From 7db8acc66d9f25caac8a2308f2bc8b9fb9e34afe Mon Sep 17 00:00:00 2001 From: Colin Date: Mon, 28 Oct 2024 09:38:01 -0400 Subject: [PATCH] Misc Misc Refactor base feature widget M2 Worked Misc Allow changing default resolution and normalization in hic --- packages/app-core/src/ui/App/ViewMenu.tsx | 36 +- .../BaseFeatureDetail/BaseCard.tsx | 41 + .../BaseFeatureDetail/CoreDetails.tsx | 53 + .../BaseFeatureDetail/FeatureDetails.tsx | 111 + .../BaseFeatureDetail/Position.tsx | 16 + .../BaseFeatureDetail/index.tsx | 241 +- .../BaseFeatureWidget/stateModelFactory.ts | 8 +- packages/core/BaseFeatureWidget/util.tsx | 4 + packages/core/ReExports/Attributes.tsx | 3 - packages/core/ReExports/BaseCard.tsx | 3 - packages/core/ReExports/FeatureDetails.tsx | 3 - packages/core/ReExports/modules.tsx | 12 +- .../src/ui/AboutDialogContents.tsx | 8 +- .../product-core/src/ui/FileInfoPanel.tsx | 6 +- .../AlignmentsFeatureDetail.tsx | 2 +- .../src/AlignmentsFeatureDetail/Flags.tsx | 2 +- .../LinkedPairedAlignments.tsx | 2 +- .../SupplementaryAlignments.tsx | 2 +- plugins/linear-comparative-view/package.json | 4 +- .../components/LaunchSyntenyViewDialog.tsx | 6 +- .../src/LGVSyntenyDisplay/components/util.ts | 32 +- .../src/LGVSyntenyDisplay/model.ts | 36 +- .../stateModelFactory.ts | 23 +- .../src/LinearSyntenyDisplay/afterAttach.ts | 3 +- .../components/LinearSyntenyRendering.tsx | 8 +- .../components/SyntenyContextMenu.tsx | 5 +- .../LinearSyntenyDisplay/components/util.ts | 28 +- .../src/LinearSyntenyDisplay/drawSynteny.ts | 8 +- .../src/LinearSyntenyDisplay/model.ts | 65 +- .../SyntenyFeatureDetail.tsx | 126 + .../src/SyntenyFeatureDetail/index.ts | 37 + .../src/{index.tsx => index.ts} | 2 + .../components/Rubberband.tsx | 5 +- .../components/TrackLabel.tsx | 36 +- .../components/TracksContainer.tsx | 11 +- .../src/LinearGenomeView/components/hooks.ts | 303 --- .../components/useRangeSelect.ts | 160 ++ .../components/useSideScroll.ts | 77 + .../components/useWheelScroll.ts | 70 + .../LaunchBreakendPanel.tsx | 2 +- .../VariantAnnotationTable.tsx | 2 +- .../VariantFeatureWidget.tsx | 2 +- .../VariantSampleGrid.tsx | 4 +- yarn.lock | 2073 +++++++++-------- 44 files changed, 2009 insertions(+), 1672 deletions(-) create mode 100644 packages/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard.tsx create mode 100644 packages/core/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.tsx create mode 100644 packages/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.tsx create mode 100644 packages/core/BaseFeatureWidget/BaseFeatureDetail/Position.tsx delete mode 100644 packages/core/ReExports/Attributes.tsx delete mode 100644 packages/core/ReExports/BaseCard.tsx delete mode 100644 packages/core/ReExports/FeatureDetails.tsx create mode 100644 plugins/linear-comparative-view/src/SyntenyFeatureDetail/SyntenyFeatureDetail.tsx create mode 100644 plugins/linear-comparative-view/src/SyntenyFeatureDetail/index.ts rename plugins/linear-comparative-view/src/{index.tsx => index.ts} (94%) delete mode 100644 plugins/linear-genome-view/src/LinearGenomeView/components/hooks.ts create mode 100644 plugins/linear-genome-view/src/LinearGenomeView/components/useRangeSelect.ts create mode 100644 plugins/linear-genome-view/src/LinearGenomeView/components/useSideScroll.ts create mode 100644 plugins/linear-genome-view/src/LinearGenomeView/components/useWheelScroll.ts diff --git a/packages/app-core/src/ui/App/ViewMenu.tsx b/packages/app-core/src/ui/App/ViewMenu.tsx index 77c71d8349..500be928e7 100644 --- a/packages/app-core/src/ui/App/ViewMenu.tsx +++ b/packages/app-core/src/ui/App/ViewMenu.tsx @@ -69,13 +69,17 @@ const ViewMenu = observer(function ({ label: 'View order', type: 'subMenu' as const, subMenu: [ - { - label: 'Move view to top', - icon: KeyboardDoubleArrowUpIcon, - onClick: () => { - session.moveViewToTop(model.id) - }, - }, + ...(session.views.length > 2 + ? [ + { + label: 'Move view to top', + icon: KeyboardDoubleArrowUpIcon, + onClick: () => { + session.moveViewToTop(model.id) + }, + }, + ] + : []), { label: 'Move view up', icon: KeyboardArrowUpIcon, @@ -90,13 +94,17 @@ const ViewMenu = observer(function ({ session.moveViewDown(model.id) }, }, - { - label: 'Move view to bottom', - icon: KeyboardDoubleArrowDownIcon, - onClick: () => { - session.moveViewToBottom(model.id) - }, - }, + ...(session.views.length > 2 + ? [ + { + label: 'Move view to bottom', + icon: KeyboardDoubleArrowDownIcon, + onClick: () => { + session.moveViewToBottom(model.id) + }, + }, + ] + : []), ], }, ] diff --git a/packages/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard.tsx b/packages/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard.tsx new file mode 100644 index 0000000000..52017c713e --- /dev/null +++ b/packages/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard.tsx @@ -0,0 +1,41 @@ +import React from 'react' +import { + Accordion, + AccordionDetails, + AccordionSummary, + Typography, +} from '@mui/material' +import { makeStyles } from 'tss-react/mui' + +// icons +import ExpandMore from '@mui/icons-material/ExpandMore' + +import { BaseCardProps } from '../types' + +const useStyles = makeStyles()(theme => ({ + expansionPanelDetails: { + display: 'block', + padding: theme.spacing(1), + }, + icon: { + color: theme.palette.tertiary.contrastText || '#fff', + }, +})) + +export default function BaseCard({ + children, + title, + defaultExpanded = true, +}: BaseCardProps) { + const { classes } = useStyles() + return ( + + }> + {title} + + + {children} + + + ) +} diff --git a/packages/core/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.tsx b/packages/core/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.tsx new file mode 100644 index 0000000000..86feba2bac --- /dev/null +++ b/packages/core/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.tsx @@ -0,0 +1,53 @@ +import React from 'react' +// locals +import { toLocale, SimpleFeatureSerialized } from '../../util' +import { BaseProps } from '../types' +import SimpleField from './SimpleField' +import Position from './Position' + +export default function CoreDetails(props: BaseProps) { + const { feature } = props + const obj = feature as SimpleFeatureSerialized & { + start: number + end: number + assemblyName?: string + strand: number + refName: string + __jbrowsefmt: { + start?: number + assemblyName?: string + end?: number + refName?: string + name?: string + } + } + + const formattedFeat = { ...obj, ...obj.__jbrowsefmt } + const { start, end } = formattedFeat + + const displayedDetails: Record = { + ...formattedFeat, + length: toLocale(end - start), + } + + const coreRenderedDetails = { + description: 'Description', + name: 'Name', + length: 'Length', + type: 'Type', + } + return ( + <> + } + /> + {Object.entries(coreRenderedDetails) + .map(([key, name]) => [name, displayedDetails[key]]) + .filter(([, value]) => value != null) + .map(([name, value]) => ( + + ))} + + ) +} diff --git a/packages/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.tsx b/packages/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.tsx new file mode 100644 index 0000000000..51be58022b --- /dev/null +++ b/packages/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.tsx @@ -0,0 +1,111 @@ +import React from 'react' +import { ErrorBoundary } from '@jbrowse/core/ui/ErrorBoundary' +import { Divider, Typography } from '@mui/material' +import { IAnyStateTreeNode } from 'mobx-state-tree' + +// locals +import { getEnv, getSession, SimpleFeatureSerialized } from '../../util' +import { ErrorMessage } from '../../ui' +import { generateTitle } from './util' +import SequenceFeatureDetails from '../SequenceFeatureDetails' +import Attributes from './Attributes' +import BaseCard from './BaseCard' +import CoreDetails from './CoreDetails' + +// coreDetails are omitted in some circumstances +const coreDetails = [ + 'name', + 'start', + 'end', + 'strand', + 'refName', + 'description', + 'type', +] + +interface PanelDescriptor { + name: string + Component: React.FC +} + +export default function FeatureDetails(props: { + model: IAnyStateTreeNode + feature: SimpleFeatureSerialized + depth?: number + omit?: string[] + descriptions?: Record + formatter?: (val: unknown, key: string) => React.ReactNode +}) { + const { omit = [], model, feature, depth = 0 } = props + const { maxDepth } = model + const { mate, name = '', id = '', type = '', subfeatures, uniqueId } = feature + const pm = getEnv(model).pluginManager + const session = getSession(model) + + const ExtraPanel = pm.evaluateExtensionPoint('Core-extraFeaturePanel', null, { + session, + feature, + model, + }) as PanelDescriptor | undefined + const m = mate as { start: number; end: number; refName: string } | undefined + return ( + + Core details + + {m ? ( + <> + + Mate details + + + ) : null} + + + Attributes + + + }> + + + + {ExtraPanel ? ( + <> + + + + + + ) : null} + + {depth < maxDepth && subfeatures?.length ? ( + + {subfeatures.map((sub, idx) => ( + + ))} + + ) : null} + + ) +} diff --git a/packages/core/BaseFeatureWidget/BaseFeatureDetail/Position.tsx b/packages/core/BaseFeatureWidget/BaseFeatureDetail/Position.tsx new file mode 100644 index 0000000000..89292e3499 --- /dev/null +++ b/packages/core/BaseFeatureWidget/BaseFeatureDetail/Position.tsx @@ -0,0 +1,16 @@ +import React from 'react' +import { assembleLocString } from '../../util' +import { BaseProps } from '../types' + +export default function Position(props: BaseProps) { + const { feature } = props + const strand = feature.strand as number + const strandMap: Record = { + '-1': '-', + '0': '', + '1': '+', + } + const str = strandMap[strand] ? `(${strandMap[strand]})` : '' + const loc = assembleLocString(feature) + return <>{`${loc} ${str}`} +} diff --git a/packages/core/BaseFeatureWidget/BaseFeatureDetail/index.tsx b/packages/core/BaseFeatureWidget/BaseFeatureDetail/index.tsx index 2fa77967b0..25007bc4ad 100644 --- a/packages/core/BaseFeatureWidget/BaseFeatureDetail/index.tsx +++ b/packages/core/BaseFeatureWidget/BaseFeatureDetail/index.tsx @@ -1,132 +1,17 @@ import React from 'react' -import { ErrorBoundary } from '@jbrowse/core/ui/ErrorBoundary' -import { - Accordion, - AccordionDetails, - AccordionSummary, - Divider, - Typography, -} from '@mui/material' -import { makeStyles } from 'tss-react/mui' import { observer } from 'mobx-react' -import { IAnyStateTreeNode } from 'mobx-state-tree' -// icons -import ExpandMore from '@mui/icons-material/ExpandMore' - -// locals -import { - getEnv, - getSession, - assembleLocString, - toLocale, - SimpleFeatureSerialized, -} from '../../util' +// utils import { ErrorMessage } from '../../ui' -import SequenceFeatureDetails from '../SequenceFeatureDetails' import { BaseCardProps, BaseProps } from '../types' -import SimpleField from './SimpleField' -import Attributes from './Attributes' -import { generateTitle, isEmpty } from './util' - -// coreDetails are omitted in some circumstances -const coreDetails = [ - 'name', - 'start', - 'end', - 'strand', - 'refName', - 'description', - 'type', -] - -const useStyles = makeStyles()(theme => ({ - expansionPanelDetails: { - display: 'block', - padding: theme.spacing(1), - }, - icon: { - color: theme.palette.tertiary.contrastText || '#fff', - }, -})) - -export function BaseCard({ - children, - title, - defaultExpanded = true, -}: BaseCardProps) { - const { classes } = useStyles() - return ( - - }> - {title} - - - {children} - - - ) -} +import { isEmpty } from './util' +import { replaceUndefinedWithNull } from '../util' -function Position(props: BaseProps) { - const { feature } = props - const strand = feature.strand as number - const strandMap: Record = { - '-1': '-', - '0': '', - '1': '+', - } - const str = strandMap[strand] ? `(${strandMap[strand]})` : '' - const loc = assembleLocString(feature) - return <>{`${loc} ${str}`} -} - -function CoreDetails(props: BaseProps) { - const { feature } = props - const obj = feature as SimpleFeatureSerialized & { - start: number - end: number - assemblyName?: string - strand: number - refName: string - __jbrowsefmt: { - start?: number - assemblyName?: string - end?: number - refName?: string - name?: string - } - } - - const formattedFeat = { ...obj, ...obj.__jbrowsefmt } - const { start, end } = formattedFeat - - const displayedDetails: Record = { - ...formattedFeat, - length: toLocale(end - start), - } - - const coreRenderedDetails = { - description: 'Description', - name: 'Name', - length: 'Length', - type: 'Type', - } - return ( - <> - } - /> - {Object.entries(coreRenderedDetails) - .map(([key, name]) => [name, displayedDetails[key]]) - .filter(([, value]) => value != null) - .map(([name, value]) => ( - - ))} - - ) -} +// locals +import Attributes from './Attributes' +import BaseCard from './BaseCard' +import CoreDetails from './CoreDetails' +import FeatureDetails from './FeatureDetails' export const BaseCoreDetails = (props: BaseProps) => { const { title = 'Primary data' } = props @@ -153,113 +38,23 @@ export interface BaseInputProps extends BaseCardProps { formatter?: (val: unknown, key: string) => React.ReactNode } -interface PanelDescriptor { - name: string - Component: React.FC -} - -export function FeatureDetails(props: { - model: IAnyStateTreeNode - feature: SimpleFeatureSerialized - depth?: number - omit?: string[] - descriptions?: Record - formatter?: (val: unknown, key: string) => React.ReactNode -}) { - const { omit = [], model, feature, depth = 0 } = props - const { maxDepth } = model - const { mate, name = '', id = '', type = '', subfeatures, uniqueId } = feature - const pm = getEnv(model).pluginManager - const session = getSession(model) - - const ExtraPanel = pm.evaluateExtensionPoint('Core-extraFeaturePanel', null, { - session, - feature, - model, - }) as PanelDescriptor | undefined - const m = mate as { start: number; end: number; refName: string } | undefined - return ( - - Core details - - {m ? ( - <> - - Mate details - - - ) : null} - - - Attributes - - - }> - - - - {ExtraPanel ? ( - <> - - - - - - ) : null} - - {depth < maxDepth && subfeatures?.length ? ( - - {subfeatures.map((sub, idx) => ( - - ))} - - ) : null} - - ) -} - const BaseFeatureDetail = observer(function ({ model }: BaseInputProps) { const { error, featureData } = model if (error) { return - } - if (!featureData) { + } else if (!featureData) { return null + } else { + // replacing undefined with null helps with allowing fields to be hidden, + // setting null is not allowed by jexl so we set it to undefined to hide. + // see config guide. this replacement happens both here and when + // snapshotting the featureData + const featureData2 = replaceUndefinedWithNull(featureData) + return isEmpty(featureData2) ? null : ( + + ) } - - // replacing undefined with null helps with allowing fields to be hidden, - // setting null is not allowed by jexl so we set it to undefined to hide. see - // config guide. this replacement happens both here and when snapshotting the - // featureData - const g = JSON.parse( - JSON.stringify(featureData, (_, v) => (v === undefined ? null : v)), - ) - return isEmpty(g) ? null : }) export default BaseFeatureDetail - -export { default as Attributes } from './Attributes' diff --git a/packages/core/BaseFeatureWidget/stateModelFactory.ts b/packages/core/BaseFeatureWidget/stateModelFactory.ts index 59c1c96d4b..9e5d8f314e 100644 --- a/packages/core/BaseFeatureWidget/stateModelFactory.ts +++ b/packages/core/BaseFeatureWidget/stateModelFactory.ts @@ -8,6 +8,7 @@ import { getConf } from '../configuration' import { getSession } from '../util' import { ElementId } from '../util/types/mst' import { SequenceFeatureDetailsF } from './SequenceFeatureDetails/model' +import { replaceUndefinedWithNull } from './util' interface Feat { subfeatures?: Record[] @@ -90,6 +91,9 @@ export function stateModelFactory(pluginManager: PluginManager) { sequenceFeatureDetails: types.optional(SequenceFeatureDetailsF(), {}), }) .volatile(() => ({ + /** + * #volatile + */ error: undefined as unknown, })) @@ -197,9 +201,7 @@ export function stateModelFactory(pluginManager: PluginManager) { // hidden, setting null is not allowed by jexl so we set it to // undefined to hide. see config guide. this replacement happens both // here and when displaying the featureData in base feature widget - finalizedFeatureData: JSON.parse( - JSON.stringify(featureData, (_, v) => (v === undefined ? null : v)), - ), + finalizedFeatureData: replaceUndefinedWithNull(featureData), ...rest, } }) diff --git a/packages/core/BaseFeatureWidget/util.tsx b/packages/core/BaseFeatureWidget/util.tsx index 5f20659e54..fe93484fd5 100644 --- a/packages/core/BaseFeatureWidget/util.tsx +++ b/packages/core/BaseFeatureWidget/util.tsx @@ -104,3 +104,7 @@ export function calculateUTRs2(cds: Feat[], parentFeat: Feat) { export function ellipses(slug: string) { return slug.length > 20 ? `${slug.slice(0, 20)}...` : slug } + +export function replaceUndefinedWithNull(obj: Record) { + return JSON.parse(JSON.stringify(obj, (_, v) => (v === undefined ? null : v))) +} diff --git a/packages/core/ReExports/Attributes.tsx b/packages/core/ReExports/Attributes.tsx deleted file mode 100644 index 7e03f6ae7a..0000000000 --- a/packages/core/ReExports/Attributes.tsx +++ /dev/null @@ -1,3 +0,0 @@ -// convert named export to default for lazy react - -export { Attributes as default } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail' diff --git a/packages/core/ReExports/BaseCard.tsx b/packages/core/ReExports/BaseCard.tsx deleted file mode 100644 index 44fea328b3..0000000000 --- a/packages/core/ReExports/BaseCard.tsx +++ /dev/null @@ -1,3 +0,0 @@ -// convert named export to default for lazy react - -export { BaseCard as default } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail' diff --git a/packages/core/ReExports/FeatureDetails.tsx b/packages/core/ReExports/FeatureDetails.tsx deleted file mode 100644 index 1fbdcf295d..0000000000 --- a/packages/core/ReExports/FeatureDetails.tsx +++ /dev/null @@ -1,3 +0,0 @@ -// convert named export to default for lazy react - -export { FeatureDetails as default } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail' diff --git a/packages/core/ReExports/modules.tsx b/packages/core/ReExports/modules.tsx index 7331e4a4f4..f875f97f84 100644 --- a/packages/core/ReExports/modules.tsx +++ b/packages/core/ReExports/modules.tsx @@ -189,9 +189,15 @@ const MuiPrefixMUI = Object.fromEntries( ]), ) -const Attributes = lazy(() => import('./Attributes')) -const FeatureDetails = lazy(() => import('./FeatureDetails')) -const BaseCard = lazy(() => import('./BaseCard')) +const Attributes = lazy( + () => import('../BaseFeatureWidget/BaseFeatureDetail/Attributes'), +) +const FeatureDetails = lazy( + () => import('../BaseFeatureWidget/BaseFeatureDetail/FeatureDetails'), +) +const BaseCard = lazy( + () => import('../BaseFeatureWidget/BaseFeatureDetail/BaseCard'), +) const DataGridEntries: Record> = { DataGrid: lazy(() => diff --git a/packages/product-core/src/ui/AboutDialogContents.tsx b/packages/product-core/src/ui/AboutDialogContents.tsx index 6596648c04..847701b6be 100644 --- a/packages/product-core/src/ui/AboutDialogContents.tsx +++ b/packages/product-core/src/ui/AboutDialogContents.tsx @@ -10,10 +10,10 @@ import { AnyConfigurationModel, } from '@jbrowse/core/configuration' import { getSession, getEnv } from '@jbrowse/core/util' -import { - BaseCard, - Attributes, -} from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail' +import Attributes from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/Attributes' +import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard' + +// locals import FileInfoPanel from './FileInfoPanel' import RefNameInfoDialog from './RefNameInfoDialog' diff --git a/packages/product-core/src/ui/FileInfoPanel.tsx b/packages/product-core/src/ui/FileInfoPanel.tsx index 365e6ecedd..bc7959fcc4 100644 --- a/packages/product-core/src/ui/FileInfoPanel.tsx +++ b/packages/product-core/src/ui/FileInfoPanel.tsx @@ -4,10 +4,8 @@ import { AnyConfigurationModel, } from '@jbrowse/core/configuration' import { getSession } from '@jbrowse/core/util' -import { - BaseCard, - Attributes, -} from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail' +import Attributes from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/Attributes' +import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard' import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui' type FileInfo = Record | string diff --git a/plugins/alignments/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx b/plugins/alignments/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx index b7150f2f6d..450ac41419 100644 --- a/plugins/alignments/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx +++ b/plugins/alignments/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx @@ -2,7 +2,7 @@ import React, { lazy } from 'react' import { Paper } from '@mui/material' import { observer } from 'mobx-react' import clone from 'clone' -import { FeatureDetails } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail' +import