({ color: green }), - C: refTheme.palette.augmentColor({ color: blue }), - G: refTheme.palette.augmentColor({ color: orange }), - T: refTheme.palette.augmentColor({ color: red }), - }, + stopCodon, + startCodon, + bases, + frames, + framesCDS, }, components: { MuiAppBar: { @@ -132,14 +200,11 @@ function getDarkMinimalTheme() { tertiary: refTheme.palette.augmentColor({ color: { main: grey[900] } }), quaternary: refTheme.palette.augmentColor({ color: { main: mandarin } }), highlight: refTheme.palette.augmentColor({ color: { main: mandarin } }), - stopCodon: '#e22', - startCodon: '#3e3', - bases: { - A: refTheme.palette.augmentColor({ color: green }), - C: refTheme.palette.augmentColor({ color: blue }), - G: refTheme.palette.augmentColor({ color: orange }), - T: refTheme.palette.augmentColor({ color: red }), - }, + stopCodon, + startCodon, + bases, + frames, + framesCDS, }, } } @@ -153,14 +218,11 @@ function getMinimalTheme() { tertiary: refTheme.palette.augmentColor({ color: { main: grey[900] } }), quaternary: refTheme.palette.augmentColor({ color: { main: mandarin } }), highlight: refTheme.palette.augmentColor({ color: { main: mandarin } }), - stopCodon: '#e22', - startCodon: '#3e3', - bases: { - A: refTheme.palette.augmentColor({ color: green }), - C: refTheme.palette.augmentColor({ color: blue }), - G: refTheme.palette.augmentColor({ color: orange }), - T: refTheme.palette.augmentColor({ color: red }), - }, + stopCodon, + startCodon, + bases, + frames, + framesCDS, }, } } @@ -391,6 +453,10 @@ function createDefaultProps(theme?: ThemeOptions): ThemeOptions { } } +function overwriteArrayMerge(_: unknown, sourceArray: unknown[]) { + return sourceArray +} + export function createJBrowseBaseTheme(theme?: ThemeOptions): ThemeOptions { return deepmerge( { @@ -400,6 +466,7 @@ export function createJBrowseBaseTheme(theme?: ThemeOptions): ThemeOptions { ...createDefaultProps(theme), }, theme || {}, + { arrayMerge: overwriteArrayMerge }, ) } @@ -413,7 +480,9 @@ export function createJBrowseTheme( return createTheme( createJBrowseBaseTheme( themeName === 'default' - ? deepmerge(themes.default, augmentTheme(configTheme)) + ? deepmerge(themes.default, augmentTheme(configTheme), { + arrayMerge: overwriteArrayMerge, + }) : augmentThemePlus(themes[themeName]) || themes.default, ), ) @@ -453,14 +522,22 @@ function augmentThemePlus(theme: ThemeOptions = {}) { if (!theme?.palette?.quaternary) { theme = deepmerge(theme, { palette: { - quaternary: refTheme.palette.augmentColor({ color: { main: '#aaa' } }), + quaternary: refTheme.palette.augmentColor({ + color: { + main: '#aaa', + }, + }), }, }) } if (!theme?.palette?.tertiary) { theme = deepmerge(theme, { palette: { - tertiary: refTheme.palette.augmentColor({ color: { main: '#aaa' } }), + tertiary: refTheme.palette.augmentColor({ + color: { + main: '#aaa', + }, + }), }, }) } diff --git a/packages/core/util/index.ts b/packages/core/util/index.ts index 24e0be058ec..070ee548ba6 100644 --- a/packages/core/util/index.ts +++ b/packages/core/util/index.ts @@ -936,6 +936,19 @@ export function measureText(str: unknown, fontSize = 10) { return total * fontSize } +export type Frame = 1 | 2 | 3 | -1 | -2 | -3 + +export function getFrame( + start: number, + end: number, + strand: 1 | -1, + phase: 0 | 1 | 2, +): Frame { + return strand === 1 + ? ((((start + phase) % 3) + 1) as 1 | 2 | 3) + : ((-1 * ((end - phase) % 3) - 1) as -1 | -2 | -3) +} + export const defaultStarts = ['ATG'] export const defaultStops = ['TAA', 'TAG', 'TGA'] export const defaultCodonTable = { diff --git a/packages/core/util/jexl.ts b/packages/core/util/jexl.ts index 1e6b41728f4..ec6949be428 100644 --- a/packages/core/util/jexl.ts +++ b/packages/core/util/jexl.ts @@ -75,6 +75,7 @@ export default function (/* config?: any*/): JexlNonBuildable { ) j.addFunction('toLowerCase', (s: string) => s.toLowerCase()) j.addFunction('toUpperCase', (s: string) => s.toUpperCase()) + j.addFunction('jsonParse', (s: string) => JSON.parse(s)) j.addFunction('trim', (s: string) => s.trim()) j.addFunction('trimEnd', (s: string) => s.trimEnd()) j.addFunction('trimStart', (s: string) => s.trimStart()) diff --git a/packages/core/util/types/index.ts b/packages/core/util/types/index.ts index 50be0d71466..ba92ec7c4e9 100644 --- a/packages/core/util/types/index.ts +++ b/packages/core/util/types/index.ts @@ -50,7 +50,7 @@ export function isViewContainer( export type NotificationLevel = 'error' | 'info' | 'warning' | 'success' export interface SnackAction { - name: string + name: React.ReactElement onClick: () => void } @@ -105,6 +105,7 @@ export interface AbstractSessionModel extends AbstractViewContainer { level?: NotificationLevel, action?: SnackAction, ) => void + notifyError: (message: string, error?: unknown, extra?: unknown) => void assemblyManager: AssemblyManager version: string getTrackActionMenuItems?: Function diff --git a/packages/web-core/src/BaseWebSession/index.ts b/packages/web-core/src/BaseWebSession/index.ts index 7abbf28b144..e320a3347f0 100644 --- a/packages/web-core/src/BaseWebSession/index.ts +++ b/packages/web-core/src/BaseWebSession/index.ts @@ -9,7 +9,6 @@ import { AnyConfiguration, } from '@jbrowse/core/configuration' import { AssemblyManager, JBrowsePlugin } from '@jbrowse/core/util/types' -import addSnackbarToModel from '@jbrowse/core/ui/SnackbarModel' import { localStorageGetItem, localStorageSetItem } from '@jbrowse/core/util' import { autorun } from 'mobx' import { @@ -22,15 +21,6 @@ import { Instance, } from 'mobx-state-tree' import TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager' -import { BaseTrackConfig } from '@jbrowse/core/pluggableElementTypes' - -// icons -import SettingsIcon from '@mui/icons-material/Settings' -import CopyIcon from '@mui/icons-material/FileCopy' -import DeleteIcon from '@mui/icons-material/Delete' -import InfoIcon from '@mui/icons-material/Info' - -// locals import PluginManager from '@jbrowse/core/PluginManager' import { DialogQueueSessionMixin, @@ -45,11 +35,21 @@ import { SessionAssembliesMixin, TemporaryAssembliesMixin, } from '@jbrowse/app-core' +import { BaseTrackConfig } from '@jbrowse/core/pluggableElementTypes' import { BaseAssemblyConfigSchema } from '@jbrowse/core/assemblyManager' +import { BaseConnectionConfigModel } from '@jbrowse/core/pluggableElementTypes/models/baseConnectionConfig' +import SnackbarModel from '@jbrowse/core/ui/SnackbarModel' + +// icons +import SettingsIcon from '@mui/icons-material/Settings' +import CopyIcon from '@mui/icons-material/FileCopy' +import DeleteIcon from '@mui/icons-material/Delete' +import InfoIcon from '@mui/icons-material/Info' + // locals import { WebSessionConnectionsMixin } from '../SessionConnections' -import { BaseConnectionConfigModel } from '@jbrowse/core/pluggableElementTypes/models/baseConnectionConfig' +// lazies const AboutDialog = lazy(() => import('./AboutDialog')) /** @@ -92,6 +92,7 @@ export function BaseWebSession({ TemporaryAssembliesMixin(pluginManager, assemblyConfigSchema), WebSessionConnectionsMixin(pluginManager), AppFocusMixin(), + SnackbarModel(), ), ) .props({ @@ -226,6 +227,7 @@ export function BaseWebSession({ renderProps() { return { theme: self.theme, + highResolutionScaling: getConf(self, 'highResolutionScaling'), } }, })) @@ -419,7 +421,7 @@ export function BaseWebSession({ sessionModel, ) as typeof sessionModel - return types.snapshotProcessor(addSnackbarToModel(extendedSessionModel), { + return types.snapshotProcessor(extendedSessionModel, { // @ts-expect-error preProcessor(snapshot) { if (snapshot) { diff --git a/plugins/alignments/src/LinearPileupDisplay/SharedLinearPileupDisplayMixin.ts b/plugins/alignments/src/LinearPileupDisplay/SharedLinearPileupDisplayMixin.ts index a86f18bf126..1fe0b669a8c 100644 --- a/plugins/alignments/src/LinearPileupDisplay/SharedLinearPileupDisplayMixin.ts +++ b/plugins/alignments/src/LinearPileupDisplay/SharedLinearPileupDisplayMixin.ts @@ -595,7 +595,7 @@ export function SharedLinearPileupDisplayMixin( } } catch (e) { console.error(e) - session.notify(`${e}`, 'error') + session.notifyError(`${e}`, e) } }), ) diff --git a/plugins/alignments/src/LinearPileupDisplay/model.ts b/plugins/alignments/src/LinearPileupDisplay/model.ts index c49e3ac03bd..b3c9c20856c 100644 --- a/plugins/alignments/src/LinearPileupDisplay/model.ts +++ b/plugins/alignments/src/LinearPileupDisplay/model.ts @@ -21,7 +21,7 @@ import SortIcon from '@mui/icons-material/Sort' import { SharedLinearPileupDisplayMixin } from './SharedLinearPileupDisplayMixin' import { observable } from 'mobx' -// async +// lzies const SortByTagDialog = lazy(() => import('./components/SortByTag')) const ModificationsDialog = lazy( () => import('./components/ColorByModifications'), @@ -152,6 +152,15 @@ function stateModelFactory(configSchema: AnyConfigurationSchemaType) { tag, } }, + /** + * #action + * overrides base from SharedLinearPileupDisplay to make sortReady false + * since changing feature height destroys the sort-induced layout + */ + setFeatureHeight(n?: number) { + self.sortReady = false + self.featureHeight = n + }, })) .actions(self => { // resets the sort object and refresh whole display on reload diff --git a/plugins/breakpoint-split-view/src/BreakpointSplitView/components/AlignmentConnections.tsx b/plugins/breakpoint-split-view/src/BreakpointSplitView/components/AlignmentConnections.tsx index 4994f57c428..787316acabc 100644 --- a/plugins/breakpoint-split-view/src/BreakpointSplitView/components/AlignmentConnections.tsx +++ b/plugins/breakpoint-split-view/src/BreakpointSplitView/components/AlignmentConnections.tsx @@ -59,13 +59,8 @@ const AlignmentConnections = observer(function ({ yOffset = rect.top } - if (!assembly) { - return null - } - - return ( + return assembly ? ( @@ -133,6 +128,7 @@ const AlignmentConnections = observer(function ({ { @@ -160,7 +156,7 @@ const AlignmentConnections = observer(function ({ return ret })} - ) + ) : null }) export default AlignmentConnections diff --git a/plugins/breakpoint-split-view/src/BreakpointSplitView/model.ts b/plugins/breakpoint-split-view/src/BreakpointSplitView/model.ts index b31d4029595..dae654075b7 100644 --- a/plugins/breakpoint-split-view/src/BreakpointSplitView/model.ts +++ b/plugins/breakpoint-split-view/src/BreakpointSplitView/model.ts @@ -351,7 +351,7 @@ export default function stateModelFactory(pluginManager: PluginManager) { ) } catch (e) { console.error(e) - getSession(self).notify(`${e}`, 'error') + getSession(self).notifyError(`${e}`, e) } }), ) diff --git a/plugins/data-management/src/ucsc-trackhub/doConnect.ts b/plugins/data-management/src/ucsc-trackhub/doConnect.ts index 3f73f302fc8..4eb1b02c247 100644 --- a/plugins/data-management/src/ucsc-trackhub/doConnect.ts +++ b/plugins/data-management/src/ucsc-trackhub/doConnect.ts @@ -132,7 +132,7 @@ export async function doConnect(self: any) { } } catch (e) { console.error(e) - session.notify(`${getConf(self, 'name')}: "${e}"`, 'error') + session.notifyError(`${getConf(self, 'name')}: "${e}"`, e) session.breakConnection?.