From 935865750c97167035d9537b8da4ec296edfdcc8 Mon Sep 17 00:00:00 2001 From: Colin Date: Wed, 18 Jan 2023 20:56:04 -0800 Subject: [PATCH] [skip ci] Matrix Updates Small updates + minor allele frequency [skip ci] Test T1 T5 Bump yarn.lock Fix some types Update snap Render block Add autogen docs Misc --- .../configSchema.ts | 27 + .../src/LinearVariantMatrixDisplay/index.ts | 22 + .../src/LinearVariantMatrixDisplay/model.ts | 77 +++ .../LinearVariantMatrixRenderer.ts | 147 ++++ .../LinearVariantMatrixRendering.tsx | 32 + .../configSchema.ts | 13 + .../src/LinearVariantMatrixRenderer/index.ts | 16 + .../variants/src/VariantTrack/configSchema.ts | 9 +- .../src/__snapshots__/index.test.ts.snap | 4 + plugins/variants/src/index.ts | 4 + .../src/CreateMultiWiggleExtension/index.ts | 65 +- test_data/config_demo.json | 80 +++ .../docs/config/LinearVariantMatrixDisplay.md | 20 + .../config/LinearVariantMatrixRenderer.md | 14 + website/docs/config/VariantTrack.md | 20 - .../docs/models/LinearVariantMatrixDisplay.md | 72 ++ yarn.lock | 627 +++++++++--------- 17 files changed, 876 insertions(+), 373 deletions(-) create mode 100644 plugins/variants/src/LinearVariantMatrixDisplay/configSchema.ts create mode 100644 plugins/variants/src/LinearVariantMatrixDisplay/index.ts create mode 100644 plugins/variants/src/LinearVariantMatrixDisplay/model.ts create mode 100644 plugins/variants/src/LinearVariantMatrixRenderer/LinearVariantMatrixRenderer.ts create mode 100644 plugins/variants/src/LinearVariantMatrixRenderer/components/LinearVariantMatrixRendering.tsx create mode 100644 plugins/variants/src/LinearVariantMatrixRenderer/configSchema.ts create mode 100644 plugins/variants/src/LinearVariantMatrixRenderer/index.ts create mode 100644 website/docs/config/LinearVariantMatrixDisplay.md create mode 100644 website/docs/config/LinearVariantMatrixRenderer.md delete mode 100644 website/docs/config/VariantTrack.md create mode 100644 website/docs/models/LinearVariantMatrixDisplay.md diff --git a/plugins/variants/src/LinearVariantMatrixDisplay/configSchema.ts b/plugins/variants/src/LinearVariantMatrixDisplay/configSchema.ts new file mode 100644 index 0000000000..c617e9d928 --- /dev/null +++ b/plugins/variants/src/LinearVariantMatrixDisplay/configSchema.ts @@ -0,0 +1,27 @@ +import { ConfigurationSchema } from '@jbrowse/core/configuration' +import PluginManager from '@jbrowse/core/PluginManager' +import { linearBasicDisplayConfigSchemaFactory } from '@jbrowse/plugin-linear-genome-view' + +// locals +import configSchema from '../LinearVariantMatrixRenderer/configSchema' + +/** + * #config LinearVariantMatrixDisplay + */ +function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars + +export default function configSchemaF(pluginManager: PluginManager) { + return ConfigurationSchema( + 'LinearVariantMatrixDisplay', + { + renderer: configSchema, + }, + { + /** + * #baseConfiguration + */ + baseConfiguration: linearBasicDisplayConfigSchemaFactory(pluginManager), + explicitlyTyped: true, + }, + ) +} diff --git a/plugins/variants/src/LinearVariantMatrixDisplay/index.ts b/plugins/variants/src/LinearVariantMatrixDisplay/index.ts new file mode 100644 index 0000000000..091a7dd1a1 --- /dev/null +++ b/plugins/variants/src/LinearVariantMatrixDisplay/index.ts @@ -0,0 +1,22 @@ +import PluginManager from '@jbrowse/core/PluginManager' +import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view' +import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType' + +// locals +import stateModelFactory from './model' +import configSchemaF from './configSchema' + +export default (pluginManager: PluginManager) => { + pluginManager.addDisplayType(() => { + const configSchema = configSchemaF(pluginManager) + return new DisplayType({ + name: 'LinearVariantMatrixDisplay', + displayName: 'Matrix display', + configSchema, + stateModel: stateModelFactory(configSchema), + trackType: 'VariantTrack', + viewType: 'LinearGenomeView', + ReactComponent: BaseLinearDisplayComponent, + }) + }) +} diff --git a/plugins/variants/src/LinearVariantMatrixDisplay/model.ts b/plugins/variants/src/LinearVariantMatrixDisplay/model.ts new file mode 100644 index 0000000000..269c0a480b --- /dev/null +++ b/plugins/variants/src/LinearVariantMatrixDisplay/model.ts @@ -0,0 +1,77 @@ +import { ConfigurationReference } from '@jbrowse/core/configuration' + +import { linearBasicDisplayModelFactory } from '@jbrowse/plugin-linear-genome-view' +import { Instance, types } from 'mobx-state-tree' + +// locals +import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration' + +/** + * #stateModel LinearVariantMatrixDisplay + * extends `LinearBasicDisplay` + */ +export default function stateModelFactory( + configSchema: AnyConfigurationSchemaType, +) { + return types + .compose( + 'LinearVariantMatrixDisplay', + linearBasicDisplayModelFactory(configSchema), + types.model({ + /** + * #property + */ + type: types.literal('LinearVariantMatrixDisplay'), + /** + * #property + */ + configuration: ConfigurationReference(configSchema), + }), + ) + .volatile(() => ({ + samples: undefined as string[] | undefined, + })) + .views(() => ({ + /** + * #getter + */ + get blockType() { + return 'dynamicBlocks' + }, + /** + * #getter + */ + get renderDelay() { + return 1000 + }, + })) + .actions(self => ({ + /** + * #action + */ + setSamples(arg: string[]) { + self.samples = arg + }, + })) + .views(self => { + const { renderProps: superRenderProps } = self + return { + /** + * #method + */ + renderProps() { + const superProps = superRenderProps() + return { + ...superProps, + height: self.height, + } + }, + } + }) +} + +export type LinearVariantMatrixDisplayStateModel = ReturnType< + typeof stateModelFactory +> +export type LinearVariantMatrixDisplayModel = + Instance diff --git a/plugins/variants/src/LinearVariantMatrixRenderer/LinearVariantMatrixRenderer.ts b/plugins/variants/src/LinearVariantMatrixRenderer/LinearVariantMatrixRenderer.ts new file