FeatureDetails from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails' // locals import { getTag } from './util' diff --git a/plugins/alignments/src/AlignmentsFeatureDetail/Flags.tsx b/plugins/alignments/src/AlignmentsFeatureDetail/Flags.tsx index e38d572e30..5239368c7a 100644 --- a/plugins/alignments/src/AlignmentsFeatureDetail/Flags.tsx +++ b/plugins/alignments/src/AlignmentsFeatureDetail/Flags.tsx @@ -1,7 +1,7 @@ import React from 'react' import { Checkbox, FormControlLabel, FormGroup } from '@mui/material' import { makeStyles } from 'tss-react/mui' -import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail' +import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard' import SimpleField from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/SimpleField' const useStyles = makeStyles()({ diff --git a/plugins/alignments/src/AlignmentsFeatureDetail/LinkedPairedAlignments.tsx b/plugins/alignments/src/AlignmentsFeatureDetail/LinkedPairedAlignments.tsx index 2afcc7f1c1..1427ca9198 100644 --- a/plugins/alignments/src/AlignmentsFeatureDetail/LinkedPairedAlignments.tsx +++ b/plugins/alignments/src/AlignmentsFeatureDetail/LinkedPairedAlignments.tsx @@ -1,5 +1,5 @@ import React from 'react' -import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail' +import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard' import { SimpleFeatureSerialized, getEnv, getSession } from '@jbrowse/core/util' import { ViewType } from '@jbrowse/core/pluggableElementTypes' diff --git a/plugins/alignments/src/AlignmentsFeatureDetail/SupplementaryAlignments.tsx b/plugins/alignments/src/AlignmentsFeatureDetail/SupplementaryAlignments.tsx index 948a88d726..bbb446f4a5 100644 --- a/plugins/alignments/src/AlignmentsFeatureDetail/SupplementaryAlignments.tsx +++ b/plugins/alignments/src/AlignmentsFeatureDetail/SupplementaryAlignments.tsx @@ -1,7 +1,7 @@ import React from 'react' -import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail' import { SimpleFeatureSerialized, getEnv, getSession } from '@jbrowse/core/util' import { ViewType } from '@jbrowse/core/pluggableElementTypes' +import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard' // locals import { AlignmentFeatureWidgetModel } from './stateModelFactory' diff --git a/plugins/linear-comparative-view/package.json b/plugins/linear-comparative-view/package.json index 95ce1bdec8..0cf9e8aa99 100644 --- a/plugins/linear-comparative-view/package.json +++ b/plugins/linear-comparative-view/package.json @@ -16,8 +16,8 @@ }, "author": "JBrowse Team", "distMain": "dist/index.js", - "srcMain": "src/index.tsx", - "main": "src/index.tsx", + "srcMain": "src/index.ts", + "main": "src/index.ts", "files": [ "dist", "esm" diff --git a/plugins/linear-comparative-view/src/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.tsx b/plugins/linear-comparative-view/src/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.tsx index c99d1878cd..20c8387b0d 100644 --- a/plugins/linear-comparative-view/src/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.tsx +++ b/plugins/linear-comparative-view/src/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.tsx @@ -9,8 +9,9 @@ import { FormControlLabel, TextField, } from '@mui/material' -import { navToSynteny } from './util' import { makeStyles } from 'tss-react/mui' +// locals +import { navToSynteny } from './util' const useStyles = makeStyles()({ padding: { @@ -22,10 +23,12 @@ const useStyles = makeStyles()({ export default function LaunchSyntenyViewDialog({ model, feature, + trackId, handleClose, }: { model: unknown feature: Feature + trackId: string handleClose: () => void }) { const { classes } = useStyles() @@ -70,6 +73,7 @@ export default function LaunchSyntenyViewDialog({ feature, windowSize: +windowSize, horizontallyFlip, + trackId, model, }) } catch (e) { diff --git a/plugins/linear-comparative-view/src/LGVSyntenyDisplay/components/util.ts b/plugins/linear-comparative-view/src/LGVSyntenyDisplay/components/util.ts index 14d57a5008..57d05d1e12 100644 --- a/plugins/linear-comparative-view/src/LGVSyntenyDisplay/components/util.ts +++ b/plugins/linear-comparative-view/src/LGVSyntenyDisplay/components/util.ts @@ -1,9 +1,4 @@ -import { - getSession, - getContainingTrack, - getContainingView, - Feature, -} from '@jbrowse/core/util' +import { getSession, Feature } from '@jbrowse/core/util' import { MismatchParser } from '@jbrowse/plugin-alignments' import { IAnyStateTreeNode } from 'mobx-state-tree' import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view' @@ -45,24 +40,24 @@ export async function navToSynteny({ feature, windowSize: ws, model, + trackId, + view, horizontallyFlip, }: { windowSize: number + trackId: string horizontallyFlip: boolean feature: Feature + view?: LinearGenomeViewModel model: IAnyStateTreeNode }) { const session = getSession(model) - const track = getContainingTrack(model) - const view = getContainingView(model) as LinearGenomeViewModel - const reg = view.dynamicBlocks.contentBlocks[0] - if (!reg) { - throw new Error('no visible region') - } + const reg = view?.dynamicBlocks.contentBlocks[0] const cigar = feature.get('CIGAR') const strand = feature.get('strand') - const regStart = reg.start - const regEnd = reg.end + + const featRef = feature.get('refName') + const featAsm = feature.get('assemblyName') const featStart = feature.get('start') const featEnd = feature.get('end') const mate = feature.get('mate') @@ -70,15 +65,15 @@ export async function navToSynteny({ const mateEnd = mate.end const mateAsm = mate.assemblyName const mateRef = mate.refName - const featAsm = reg.assemblyName - const featRef = reg.refName let rMateStart: number let rMateEnd: number let rFeatStart: number let rFeatEnd: number - if (cigar) { + if (reg && cigar) { + const regStart = reg.start + const regEnd = reg.end const p = parseCigar(cigar) const [fStartX, mStartX] = findPosInCigar(p, regStart - featStart) const [fEndX, mEndX] = findPosInCigar(p, regEnd - featStart) @@ -95,18 +90,15 @@ export async function navToSynteny({ rMateStart = mateStart rMateEnd = mateEnd } - const trackId = track.configuration.trackId const view2 = session.addView('LinearSyntenyView', { type: 'LinearSyntenyView', views: [ { - id: `${Math.random()}`, type: 'LinearGenomeView', hideHeader: true, }, { - id: `${Math.random()}`, type: 'LinearGenomeView', hideHeader: true, }, diff --git a/plugins/linear-comparative-view/src/LGVSyntenyDisplay/model.ts b/plugins/linear-comparative-view/src/LGVSyntenyDisplay/model.ts index 04a03b5c3d..ed9994da20 100644 --- a/plugins/linear-comparative-view/src/LGVSyntenyDisplay/model.ts +++ b/plugins/linear-comparative-view/src/LGVSyntenyDisplay/model.ts @@ -2,8 +2,15 @@ import { lazy } from 'react' import { ConfigurationReference, AnyConfigurationSchemaType, + getConf, } from '@jbrowse/core/configuration' -import { getSession } from '@jbrowse/core/util' +import { + Feature, + getContainingTrack, + getContainingView, + getSession, + isSessionModelWithWidgets, +} from '@jbrowse/core/util' import { SharedLinearPileupDisplayMixin } from '@jbrowse/plugin-alignments' import { types } from 'mobx-state-tree' @@ -48,12 +55,13 @@ function stateModelFactory(schema: AnyConfigurationSchemaType) { ...(feature ? [ { - label: 'Open synteny view for this position', + label: 'Launch synteny view for this position', onClick: () => { getSession(self).queueDialog(handleClose => [ LaunchSyntenyViewDialog, { model: self, + trackId: getConf(getContainingTrack(self), 'trackId'), handleClose, feature, }, @@ -87,6 +95,30 @@ function stateModelFactory(schema: AnyConfigurationSchemaType) { } }) .actions(self => ({ + /** + * #action + */ + selectFeature(feature: Feature) { + const session = getSession(self) + if (isSessionModelWithWidgets(session)) { + const r2 = getContainingView(self) + let r3 = r2 + try { + r3 = getContainingView(r3) + } catch (e) {} + const featureWidget = session.addWidget( + 'SyntenyFeatureWidget', + 'syntenyFeature', + { + featureData: feature.toJSON(), + view: r3, + track: getContainingTrack(self), + }, + ) + session.showWidget(featureWidget) + } + session.setSelection(feature) + }, afterCreate() { // use color by stand to help indicate inversions better on first load, // otherwise use selected orientation diff --git a/plugins/linear-comparative-view/src/LinearComparativeDisplay/stateModelFactory.ts b/plugins/linear-comparative-view/src/LinearComparativeDisplay/stateModelFactory.ts index 3023c9bb75..0281de9a8b 100644 --- a/plugins/linear-comparative-view/src/LinearComparativeDisplay/stateModelFactory.ts +++ b/plugins/linear-comparative-view/src/LinearComparativeDisplay/stateModelFactory.ts @@ -42,6 +42,24 @@ function stateModelFactory(configSchema: AnyConfigurationSchemaType) { message: undefined as string | undefined, })) .views(self => ({ + /** + * #getter + */ + get parentTrack() { + return getParent<{ height: number; level: number }>(self, 4) + }, + /** + * #getter + */ + get level() { + return this.parentTrack.level + }, + /** + * #getter + */ + get height() { + return this.parentTrack.height + }, /** * #getter */ @@ -166,7 +184,7 @@ function renderBlockData(self: LinearComparativeDisplay) { // serverSideRenderedBlock readConfObject(self.configuration) - const { adapterConfig } = self + const { level, adapterConfig } = self const parent = getContainingView(self) as LinearComparativeViewModel const sessionId = getRpcSessionId(self) getSnapshot(parent) @@ -175,8 +193,7 @@ function renderBlockData(self: LinearComparativeDisplay) { rpcManager, renderProps: { ...display.renderProps(), - // @ts-expect-error - level: getParent(self, 4).level as number, + level, view: parent, adapterConfig, sessionId, diff --git a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/afterAttach.ts b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/afterAttach.ts index d41449edc8..58d56c48b4 100644 --- a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/afterAttach.ts +++ b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/afterAttach.ts @@ -84,10 +84,9 @@ export function doAfterAttach(self: LinearSyntenyDisplayModel) { if (!initialized) { return } + const { level } = self const { assemblyManager } = getSession(self) const view = getContainingView(self) as LSV - // @ts-expect-error - const level = getParent(self, 4).level const viewSnaps = view.views.map(view => ({ ...getSnapshot(view), width: view.width, diff --git a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/LinearSyntenyRendering.tsx b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/LinearSyntenyRendering.tsx