(self.configuration) } } diff --git a/plugins/dotplot-view/src/DotplotReadVsRef/DotplotReadVsRef.ts b/plugins/dotplot-view/src/DotplotReadVsRef/DotplotReadVsRef.ts index 5156266a710..632fa68c8b6 100644 --- a/plugins/dotplot-view/src/DotplotReadVsRef/DotplotReadVsRef.ts +++ b/plugins/dotplot-view/src/DotplotReadVsRef/DotplotReadVsRef.ts @@ -110,6 +110,6 @@ export function onClick(feature: Feature, self: LinearPileupDisplayModel) { }) } catch (e) { console.error(e) - session.notify(`${e}`, 'error') + session.notifyError(`${e}`, e) } } diff --git a/plugins/dotplot-view/src/LaunchDotplotView.ts b/plugins/dotplot-view/src/LaunchDotplotView.ts index 99781be0ad4..ba97799d0ff 100644 --- a/plugins/dotplot-view/src/LaunchDotplotView.ts +++ b/plugins/dotplot-view/src/LaunchDotplotView.ts @@ -39,7 +39,7 @@ export default function LaunchDotplotView(pluginManager: PluginManager) { ) } } catch (e) { - session.notify(`${e}`, 'error') + session.notifyError(`${e}`, e) throw e } }, diff --git a/plugins/grid-bookmark/src/GridBookmarkWidget/components/BookmarkGrid.tsx b/plugins/grid-bookmark/src/GridBookmarkWidget/components/BookmarkGrid.tsx index e87b9fbd12d..8548af53951 100644 --- a/plugins/grid-bookmark/src/GridBookmarkWidget/components/BookmarkGrid.tsx +++ b/plugins/grid-bookmark/src/GridBookmarkWidget/components/BookmarkGrid.tsx @@ -148,7 +148,7 @@ const BookmarkGrid = observer(function ({ model.updateBookmarkLabel(target, row.label) return row }} - onProcessRowUpdateError={e => session.notify(e.message, 'error')} + onProcessRowUpdateError={e => session.notifyError(`${e}`, e)} checkboxSelection onRowSelectionModelChange={newRowSelectionModel => { if (bookmarksWithValidAssemblies.length > 0) { diff --git a/plugins/grid-bookmark/src/GridBookmarkWidget/components/Highlight/OverviewHighlight.tsx b/plugins/grid-bookmark/src/GridBookmarkWidget/components/Highlight/OverviewHighlight.tsx index d651920a56e..442a40d652a 100644 --- a/plugins/grid-bookmark/src/GridBookmarkWidget/components/Highlight/OverviewHighlight.tsx +++ b/plugins/grid-bookmark/src/GridBookmarkWidget/components/Highlight/OverviewHighlight.tsx @@ -25,9 +25,9 @@ const OverviewHighlight = observer(function OverviewHighlight({ model: LGV overview: Base1DViewModel }) { - const { classes } = useStyles() const { cytobandOffset } = model const session = getSession(model) as SessionWithWidgets + const { classes } = useStyles() const { showBookmarkHighlights, showBookmarkLabels } = model const assemblyNames = new Set(session.assemblyNames) @@ -48,64 +48,45 @@ const OverviewHighlight = observer(function OverviewHighlight({ } }, [session, bookmarkWidget]) - return ( - <> - {showBookmarkHighlights && bookmarks.current - ? bookmarks.current - .filter(value => assemblyNames.has(value.assemblyName)) - .map(r => { - const s = overview.bpToPx({ - ...r, - coord: r.reversed ? r.end : r.start, - }) - const e = overview.bpToPx({ - ...r, - coord: r.reversed ? r.start : r.end, - }) - return s !== undefined && e !== undefined - ? { - width: Math.abs(e - s), - left: s + cytobandOffset, - highlight: r.highlight, - label: r.label, - } - : undefined - }) - .filter(notEmpty) - .map(({ left, width, highlight, label }, idx) => ( - <> - {showBookmarkLabels ? ( - -
- - ) : ( -
- )} - - )) - : null} - - ) + return showBookmarkHighlights && bookmarks.current + ? bookmarks.current + .filter(value => assemblyNames.has(value.assemblyName)) + .map(r => { + const rev = r.reversed + const s = overview.bpToPx({ ...r, coord: rev ? r.end : r.start }) + const e = overview.bpToPx({ ...r, coord: rev ? r.start : r.end }) + return s !== undefined && e !== undefined + ? { + width: Math.abs(e - s), + left: s + cytobandOffset, + highlight: r.highlight, + label: r.label, + } + : undefined + }) + .filter(notEmpty) + .map((obj, idx) => { + const { left, width, highlight, label } = obj + return ( + +
+ + ) + }) + : null }) export default OverviewHighlight diff --git a/plugins/grid-bookmark/src/GridBookmarkWidget/utils.ts b/plugins/grid-bookmark/src/GridBookmarkWidget/utils.ts index 5eb43f9dcd0..19835801cce 100644 --- a/plugins/grid-bookmark/src/GridBookmarkWidget/utils.ts +++ b/plugins/grid-bookmark/src/GridBookmarkWidget/utils.ts @@ -41,7 +41,7 @@ export async function navToBookmark( await view.navToLocString(locString, assembly) } catch (e) { console.error(e) - session.notify(`${e}`, 'error') + session.notifyError(`${e}`, e) } } diff --git a/plugins/legacy-jbrowse/src/JBrowse1Connection/model.ts b/plugins/legacy-jbrowse/src/JBrowse1Connection/model.ts index 3c5e147bf04..ee86b264815 100644 --- a/plugins/legacy-jbrowse/src/JBrowse1Connection/model.ts +++ b/plugins/legacy-jbrowse/src/JBrowse1Connection/model.ts @@ -55,9 +55,9 @@ export default function (pluginManager: PluginManager) { self.setTrackConfs(jb2Tracks) } catch (error) { console.error(error) - session.notify( + session.notifyError( `There was a problem connecting to the JBrowse 1 data directory "${self.name}". Please make sure you have entered a valid location. The error that was thrown is: "${error}"`, - 'error', + error, ) session.breakConnection?.(self.configuration) } diff --git a/plugins/linear-comparative-view/src/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.tsx b/plugins/linear-comparative-view/src/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.tsx index 94c77ee68e4..aae9026be43 100644 --- a/plugins/linear-comparative-view/src/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.tsx +++ b/plugins/linear-comparative-view/src/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.tsx @@ -69,7 +69,8 @@ export default function LaunchSyntenyViewDialog({ model, }) } catch (e) { - getSession(model).notify(`${e}`, 'error') + console.error(e) + getSession(model).notifyError(`${e}`, e) } })() handleClose() diff --git a/plugins/linear-comparative-view/src/LaunchLinearSyntenyView.ts b/plugins/linear-comparative-view/src/LaunchLinearSyntenyView.ts index f86cbca3458..4e7d11302f0 100644 --- a/plugins/linear-comparative-view/src/LaunchLinearSyntenyView.ts +++ b/plugins/linear-comparative-view/src/LaunchLinearSyntenyView.ts @@ -67,7 +67,7 @@ export default function LaunchLinearSyntenyView(pluginManager: PluginManager) { ) } } catch (e) { - session.notify(`${e}`, 'error') + session.notifyError(`${e}`, e) throw e } }, diff --git a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/SyntenyContextMenu.tsx b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/SyntenyContextMenu.tsx index d1ada8428c4..2c3a0077fd5 100644 --- a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/SyntenyContextMenu.tsx +++ b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/SyntenyContextMenu.tsx @@ -62,13 +62,13 @@ export default function SyntenyContextMenu({ .navToLocString(`${refName}:${start}-${end}`) .catch(e => { console.error(e) - getSession(model).notify(`${e}`, 'error') + getSession(model).notifyError(`${e}`, e) }) view.views[1] .navToLocString(`${mate.refName}:${mate.start}-${mate.end}`) .catch(e => { console.error(e) - getSession(model).notify(`${e}`, 'error') + getSession(model).notifyError(`${e}`, e) }) }, }, diff --git a/plugins/linear-genome-view/src/LaunchLinearGenomeView/index.ts b/plugins/linear-genome-view/src/LaunchLinearGenomeView/index.ts index e0f45cd0166..7fb2a5884cc 100644 --- a/plugins/linear-genome-view/src/LaunchLinearGenomeView/index.ts +++ b/plugins/linear-genome-view/src/LaunchLinearGenomeView/index.ts @@ -85,7 +85,7 @@ export default (pluginManager: PluginManager) => { ) } } catch (e) { - session.notify(`${e}`, 'error') + session.notifyError(`${e}`, e) throw e } }, diff --git a/plugins/linear-genome-view/src/LinearGenomeView/components/MiniControls.tsx b/plugins/linear-genome-view/src/LinearGenomeView/components/MiniControls.tsx index c328ab8e750..5fce00deffe 100644 --- a/plugins/linear-genome-view/src/LinearGenomeView/components/MiniControls.tsx +++ b/plugins/linear-genome-view/src/LinearGenomeView/components/MiniControls.tsx @@ -1,6 +1,6 @@ import React from 'react' import { observer } from 'mobx-react' -import { IconButton, Paper } from '@mui/material' +import { IconButton, Paper, alpha } from '@mui/material' // icons import ZoomIn from '@mui/icons-material/ZoomIn' @@ -20,10 +20,7 @@ const useStyles = makeStyles()(theme => ({ background: theme.palette.background.paper, }, focusedBackground: { - background: theme.palette.secondary.light, - svg: { - fill: theme.palette.secondary.contrastText, - }, + background: alpha(theme.palette.secondary.light, 0.2), }, })) @@ -32,33 +29,32 @@ const MiniControls = observer(function ({ }: { model: LinearGenomeViewModel }) { - const { classes, cx } = useStyles() + const { classes } = useStyles() const { id, bpPerPx, maxBpPerPx, minBpPerPx, scaleFactor, hideHeader } = model const { focusedViewId } = getSession(model) return hideHeader ? ( - - - - - model.zoom(bpPerPx * 2)} - disabled={bpPerPx >= maxBpPerPx - 0.0001 || scaleFactor !== 1} + + - - - model.zoom(bpPerPx / 2)} - disabled={bpPerPx <= minBpPerPx + 0.0001 || scaleFactor !== 1} - > - - + + + + model.zoom(bpPerPx * 2)} + disabled={bpPerPx >= maxBpPerPx - 0.0001 || scaleFactor !== 1} + > + + + model.zoom(bpPerPx / 2)} + disabled={bpPerPx <= minBpPerPx + 0.0001 || scaleFactor !