mode 100644 index 0000000000..44cbd0c4a9 --- /dev/null +++ b/plugins/variants/src/LinearVariantMatrixRenderer/LinearVariantMatrixRenderer.ts @@ -0,0 +1,147 @@ +import BoxRendererType, { + RenderArgs, + RenderArgsSerialized, + RenderArgsDeserialized as BoxRenderArgsDeserialized, + RenderResults, + ResultsSerialized, + ResultsDeserialized, +} from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType' +import { Feature, renderToAbstractCanvas } from '@jbrowse/core/util' + +export interface SortParams { + type: string + pos: number + refName: string + assemblyName: string + tag?: string +} + +export interface RenderArgsDeserialized extends BoxRenderArgsDeserialized { + highResolutionScaling: number + height: number +} + +export interface RenderArgsDeserializedWithFeaturesAndLayout + extends RenderArgsDeserialized { + features: Map +} + +const fudgeFactor = 0.6 +const f2 = fudgeFactor / 2 + +export default class LinearVariantMatrixRenderer extends BoxRendererType { + supportsSVG = true + + makeImageData({ + ctx, + canvasWidth, + canvasHeight, + renderArgs, + }: { + ctx: CanvasRenderingContext2D + canvasWidth: number + canvasHeight: number + renderArgs: RenderArgsDeserializedWithFeaturesAndLayout + }) { + const { features } = renderArgs + const feats = [...features.values()] + if (!feats.length) { + return + } + const samples = feats[0].get('samples') + const keys = Object.keys(samples) + const h = canvasHeight / keys.length + + const mafs = [] as number[] + for (let i = 0; i < feats.length; i++) { + let c = 0 + let c2 = 0 + for (let j = 0; j < keys.length; j++) { + const key = keys[j] + const samp = feats[i].get('samples') + const s = samp[key].GT[0] + if (s === '0|0') { + } else if (s === '1|0' || s === '0|1') { + c++ + } else if (s === '1|1') { + c++ + c2++ + } else { + c++ + } + } + if (c / keys.length > 0.15 && c2 / keys.length < 0.85) { + mafs.push(i) + } + } + + const w = canvasWidth / mafs.length + for (let i = 0; i < mafs.length; i++) { + const m = mafs[i] + const f = feats[m] + const x = (i / mafs.length) * canvasWidth + for (let j = 0; j < keys.length; j++) { + const y = (j / keys.length) * canvasHeight + const key = keys[j] + const samp = f.get('samples') + const s = samp[key].GT[0] + if (s === '0|0') { + ctx.fillStyle = 'grey' + } else if (s === '1|0' || s === '0|1') { + ctx.fillStyle = 'teal' + } else if (s === '1|1') { + ctx.fillStyle = 'blue' + } else { + ctx.fillStyle = 'purple' + } + ctx.fillRect(x - f2, y - f2, w + f2, h + f2) + } + } + return { samples: Object.keys(samples) } + } + + async render(renderProps: RenderArgsDeserialized) { + const features = await this.getFeatures(renderProps) + const { height, regions, bpPerPx } = renderProps + const [region] = regions + + const { end, start } = region + + const width = (end - start) / bpPerPx + const res = await renderToAbstractCanvas(width, height, renderProps, ctx => + this.makeImageData({ + ctx, + canvasWidth: width, + canvasHeight: height, + renderArgs: { + ...renderProps, + features, + }, + }), + ) + + const results = await super.render({ + ...renderProps, + ...res, + features, + height, + width, + }) + + return { + ...results, + ...res, + features: new Map(), + height, + width, + } + } +} + +export type { + RenderArgs, + RenderArgsSerialized, + RenderResults, + ResultsSerialized, + ResultsDeserialized, +} diff --git a/plugins/variants/src/LinearVariantMatrixRenderer/components/LinearVariantMatrixRendering.tsx b/plugins/variants/src/LinearVariantMatrixRenderer/components/LinearVariantMatrixRendering.tsx new file mode 100644 index 0000000000..9c6ee2583e --- /dev/null +++ b/plugins/variants/src/LinearVariantMatrixRenderer/components/LinearVariantMatrixRendering.tsx @@ -0,0 +1,32 @@ +import React, { useEffect } from 'react' +import { PrerenderedCanvas } from '@jbrowse/core/ui' +import { Region } from '@jbrowse/core/util' +import { observer } from 'mobx-react' +import { LinearVariantMatrixDisplayModel } from '../../LinearVariantMatrixDisplay/model' + +export default observer(function LinearVariantMatrixRendering(props: { + blockKey: string + displayModel: LinearVariantMatrixDisplayModel + width: number + height: number + regions: Region[] + bpPerPx: number + onMouseMove?: (event: React.MouseEvent, featureId?: string) => void + samples: string[] +}) { + const { displayModel, width, height, samples } = props + + useEffect(() => { + displayModel.setSamples(samples) + }, [samples, displayModel]) + const canvasWidth = Math.ceil(width) + + return ( +
+ +
+ ) +}) diff --git a/plugins/variants/src/LinearVariantMatrixRenderer/configSchema.ts b/plugins/variants/src/LinearVariantMatrixRenderer/configSchema.ts new file mode 100644 index 0000000000..71e751baf1 --- /dev/null +++ b/plugins/variants/src/LinearVariantMatrixRenderer/configSchema.ts @@ -0,0 +1,13 @@ +import { ConfigurationSchema } from '@jbrowse/core/configuration' + +/** + * #config LinearVariantMatrixRenderer + */ +function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars + +const LinearVariantMatrixRenderer = ConfigurationSchema( + 'LinearVariantMatrixRenderer', + {}, + { explicitlyTyped: true }, +) +export default LinearVariantMatrixRenderer diff --git a/plugins/variants/src/LinearVariantMatrixRenderer/index.ts b/plugins/variants/src/LinearVariantMatrixRenderer/index.ts new file mode 100644 index 0000000000..267d40ab07 --- /dev/null +++ b/plugins/variants/src/LinearVariantMatrixRenderer/index.ts @@ -0,0 +1,16 @@ +import PluginManager from '@jbrowse/core/PluginManager' +import LinearVariantMatrixRenderer from './LinearVariantMatrixRenderer' +import ReactComponent from './components/LinearVariantMatrixRendering' +import configSchema from './configSchema' + +export default function register(pluginManager: PluginManager) { + pluginManager.addRendererType(() => { + return new LinearVariantMatrixRenderer({ + name: 'LinearVariantMatrixRenderer', + displayName: 'Linear variant matrix