diff --git a/CHANGELOG.md b/CHANGELOG.md index aae20f2fca..90e053108c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,46 @@ +yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.16.1 + +## 2.16.1 (2024-11-03) + +#### :rocket: Enhancement + +- `app-core`, `core`, `product-core`, `text-indexing` + - [#4624](https://github.com/GMOD/jbrowse-components/pull/4624) Add utility + links to synteny feature details to allow centering a view on a feature + ([@cmdcolin](https://github.com/cmdcolin)) +- Other + - [#4628](https://github.com/GMOD/jbrowse-components/pull/4628) Allow + configuring Hi-C normalization and default resolution multiplier + ([@cmdcolin](https://github.com/cmdcolin)) + - [#4619](https://github.com/GMOD/jbrowse-components/pull/4619) Add + resolutionMultiplier config slot to BigWigAdapter + ([@cmdcolin](https://github.com/cmdcolin)) + +#### :bug: Bug Fix + +- [#4634](https://github.com/GMOD/jbrowse-components/pull/4634) Fix opening + local files in the multi-wiggle add track selector + ([@cmdcolin](https://github.com/cmdcolin)) +- [#4633](https://github.com/GMOD/jbrowse-components/pull/4633) Fix "Add track" + select box not going away after selecting element + ([@cmdcolin](https://github.com/cmdcolin)) +- [#4632](https://github.com/GMOD/jbrowse-components/pull/4632) Standardize + modification colors between alignments track coverage and pileup subtracks + ([@cmdcolin](https://github.com/cmdcolin)) +- [#4631](https://github.com/GMOD/jbrowse-components/pull/4631) Fix config + description of assembly name ordering for synteny data adapters + ([@cmdcolin](https://github.com/cmdcolin)) +- [#4630](https://github.com/GMOD/jbrowse-components/pull/4630) Fix MM tag + modifications from particular BAM file failing to render on the negative + strand ([@cmdcolin](https://github.com/cmdcolin)) +- [#4626](https://github.com/GMOD/jbrowse-components/pull/4626) Fix dark redraw + on selected features after vertical resize of the synteny canvas + ([@cmdcolin](https://github.com/cmdcolin)) + +#### Committers: 1 + +- Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 1.20s. + yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.16.0 ## 2.16.0 (2024-10-23) diff --git a/lerna.json b/lerna.json index bd3fefa861..b03141ea35 100644 --- a/lerna.json +++ b/lerna.json @@ -1,5 +1,5 @@ { - "version": "2.16.0", + "version": "2.16.1", "npmClient": "yarn", "$schema": "node_modules/lerna/schemas/lerna-schema.json" } diff --git a/package.json b/package.json index 1b61fe42b3..cbac328f70 100644 --- a/package.json +++ b/package.json @@ -24,7 +24,8 @@ "configdocs": "rm -rf website/docs/config && mkdir website/docs/config && yarn tsx docs/generateConfigDocs.ts", "statedocs": "rm -rf website/docs/models && mkdir website/docs/models && yarn tsx docs/generateStateModelDocs.ts", "autogen": "yarn statedocs && yarn configdocs && yarn prettier --write website", - "releasenotes": "npx prettier --prose-wrap never website/blog/$(ls -Art website/blog/ | tail -n 1)|sed -e '/## Downloads/,+7d'|tail -n +7" + "releasenotes": "yarn prettier --prose-wrap never website/blog/$(ls -Art website/blog/ | tail -n 1)|sed -e '/## Downloads/,+7d'|tail -n +7", + "copynotes": "yarn --silent releasenotes | xclip -selection clipboard" }, "devDependencies": { "@babel/core": "^7.3.4", @@ -100,7 +101,7 @@ "dependency-graph": "^1.0.0", "dotenv": "^16.3.1", "dotenv-expand": "^11.0.3", - "electron": "32.1.0", + "electron": "33.0.2", "electron-builder": "^25.1.6", "electron-mock-ipc": "^0.3.8", "eslint": "^9.0.0", diff --git a/packages/app-core/package.json b/packages/app-core/package.json index 4a72a8b5ee..cd8ec69f01 100644 --- a/packages/app-core/package.json +++ b/packages/app-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/app-core", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 code shared between the 'full featured' apps e.g. jbrowse-web and jbrowse-desktop", "keywords": [ "jbrowse", @@ -42,7 +42,7 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/product-core": "^2.16.0", + "@jbrowse/product-core": "^2.16.1", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "copy-to-clipboard": "^3.3.1" 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} ${str}`} +} diff --git a/packages/core/BaseFeatureWidget/BaseFeatureDetail/index.tsx b/packages/core/BaseFeatureWidget/BaseFeatureDetail/index.tsx index 2fa77967b0..81ea0fa034 100644 --- a/packages/core/BaseFeatureWidget/BaseFeatureDetail/index.tsx +++ b/packages/core/BaseFeatureWidget/BaseFeatureDetail/index.tsx @@ -1,132 +1,17 @@ import React from 'react' -import { ErrorBoundary } from '@jbrowse/core/ui/ErrorBoundary' -import { - Accordion, - AccordionDetails, - AccordionSummary, - Divider, - Typography, -} from '@mui/material' -import { makeStyles } from 'tss-react/mui' import { observer } from 'mobx-react' -import { IAnyStateTreeNode } from 'mobx-state-tree' -// icons -import ExpandMore from '@mui/icons-material/ExpandMore' - -// locals -import { - getEnv, - getSession, - assembleLocString, - toLocale, - SimpleFeatureSerialized, -} from '../../util' +// utils import { ErrorMessage } from '../../ui' -import SequenceFeatureDetails from '../SequenceFeatureDetails' import { BaseCardProps, BaseProps } from '../types' -import SimpleField from './SimpleField' -import Attributes from './Attributes' -import { generateTitle, isEmpty } from './util' - -// coreDetails are omitted in some circumstances -const coreDetails = [ - 'name', - 'start', - 'end', - 'strand', - 'refName', - 'description', - 'type', -] - -const useStyles = makeStyles()(theme => ({ - expansionPanelDetails: { - display: 'block', - padding: theme.spacing(1), - }, - icon: { - color: theme.palette.tertiary.contrastText || '#fff', - }, -})) - -export function BaseCard({ - children, - title, - defaultExpanded = true, -}: BaseCardProps) { - const { classes } = useStyles() - return ( - - }> - {title} - - - {children} - - - ) -} - -function Position(props: BaseProps) { - const { feature } = props - const strand = feature.strand as number - const strandMap: Record = { - '-1': '-', - '0': '', - '1': '+', - } - const str = strandMap[strand] ? `(${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 +import { isEmpty } from './util' +import { replaceUndefinedWithNull } from '../util' - 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 +38,26 @@ 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' +export { default as BaseCard } from './BaseCard' +export { default as FeatureDetails } from './FeatureDetails' 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/core/package.json b/packages/core/package.json index f275b9d515..de511578dd 100644 --- a/packages/core/package.json +++ b/packages/core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/core", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 core libraries used by plugins", "keywords": [ "jbrowse", diff --git a/packages/embedded-core/package.json b/packages/embedded-core/package.json index aa0eacb411..f05863e3de 100644 --- a/packages/embedded-core/package.json +++ b/packages/embedded-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/embedded-core", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 code shared between embedded products", "keywords": [ "jbrowse", @@ -42,8 +42,8 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/core": "^2.16.0", - "@jbrowse/product-core": "^2.16.0", + "@jbrowse/core": "^2.16.1", + "@jbrowse/product-core": "^2.16.1", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "copy-to-clipboard": "^3.3.1" diff --git a/packages/product-core/package.json b/packages/product-core/package.json index bd28ed70d9..f5e064740b 100644 --- a/packages/product-core/package.json +++ b/packages/product-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/product-core", - "version": "2.16.0", + "version": "2.16.1", "sideEffects": false, "description": "JBrowse 2 code shared between products but not used by plugins", "keywords": [ @@ -43,7 +43,7 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/core": "^2.16.0", + "@jbrowse/core": "^2.16.1", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "copy-to-clipboard": "^3.3.1", 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/packages/sv-core/package.json b/packages/sv-core/package.json index 9b5b9e3723..3f1fd429f9 100644 --- a/packages/sv-core/package.json +++ b/packages/sv-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/sv-core", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 code shared between sv type code", "keywords": [ "jbrowse", @@ -41,7 +41,7 @@ "useSrc": "node ../../scripts/useSrc.js" }, "dependencies": { - "@jbrowse/plugin-linear-genome-view": "^2.16.0", + "@jbrowse/plugin-linear-genome-view": "^2.16.1", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0" }, diff --git a/packages/text-indexing/package.json b/packages/text-indexing/package.json index 6524e12898..41c32f0b4a 100644 --- a/packages/text-indexing/package.json +++ b/packages/text-indexing/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/text-indexing", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 text indexing for desktop", "keywords": [ "jbrowse", @@ -42,7 +42,7 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/core": "^2.16.0", + "@jbrowse/core": "^2.16.1", "ixixx": "^2.0.1", "node-fetch": "^2.6.0", "sanitize-filename": "^1.6.3" diff --git a/packages/text-indexing/src/types/common.ts