index 7ee39b5186..1a586f2513 100644 --- a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/LinearSyntenyRendering.tsx +++ b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/LinearSyntenyRendering.tsx @@ -200,7 +200,13 @@ const LinearSyntenyRendering = observer(function ({ const { f, cigar } = model.featPositions[id] const unitMultiplier2 = Math.floor(MAX_COLOR_RANGE / cigar.length) const cigarIdx = getId(r2!, g2!, b2!, unitMultiplier2) - setTooltip(getTooltip(f, cigar[cigarIdx], cigar[cigarIdx + 1])) + setTooltip( + getTooltip({ + feature: f, + cigarOp: cigar[cigarIdx], + cigarOpLen: cigar[cigarIdx + 1], + }), + ) } } }} diff --git a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/SyntenyContextMenu.tsx b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/SyntenyContextMenu.tsx index 9df93e7adf..6b6d5c42d3 100644 --- a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/SyntenyContextMenu.tsx +++ b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/SyntenyContextMenu.tsx @@ -55,14 +55,13 @@ export default function SyntenyContextMenu({ label: 'Center on feature', onClick: () => { const { f } = feature - const track = getParent<{ level: number }>(model, 4) const start = f.get('start') const end = f.get('end') const refName = f.get('refName') const mate = f.get('mate') - const l1 = view.views[track.level]! - const l2 = view.views[track.level + 1]! + const l1 = view.views[model.level]! + const l2 = view.views[model.level + 1]! l1.navToLocString(`${refName}:${start}-${end}`).catch( (e: unknown) => { const err = `${l1.assemblyNames[0]}:${e}` diff --git a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/util.ts b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/util.ts index 210a38824e..a4f21d45f9 100644 --- a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/util.ts +++ b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/util.ts @@ -166,8 +166,13 @@ export function onSynClick( ) { const view = getContainingView(model) const track = getContainingTrack(model) - const ref1 = model.clickMapCanvas - const ref2 = model.cigarClickMapCanvas + const { + featPositions, + numFeats, + clickMapCanvas: ref1, + cigarClickMapCanvas: ref2, + level, + } = model if (!ref1 || !ref2) { return } @@ -180,19 +185,20 @@ export function onSynClick( const x = event.clientX - rect.left const y = event.clientY - rect.top const [r1, g1, b1] = ctx1.getImageData(x, y, 1, 1).data - const unitMultiplier = Math.floor(MAX_COLOR_RANGE / model.numFeats) + const unitMultiplier = Math.floor(MAX_COLOR_RANGE / numFeats) const id = getId(r1!, g1!, b1!, unitMultiplier) - const feat = model.featPositions[id] + const feat = featPositions[id] if (feat) { const { f } = feat model.setClickId(f.id()) const session = getSession(model) if (isSessionModelWithWidgets(session)) { session.showWidget( - session.addWidget('BaseFeatureWidget', 'baseFeature', { + session.addWidget('SyntenyFeatureWidget', 'syntenyFeature', { view, track, featureData: f.toJSON(), + level, }), ) } @@ -230,9 +236,17 @@ export function onSynContextClick( } } -export function getTooltip(f: Feature, cigarOp?: string, cigarOpLen?: string) { +export function getTooltip({ + feature, + cigarOp, + cigarOpLen, +}: { + feature: Feature + cigarOp?: string + cigarOpLen?: string +}) { // @ts-expect-error - const f1 = f.toJSON() as { + const f1 = feature.toJSON() as { refName: string start: number end: number diff --git a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/drawSynteny.ts b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/drawSynteny.ts index 68cc750940..cf3c6cafbf 100644 --- a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/drawSynteny.ts +++ b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/drawSynteny.ts @@ -37,11 +37,9 @@ export function drawRef( ctx3?: CanvasRenderingContext2D, ) { const view = getContainingView(model) as LinearSyntenyViewModel - // @ts-expect-error - const level = getParent(model, 4).level const drawCurves = view.drawCurves const drawCIGAR = view.drawCIGAR - const { height, featPositions } = model + const { level, height, featPositions } = model const width = view.width const bpPerPxs = view.views.map(v => v.bpPerPx) @@ -226,7 +224,7 @@ export function drawRef( } export function drawMouseoverSynteny(model: LinearSyntenyDisplayModel) { - const { clickId, mouseoverId } = model + const { level, clickId, mouseoverId } = model const highResolutionScaling = 1 const view = getContainingView(model) as LinearSyntenyViewModel const drawCurves = view.drawCurves @@ -234,8 +232,6 @@ export function drawMouseoverSynteny(model: LinearSyntenyDisplayModel) { const width = view.width const ctx = model.mouseoverCanvas?.getContext('2d') const offsets = view.views.map(v => v.offsetPx) - // @ts-expect-error - const level = getParent(model, 4).level if (!ctx) { return diff --git a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/model.ts b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/model.ts index a95d5fdc8c..4e8260e352 100644 --- a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/model.ts +++ b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/model.ts @@ -1,4 +1,4 @@ -import { types, Instance, getParent } from 'mobx-state-tree' +import { types, Instance } from 'mobx-state-tree' import { getConf, ConfigurationReference, @@ -44,35 +44,58 @@ function stateModelFactory(configSchema: AnyConfigurationSchemaType) { }), ) .volatile(() => ({ - // canvas used for drawing visible screen + /** + * #volatile + * canvas used for drawing visible screen + */ mainCanvas: null as HTMLCanvasElement | null, - // canvas used for drawing click map with feature ids - // this renders a unique color per alignment, so that it can be re-traced - // after a feature click with getImageData at that pixel + /** + * #volatile + * canvas used for drawing click map with feature ids this renders a + * unique color per alignment, so that it can be re-traced after a + * feature click with getImageData at that pixel + */ clickMapCanvas: null as HTMLCanvasElement | null, - // canvas used for drawing click map with cigar data - // this can show if you are mousing over a insertion/deletion. it is similar - // in purpose to the clickMapRef but was not feasible to pack this into the - // clickMapRef + /** + * #volatile + * canvas used for drawing click map with cigar data this can show if you + * are mousing over a insertion/deletion. it is similar in purpose to the + * clickMapRef but was not feasible to pack this into the clickMapRef + */ cigarClickMapCanvas: null as HTMLCanvasElement | null, - // canvas for drawing mouseover shading - // this is separate from the other code for speed: don't have to redraw - // entire canvas to do a feature's mouseover shading + /** + * #volatile + * canvas for drawing mouseover shading this is separate from the other + * code for speed: don't have to redraw entire canvas to do a feature's + * mouseover shading + */ mouseoverCanvas: null as HTMLCanvasElement | null, - // assigned by reaction + /** + * #volatile + * assigned by reaction + */ featPositions: [] as FeatPos[], - // currently mouse'd over feature + /** + * #volatile + * currently mouse'd over feature + */ mouseoverId: undefined as string | undefined, - // currently click'd over feature + /** + * #volatile + * currently click'd over feature + */ clickId: undefined as string | undefined, - // currently mouseover'd CIGAR subfeature + /** + * #volatile + * currently mouseover'd CIGAR subfeature + */ cigarMouseoverId: -1, })) .actions(self => ({ @@ -137,25 +160,21 @@ function stateModelFactory(configSchema: AnyConfigurationSchemaType) { ...getConf(self.parentTrack, 'adapter'), } }, + /** * #getter */ get trackIds() { return getConf(self, 'trackIds') as string[] }, - /** - * #getter - */ - get height() { - // @ts-expect-error - return getParent(self, 4).height as number - }, + /** * #getter */ get numFeats() { return self.featPositions.length }, + /** * #getter * used for synteny svg rendering diff --git a/plugins/linear-comparative-view/src/SyntenyFeatureDetail/SyntenyFeatureDetail.tsx b/plugins/linear-comparative-view/src/SyntenyFeatureDetail/SyntenyFeatureDetail.tsx new file mode 100644 index 0000000000..0358823855 --- /dev/null +++ b/plugins/linear-comparative-view/src/SyntenyFeatureDetail/SyntenyFeatureDetail.tsx @@ -0,0 +1,126 @@ +import React, { lazy } from 'react' +import { Link, Paper } from '@mui/material' +import { observer } from 'mobx-react' + +// locals +import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard' +import BaseFeatureDetail from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail' +import { + assembleLocString, + getSession, + SimpleFeature, + SimpleFeatureSerialized, +} from '@jbrowse/core/util' +import { LinearSyntenyViewModel } from '../LinearSyntenyView/model' + +// lazies +const LaunchSyntenyViewDialog = lazy( + () => import('../LGVSyntenyDisplay/components/LaunchSyntenyViewDialog'), +) + +interface SyntenyFeatureDetailModel { + trackId: string + featureData: SimpleFeatureSerialized + level?: number + view: { + type: string + } +} + +const CustomLinker = observer(function ({ + model, +}: { + model: SyntenyFeatureDetailModel +}) { + const { featureData, view, level, trackId } = model + return ( +
    + {view.type === 'LinearSyntenyView' ? ( +
  • + { + event.preventDefault() + const { views } = view as LinearSyntenyViewModel + if (level !== undefined) { + // level is "pre-known", and stored in the SyntenyFeatureWidget + // model state e.g. when clicking on a feature from a + // LinearSyntenyRendering + views[level]?.navTo(featureData) + views[level + 1]?.navTo( + featureData.mate as SimpleFeatureSerialized, + ) + } else { + // best effort to find the right level. this is triggered for + // example if a user clicks on a feature in a LGVSyntenyDisplay + // in an existing LinearSyntenyView, there is no real proper + // level "pre-known" to this situation + const f1 = featureData + const f2 = featureData.mate as SimpleFeatureSerialized + const r1 = f1.assemblyName as string + const r2 = f2.assemblyName as string + const v1 = views.find(view => view.assemblyNames[0] === r1) + const v2 = views.find(view => view.assemblyNames[0] === r2) + if (!v1 || !v2) { + getSession(model).notify( + [ + v1 + ? `Unable to find ${assembleLocString(f1)} in synteny view` + : '', + v2 + ? `Unable to find ${assembleLocString(f2)} in synteny view` + : '', + ].join(' ... '), + ) + } + v1?.navTo(f1) + v2?.navTo(f2) + } + }} + > + Center view on this feature + +
