From b345bc461ea8c230b2573f467305c813dedda7dd Mon Sep 17 00:00:00 2001 From: Colin Date: Fri, 24 Jan 2025 02:03:20 -0500 Subject: [PATCH] Colors from csv --- .../src/UCSCTrackHub/ucscTrackHub.ts | 2 +- .../components/VariantDisplayComponent.tsx | 2 +- .../src/MultiLinearVariantDisplay/model.ts | 18 +- .../components/VariantDisplayComponent.tsx | 2 +- .../MultiLinearVariantMatrixDisplay/model.ts | 18 +- .../StructuralVariantChordRenderer/Chord.tsx | 2 +- plugins/variants/src/VcfAdapter/VcfAdapter.ts | 31 +- .../variants/src/VcfAdapter/configSchema.ts | 11 +- .../src/VcfTabixAdapter/VcfTabixAdapter.ts | 24 +- .../src/VcfTabixAdapter/configSchema.ts | 11 +- .../src/getMultiVariantFeaturesAutorun.ts | 2 +- plugins/variants/src/shared/BulkEditPanel.tsx | 250 ++-- plugins/variants/src/shared/HelpfulTips.tsx | 19 + plugins/variants/src/shared/RowPalettizer.tsx | 66 +- .../variants/src/shared/SetColorDialog.tsx | 176 ++- .../src/MultiLinearWiggleDisplay/util.ts | 8 + .../__snapshots__/jbrowseModel.test.ts.snap | 40 + .../jbrowse-web/src/tests/VcfMatrix.test.tsx | 37 + .../vcf-matrix-test-tsx-matrix-1-snap.png | Bin 0 -> 46618 bytes .../vcf-matrix-test-tsx-regular-1-snap.png | Bin 0 -> 3986 bytes test_data/volvox/1000genomes.tsv | 1095 +++++++++++++++++ test_data/volvox/config.json | 13 +- .../volvox/trix/volvox-rev-del_meta.json | 2 +- test_data/volvox/trix/volvox_meta.json | 6 +- yarn.lock | 142 +-- 25 files changed, 1618 insertions(+), 359 deletions(-) create mode 100644 plugins/variants/src/shared/HelpfulTips.tsx create mode 100644 plugins/wiggle/src/MultiLinearWiggleDisplay/util.ts create mode 100644 products/jbrowse-web/src/tests/VcfMatrix.test.tsx create mode 100644 products/jbrowse-web/src/tests/__image_snapshots__/vcf-matrix-test-tsx-matrix-1-snap.png create mode 100644 products/jbrowse-web/src/tests/__image_snapshots__/vcf-matrix-test-tsx-regular-1-snap.png create mode 100644 test_data/volvox/1000genomes.tsv diff --git a/plugins/data-management/src/UCSCTrackHub/ucscTrackHub.ts b/plugins/data-management/src/UCSCTrackHub/ucscTrackHub.ts index 2135ea3e49..bdb840d26e 100644 --- a/plugins/data-management/src/UCSCTrackHub/ucscTrackHub.ts +++ b/plugins/data-management/src/UCSCTrackHub/ucscTrackHub.ts @@ -3,7 +3,7 @@ import { generateUnknownTrackConf } from '@jbrowse/core/util/tracks' import { makeLoc2, makeLoc, makeLocAlt } from './util' -import type { RaStanza, TrackDbFile } from '@gmod/ucsc-hub' +import type { RaStanza, TrackDbFile } from '@gmod/ucsc-hub' import type { FileLocation } from '@jbrowse/core/util' export function generateTracks({ diff --git a/plugins/variants/src/MultiLinearVariantDisplay/components/VariantDisplayComponent.tsx b/plugins/variants/src/MultiLinearVariantDisplay/components/VariantDisplayComponent.tsx index 66b6119fd5..fda5262107 100644 --- a/plugins/variants/src/MultiLinearVariantDisplay/components/VariantDisplayComponent.tsx +++ b/plugins/variants/src/MultiLinearVariantDisplay/components/VariantDisplayComponent.tsx @@ -70,7 +70,7 @@ const MultiLinearVariantDisplayComponent = observer(function (props: { ) .filter(([key]) => key !== 'color') .map(([key, value]) => `${key}:${value}`) - .join('\n')} + .join('
')} /> diff --git a/plugins/variants/src/MultiLinearVariantDisplay/model.ts b/plugins/variants/src/MultiLinearVariantDisplay/model.ts index fef99141a8..202eefbb1f 100644 --- a/plugins/variants/src/MultiLinearVariantDisplay/model.ts +++ b/plugins/variants/src/MultiLinearVariantDisplay/model.ts @@ -1,14 +1,11 @@ import { lazy } from 'react' -import { set1 } from '@jbrowse/core/ui/colors' import { getSession } from '@jbrowse/core/util' import { stopStopToken } from '@jbrowse/core/util/stopToken' import { linearBareDisplayStateModelFactory } from '@jbrowse/plugin-linear-genome-view' import deepEqual from 'fast-deep-equal' import { isAlive, types } from 'mobx-state-tree' -import { randomColor } from '../util' - import type { Source } from '../types' import type PluginManager from '@jbrowse/core/PluginManager' import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration' @@ -24,7 +21,7 @@ const ClusterDialog = lazy(() => import('../shared/ClusterDialog')) /** * #stateModel MultiLinearVariantDisplay * extends - * - [SharedVariantMixin](../sharedvariantmixin) + * - [LinearBareDisplay](../linearbaredisplay) */ export function stateModelFactory( pluginManager: PluginManager, @@ -160,15 +157,10 @@ export function stateModelFactory( self.sourcesVolatile?.map(s => [s.name, s]) || [], ) const iter = self.layout.length ? self.layout : self.sourcesVolatile - return iter - ?.map(s => ({ - ...sources[s.name], - ...s, - })) - .map((s, i) => ({ - ...s, - color: s.color || set1[i] || randomColor(s.name), - })) + return iter?.map(s => ({ + ...sources[s.name], + ...s, + })) }, })) diff --git a/plugins/variants/src/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.tsx b/plugins/variants/src/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.tsx index 842dfec511..7bed1bf5ac 100644 --- a/plugins/variants/src/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.tsx +++ b/plugins/variants/src/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.tsx @@ -70,7 +70,7 @@ const MultiLinearVariantMatrixDisplayComponent = observer(function (props: { ) .filter(([key]) => key !== 'color') .map(([key, value]) => `${key}:${value}`) - .join('\n')} + .join('
')} /> diff --git a/plugins/variants/src/MultiLinearVariantMatrixDisplay/model.ts b/plugins/variants/src/MultiLinearVariantMatrixDisplay/model.ts index e14fb93781..d570842d97 100644 --- a/plugins/variants/src/MultiLinearVariantMatrixDisplay/model.ts +++ b/plugins/variants/src/MultiLinearVariantMatrixDisplay/model.ts @@ -1,15 +1,12 @@ import { lazy } from 'react' import { ConfigurationReference } from '@jbrowse/core/configuration' -import { set1 } from '@jbrowse/core/ui/colors' import { getSession } from '@jbrowse/core/util' import { stopStopToken } from '@jbrowse/core/util/stopToken' import { linearBareDisplayStateModelFactory } from '@jbrowse/plugin-linear-genome-view' import deepEqual from 'fast-deep-equal' import { isAlive, types } from 'mobx-state-tree' -import { randomColor } from '../util' - import type { Source } from '../types' import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration' import type { Feature } from '@jbrowse/core/util' @@ -24,7 +21,7 @@ const ClusterDialog = lazy(() => import('../shared/ClusterDialog')) /** * #stateModel LinearVariantMatrixDisplay * extends - * - [LinearBasicDisplay](../linearbasicdisplay) + * - [LinearBareDisplay](../linearbaredisplay) */ export default function stateModelFactory( configSchema: AnyConfigurationSchemaType, @@ -142,15 +139,10 @@ export default function stateModelFactory( const sources = Object.fromEntries( self.sourcesVolatile?.map(s => [s.name, s]) || [], ) - return this.preSources - ?.map(s => ({ - ...sources[s.name], - ...s, - })) - .map((s, i) => ({ - ...s, - color: s.color || set1[i] || randomColor(s.name), - })) + return this.preSources?.map(s => ({ + ...sources[s.name], + ...s, + })) }, })) .views(self => { diff --git a/plugins/variants/src/StructuralVariantChordRenderer/Chord.tsx b/plugins/variants/src/StructuralVariantChordRenderer/Chord.tsx index cfb8a5f90a..baeffe10a5 100644 --- a/plugins/variants/src/StructuralVariantChordRenderer/Chord.tsx +++ b/plugins/variants/src/StructuralVariantChordRenderer/Chord.tsx @@ -5,9 +5,9 @@ import { readConfObject } from '@jbrowse/core/configuration' import { getStrokeProps, polarToCartesian } from '@jbrowse/core/util' import { observer } from 'mobx-react' +import type { AnyRegion, Block } from './types' import type { AnyConfigurationModel } from '@jbrowse/core/configuration' import type { Feature } from '@jbrowse/core/util' -import type { AnyRegion, Block } from './types' function bpToRadians(block: Block, pos: number) { const blockStart = block.region.elided ? 