== 1} + > + + + ) : null }) diff --git a/plugins/linear-genome-view/src/LinearGenomeView/components/RefNameAutocomplete/index.tsx b/plugins/linear-genome-view/src/LinearGenomeView/components/RefNameAutocomplete/index.tsx index 91dda7ba74e..42f6f22b938 100644 --- a/plugins/linear-genome-view/src/LinearGenomeView/components/RefNameAutocomplete/index.tsx +++ b/plugins/linear-genome-view/src/LinearGenomeView/components/RefNameAutocomplete/index.tsx @@ -48,8 +48,6 @@ const RefNameAutocomplete = observer(function ({ const { coarseVisibleLocStrings, hasDisplayedRegions } = model useEffect(() => { - let active = true - // eslint-disable-next-line @typescript-eslint/no-floating-promises ;(async () => { try { @@ -59,21 +57,13 @@ const RefNameAutocomplete = observer(function ({ setLoaded(false) const results = await fetchResults(debouncedSearch) - if (active) { - setLoaded(true) - setSearchOptions(getDeduplicatedResult(results)) - } + setLoaded(true) + setSearchOptions(getDeduplicatedResult(results)) } catch (e) { console.error(e) - if (active) { - session.notify(`${e}`, 'error') - } + session.notifyError(`${e}`, e) } })() - - return () => { - active = false - } }, [assemblyName, fetchResults, debouncedSearch, session, model]) const inputBoxVal = coarseVisibleLocStrings || value || '' diff --git a/plugins/linear-genome-view/src/LinearGenomeView/components/SearchResultsTable.tsx b/plugins/linear-genome-view/src/LinearGenomeView/components/SearchResultsTable.tsx index 60553e04b82..ec31deeccfe 100644 --- a/plugins/linear-genome-view/src/LinearGenomeView/components/SearchResultsTable.tsx +++ b/plugins/linear-genome-view/src/LinearGenomeView/components/SearchResultsTable.tsx @@ -102,7 +102,7 @@ export default function SearchResultsTable({ } } catch (e) { console.error(e) - session.notify(`${e}`, 'error') + session.notifyError(`${e}`, e) } handleClose() }} diff --git a/plugins/linear-genome-view/src/LinearGenomeView/model.ts b/plugins/linear-genome-view/src/LinearGenomeView/model.ts index 2745ed75ba2..e715754e9b0 100644 --- a/plugins/linear-genome-view/src/LinearGenomeView/model.ts +++ b/plugins/linear-genome-view/src/LinearGenomeView/model.ts @@ -14,6 +14,7 @@ import { isSessionModelWithWidgets, isSessionWithAddTracks, localStorageGetItem, + localStorageSetItem, measureText, springAnimate, sum, @@ -50,6 +51,7 @@ import FolderOpenIcon from '@mui/icons-material/FolderOpen' import PhotoCameraIcon from '@mui/icons-material/PhotoCamera' import ZoomInIcon from '@mui/icons-material/ZoomIn' import MenuOpenIcon from '@mui/icons-material/MenuOpen' +import PaletteIcon from '@mui/icons-material/Palette' import MiniControls from './components/MiniControls' import Header from './components/Header' @@ -249,6 +251,14 @@ export function stateModelFactory(pluginManager: PluginManager) { * highlights on the LGV from the URL parameters */ highlight: types.maybe(types.frozen>()), + + /** + * #property + * color by CDS + */ + colorByCDS: types.optional(types.boolean, () => + Boolean(JSON.parse(localStorageGetItem('lgv-colorByCDS') || 'false')), + ), }), ) .volatile(() => ({ @@ -464,10 +474,7 @@ export function stateModelFactory(pluginManager: PluginManager) { return { ...getParentRenderProps(self), bpPerPx: self.bpPerPx, - highResolutionScaling: getConf( - getSession(self), - 'highResolutionScaling', - ), + colorByCDS: self.colorByCDS, } }, @@ -545,6 +552,12 @@ export function stateModelFactory(pluginManager: PluginManager) { }, })) .actions(self => ({ + /** + * #action + */ + setColorByCDS(flag: boolean) { + self.colorByCDS = flag + }, /** * #action */ @@ -1102,6 +1115,13 @@ export function stateModelFactory(pluginManager: PluginManager) { icon: SyncAltIcon, onClick: self.horizontallyFlip, }, + { + label: 'Color by CDS', + type: 'checkbox', + checked: self.colorByCDS, + icon: PaletteIcon, + onClick: () => self.setColorByCDS(!self.colorByCDS), + }, { label: 'Show...', icon: VisibilityIcon, @@ -1122,6 +1142,7 @@ export function stateModelFactory(pluginManager: PluginManager) { checked: !self.hideHeader, onClick: () => self.setHideHeader(!self.hideHeader), }, + { label: 'Show header overview', type: 'checkbox', @@ -1288,11 +1309,10 @@ export function stateModelFactory(pluginManager: PluginManager) { self, autorun(() => { const s = (s: unknown) => JSON.stringify(s) - const { showCytobandsSetting, showCenterLine } = self - if (typeof localStorage !== 'undefined') { - localStorage.setItem('lgv-showCytobands', s(showCytobandsSetting)) - localStorage.setItem('lgv-showCenterLine', s(showCenterLine)) - } + const { showCytobandsSetting, showCenterLine, colorByCDS } = self + localStorageSetItem('lgv-showCytobands', s(showCytobandsSetting)) + localStorageSetItem('lgv-showCenterLine', s(showCenterLine)) + localStorageSetItem('lgv-colorByCDS', s(colorByCDS)) }), ) }, diff --git a/plugins/sequence/src/DivSequenceRenderer/components/DivSequenceRendering.test.tsx b/plugins/sequence/src/DivSequenceRenderer/components/DivSequenceRendering.test.tsx index bafbf15f337..fd7bbe868d9 100644 --- a/plugins/sequence/src/DivSequenceRenderer/components/DivSequenceRendering.test.tsx +++ b/plugins/sequence/src/DivSequenceRenderer/components/DivSequenceRendering.test.tsx @@ -1,38 +1,16 @@ import React from 'react' import { render } from '@testing-library/react' -import SimpleFeature from '@jbrowse/core/util/simpleFeature' +import { SimpleFeature } from '@jbrowse/core/util' import DivSequenceRendering from './DivSequenceRendering' import DivRenderingConfigSchema from '../configSchema' -// This just keeps our testing logs clean by not displaying `console.error`s -// from errors we intentionally throw in our tests. Hopefully React will -// someday provide a way for error boundaries to prevent error logging so we -// won't have to do this: https://github.com/facebook/react/issues/15069 -const originalError = console.error -beforeAll(() => { - console.error = (...args) => { - if ( - args[0].includes('feature one did not contain a valid `seq` attribute') || - args[0].includes( - 'The above error occurred in the component', - ) - ) { - return - } - originalError.call(console, ...args) - } -}) - -afterAll(() => { - console.error = originalError -}) - test('renders with one, zoomed way out', () => { const { container } = render( { regions={[ { assemblyName: 'volvox', refName: 'zonk', start: 0, end: 1000 }, ]} + colorByCDS={false} features={ new Map([ ['one', new SimpleFeature({ uniqueId: 'one', start: 1, end: 3 })], @@ -83,6 +62,7 @@ test('renders with one feature with an incorrect seq, zoomed in, should throw', regions={[ { assemblyName: 'volvox', refName: 'zonk', start: 0, end: 1000 }, ]} + colorByCDS={false} features={ new Map([ [ @@ -112,6 +92,7 @@ test('renders with one feature with a correct seq, zoomed in, should render nice regions={[ { assemblyName: 'volvox', refName: 'zonk', start: 0, end: 1000 }, ]} + colorByCDS={false} features={ new Map([ [ @@ -147,6 +128,7 @@ test('renders with one feature reversed with a correct seq, zoomed in, should re reversed: true, }, ]} + colorByCDS={false} features={ new Map([ [ diff --git a/plugins/sequence/src/DivSequenceRenderer/components/DivSequenceRendering.tsx b/plugins/sequence/src/DivSequenceRenderer/components/DivSequenceRendering.tsx index f4c9ae4a1b8..46039319a89 100644 --- a/plugins/sequence/src/DivSequenceRenderer/components/DivSequenceRendering.tsx +++ b/plugins/sequence/src/DivSequenceRenderer/components/DivSequenceRendering.tsx @@ -12,90 +12,101 @@ import { defaultStops, defaultCodonTable, generateCodonTable, + Frame, } from '@jbrowse/core/util' import { Theme } from '@mui/material' -function Translation(props: { +function Translation({ + codonTable, + seq, + frame, + bpPerPx, + colorByCDS, + region, + seqStart, + height, + y, + reverse = false, + theme, +}: { codonTable: Record seq: string - frame: number + frame: Frame + colorByCDS: boolean bpPerPx: number region: Region + seqStart: number reverse?: boolean height: number y: number theme?: Theme }) { - const { - codonTable, - seq, - frame, - bpPerPx, - region, - height, - y, - reverse = false, - theme, - } = props - const scale = bpPerPx - - // the tilt variable normalizes the frame to where we are starting from, - // which increases consistency across blocks - const tilt = 3 - (region.start % 3) + const normalizedFrame = Math.abs(frame) - 1 + const seqFrame = seqStart % 3 + const frameShift = (normalizedFrame - seqFrame + 3) % 3 - // the effectiveFrame incorporates tilt and the frame to say what the - // effective frame that is plotted. The +3 is for when frame is -2 and this - // can otherwise result in effectiveFrame -1 - const effectiveFrame = (frame + tilt + 3) % 3 - - const seqSliced = seq.slice(effectiveFrame) + const frameShiftAdjustedSeqLength = seq.length - frameShift + const multipleOfThreeLength = + frameShiftAdjustedSeqLength - (frameShiftAdjustedSeqLength % 3) + const seqSliced = seq.slice(frameShift, frameShift + multipleOfThreeLength) const translated: { letter: string; codon: string }[] = [] for (let i = 0; i < seqSliced.length; i += 3) { const codon = seqSliced.slice(i, i + 3) const normalizedCodon = reverse ? revcom(codon) : codon const aminoAcid = codonTable[normalizedCodon] || '' - translated.push({ letter: aminoAcid, codon: normalizedCodon.toUpperCase() }) + translated.push({ + letter: aminoAcid, + codon: normalizedCodon.toUpperCase(), + }) } - const w = (1 / scale) * 3 - const drop = region.start === 0 ? 0 : w - const render = 1 / bpPerPx >= 12 const width = (region.end - region.start) / bpPerPx - - const map = ['#d8d8d8', '#adadad', '#8f8f8f'].reverse() + const codonWidth = (1 / bpPerPx) * 3 + const renderLetter = 1 / bpPerPx >= 12 + const frameOffset = frameShift / bpPerPx + const startOffset = (region.start - seqStart) / bpPerPx + const offset = frameOffset - startOffset + const defaultFill = colorByCDS + ? theme?.palette.framesCDS.at(frame)?.main + : theme?.palette.frames.at(frame)?.main return ( <> + {translated.map((element, index) => { const x = region.reversed - ? width - (w * (index + 1) + effectiveFrame / scale - drop) - : w * index + effectiveFrame / scale - drop + ? width - (index + 1) * codonWidth - offset + : codonWidth * index + offset const { letter, codon } = element + const codonFill = defaultStarts.includes(codon) + ? theme?.palette.startCodon + : defaultStops.includes(codon) + ? theme?.palette.stopCodon + : undefined + if (!