    • + ) : null} +
  • + { + event.preventDefault() + + const session = getSession(model) + const feature = new SimpleFeature(featureData) + session.queueDialog(handleClose => [ + LaunchSyntenyViewDialog, + { + model, + feature, + trackId, + handleClose, + }, + ]) + }} + > + Launch new linear synteny view on this feature + +
    • +
+ ) +}) + +const SyntenyFeatureDetail = observer(function ({ + model, +}: { + model: SyntenyFeatureDetailModel +}) { + return ( + + + + + + + ) +}) + +export default SyntenyFeatureDetail diff --git a/plugins/linear-comparative-view/src/SyntenyFeatureDetail/index.ts b/plugins/linear-comparative-view/src/SyntenyFeatureDetail/index.ts new file mode 100644 index 0000000000..b7cbb8d739 --- /dev/null +++ b/plugins/linear-comparative-view/src/SyntenyFeatureDetail/index.ts @@ -0,0 +1,37 @@ +import { lazy } from 'react' +import { ConfigurationSchema } from '@jbrowse/core/configuration' +import WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType' +import PluginManager from '@jbrowse/core/PluginManager' +import { types } from 'mobx-state-tree' +import { stateModelFactory as BaseFeatureWidgetStateModelF } from '@jbrowse/core/BaseFeatureWidget' + +const configSchema = ConfigurationSchema('SyntenyFeatureWidget', {}) + +function stateModelF(pluginManager: PluginManager) { + return types.compose( + BaseFeatureWidgetStateModelF(pluginManager), + types.model('SyntenyFeatureWidget', { + /** + * #property + */ + type: types.literal('SyntenyFeatureWidget'), + /** + * #property + */ + level: types.maybe(types.number), + }), + ) +} + +export default function SyntenyFeatureWidgetF(pluginManager: PluginManager) { + pluginManager.addWidgetType( + () => + new WidgetType({ + name: 'SyntenyFeatureWidget', + heading: 'Synteny feature details', + configSchema, + stateModel: stateModelF(pluginManager), + ReactComponent: lazy(() => import('./SyntenyFeatureDetail')), + }), + ) +} diff --git a/plugins/linear-comparative-view/src/index.tsx b/plugins/linear-comparative-view/src/index.ts similarity index 94% rename from plugins/linear-comparative-view/src/index.tsx rename to plugins/linear-comparative-view/src/index.ts index b1502789cd..1ffa87d204 100644 --- a/plugins/linear-comparative-view/src/index.tsx +++ b/plugins/linear-comparative-view/src/index.ts @@ -12,6 +12,7 @@ import LinearSyntenyViewHelperF from './LinearSyntenyViewHelper' import LaunchLinearSyntenyViewF from './LaunchLinearSyntenyView' import SyntenyTrackF from './SyntenyTrack' import LinearReadVsRefMenuItemF from './LinearReadVsRef' +import SyntenyFeatureWidgetF from './SyntenyFeatureDetail' export default class LinearComparativeViewPlugin extends Plugin { name = 'LinearComparativeViewPlugin' @@ -22,6 +23,7 @@ export default class LinearComparativeViewPlugin extends Plugin { LinearSyntenyViewF(pluginManager) LinearComparativeDisplayF(pluginManager) LinearSyntenyDisplayF(pluginManager) + SyntenyFeatureWidgetF(pluginManager) LGVSyntenyDisplayF(pluginManager) LaunchLinearSyntenyViewF(pluginManager) SyntenyTrackF(pluginManager) diff --git a/plugins/linear-genome-view/src/LinearGenomeView/components/Rubberband.tsx b/plugins/linear-genome-view/src/LinearGenomeView/components/Rubberband.tsx index 65b2c46338..b46f7cbeb2 100644 --- a/plugins/linear-genome-view/src/LinearGenomeView/components/Rubberband.tsx +++ b/plugins/linear-genome-view/src/LinearGenomeView/components/Rubberband.tsx @@ -6,7 +6,8 @@ import { Menu } from '@jbrowse/core/ui' // locals import VerticalGuide from './VerticalGuide' import RubberbandSpan from './RubberbandSpan' -import { useRangeSelect } from './hooks' +// hooks +import { useRangeSelect } from './useRangeSelect' import { LinearGenomeViewModel } from '..' type LGV = LinearGenomeViewModel @@ -38,8 +39,8 @@ const Rubberband = observer(function ({ width, left, anchorPosition, - handleMenuItemClick, open, + handleMenuItemClick, handleClose, mouseMove, mouseDown, diff --git a/plugins/linear-genome-view/src/LinearGenomeView/components/TrackLabel.tsx b/plugins/linear-genome-view/src/LinearGenomeView/components/TrackLabel.tsx index 9d5898612a..7efe400d0d 100644 --- a/plugins/linear-genome-view/src/LinearGenomeView/components/TrackLabel.tsx +++ b/plugins/linear-genome-view/src/LinearGenomeView/components/TrackLabel.tsx @@ -69,13 +69,17 @@ const TrackLabel = observer( track.setMinimized(!minimized) }, }, - { - label: 'Move track to top', - icon: KeyboardDoubleArrowUpIcon, - onClick: () => { - view.moveTrackToTop(track.id) - }, - }, + ...(view.tracks.length > 2 + ? [ + { + label: 'Move track to top', + icon: KeyboardDoubleArrowUpIcon, + onClick: () => { + view.moveTrackToTop(track.id) + }, + }, + ] + : []), { label: 'Move track up', @@ -91,13 +95,17 @@ const TrackLabel = observer( view.moveTrackDown(track.id) }, }, - { - label: 'Move track to bottom', - icon: KeyboardDoubleArrowDownIcon, - onClick: () => { - view.moveTrackToBottom(track.id) - }, - }, + ...(view.tracks.length > 2 + ? [ + { + label: 'Move track to bottom', + icon: KeyboardDoubleArrowDownIcon, + onClick: () => { + view.moveTrackToBottom(track.id) + }, + }, + ] + : []), ], }, ...(session.getTrackActionMenuItems?.(trackConf) || []), diff --git a/plugins/linear-genome-view/src/LinearGenomeView/components/TracksContainer.tsx b/plugins/linear-genome-view/src/LinearGenomeView/components/TracksContainer.tsx index 29151f3a2f..800ed52bc0 100644 --- a/plugins/linear-genome-view/src/LinearGenomeView/components/TracksContainer.tsx +++ b/plugins/linear-genome-view/src/LinearGenomeView/components/TracksContainer.tsx @@ -6,7 +6,6 @@ import { getEnv } from '@jbrowse/core/util' // local utils import { LinearGenomeViewModel } from '..' -import { useSideScroll, useRangeSelect, useWheelScroll } from './hooks' // local components import Rubberband from './Rubberband' @@ -18,6 +17,11 @@ import RubberbandSpan from './RubberbandSpan' import HighlightGroup from './Highlight' import { SCALE_BAR_HEIGHT } from '../consts' +// hooks +import { useSideScroll } from './useSideScroll' +import { useWheelScroll } from './useWheelScroll' +import { useRangeSelect } from './useRangeSelect' + const useStyles = makeStyles()({ tracksContainer: { position: 'relative', @@ -37,6 +41,7 @@ const TracksContainer = observer(function TracksContainer({ const { classes } = useStyles() const { pluginManager } = getEnv(model) const { mouseDown: mouseDown1, mouseUp } = useSideScroll(model) + const { showGridlines, showCenterLine } = model const ref = useRef(null) const { guideX, @@ -73,8 +78,8 @@ const TracksContainer = observer(function TracksContainer({ onMouseMove={mouseMove} onMouseUp={mouseUp} > - {model.showGridlines ? : null} - {model.showCenterLine ? : null} + {showGridlines ? : null} + {showCenterLine ? : null} {guideX !== undefined ? ( ) : rubberbandOn ? ( diff --git a/plugins/linear-genome-view/src/LinearGenomeView/components/hooks.ts b/plugins/linear-genome-view/src/LinearGenomeView/components/hooks.ts deleted file mode 100644 index 1f36223700..0000000000 --- a/plugins/linear-genome-view/src/LinearGenomeView/components/hooks.ts +++ /dev/null @@ -1,303 +0,0 @@ -import React, { useRef, useEffect, useState } from 'react' - -// locals -import { LinearGenomeViewModel } from '..' -import { getRelativeX } from './util' - -type LGV = LinearGenomeViewModel -type Timer = ReturnType - -export function useSideScroll(model: LGV) { - const [mouseDragging, setMouseDragging] = useState(false) - // refs are to store these variables to avoid repeated rerenders associated - // with useState/setState - const scheduled = useRef(false) - - const prevX = useRef(0) - - useEffect(() => { - let cleanup = () => {} - - function globalMouseMove(event: MouseEvent) { - event.preventDefault() - const currX = event.clientX - const distance = currX - prevX.current - if (distance) { - // use rAF to make it so multiple event handlers aren't fired per-frame - // see https://calendar.perfplanet.com/2013/the-runtime-performance-checklist/ - if (!scheduled.current) { - scheduled.current = true - window.requestAnimationFrame(() => { - model.horizontalScroll(-distance) - scheduled.current = false - prevX.current = event.clientX - }) - } - } - } - - function globalMouseUp() { - prevX.current = 0 - if (mouseDragging) { - setMouseDragging(false) - } - } - - if (mouseDragging) { - window.addEventListener('mousemove', globalMouseMove, true) - window.addEventListener('mouseup', globalMouseUp, true) - cleanup = () => { - window.removeEventListener('mousemove', globalMouseMove, true) - window.removeEventListener('mouseup', globalMouseUp, true) - } - } - return cleanup - }, [model, mouseDragging]) - - function mouseDown(event: React.MouseEvent) { - if (event.shiftKey) { - return - } - // check if clicking a draggable element or a resize handle - const target = event.target as HTMLElement - if (target.draggable || target.dataset.resizer) { - return - } - - // otherwise do click and drag scroll - if (event.button === 0) { - prevX.current = event.clientX - setMouseDragging(true) - } - } - - // this local mouseup is used in addition to the global because sometimes - // the global add/remove are not called in time, resulting in issue #533 - function mouseUp(event: React.MouseEvent) { - event.preventDefault() - setMouseDragging(false) - } - return { mouseDown, mouseUp } -} - -interface AnchorPosition { - offsetX: number - clientX: number - clientY: number -} - -export function useRangeSelect( - ref: React.RefObject, - model: LGV, - shiftOnly?: boolean, -) { - const [startX, setStartX] = useState() - const [currentX, setCurrentX] = useState() - - // clientX and clientY used for anchorPosition for menu - // offsetX used for calculations about width of selection - const [anchorPosition, setAnchorPosition] = useState() - const [guideX, setGuideX] = useState() - const mouseDragging = startX !== undefined && anchorPosition === undefined - - useEffect(() => { - function computeOffsets(offsetX: number) { - if (startX === undefined) { - return - } - const leftPx = Math.min(startX, offsetX) - const rightPx = Math.max(startX, offsetX) - return { - leftOffset: model.pxToBp(leftPx), - rightOffset: model.pxToBp(rightPx), - } - } - - function globalMouseMove(event: MouseEvent) { - if (ref.current && mouseDragging) { - const relativeX = getRelativeX(event, ref.current) - setCurrentX(relativeX) - } - } - - function globalMouseUp(event: MouseEvent) { - if (startX !