renderer', + ReactComponent, + configSchema, + pluginManager, + }) + }) +} diff --git a/plugins/variants/src/VariantTrack/configSchema.ts b/plugins/variants/src/VariantTrack/configSchema.ts index 8ea8a45adf..bcbe18abc5 100644 --- a/plugins/variants/src/VariantTrack/configSchema.ts +++ b/plugins/variants/src/VariantTrack/configSchema.ts @@ -7,10 +7,8 @@ import PluginManager from '@jbrowse/core/PluginManager' * Mostly similar to feature track, but has `ChordDisplayType` registered to it, * and custom feature details in `LinearVariantDisplay` */ -function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars - -const configSchema = (pluginManager: PluginManager) => - ConfigurationSchema( +export default function (pluginManager: PluginManager) { + return ConfigurationSchema( 'VariantTrack', {}, { @@ -20,5 +18,4 @@ const configSchema = (pluginManager: PluginManager) => baseConfiguration: createBaseTrackConfig(pluginManager), }, ) - -export default configSchema +} diff --git a/plugins/variants/src/__snapshots__/index.test.ts.snap b/plugins/variants/src/__snapshots__/index.test.ts.snap index 34004264d3..3a2ed5fb3a 100644 --- a/plugins/variants/src/__snapshots__/index.test.ts.snap +++ b/plugins/variants/src/__snapshots__/index.test.ts.snap @@ -9,6 +9,10 @@ exports[`plugin in a stock JBrowse 2`] = ` "displayId": "trackId0-LinearVariantDisplay", "type": "LinearVariantDisplay", }, + { + "displayId": "trackId0-LinearVariantMatrixDisplay", + "type": "LinearVariantMatrixDisplay", + }, { "displayId": "trackId0-ChordVariantDisplay", "type": "ChordVariantDisplay", diff --git a/plugins/variants/src/index.ts b/plugins/variants/src/index.ts index 69ce13a9f7..cdacf0b0fe 100644 --- a/plugins/variants/src/index.ts +++ b/plugins/variants/src/index.ts @@ -6,6 +6,8 @@ import Plugin from '@jbrowse/core/Plugin' import PluginManager from '@jbrowse/core/PluginManager' import ChordVariantDisplayF from './ChordVariantDisplay' import LinearVariantDisplayF from './LinearVariantDisplay' +import LinearVariantMatrixDisplayF from './LinearVariantMatrixDisplay' +import LinearVariantMatrixRendererF from './LinearVariantMatrixRenderer' import StructuralVariantChordRendererF from './StructuralVariantChordRenderer' import VariantFeatureWidgetF from './VariantFeatureWidget' @@ -19,6 +21,8 @@ export default class VariantsPlugin extends Plugin { VariantTrackF(pluginManager) ExtensionPointsF(pluginManager) LinearVariantDisplayF(pluginManager) + LinearVariantMatrixDisplayF(pluginManager) + LinearVariantMatrixRendererF(pluginManager) StructuralVariantChordRendererF(pluginManager) ChordVariantDisplayF(pluginManager) } diff --git a/plugins/wiggle/src/CreateMultiWiggleExtension/index.ts b/plugins/wiggle/src/CreateMultiWiggleExtension/index.ts index f192470dfb..976ae5f90e 100644 --- a/plugins/wiggle/src/CreateMultiWiggleExtension/index.ts +++ b/plugins/wiggle/src/CreateMultiWiggleExtension/index.ts @@ -4,8 +4,44 @@ import { readConfObject } from '@jbrowse/core/configuration' import { getSession, isSessionWithAddTracks } from '@jbrowse/core/util' import { HierarchicalTrackSelectorModel } from '@jbrowse/plugin-data-management' +// lazies const ConfirmDialog = lazy(() => import('./ConfirmDialog')) +function makeTrack({ + model, + arg, +}: { + model: HierarchicalTrackSelectorModel + arg: { + name: string + } +}) { + const tracks = model.selection + const trackIds = tracks.map(c => readConfObject(c, 'name')) + const subadapters = tracks + .map(c => readConfObject(c, 'adapter')) + .map((c, idx) => ({ ...c, source: trackIds[idx] })) + const now = +Date.now() + const trackId = `multitrack-${now}-sessionTrack` + + const session = getSession(model) + if (isSessionWithAddTracks(session)) { + session.addTrackConf({ + type: 'MultiQuantitativeTrack', + trackId, + name: arg.name, + assemblyNames: [ + ...new Set(tracks.flatMap(c => readConfObject(c, 'assemblyNames'))), + ], + adapter: { + type: 'MultiWiggleAdapter', + subadapters, + }, + }) + model.view.showTrack(trackId) + } +} + export default function CreateMultiWiggleExtensionF(pm: PluginManager) { pm.addToExtensionPoint( 'TrackSelector-multiTrackMenuItems', @@ -19,41 +55,14 @@ export default function CreateMultiWiggleExtensionF(pm: PluginManager) { label: 'Create multi-wiggle track', onClick: (model: HierarchicalTrackSelectorModel) => { const tracks = model.selection - const trackIds = tracks.map(c => readConfObject(c, 'name')) - function makeTrack(arg: { name: string }) { - const subadapters = tracks - .map(c => readConfObject(c, 'adapter')) - .map((c, idx) => ({ ...c, source: trackIds[idx] })) - const assemblyNames = [ - ...new Set( - tracks.flatMap(c => readConfObject(c, 'assemblyNames')), - ), - ] - const now = +Date.now() - const trackId = `multitrack-${now}-sessionTrack` - const session = getSession(model) - if (isSessionWithAddTracks(session)) { - session.addTrackConf({ - type: 'MultiQuantitativeTrack', - trackId, - name: arg.name, - assemblyNames, - adapter: { - type: 'MultiWiggleAdapter', - subadapters, - }, - }) - model.view.showTrack(trackId) - } - } getSession(model).queueDialog(handleClose => [ ConfirmDialog, { tracks, onClose: (arg: boolean, arg1?: { name: string }) => { if (arg && arg1) { - makeTrack(arg1) + makeTrack({ model, arg: arg1 }) } handleClose() }, diff --git a/test_data/config_demo.json b/test_data/config_demo.json index 89a08cde1a..91e88347da 100644 --- a/test_data/config_demo.json +++ b/test_data/config_demo.json @@ -4486,6 +4486,86 @@ } }, "assemblyNames": ["hg38"] + }, + { + "type": "VariantTrack", + "trackId": "ALL.chr1.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf", + "name": "ALL.chr1.