(renderLetter || codonFill)) { + return null + } return ( - {render ? ( + {renderLetter ? ( {letter} @@ -169,6 +180,7 @@ function DNA(props: { function SequenceSVG({ regions, theme: configTheme, + colorByCDS, features = new Map(), showReverse = true, showForward = true, @@ -179,6 +191,7 @@ function SequenceSVG({ regions: Region[] theme?: Theme features: Map + colorByCDS: boolean showReverse?: boolean showForward?: boolean showTranslation?: boolean @@ -201,28 +214,36 @@ function SequenceSVG({ // (applies to both translation rows and dna rows) let currY = -rowHeight + const showDNA = bpPerPx <= 1 + + const forwardFrames: Frame[] = showTranslation && showForward ? [3, 2, 1] : [] + const reverseFrames: Frame[] = + showTranslation && showReverse ? [-1, -2, -3] : [] + + // if region.reversed, the forward translation is on bottom, reverse on top + const [topFrames, bottomFrames] = region.reversed + ? [reverseFrames.toReversed(), forwardFrames.toReversed()] + : [forwardFrames, reverseFrames] return ( <> - {/* the upper translation row. if the view is reversed, the reverse - translation is on the top */} - {showTranslation && (region.reversed ? showReverse : showForward) - ? [2, 1, 0].map(index => ( - - )) - : null} + {topFrames.map(index => ( + + ))} - {showForward ? ( + {showForward && showDNA ? ( ) : null} - {showReverse ? ( + {showReverse && showDNA ? ( ) : null} - {/* the lower translation row. if the view is reversed, the forward - translation is on the bottom */} - {showTranslation && (region.reversed ? showForward : showReverse) - ? [0, -1, -2].map(index => ( - - )) - : null} + {bottomFrames.map(index => ( + + ))} ) } @@ -287,11 +306,11 @@ function Wrapper({ width={width} height={totalHeight} style={{ + // use block because svg by default is inline, which adds a margin + display: 'block', width, height: totalHeight, userSelect: 'none', - // use block because svg by default is inline, which adds a margin - display: 'block', }} > {children} @@ -303,6 +322,7 @@ const DivSequenceRendering = observer(function (props: { exportSVG?: { rasterizeLayers: boolean } features: Map regions: Region[] + colorByCDS: boolean bpPerPx: number rowHeight: number sequenceHeight: number diff --git a/plugins/sequence/src/DivSequenceRenderer/components/__snapshots__/DivSequenceRendering.test.tsx.snap b/plugins/sequence/src/DivSequenceRenderer/components/__snapshots__/DivSequenceRendering.test.tsx.snap index 59db00aaed0..7538bd85974 100644 --- a/plugins/sequence/src/DivSequenceRenderer/components/__snapshots__/DivSequenceRendering.test.tsx.snap +++ b/plugins/sequence/src/DivSequenceRenderer/components/__snapshots__/DivSequenceRendering.test.tsx.snap @@ -5,12 +5,19 @@ exports[`renders with one feature reversed with a correct seq, zoomed in, should + - - - + - @@ -611,12 +593,19 @@ exports[`renders with one feature with a correct seq, zoomed in, should render n + - - - + - @@ -1217,27 +1181,26 @@ exports[`renders with one feature with an incorrect seq, zoomed in, should throw - + - - + -
`; @@ -1427,7 +1373,7 @@ exports[`renders with one feature with no seq, zoomed in, should throw 1`] = `
@@ -1438,73 +1384,51 @@ exports[`renders with one, zoomed way out 1`] = ` + - - -
`; diff --git a/plugins/sequence/src/LinearReferenceSequenceDisplay/model.ts b/plugins/sequence/src/LinearReferenceSequenceDisplay/model.ts index b76f1d8d921..fb103e27c19 100644 --- a/plugins/sequence/src/LinearReferenceSequenceDisplay/model.ts +++ b/plugins/sequence/src/LinearReferenceSequenceDisplay/model.ts @@ -7,6 +7,7 @@ import { AnyConfigurationSchemaType, ConfigurationReference, } from '@jbrowse/core/configuration' +import { getParentRenderProps } from '@jbrowse/core/util/tracks' import { getContainingView } from '@jbrowse/core/util' import { autorun } from 'mobx' @@ -81,6 +82,7 @@ export function modelFactory(configSchema: AnyConfigurationSchemaType) { } = self return { ...superRenderProps(), + ...getParentRenderProps(self), config: self.configuration.renderer, rpcDriverName, showForward, @@ -98,7 +100,7 @@ export function modelFactory(configSchema: AnyConfigurationSchemaType) { */ regionCannotBeRendered(/* region */) { const view = getContainingView(self) as LGV - return view?.bpPerPx >= 1 ? 'Zoom in to see sequence' : undefined + return view?.bpPerPx > 3 ? 'Zoom in to see sequence' : undefined }, /** * #getter @@ -131,7 +133,7 @@ export function modelFactory(configSchema: AnyConfigurationSchemaType) { self, autorun(() => { const view = getContainingView(self) as LGV - if (view?.bpPerPx >= 1) { + if (view?.bpPerPx > 3) { self.setHeight(50) } else { self.setHeight(self.sequenceHeight) diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/LocString.tsx b/plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/LocString.tsx index 742c4231b50..77d4783ee38 100644 --- a/plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/LocString.tsx +++ b/plugins/spreadsheet-view/src/SpreadsheetView/models/ColumnDataTypes/LocString.tsx @@ -302,7 +302,7 @@ const DataCellReactComponent = observer(function ({ await locationLinkClick(spreadsheet, columnNumber, cell) } catch (e) { console.error(e) - session.notify(`${e}`, 'error') + session.notifyError(`${e}`, e) } }} title="open a new linear genome view here" diff --git a/plugins/svg/src/SvgFeatureRenderer/components/Box.tsx b/plugins/svg/src/SvgFeatureRenderer/components/Box.tsx index a8bae0cfdbd..65ef77a045b 100644 --- a/plugins/svg/src/SvgFeatureRenderer/components/Box.tsx +++ b/plugins/svg/src/SvgFeatureRenderer/components/Box.tsx @@ -4,8 +4,9 @@ import { AnyConfigurationModel, readConfObject, } from '@jbrowse/core/configuration' -import { Region, Feature } from '@jbrowse/core/util' +import { Region, Feature, getFrame } from '@jbrowse/core/util' import { SceneGraph } from '@jbrowse/core/util/layouts' +import { useTheme } from '@mui/material' // locals import { isUTR } from './util' @@ -21,12 +22,26 @@ const Box = observer(function Box(props: { bpPerPx: number selected?: boolean topLevel?: boolean - children?: React.ReactNode + colorByCDS: boolean }) { - const { feature, region, config, featureLayout, bpPerPx, topLevel } = props + const theme = useTheme() + const { + colorByCDS, + feature, + region, + config, + featureLayout, + bpPerPx, + topLevel, + } = props const { start, end } = region const screenWidth = (end - start) / bpPerPx - const width = (feature.get('end') - feature.get('start')) / bpPerPx + const featureStart = feature.get('start') + const featureEnd = feature.get('end') + const featureType: string | undefined = feature.get('type') + const featureStrand: -1 | 1 | undefined = feature.get('strand') + const featurePhase: 0 | 1 | 2 | undefined = feature.get('phase') + const width = (featureEnd - featureStart) / bpPerPx const { left = 0 } = featureLayout.absolute let { top = 0, height = 0 } = featureLayout.absolute @@ -42,10 +57,31 @@ const Box = observer(function Box(props: { const diff = leftWithinBlock - left const widthWithinBlock = Math.max(2, Math.min(width - diff, screenWidth)) + let fill: string = isUTR(feature) + ? readConfObject(config, 'color3', { feature }) + : readConfObject(config, 'color1', { feature }) + if ( + colorByCDS && + featureType === 'CDS' && + featureStrand !== undefined && + featurePhase !== undefined + ) { + const frame = getFrame( + featureStart, + featureEnd, + featureStrand, + featurePhase, + ) + const frameColor = theme.palette.framesCDS.at(frame)?.main + if (frameColor) { + fill = frameColor + } + } + // if feature has parent and type is intron, then don't render the intron // subfeature (if it doesn't have a parent, then maybe the introns are // separately displayed features that should be displayed) - return feature.parent() && feature.get('type') === 'intron' ? null : ( + return feature.parent() && featureType === 'intron' ? null : ( <> {topLevel ? : null} diff --git a/plugins/svg/src/SvgFeatureRenderer/components/FeatureGlyph.tsx b/plugins/svg/src/SvgFeatureRenderer/components/FeatureGlyph.tsx index 139d5788f25..cef2cc6051a 100644 --- a/plugins/svg/src/SvgFeatureRenderer/components/FeatureGlyph.tsx +++ b/plugins/svg/src/SvgFeatureRenderer/components/FeatureGlyph.tsx @@ -19,6 +19,7 @@ const FeatureGlyph = observer(function (props: { description: string shouldShowName: boolean shouldShowDescription: boolean + colorByCDS: boolean fontHeight: number allowedWidthExpansion: number exportSVG?: unknown diff --git a/plugins/svg/src/SvgFeatureRenderer/components/ProcessedTranscript.tsx b/plugins/svg/src/SvgFeatureRenderer/components/ProcessedTranscript.tsx index 8b018edcb98..36192e51bb2 100644 --- a/plugins/svg/src/SvgFeatureRenderer/components/ProcessedTranscript.tsx +++ b/plugins/svg/src/SvgFeatureRenderer/components/ProcessedTranscript.tsx @@ -16,15 +16,11 @@ function makeSubpartsFilter( confKey = 'subParts', config: AnyConfigurationModel, ) { - let filter = readConfObject(config, confKey) as string[] | string - - if (typeof filter == 'string') { - // convert to array - filter = filter.split(/\s*,\s*/) - } + const filter = readConfObject(config, confKey) as string[] | string + const ret = typeof filter == 'string' ? filter.split(/\s*,\s*/) : filter return (feature: Feature) => - filter + ret .map(typeName => typeName.toLowerCase()) .includes(feature.get('type').toLowerCase()) } diff --git a/plugins/svg/src/SvgFeatureRenderer/components/SvgFeatureRendering.test.tsx b/plugins/svg/src/SvgFeatureRenderer/components/SvgFeatureRendering.test.tsx index 8dbe2b98a38..78c2d2d74be 100644 --- a/plugins/svg/src/SvgFeatureRenderer/components/SvgFeatureRendering.test.tsx +++ b/plugins/svg/src/SvgFeatureRenderer/components/SvgFeatureRendering.test.tsx @@ -15,6 +15,7 @@ test('no features', () => { const { container } = render( { const { container } = render( { const { container, getByTestId } = render( { const { container } = render( { const { container } = render( { const { container } = render( { const { container } = render( { assemblyName: 'volvox', }} displayModel={{ - getFeatureByID: () => { - return [0, 0, 10, 10] - }, + getFeatureByID: () => [0, 0, 10, 10], featureIdUnderMouse: 'one', selectedFeatureId: 'one', }} diff --git a/plugins/svg/src/SvgFeatureRenderer/components/SvgFeatureRendering.tsx b/plugins/svg/src/SvgFeatureRenderer/components/SvgFeatureRendering.tsx index f35e145674d..93785736d87 100644 --- a/plugins/svg/src/SvgFeatureRenderer/components/SvgFeatureRendering.tsx +++ b/plugins/svg/src/SvgFeatureRenderer/components/SvgFeatureRendering.tsx @@ -30,6 +30,7 @@ function RenderedFeatureGlyph(props: { bpPerPx: number region: Region config: AnyConfigurationModel + colorByCDS: boolean layout: BaseLayout extraGlyphs?: ExtraGlyphValidator[] displayMode: string @@ -157,6 +158,7 @@ const RenderedFeatures = observer( bpPerPx: number config: AnyConfigurationModel displayMode: string + colorByCDS: boolean displayModel?: DisplayModel region: Region exportSVG?: unknown @@ -196,6 +198,7 @@ const SvgFeatureRendering = observer(function SvgFeatureRendering(props: { bpPerPx: number detectRerender?: () => void config: AnyConfigurationModel + colorByCDS: boolean features: Map displayModel?: DisplayModel exportSVG?: boolean diff --git a/plugins/svg/src/SvgFeatureRenderer/components/util.ts b/plugins/svg/src/SvgFeatureRenderer/components/util.ts index 9cc9bfbbd29..abbf2a167e9 100644 --- a/plugins/svg/src/SvgFeatureRenderer/components/util.ts +++ b/plugins/svg/src/SvgFeatureRenderer/components/util.ts @@ -14,7 +14,7 @@ import Subfeatures from './Subfeatures' export interface Glyph extends React.FC<{ - children: React.ReactNode + colorByCDS: boolean feature: Feature featureLayout: SceneGraph selected?: boolean @@ -118,7 +118,7 @@ export function layOut({ return subLayout } -export function layOutFeature(args: FeatureLayOutArgs): SceneGraph { +export function layOutFeature(args: FeatureLayOutArgs) { const { layout, feature, bpPerPx, reversed, config, extraGlyphs } = args const displayMode = readConfObject(config, 'displayMode') as string const GlyphComponent = diff --git a/products/jbrowse-cli/README.md b/products/jbrowse-cli/README.md index 61a34db1e5a..017f50bb2d6 100644 --- a/products/jbrowse-cli/README.md +++ b/products/jbrowse-cli/README.md @@ -477,7 +477,7 @@ DESCRIPTION ``` _See code: -[@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v6.0.17/src/commands/help.ts)_ +[@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v6.0.18/src/commands/help.ts)_ ## `jbrowse make-pif FILE` diff --git a/products/jbrowse-cli/src/commands/add-connection.ts b/products/jbrowse-cli/src/commands/add-connection.ts index 038ddc279db..bb66177897a 100644 --- a/products/jbrowse-cli/src/commands/add-connection.ts +++ b/products/jbrowse-cli/src/commands/add-connection.ts @@ -136,8 +136,9 @@ export default class AddConnection extends JBrowseCommand { } : {}), connectionId: id, - assemblyNames: - assemblyNames || type === 'JBrowse1Connection' + assemblyNames: assemblyNames + ? assemblyNames.split(',') + : type === 'JBrowse1Connection' ? [configContents.assemblies[0]?.name] : undefined, ...