== undefined && ref.current) { - const { clientX, clientY } = event - const offsetX = getRelativeX(event, ref.current) - // as stated above, store both clientX/Y and offsetX for different - // purposes - setAnchorPosition({ - offsetX, - clientX, - clientY, - }) - const args = computeOffsets(offsetX) - if (args) { - model.setOffsets(args.leftOffset, args.rightOffset) - } - setGuideX(undefined) - } - } - if (mouseDragging) { - window.addEventListener('mousemove', globalMouseMove) - window.addEventListener('mouseup', globalMouseUp) - return () => { - window.removeEventListener('mousemove', globalMouseMove) - window.removeEventListener('mouseup', globalMouseUp) - } - } - return () => {} - }, [startX, mouseDragging, model, ref]) - - useEffect(() => { - if ( - !mouseDragging && - currentX !== undefined && - startX !== undefined && - Math.abs(currentX - startX) <= 3 - ) { - handleClose() - } - }, [mouseDragging, currentX, startX]) - - function mouseDown(event: React.MouseEvent) { - if (shiftOnly && !event.shiftKey) { - return - } - - event.preventDefault() - event.stopPropagation() - const relativeX = getRelativeX(event, ref.current) - setStartX(relativeX) - setCurrentX(relativeX) - } - - function mouseMove(event: React.MouseEvent) { - if (shiftOnly) { - if (event.shiftKey) { - setGuideX(getRelativeX(event, ref.current)) - } else { - setGuideX(undefined) - } - } else { - setGuideX(getRelativeX(event, ref.current)) - } - } - - function mouseOut() { - setGuideX(undefined) - model.setOffsets(undefined, undefined) - } - - function handleClose() { - setAnchorPosition(undefined) - setStartX(undefined) - setCurrentX(undefined) - } - - function handleMenuItemClick(_: unknown, callback: () => void) { - callback() - handleClose() - } - - const open = Boolean(anchorPosition) - if (startX === undefined) { - return { - open, - guideX, - mouseDown, - mouseMove, - mouseOut, - handleMenuItemClick, - } - } - const right = anchorPosition ? anchorPosition.offsetX : currentX || 0 - const left = Math.min(right, startX) - const width = Math.abs(right - startX) - const leftBpOffset = model.pxToBp(left) - const rightBpOffset = model.pxToBp(left + width) - const numOfBpSelected = Math.ceil(width * model.bpPerPx) - - return { - open, - rubberbandOn: true, - mouseDown, - mouseMove, - mouseOut, - handleClose, - handleMenuItemClick, - leftBpOffset, - rightBpOffset, - anchorPosition, - numOfBpSelected, - width, - left, - } -} - -export function useWheelScroll( - ref: React.RefObject, - model: { - bpPerPx: number - zoomTo: (arg: number, arg2?: number) => void - setScaleFactor: (arg: number) => void - horizontalScroll: (arg: number) => void - }, -) { - const delta = useRef(0) - const timeout = useRef() - const scheduled = useRef(false) - useEffect(() => { - const curr = ref.current - - // if ctrl is held down, zoom in with y-scroll - // else scroll horizontally with x-scroll - function onWheel(event: WheelEvent) { - if (event.ctrlKey) { - event.preventDefault() - delta.current += event.deltaY / 500 - model.setScaleFactor( - delta.current < 0 ? 1 - delta.current : 1 / (1 + delta.current), - ) - if (timeout.current) { - clearTimeout(timeout.current) - } - timeout.current = setTimeout(() => { - model.setScaleFactor(1) - model.zoomTo( - delta.current > 0 - ? model.bpPerPx * (1 + delta.current) - : model.bpPerPx / (1 - delta.current), - event.clientX - (curr?.getBoundingClientRect().left || 0), - ) - delta.current = 0 - }, 300) - } else { - // this is needed to stop the event from triggering "back button - // action" on MacOSX etc. but is a heuristic to avoid preventing the - // inner-track scroll behavior - if (Math.abs(event.deltaX) > Math.abs(2 * event.deltaY)) { - event.preventDefault() - } - delta.current += event.deltaX - if (!scheduled.current) { - // use rAF to make it so multiple event handlers aren't fired per-frame - // see https://calendar.perfplanet.com/2013/the-runtime-performance-checklist/ - scheduled.current = true - window.requestAnimationFrame(() => { - model.horizontalScroll(delta.current) - delta.current = 0 - scheduled.current = false - }) - } - } - } - if (curr) { - curr.addEventListener('wheel', onWheel) - return () => { - curr.removeEventListener('wheel', onWheel) - } - } - return () => {} - }, [model, ref]) -} diff --git a/plugins/linear-genome-view/src/LinearGenomeView/components/useRangeSelect.ts b/plugins/linear-genome-view/src/LinearGenomeView/components/useRangeSelect.ts new file mode 100644 index 0000000000..17465df8c6 --- /dev/null +++ b/plugins/linear-genome-view/src/LinearGenomeView/components/useRangeSelect.ts @@ -0,0 +1,160 @@ +import React, { useEffect, useState } from 'react' + +// locals +import { LinearGenomeViewModel } from '..' +import { getRelativeX } from './util' + +interface AnchorPosition { + offsetX: number + clientX: number + clientY: number +} + +export function useRangeSelect( + ref: React.RefObject, + model: LinearGenomeViewModel, + shiftOnly?: boolean, +) { + const [startX, setStartX] = useState() + const [currentX, setCurrentX] = useState() + + // clientX and clientY used for anchorPosition for menu + // offsetX used for calculations about width of selection + const [anchorPosition, setAnchorPosition] = useState() + const [guideX, setGuideX] = useState() + const mouseDragging = startX !== undefined && anchorPosition === undefined + + useEffect(() => { + function computeOffsets(offsetX: number) { + if (startX === undefined) { + return + } + const leftPx = Math.min(startX, offsetX) + const rightPx = Math.max(startX, offsetX) + return { + leftOffset: model.pxToBp(leftPx), + rightOffset: model.pxToBp(rightPx), + } + } + + function globalMouseMove(event: MouseEvent) { + if (ref.current && mouseDragging) { + const relativeX = getRelativeX(event, ref.current) + setCurrentX(relativeX) + } + } + + function globalMouseUp(event: MouseEvent) { + if (startX !== undefined && ref.current) { + const { clientX, clientY } = event + const offsetX = getRelativeX(event, ref.current) + // as stated above, store both clientX/Y and offsetX for different + // purposes + setAnchorPosition({ + offsetX, + clientX, + clientY, + }) + const args = computeOffsets(offsetX) + if (args) { + model.setOffsets(args.leftOffset, args.rightOffset) + } + setGuideX(undefined) + } + } + if (mouseDragging) { + window.addEventListener('mousemove', globalMouseMove) + window.addEventListener('mouseup', globalMouseUp) + return () => { + window.removeEventListener('mousemove', globalMouseMove) + window.removeEventListener('mouseup', globalMouseUp) + } + } + return () => {} + }, [startX, mouseDragging, model, ref]) + + useEffect(() => { + if ( + !mouseDragging && + currentX !== undefined && + startX !== undefined && + Math.abs(currentX - startX) <= 3 + ) { + handleClose() + } + }, [mouseDragging, currentX, startX]) + + function mouseDown(event: React.MouseEvent) { + if (shiftOnly && !event.shiftKey) { + return + } + + event.preventDefault() + event.stopPropagation() + const relativeX = getRelativeX(event, ref.current) + setStartX(relativeX) + setCurrentX(relativeX) + } + + function mouseMove(event: React.MouseEvent) { + if (shiftOnly) { + if (event.shiftKey) { + setGuideX(getRelativeX(event, ref.current)) + } else { + setGuideX(undefined) + } + } else { + setGuideX(getRelativeX(event, ref.current)) + } + } + + function mouseOut() { + setGuideX(undefined) + model.setOffsets(undefined, undefined) + } + + function handleClose() { + setAnchorPosition(undefined) + setStartX(undefined) + setCurrentX(undefined) + } + + function handleMenuItemClick(_: unknown, callback: () => void) { + callback() + handleClose() + } + + const open = Boolean(anchorPosition) + if (startX === undefined) { + return { + open, + guideX, + mouseDown, + mouseMove, + mouseOut, + handleMenuItemClick, + } + } + const right = anchorPosition ? anchorPosition.offsetX : currentX || 0 + const left = Math.min(right, startX) + const width = Math.abs(right - startX) + const leftBpOffset = model.pxToBp(left) + const rightBpOffset = model.pxToBp(left + width) + const numOfBpSelected = Math.ceil(width * model.bpPerPx) + + return { + open, + rubberbandOn: true, + mouseDown, + mouseMove, + mouseOut, + handleClose, + handleMenuItemClick, + leftBpOffset, + rightBpOffset, + anchorPosition, + numOfBpSelected, + width, + left, + } +} diff --git a/plugins/linear-genome-view/src/LinearGenomeView/components/useSideScroll.ts b/plugins/linear-genome-view/src/LinearGenomeView/components/useSideScroll.ts new file mode 100644 index 0000000000..b83858dca2 --- /dev/null +++ b/plugins/linear-genome-view/src/LinearGenomeView/components/useSideScroll.ts @@ -0,0 +1,77 @@ +import React, { useRef, useEffect, useState } from 'react' + +// locals +import { LinearGenomeViewModel } from '..' + +export function useSideScroll(model: LinearGenomeViewModel) { + const [mouseDragging, setMouseDragging] = useState(false) + // refs are to store these variables to avoid repeated rerenders associated + // with useState/setState + const scheduled = useRef(false) + + const prevX = useRef(0) + + useEffect(() => { + let cleanup = () => {} + + function globalMouseMove(event: MouseEvent) { + event.preventDefault() + const currX = event.clientX + const distance = currX - prevX.current + if (distance) { + // use rAF to make it so multiple event handlers aren't fired per-frame + // see https://calendar.perfplanet.com/2013/the-runtime-performance-checklist/ + if (!scheduled.current) { + scheduled.current = true + window.requestAnimationFrame(() => { + model.horizontalScroll(-distance) + scheduled.current = false + prevX.current = event.clientX + }) + } + } + } + + function globalMouseUp() { + prevX.current = 0 + if (mouseDragging) { + setMouseDragging(false) + } + } + + if (mouseDragging) { + window.addEventListener('mousemove', globalMouseMove, true) + window.addEventListener('mouseup', globalMouseUp, true) + cleanup = () => { + window.removeEventListener('mousemove', globalMouseMove, true) + window.removeEventListener('mouseup', globalMouseUp, true) + } + } + return cleanup + }, [model, mouseDragging]) + + function mouseDown(event: React.MouseEvent) { + if (event.shiftKey) { + return + } + // check if clicking a draggable element or a resize handle + const target = event.target as HTMLElement + if (target.draggable || target.dataset.resizer) { + return + } + + // otherwise do click and drag scroll + if (event.button === 0) { + prevX.current = event.clientX + setMouseDragging(true) + } + } + + // this local mouseup is used in addition to the global because sometimes + // the global add/remove are not called in time, resulting in issue #533 + function mouseUp(event: React.MouseEvent) { + event.preventDefault() + setMouseDragging(false) + } + return { mouseDown, mouseUp } +} diff --git a/plugins/linear-genome-view/src/LinearGenomeView/components/useWheelScroll.ts b/plugins/linear-genome-view/src/LinearGenomeView/components/useWheelScroll.ts new file mode 100644 index 0000000000..0474be52b0 --- /dev/null +++ b/plugins/linear-genome-view/src/LinearGenomeView/components/useWheelScroll.ts @@ -0,0 +1,70 @@ +import React, { useRef, useEffect } from 'react' + +type Timer = ReturnType + +export function useWheelScroll( + ref: React.RefObject, + model: { + bpPerPx: number + zoomTo: (arg: number, arg2?: number) => void + setScaleFactor: (arg: number) => void + horizontalScroll: (arg: number) => void + }, +) { + const delta = useRef(0) + const timeout = useRef() + const scheduled = useRef(false) + useEffect(() => { + const curr = ref.current + + // if ctrl is held down, zoom in with y-scroll, else scroll horizontally + // with x-scroll + function onWheel(event: WheelEvent) { + if (event.ctrlKey) { + event.preventDefault() + delta.current += event.deltaY / 500 + model.setScaleFactor( + delta.current < 0 ? 