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf", + "adapter": { + "type": "VcfTabixAdapter", + "vcfGzLocation": { + "uri": "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz", + "locationType": "UriLocation" + }, + "index": { + "location": { + "uri": "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz.tbi", + "locationType": "UriLocation" + }, + "indexType": "TBI" + } + }, + "assemblyNames": ["hg19"] + }, + { + "type": "VariantTrack", + "trackId": "CCDG_14151_B01_GRM_WGS_2020-08-05_chr1.filtered.shapeit2-duohmm-phased.vcf", + "name": "CCDG_14151_B01_GRM_WGS_2020-08-05_chr1.filtered.shapeit2-duohmm-phased.vcf", + "adapter": { + "type": "VcfTabixAdapter", + "vcfGzLocation": { + "uri": "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20201028_3202_phased/CCDG_14151_B01_GRM_WGS_2020-08-05_chr1.filtered.shapeit2-duohmm-phased.vcf.gz", + "locationType": "UriLocation" + }, + "index": { + "location": { + "uri": "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20201028_3202_phased/CCDG_14151_B01_GRM_WGS_2020-08-05_chr1.filtered.shapeit2-duohmm-phased.vcf.gz.tbi", + "locationType": "UriLocation" + }, + "indexType": "TBI" + } + }, + "assemblyNames": ["hg38"] + }, + { + "type": "VariantTrack", + "trackId": "1KGP_3202.Illumina_ensemble_callset.freeze_V1.vcf", + "name": "1KGP_3202.Illumina_ensemble_callset.freeze_V1.vcf", + "adapter": { + "type": "VcfTabixAdapter", + "vcfGzLocation": { + "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/1000genomes/1KGP_3202.Illumina_ensemble_callset.freeze_V1.vcf.gz", + "locationType": "UriLocation" + }, + "index": { + "location": { + "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/1000genomes/1KGP_3202.Illumina_ensemble_callset.freeze_V1.vcf.gz.tbi", + "locationType": "UriLocation" + }, + "indexType": "TBI" + } + }, + "assemblyNames": ["hg38"] + }, + { + "type": "VariantTrack", + "trackId": "1kGP_high_coverage_Illumina.chr1.filtered.SNV_INDEL_SV_phased_panel.vcf", + "name": "1kGP_high_coverage_Illumina.chr1.filtered.SNV_INDEL_SV_phased_panel.vcf", + "adapter": { + "type": "VcfTabixAdapter", + "vcfGzLocation": { + "uri": "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20220422_3202_phased_SNV_INDEL_SV/1kGP_high_coverage_Illumina.chr1.filtered.SNV_INDEL_SV_phased_panel.vcf.gz", + "locationType": "UriLocation" + }, + "index": { + "location": { + "uri": "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20220422_3202_phased_SNV_INDEL_SV/1kGP_high_coverage_Illumina.chr1.filtered.SNV_INDEL_SV_phased_panel.vcf.gz.tbi", + "locationType": "UriLocation" + }, + "indexType": "TBI" + } + }, + "assemblyNames": ["hg38"] } ], "connections": [], diff --git a/website/docs/config/LinearVariantMatrixDisplay.md b/website/docs/config/LinearVariantMatrixDisplay.md new file mode 100644 index 0000000000..271422b67b --- /dev/null +++ b/website/docs/config/LinearVariantMatrixDisplay.md @@ -0,0 +1,20 @@ +--- +id: linearvariantmatrixdisplay +title: LinearVariantMatrixDisplay +toplevel: true +--- + +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info + +## Source file + +[plugins/variants/src/LinearVariantMatrixDisplay/configSchema.ts](https://github.com/GMOD/jbrowse-components/blob/main/plugins/variants/src/LinearVariantMatrixDisplay/configSchema.ts) + +## Docs + +## LinearVariantMatrixDisplay - Derives from + +```js +baseConfiguration: linearBasicDisplayConfigSchemaFactory(pluginManager) +``` diff --git a/website/docs/config/LinearVariantMatrixRenderer.md b/website/docs/config/LinearVariantMatrixRenderer.md new file mode 100644 index 0000000000..9519040016 --- /dev/null +++ b/website/docs/config/LinearVariantMatrixRenderer.md @@ -0,0 +1,14 @@ +--- +id: linearvariantmatrixrenderer +title: LinearVariantMatrixRenderer +toplevel: true +--- + +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info + +## Source file + +[plugins/variants/src/LinearVariantMatrixRenderer/configSchema.ts](https://github.com/GMOD/jbrowse-components/blob/main/plugins/variants/src/LinearVariantMatrixRenderer/configSchema.ts) + +## Docs diff --git a/website/docs/config/VariantTrack.md b/website/docs/config/VariantTrack.md deleted file mode 100644 index 2d606a2065..0000000000 --- a/website/docs/config/VariantTrack.md +++ /dev/null @@ -1,20 +0,0 @@ ---- -id: varianttrack -title: VariantTrack ---- - -Note: this document is automatically generated from configuration objects in our -source code. See [Config guide](/docs/config_guide) for more info - -### Source file - -[plugins/variants/src/VariantTrack/configSchema.ts](https://github.com/GMOD/jbrowse-components/blob/main/plugins/variants/src/VariantTrack/configSchema.ts) - -Mostly similar to feature track, but has `ChordDisplayType` registered to it, -and custom feature details in `LinearVariantDisplay` - -### VariantTrack - Derives from - -```js -baseConfiguration: createBaseTrackConfig(pluginManager) -``` diff --git a/website/docs/models/LinearVariantMatrixDisplay.md b/website/docs/models/LinearVariantMatrixDisplay.md new file mode 100644 index 0000000000..a84e86ba72 --- /dev/null +++ b/website/docs/models/LinearVariantMatrixDisplay.md @@ -0,0 +1,72 @@ +--- +id: linearvariantmatrixdisplay +title: LinearVariantMatrixDisplay +toplevel: true +--- + +Note: this document is automatically generated from mobx-state-tree objects in +our source code. See +[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more +info + +## Source file + +[plugins/variants/src/LinearVariantMatrixDisplay/model.ts](https://github.com/GMOD/jbrowse-components/blob/main/plugins/variants/src/LinearVariantMatrixDisplay/model.ts) + +## Docs + +extends `LinearBasicDisplay` + +### LinearVariantMatrixDisplay - Properties + +#### property: type + +```js +// type signature +ISimpleType<"LinearVariantMatrixDisplay"> +// code +type: types.literal('LinearVariantMatrixDisplay') +``` + +#### property: configuration + +```js +// type signature +ITypeUnion +// code +configuration: ConfigurationReference(configSchema) +``` + +### LinearVariantMatrixDisplay - Getters + +#### getter: blockType + +```js +// type +string +``` + +#### getter: renderDelay + +```js +// type +number +``` + +### LinearVariantMatrixDisplay - Methods + +#### method: renderProps + +```js +// type signature +renderProps: () => any +``` + +### LinearVariantMatrixDisplay - Actions + +#### action: setSamples + +```js +// type signature +setSamples: (arg: string[]) => void +``` diff --git a/yarn.lock b/yarn.lock index 4c97ba3ca9..f4ef487e5f 100644 --- a/yarn.lock +++ b/yarn.lock @@ -138,10 +138,10 @@ "@smithy/util-waiter" "^3.1.6" tslib "^2.6.2" -"@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== +"@aws-sdk/client-s3@^3.676.0": + version "3.682.0" + resolved "https://registry.yarnpkg.com/@aws-sdk/client-s3/-/client-s3-3.682.0.tgz#b7a6148f12bc6a5a44562a44dd6af733a83af1d7" + integrity sha512-gn8yPhOmExhqRENnR/vKvsbTw9jaRPbfNE8fQ2j91ejXhpj632QDNdobY8TxxPm2UEW2ISAVM55r2/UPl0YP1Q== dependencies: "@aws-crypto/sha1-browser" "5.2.0" "@aws-crypto/sha256-browser" "5.2.0" @@ -157,11 +157,11 @@ "@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-sdk-s3" "3.682.0" "@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/signature-v4-multi-region" "3.682.0" "@aws-sdk/types" "3.679.0" "@aws-sdk/util-endpoints" "3.679.0" "@aws-sdk/util-user-agent-browser" "3.679.0" @@ -532,10 +532,10 @@ "@smithy/types" "^3.5.0" tslib "^2.6.2" -"@aws-sdk/middleware-sdk-s3@3.685.0": - version "3.685.0" - resolved "https://registry.yarnpkg.com/@aws-sdk/middleware-sdk-s3/-/middleware-sdk-s3-3.685.0.tgz#9e198973cc8d7ead142e5b5ba38694a957cf462b" - integrity sha512-C4w92b3A99NbghrA2Ssw6y1RbDF3I3Bgzi2Izh0pXgyIoDiX0xs9bUs/FGYLK4uepYr78DAZY8DwEpzjWIXkSA== +"@aws-sdk/middleware-sdk-s3@3.682.0": + version "3.682.0" + resolved "https://registry.yarnpkg.com/@aws-sdk/middleware-sdk-s3/-/middleware-sdk-s3-3.682.0.tgz#a3dc95c44454b1d52c581955b3c2fdad17d0f757" + integrity sha512-Tqndx8elRD4xDR8f5Cng6jpZ/odcm1ZTOtGRFMzHgOCij4BeMf4+/+ecQScobcrAZpUTCUTCzaTvdCdJw8MYJA== dependencies: "@aws-sdk/core" "3.679.0" "@aws-sdk/types" "3.679.0" @@ -586,12 +586,12 @@ "@smithy/util-middleware" "^3.0.7" tslib "^2.6.2" -"@aws-sdk/signature-v4-multi-region@3.685.0": - version "3.685.0" - resolved "https://registry.yarnpkg.com/@aws-sdk/signature-v4-multi-region/-/signature-v4-multi-region-3.685.0.tgz#8bf6ae3d535666dd30ac255c9ba3bbde991b13df" - integrity sha512-IHLwuAZGqfUWVrNqw0ugnBa7iL8uBP4x6A7bfBDXRXWCWjUCed/1/D//0lKDHwpFkV74fGW6KoBacnWSUlXmwA== +"@aws-sdk/signature-v4-multi-region@3.682.0": + version "3.682.0" + resolved "https://registry.yarnpkg.com/@aws-sdk/signature-v4-multi-region/-/signature-v4-multi-region-3.682.0.tgz#3eae1705be68bb85ecaeb978c82a51f5e9d6a079" + integrity sha512-y7RAQSCb9pH8wCX5We9UXfiqPVwBLLvSljhuXC31mibHmYaZnpNEwHiQlRNQPblyaNpiKnXXQ0H3Ns3FDyDYdQ== dependencies: - "@aws-sdk/middleware-sdk-s3" "3.685.0" + "@aws-sdk/middleware-sdk-s3" "3.682.0" "@aws-sdk/types" "3.679.0" "@smithy/protocol-http" "^4.1.4" "@smithy/signature-v4" "^4.2.0" @@ -2119,7 +2119,7 @@ dependencies: eslint-visitor-keys "^3.4.3" -"@eslint-community/regexpp@^4.10.0", "@eslint-community/regexpp@^4.12.1": +"@eslint-community/regexpp@^4.10.0", "@eslint-community/regexpp@^4.11.0": version "4.12.1" resolved "https://registry.yarnpkg.com/@eslint-community/regexpp/-/regexpp-4.12.1.tgz#cfc6cffe39df390a3841cde2abccf92eaa7ae0e0" integrity sha512-CCZCDJuduB9OUkFkY2IgppNZMi2lBQgD2qzwXkEia16cge2pijY/aXi96CJMquDMn3nJdlPV1A5KrJEXwfLNzQ== @@ -2153,10 +2153,10 @@ minimatch "^3.1.2" strip-json-comments "^3.1.1" -"@eslint/js@9.14.0": - version "9.14.0" - resolved "https://registry.yarnpkg.com/@eslint/js/-/js-9.14.0.tgz#2347a871042ebd11a00fd8c2d3d56a265ee6857e" - integrity sha512-pFoEtFWCPyDOl+C6Ift+wC7Ro89otjigCf5vcuWqWgqNSQbRrpjSvdeE6ofLz4dHmyxD5f7gIdGT4+p36L6Twg== +"@eslint/js@9.13.0": + version "9.13.0" + resolved "https://registry.yarnpkg.com/@eslint/js/-/js-9.13.0.tgz#c5f89bcd57eb54d5d4fa8b77693e9c28dc97e547" + integrity sha512-IFLyoY4d72Z5y/6o/BazFBezupzI/taV8sGumxTAVw3lXG9A6md1Dc34T9s1FoD/an9pJH8RHbAxsaEbBed9lA== "@eslint/object-schema@^2.1.4": version "2.1.4" @@ -2198,9 +2198,9 @@ "@floating-ui/dom" "^1.0.0" "@floating-ui/react@^0.26.3": - version "0.26.27" - resolved "https://registry.yarnpkg.com/@floating-ui/react/-/react-0.26.27.tgz#402f7b4b2702650662705fe9cbe0f1d5607846a1" - integrity sha512-jLP72x0Kr2CgY6eTYi/ra3VA9LOkTo4C+DUTrbFgFOExKy3omYVmwMjNKqxAHdsnyLS96BIDLcO2SlnsNf8KUQ== + version "0.26.26" + resolved "https://registry.yarnpkg.com/@floating-ui/react/-/react-0.26.26.tgz#ab4b8675b21a61c1c868c392d44b2ccb5d5359a2" + integrity sha512-iv2BjdcyoF1j1708Z9CrGtMc9ZZvMPZnDqyB1FrSWYCi+/nlPArUO/u9QhwC4E1Pi4T0g18GZ4W702m0NDh9bw== dependencies: "@floating-ui/react-dom" "^2.1.2" "@floating-ui/utils" "^0.2.8" @@ -2349,7 +2349,7 @@ resolved "https://registry.yarnpkg.com/@humanfs/core/-/core-0.19.1.tgz#17c55ca7d426733fe3c561906b8173c336b40a77" integrity sha512-5DyQ4+1JEUzejeK1JGICcideyfUbGixgS9jNgex5nqkW+cY7WZhxBigmieN5Qnw9ZosSNVC9KQKyb+GUaGyKUA== -"@humanfs/node@^0.16.6": +"@humanfs/node@^0.16.5": version "0.16.6" resolved "https://registry.yarnpkg.com/@humanfs/node/-/node-0.16.6.tgz#ee2a10eaabd1131987bf0488fd9b820174cd765e" integrity sha512-YuI2ZHQL78Q5HbhDiBA1X4LmYdXCKCMQIfw0pw7piHJwyREFebJUvrQN4cMssyES6x+vfUbx1CIpaQUKYdQZOw== @@ -2362,16 +2362,11 @@ resolved "https://registry.yarnpkg.com/@humanwhocodes/module-importer/-/module-importer-1.0.1.tgz#af5b2691a22b44be847b0ca81641c5fb6ad0172c" integrity sha512-bxveV4V8v5Yb4ncFTT3rPSgZBOpCkjfK0y4oVVVJwIuDVBRMDXrPyXRL988i5ap9m9bnyEEjWfm5WkBmtffLfA== -"@humanwhocodes/retry@^0.3.0": +"@humanwhocodes/retry@^0.3.0", "@humanwhocodes/retry@^0.3.1": version "0.3.1" resolved "https://registry.yarnpkg.com/@humanwhocodes/retry/-/retry-0.3.1.tgz#c72a5c76a9fbaf3488e231b13dc52c0da7bab42a" integrity sha512-JBxkERygn7Bv/GbN5Rv8Ul6LVknS+5Bp6RgDC/O8gEBU/yeH5Ui5C/OlWrTb6qct7LjjfT6Re2NxB0ln0yYybA== -"@humanwhocodes/retry@^0.4.0": - 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version "20.0.7" - resolved "https://registry.yarnpkg.com/@nx/devkit/-/devkit-20.0.7.tgz#c610eb5171bc8cc7681d45eda22ad21cb5409f1a" - integrity sha512-h+B5S+tkHObtKj2pQYUkbiaiYdcim95iS27CaZgasq7FiIXQOoupQ6jrIKduQJKx+GfYbuCCd60zrAYbkyvxiA== + version "20.0.6" + resolved "https://registry.yarnpkg.com/@nx/devkit/-/devkit-20.0.6.tgz#75d4fd9284642fd791a308c617e5b5c5e1f527be" + integrity sha512-vUjVVEJgfq/roCzDDZDXduwnhVXl1MM5No2UELUka2oNBK09pPigdFxzUNh8XvmOyFskCGDTLKH/dAO5yTD5Bg== dependencies: ejs "^3.1.7" enquirer "~2.3.6" @@ -3393,55 +3388,55 @@ tslib "^2.3.0" yargs-parser "21.1.1" -"@nx/nx-darwin-arm64@20.0.7": - version "20.0.7" - resolved "https://registry.yarnpkg.com/@nx/nx-darwin-arm64/-/nx-darwin-arm64-20.0.7.tgz#535f3539a59daf52b1e7415b5d54f8ed732a4e6f" - integrity sha512-QLD0DlyT343okCMHNg4EyM1s9HWU55RGiD36OxopaAmDcJ45j4p7IgmYlwbWCC5TyjIXSnLnZyIAs5DrqaKwrg== - -"@nx/nx-darwin-x64@20.0.7": - version "20.0.7" - resolved "https://registry.yarnpkg.com/@nx/nx-darwin-x64/-/nx-darwin-x64-20.0.7.tgz#a6f552aadd5d2abd2d775e39558a4f4ea5f4a20e" - 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version "8.5.13" - resolved "https://registry.yarnpkg.com/@types/ws/-/ws-8.5.13.tgz#6414c280875e2691d0d1e080b05addbf5cb91e20" - integrity sha512-osM/gWBTPKgHV8XkTunnegTRIsvF6owmf5w+JtAfOw472dptdm0dlGv4xCt6GwQRcC2XVOvvRE/0bAoQcL2QkA== + version "8.5.12" + resolved "https://registry.yarnpkg.com/@types/ws/-/ws-8.5.12.tgz#619475fe98f35ccca2a2f6c137702d85ec247b7e" + integrity sha512-3tPRkv1EtkDpzlgyKyI8pGsGZAGPEaXeu0DOj5DI25Ja91bdAYddYHbADRYVrZMRbfW+1l5YwXVDKohDJNQxkQ== dependencies: "@types/node" "*" @@ -5604,7 +5583,7 @@ abbrev@^2.0.0: resolved "https://registry.yarnpkg.com/abbrev/-/abbrev-2.0.0.tgz#cf59829b8b4f03f89dda2771cb7f3653828c89bf" integrity sha512-6/mh1E2u2YgEsCHdY0Yx5oW+61gZU+1vXaoiHHrpKeuRNNgFvS+/jrwHiQhB5apAf5oB7UB7E19ol2R2LKH8hQ== -accepts@~1.3.4, accepts@~1.3.8: +accepts@~1.3.4, accepts@~1.3.5, accepts@~1.3.8: version "1.3.8" resolved "https://registry.yarnpkg.com/accepts/-/accepts-1.3.8.tgz#0bf0be125b67014adcb0b0921e62db7bffe16b2e" integrity sha512-PYAthTa2m2VKxuvSD3DPC/Gy+U+sOA1LAuT8mkmRuvw+NACSaeXEQ+NHcVF7rONl6qcaxV3Uuemwawk+7+SJLw== @@ -5620,6 +5599,11 @@ acorn-globals@^7.0.0: acorn "^8.1.0" acorn-walk "^8.0.2" +acorn-import-attributes@^1.9.5: + version "1.9.5" + resolved "https://registry.yarnpkg.com/acorn-import-attributes/-/acorn-import-attributes-1.9.5.tgz#7eb1557b1ba05ef18b5ed0ec67591bfab04688ef" + integrity sha512-n02Vykv5uA3eHGM/Z2dQrcD56kL8TyDb2p1+0P83PClMnC/nc+anbQRhIOWnSq4Ke/KvDPrY3C9hDtC/A3eHnQ== + acorn-jsx@^5.3.2: version "5.3.2" resolved "https://registry.yarnpkg.com/acorn-jsx/-/acorn-jsx-5.3.2.tgz#7ed5bb55908b3b2f1bc55c6af1653bada7f07937" @@ -5632,7 +5616,7 @@ acorn-walk@^8.0.2, acorn-walk@^8.1.1: dependencies: acorn "^8.11.0" -acorn@^8.1.0, acorn@^8.11.0, acorn@^8.14.0, acorn@^8.4.1, acorn@^8.8.1, acorn@^8.8.2: +acorn@^8.1.0, acorn@^8.11.0, acorn@^8.14.0, acorn@^8.4.1, acorn@^8.7.1, acorn@^8.8.1, acorn@^8.8.2: version "8.14.0" resolved "https://registry.yarnpkg.com/acorn/-/acorn-8.14.0.tgz#063e2c70cac5fb4f6467f0b11152e04c682795b0" integrity sha512-cl669nCJTZBsL97OF4kUQm5g5hC2uihk0NxY3WENAC0TYdILVkAyHymAntgxGkl7K+t0cXIrH5siy5S4XkFycA== @@ -6050,7 +6034,7 @@ at-least-node@^1.0.0: resolved "https://registry.yarnpkg.com/at-least-node/-/at-least-node-1.0.0.tgz#602cd4b46e844ad4effc92a8011a3c46e0238dc2" integrity sha512-+q/t7Ekv1EDY2l6Gda6LLiX14rU9TV20Wa3ofeQmwPFZbOMo9DXrLbOjFaaclkXKWidIaopwAObQDqwWtGUjqg== -attr-accept@^2.2.4: +attr-accept@^2.2.2: version "2.2.4" resolved "https://registry.yarnpkg.com/attr-accept/-/attr-accept-2.2.4.tgz#e28749d5975732586aea03c8912e2d0f1d1d77e7" integrity sha512-2pA6xFIbdTUDCAwjN8nQwI+842VwzbDUXO2IYlpPXQIORgKnavorcr4Ce3rwh+zsNg9zK7QPsdvDj3Lum4WX4w== @@ -6340,7 +6324,7 @@ browser-assert@^1.2.1: resolved "https://registry.yarnpkg.com/browser-assert/-/browser-assert-1.2.1.tgz#9aaa5a2a8c74685c2ae05bfe46efd606f068c200" integrity sha512-nfulgvOR6S4gt9UKCeGJOuSGBPGiFT6oQ/2UBnvTY/5aQ1PnksW72fhZkM30DzoRRv2WpwZf1vHHEr3mtuXIWQ== -browserslist@^4.0.0, browserslist@^4.18.1, browserslist@^4.23.0, browserslist@^4.24.0, browserslist@^4.24.2: +browserslist@^4.0.0, browserslist@^4.18.1, browserslist@^4.21.10, browserslist@^4.23.0, browserslist@^4.24.0, browserslist@^4.24.2: version "4.24.2" resolved "https://registry.yarnpkg.com/browserslist/-/browserslist-4.24.2.tgz#f5845bc91069dbd55ee89faf9822e1d885d16580" integrity sha512-ZIc+Q62revdMcqC6aChtW4jz3My3klmCO1fEmINZY/8J3EpBg5/A/D0AKmBveUh6pgoeycoMkVMko84tuYS+Gg== @@ -6448,6 +6432,11 @@ byte-size@8.1.1: resolved "https://registry.yarnpkg.com/byte-size/-/byte-size-8.1.1.tgz#3424608c62d59de5bfda05d31e0313c6174842ae" integrity sha512-tUkzZWK0M/qdoLEqikxBWe4kumyuwjl3HO6zHTr4yEI23EojPtLYXdG1+AQY7MN0cGyNDvEaJ8wiYQm6P2bPxg== +bytes@3.0.0: + version "3.0.0" + resolved "https://registry.yarnpkg.com/bytes/-/bytes-3.0.0.tgz#d32815404d689699f85a4ea4fa8755dd13a96048" + integrity sha512-pMhOfFDPiv9t5jjIXkHosWmkSyQbvsgEVNkz0ERHbuLh2T/7j4Mqqpz523Fe8MVY89KC6Sh/QfS2sM+SjgFDcw== + bytes@3.1.2: version "3.1.2" resolved "https://registry.yarnpkg.com/bytes/-/bytes-3.1.2.tgz#8b0beeb98605adf1b128fa4386403c009e0221a5" @@ -6614,9 +6603,9 @@ caniuse-api@^3.0.0: lodash.uniq "^4.5.0" caniuse-lite@^1.0.0, caniuse-lite@^1.0.30001669: - version "1.0.30001677" - resolved "https://registry.yarnpkg.com/caniuse-lite/-/caniuse-lite-1.0.30001677.tgz#27c2e2c637e007cfa864a16f7dfe7cde66b38b5f" - integrity sha512-fmfjsOlJUpMWu+mAAtZZZHz7UEwsUxIIvu1TJfO1HqFQvB/B+ii0xr9B5HpbZY/mC4XZ8SvjHJqtAY6pDPQEog== + version "1.0.30001676" + resolved "https://registry.yarnpkg.com/caniuse-lite/-/caniuse-lite-1.0.30001676.tgz#fe133d41fe74af8f7cc93b8a714c3e86a86e6f04" + integrity sha512-Qz6zwGCiPghQXGJvgQAem79esjitvJ+CxSbSQkW9H/UX5hg8XM88d4lp2W+MEQ81j+Hip58Il+jGVdazk1z9cw== canvas-sequencer@^3.1.0: version "3.1.0" @@ -7033,7 +7022,7 @@ 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@~2.0.18: +compressible@~2.0.16: version "2.0.18" resolved "https://registry.yarnpkg.com/compressible/-/compressible-2.0.18.tgz#af53cca6b070d4c3c0750fbd77286a6d7cc46fba" integrity sha512-AF3r7P5dWxL8MxyITRMlORQNaOA2IkAFaTr4k7BUumjPtRpGDTZpl0Pb1XCO6JeDCBdp126Cgs9sMxqSjgYyRg== @@ -7041,16 +7030,16 @@ compressible@~2.0.18: mime-db ">= 1.43.0 < 