b/packages/text-indexing/src/types/common.ts index 1fdfb3b38e..f8b57c0a1d 100644 --- a/packages/text-indexing/src/types/common.ts +++ b/packages/text-indexing/src/types/common.ts @@ -29,19 +29,35 @@ export function isURL(FileName: string) { return url.protocol === 'http:' || url.protocol === 'https:' } -export async function getLocalOrRemoteStream(uri: string, out: string) { - if (isURL(uri)) { - const result = await createRemoteStream(uri) - return { - totalBytes: +(result.headers.get('Content-Length') || 0), - stream: result.body, - } +export async function getLocalOrRemoteStream({ + file, + out, + onBytesReceived, + onTotalBytes, +}: { + file: string + out: string + onBytesReceived: (totalBytesReceived: number) => void + onTotalBytes: (totalBytes: number) => void +}) { + let receivedBytes = 0 + if (isURL(file)) { + const result = await createRemoteStream(file) + result.body.on('data', chunk => { + receivedBytes += chunk.length + onBytesReceived(receivedBytes) + }) + onTotalBytes(+(result.headers.get('Content-Length') || 0)) + return result.body } else { - const filename = path.isAbsolute(uri) ? uri : path.join(out, uri) - return { - totalBytes: fs.statSync(filename).size, - stream: fs.createReadStream(filename), - } + const filename = path.isAbsolute(file) ? file : path.join(out, file) + const stream = fs.createReadStream(filename) + stream.on('data', chunk => { + receivedBytes += chunk.length + onBytesReceived(receivedBytes) + }) + onTotalBytes(fs.statSync(filename).size) + return stream } } diff --git a/packages/text-indexing/src/types/gff3Adapter.ts b/packages/text-indexing/src/types/gff3Adapter.ts index a9030457b8..c8383ab671 100644 --- a/packages/text-indexing/src/types/gff3Adapter.ts +++ b/packages/text-indexing/src/types/gff3Adapter.ts @@ -23,17 +23,11 @@ export async function* indexGff3({ onUpdate: (progressBytes: number) => void }) { const { trackId } = config - - let receivedBytes = 0 - const { totalBytes, stream } = await getLocalOrRemoteStream( - inLocation, - outDir, - ) - onStart(totalBytes) - - stream.on('data', chunk => { - receivedBytes += chunk.length - onUpdate(receivedBytes) + const stream = await getLocalOrRemoteStream({ + file: inLocation, + out: outDir, + onTotalBytes: onStart, + onBytesReceived: onUpdate, }) const rl = readline.createInterface({ diff --git a/packages/text-indexing/src/types/vcfAdapter.ts b/packages/text-indexing/src/types/vcfAdapter.ts index 3864c6290c..4767757251 100644 --- a/packages/text-indexing/src/types/vcfAdapter.ts +++ b/packages/text-indexing/src/types/vcfAdapter.ts @@ -21,17 +21,11 @@ export async function* indexVcf({ onUpdate: (progressBytes: number) => void }) { const { trackId } = config - let receivedBytes = 0 - const { totalBytes, stream } = await getLocalOrRemoteStream( - inLocation, - outDir, - ) - - onStart(totalBytes) - - stream.on('data', chunk => { - receivedBytes += chunk.length - onUpdate(receivedBytes) + const stream = await getLocalOrRemoteStream({ + file: inLocation, + out: outDir, + onTotalBytes: onStart, + onBytesReceived: onUpdate, }) const gzStream = /.b?gz$/.exec(inLocation) diff --git a/packages/web-core/package.json b/packages/web-core/package.json index 3a68530040..bb81e8e410 100644 --- a/packages/web-core/package.json +++ b/packages/web-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/web-core", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 code shared between web-app type products", "keywords": [ "jbrowse", @@ -42,8 +42,8 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/app-core": "^2.16.0", - "@jbrowse/product-core": "^2.16.0", + "@jbrowse/app-core": "^2.16.1", + "@jbrowse/product-core": "^2.16.1", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "clone": "^2.0.0", diff --git a/plugins/alignments/package.json b/plugins/alignments/package.json index 7343e0aa39..67f7c6137a 100644 --- a/plugins/alignments/package.json +++ b/plugins/alignments/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-alignments", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 alignments adapters, tracks, etc.", "keywords": [ "jbrowse", @@ -38,7 +38,7 @@ "dependencies": { "@gmod/bam": "^2.0.0", "@gmod/cram": "^3.0.3", - "@jbrowse/sv-core": "^2.16.0", + "@jbrowse/sv-core": "^2.16.1", "@mui/icons-material": "^6.0.0", "canvas2svg": "^1.0.16", "clone": "^2.1.2", 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/alignments/src/LinearPileupDisplay/model.ts b/plugins/alignments/src/LinearPileupDisplay/model.ts index caa6da578e..51c5c2f5cd 100644 --- a/plugins/alignments/src/LinearPileupDisplay/model.ts +++ b/plugins/alignments/src/LinearPileupDisplay/model.ts @@ -96,7 +96,7 @@ function stateModelFactory(configSchema: AnyConfigurationSchemaType) { if (!self.modificationTagMap.has(value)) { self.modificationTagMap.set( value, - modificationColors[value] || randomColor(), + modificationColors[value] || randomColor(value), ) } }) diff --git a/plugins/alignments/src/LinearSNPCoverageDisplay/models/model.ts b/plugins/alignments/src/LinearSNPCoverageDisplay/models/model.ts index b8e2b1917c..6da467f996 100644 --- a/plugins/alignments/src/LinearSNPCoverageDisplay/models/model.ts +++ b/plugins/alignments/src/LinearSNPCoverageDisplay/models/model.ts @@ -115,7 +115,7 @@ function stateModelFactory( if (!self.modificationTagMap.has(value)) { self.modificationTagMap.set( value, - modificationColors[value] || randomColor(), + modificationColors[value] || randomColor(value), ) } }) diff --git a/plugins/alignments/src/MismatchParser/index.ts b/plugins/alignments/src/MismatchParser/index.ts index cd7d61f405..4573515930 100644 --- a/plugins/alignments/src/MismatchParser/index.ts +++ b/plugins/alignments/src/MismatchParser/index.ts @@ -351,13 +351,18 @@ export function getModificationPositions( } i++ } while (delta >= 0 && i < seq.length) - - const temp = i - 1 - positions.push(fstrand === -1 ? seq.length - 1 - temp : temp) - } - if (fstrand === -1) { - positions.sort((a, b) => a - b) + if (fstrand === -1) { + const pos = seq.length - i + if (pos >= 0) { + // avoid negative-number-positions in array, seen in #4629 cause + // unknown, could warrant some further investigation + positions.unshift(pos) + } + } else { + positions.push(i - 1) + } } + result.push({ type, positions, diff --git a/plugins/alignments/src/util.ts b/plugins/alignments/src/util.ts index aa23ccd51b..8313836e7b 100644 --- a/plugins/alignments/src/util.ts +++ b/plugins/alignments/src/util.ts @@ -127,6 +127,7 @@ export const modificationColors = { g: 'rgb(255, 160, 86)', e: 'rgb(141, 221, 208)', b: 'rgb(202, 71, 47)', + a: 'hsl(136, 50%, 50%)', } as Record type DisplayModel = IAnyStateTreeNode & { setError: (arg: unknown) => void } @@ -149,6 +150,12 @@ export function createAutorun( }, opts), ) } -export function randomColor() { - return `hsl(${Math.random() * 200}, 50%, 50%)` + +export function randomColor(str: string) { + let sum = 0 + + for (let i = 0; i < str.length; i++) { + sum += str.charCodeAt(i) + } + return `hsl(${sum * 10}, 20%, 50%)` } diff --git a/plugins/arc/package.json b/plugins/arc/package.json index d68f54a117..6b96604bb0 100644 --- a/plugins/arc/package.json +++ b/plugins/arc/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-arc", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 arc adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/authentication/package.json b/plugins/authentication/package.json index d47b775933..c016d89a41 100644 --- a/plugins/authentication/package.json +++ b/plugins/authentication/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-authentication", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 Authentication", "keywords": [ "jbrowse", diff --git a/plugins/bed/package.json b/plugins/bed/package.json index d911ea9413..66446f11f9 100644 --- a/plugins/bed/package.json +++ b/plugins/bed/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-bed", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 bed adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/breakpoint-split-view/package.json b/plugins/breakpoint-split-view/package.json index a047fc0de4..18794f04f8 100644 --- a/plugins/breakpoint-split-view/package.json +++ b/plugins/breakpoint-split-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-breakpoint-split-view", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 breakpoint detail split view", "keywords": [ "jbrowse", diff --git a/plugins/canvas/package.json b/plugins/canvas/package.json index 1c5b278a32..2aa7e11577 100644 --- a/plugins/canvas/package.json +++ b/plugins/canvas/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-canvas", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 plugin for canvas features", "keywords": [ "jbrowse", diff --git a/plugins/canvas/src/CanvasFeatureRenderer/index.ts b/plugins/canvas/src/CanvasFeatureRenderer/index.ts index ab53629135..386d532391 100644 --- a/plugins/canvas/src/CanvasFeatureRenderer/index.ts +++ b/plugins/canvas/src/CanvasFeatureRenderer/index.ts @@ -1,7 +1,4 @@ - - export { default as ReactComponent } from './components/CanvasFeatureRendering' export { default as configSchema } from './configSchema' - -export {default} from './CanvasFeatureRenderer' \ No newline at end of file +export { default } from './CanvasFeatureRenderer' diff --git a/plugins/canvas/src/index.ts b/plugins/canvas/src/index.ts index 5632fd7dd7..0d9af50e83 