(config ? parseJSON(config) : {}), diff --git a/products/jbrowse-desktop/package.json b/products/jbrowse-desktop/package.json index aefa8026e35..4c368bcc1b9 100644 --- a/products/jbrowse-desktop/package.json +++ b/products/jbrowse-desktop/package.json @@ -104,32 +104,19 @@ "use-query-params": "^2.0.0" }, "devDependencies": { - "electron": "29.1.0" + "electron": "29.1.2" }, "browserslist": [ "last 1 chrome version" ], "build": { - "electronVersion": "29.1.0", + "electronVersion": "29.1.2", "extraMetadata": { "main": "build/electron.js" }, "appId": "org.jbrowse2.app", "productName": "JBrowse 2", "copyright": "Copyright © 2019", - "snap": { - "confinement": "strict", - "plugs": [ - "default", - "removable-media" - ], - "publish": [ - "github" - ], - "slots": [ - "default" - ] - }, "win": { "publish": [ "github" @@ -140,9 +127,33 @@ "publish": [ "github" ], + "target": [ + { + "target": "AppImage" + }, + { + "target": "snap" + }, + { + "target": "deb" + } + ], "executableName": "jbrowse-desktop", "artifactName": "jbrowse-desktop-v${version}-linux.${ext}" }, + "deb": { + "maintainer": "colin.diesh@gmail.com" + }, + "snap": { + "confinement": "strict", + "plugs": [ + "default", + "removable-media" + ], + "slots": [ + "default" + ] + }, "mac": { "mergeASARs": false, "target": [ diff --git a/products/jbrowse-desktop/src/rootModel/Menus.ts b/products/jbrowse-desktop/src/rootModel/Menus.ts index 0379ffe23b6..849c862862a 100644 --- a/products/jbrowse-desktop/src/rootModel/Menus.ts +++ b/products/jbrowse-desktop/src/rootModel/Menus.ts @@ -54,7 +54,7 @@ export function DesktopMenusMixin(_pluginManager: PluginManager) { } } catch (e) { console.error(e) - self.session?.notify(`${e}`, 'error') + self.session?.notifyError(`${e}`, e) } }, }, @@ -67,7 +67,7 @@ export function DesktopMenusMixin(_pluginManager: PluginManager) { await self.saveSession(getSaveSession(self)) } catch (e) { console.error(e) - self.session?.notify(`${e}`, 'error') + self.session?.notifyError(`${e}`, e) } } }, @@ -84,7 +84,7 @@ export function DesktopMenusMixin(_pluginManager: PluginManager) { await self.saveSession(getSaveSession(self)) } catch (e) { console.error(e) - self.session?.notify(`${e}`, 'error') + self.session?.notifyError(`${e}`, e) } }, }, @@ -110,7 +110,7 @@ export function DesktopMenusMixin(_pluginManager: PluginManager) { }) } catch (e) { console.error(e) - self.session?.notify(`${e}`) + self.session?.notifyError(`${e}`, e) } doneCallback() }, diff --git a/products/jbrowse-desktop/src/sessionModel/index.ts b/products/jbrowse-desktop/src/sessionModel/index.ts index d67a55a7b82..571aa4a9a0e 100644 --- a/products/jbrowse-desktop/src/sessionModel/index.ts +++ b/products/jbrowse-desktop/src/sessionModel/index.ts @@ -1,12 +1,7 @@ -import { readConfObject } from '@jbrowse/core/configuration' -import addSnackbarToModel from '@jbrowse/core/ui/SnackbarModel' +import { getConf, readConfObject } from '@jbrowse/core/configuration' import { types, Instance, getParent } from 'mobx-state-tree' import PluginManager from '@jbrowse/core/PluginManager' - -// icons -import { DesktopSessionTrackMenuMixin } from './TrackMenu' import { BaseTrackConfig } from '@jbrowse/core/pluggableElementTypes' -import { DesktopRootModel } from '../rootModel' import { ConnectionManagementSessionMixin, DialogQueueSessionMixin, @@ -16,7 +11,6 @@ import { ThemeManagerSessionMixin, TracksManagerSessionMixin, } from '@jbrowse/product-core' -import { DesktopSessionFactory } from './DesktopSession' import { AppFocusMixin, SessionAssembliesMixin, @@ -24,6 +18,14 @@ import { } from '@jbrowse/app-core' import { BaseAssemblyConfigSchema } from '@jbrowse/core/assemblyManager/assemblyConfigSchema' import { AbstractSessionModel } from '@jbrowse/core/util' +import SnackbarModel from '@jbrowse/core/ui/SnackbarModel' + +// icons +import { DesktopSessionTrackMenuMixin } from './TrackMenu' + +// locals +import { DesktopRootModel } from '../rootModel' +import { DesktopSessionFactory } from './DesktopSession' /** * #stateModel JBrowseDesktopSessionModel @@ -67,6 +69,7 @@ export default function sessionModelFactory({ TemporaryAssembliesMixin(pluginManager, assemblyConfigSchema), DesktopSessionTrackMenuMixin(pluginManager), AppFocusMixin(), + SnackbarModel(), ) .views(self => ({ /** @@ -138,7 +141,10 @@ export default function sessionModelFactory({ * #method */ renderProps() { - return { theme: readConfObject(self.configuration, 'theme') } + return { + theme: getConf(self, 'theme'), + highResolutionScaling: getConf(self, 'highResolutionScaling'), + } }, })) @@ -147,7 +153,7 @@ export default function sessionModelFactory({ sessionModel, ) as typeof sessionModel - return types.snapshotProcessor(addSnackbarToModel(extendedSessionModel), { + return types.snapshotProcessor(extendedSessionModel, { // @ts-expect-error preProcessor(snapshot) { if (snapshot) { diff --git a/products/jbrowse-react-circular-genome-view/src/createModel/createSessionModel.ts b/products/jbrowse-react-circular-genome-view/src/createModel/createSessionModel.ts index 0547c974d41..60739f4104c 100644 --- a/products/jbrowse-react-circular-genome-view/src/createModel/createSessionModel.ts +++ b/products/jbrowse-react-circular-genome-view/src/createModel/createSessionModel.ts @@ -3,9 +3,9 @@ import { lazy } from 'react' import { AbstractSessionModel } from '@jbrowse/core/util/types' import { getParent, types, Instance } from 'mobx-state-tree' import PluginManager from '@jbrowse/core/PluginManager' -import { readConfObject } from '@jbrowse/core/configuration' +import SnackbarModel from '@jbrowse/core/ui/SnackbarModel' +import { getConf } from '@jbrowse/core/configuration' import InfoIcon from '@mui/icons-material/Info' -import addSnackbarToModel from '@jbrowse/core/ui/SnackbarModel' import { BaseSessionModel, ConnectionManagementSessionMixin, @@ -29,7 +29,7 @@ const AboutDialog = lazy(() => import('./AboutDialog')) * - [SnackbarModel](../snackbarmodel) */ export default function sessionModelFactory(pluginManager: PluginManager) { - const model = types + return types .compose( 'ReactCircularGenomeViewSession', BaseSessionModel(pluginManager), @@ -38,6 +38,7 @@ export default function sessionModelFactory(pluginManager: PluginManager) { DialogQueueSessionMixin(pluginManager), TracksManagerSessionMixin(pluginManager), ReferenceManagementSessionMixin(pluginManager), + SnackbarModel(), ) .props({ /** @@ -94,7 +95,10 @@ export default function sessionModelFactory(pluginManager: PluginManager) { * #method */ renderProps() { - return { theme: readConfObject(self.configuration, 'theme') } + return { + theme: getConf(self, 'theme'), + highResolutionScaling: getConf(self, 'highResolutionScaling'), + } }, })) .actions(self => ({ @@ -140,8 +144,6 @@ export default function sessionModelFactory(pluginManager: PluginManager) { ] }, })) - - return addSnackbarToModel(model) } export type SessionStateModel = ReturnType diff --git a/products/jbrowse-react-linear-genome-view/src/JBrowseLinearGenomeView/__snapshots__/JBrowseLinearGenomeView.test.tsx.snap b/products/jbrowse-react-linear-genome-view/src/JBrowseLinearGenomeView/__snapshots__/JBrowseLinearGenomeView.test.tsx.snap index 3c971649e50..b9f966b9014 100644 --- a/products/jbrowse-react-linear-genome-view/src/JBrowseLinearGenomeView/__snapshots__/JBrowseLinearGenomeView.test.tsx.snap +++ b/products/jbrowse-react-linear-genome-view/src/JBrowseLinearGenomeView/__snapshots__/JBrowseLinearGenomeView.test.tsx.snap @@ -1395,12 +1395,19 @@ exports[` renders successfully 1`] = ` + renders successfully 1`] = ` L renders successfully 1`] = ` L renders successfully 1`] = ` R renders successfully 1`] = ` * renders successfully 1`] = ` T renders successfully 1`] = ` T renders successfully 1`] = ` A renders successfully 1`] = ` L renders successfully 1`] = ` G renders successfully 1`] = ` T renders successfully 1`] = ` L renders successfully 1`] = ` P - renders successfully 1`] = ` I renders successfully 1`] = ` V renders successfully 1`] = ` A renders successfully 1`] = ` E renders successfully 1`] = ` L renders successfully 1`] = ` N renders successfully 1`] = ` N renders successfully 1`] = ` G renders successfully 1`] = ` I renders successfully 1`] = ` R renders successfully 1`] = ` N renders successfully 1`] = ` T renders successfully 1`] = ` S renders successfully 1`] = ` + renders successfully 1`] = ` H renders successfully 1`] = ` C renders successfully 1`] = ` C renders successfully 1`] = ` G renders successfully 1`] = ` V renders successfully 1`] = ` E renders successfully 1`] = ` Q renders successfully 1`] = ` R renders successfully 1`] = ` * renders successfully 1`] = ` E renders successfully 1`] = ` H renders successfully 1`] = ` F renders successfully 1`] = ` > R - - renders successfully 1`] = ` > G + renders successfully 1`] = ` M renders successfully 1`] = ` T renders successfully 1`] = ` A renders successfully 1`] = ` S renders successfully 1`] = ` N renders successfully 1`] = ` F renders successfully 1`] = ` L renders successfully 1`] = ` M renders successfully 1`] = ` L renders successfully 1`] = ` F renders successfully 1`] = ` V renders successfully 1`] = ` E renders successfully 1`] = ` T - - Q + N - Q + N - P + R - T + L - S + Q - C + V - R + V - C + A - * + N - S + P - C + V - K + S - R + G + > + D + + - N + Q - N + Q - R + P - L + T - Q + S - V + C - - V - - - A + R - N + C - P + * - V + S - S + C - G + K - D + R @@ -4409,12 +4391,19 @@ exports[` renders successfully 1`] = ` + renders successfully 1`] = ` P renders successfully 1`] = ` S renders successfully 1`] = ` L renders successfully 1`] = ` T renders successfully 1`] = ` F renders successfully 1`] = ` I renders successfully 1`] = ` R renders successfully 1`] = ` * renders successfully 1`] = ` L renders successfully 1`] = ` V renders successfully 1`] = ` * renders successfully 1`] = ` P renders successfully 1`] = ` + renders successfully 1`] = ` S renders successfully 1`] = ` V renders successfully 1`] = ` S renders successfully 1`] = ` H renders successfully 1`] = ` F renders successfully 1`] = ` Y renders successfully 1`] = ` T renders successfully 1`] = ` M renders successfully 1`] = ` I renders successfully 1`] = ` G renders successfully 1`] = ` S renders successfully 1`] = ` L renders successfully 1`] = ` A renders successfully 1`] = ` L - renders successfully 1`] = ` R renders successfully 1`] = ` L renders successfully 1`] = ` S renders successfully 1`] = ` L renders successfully 1`] = ` L renders successfully 1`] = ` Y renders successfully 1`] = ` D renders successfully 1`] = ` Y renders successfully 1`] = ` D renders successfully 1`] = ` W renders successfully 1`] = ` F renders successfully 1`] = ` F renders successfully 1`] = ` S renders successfully 1`] = ` > L - - renders successfully 1`] = ` + renders successfully 1`] = ` T renders successfully 1`] = ` * renders successfully 1`] = ` * renders successfully 1`] = ` V renders successfully 1`] = ` I renders successfully 1`] = ` I renders successfully 1`] = ` I renders successfully 1`] = ` P renders successfully 1`] = ` E renders successfully 1`] = ` K renders successfully 1`] = ` A renders successfully 1`] = ` K - - R + G - R + D - E + R - S + V K - Y + I - S + R - * + N - S + H - Q + N - N + T - K + R - L + * - R + G - P + Q - - G - - D + R R - V + E - K + S - I + K - R + Y - N + S - H + * - N + S - T + Q - R + N - * + K - G + L - Q + R + > + P + diff --git a/products/jbrowse-react-linear-genome-view/src/createModel/createSessionModel.ts b/products/jbrowse-react-linear-genome-view/src/createModel/createSessionModel.ts index 0bc650494fb..38214adde5c 100644 --- a/products/jbrowse-react-linear-genome-view/src/createModel/createSessionModel.ts +++ b/products/jbrowse-react-linear-genome-view/src/createModel/createSessionModel.ts @@ -1,8 +1,8 @@ /* eslint-disable @typescript-eslint/no-explicit-any */ import { lazy } from 'react' import { AbstractSessionModel } from '@jbrowse/core/util/types' -import addSnackbarToModel from '@jbrowse/core/ui/SnackbarModel' -import { readConfObject } from '@jbrowse/core/configuration' +import SnackbarModel from '@jbrowse/core/ui/SnackbarModel' +import { getConf } from '@jbrowse/core/configuration' import { cast, getParent, types, Instance } from 'mobx-state-tree' import PluginManager from '@jbrowse/core/PluginManager' import InfoIcon from '@mui/icons-material/Info' @@ -34,7 +34,7 @@ const AboutDialog = lazy(() => import('./AboutDialog')) function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars export default function sessionModelFactory(pluginManager: PluginManager) { - const model = types + return types .compose( 'ReactLinearGenomeViewSession', BaseSessionModel(pluginManager), @@ -44,6 +44,7 @@ export default function sessionModelFactory(pluginManager: PluginManager) { TracksManagerSessionMixin(pluginManager), ReferenceManagementSessionMixin(pluginManager), SessionTracksManagerSessionMixin(pluginManager), + SnackbarModel(), ) .props({ /** @@ -105,7 +106,10 @@ export default function sessionModelFactory(pluginManager: PluginManager) { * #method */ renderProps() { - return { theme: readConfObject(self.configuration, 'theme') } + return { + theme: getConf(self, 'theme'), + highResolutionScaling: getConf(self, 'highResolutionScaling'), + } }, })) .actions(self => ({ @@ -146,8 +150,6 @@ export default function sessionModelFactory(pluginManager: PluginManager) { ] }, })) - - return addSnackbarToModel(model) } export type SessionStateModel = ReturnType diff --git a/products/jbrowse-react-linear-genome-view/src/createViewState.ts b/products/jbrowse-react-linear-genome-view/src/createViewState.ts index 2f48bccc714..9c8e0acb162 100644 --- a/products/jbrowse-react-linear-genome-view/src/createViewState.ts +++ b/products/jbrowse-react-linear-genome-view/src/createViewState.ts @@ -112,7 +112,7 @@ export default function createViewState(opts: ViewStateOptions) { assembly.name, ) } catch (e) { - session.notify(`${e}`, 'error') + session.notifyError(`${e}`, e) } })() } diff --git a/products/jbrowse-web/src/createPluginManager.ts b/products/jbrowse-web/src/createPluginManager.ts index 0f12ec234d8..6c9681c7844 100644 --- a/products/jbrowse-web/src/createPluginManager.ts +++ b/products/jbrowse-web/src/createPluginManager.ts @@ -52,15 +52,11 @@ export function createPluginManager(self: SessionLoaderModel) { let afterInitializedCb = () => {} - // in order: saves the previous autosave for recovery, tries to - // load the local session if session in query, or loads the default - // session + // in order: saves the previous autosave for recovery, tries to load the + // local session if session in query, or loads the default session try { if (self.sessionError) { - rootModel.setDefaultSession() - rootModel.session.notify( - `Error loading session: ${self.sessionError}. If you received this URL from another user, request that they send you a session generated with the "Share" button instead of copying and pasting their URL`, - ) + throw self.sessionError } else if (self.sessionSnapshot) { rootModel.setSession(self.sessionSnapshot) } else if (self.sessionSpec) { @@ -72,15 +68,13 @@ export function createPluginManager(self: SessionLoaderModel) { } catch (e) { rootModel.setDefaultSession() const str = `${e}` - const errorMessage = str - .replace('[mobx-state-tree] ', '') - .replace(/\(.+/, '') - rootModel.session?.notify( - `Session could not be loaded. ${ - errorMessage.length > 1000 - ? `${errorMessage.slice(0, 1000)}...see more in console` - : errorMessage - }`, + const m = str.replace('[mobx-state-tree] ', '').replace(/\(.+/, '') + const r = m.length > 1000 ? `${m.slice(0, 1000)}...see more in console` : m + const s = r.startsWith('Error:') ? r : `Error: ${r}` + rootModel.session?.notifyError( + `${s}. If you received this URL from another user, request that they send you a session generated with the "Share" button instead of copying and pasting their URL`, + self.sessionError, + self.sessionSnapshot, ) console.error(e) } diff --git a/products/jbrowse-web/src/tests/__image_snapshots__/breakpoint_split_view_snapshot.svg b/products/jbrowse-web/src/tests/__image_snapshots__/breakpoint_split_view_snapshot.svg index c825f7c5b8b..6466ca42d0c 100644 --- a/products/jbrowse-web/src/tests/__image_snapshots__/breakpoint_split_view_snapshot.svg +++ b/products/jbrowse-web/src/tests/__image_snapshots__/breakpoint_split_view_snapshot.svg @@ -1 +1 @@ -hg19chr3186,698,000186,700,000chr3186,702,000186,704,0000077HG002.hs37d5.11kbpbsv.BND.3:186700648-6:56758392T[6:56758392[pbsv.BND.3:186700648-6:56758392T[6:56758392[HG002.hs37d5.bndshg19chr656,754,00056,756,00056,758,000chr656,758,00056,760,00056,762,0000088HG002.hs37d5.11kbpbsv.BND.6:56758392-3:186700648]3:186700648]Tpbsv.BND.6:56758392-3:186700648]3:186700648]THG002.hs37d5.bnds \ No newline at end of file +hg19chr3186,698,000186,700,000chr3186,702,000186,704,0000077HG002.hs37d5.11kbpbsv.BND.3:186700648-6:56758392T[6:56758392[pbsv.BND.3:186700648-6:56758392T[6:56758392[HG002.hs37d5.bndshg19chr656,754,00056,756,00056,758,000chr656,758,00056,760,00056,762,0000088HG002.hs37d5.11kbpbsv.BND.6:56758392-3:186700648]3:186700648]Tpbsv.BND.6:56758392-3:186700648]3:186700648]THG002.hs37d5.bnds \ No newline at end of file diff --git a/products/jbrowse-web/src/tests/__snapshots__/BreakpointSplitView.test.tsx.snap b/products/jbrowse-web/src/tests/__snapshots__/BreakpointSplitView.test.tsx.snap index ca234a5f218..db7c352ce4b 100644 --- a/products/jbrowse-web/src/tests/__snapshots__/BreakpointSplitView.test.tsx.snap +++ b/products/jbrowse-web/src/tests/__snapshots__/BreakpointSplitView.test.tsx.snap @@ -4,16 +4,17 @@ exports[`breakpoint split view 1`] = ` diff --git a/products/jbrowse-web/src/tests/__snapshots__/ExportSvgBreakpointSplitView.test.tsx.snap b/products/jbrowse-web/src/tests/__snapshots__/ExportSvgBreakpointSplitView.test.tsx.snap index b0e858bda72..0d8a41a9c58 100644 --- a/products/jbrowse-web/src/tests/__snapshots__/ExportSvgBreakpointSplitView.test.tsx.snap +++ b/products/jbrowse-web/src/tests/__snapshots__/ExportSvgBreakpointSplitView.test.tsx.snap @@ -1,3 +1,3 @@ // Jest Snapshot v1, https://goo.gl/fbAQLP -exports[`export svg of breakpoint split view 1`] = `"hg19chr3186,698,000186,700,000chr3186,702,000186,704,0000077HG002.hs37d5.11kbpbsv.BND.3:186700648-6:56758392T[6:56758392[pbsv.BND.3:186700648-6:56758392T[6:56758392[HG002.hs37d5.bndshg19chr656,754,00056,756,00056,758,000chr656,758,00056,760,00056,762,0000088HG002.hs37d5.11kbpbsv.BND.6:56758392-3:186700648]3:186700648]Tpbsv.BND.6:56758392-3:186700648]3:186700648]THG002.hs37d5.bnds"`; +exports[`export svg of breakpoint split view 1`] = `"hg19chr3186,698,000186,700,000chr3186,702,000186,704,0000077HG002.hs37d5.11kbpbsv.BND.3:186700648-6:56758392T[6:56758392[pbsv.BND.3:186700648-6:56758392T[6:56758392[HG002.hs37d5.bndshg19chr656,754,00056,756,00056,758,000chr656,758,00056,760,00056,762,0000088HG002.hs37d5.11kbpbsv.BND.6:56758392-3:186700648]3:186700648]Tpbsv.BND.6:56758392-3:186700648]3:186700648]THG002.hs37d5.bnds"`; diff --git a/test_data/volvox/volvox.sort.gff3 b/test_data/volvox/volvox.sort.gff3 index 30f55ef28d2..b28d4b0dc89 100644 --- a/test_data/volvox/volvox.sort.gff3 +++ b/test_data/volvox/volvox.sort.gff3 @@ -2,7 +2,7 @@ # multi-exon gene - several linked CDSs # single exon gene - one CDS only ##gff-version 3 -ctgA example contig 1 50001 . . . Name=ctgA;multivalue=val1,val2,val3 +ctgA example contig 1 50001 . . . Name=ctgA;multivalue=val1,val2,val3;table=%5B%7B%22name%22%3A%22hello1%22%2C%22value%22%3A1%7D%2C%7B%22name%22%3A%22hello2%22%2C%22value%22%3A2%7D%2C%7B%22name%22%3A%22hello3%22%2C%22value%22%3A3%7D%2C%7B%22name%22%3A%22hello4%22%2C%22value%22%3A4%7D%2C%7B%22name%22%3A%22hello5%22%2C%22value%22%3A5%7D%5D ctgA example BAC 1000 20000 . . . ID=b101.2;Name=b101.2;Note=Fingerprinted BAC with end reads ctgA example SNP 1000 1000 0.987 . . ID=FakeSNP1;Name=FakeSNP;Note=This