2" compression@^1.7.4: - version "1.7.5" - resolved "https://registry.yarnpkg.com/compression/-/compression-1.7.5.tgz#fdd256c0a642e39e314c478f6c2cd654edd74c93" - integrity sha512-bQJ0YRck5ak3LgtnpKkiabX5pNF7tMUh1BSy2ZBOTh0Dim0BUu6aPPwByIns6/A5Prh8PufSPerMDUklpzes2Q== + version "1.7.4" + resolved "https://registry.yarnpkg.com/compression/-/compression-1.7.4.tgz#95523eff170ca57c29a0ca41e6fe131f41e5bb8f" + integrity sha512-jaSIDzP9pZVS4ZfQ+TzvtiWhdpFhE2RDHz8QJkpX9SIpLq88VueF5jJw6t+6CUQcAoA6t+x89MLrWAqpfDE8iQ== dependencies: - bytes "3.1.2" - compressible "~2.0.18" + accepts "~1.3.5" + bytes "3.0.0" + compressible "~2.0.16" debug "2.6.9" - negotiator "~0.6.4" on-headers "~1.0.2" - safe-buffer "5.2.1" + safe-buffer "5.1.2" vary "~1.1.2" concat-map@0.0.1: @@ -8196,9 +8185,9 @@ electron-publish@25.1.7: mime "^2.5.2" electron-to-chromium@^1.5.41: - version "1.5.50" - resolved "https://registry.yarnpkg.com/electron-to-chromium/-/electron-to-chromium-1.5.50.tgz#d9ba818da7b2b5ef1f3dd32bce7046feb7e93234" - integrity sha512-eMVObiUQ2LdgeO1F/ySTXsvqvxb6ZH2zPGaMYsWzRDdOddUa77tdmI0ltg+L16UpbWdhPmuF3wIQYyQq65WfZw== + version "1.5.49" + resolved "https://registry.yarnpkg.com/electron-to-chromium/-/electron-to-chromium-1.5.49.tgz#9358f514ab6eeed809a8689f4b39ea5114ae729c" + integrity sha512-ZXfs1Of8fDb6z7WEYZjXpgIRF6MEu8JdeGA0A40aZq6OQbS+eJpnnV49epZRna2DU/YsEjSQuGtQPPtvt6J65A== electron-updater@^6.1.1: version "6.3.9" @@ -8654,7 +8643,7 @@ eslint-scope@5.1.1: esrecurse "^4.3.0" estraverse "^4.1.1" -eslint-scope@^8.2.0: +eslint-scope@^8.1.0: version "8.2.0" resolved "https://registry.yarnpkg.com/eslint-scope/-/eslint-scope-8.2.0.tgz#377aa6f1cb5dc7592cfd0b7f892fd0cf352ce442" integrity sha512-PHlWUfG6lvPc3yvP5A4PNyBL1W8fkDUccmI21JUu/+GKZBoH/W5u6usENXUrWFRsyoW5ACUjFGgAFQp5gUlb/A== @@ -8667,26 +8656,26 @@ eslint-visitor-keys@^3.4.3: resolved "https://registry.yarnpkg.com/eslint-visitor-keys/-/eslint-visitor-keys-3.4.3.tgz#0cd72fe8550e3c2eae156a96a4dddcd1c8ac5800" integrity sha512-wpc+LXeiyiisxPlEkUzU6svyS1frIO3Mgxj1fdy7Pm8Ygzguax2N3Fa/D/ag1WqbOprdI+uY6wMUl8/a2G+iag== -eslint-visitor-keys@^4.2.0: +eslint-visitor-keys@^4.1.0, eslint-visitor-keys@^4.2.0: version "4.2.0" resolved "https://registry.yarnpkg.com/eslint-visitor-keys/-/eslint-visitor-keys-4.2.0.tgz#687bacb2af884fcdda8a6e7d65c606f46a14cd45" integrity sha512-UyLnSehNt62FFhSwjZlHmeokpRK59rcz29j+F1/aDgbkbRTk7wIc9XzdoasMUbRNKDM0qQt/+BJ4BrpFeABemw== eslint@^9.0.0: - version "9.14.0" - resolved "https://registry.yarnpkg.com/eslint/-/eslint-9.14.0.tgz#534180a97c00af08bcf2b60b0ebf0c4d6c1b2c95" - integrity sha512-c2FHsVBr87lnUtjP4Yhvk4yEhKrQavGafRA/Se1ouse8PfbfC/Qh9Mxa00yWsZRlqeUB9raXip0aiiUZkgnr9g== + version "9.13.0" + resolved "https://registry.yarnpkg.com/eslint/-/eslint-9.13.0.tgz#7659014b7dda1ff876ecbd990f726e11c61596e6" + integrity sha512-EYZK6SX6zjFHST/HRytOdA/zE72Cq/bfw45LSyuwrdvcclb/gqV8RRQxywOBEWO2+WDpva6UZa4CcDeJKzUCFA== dependencies: "@eslint-community/eslint-utils" "^4.2.0" - "@eslint-community/regexpp" "^4.12.1" + "@eslint-community/regexpp" "^4.11.0" "@eslint/config-array" "^0.18.0" "@eslint/core" "^0.7.0" "@eslint/eslintrc" "^3.1.0" - "@eslint/js" "9.14.0" + "@eslint/js" "9.13.0" "@eslint/plugin-kit" "^0.2.0" - "@humanfs/node" "^0.16.6" + "@humanfs/node" "^0.16.5" "@humanwhocodes/module-importer" "^1.0.1" - "@humanwhocodes/retry" "^0.4.0" + "@humanwhocodes/retry" "^0.3.1" "@types/estree" "^1.0.6" "@types/json-schema" "^7.0.15" ajv "^6.12.4" @@ -8694,9 +8683,9 @@ eslint@^9.0.0: cross-spawn "^7.0.2" debug "^4.3.2" escape-string-regexp "^4.0.0" - eslint-scope "^8.2.0" - eslint-visitor-keys "^4.2.0" - espree "^10.3.0" + eslint-scope "^8.1.0" + eslint-visitor-keys "^4.1.0" + espree "^10.2.0" esquery "^1.5.0" esutils "^2.0.2" fast-deep-equal "^3.1.3" @@ -8713,7 +8702,7 @@ eslint@^9.0.0: optionator "^0.9.3" text-table "^0.2.0" -espree@^10.0.1, espree@^10.3.0: +espree@^10.0.1, espree@^10.2.0: version "10.3.0" resolved "https://registry.yarnpkg.com/espree/-/espree-10.3.0.tgz#29267cf5b0cb98735b65e64ba07e0ed49d1eed8a" integrity sha512-0QYC8b24HWY8zjRnDTL6RiHfDbAWn63qb4LMj1Z4b076A4une81+z03Kg7l7mn/48PUTqoLptSXez8oknU8Clg== @@ -9005,12 +8994,12 @@ file-saver@^2.0.0: resolved "https://registry.yarnpkg.com/file-saver/-/file-saver-2.0.5.tgz#d61cfe2ce059f414d899e9dd6d4107ee25670c38" integrity sha512-P9bmyZ3h/PRG+Nzga+rbdI4OEpNDzAVyy74uVO9ATgzLK6VtAsYybF/+TOCvrc0MO793d6+42lLyZTw7/ArVzA== -file-selector@^2.1.0: - version "2.1.0" - resolved "https://registry.yarnpkg.com/file-selector/-/file-selector-2.1.0.tgz#beb164ca5ce48af8a48d3e632c94750bc573581a" - integrity sha512-ZuXAqGePcSPz4JuerOY06Dzzq0hrmQ6VGoXVzGyFI1npeOfBgqGIKKpznfYWRkSLJlXutkqVC5WvGZtkFVhu9Q== +file-selector@^0.6.0: + version "0.6.0" + resolved "https://registry.yarnpkg.com/file-selector/-/file-selector-0.6.0.tgz#fa0a8d9007b829504db4d07dd4de0310b65287dc" + integrity sha512-QlZ5yJC0VxHxQQsQhXvBaC7VRJ2uaxTf+Tfpu4Z/OcVQJVpZO+DGU0rkoVW5ce2SccxugvpBJoMvUs59iILYdw== dependencies: - tslib "^2.7.0" + tslib "^2.4.0" file-type@^3.8.0: version "3.9.0" @@ -12058,9 +12047,9 @@ min-indent@^1.0.0, min-indent@^1.0.1: integrity sha512-I9jwMn07Sy/IwOj3zVkVik2JTvgpaykDZEigL6Rx6N9LbMywwUSMtxET+7lVoDLLd3O3IXwJwvuuns8UB/HeAg== mini-css-extract-plugin@^2.4.5: - version "2.9.2" - resolved "https://registry.yarnpkg.com/mini-css-extract-plugin/-/mini-css-extract-plugin-2.9.2.tgz#966031b468917a5446f4c24a80854b2947503c5b" - integrity sha512-GJuACcS//jtq4kCtd5ii/M0SZf7OZRH+BxdqXZHaJfb8TJiVl+NgQRPwiYt2EuqeSkNydn/7vP+bcE27C5mb9w== + version "2.9.1" + resolved "https://registry.yarnpkg.com/mini-css-extract-plugin/-/mini-css-extract-plugin-2.9.1.tgz#4d184f12ce90582e983ccef0f6f9db637b4be758" + integrity sha512-+Vyi+GCCOHnrJ2VPS+6aPoXN2k2jgUzDRhTFLjjTBn23qyXJXkjUWQgTL+mXpF5/A8ixLdCc6kWsoeOjKGejKQ== dependencies: schema-utils "^4.0.0" tapable "^2.2.1" @@ -12345,7 +12334,7 @@ negotiator@0.6.3: resolved "https://registry.yarnpkg.com/negotiator/-/negotiator-0.6.3.tgz#58e323a72fedc0d6f9cd4d31fe49f51479590ccd" integrity