1 - delta.current : 1 / (1 + delta.current), + ) + if (timeout.current) { + clearTimeout(timeout.current) + } + timeout.current = setTimeout(() => { + model.setScaleFactor(1) + model.zoomTo( + delta.current > 0 + ? model.bpPerPx * (1 + delta.current) + : model.bpPerPx / (1 - delta.current), + event.clientX - (curr?.getBoundingClientRect().left || 0), + ) + delta.current = 0 + }, 300) + } else { + // this is needed to stop the event from triggering "back button + // action" on MacOSX etc. but is a heuristic to avoid preventing the + // inner-track scroll behavior + if (Math.abs(event.deltaX) > Math.abs(2 * event.deltaY)) { + event.preventDefault() + } + delta.current += event.deltaX + if (!scheduled.current) { + // use rAF to make it so multiple event handlers aren't fired per-frame + // see https://calendar.perfplanet.com/2013/the-runtime-performance-checklist/ + scheduled.current = true + window.requestAnimationFrame(() => { + model.horizontalScroll(delta.current) + delta.current = 0 + scheduled.current = false + }) + } + } + } + if (curr) { + curr.addEventListener('wheel', onWheel) + return () => { + curr.removeEventListener('wheel', onWheel) + } + } + return () => {} + }, [model, ref]) +} diff --git a/plugins/variants/src/VariantFeatureWidget/LaunchBreakendPanel.tsx b/plugins/variants/src/VariantFeatureWidget/LaunchBreakendPanel.tsx index 26c0c8da1c..e35e7e361d 100644 --- a/plugins/variants/src/VariantFeatureWidget/LaunchBreakendPanel.tsx +++ b/plugins/variants/src/VariantFeatureWidget/LaunchBreakendPanel.tsx @@ -6,7 +6,7 @@ import { SimpleFeature, SimpleFeatureSerialized, } from '@jbrowse/core/util' -import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail' +import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard' import { ViewType } from '@jbrowse/core/pluggableElementTypes' // locals diff --git a/plugins/variants/src/VariantFeatureWidget/VariantAnnotationTable.tsx b/plugins/variants/src/VariantFeatureWidget/VariantAnnotationTable.tsx index eff8c7d93d..007632930d 100644 --- a/plugins/variants/src/VariantFeatureWidget/VariantAnnotationTable.tsx +++ b/plugins/variants/src/VariantFeatureWidget/VariantAnnotationTable.tsx @@ -1,6 +1,6 @@ import React from 'react' -import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail' import AnnotGrid from './AnnotGrid' +import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard' export default function VariantAnnotationTable({ data, diff --git a/plugins/variants/src/VariantFeatureWidget/VariantFeatureWidget.tsx b/plugins/variants/src/VariantFeatureWidget/VariantFeatureWidget.tsx index b069c451db..d7d57c6d94 100644 --- a/plugins/variants/src/VariantFeatureWidget/VariantFeatureWidget.tsx +++ b/plugins/variants/src/VariantFeatureWidget/VariantFeatureWidget.tsx @@ -1,7 +1,7 @@ import React, { lazy, Suspense } from 'react' import { observer } from 'mobx-react' import { Paper } from '@mui/material' -import { FeatureDetails } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail' +import FeatureDetails from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails' import { parseBreakend } from '@gmod/vcf' // locals diff --git a/plugins/variants/src/VariantFeatureWidget/VariantSampleGrid.tsx b/plugins/variants/src/VariantFeatureWidget/VariantSampleGrid.tsx index 8bb4f21e9e..4648b40601 100644 --- a/plugins/variants/src/VariantFeatureWidget/VariantSampleGrid.tsx +++ b/plugins/variants/src/VariantFeatureWidget/VariantSampleGrid.tsx @@ -8,8 +8,8 @@ import { } from '@mui/material' import { DataGrid, GridToolbar } from '@mui/x-data-grid' -import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail' import { measureGridWidth, SimpleFeatureSerialized } from '@jbrowse/core/util' +import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard' interface Entry { sample: string @@ -92,8 +92,8 @@ export default function VariantSamples(props: { error = e } - const keys = ['sample', ...Object.keys(preFilteredRows[0]?.[1] || {})] const [checked, setChecked] = useState(false) + const keys = ['sample', ...Object.keys(preFilteredRows[0]?.[1] || {})] const widths = keys.map(e => measureGridWidth(rows.map(r => r[e]))) const columns = keys.map((field, index) => ({ field, diff --git a/yarn.lock b/yarn.lock index ad3f88d3db..16d077594b 100644 --- a/yarn.lock +++ b/yarn.lock @@ -88,27 +88,27 @@ "@smithy/util-utf8" "^2.0.0" tslib "^2.6.2" -"@aws-sdk/client-cloudfront@^3.675.0": - version "3.677.0" - resolved "https://registry.yarnpkg.com/@aws-sdk/client-cloudfront/-/client-cloudfront-3.677.0.tgz#bce261352d0e9a8c0dbcdc1e1327e4612aa6f830" - integrity sha512-0g1e2HGg8qKDkWiq1ugWyWMJqMBXkD0vszRaFBgCwaSktxXNRv2QG7NxoVgPbjbd1rGhnRHvJsAdSNDvJfp79w== +"@aws-sdk/client-cloudfront@^3.679.0": + version "3.682.0" + resolved "https://registry.yarnpkg.com/@aws-sdk/client-cloudfront/-/client-cloudfront-3.682.0.tgz#bc7a0b298492407c6f515459fa8f5accbe3782b2" + integrity sha512-K4RXR+6mlQe4XEp+tBj0nkoiQ5yDPdef0StEfcJQ9NbwwJb2Vdm8ImeEkJjisPcc0h3D6NhaZHumYwWAKb3BpA== dependencies: "@aws-crypto/sha256-browser" "5.2.0" "@aws-crypto/sha256-js" "5.2.0" - "@aws-sdk/client-sso-oidc" "3.677.0" - "@aws-sdk/client-sts" "3.677.0" - "@aws-sdk/core" "3.677.0" - "@aws-sdk/credential-provider-node" "3.677.0" - "@aws-sdk/middleware-host-header" "3.667.0" - "@aws-sdk/middleware-logger" "3.667.0" - "@aws-sdk/middleware-recursion-detection" "3.667.0" - "@aws-sdk/middleware-user-agent" "3.677.0" - "@aws-sdk/region-config-resolver" "3.667.0" - "@aws-sdk/types" "3.667.0" - "@aws-sdk/util-endpoints" "3.667.0" - "@aws-sdk/util-user-agent-browser" "3.675.0" - "@aws-sdk/util-user-agent-node" "3.677.0" - "@aws-sdk/xml-builder" "3.662.0" + "@aws-sdk/client-sso-oidc" "3.682.0" + "@aws-sdk/client-sts" "3.682.0" + "@aws-sdk/core" "3.679.0" + "@aws-sdk/credential-provider-node" "3.682.0" + "@aws-sdk/middleware-host-header" "3.679.0" + "@aws-sdk/middleware-logger" "3.679.0" + "@aws-sdk/middleware-recursion-detection" "3.679.0" + "@aws-sdk/middleware-user-agent" "3.682.0" + "@aws-sdk/region-config-resolver" "3.679.0" + "@aws-sdk/types" "3.679.0" + "@aws-sdk/util-endpoints" "3.679.0" + "@aws-sdk/util-user-agent-browser" "3.679.0" + "@aws-sdk/util-user-agent-node" "3.682.0" + "@aws-sdk/xml-builder" "3.679.0" "@smithy/config-resolver" "^3.0.9" "@smithy/core" "^2.4.8" "@smithy/fetch-http-handler" "^3.2.9" @@ -139,34 +139,34 @@ tslib 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+"@aws-sdk/client-sso-oidc@3.682.0": + version "3.682.0" + resolved "https://registry.yarnpkg.com/@aws-sdk/client-sso-oidc/-/client-sso-oidc-3.682.0.tgz#423d6b3179fe560a515e3b286689414590f3263b" + integrity sha512-ZPZ7Y/r/w3nx/xpPzGSqSQsB090Xk5aZZOH+WBhTDn/pBEuim09BYXCLzvvxb7R7NnuoQdrTJiwimdJAhHl7ZQ== dependencies: "@aws-crypto/sha256-browser" "5.2.0" "@aws-crypto/sha256-js" "5.2.0" - "@aws-sdk/core" "3.677.0" - "@aws-sdk/credential-provider-node" "3.677.0" - "@aws-sdk/middleware-host-header" "3.667.0" - "@aws-sdk/middleware-logger" "3.667.0" - "@aws-sdk/middleware-recursion-detection" "3.667.0" - "@aws-sdk/middleware-user-agent" "3.677.0" - "@aws-sdk/region-config-resolver" "3.667.0" - "@aws-sdk/types" "3.667.0" - "@aws-sdk/util-endpoints" "3.667.0" - "@aws-sdk/util-user-agent-browser" "3.675.0" - "@aws-sdk/util-user-agent-node" "3.677.0" + "@aws-sdk/core" "3.679.0" + "@aws-sdk/credential-provider-node" "3.682.0" + "@aws-sdk/middleware-host-header" "3.679.0" + 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sha512-PYH9RFUMYLFl66HSBq4tIx6fHViMLkhJHTYJoJONpBs+Td+NwVJ895AdLtDsBIhMS0YseCbPpuyjUCJgsUrwUw== dependencies: "@aws-crypto/sha256-browser" "5.2.0" "@aws-crypto/sha256-js" "5.2.0" - "@aws-sdk/core" "3.677.0" - "@aws-sdk/middleware-host-header" "3.667.0" - "@aws-sdk/middleware-logger" "3.667.0" - "@aws-sdk/middleware-recursion-detection" "3.667.0" - "@aws-sdk/middleware-user-agent" "3.677.0" - "@aws-sdk/region-config-resolver" "3.667.0" - "@aws-sdk/types" "3.667.0" - "@aws-sdk/util-endpoints" "3.667.0" - "@aws-sdk/util-user-agent-browser" "3.675.0" - "@aws-sdk/util-user-agent-node" "3.677.0" + "@aws-sdk/core" "3.679.0" + "@aws-sdk/middleware-host-header" "3.679.0" + "@aws-sdk/middleware-logger" "3.679.0" + "@aws-sdk/middleware-recursion-detection" "3.679.0" + "@aws-sdk/middleware-user-agent" "3.682.0" + "@aws-sdk/region-config-resolver" "3.679.0" + "@aws-sdk/types" "3.679.0" + "@aws-sdk/util-endpoints" "3.679.0" + "@aws-sdk/util-user-agent-browser" "3.679.0" + 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+337,12 @@ "@smithy/util-utf8" "^3.0.0" tslib "^2.6.2" -"@aws-sdk/core@3.677.0": - version "3.677.0" - resolved "https://registry.yarnpkg.com/@aws-sdk/core/-/core-3.677.0.tgz#4782cc573b28407e892db111cd730a5183a207ec" - integrity sha512-5auvc1wmXmd7u9Y9nM95Ia+VX7J2FiZLuADitHqE4mHPH9riDgOY+uK/yM+UKr+lfq4zKiZQG7i8cfabZlCY8g== +"@aws-sdk/core@3.679.0": + version "3.679.0" + resolved "https://registry.yarnpkg.com/@aws-sdk/core/-/core-3.679.0.tgz#102aa1d19db5bdcabefc2dcd044f2fb5d0771568" + integrity sha512-CS6PWGX8l4v/xyvX8RtXnBisdCa5+URzKd0L6GvHChype9qKUVxO/Gg6N/y43Hvg7MNWJt9FBPNWIxUB+byJwg== dependencies: - "@aws-sdk/types" "3.667.0" + "@aws-sdk/types" "3.679.0" "@smithy/core" "^2.4.8" "@smithy/node-config-provider" "^3.1.8" "@smithy/property-provider" "^3.1.7" @@ -354,24 +354,24 @@ fast-xml-parser "4.4.1" tslib "^2.6.2" -"@aws-sdk/credential-provider-env@3.677.0": - version "3.677.0" - resolved 