100644 --- a/plugins/canvas/src/index.ts +++ b/plugins/canvas/src/index.ts @@ -21,6 +21,7 @@ export default class CanvasPlugin extends Plugin { } } - - -export {configSchema as canvasFeatureRendererConfigSchema, ReactComponent as CanvasFeatureRendererReactComponent} from './CanvasFeatureRenderer' \ No newline at end of file +export { + configSchema as canvasFeatureRendererConfigSchema, + ReactComponent as CanvasFeatureRendererReactComponent, +} from './CanvasFeatureRenderer' diff --git a/plugins/circular-view/package.json b/plugins/circular-view/package.json index 009255b9d6..f4ef5afd8f 100644 --- a/plugins/circular-view/package.json +++ b/plugins/circular-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-circular-view", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 circular view", "keywords": [ "jbrowse", diff --git a/plugins/comparative-adapters/package.json b/plugins/comparative-adapters/package.json index d88b9c0a83..e9ba006a03 100644 --- a/plugins/comparative-adapters/package.json +++ b/plugins/comparative-adapters/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-comparative-adapters", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 comparative adapters", "keywords": [ "jbrowse", diff --git a/plugins/comparative-adapters/src/ChainAdapter/configSchema.ts b/plugins/comparative-adapters/src/ChainAdapter/configSchema.ts index 82bda25fe0..42caf12d76 100644 --- a/plugins/comparative-adapters/src/ChainAdapter/configSchema.ts +++ b/plugins/comparative-adapters/src/ChainAdapter/configSchema.ts @@ -16,7 +16,7 @@ const ChainAdapter = ConfigurationSchema( type: 'stringArray', defaultValue: [], description: - 'Target is the first value in the array, query is the second', + 'Array of assembly names to use for this file. The query assembly name is the first value in the array, target assembly name is the second', }, /** * #slot diff --git a/plugins/comparative-adapters/src/DeltaAdapter/configSchema.ts b/plugins/comparative-adapters/src/DeltaAdapter/configSchema.ts index ff299a2a59..94a24ff012 100644 --- a/plugins/comparative-adapters/src/DeltaAdapter/configSchema.ts +++ b/plugins/comparative-adapters/src/DeltaAdapter/configSchema.ts @@ -16,7 +16,7 @@ const DeltaAdapter = ConfigurationSchema( type: 'stringArray', defaultValue: [], description: - 'Array of assembly names to use for this file. The target assembly name is the first value in the array, query assembly name is the second', + 'Array of assembly names to use for this file. The query assembly name is the first value in the array, target assembly name is the second', }, /** * #slot @@ -41,7 +41,10 @@ const DeltaAdapter = ConfigurationSchema( */ deltaLocation: { type: 'fileLocation', - defaultValue: { uri: '/path/to/file.delta', locationType: 'UriLocation' }, + defaultValue: { + uri: '/path/to/file.delta', + locationType: 'UriLocation', + }, }, }, { explicitlyTyped: true }, diff --git a/plugins/comparative-adapters/src/MashMapAdapter/configSchema.ts b/plugins/comparative-adapters/src/MashMapAdapter/configSchema.ts index cc53fa158b..9aa98e8c3a 100644 --- a/plugins/comparative-adapters/src/MashMapAdapter/configSchema.ts +++ b/plugins/comparative-adapters/src/MashMapAdapter/configSchema.ts @@ -15,7 +15,7 @@ const MashMapAdapter = ConfigurationSchema( type: 'stringArray', defaultValue: [], description: - 'Target is the first value in the array, query is the second', + 'Array of assembly names to use for this file. The query assembly name is the first value in the array, target assembly name is the second', }, /** diff --git a/plugins/comparative-adapters/src/PAFAdapter/configSchema.ts b/plugins/comparative-adapters/src/PAFAdapter/configSchema.ts index 91f305a591..bfcae985e1 100644 --- a/plugins/comparative-adapters/src/PAFAdapter/configSchema.ts +++ b/plugins/comparative-adapters/src/PAFAdapter/configSchema.ts @@ -15,7 +15,7 @@ const PAFAdapter = ConfigurationSchema( type: 'stringArray', defaultValue: [], description: - 'Array of assembly names to use for this file. The target assembly name is the first value in the array, query assembly name is the second', + 'Array of assembly names to use for this file. The query assembly name is the first value in the array, target assembly name is the second', }, /** * #slot diff --git a/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/configSchema.ts b/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/configSchema.ts index 6c9009291d..ca6aef705d 100644 --- a/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/configSchema.ts +++ b/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/configSchema.ts @@ -16,7 +16,7 @@ const PairwiseIndexedPAFAdapter = ConfigurationSchema( type: 'stringArray', defaultValue: [], description: - 'Array of assembly names to use for this file. The target assembly name is the first value in the array, query assembly name is the second', + 'Array of assembly names to use for this file. The query assembly name is the first value in the array, target assembly name is the second', }, /** * #slot diff --git a/plugins/config/package.json b/plugins/config/package.json index 4633fb052d..f1ee5a42e6 100644 --- a/plugins/config/package.json +++ b/plugins/config/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-config", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 config utilities", "keywords": [ "jbrowse", diff --git a/plugins/data-management/package.json b/plugins/data-management/package.json index 8eb89f2183..be3b160ae1 100644 --- a/plugins/data-management/package.json +++ b/plugins/data-management/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-data-management", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 linear genome view", "keywords": [ "jbrowse", diff --git a/plugins/data-management/src/AddTrackWidget/components/AddTrackWidget.tsx b/plugins/data-management/src/AddTrackWidget/components/AddTrackWidget.tsx index 8e1136e5aa..f2c5f552d7 100644 --- a/plugins/data-management/src/AddTrackWidget/components/AddTrackWidget.tsx +++ b/plugins/data-management/src/AddTrackWidget/components/AddTrackWidget.tsx @@ -1,4 +1,4 @@ -import React, { useState } from 'react' +import React, { Suspense, useState } from 'react' import { observer } from 'mobx-react' import { FormControl, FormHelperText, Select, MenuItem } from '@mui/material' import { getEnv } from '@jbrowse/core/util' @@ -14,12 +14,14 @@ const AddTrackSelector = observer(function ({ model: AddTrackModel }) { const [val, setVal] = useState('Default add track workflow') - const { pluginManager } = getEnv(model) - const widgets = pluginManager.getAddTrackWorkflowElements() const ComponentMap = { 'Default add track workflow': DefaultAddTrackWorkflow, 'Add track JSON': PasteConfigWorkflow, - ...Object.fromEntries(widgets.map(w => [w.name, w.ReactComponent])), + ...Object.fromEntries( + getEnv(model) + .pluginManager.getAddTrackWorkflowElements() + .map(w => [w.name, w.ReactComponent]), + ), } as Record> // make sure the selected value is in the list @@ -43,8 +45,9 @@ const AddTrackSelector = observer(function ({ Type of add track workflow -
- + + + ) }) diff --git a/plugins/dotplot-view/package.json b/plugins/dotplot-view/package.json index 129bc17142..8e6275f149 100644 --- a/plugins/dotplot-view/package.json +++ b/plugins/dotplot-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-dotplot-view", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 dotplot view", "keywords": [ "jbrowse", diff --git a/plugins/gccontent/package.json b/plugins/gccontent/package.json index 3bb59d51af..fefec029a0 100644 --- a/plugins/gccontent/package.json +++ b/plugins/gccontent/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-gccontent", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 gccontent concepts", "keywords": [ "jbrowse", diff --git a/plugins/gff3/package.json b/plugins/gff3/package.json index 95b01d1120..afe1d349d5 100644 --- a/plugins/gff3/package.json +++ b/plugins/gff3/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-gff3", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 gff3.", "keywords": [ "jbrowse", diff --git a/plugins/grid-bookmark/package.json b/plugins/grid-bookmark/package.json index 00a78938ad..3fcd60ee1e 100644 --- a/plugins/grid-bookmark/package.json +++ b/plugins/grid-bookmark/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-grid-bookmark", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 grid bookmark widget", "keywords": [ "jbrowse", diff --git a/plugins/gtf/package.json b/plugins/gtf/package.json index 0672c0efd5..b4dbaab5c1 100644 --- a/plugins/gtf/package.json +++ b/plugins/gtf/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-gtf", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 gtf feature adapter", "keywords": [ "jbrowse", diff --git a/plugins/hic/package.json b/plugins/hic/package.json index b541c43ce9..db766ea7f8 100644 --- a/plugins/hic/package.json +++ b/plugins/hic/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-hic", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 hic adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/hic/src/HicAdapter/HicAdapter.ts b/plugins/hic/src/HicAdapter/HicAdapter.ts index aea060b40c..9ba3437b0e 100644 --- a/plugins/hic/src/HicAdapter/HicAdapter.ts +++ b/plugins/hic/src/HicAdapter/HicAdapter.ts @@ -2,15 +2,16 @@ import { BaseFeatureDataAdapter, BaseOptions, } from '@jbrowse/core/data_adapters/BaseAdapter' -import { Region, FileLocation } from '@jbrowse/core/util/types' +import { Region } from '@jbrowse/core/util/types' import { ObservableCreate } from '@jbrowse/core/util/rxjs' -import { openLocation } from '@jbrowse/core/util/io' -import type { GenericFilehandle } from 'generic-filehandle' import HicStraw from 'hic-straw' import PluginManager from '@jbrowse/core/PluginManager' import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache' import { AnyConfigurationModel } from '@jbrowse/core/configuration' -import { Buffer } from 'buffer' +import { updateStatus } from '@jbrowse/core/util' + +// locals +import { openHicFilehandle } from './HicFilehandle' interface ContactRecord { bin1: number @@ -35,32 +36,7 @@ interface Ref { interface HicOptions extends BaseOptions { resolution?: number bpPerPx?: number -} - -// wraps generic-filehandle so the read function only takes a position and -// length in some ways, generic-filehandle wishes it was just this but it has -// to adapt to the node.js fs promises API -class GenericFilehandleWrapper { - constructor(private filehandle: GenericFilehandle) {} - - async read(position: number, length: number) { - const { buffer } = await this.filehandle.read( - Buffer.alloc(length), - 0, - length, - position, - ) - return buffer.buffer.slice( - buffer.byteOffset, - buffer.byteOffset + buffer.byteLength, - ) - } -} -export function openFilehandleWrapper( - location: FileLocation, - pluginManager?: PluginManager, -) { - return new GenericFilehandleWrapper(openLocation(location, pluginManager)) + normalization?: string } interface HicParser { @@ -83,24 +59,23 @@ export default class HicAdapter extends BaseFeatureDataAdapter { pluginManager?: PluginManager, ) { super(config, getSubAdapter, pluginManager) - const hicLocation = this.getConf('hicLocation') this.hic = new HicStraw({ - file: openFilehandleWrapper(hicLocation, this.pluginManager), + file: openHicFilehandle(this.getConf('hicLocation'), this.pluginManager), }) } private async setup(opts?: BaseOptions) { const { statusCallback = () => {} } = opts || {} - statusCallback('Downloading .hic header') - const result = await this.hic.getMetaData() - statusCallback('') - return result + return updateStatus('Downloading .hic header', statusCallback, () => + this.hic.getMetaData(), + ) } public async getHeader(opts?: BaseOptions) { - const ret = await this.setup(opts) - const { chromosomes, ...rest } = ret - return rest + const { chromosomes, ...rest } = await this.setup(opts) + // @ts-expect-error + const norms = await this.hic.getNormalizationOptions() + return { ...rest, norms } } async getRefNames(opts?: BaseOptions) { @@ -108,14 +83,13 @@ export default class HicAdapter extends BaseFeatureDataAdapter { return metadata.chromosomes.map(chr => chr.name) } - async getResolution(bpPerPx: number, opts?: BaseOptions) { + async getResolution(res: number, opts?: BaseOptions) { const { resolutions } = await this.setup(opts) - + const resolutionMultiplier = this.getConf('resolutionMultiplier') let chosenResolution = resolutions.at(-1)! - for (let i = resolutions.length - 1; i >= 0; i -= 1) { const r = resolutions[i]! - if (r <= 2 * bpPerPx) { + if (r <= 2 * res * resolutionMultiplier) { chosenResolution = r } } @@ -125,28 +99,35 @@ export default class HicAdapter extends BaseFeatureDataAdapter { getFeatures(region: Region, opts: HicOptions = {}) { return ObservableCreate(async observer => { const { refName: chr, start, end } = region - const { resolution, bpPerPx = 1, statusCallback = () => {} } = opts + const { + resolution, + normalization = 'KR', + bpPerPx = 1, + statusCallback = () => {}, + } = opts const res = await this.getResolution(bpPerPx / (resolution || 1000), opts) - statusCallback('Downloading .hic data') - const records = await this.hic.getContactRecords( - 'KR', - { start, chr, end }, - { start, chr, end }, - 'BP', - res, - ) - for (const record of records) { - observer.next(record) - } - statusCallback('') + await updateStatus('Downloading .hic data', statusCallback, async () => { + const records = await this.hic.getContactRecords( + normalization, + { start, chr, end }, + { start, chr, end }, + 'BP', + res, + ) + for (const record of records) { + observer.next(record) + } + }) observer.complete() }, opts.signal) as any } // don't do feature stats estimation, similar to bigwigadapter async getMultiRegionFeatureDensityStats(_regions: Region[]) { - return { featureDensity: 0 } + return { + featureDensity: 0, + } } freeResources(/* { region } */): void {} diff --git a/plugins/hic/src/HicAdapter/HicFilehandle.ts b/plugins/hic/src/HicAdapter/HicFilehandle.ts new file mode 100644 index 0000000000..a55f52ff58 --- /dev/null +++ b/plugins/hic/src/HicAdapter/HicFilehandle.ts @@ -0,0 +1,35 @@ +import { FileLocation } from '@jbrowse/core/util' +import { openLocation } from '@jbrowse/core/util/io' +import type { GenericFilehandle } from 'generic-filehandle' + +import { Buffer } from 'buffer' +import PluginManager from '@jbrowse/core/PluginManager' + +// wraps generic-filehandle so the read function only takes a position and +// length +// +// in some ways, generic-filehandle wishes it was just this but it has +// to adapt to the node.js fs promises API +class HicFilehandle { + constructor(private filehandle: GenericFilehandle) {} + + async read(position: number, length: number) { + const { buffer } = await this.filehandle.read( + Buffer.alloc(length), + 0, + length, + position, + ) + return buffer.buffer.slice( + buffer.byteOffset, + buffer.byteOffset + buffer.byteLength, + ) + } +} + +export function openHicFilehandle( + location: FileLocation, + pluginManager?: PluginManager, +) { + return new HicFilehandle(openLocation(location, pluginManager)) +} diff --git a/plugins/hic/src/HicAdapter/configSchema.ts b/plugins/hic/src/HicAdapter/configSchema.ts index a139482fac..a58c4d870b 100644 --- a/plugins/hic/src/HicAdapter/configSchema.ts +++ b/plugins/hic/src/HicAdapter/configSchema.ts @@ -19,6 +19,14 @@ const HicAdapter = ConfigurationSchema( locationType: 'UriLocation', }, }, + /** + * #slot + */ + resolutionMultiplier: { + type: 'number', + defaultValue: 1, + description: 'Initial resolution multiplier', + }, }, { explicitlyTyped: true }, ) diff --git a/plugins/hic/src/HicRenderer/HicRenderer.tsx b/plugins/hic/src/HicRenderer/HicRenderer.tsx index d064eea21d..9b955c4c79 100644 --- a/plugins/hic/src/HicRenderer/HicRenderer.tsx +++ b/plugins/hic/src/HicRenderer/HicRenderer.tsx @@ -101,7 +101,7 @@ export default class HicRenderer extends ServerSideRendererType { } } -export { - type RenderArgsSerialized, - type RenderResults, +export type { + RenderArgsSerialized, + RenderResults, } from '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType' diff --git a/plugins/hic/src/LinearHicDisplay/model.ts b/plugins/hic/src/LinearHicDisplay/model.ts index b9e8e7065b..03e5b3035f 100644 --- a/plugins/hic/src/LinearHicDisplay/model.ts +++ b/plugins/hic/src/LinearHicDisplay/model.ts @@ -1,7 +1,9 @@ import { ConfigurationReference, getConf } from '@jbrowse/core/configuration' import { BaseLinearDisplay } from '@jbrowse/plugin-linear-genome-view' -import { types, getEnv } from 'mobx-state-tree' +import { types, getEnv, addDisposer } from 'mobx-state-tree' import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration' +import { autorun } from 'mobx' +import { getContainingTrack, getSession } from '@jbrowse/core/util' /** * #stateModel LinearHicDisplay @@ -38,8 +40,18 @@ export default function stateModelFactory( * #property */ colorScheme: types.maybe(types.string), + /** + * #property + */ + activeNormalization: 'KR', }), ) + .volatile(() => ({ + /** + * #volatile + */ + availableNormalizations: undefined as string[] | undefined, + })) .views(self => { const { renderProps: superRenderProps } = self return { @@ -74,6 +86,7 @@ export default function stateModelFactory( return { ...superRenderProps(), config, + normalization: self.activeNormalization, rpcDriverName: self.rpcDriverName, displayModel: self, resolution: self.resolution, @@ -102,6 +115,18 @@ export default function stateModelFactory( setColorScheme(f?: string) { self.colorScheme = f }, + /** + * #action + */ + setActiveNormalization(f: string) { + self.activeNormalization = f + }, + /** + * #action + */ + setAvailableNormalizations(f: string[]) { + self.availableNormalizations = f + }, })) .views(self => { const { trackMenuItems: superTrackMenuItems } = self @@ -167,8 +192,50 @@ export default function stateModelFactory( }, ], }, + ...