sha512-+EUsqGPLsM+j/zdChZjsnX51g4XrHFOIXwfnCVPGlQk/k5giakcKsuxCObBRu6DSm9opw/O6slWbJdghQM4bBg== -negotiator@^0.6.2, negotiator@^0.6.3, negotiator@~0.6.4: +negotiator@^0.6.2, negotiator@^0.6.3: version "0.6.4" resolved "https://registry.yarnpkg.com/negotiator/-/negotiator-0.6.4.tgz#777948e2452651c570b712dd01c23e262713fff7" integrity sha512-myRT3DiWPHqho5PrJaIRyaMv2kgYf0mUVgBNOYMuCH5Ki1yEiQaf/ZJuQ62nvpc44wL5WDbTX7yGJi1Neevw8w== @@ -12663,9 +12652,9 @@ nwsapi@^2.2.12, nwsapi@^2.2.2: integrity sha512-cTGB9ptp9dY9A5VbMSe7fQBcl/tt22Vcqdq8+eN93rblOuE0aCFu4aZ2vMwct/2t+lFnosm8RkQW1I0Omb1UtQ== "nx@>=17.1.2 < 21": - version "20.0.7" - resolved "https://registry.yarnpkg.com/nx/-/nx-20.0.7.tgz#ddf2fc19b8d91f97db0256202307a29bfbeba39e" - integrity sha512-Un7eMAqTx+gRB4j6hRWafMvOso4pmFg3Ff+BmfFOgqD8XdE+xV/+Ke9mPTfi4qYD5eQiY1lO15l3dRuBH7+AJw== + version "20.0.6" + resolved "https://registry.yarnpkg.com/nx/-/nx-20.0.6.tgz#640f0f058f94bbb52918571e7f788f6c3247288f" + integrity sha512-z8PMPEXxtADwxsNXamZdDbx65fcNcR4gTmX7N94GKmpZNrjwd3m7RcnoYgQp5vA8kFQkMR+320mtq5NkGJPZvg== dependencies: "@napi-rs/wasm-runtime" "0.2.4" "@yarnpkg/lockfile" "^1.1.0" @@ -12700,16 +12689,16 @@ nwsapi@^2.2.12, nwsapi@^2.2.2: yargs "^17.6.2" yargs-parser "21.1.1" optionalDependencies: - "@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" + "@nx/nx-darwin-arm64" "20.0.6" + "@nx/nx-darwin-x64" "20.0.6" + "@nx/nx-freebsd-x64" "20.0.6" + "@nx/nx-linux-arm-gnueabihf" "20.0.6" + "@nx/nx-linux-arm64-gnu" "20.0.6" + "@nx/nx-linux-arm64-musl" "20.0.6" + "@nx/nx-linux-x64-gnu" "20.0.6" + "@nx/nx-linux-x64-musl" "20.0.6" + "@nx/nx-win32-arm64-msvc" "20.0.6" + "@nx/nx-win32-x64-msvc" "20.0.6" object-assign@^4, object-assign@^4.0.1, object-assign@^4.1.1: version "4.1.1" @@ -12775,18 +12764,18 @@ obuf@^1.0.0, obuf@^1.1.2: integrity sha512-PX1wu0AmAdPqOL1mWhqmlOd8kOIZQwGZw6rh7uby9fTc5lhaOWFLX3I6R1hrF9k3zUY40e6igsLGkDXK92LJNg== oclif@^4.0.0: - version "4.15.19" - resolved "https://registry.yarnpkg.com/oclif/-/oclif-4.15.19.tgz#3a3c51cb021df51cd4a14250f9e5a666dd3a6d52" - integrity sha512-FM3hIgmCtKc7YTUPCdHGILI/UgtYC7IjYlUJ0xGVCcpfhsAmwj6DieJC+HmuMczY+bhWLxfKEw5SbZDy8w4VSA== + version "4.15.16" + resolved "https://registry.yarnpkg.com/oclif/-/oclif-4.15.16.tgz#02c9f8690eac3b625a40fabbf3e21312461207d1" + integrity sha512-y/xBQpFrYZihmEoCUwCzGM2aoKKWHMEcnEHrXrsrTOmDIcS8diwk7IoL8k72Ztp7kbD+GrAVhUXfsbo1jUZCaQ== dependencies: "@aws-sdk/client-cloudfront" "^3.679.0" - "@aws-sdk/client-s3" "^3.685.0" + "@aws-sdk/client-s3" "^3.676.0" "@inquirer/confirm" "^3.1.22" "@inquirer/input" "^2.2.4" "@inquirer/select" "^2.5.0" - "@oclif/core" "^4.0.31" + "@oclif/core" "^4.0.30" "@oclif/plugin-help" "^6.2.16" - "@oclif/plugin-not-found" "^3.2.24" + "@oclif/plugin-not-found" "^3.2.21" "@oclif/plugin-warn-if-update-available" "^3.1.20" async-retry "^1.3.3" chalk "^4" @@ -13922,12 +13911,12 @@ react-draggable@^4.4.5: prop-types "^15.8.1" react-dropzone@^14.2.1: - version "14.3.3" - resolved "https://registry.yarnpkg.com/react-dropzone/-/react-dropzone-14.3.3.tgz#8f2cf46567615123c91e1ba59b07e6c815e5aef0" - integrity sha512-38yaWovqDqZdtn7LKTE5lFdqc57hYbPdS/oIxyhmaTP/yzC0yztPxnNy+poxew5HKF44gzGCNcNDBYjqlCXr6g== + version "14.2.10" + resolved "https://registry.yarnpkg.com/react-dropzone/-/react-dropzone-14.2.10.tgz#b8d86775c616534b44a30bd9c962044d2925c1a2" + integrity sha512-Y98LOCYxGO2jOFWREeKJlL7gbrHcOlTBp+9DCM1dh9XQ8+P/8ThhZT7kFb05C+bPcTXq/rixpU+5+LzwYrFLUw== dependencies: - attr-accept "^2.2.4" - file-selector "^2.1.0" + attr-accept "^2.2.2" + file-selector "^0.6.0" prop-types "^15.8.1" react-error-overlay@^6.0.11: @@ -15054,11 +15043,11 @@ statuses@2.0.1: integrity sha512-OpZ3zP+jT1PI7I8nemJX4AKmAX070ZkYPVWV/AaKTJl+tXCTGyVdC1a4SL8RUQYEwk/f34ZX8UTykN68FwrqAA== storybook@^8.0.0: - version "8.4.1" - resolved "https://registry.yarnpkg.com/storybook/-/storybook-8.4.1.tgz#97baa471677566d614a5677deab0cd243c0142dc" - integrity sha512-0tfFIFghjho9FtnFoiJMoxhcs2iIdvEF81GTSVnTsDVJrYA84nB+FxN3UY1fT0BcQ8BFlbf+OhSjZL7ufqqWKA== + version "8.4.0" + resolved "https://registry.yarnpkg.com/storybook/-/storybook-8.4.0.tgz#8e89485906e58fa5531679f7055aaecedfbb3d8e" + integrity sha512-hLfXPtqfoQUMKVortxXdnQoUwDwtH85eSj9LbqGT/z1f/gLLYGNG3Mv3QbsRjHXhn+EfYffh7wuLpAn+Cicijw== dependencies: - "@storybook/core" "8.4.1" + "@storybook/core" "8.4.0" string-length@^4.0.1: version "4.0.2" @@ -15631,10 +15620,10 @@ tsconfig-paths@^4.1.2, tsconfig-paths@^4.2.0: minimist "^1.2.6" strip-bom "^3.0.0" -tslib@^2.0.0, tslib@^2.0.1, tslib@^2.0.3, 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== +tslib@^2.0.0, tslib@^2.0.1, tslib@^2.0.3, tslib@^2.1.0, tslib@^2.3.0, tslib@^2.3.1, tslib@^2.4.0, tslib@^2.6.2: + version "2.8.0" + resolved "https://registry.yarnpkg.com/tslib/-/tslib-2.8.0.tgz#d124c86c3c05a40a91e6fdea4021bd31d377971b" + integrity sha512-jWVzBLplnCmoaTr13V9dYbiQ99wvZRd0vNWaDRg+aVYRcjDF3nDksxFDE/+fkXnKhpnUUkmx5pK/v8mCtLVqZA== tss-react@^4.0.0, tss-react@^4.4.1: version "4.9.13" @@ -16248,17 +16237,17 @@ 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 "5.96.1" - resolved "https://registry.yarnpkg.com/webpack/-/webpack-5.96.1.tgz#3676d1626d8312b6b10d0c18cc049fba7ac01f0c" - integrity sha512-l2LlBSvVZGhL4ZrPwyr8+37AunkcYj5qh8o6u2/2rzoPc8gxFJkLj1WxNgooi9pnoc06jh0BjuXnamM4qlujZA== + version "5.95.0" + resolved "https://registry.yarnpkg.com/webpack/-/webpack-5.95.0.tgz#8fd8c454fa60dad186fbe36c400a55848307b4c0" + integrity sha512-2t3XstrKULz41MNMBF+cJ97TyHdyQ8HCt//pqErqDvNjU9YQBnZxIHa11VXsi7F3mb5/aO2tuDxdeTPdU7xu9Q== dependencies: - "@types/eslint-scope" "^3.7.7" - "@types/estree" "^1.0.6" + "@types/estree" "^1.0.5" "@webassemblyjs/ast" "^1.12.1" "@webassemblyjs/wasm-edit" "^1.12.1" "@webassemblyjs/wasm-parser" "^1.12.1" - acorn "^8.14.0" - browserslist "^4.24.0" + acorn "^8.7.1" + acorn-import-attributes "^1.9.5" + browserslist "^4.21.10" chrome-trace-event "^1.0.2" enhanced-resolve "^5.17.1" es-module-lexer "^1.2.1"