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-browserslist@^4.0.0, browserslist@^4.18.1, browserslist@^4.21.10, browserslist@^4.23.0, browserslist@^4.23.3, browserslist@^4.24.0: +browserslist@^4.0.0, browserslist@^4.18.1, browserslist@^4.21.10, browserslist@^4.23.0, browserslist@^4.24.0, browserslist@^4.24.2: version "4.24.2" resolved "https://registry.yarnpkg.com/browserslist/-/browserslist-4.24.2.tgz#f5845bc91069dbd55ee89faf9822e1d885d16580" integrity sha512-ZIc+Q62revdMcqC6aChtW4jz3My3klmCO1fEmINZY/8J3EpBg5/A/D0AKmBveUh6pgoeycoMkVMko84tuYS+Gg== @@ -6471,9 +6603,9 @@ caniuse-api@^3.0.0: lodash.uniq "^4.5.0" caniuse-lite@^1.0.0, caniuse-lite@^1.0.30001669: - version "1.0.30001669" - resolved "https://registry.yarnpkg.com/caniuse-lite/-/caniuse-lite-1.0.30001669.tgz#fda8f1d29a8bfdc42de0c170d7f34a9cf19ed7a3" - integrity sha512-DlWzFDJqstqtIVx1zeSpIMLjunf5SmwOw0N2Ck/QSQdS8PLS4+9HrLaYei4w8BIAL7IB/UEDu889d8vhCTPA0w== + version "1.0.30001676" + resolved 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version "3.39.0" + resolved "https://registry.yarnpkg.com/core-js-compat/-/core-js-compat-3.39.0.tgz#b12dccb495f2601dc860bdbe7b4e3ffa8ba63f61" + integrity sha512-VgEUx3VwlExr5no0tXlBt+silBvhTryPwCXRI2Id1PN8WTKu7MreethvddqOubrYxkFdv/RnYrqlv1sFNAUelw== dependencies: - browserslist "^4.23.3" + browserslist "^4.24.2" core-js-pure@^3.23.3: - version "3.38.1" - resolved "https://registry.yarnpkg.com/core-js-pure/-/core-js-pure-3.38.1.tgz#e8534062a54b7221344884ba9b52474be495ada3" - integrity sha512-BY8Etc1FZqdw1glX0XNOq2FDwfrg/VGqoZOZCdaL+UmdaqDwQwYXkMJT4t6In+zfEfOJDcM9T0KdbBeJg8KKCQ== + version "3.39.0" + resolved "https://registry.yarnpkg.com/core-js-pure/-/core-js-pure-3.39.0.tgz#aa0d54d70a15bdc13e7c853db87c10abc30d68f3" + integrity sha512-7fEcWwKI4rJinnK+wLTezeg2smbFFdSBP6E2kQZNbnzM2s1rpKQ6aaRteZSSg7FLU3P0HGGVo/gbpfanU36urg== core-util-is@1.0.2: version "1.0.2" @@ -7107,6 +7239,16 @@ cors@^2.8.5: object-assign "^4" vary "^1" +cosmiconfig@9.0.0: + version "9.0.0" + resolved "https://registry.yarnpkg.com/cosmiconfig/-/cosmiconfig-9.0.0.tgz#34c3fc58287b915f3ae905ab6dc3de258b55ad9d" + integrity sha512-itvL5h8RETACmOTFc4UfIyB2RfEHi71Ax6E/PivVxq9NseKbOWpeyHEOIbmAw1rs8Ak0VursQNww7lf7YtUwzg== + dependencies: + env-paths "^2.2.1" + import-fresh "^3.3.0" + js-yaml "^4.1.0" + parse-json "^5.2.0" + cosmiconfig@^6.0.0: version "6.0.0" resolved "https://registry.yarnpkg.com/cosmiconfig/-/cosmiconfig-6.0.0.tgz#da4fee853c52f6b1e6935f41c1a2fc50bd4a9982" @@ -7129,16 +7271,6 @@ cosmiconfig@^7.0.0, cosmiconfig@^7.0.1: path-type "^4.0.0" yaml "^1.10.0" -cosmiconfig@^8.2.0: - version "8.3.6" - resolved "https://registry.yarnpkg.com/cosmiconfig/-/cosmiconfig-8.3.6.tgz#060a2b871d66dba6c8538ea1118ba1ac16f5fae3" - integrity sha512-kcZ6+W5QzcJ3P1Mt+83OUv/oHFqZHIx8DuxG6eZ5RGMERoLqp4BuGjhHLYGK+Kf5XVkQvqBSmAy/nGWN3qDgEA== - dependencies: - import-fresh "^3.3.0" - js-yaml "^4.1.0" - parse-json "^5.2.0" - path-type "^4.0.0" - crc@^3.8.0: version "3.8.0" resolved "https://registry.yarnpkg.com/crc/-/crc-3.8.0.tgz#ad60269c2c856f8c299e2c4cc0de4556914056c6" @@ -8053,9 +8185,9 @@ electron-publish@25.1.7: mime "^2.5.2" electron-to-chromium@^1.5.41: - version "1.5.43" - resolved "https://registry.yarnpkg.com/electron-to-chromium/-/electron-to-chromium-1.5.43.tgz#d9e69fc709ddebd521416de9d17cdef81d2d4718" - integrity sha512-NxnmFBHDl5Sachd2P46O7UJiMaMHMLSofoIWVJq3mj8NJgG0umiSeljAVP9lGzjI0UDLJJ5jjoGjcrB8RSbjLQ== + version "1.5.49" + resolved "https://registry.yarnpkg.com/electron-to-chromium/-/electron-to-chromium-1.5.49.tgz#9358f514ab6eeed809a8689f4b39ea5114ae729c" + integrity sha512-ZXfs1Of8fDb6z7WEYZjXpgIRF6MEu8JdeGA0A40aZq6OQbS+eJpnnV49epZRna2DU/YsEjSQuGtQPPtvt6J65A== electron-updater@^6.1.1: version "6.3.9" @@ -8166,7 +8298,7 @@ entities@^4.2.0, entities@^4.5.0: resolved "https://registry.yarnpkg.com/entities/-/entities-4.5.0.tgz#5d268ea5e7113ec74c4d033b79ea5a35a488fb48" integrity sha512-V0hjH4dGPh9Ao5p0MoRY6BVqtwCjhz6vI5LT8AJ55H+4g9/4vbHx1I54fS0XuclLhDHArPQCiMjDxjaL8fPxhw== -env-paths@^2.2.0: +env-paths@^2.2.0, env-paths@^2.2.1: version "2.2.1" resolved "https://registry.yarnpkg.com/env-paths/-/env-paths-2.2.1.tgz#420399d416ce1fbe9bc0a07c62fa68d67fd0f8f2" integrity sha512-+h1lkLKhZMTYjog1VEpJNG7NZJWcuc2DDk/qsqSTRRCOXiLjeQ1d1/udrUGhqMxUgAlwKNZ0cf2uqan5GLuS2A== @@ -8343,7 +8475,37 @@ esbuild-register@^3.5.0: dependencies: debug "^4.3.4" -"esbuild@^0.18.0 || ^0.19.0 || ^0.20.0 || ^0.21.0 || ^0.22.0 || ^0.23.0", esbuild@~0.23.0: +"esbuild@^0.18.0 || ^0.19.0 || ^0.20.0 || ^0.21.0 || ^0.22.0 || ^0.23.0 || ^0.24.0": + version "0.24.0" + resolved "https://registry.yarnpkg.com/esbuild/-/esbuild-0.24.0.tgz#f2d470596885fcb2e91c21eb3da3b3c89c0b55e7" + integrity sha512-FuLPevChGDshgSicjisSooU0cemp/sGXR841D5LHMB7mTVOmsEHcAxaH3irL53+8YDIeVNQEySh4DaYU/iuPqQ== + optionalDependencies: + "@esbuild/aix-ppc64" "0.24.0" + "@esbuild/android-arm" "0.24.0" + "@esbuild/android-arm64" 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-external-editor@^3.0.3: +external-editor@^3.0.3, external-editor@^3.1.0: version "3.1.0" resolved "https://registry.yarnpkg.com/external-editor/-/external-editor-3.1.0.tgz#cb03f740befae03ea4d283caed2741a83f335495" integrity sha512-hMQ4CX1p1izmuLYyZqLMO/qGNw10wSv9QDCPfzXfyFrOaCSSoRfqE1Kf1s5an66J5JZC62NewG+mK49jOCtQew== @@ -9082,7 +9244,7 @@ fs-extra@^10.0.0, fs-extra@^10.1.0: jsonfile "^6.0.1" universalify "^2.0.0" -fs-extra@^11.1.0, fs-extra@^11.1.1, fs-extra@^11.2.0: +fs-extra@^11.1.1, fs-extra@^11.2.0: version "11.2.0" resolved "https://registry.yarnpkg.com/fs-extra/-/fs-extra-11.2.0.tgz#e70e17dfad64232287d01929399e0ea7c86b0e5b" integrity sha512-PmDi3uwK5nFuXh7XDTlVnS17xJS7vW36is2+w3xcv8SVxiB4NyATf4ctkVY5bkSjX0Y4nbvZCq1/EjtEyr9ktw== @@ -9351,7 +9513,7 @@ gitconfiglocal@^1.0.0: dependencies: ini "^1.3.2" -github-slugger@^2, github-slugger@^2.0.0: +github-slugger@^2: version "2.0.0" resolved 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- -hast-util-to-string@^3.0.0: - version "3.0.1" - resolved "https://registry.yarnpkg.com/hast-util-to-string/-/hast-util-to-string-3.0.1.tgz#a4f15e682849326dd211c97129c94b0c3e76527c" - integrity sha512-XelQVTDWvqcl3axRfI0xSeoVKzyIFPwsAGSLIsKdJKQMXDYJS4WYrBNF/8J7RdhIcFI2BOHgAifggsvsxp/3+A== - dependencies: - "@types/hast" "^3.0.0" - he@^1.2.0: version "1.2.0" resolved "https://registry.yarnpkg.com/he/-/he-1.2.0.tgz#84ae65fa7eafb165fddb61566ae14baf05664f0f" @@ -9757,11 +9898,6 @@ html-minifier-terser@^6.0.2: relateurl "^0.2.7" terser "^5.10.0" -html-tags@^3.1.0: - version "3.3.1" - resolved "https://registry.yarnpkg.com/html-tags/-/html-tags-3.3.1.tgz#a04026a18c882e4bba8a01a3d39cfe465d40b5ce" - integrity sha512-ztqyC3kLto0e9WbNp0aeP+M3kTt+nbaIveGmUxAtZa+8iFgKLUOD4YKM5j+f3QD89bra7UeumolZHKuOXnTmeQ== - html-webpack-plugin@^5.5.0: version "5.6.3" resolved "https://registry.yarnpkg.com/html-webpack-plugin/-/html-webpack-plugin-5.6.3.tgz#a31145f0fee4184d53a794f9513147df1e653685" @@ -10118,11 +10254,6 @@ ipaddr.js@^2.1.0: resolved "https://registry.yarnpkg.com/ipaddr.js/-/ipaddr.js-2.2.0.tgz#d33fa7bac284f4de7af949638c9d68157c6b92e8" integrity sha512-Ag3wB2o37wslZS19hZqorUnrnzSkpOVy+IiiDEiTqNubEYpYuHWIf6K4psgN2ZWKExS4xhVCrRVfb/wfW8fWJA== -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 sha512-/51/TKE88Lmm7Gc4/8btclNXWS+g50wXhYJq8HWIBAGUBnoAdRu1aXeh364t/O7wXDAcTJDP8PNuNKWUDWie+A== - is-arguments@^1.0.4: version "1.1.1" resolved "https://registry.yarnpkg.com/is-arguments/-/is-arguments-1.1.1.tgz#15b3f88fda01f2a97fec84ca761a560f123efa9b" @@ -10338,11 +10469,6 @@ is-plain-obj@^4.1.0: resolved "https://registry.yarnpkg.com/is-plain-obj/-/is-plain-obj-4.1.0.tgz#d65025edec3657ce032fd7db63c97883eaed71f0" integrity sha512-+Pgi+vMuUNkJyExiMBt5IlFoMyKnr5zhJ4Uspz58WOhBF5QoIZkFyNHIbBAtHwzVAgk5RtndVNsDRN61/mmDqg== -is-plain-object@5.0.0, is-plain-object@^5.0.0: - version "5.0.0" - resolved "https://registry.yarnpkg.com/is-plain-object/-/is-plain-object-5.0.0.tgz#4427f50ab3429e9025ea7d52e9043a9ef4159344" - integrity sha512-VRSzKkbMm5jMDoKLbltAkFQ5Qr7VDiTFGXxYFXXowVj387GeGNOCsOH6Msy00SGZ3Fp84b1Naa1psqgcCIEP5Q== - is-plain-object@^2.0.4: version "2.0.4" resolved "https://registry.yarnpkg.com/is-plain-object/-/is-plain-object-2.0.4.tgz#2c163b3fafb1b606d9d17928f05c2a1c38e07677" @@ -10350,6 +10476,11 @@ is-plain-object@^2.0.4: dependencies: isobject "^3.0.1" +is-plain-object@^5.0.0: + version "5.0.0" + resolved "https://registry.yarnpkg.com/is-plain-object/-/is-plain-object-5.0.0.tgz#4427f50ab3429e9025ea7d52e9043a9ef4159344" + integrity sha512-VRSzKkbMm5jMDoKLbltAkFQ5Qr7VDiTFGXxYFXXowVj387GeGNOCsOH6Msy00SGZ3Fp84b1Naa1psqgcCIEP5Q== + is-potential-custom-element-name@^1.0.1: version "1.0.1" resolved "https://registry.yarnpkg.com/is-potential-custom-element-name/-/is-potential-custom-element-name-1.0.1.tgz#171ed6f19e3ac554394edf78caa05784a45bebb5" @@ -10477,7 +10608,7 @@ is-wsl@^2.2.0: dependencies: is-docker "^2.0.0" -is-wsl@^3, is-wsl@^3.1.0: +is-wsl@^3.1.0: version "3.1.0" resolved "https://registry.yarnpkg.com/is-wsl/-/is-wsl-3.1.0.tgz#e1c657e39c10090afcbedec61720f6b924c3cbd2" integrity sha512-UcVfVfaK4Sc4m7X3dUSoHoozQGBEFeDC+zVo06t98xe8CzHSZZBekNXH+tu0NalHolcJ/QAGqS46Hef7QXBIMw== @@ -11282,15 +11413,15 @@ lerna-changelog@^2.2.0: yargs "^17.1.0" lerna@^8.0.0: - version "8.1.8" - resolved "https://registry.yarnpkg.com/lerna/-/lerna-8.1.8.tgz#9edc9ce4fb4b6c7e22c994e9ef91d4e0370595b2" - integrity sha512-Rmo5ShMx73xM2CUcRixjmpZIXB7ZFlWEul1YvJyx/rH4onAwDHtUGD7Rx4NZYL8QSRiQHroglM2Oyq+WqA4BYg== + version "8.1.9" + resolved "https://registry.yarnpkg.com/lerna/-/lerna-8.1.9.tgz#1233c3cfacca3b85b23c292235e246d79de3de32" + integrity sha512-ZRFlRUBB2obm+GkbTR7EbgTMuAdni6iwtTQTMy7LIrQ4UInG44LyfRepljtgUxh4HA0ltzsvWfPkd5J1DKGCeQ== dependencies: - "@lerna/create" "8.1.8" + "@lerna/create" "8.1.9" "@npmcli/arborist" "7.5.4" "@npmcli/package-json" "5.2.0" "@npmcli/run-script" "8.1.0" - "@nx/devkit" ">=17.1.2 < 20" + "@nx/devkit" ">=17.1.2 < 21" "@octokit/plugin-enterprise-rest" "6.0.1" "@octokit/rest" "19.0.11" aproba "2.0.0" @@ -11304,7 +11435,7 @@ lerna@^8.0.0: conventional-changelog-angular "7.0.0" conventional-changelog-core "5.0.1" conventional-recommended-bump "7.0.1" - cosmiconfig "^8.2.0" + cosmiconfig "9.0.0" dedent "1.5.3" envinfo "7.13.0" execa "5.0.0" @@ -11335,7 +11466,7 @@ lerna@^8.0.0: npm-package-arg "11.0.2" npm-packlist "8.0.2" npm-registry-fetch "^17.1.0" - nx ">=17.1.2 < 20" + nx ">=17.1.2 < 21" p-map "4.0.0" p-map-series "2.1.0" p-pipe "3.1.0" @@ -11737,11 +11868,6 @@ map-or-similar@^1.5.0: resolved 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