(self.availableNormalizations + ? [ + { + label: 'Normalization scheme', + subMenu: self.availableNormalizations.map(norm => ({ + label: norm, + type: 'checkbox', + checked: norm === self.activeNormalization, + onClick: () => { + self.setActiveNormalization(norm) + }, + })), + }, + ] + : []), ] }, } }) + .actions(self => ({ + afterAttach() { + addDisposer( + self, + autorun(async () => { + try { + const { rpcManager } = getSession(self) + const track = getContainingTrack(self) + const adapterConfig = getConf(track, 'adapter') + const { norms } = (await rpcManager.call( + getConf(track, 'trackId'), + 'CoreGetInfo', + { + adapterConfig, + }, + )) as { norms?: string[] } + if (norms) { + self.setAvailableNormalizations(norms) + } + } catch (e) { + console.error(e) + getSession(self).notifyError(`${e}`, e) + } + }), + ) + }, + })) } diff --git a/plugins/jobs-management/package.json b/plugins/jobs-management/package.json index 3d0df6378c..9ba007e158 100644 --- a/plugins/jobs-management/package.json +++ b/plugins/jobs-management/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-jobs-management", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 jobs management", "keywords": [ "jbrowse", @@ -36,7 +36,7 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { - "@jbrowse/text-indexing": "^2.16.0", + "@jbrowse/text-indexing": "^2.16.1", "@mui/icons-material": "^6.0.0" }, "peerDependencies": { diff --git a/plugins/legacy-jbrowse/package.json b/plugins/legacy-jbrowse/package.json index a4d55b9f61..b7946ad678 100644 --- a/plugins/legacy-jbrowse/package.json +++ b/plugins/legacy-jbrowse/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-legacy-jbrowse", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data", "keywords": [ "jbrowse", diff --git a/plugins/linear-comparative-view/package.json b/plugins/linear-comparative-view/package.json index 95ce1bdec8..34b768c951 100644 --- a/plugins/linear-comparative-view/package.json +++ b/plugins/linear-comparative-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-linear-comparative-view", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 linear comparative view", "keywords": [ "jbrowse", @@ -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..210ed400aa 100644 --- a/plugins/linear-comparative-view/src/LinearComparativeDisplay/stateModelFactory.ts +++ b/plugins/linear-comparative-view/src/LinearComparativeDisplay/stateModelFactory.ts @@ -42,6 +42,18 @@ function stateModelFactory(configSchema: AnyConfigurationSchemaType) { message: undefined as string | undefined, })) .views(self => ({ + /** + * #getter + */ + get level() { + return getParent<{ height: number; level: number }>(self, 4).level + }, + /** + * #getter + */ + get height() { + return getParent<{ height: number; level: number }>(self, 4).height + }, /** * #getter */ @@ -166,7 +178,7 @@ 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 +187,7 @@ 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..8696c56485 100644 --- a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/afterAttach.ts +++ b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/afterAttach.ts @@ -1,9 +1,8 @@ -import { addDisposer, getParent, getSnapshot } from 'mobx-state-tree' - +import { reaction, autorun } from 'mobx' +import { addDisposer, getSnapshot } from 'mobx-state-tree' import { Feature, getContainingView, getSession } from '@jbrowse/core/util' import { bpToPx } from '@jbrowse/core/util/Base1DUtils' import { MismatchParser } from '@jbrowse/plugin-alignments' -import { reaction, autorun } from 'mobx' // locals import { LinearSyntenyViewModel } from '../LinearSyntenyView/model' @@ -84,10 +83,9 @@ 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 6ecceb84a9..1a586f2513 100644 --- a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/LinearSyntenyRendering.tsx +++ b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/LinearSyntenyRendering.tsx @@ -26,6 +26,7 @@ const useStyles = makeStyles()({ position: 'relative', }, mouseoverCanvas: { + imageRendering: 'pixelated', position: 'absolute', pointEvents: 'none', }, @@ -40,11 +41,11 @@ const LinearSyntenyRendering = observer(function ({ model: LinearSyntenyDisplayModel }) { const { classes } = useStyles() + const { mouseoverId, height } = model const xOffset = useRef(0) const view = getContainingView(model) as LinearSyntenyViewModel const width = view.width const delta = useRef(0) - const scheduled = useRef(false) const timeout = useRef() const [anchorEl, setAnchorEl] = useState() @@ -53,13 +54,12 @@ const LinearSyntenyRendering = observer(function ({ const [mouseCurrDownX, setMouseCurrDownX] = useState() const [mouseInitialDownX, setMouseInitialDownX] = useState() const [currY, setCurrY] = useState() - const { mouseoverId, height } = model - const k2p = useRef() + const mainSyntenyCanvasRefp = useRef() // these useCallbacks avoid new refs from being created on any mouseover, // etc. // biome-ignore lint/correctness/useExhaustiveDependencies: - const k1 = useCallback( + const mouseoverDetectionCanvasRef = useCallback( (ref: HTMLCanvasElement | null) => { model.setMouseoverCanvasRef(ref) }, @@ -68,10 +68,10 @@ const LinearSyntenyRendering = observer(function ({ ) // biome-ignore lint/correctness/useExhaustiveDependencies: - const k2 = useCallback( + const mainSyntenyCanvasRef = useCallback( (ref: HTMLCanvasElement | null) => { model.setMainCanvasRef(ref) - k2p.current = ref // this ref is additionally used in useEffect below + mainSyntenyCanvasRefp.current = ref // this ref is additionally used in useEffect below }, // eslint-disable-next-line react-hooks/exhaustive-deps [model, height, width], @@ -97,7 +97,9 @@ const LinearSyntenyRendering = observer(function ({ delta.current > 0 ? v.bpPerPx * (1 + delta.current) : v.bpPerPx / (1 - delta.current), - event.clientX - (k2p.current?.getBoundingClientRect().left || 0), + event.clientX - + (mainSyntenyCanvasRefp.current?.getBoundingClientRect().left || + 0), ) } delta.current = 0 @@ -120,15 +122,15 @@ const LinearSyntenyRendering = observer(function ({ } } } - k2p.current?.addEventListener('wheel', onWheel) + mainSyntenyCanvasRefp.current?.addEventListener('wheel', onWheel) return () => { - k2p.current?.removeEventListener('wheel', onWheel) + mainSyntenyCanvasRefp.current?.removeEventListener('wheel', onWheel) } // eslint-disable-next-line react-hooks/exhaustive-deps }, [model, height, width]) // biome-ignore lint/correctness/useExhaustiveDependencies: - const k3 = useCallback( + const clickMapCanvasRef = useCallback( (ref: HTMLCanvasElement | null) => { model.setClickMapCanvasRef(ref) }, @@ -136,7 +138,7 @@ const LinearSyntenyRendering = observer(function ({ [model, height, width], ) // biome-ignore lint/correctness/useExhaustiveDependencies: - const k4 = useCallback( + const cigarClickMapCanvasRef = useCallback( (ref: HTMLCanvasElement | null) => { model.setCigarClickMapCanvasRef(ref) }, @@ -147,13 +149,13 @@ const LinearSyntenyRendering = observer(function ({ return (
{ if (mouseCurrDownX !== undefined) { xOffset.current += mouseCurrDownX - event.clientX @@ -198,7 +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], + }), + ) } } }} @@ -228,8 +236,18 @@ const LinearSyntenyRendering = observer(function ({ width={width} height={height} /> - - + + {mouseoverId && tooltip && currX && currY ? ( ) : null} diff --git a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/SyntenyContextMenu.tsx b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/SyntenyContextMenu.tsx index 9df93e7adf..27107aa049 100644 --- a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/SyntenyContextMenu.tsx +++ b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/SyntenyContextMenu.tsx @@ -1,7 +1,6 @@ import React from 'react' import { getContainingView, getSession, Feature } from '@jbrowse/core/util' import { Menu } from '@jbrowse/core/ui' -import { getParent } from 'mobx-state-tree' // locals import { LinearSyntenyDisplayModel } from '../model' @@ -55,14 +54,13 @@ 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 c626d74300..a4f21d45f9 100644 --- a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/util.ts +++ b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/components/util.ts @@ -128,7 +128,6 @@ export function drawBox( ctx.lineTo(x3, y2) ctx.lineTo(x4, y2) ctx.closePath() - ctx.fill() } export function drawBezierBox( @@ -159,7 +158,6 @@ export function drawBezierBox( ctx.lineTo(x4, y2) ctx.bezierCurveTo(x4, mid, x1, mid, x1, y1) ctx.closePath() - ctx.fill() } export function onSynClick( @@ -168,8 +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 } @@ -182,19 +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, }), ) } @@ -232,9 +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 759896da7c..46f75d0eef 100644 --- a/plugins/linear-comparative-view/src/LinearSyntenyDisplay/drawSynteny.ts +++ b/plugins/linear-comparative-view/src/LinearSyntenyDisplay/drawSynteny.ts @@ -3,7 +3,6 @@ import { doesIntersect2, getContainingView } from '@jbrowse/core/util' import { LinearSyntenyViewModel } from '../LinearSyntenyView/model' import { LinearSyntenyDisplayModel } from './model' import { draw, drawMatchSimple } from './components/util' -import { getParent } from 'mobx-state-tree' export const MAX_COLOR_RANGE = 255 * 255 * 255 // max color range @@ -37,11 +36,9 @@ 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) @@ -179,15 +176,18 @@ export function drawRef( continuingFlag = false draw(ctx1, px1, cx1, y1, cx2, px2, y2, mid, drawCurves) + ctx1.fill() if (ctx3) { ctx3.fillStyle = makeColor(idx) draw(ctx3, px1, cx1, y1, cx2, px2, y2, mid, drawCurves) + ctx3.fill() } } } } } else { draw(ctx1, x11, x12, y1, x22, x21, y2, mid, drawCurves) + ctx1.fill() } } } @@ -223,7 +223,7 @@ 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 @@ -231,8 +231,6 @@ 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 @@ -240,9 +238,10 @@ export function drawMouseoverSynteny(model: LinearSyntenyDisplayModel) { ctx.resetTransform() ctx.scale(highResolutionScaling, highResolutionScaling) ctx.clearRect(0, 0, width, height) + ctx.strokeStyle = 'rgba(0, 0, 0, 0.9)' + ctx.fillStyle = 'rgba(0, 0, 0, 0.1)' const