is a fake SNP that should appear at 1000 with length 1 ctgA example clone_start 1000 1500 . + . Parent=b101.2 diff --git a/yarn.lock b/yarn.lock index 759ad142ddf..6e676d024fd 100644 --- a/yarn.lock +++ b/yarn.lock @@ -792,6 +792,17 @@ lodash.debounce "^4.0.8" resolve "^1.14.2" +"@babel/helper-define-polyfill-provider@^0.6.1": + version "0.6.1" + resolved "https://registry.yarnpkg.com/@babel/helper-define-polyfill-provider/-/helper-define-polyfill-provider-0.6.1.tgz#fadc63f0c2ff3c8d02ed905dcea747c5b0fb74fd" + integrity sha512-o7SDgTJuvx5vLKD6SFvkydkSMBvahDKGiNJzG22IZYXhiqoe9efY7zocICBgzHV4IRg5wdgl2nEL/tulKIEIbA== + dependencies: + "@babel/helper-compilation-targets" "^7.22.6" + "@babel/helper-plugin-utils" "^7.22.5" + debug "^4.1.1" + lodash.debounce "^4.0.8" + resolve "^1.14.2" + "@babel/helper-environment-visitor@^7.22.20": version "7.22.20" resolved "https://registry.yarnpkg.com/@babel/helper-environment-visitor/-/helper-environment-visitor-7.22.20.tgz#96159db61d34a29dba454c959f5ae4a649ba9167" @@ -1662,7 +1673,7 @@ "@babel/types" "^7.4.4" esutils "^2.0.2" 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-"@floating-ui/react-dom@^2.0.0", "@floating-ui/react-dom@^2.0.8": +"@floating-ui/react-dom@^2.0.8": version "2.0.8" resolved "https://registry.yarnpkg.com/@floating-ui/react-dom/-/react-dom-2.0.8.tgz#afc24f9756d1b433e1fe0d047c24bd4d9cefaa5d" integrity sha512-HOdqOt3R3OGeTKidaLvJKcgg75S6tibQ3Tif4eyd91QnIJWr0NLvoXFpJA/j8HqkFSL68GDca9AuyWEHlhyClw== @@ -2500,7 +2516,7 @@ jest-haste-map "^29.7.0" slash "^3.0.0" -"@jest/transform@^29.3.1", "@jest/transform@^29.7.0": +"@jest/transform@^29.7.0": version "29.7.0" resolved "https://registry.yarnpkg.com/@jest/transform/-/transform-29.7.0.tgz#df2dd9c346c7d7768b8a06639994640c642e284c" integrity sha512-ok/BTPFzFKVMwO5eOHRrvnBVHdRy9IrsrW1GpMaQ9MCnilNLXQKmAX8s1YXDFaai9xJpac2ySzV0YeRRECr2Vw== @@ -2538,7 +2554,7 @@ resolved "https://registry.yarnpkg.com/@jkbonfield/htscodecs/-/htscodecs-0.5.1.tgz#a8b16be1076883837640234fe4fdd8e0187c094c" integrity sha512-1qNMsatU8i6qOsbtZnZxQwJnCRPMeviRo8+i44hoZ7W5OWUnXSKSx9273aLv9M6DxcuLapIiFvWAaoi5x7Loiw== 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"https://registry.yarnpkg.com/async-retry/-/async-retry-1.3.3.tgz#0e7f36c04d8478e7a58bdbed80cedf977785f280" @@ -6836,7 +6454,7 @@ attr-accept@^2.2.2: resolved "https://registry.yarnpkg.com/attr-accept/-/attr-accept-2.2.2.tgz#646613809660110749e92f2c10833b70968d929b" integrity sha512-7prDjvt9HmqiZ0cl5CRjtS84sEyhsHP2coDkaZKRKVfCDo9s7iw7ChVmar78Gu9pC4SoR/28wFu/G5JJhTnqEg== -available-typed-arrays@^1.0.6, available-typed-arrays@^1.0.7: +available-typed-arrays@^1.0.7: version "1.0.7" resolved "https://registry.yarnpkg.com/available-typed-arrays/-/available-typed-arrays-1.0.7.tgz#a5cc375d6a03c2efc87a553f3e0b1522def14846" integrity sha512-wvUjBtSGN7+7SjNpq/9M2Tg350UZD3q62IFZLbRAR1bSMlCo1ZaeW+BJ+D090e4hIIZLBcTDWe4Mh4jvUDajzQ== @@ -6870,7 +6488,7 @@ babel-jest@^29.7.0: graceful-fs "^4.2.9" slash "^3.0.0" -babel-loader@^9.0.0, babel-loader@^9.1.0: +babel-loader@^9.1.0: version "9.1.3" resolved 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+ "@esbuild/aix-ppc64" "0.20.1" + "@esbuild/android-arm" "0.20.1" + "@esbuild/android-arm64" "0.20.1" + "@esbuild/android-x64" "0.20.1" + "@esbuild/darwin-arm64" "0.20.1" + "@esbuild/darwin-x64" "0.20.1" + "@esbuild/freebsd-arm64" "0.20.1" + "@esbuild/freebsd-x64" "0.20.1" + "@esbuild/linux-arm" "0.20.1" + "@esbuild/linux-arm64" "0.20.1" + "@esbuild/linux-ia32" "0.20.1" + "@esbuild/linux-loong64" "0.20.1" + "@esbuild/linux-mips64el" "0.20.1" + "@esbuild/linux-ppc64" "0.20.1" + "@esbuild/linux-riscv64" "0.20.1" + "@esbuild/linux-s390x" "0.20.1" + "@esbuild/linux-x64" "0.20.1" + "@esbuild/netbsd-x64" "0.20.1" + "@esbuild/openbsd-x64" "0.20.1" + "@esbuild/sunos-x64" "0.20.1" + "@esbuild/win32-arm64" "0.20.1" + "@esbuild/win32-ia32" "0.20.1" + "@esbuild/win32-x64" "0.20.1" escalade@^3.1.1: version "3.1.2" @@ -9850,9 +9449,9 @@ eslint-plugin-react-hooks@^4.3.0: integrity sha512-oFc7Itz9Qxh2x4gNHStv3BqJq54ExXmfC+a1NjAta66IAN87Wu0R/QArgIS9qKzX3dXKPI9H5crl9QchNMY9+g== eslint-plugin-react-refresh@^0.4.3: - version "0.4.5" - resolved "https://registry.yarnpkg.com/eslint-plugin-react-refresh/-/eslint-plugin-react-refresh-0.4.5.tgz#6b9b307bad3feba2244ef64a1a15485ac70a2d0f" - integrity sha512-D53FYKJa+fDmZMtriODxvhwrO+IOqrxoEo21gMA0sjHdU6dPVH4OhyFip9ypl8HOF5RV5KdTo+rBQLvnY2cO8w== + version "0.4.6" + resolved "https://registry.yarnpkg.com/eslint-plugin-react-refresh/-/eslint-plugin-react-refresh-0.4.6.tgz#e8e8accab681861baed00c5c12da70267db0936f" + integrity sha512-NjGXdm7zgcKRkKMua34qVO9doI7VOxZ6ancSvBELJSSoX97jyndXcSoa8XBh69JoB31dNz3EEzlMcizZl7LaMA== eslint-plugin-react@^7.33.2: version "7.34.0" @@ -10154,11 +9753,6 @@ express@^4.17.1, express@^4.17.3, express@^4.18.2: utils-merge "1.0.1" vary "~1.1.2" -extend@^3.0.0: - version "3.0.2" - resolved "https://registry.yarnpkg.com/extend/-/extend-3.0.2.tgz#f8b1136b4071fbd8eb140aff858b1019ec2915fa" - integrity sha512-fjquC59cD7CyW6urNXK0FBufkZcoiGG80wTuPujX590cB5Ttln20E2UB4S/WARVqhXffZl2LNgS+gQdPIIim/g== - external-editor@^3.0.3: version "3.1.0" resolved "https://registry.yarnpkg.com/external-editor/-/external-editor-3.1.0.tgz#cb03f740befae03ea4d283caed2741a83f335495" @@ -10175,16 +9769,6 @@ external-sorting@^1.3.1: dependencies: fast-sort "^2.0.1" -extract-zip@^1.6.6: - version "1.7.0" - resolved "https://registry.yarnpkg.com/extract-zip/-/extract-zip-1.7.0.tgz#556cc3ae9df7f452c493a0cfb51cc30277940927" - integrity sha512-xoh5G1W/PB0/27lXgMQyIhP5DSY/LhoCsOyZgb+6iMmRtCwVBo55uKaMoEYrDCKQhWvqEip5ZPKAc6eFNyf/MA== - dependencies: - concat-stream "^1.6.2" - debug "^2.6.9" - mkdirp "^0.5.4" - yauzl "^2.10.0" - extract-zip@^2.0.1: version "2.0.1" resolved "https://registry.yarnpkg.com/extract-zip/-/extract-zip-2.0.1.tgz#663dca56fe46df890d5f131ef4a06d22bb8ba13a" @@ -10201,10 +9785,10 @@ extsprintf@^1.2.0: resolved "https://registry.yarnpkg.com/extsprintf/-/extsprintf-1.4.1.tgz#8d172c064867f235c0c84a596806d279bf4bcc07" integrity 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get-intrinsic@^1.1.3, get-intrinsic@^1.2.1, get-intrinsic@^1.2.2, get-intrinsic@^1.2.3, get-intrinsic@^1.2.4: +get-intrinsic@^1.1.3, get-intrinsic@^1.2.1, get-intrinsic@^1.2.2, 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== @@ -10751,11 +10335,6 @@ get-intrinsic@^1.1.1, get-intrinsic@^1.1.3, get-intrinsic@^1.2.1, get-intrinsic@ has-symbols "^1.0.3" hasown "^2.0.0" -get-nonce@^1.0.0: - version "1.0.1" - resolved "https://registry.yarnpkg.com/get-nonce/-/get-nonce-1.0.1.tgz#fdf3f0278073820d2ce9426c18f07481b1e0cdf3" - integrity sha512-FJhYRoDaiatfEkUK8HKlicmu/3SGFD51q3itKDGoSTysQJBnfOcxU5GxnhE1E6soB76MbT0MBtnKJuXyAx+96Q== - get-npm-tarball-url@^2.0.3: version "2.1.0" resolved "https://registry.yarnpkg.com/get-npm-tarball-url/-/get-npm-tarball-url-2.1.0.tgz#cbd6bb25884622bc3191c761466c93ac83343213" @@ -10776,7 +10355,7 @@ get-pkg-repo@^4.2.1: through2 "^2.0.0" yargs "^16.2.0" -get-port@5.1.1, get-port@^5.1.1: +get-port@5.1.1: version "5.1.1" resolved "https://registry.yarnpkg.com/get-port/-/get-port-5.1.1.tgz#0469ed07563479de6efb986baf053dcd7d4e3193" integrity sha512-g/Q1aTSDOxFpchXC4i8ZWvxA1lnPqx/JHqcpIw0/LX9T8x/GBbi6YnlN5nhaKIFkT8oFsscUKgDJYxfwfS6QsQ== @@ -10913,11 +10492,16 @@ gitconfiglocal@^1.0.0: dependencies: ini "^1.3.2" -github-slugger@^1.0.0, github-slugger@^1.5.0: +github-slugger@^1.5.0: version "1.5.0" resolved "https://registry.yarnpkg.com/github-slugger/-/github-slugger-1.5.0.tgz#17891bbc73232051474d68bd867a34625c955f7d" integrity sha512-wIh+gKBI9Nshz2o46B0B3f5k/W+WI9ZAv6y5Dn5WJ5SK1t0TnDimB4WE5rmTD05ZAIn8HALCZVmCsvj0w0v0lw== +github-slugger@^2.0.0: + version "2.0.0" + resolved 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dependencies: - loose-envify "^1.0.0" - ip-address@^9.0.5: version "9.0.5" resolved "https://registry.yarnpkg.com/ip-address/-/ip-address-9.0.5.tgz#117a960819b08780c3bd1f14ef3c1cc1d3f3ea5a" @@ -11735,10 +11325,10 @@ ipaddr.js@^2.1.0: resolved "https://registry.yarnpkg.com/ipaddr.js/-/ipaddr.js-2.1.0.tgz#2119bc447ff8c257753b196fc5f1ce08a4cdf39f" integrity sha512-LlbxQ7xKzfBusov6UMi4MFpEg0m+mAm9xyNGEduwXMEDuf4WfzB/RZwMVYEd7IKGvh4IUkEXYxtAVu9T3OelJQ== -is-absolute-url@^3.0.0: - version "3.0.3" - resolved "https://registry.yarnpkg.com/is-absolute-url/-/is-absolute-url-3.0.3.tgz#96c6a22b6a23929b11ea0afb1836c36ad4a5d698" - integrity sha512-opmNIX7uFnS96NtPmhWQgQx6/NYFgsUXYMllcfzwWKUMwfo8kku1TvE6hkNcH+Q1ts5cMVrsY7j0bxXQDciu9Q== +is-absolute-url@^4.0.0: + version "4.0.1" + resolved "https://registry.yarnpkg.com/is-absolute-url/-/is-absolute-url-4.0.1.tgz#16e4d487d4fded05cfe0685e53ec86804a5e94dc" + integrity 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+ version "4.0.6" + resolved "https://registry.yarnpkg.com/mobx-react-lite/-/mobx-react-lite-4.0.6.tgz#a7f128914e3d67dac80819068b749ffdd4a18705" + integrity sha512-0rOE0KDMwV9CzsstYC86ZxxrUpKLGBN0/T3WpKZibLnJcukdb9HVL8VKHoDxaBPbInLZ5azPKUod4mXTsi+u+A== dependencies: use-sync-external-store "^1.2.0" @@ -14527,12 +14105,12 @@ nwsapi@^2.2.2, nwsapi@^2.2.7: resolved "https://registry.yarnpkg.com/nwsapi/-/nwsapi-2.2.7.tgz#738e0707d3128cb750dddcfe90e4610482df0f30" integrity sha512-ub5E4+FBPKwAZx0UwIQOjYWGHTEq5sPqHQNRN8Z9e4A7u3Tj1weLJsL59yH9vmvqEtBHaOmT6cYQKIZOxp35FQ== -nx@18.0.7, "nx@>=17.1.2 < 19": - version "18.0.7" - resolved "https://registry.yarnpkg.com/nx/-/nx-18.0.7.tgz#4451f810743f68108912c1a062d968b60e05d492" - integrity sha512-jcJ7ohP/rgqI9X6FJ8WnsPHpzm99oBV9qmaUeOUHWsdjp8r+2ptSHDmMmA67BPT+J6T+/ILhVlgzboXV1W7Ccg== +nx@18.0.8, "nx@>=17.1.2 < 19": + version "18.0.8" + resolved "https://registry.yarnpkg.com/nx/-/nx-18.0.8.tgz#5d0ac8b53663cc53045c63005ff3fc7592a0bc5d" + integrity 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"@nx/nx-win32-arm64-msvc" "18.0.8" + "@nx/nx-win32-x64-msvc" "18.0.8" nypm@^0.3.3: version "0.3.8" @@ -14673,15 +14251,15 @@ obuf@^1.0.0, obuf@^1.1.2: integrity sha512-PX1wu0AmAdPqOL1mWhqmlOd8kOIZQwGZw6rh7uby9fTc5lhaOWFLX3I6R1hrF9k3zUY40e6igsLGkDXK92LJNg== oclif@^4.0.0: - version "4.5.2" - resolved "https://registry.yarnpkg.com/oclif/-/oclif-4.5.2.tgz#b90f9bb624fccb73e57dd733e3a5146f3eeb7599" - integrity sha512-9xUwaaNvdrN1tSx/jxKD1tsu/sR3ZHFv1f72S8GAZ01xmp5EGyRw97xUT64TFLPQLp/6h3zXm3VUwhZyCv9bkw== + version "4.5.4" + resolved "https://registry.yarnpkg.com/oclif/-/oclif-4.5.4.tgz#8b874dd3bbab1a16a4a72a1e7e3babd34c3614c4" + integrity sha512-3WVlr9FtTXiS5+kBmMdENvWwSHzhrfEpML6HgXDvyEYub3YeapbE60/sCvvNmgBDZ8vYnbOTf3RgqBt1oFo05Q== dependencies: "@aws-sdk/client-cloudfront" "^3.525.0" "@aws-sdk/client-s3" "^3.515.0" "@oclif/core" "^3.21.0" "@oclif/plugin-help" "^6.0.14" - "@oclif/plugin-not-found" "^3.0.10" + "@oclif/plugin-not-found" "^3.0.14" "@oclif/plugin-warn-if-update-available" "^3.0.12" async-retry "^1.3.3" change-case "^4" @@ -14737,9 +14315,9 @@ onetime@^6.0.0: mimic-fn "^4.0.0" open@^10.0.3: - version "10.0.4" - resolved "https://registry.yarnpkg.com/open/-/open-10.0.4.tgz#4869d009dc5b706ae6585699e15d8ccc6cb73629" - integrity sha512-oujJ/FFr7ra6/7gJuQ4ZJJ8Gf2VHM0J3J/W7IvH++zaqEzacWVxzK++NiVY5NLHTTj7u/jNH5H3Ei9biL31Lng== + version "10.1.0" + resolved "https://registry.yarnpkg.com/open/-/open-10.1.0.tgz#a7795e6e5d519abe4286d9937bb24b51122598e1" + integrity sha512-mnkeQ1qP5Ue2wd+aivTD3NHd/lZ96Lu0jgf0pwktLPtx6cTZiH7tyeGRRHs0zX0rbrahXPnXlUnbeXyaBBuIaw== dependencies: default-browser "^5.2.1" define-lazy-prop "^3.0.0" @@ -15638,9 +15216,9 @@ postcss-reduce-transforms@^6.0.2: postcss-value-parser "^4.2.0" postcss-selector-parser@^6.0.11, postcss-selector-parser@^6.0.15, postcss-selector-parser@^6.0.2, postcss-selector-parser@^6.0.4: - version "6.0.15" - resolved 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"https://registry.yarnpkg.com/prettier/-/prettier-3.2.5.tgz#e52bc3090586e824964a8813b09aba6233b28368" integrity sha512-3/GWa9aOC0YeD7LUfvOG2NiDyhOWRvt1k+rcKhOuYnMY24iiCphgneUfJDyFXd6rZCAnuLBv6UeAULtrhT/F4A== @@ -15762,7 +15335,7 @@ process@^0.11.10: resolved "https://registry.yarnpkg.com/process/-/process-0.11.10.tgz#7332300e840161bda3e69a1d1d91a7d4bc16f182" integrity sha512-cdGef/drWFoydD1JsMzuFf8100nZl+GT+yacc2bEced5f9Rjk4z+WtFUTBu9PhOi9j/jfmBPu0mMEY4wIdAF8A== -progress@^2.0.0, progress@^2.0.1, progress@^2.0.3: +progress@^2.0.0, progress@^2.0.3: version "2.0.3" resolved "https://registry.yarnpkg.com/progress/-/progress-2.0.3.tgz#7e8cf8d8f5b8f239c1bc68beb4eb78567d572ef8" integrity sha512-7PiHtLll5LdnKIMw100I+8xJXR5gW2QwWYkT6iJva0bXitZKa/XMrSbdmg3r2Xnaidz9Qumd0VPaMrZlF9V9sA== @@ -15851,7 +15424,7 @@ proxy-agent@^6.2.1: proxy-from-env "^1.1.0" socks-proxy-agent "^8.0.2" -proxy-from-env@^1.0.0, proxy-from-env@^1.1.0: +proxy-from-env@^1.1.0: version "1.1.0" resolved "https://registry.yarnpkg.com/proxy-from-env/-/proxy-from-env-1.1.0.tgz#e102f16ca355424865755d2c9e8ea4f24d58c3e2" integrity sha512-D+zkORCbA9f1tdWRK0RaCR3GPv50cMxcrz4X8k5LTSUD1Dkw47mKJEZQNunItRTkWwgtaUSo1RVFRIG9ZXiFYg== @@ -15908,22 +15481,6 @@ punycode@^2.1.0, punycode@^2.1.1, punycode@^2.3.0, punycode@^2.3.1: resolved "https://registry.yarnpkg.com/punycode/-/punycode-2.3.1.tgz#027422e2faec0b25e1549c3e1bd8309b9133b6e5" integrity sha512-vYt7UD1U9Wg6138shLtLOvdAu+8DsC/ilFtEVHcH+wydcSpNE20AfSOduf6MkRFahL5FY7X1oU7nKVZFtfq8Fg== -puppeteer-core@^2.1.1: - version "2.1.1" - resolved "https://registry.yarnpkg.com/puppeteer-core/-/puppeteer-core-2.1.1.tgz#e9b3fbc1237b4f66e25999832229e9db3e0b90ed" - integrity sha512-n13AWriBMPYxnpbb6bnaY5YoY6rGj8vPLrz6CZF3o0qJNEwlcfJVxBzYZ0NJsQ21UbdJoijPCDrM++SUVEz7+w== - dependencies: - "@types/mime-types" "^2.1.0" - debug "^4.1.0" - extract-zip "^1.6.6" - https-proxy-agent "^4.0.0" - mime "^2.0.3" - mime-types "^2.1.25" - progress "^2.0.1" - proxy-from-env "^1.0.0" - rimraf "^2.6.1" - ws "^6.1.0" - pure-rand@^6.0.0: version "6.0.4" resolved "https://registry.yarnpkg.com/pure-rand/-/pure-rand-6.0.4.tgz#50b737f6a925468679bff00ad20eade53f37d5c7" @@ -16076,7 +15633,7 @@ react-docgen@^7.0.0: resolve "^1.22.1" strip-indent "^4.0.0" -react-dom@^18.0.0: +"react-dom@^16.8.0 || ^17.0.0 || ^18.0.0", react-dom@^18.0.0: version "18.2.0" resolved "https://registry.yarnpkg.com/react-dom/-/react-dom-18.2.0.tgz#22aaf38708db2674ed9ada224ca4aa708d821e3d" integrity sha512-6IMTriUmvsjHUjNtEDudZfuDQUoWXVxKHhlEGSk81n4YFS+r/Kl99wXiwlVXtPBtJenozv2P+hxDsw9eA7Xo6g== @@ -16152,34 +15709,6 @@ react-refresh@^0.14.0: resolved "https://registry.yarnpkg.com/react-refresh/-/react-refresh-0.14.0.tgz#4e02825378a5f227079554d4284889354e5f553e" integrity sha512-wViHqhAd8OHeLS/IRMJjTSDHF3U9eWi62F/MledQGPdJGDhodXJ9PBLNGr6WWL7qlH12Mt3TyTpbS+hGXMjCzQ== -react-remove-scroll-bar@^2.3.3: - version "2.3.5" - resolved 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readable-stream@~2.3.6: +readable-stream@^2.0.0, readable-stream@^2.0.1, readable-stream@^2.0.2, readable-stream@^2.3.0, readable-stream@^2.3.5, readable-stream@^2.3.8, readable-stream@~2.3.6: version "2.3.8" resolved "https://registry.yarnpkg.com/readable-stream/-/readable-stream-2.3.8.tgz#91125e8042bba1b9887f49345f6277027ce8be9b" integrity sha512-8p0AUk4XODgIewSi0l8Epjs+EVnWiK7NoDIEGU0HhE7+ZyY8D1IMY7odu5lRrFXGg71L15KG8QrPmum45RTtdA== @@ -16369,10 +15898,10 @@ readdirp@~3.6.0: dependencies: picomatch "^2.2.1" -recast@^0.23.1, recast@^0.23.3: - version "0.23.5" - resolved "https://registry.yarnpkg.com/recast/-/recast-0.23.5.tgz#07f5594a0d36e7754356160b70e90393cca0406d" - integrity sha512-M67zIddJiwXdfPQRYKJ0qZO1SLdH1I0hYeb0wzxA+pNOvAZiQHulWzuk+fYsEWRQ8VfZrgjyucqsCOtCyM01/A== +recast@^0.23.3, recast@^0.23.5: + version "0.23.6" + resolved "https://registry.yarnpkg.com/recast/-/recast-0.23.6.tgz#198fba74f66143a30acc81929302d214ce4e3bfa" + integrity 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version "1.3.0" + resolved "https://registry.yarnpkg.com/ts-api-utils/-/ts-api-utils-1.3.0.tgz#4b490e27129f1e8e686b45cc4ab63714dc60eea1" + integrity sha512-UQMIo7pb8WRomKR1/+MFVLTroIvDVtMX3K6OUir8ynLyzB8Jeriont2bTAtmNPa1ekAgN7YPDyf6V+ygrdU+eQ== ts-dedent@^2.0.0: version "2.2.0" @@ -18137,7 +17673,7 @@ ts-node@^10.4.0: v8-compile-cache-lib "^3.0.1" yn "3.1.1" -tsconfig-paths@^4.1.2: +tsconfig-paths@^4.1.2, tsconfig-paths@^4.2.0: version "4.2.0" resolved "https://registry.yarnpkg.com/tsconfig-paths/-/tsconfig-paths-4.2.0.tgz#ef78e19039133446d244beac0fd6a1632e2d107c" integrity sha512-NoZ4roiN7LnbKn9QqE1amc9DJfzvZXxF4xDavcOWt1BPkdx+m+0gJuPM+S0vCe7zTJMYUP0R8pO2XMr+Y8oLIg== @@ -18253,9 +17789,9 @@ type-fest@^2.19.0, type-fest@~2.19: integrity sha512-RAH822pAdBgcNMAfWnCBU3CFZcfZ/i1eZjwFU/dsLKumyuuP3niueg2UAukXYF0E2AAoc82ZSSf9J0WQBinzHA== type-fest@^4.4.0: - version "4.11.1" - resolved "https://registry.yarnpkg.com/type-fest/-/type-fest-4.11.1.tgz#7de27117459b926cb56922a4fd565423041e06d3" - 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"https://registry.yarnpkg.com/use-query-params/-/use-query-params-2.2.1.tgz#c558ab70706f319112fbccabf6867b9f904e947d" @@ -18550,21 +18081,6 @@ use-query-params@^2.0.0: dependencies: serialize-query-params "^2.0.2" -use-resize-observer@^9.1.0: - version "9.1.0" - resolved "https://registry.yarnpkg.com/use-resize-observer/-/use-resize-observer-9.1.0.tgz#14735235cf3268569c1ea468f8a90c5789fc5c6c" - integrity sha512-R25VqO9Wb3asSD4eqtcxk8sJalvIOYBqS8MNZlpDSQ4l4xMQxC/J7Id9HoTqPq8FwULIn0PVW+OAqF2dyYbjow== - dependencies: - "@juggle/resize-observer" "^3.3.1" - -use-sidecar@^1.1.2: - version "1.1.2" - resolved "https://registry.yarnpkg.com/use-sidecar/-/use-sidecar-1.1.2.tgz#2f43126ba2d7d7e117aa5855e5d8f0276dfe73c2" - integrity sha512-epTbsLuzZ7lPClpz2TyryBfztm7m+28DlEv2ZCQ3MDr5ssiwyOwGH/e5F9CkfWjJ1t4clvI58yF822/GUkjjhw== - dependencies: - detect-node-es "^1.1.0" - tslib "^2.0.0" - use-sync-external-store@^1.2.0: version "1.2.0" resolved "https://registry.yarnpkg.com/use-sync-external-store/-/use-sync-external-store-1.2.0.tgz#7dbefd6ef3fe4e767a0cf5d7287aacfb5846928a" @@ -18716,9 +18232,9 @@ walker@^1.0.8: makeerror "1.0.12" watchpack@^2.2.0, watchpack@^2.4.0: - version "2.4.0" - resolved "https://registry.yarnpkg.com/watchpack/-/watchpack-2.4.0.tgz#fa33032374962c78113f93c7f2fb4c54c9862a5d" - integrity sha512-Lcvm7MGST/4fup+ifyKi2hjyIAwcdI4HRgtvTpIUxBRhB+RFtUh8XtDOxUfctVCnhVi+QQj49i91OyvzkJl6cg== + version "2.4.1" + resolved "https://registry.yarnpkg.com/watchpack/-/watchpack-2.4.1.tgz#29308f2cac150fa8e4c92f90e0ec954a9fed7fff" + integrity sha512-8wrBCMtVhqcXP2Sup1ctSkga6uc2Bx0IIvKyT7yTFier5AXHooSI+QyQQAtTb7+E0IUCCKyTFmXqdqgum2XWGg== dependencies: glob-to-regexp "^0.4.1" graceful-fs "^4.1.2" @@ -18798,9 +18314,9 @@ webpack-dev-middleware@^7.0.0: schema-utils "^4.0.0" webpack-dev-server@^5.0.0: - version "5.0.2" - resolved 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"https://registry.yarnpkg.com/which-collection/-/which-collection-1.0.2.tgz#627ef76243920a107e7ce8e96191debe4b16c2a0" + integrity sha512-K4jVyjnBdgvc86Y6BkaLZEN933SwYOuBFkdmBu9ZfkcAbdVbpITnDmjvZ/aQjRXQrv5EPkTnD1s39GiiqbngCw== dependencies: - is-map "^2.0.1" - is-set "^2.0.1" - is-weakmap "^2.0.1" - is-weakset "^2.0.1" + is-map "^2.0.3" + is-set "^2.0.3" + is-weakmap "^2.0.2" + is-weakset "^2.0.3" which-pm@2.0.0: version "2.0.0" @@ -19022,15 +18538,15 @@ which-pm@2.0.0: path-exists "^4.0.0" which-typed-array@^1.1.13, which-typed-array@^1.1.14, which-typed-array@^1.1.2, which-typed-array@^1.1.9: - version "1.1.14" - resolved "https://registry.yarnpkg.com/which-typed-array/-/which-typed-array-1.1.14.tgz#1f78a111aee1e131ca66164d8bdc3ab062c95a06" - integrity sha512-VnXFiIW8yNn9kIHN88xvZ4yOWchftKDsRJ8fEPacX/wl1lOvBrhsJ/OeJCXq7B0AaijRuqgzSKalJoPk+D8MPg== + version "1.1.15" + resolved "https://registry.yarnpkg.com/which-typed-array/-/which-typed-array-1.1.15.tgz#264859e9b11a649b388bfaaf4f767df1f779b38d" + integrity sha512-oV0jmFtUky6CXfkqehVvBP/LSWJ2sy4vWMioiENyJLePrBO/yKyV9OyJySfAKosh+RYkIl5zJCNZ8/4JncrpdA== dependencies: - available-typed-arrays "^1.0.6" - call-bind "^1.0.5" + available-typed-arrays "^1.0.7" + call-bind "^1.0.7" for-each "^0.3.3" gopd "^1.0.1" - has-tostringtag "^1.0.1" + has-tostringtag "^1.0.2" which@^1.2.9, which@^1.3.1: version "1.3.1" @@ -19084,7 +18600,7 @@ wordwrap@^1.0.0: resolved "https://registry.yarnpkg.com/wordwrap/-/wordwrap-1.0.0.tgz#27584810891456a4171c8d0226441ade90cbcaeb" integrity sha512-gvVzJFlPycKc5dZN4yPkP8w7Dc37BtP1yczEneOb4uq34pXZcvrtRTmWV8W+Ume+XCxKgbjM+nevkyFPMybd4Q== -"wrap-ansi-cjs@npm:wrap-ansi@^7.0.0", wrap-ansi@^7.0.0: +"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== @@ -19102,6 +18618,15 @@ wrap-ansi@^6.0.1: string-width "^4.1.0" strip-ansi "^6.0.0" +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@^8.1.0: version "8.1.0" resolved "https://registry.yarnpkg.com/wrap-ansi/-/wrap-ansi-8.1.0.tgz#56dc22368ee570face1b49819975d9b9a5ead214" @@ -19162,13 +18687,6 @@ write-pkg@4.0.0: type-fest "^0.4.1" write-json-file "^3.2.0" -ws@^6.1.0: - version "6.2.2" - resolved "https://registry.yarnpkg.com/ws/-/ws-6.2.2.tgz#dd5cdbd57a9979916097652d78f1cc5faea0c32e" - integrity sha512-zmhltoSR8u1cnDsD43TX59mzoMZsLKqUweyYBAIvTngR3shc0W6aOZylZmq/7hqyVxPdi+5Ud2QInblgyE72fw== - dependencies: - async-limiter "~1.0.0" - ws@^8.11.0, ws@^8.16.0, ws@^8.2.3: version "8.16.0" resolved "https://registry.yarnpkg.com/ws/-/ws-8.16.0.tgz#d1cd774f36fbc07165066a60e40323eab6446fd4"