feature1 = model.featMap[mouseoverId || ''] if (feature1) { - ctx.fillStyle = 'rgb(0,0,0,0.1)' drawMatchSimple({ cb: ctx => { ctx.fill() @@ -259,8 +258,6 @@ export function drawMouseoverSynteny(model: LinearSyntenyDisplayModel) { } const feature2 = model.featMap[clickId || ''] if (feature2) { - ctx.strokeStyle = 'rgb(0, 0, 0, 0.9)' - drawMatchSimple({ cb: ctx => { ctx.stroke() 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/package.json b/plugins/linear-genome-view/package.json index ef0a9ad997..54eda6be7c 100644 --- a/plugins/linear-genome-view/package.json +++ b/plugins/linear-genome-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-linear-genome-view", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 linear genome view", "keywords": [ "jbrowse", 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/lollipop/package.json b/plugins/lollipop/package.json index 53f73bbad2..0bb35b16d4 100644 --- a/plugins/lollipop/package.json +++ b/plugins/lollipop/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-lollipop", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 plugin for lollipops", "keywords": [ "jbrowse", diff --git a/plugins/menus/package.json b/plugins/menus/package.json index b0b32618e6..be5cc9645c 100644 --- a/plugins/menus/package.json +++ b/plugins/menus/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-menus", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 basic menus", "keywords": [ "jbrowse", diff --git a/plugins/rdf/package.json b/plugins/rdf/package.json index 974451fd48..895528a1ea 100644 --- a/plugins/rdf/package.json +++ b/plugins/rdf/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-rdf", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 RDF resources", "keywords": [ "jbrowse", diff --git a/plugins/sequence/package.json b/plugins/sequence/package.json index 4d6d7d7c5a..d45b51023c 100644 --- a/plugins/sequence/package.json +++ b/plugins/sequence/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-sequence", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 sequence adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/spreadsheet-view/package.json b/plugins/spreadsheet-view/package.json index 81f035bcc9..06a5925ec5 100644 --- a/plugins/spreadsheet-view/package.json +++ b/plugins/spreadsheet-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-spreadsheet-view", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 spreadsheet view", "keywords": [ "jbrowse", @@ -38,7 +38,7 @@ "dependencies": { "@gmod/bgzf-filehandle": "^1.4.3", "@gmod/vcf": "^5.0.9", - "@jbrowse/plugin-variants": "^2.16.0", + "@jbrowse/plugin-variants": "^2.16.1", "@mui/icons-material": "^6.0.0", "csvtojson": "^2.0.10" }, diff --git a/plugins/sv-inspector/package.json b/plugins/sv-inspector/package.json index 8f81e476e4..0c963ef695 100644 --- a/plugins/sv-inspector/package.json +++ b/plugins/sv-inspector/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-sv-inspector", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 SV inspector view", "keywords": [ "jbrowse", diff --git a/plugins/svg/package.json b/plugins/svg/package.json index 76d773793c..3cafc8320f 100644 --- a/plugins/svg/package.json +++ b/plugins/svg/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-svg", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 plugin for svg features", "keywords": [ "jbrowse", diff --git a/plugins/text-indexing/package.json b/plugins/text-indexing/package.json index f0a53d60e1..290bf96bcb 100644 --- a/plugins/text-indexing/package.json +++ b/plugins/text-indexing/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-text-indexing", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 text indexing rpc method", "keywords": [ "jbrowse", @@ -36,7 +36,7 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { - "@jbrowse/text-indexing": "^2.16.0" + "@jbrowse/text-indexing": "^2.16.1" }, "peerDependencies": { "@jbrowse/core": "^2.0.0", diff --git a/plugins/trix/package.json b/plugins/trix/package.json index 30afa8b655..486fc8711c 100644 --- a/plugins/trix/package.json +++ b/plugins/trix/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-trix", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 trix text search adapter", "keywords": [ "jbrowse", diff --git a/plugins/variants/package.json b/plugins/variants/package.json index 95742f1992..9d1e935d76 100644 --- a/plugins/variants/package.json +++ b/plugins/variants/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-variants", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 variant adapters, tracks, etc.", "keywords": [ "jbrowse", @@ -40,7 +40,7 @@ "@gmod/bgzf-filehandle": "^1.4.3", "@gmod/tabix": "^1.5.6", "@gmod/vcf": "^5.0.9", - "@jbrowse/sv-core": "^2.16.0", + "@jbrowse/sv-core": "^2.16.1", "@mui/icons-material": "^6.0.0", "@mui/x-data-grid": "^7.0.0", "generic-filehandle": "^3.0.0" 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/plugins/wiggle/package.json b/plugins/wiggle/package.json index 7d60db90a3..adb51e2e6e 100644 --- a/plugins/wiggle/package.json +++ b/plugins/wiggle/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-wiggle", - "version": "2.16.0", + "version": "2.16.1", "description": "JBrowse 2 wiggle adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/wiggle/src/BigWigAdapter/BigWigAdapter.ts b/plugins/wiggle/src/BigWigAdapter/BigWigAdapter.ts index 307f400144..59a6b3f389 100644 --- a/plugins/wiggle/src/BigWigAdapter/BigWigAdapter.ts +++ b/plugins/wiggle/src/BigWigAdapter/BigWigAdapter.ts @@ -78,10 +78,11 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter { return ObservableCreate(async observer => { statusCallback('Downloading bigwig data') const source = this.getConf('source') + const resolutionMultiplier = this.getConf('resolutionMultiplier') const { bigwig } = await this.setup(opts) const feats = await bigwig.getFeatures(refName, start, end, { ...opts, - basesPerSpan: bpPerPx / resolution, + basesPerSpan: (bpPerPx / resolution) * resolutionMultiplier, }) for (const data of feats) { diff --git a/plugins/wiggle/src/BigWigAdapter/configSchema.ts b/plugins/wiggle/src/BigWigAdapter/configSchema.ts index 7e85296ecf..1337051c3a 100644 --- a/plugins/wiggle/src/BigWigAdapter/configSchema.ts +++ b/plugins/wiggle/src/BigWigAdapter/configSchema.ts @@ -27,6 +27,15 @@ const BigWigAdapter = ConfigurationSchema( defaultValue: '', description: 'Used for multiwiggle', }, + + /** + * #slot + */ + resolutionMultiplier: { + type: 'number', + defaultValue: 1, + description: 'Initial resolution multiplier', + }, }, { explicitlyTyped: true }, ) diff --git a/plugins/wiggle/src/MultiWiggleAddTrackWorkflow/AddTrackWorkflow.tsx b/plugins/wiggle/src/MultiWiggleAddTrackWorkflow/AddTrackWorkflow.tsx index 7706f27dbc..d7e68d3ab0 100644 --- a/plugins/wiggle/src/MultiWiggleAddTrackWorkflow/AddTrackWorkflow.tsx +++ b/plugins/wiggle/src/MultiWiggleAddTrackWorkflow/AddTrackWorkflow.tsx @@ -11,9 +11,6 @@ import { storeBlobLocation } from '@jbrowse/core/util/tracks' import { AddTrackModel } from '@jbrowse/plugin-data-management' const useStyles = makeStyles()(theme => ({ - textbox: { - width: '100%', - }, paper: { margin: theme.spacing(), padding: theme.spacing(), @@ -25,6 +22,17 @@ const useStyles = makeStyles()(theme => ({ }, })) +// on electron, use path to LocalFileLocation, on web, use the BlobLocation +function makeFileLocation(file: File) { + const { webUtils } = window.require('electron') + return isElectron + ? { + localPath: webUtils.getPathForFile(file), + locationType: 'LocalPathLocation', + } + : storeBlobLocation({ blob: file }) +} + export default function MultiWiggleWidget({ model }: { model: AddTrackModel }) { const { classes } = useStyles() const [val, setVal] = useState('') @@ -41,14 +49,14 @@ export default function MultiWiggleWidget({ model }: { model: AddTrackModel }) { { setVal(event.target.value) }} - placeholder={'Paste list of URLs here, or use file selector below'} - variant="outlined" - className={classes.textbox} /> { setTrackName(event.target.value) }} - helperText="Track name" /> @@ -371,7 +381,7 @@ function LocalFileChooser(props: { }) { const { classes } = useStyles() const { location, setLocation, setName } = props - const [filename, setFilename] = useState(``) + const [filename, setFilename] = useState('') const needToReload = location && isBlobLocation(location) && !getBlob(location.blobId) @@ -390,17 +400,19 @@ function LocalFileChooser(props: { const file = target && target.files && target.files[0] if (file) { if (isElectron) { + const { webUtils } = window.require('electron') + const path = webUtils.getPathForFile(file) // here we are setting the location information for the file selected // these features are necessary for the VcfTabixAdapter setLocation({ - localPath: (file as File & { path: string }).path, + localPath: path, locationType: 'LocalPathLocation', }) } else { setLocation(storeBlobLocation({ blob: file })) } // these set ui elements - setFilename((file as File & { path: string }).path) + setFilename(file.name) setName(file.name) } }} diff --git a/website/docusaurus.config.json b/website/docusaurus.config.json index 7e3a8e460b..e08f61fbec 100644 --- a/website/docusaurus.config.json +++ b/website/docusaurus.config.json @@ -9,6 +9,6 @@ "organizationName": "GMOD", "projectName": "jbrowse-components", "customFields": { - "currentVersion": "v2.16.0" + "currentVersion": "v2.16.1" } } diff --git a/website/release_announcement_drafts/v2.16.1.md b/website/release_announcement_drafts/v2.16.1.md new file mode 100644 index 0000000000..81f60b4c92 --- /dev/null +++ b/website/release_announcement_drafts/v2.16.1.md @@ -0,0 +1,3 @@ +Hi all, + +This is a bugfix release! See notes below diff --git a/yarn.lock b/yarn.lock index ad3f88d3db..4c97ba3ca9 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" @@ -138,35 +138,35 @@ "@smithy/util-waiter" "^3.1.6" tslib "^2.6.2" -"@aws-sdk/client-s3@^3.676.0": - version "3.677.0" - resolved "https://registry.yarnpkg.com/@aws-sdk/client-s3/-/client-s3-3.677.0.tgz#b6218ff19bdf83102cad5bfae8f3da5c685cf404" - integrity sha512-TrfT7hyjs0FRh5MosduFZsskHhjvBKL451Wo5f80IcnxvNL8YZouh6kblUSiHKUxuc32WSiAKbXJJaPWdXs75Q== +"@aws-sdk/client-s3@^3.685.0": + version "3.685.0" + resolved "https://registry.yarnpkg.com/@aws-sdk/client-s3/-/client-s3-3.685.0.tgz#bf2fd9fe310a2d20fdaf3585755e9a8416d08c2b" + integrity sha512-ClvMeQHbLhWkpxnVymo4qWS5/yZcPXjorDbSday3joCWYWCSHTO409nWd+jx6eA4MKT/EY/uJ6ZBJRFfByKLuA== dependencies: "@aws-crypto/sha1-browser" "5.2.0" "@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-bucket-endpoint" "3.667.0" - "@aws-sdk/middleware-expect-continue" "3.667.0" - "@aws-sdk/middleware-flexible-checksums" "3.677.0" - "@aws-sdk/middleware-host-header" "3.667.0" - "@aws-sdk/middleware-location-constraint" "3.667.0" - "@aws-sdk/middleware-logger" "3.667.0" - "@aws-sdk/middleware-recursion-detection" "3.667.0" - "@aws-sdk/middleware-sdk-s3" "3.677.0" - "@aws-sdk/middleware-ssec" "3.667.0" - "@aws-sdk/middleware-user-agent" "3.677.0" - "@aws-sdk/region-config-resolver" "3.667.0" - "@aws-sdk/signature-v4-multi-region" "3.677.0" - "@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-bucket-endpoint" "3.679.0" + "@aws-sdk/middleware-expect-continue" "3.679.0" + "@aws-sdk/middleware-flexible-checksums" "3.682.0" + "@aws-sdk/middleware-host-header" "3.679.0" + "@aws-sdk/middleware-location-constraint" "3.679.0" + "@aws-sdk/middleware-logger" "3.679.0" + "@aws-sdk/middleware-recursion-detection" "3.679.0" + "@aws-sdk/middleware-sdk-s3" "3.685.0" + "@aws-sdk/middleware-ssec" "3.679.0" + "@aws-sdk/middleware-user-agent" "3.682.0" + "@aws-sdk/region-config-resolver" "3.679.0" + "@aws-sdk/signature-v4-multi-region" "3.685.0" + "@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/eventstream-serde-browser" "^3.0.10" @@ -202,24 +202,24 @@ "@smithy/util-waiter" "^3.1.6" tslib "^2.6.2" -"@aws-sdk/client-sso-oidc@3.677.0": - version "3.677.0" - resolved "https://registry.yarnpkg.com/@aws-sdk/client-sso-oidc/-/client-sso-oidc-3.677.0.tgz#5557cb45ded0ebe0d25cf62611507f36d4b45afd" - integrity sha512-2zgZkRIU7DsnUVOy+9bjfJ0IYMzi9ONWXQt/WqMa7HOnj4RfenfpipyhHYxGZR5kmehgv53EI79yvUu+SAfGNg== +"@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" + "@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" "@smithy/config-resolver" "^3.0.9" "@smithy/core" "^2.4.8" "@smithy/fetch-http-handler" "^3.2.9" @@ -247,23 +247,23 @@ "@smithy/util-utf8" "^3.0.0" tslib "^2.6.2" -"@aws-sdk/client-sso@3.677.0": - version "3.677.0" - resolved "https://registry.yarnpkg.com/@aws-sdk/client-sso/-/client-sso-3.677.0.tgz#a099a0e39b807cd93f3ead5ddf52bcd27a6f6338" - integrity sha512-/y6EskFhOa2w9VwXaXoyOrGeBjnOj/72wsxDOslS908qH+nf7m40pBK6e/iBelg04vlx0gqhlbfK8hLbaT6KHA== +"@aws-sdk/client-sso@3.682.0": + version "3.682.0" + resolved "https://registry.yarnpkg.com/@aws-sdk/client-sso/-/client-sso-3.682.0.tgz#7533f677456d5f79cfcceed44a3481bcd86b560e" + integrity 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" + "@aws-sdk/util-user-agent-node" "3.682.0" "@smithy/config-resolver" "^3.0.9" "@smithy/core" "^2.4.8" "@smithy/fetch-http-handler" "^3.2.9" @@ -291,25 +291,25 @@ "@smithy/util-utf8" "^3.0.0" tslib "^2.6.2" -"@aws-sdk/client-sts@3.677.0": - version "3.677.0" - resolved "https://registry.yarnpkg.com/@aws-sdk/client-sts/-/client-sts-3.677.0.tgz#70f57f2fc6bb709b854d384e825e408109af589d" - integrity sha512-N5fs1GLSthnwrs44b4IJI//dcShuIT42g4pM8FCUJZwbrWn9Sp9F876R1mvb8A9TAy2S4qCXi7TkHS0REnuicQ== +"@aws-sdk/client-sts@3.682.0": + version "3.682.0" + resolved "https://registry.yarnpkg.com/@aws-sdk/client-sts/-/client-sts-3.682.0.tgz#97ff70ca141aa6ef48a22f14ef9727bd6ae17b03" + integrity sha512-xKuo4HksZ+F8m9DOfx/ZuWNhaPuqZFPwwy0xqcBT6sWH7OAuBjv/fnpOTzyQhpVTWddlf+ECtMAMrxjxuOExGQ== 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/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/client-sso-oidc" "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" "@smithy/config-resolver" "^3.0.9" "@smithy/core" "^2.4.8" "@smithy/fetch-http-handler" "^3.2.9" @@ -337,12 +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 "https://registry.yarnpkg.com/@aws-sdk/credential-provider-env/-/credential-provider-env-3.677.0.tgz#ee5b6a7fb30fad6363f57d9df88779cda5981930" - integrity sha512-0ctcqKzclr9TiNIkB8I+YRogjWH/4mLWQGv/bgb8ElHqph+rPy4pOubj1Ax01sbs7XdwDaImjBYV5xXE+BEsYw== +"@aws-sdk/credential-provider-env@3.679.0": + version "3.679.0" + resolved "https://registry.yarnpkg.com/@aws-sdk/credential-provider-env/-/credential-provider-env-3.679.0.tgz#abf297714b77197a9da0d3d95a0f5687ae28e5b3" + integrity sha512-EdlTYbzMm3G7VUNAMxr9S1nC1qUNqhKlAxFU8E7cKsAe8Bp29CD5HAs3POc56AVo9GC4yRIS+/mtlZSmrckzUA== dependencies: - "@aws-sdk/core" "3.677.0" - "@aws-sdk/types" "3.667.0" + "@aws-sdk/core" "3.679.0" + "@aws-sdk/types" "3.679.0" "@smithy/property-provider" "^3.1.7" "@smithy/types" "^3.5.0" tslib "^2.6.2" -"@aws-sdk/credential-provider-http@3.677.0": - version "3.677.0" - resolved "https://registry.yarnpkg.com/@aws-sdk/credential-provider-http/-/credential-provider-http-3.677.0.tgz#d0b3ad71409f8ac80d70c19cd2d96d5f22d760c2" - integrity sha512-c4TnShdzk37dhL1HGGzZ2PDKIIEmo1IbT/4y5hSRdNc8Z8fu6spE5GoeVsv6p/HdSGPS7XTy6aOFCMCk4AeIzQ== +"@aws-sdk/credential-provider-http@3.679.0": + version "3.679.0" + resolved "https://registry.yarnpkg.com/@aws-sdk/credential-provider-http/-/credential-provider-http-3.679.0.tgz#9fc29f4ec7ab52ecf394288c05295823e818d812" + integrity sha512-ZoKLubW5DqqV1/2a3TSn+9sSKg0T8SsYMt1JeirnuLJF0mCoYFUaWMyvxxKuxPoqvUsaycxKru4GkpJ10ltNBw== dependencies: - "@aws-sdk/core" "3.677.0" - "@aws-sdk/types" "3.667.0" + "@aws-sdk/core" "3.679.0" + "@aws-sdk/types" "3.679.0" "@smithy/fetch-http-handler" "^3.2.9" "@smithy/node-http-handler" "^3.2.4" "@smithy/property-provider" "^3.1.7" @@ -381,111 +381,111 @@ "@smithy/util-stream" "^3.1.9" tslib "^2.6.2" 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integrity sha512-wi72R01tgjBjzG2kjRyTHl4yCTKDfDMIXRyKz9E/FBa9SkFvUOAE4bdyY9MhEsRZmSWL7+CYE8Flv/HScRpBbA== +"@lerna/create@8.1.9": + version "8.1.9" + resolved "https://registry.yarnpkg.com/@lerna/create/-/create-8.1.9.tgz#6ab7b8514a9a200a4bacb7fa6cf6f01d82d3a154" + integrity sha512-DPnl5lPX4v49eVxEbJnAizrpMdMTBz1qykZrAbBul9rfgk531v8oAt+Pm6O/rpAleRombNM7FJb5rYGzBJatOQ== dependencies: "@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" @@ -2654,7 +2893,7 @@ console-control-strings "^1.1.0" conventional-changelog-core "5.0.1" conventional-recommended-bump "7.0.1" - cosmiconfig "^8.2.0" + cosmiconfig "9.0.0" dedent "1.5.3" execa "5.0.0" fs-extra "^11.2.0" @@ -2680,7 +2919,7 @@ 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" 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resolved "https://registry.yarnpkg.com/caniuse-lite/-/caniuse-lite-1.0.30001677.tgz#27c2e2c637e007cfa864a16f7dfe7cde66b38b5f" + integrity sha512-fmfjsOlJUpMWu+mAAtZZZHz7UEwsUxIIvu1TJfO1HqFQvB/B+ii0xr9B5HpbZY/mC4XZ8SvjHJqtAY6pDPQEog== canvas-sequencer@^3.1.0: version "3.1.0" @@ -6516,7 +6659,7 @@ chalk@4.1.0: ansi-styles "^4.1.0" supports-color "^7.1.0" -chalk@^2.4.1, chalk@^2.4.2: +chalk@^2.4.1: version "2.4.2" resolved "https://registry.yarnpkg.com/chalk/-/chalk-2.4.2.tgz#cd42541677a54333cf541a49108c1432b44c9424" integrity sha512-Mti+f9lpJNcwF4tWV8/OrTTtF1gZi+f8FqlyAdouralcFWFQWF2+NgCHShjkCb+IFBLq9buZwE1xckQU4peSuQ== @@ -6890,7 +7033,7 @@ compare-version@^0.1.2: resolved "https://registry.yarnpkg.com/compare-version/-/compare-version-0.1.2.tgz#0162ec2d9351f5ddd59a9202cba935366a725080" integrity sha512-pJDh5/4wrEnXX/VWRZvruAGHkzKdr46z11OlTPN+VrATlWWhSKewNCJ1futCO5C7eJB3nPMFZA1LeYtcFboZ2A== -compressible@~2.0.16: +compressible@~2.0.18: version "2.0.18" resolved 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sha512-FuLPevChGDshgSicjisSooU0cemp/sGXR841D5LHMB7mTVOmsEHcAxaH3irL53+8YDIeVNQEySh4DaYU/iuPqQ== + optionalDependencies: + "@esbuild/aix-ppc64" "0.24.0" + "@esbuild/android-arm" "0.24.0" + "@esbuild/android-arm64" "0.24.0" + "@esbuild/android-x64" "0.24.0" + "@esbuild/darwin-arm64" "0.24.0" + "@esbuild/darwin-x64" "0.24.0" + "@esbuild/freebsd-arm64" "0.24.0" + "@esbuild/freebsd-x64" "0.24.0" + "@esbuild/linux-arm" "0.24.0" + "@esbuild/linux-arm64" "0.24.0" + "@esbuild/linux-ia32" "0.24.0" + "@esbuild/linux-loong64" "0.24.0" + "@esbuild/linux-mips64el" "0.24.0" + "@esbuild/linux-ppc64" "0.24.0" + "@esbuild/linux-riscv64" "0.24.0" + "@esbuild/linux-s390x" "0.24.0" + "@esbuild/linux-x64" "0.24.0" + "@esbuild/netbsd-x64" "0.24.0" + "@esbuild/openbsd-arm64" "0.24.0" + "@esbuild/openbsd-x64" "0.24.0" + "@esbuild/sunos-x64" "0.24.0" + "@esbuild/win32-arm64" "0.24.0" + "@esbuild/win32-ia32" "0.24.0" + "@esbuild/win32-x64" "0.24.0" + +esbuild@~0.23.0: version "0.23.1" resolved 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dependencies: - "@types/hast" "^3.0.0" - -hast-util-is-element@^3.0.0: - version "3.0.0" - resolved "https://registry.yarnpkg.com/hast-util-is-element/-/hast-util-is-element-3.0.0.tgz#6e31a6532c217e5b533848c7e52c9d9369ca0932" - integrity sha512-Val9mnv2IWpLbNPqc/pUem+a7Ipj2aHacCwgNfTiK0vJKl0LF+4Ba4+v1oPHFpf3bLYmreq0/l3Gud9S5OH42g== - dependencies: - "@types/hast" "^3.0.0" - -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 +9909,6 @@ 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 +10265,6 @@ 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 +10480,6 @@ 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 +10487,11 @@ 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 +10619,7 @@ 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 +11424,15 @@ 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 +11446,7 @@ 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 +11477,7 @@ 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 +11879,6 @@ map-or-similar@^1.5.0: resolved "https://registry.yarnpkg.com/map-or-similar/-/map-or-similar-1.5.0.tgz#6de2653174adfb5d9edc33c69d3e92a1b76faf08" integrity sha512-0aF7ZmVon1igznGI4VS30yugpduQW3y3GkcgGJOp7d8x8QrizhigUxjI/m2UojsXXto+jLAH3KSz+xOJTiORjg== -markdown-to-jsx@^7.4.5: - version "7.5.0" - resolved "https://registry.yarnpkg.com/markdown-to-jsx/-/markdown-to-jsx-7.5.0.tgz#42ece0c71e842560a7d8bd9f81e7a34515c72150" - integrity sha512-RrBNcMHiFPcz/iqIj0n3wclzHXjwS7mzjBNWecKKVhNTIxQepIix6Il/wZCn2Cg5Y1ow2Qi84+eJrryFRWBEWw== - matcher@^3.0.0: version "3.0.0" resolved "https://registry.yarnpkg.com/matcher/-/matcher-3.0.0.tgz#bd9060f4c5b70aa8041ccc6f80368760994f30ca" @@ -11921,9 +12058,9 @@ min-indent@^1.0.0, min-indent@^1.0.1: integrity sha512-I9jwMn07Sy/IwOj3zVkVik2JTvgpaykDZEigL6Rx6N9LbMywwUSMtxET+7lVoDLLd3O3IXwJwvuuns8UB/HeAg== mini-css-extract-plugin@^2.4.5: - version 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strong-log-transformer "^2.1.0" tar-stream "~2.2.0" tmp "~0.2.1" tsconfig-paths "^4.1.2" @@ -12560,16 +12700,16 @@ nx@19.8.6, "nx@>=17.1.2 < 20": yargs "^17.6.2" yargs-parser "21.1.1" optionalDependencies: - "@nx/nx-darwin-arm64" "19.8.6" - "@nx/nx-darwin-x64" "19.8.6" - "@nx/nx-freebsd-x64" "19.8.6" - "@nx/nx-linux-arm-gnueabihf" "19.8.6" - "@nx/nx-linux-arm64-gnu" "19.8.6" - "@nx/nx-linux-arm64-musl" "19.8.6" - "@nx/nx-linux-x64-gnu" "19.8.6" - "@nx/nx-linux-x64-musl" "19.8.6" - "@nx/nx-win32-arm64-msvc" "19.8.6" - "@nx/nx-win32-x64-msvc" "19.8.6" + "@nx/nx-darwin-arm64" "20.0.7" + "@nx/nx-darwin-x64" "20.0.7" + "@nx/nx-freebsd-x64" "20.0.7" + "@nx/nx-linux-arm-gnueabihf" "20.0.7" + "@nx/nx-linux-arm64-gnu" "20.0.7" + "@nx/nx-linux-arm64-musl" "20.0.7" + "@nx/nx-linux-x64-gnu" "20.0.7" + "@nx/nx-linux-x64-musl" "20.0.7" + "@nx/nx-win32-arm64-msvc" "20.0.7" + "@nx/nx-win32-x64-msvc" "20.0.7" object-assign@^4, object-assign@^4.0.1, object-assign@^4.1.1: version "4.1.1" @@ -12635,19 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-rehype-external-links@^3.0.0: - version "3.0.0" - resolved "https://registry.yarnpkg.com/rehype-external-links/-/rehype-external-links-3.0.0.tgz#2b28b5cda1932f83f045b6f80a3e1b15f168c6f6" - integrity sha512-yp+e5N9V3C6bwBeAC4n796kc86M4gJCdlVhiMTxIrJG5UHDMh+PJANf9heqORJbt1nrCbDwIlAZKjANIaVBbvw== - dependencies: - "@types/hast" "^3.0.0" - "@ungap/structured-clone" "^1.0.0" - hast-util-is-element "^3.0.0" - is-absolute-url "^4.0.0" - space-separated-tokens "^2.0.0" - unist-util-visit "^5.0.0" - -rehype-slug@^6.0.0: - version "6.0.0" - resolved "https://registry.yarnpkg.com/rehype-slug/-/rehype-slug-6.0.0.tgz#1d21cf7fc8a83ef874d873c15e6adaee6344eaf1" - integrity sha512-lWyvf/jwu+oS5+hL5eClVd3hNdmwM1kAC0BUvEGD19pajQMIzcNUd/k9GsfQ+FfECvX+JE+e9/btsKH0EjJT6A== - dependencies: - "@types/hast" "^3.0.0" - github-slugger "^2.0.0" - hast-util-heading-rank "^3.0.0" - hast-util-to-string "^3.0.0" - unist-util-visit "^5.0.0" - relateurl@^0.2.7: version "0.2.7" resolved "https://registry.yarnpkg.com/relateurl/-/relateurl-0.2.7.tgz#54dbf377e51440aca90a4cd274600d3ff2d888a9" @@ -14824,11 +14922,6 @@ source-map@^0.7.3: resolved "https://registry.yarnpkg.com/source-map/-/source-map-0.7.4.tgz#a9bbe705c9d8846f4e08ff6765acf0f1b0898656" integrity sha512-l3BikUxvPOcn5E74dZiq5BGsTb5yEwhaTSzccU6t4sDOH8NWJCstKO5QT2CvtFoK6F0saL7p9xHAqHOlCPJygA== -space-separated-tokens@^2.0.0: - version "2.0.2" - resolved "https://registry.yarnpkg.com/space-separated-tokens/-/space-separated-tokens-2.0.2.tgz#1ecd9d2350a3844572c3f4a312bceb018348859f" - integrity sha512-PEGlAwrG8yXGXRjW32fGbg66JAlOAwbObuqVoJpv/mRgoWDQfgH1wDPvtzWyUSNAXBGSk8h755YDbbcEy3SH2Q== - spdx-correct@^3.0.0: version "3.2.0" resolved "https://registry.yarnpkg.com/spdx-correct/-/spdx-correct-3.2.0.tgz#4f5ab0668f0059e34f9c00dce331784a12de4e9c" @@ -14961,11 +15054,11 @@ statuses@2.0.1: integrity sha512-OpZ3zP+jT1PI7I8nemJX4AKmAX070ZkYPVWV/AaKTJl+tXCTGyVdC1a4SL8RUQYEwk/f34ZX8UTykN68FwrqAA== storybook@^8.0.0: - 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tslib@^2.1.0, tslib@^2.3.0, tslib@^2.3.1, tslib@^2.4.0, tslib@^2.6.2, tslib@^2.7.0: + version "2.8.1" + resolved "https://registry.yarnpkg.com/tslib/-/tslib-2.8.1.tgz#612efe4ed235d567e8aba5f2a5fab70280ade83f" + integrity sha512-oJFu94HQb+KVduSUQL7wnpmqnfmLsOA/nAh6b6EH0wCEoK0/mPeXU6c3wKDV83MkOuHPRHtSXKKU99IBazS/2w== tss-react@^4.0.0, tss-react@^4.4.1: version "4.9.13" @@ -15560,9 +15646,9 @@ tss-react@^4.0.0, tss-react@^4.4.1: "@emotion/utils" "*" tsx@^4.17.0: - version "4.19.1" - resolved "https://registry.yarnpkg.com/tsx/-/tsx-4.19.1.tgz#b7bffdf4b565813e4dea14b90872af279cd0090b" - integrity sha512-0flMz1lh74BR4wOvBjuh9olbnwqCPc35OOlfyzHba0Dc+QNUeWX/Gq2YTbnwcWPO3BMd8fkzRVrHcsR+a7z7rA== + version "4.19.2" + resolved "https://registry.yarnpkg.com/tsx/-/tsx-4.19.2.tgz#2d7814783440e0ae42354d0417d9c2989a2ae92c" + integrity sha512-pOUl6Vo2LUq/bSa8S5q7b91cgNSjctn9ugq/+Mvow99qW6x/UZYwzxy/3NmqoT66eHYfCVvFvACC58UBPFf28g== dependencies: esbuild "~0.23.0" get-tsconfig "^4.7.5" @@ -15632,7 +15718,7 @@ type-fest@^0.8.1: resolved "https://registry.yarnpkg.com/type-fest/-/type-fest-0.8.1.tgz#09e249ebde851d3b1e48d27c105444667f17b83d" integrity sha512-4dbzIzqvjtgiM5rw1k5rEHtBANKmdudhGyBEajN01fEyhaAIhsoKNy6y7+IN93IfpFtwY9iqi7kD+xwKhQsNJA== -type-fest@^2.19.0, type-fest@~2.19: +type-fest@^2.19.0: version "2.19.0" resolved "https://registry.yarnpkg.com/type-fest/-/type-fest-2.19.0.tgz#88068015bb33036a598b952e55e9311a60fd3a9b" integrity sha512-RAH822pAdBgcNMAfWnCBU3CFZcfZ/i1eZjwFU/dsLKumyuuP3niueg2UAukXYF0E2AAoc82ZSSf9J0WQBinzHA== @@ -15695,13 +15781,13 @@ typedarray@^0.0.6: integrity sha512-/aCDEGatGvZ2BIk+HmLf4ifCJFwvKFNb9/JeZPMulfgFracn9QFcAf5GO8B/mweUjSoblS5In0cWhqpfs/5PQA== typescript-eslint@^8.0.1: - version "8.11.0" - resolved "https://registry.yarnpkg.com/typescript-eslint/-/typescript-eslint-8.11.0.tgz#74a0551972d675b4141672cec3acc5139b7399c0" - integrity sha512-cBRGnW3FSlxaYwU8KfAewxFK5uzeOAp0l2KebIlPDOT5olVi65KDG/yjBooPBG0kGW/HLkoz1c/iuBFehcS3IA== + version "8.12.2" + resolved 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sha512-MR04uvD+07cwl/yhVuVWAtw+3GOR/knlL55Nd/wAdblk27GCVt3lqpTivy/tkJcZoNPzTwS1Y+KMojlLDhoTzg== - dependencies: - "@types/unist" "^3.0.0" - unist-util-is "^6.0.0" - unist-util-visit-parents "^6.0.0" - universal-user-agent@^6.0.0: version "6.0.1" resolved "https://registry.yarnpkg.com/universal-user-agent/-/universal-user-agent-6.0.1.tgz#15f20f55da3c930c57bddbf1734c6654d5fd35aa" @@ -15851,11 +15913,11 @@ unpipe@1.0.0, unpipe@~1.0.0: integrity sha512-pjy2bYhSsufwWlKwPc+l3cN7+wuJlK6uz0YdJEOlQDbl6jo/YlPi4mb8agUkVC8BF7V8NuzeyPNqRksA3hztKQ== unplugin@^1.3.1: - version "1.14.1" - resolved "https://registry.yarnpkg.com/unplugin/-/unplugin-1.14.1.tgz#c76d6155a661e43e6a897bce6b767a1ecc344c1a" - integrity sha512-lBlHbfSFPToDYp9pjXlUEFVxYLaue9f9T1HC+4OHlmj+HnMDdz9oZY+erXfoCe/5V/7gKUSY2jpXPb9S7f0f/w== + version "1.15.0" + resolved "https://registry.yarnpkg.com/unplugin/-/unplugin-1.15.0.tgz#cd1e92e537ab14a03354d6f83f29d536fac2e5a9" + integrity sha512-jTPIs63W+DUEDW207ztbaoO7cQ4p5aVaB823LSlxpsFEU3Mykwxf3ZGC/wzxFJeZlASZYgVrWeo7LgOrqJZ8RA== dependencies: - acorn "^8.12.1" + acorn "^8.14.0" webpack-virtual-modules "^0.6.2" upath@2.0.1: @@ -16186,17 +16248,17 @@ webpack-virtual-modules@^0.6.0, webpack-virtual-modules@^0.6.2: integrity sha512-66/V2i5hQanC51vBQKPH4aI8NMAcBW59FVBs+rC7eGHupMyfn34q7rZIE+ETlJ+XTevqfUhVVBgSUNSW2flEUQ== webpack@5, webpack@^5.64.4, webpack@^5.72.0: - version "5.95.0" - resolved "https://registry.yarnpkg.com/webpack/-/webpack-5.95.0.tgz#8fd8c454fa60dad186fbe36c400a55848307b4c0" - integrity sha512-2t3XstrKULz41MNMBF+cJ97TyHdyQ8HCt//pqErqDvNjU9YQBnZxIHa11VXsi7F3mb5/aO2tuDxdeTPdU7xu9Q== + version "5.96.1" + resolved "https://registry.yarnpkg.com/webpack/-/webpack-5.96.1.tgz#3676d1626d8312b6b10d0c18cc049fba7ac01f0c" + integrity sha512-l2LlBSvVZGhL4ZrPwyr8+37AunkcYj5qh8o6u2/2rzoPc8gxFJkLj1WxNgooi9pnoc06jh0BjuXnamM4qlujZA== dependencies: - "@types/estree" "^1.0.5" + "@types/eslint-scope" "^3.7.7" + "@types/estree" "^1.0.6" "@webassemblyjs/ast" "^1.12.1" "@webassemblyjs/wasm-edit" "^1.12.1" "@webassemblyjs/wasm-parser" "^1.12.1" - acorn "^8.7.1" - acorn-import-attributes "^1.9.5" - browserslist "^4.21.10" + acorn "^8.14.0" + browserslist "^4.24.0" chrome-trace-event "^1.0.2" enhanced-resolve "^5.17.1" es-module-lexer "^1.2.1"