0 : block.region.start diff --git a/plugins/variants/src/VcfAdapter/VcfAdapter.ts b/plugins/variants/src/VcfAdapter/VcfAdapter.ts index 3ef1560bc0..a8a122c3f8 100644 --- a/plugins/variants/src/VcfAdapter/VcfAdapter.ts +++ b/plugins/variants/src/VcfAdapter/VcfAdapter.ts @@ -1,11 +1,10 @@ import IntervalTree from '@flatten-js/interval-tree' -import VCF from '@gmod/vcf' +import VcfParser from '@gmod/vcf' import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter' import { fetchAndMaybeUnzip } from '@jbrowse/core/util' import { openLocation } from '@jbrowse/core/util/io' import { ObservableCreate } from '@jbrowse/core/util/rxjs' -// local import VcfFeature from '../VcfFeature' import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter' @@ -18,6 +17,7 @@ export default class VcfAdapter extends BaseFeatureDataAdapter { vcfFeatures?: Promise<{ header: string + parser: VcfParser intervalTreeMap: Record IntervalTree> }> @@ -29,8 +29,7 @@ export default class VcfAdapter extends BaseFeatureDataAdapter { } async getMetadata() { - const { header } = await this.setup() - const parser = new VCF({ header }) + const { parser } = await this.setup() return parser.getMetadata() } @@ -72,7 +71,7 @@ export default class VcfAdapter extends BaseFeatureDataAdapter { } const header = headerLines.join('\n') - const parser = new VCF({ header }) + const parser = new VcfParser({ header }) const intervalTreeMap = Object.fromEntries( Object.entries(featureMap).map(([refName, lines]) => [ @@ -99,6 +98,7 @@ export default class VcfAdapter extends BaseFeatureDataAdapter { return { header, + parser, intervalTreeMap, } } @@ -135,5 +135,26 @@ export default class VcfAdapter extends BaseFeatureDataAdapter { }, opts.stopToken) } + async getSources() { + const conf = this.getConf('samplesTsvLocation') + if (conf.uri === '' || conf.uri === '/path/to/samples.tsv') { + const { parser } = await this.setup() + return parser.samples.map(name => ({ + name, + })) + } else { + const txt = await openLocation(conf).readFile('utf8') + const lines = txt.split(/\n|\r\n|\r/) + const header = lines[0]!.split('\t') + return lines.slice(1).map(line => + Object.fromEntries( + line + .split('\t') + // force col 0 to be called name + .map((c, idx) => [idx === 0 ? 'name' : header[idx], c]), + ), + ) + } + } public freeResources(): void {} } diff --git a/plugins/variants/src/VcfAdapter/configSchema.ts b/plugins/variants/src/VcfAdapter/configSchema.ts index 2e964778ec..49ad5f0030 100644 --- a/plugins/variants/src/VcfAdapter/configSchema.ts +++ b/plugins/variants/src/VcfAdapter/configSchema.ts @@ -21,9 +21,14 @@ const VcfAdapter = ConfigurationSchema( /** * #slot */ - samples: { - type: 'frozen', - defaultValue: [], + samplesTsvLocation: { + type: 'fileLocation', + defaultValue: { + uri: '/path/to/samples.tsv', + description: + 'tsv with header like name\tpopulation\tetc. where the first column is required, and is the sample names', + locationType: 'UriLocation', + }, }, }, { explicitlyTyped: true }, diff --git a/plugins/variants/src/VcfTabixAdapter/VcfTabixAdapter.ts b/plugins/variants/src/VcfTabixAdapter/VcfTabixAdapter.ts index 17e57e4d77..394f6ec684 100644 --- a/plugins/variants/src/VcfTabixAdapter/VcfTabixAdapter.ts +++ b/plugins/variants/src/VcfTabixAdapter/VcfTabixAdapter.ts @@ -83,12 +83,26 @@ export default class VcfTabixAdapter extends BaseFeatureDataAdapter { observer.complete() }, opts.stopToken) } - async getSources() { - const { parser } = await this.configure() - return parser.samples.map(name => ({ - name, - })) + const conf = this.getConf('samplesTsvLocation') + if (conf.uri === '' || conf.uri === '/path/to/samples.tsv') { + const { parser } = await this.configure() + return parser.samples.map(name => ({ + name, + })) + } else { + const txt = await openLocation(conf).readFile('utf8') + const lines = txt.split(/\n|\r\n|\r/) + const header = lines[0]!.split('\t') + return lines.slice(1).map(line => + Object.fromEntries( + line + .split('\t') + // force col 0 to be called name + .map((c, idx) => [idx === 0 ? 'name' : header[idx], c]), + ), + ) + } } public freeResources(/* { region } */): void {} diff --git a/plugins/variants/src/VcfTabixAdapter/configSchema.ts b/plugins/variants/src/VcfTabixAdapter/configSchema.ts index b41d2cfcb5..beb08f05a6 100644 --- a/plugins/variants/src/VcfTabixAdapter/configSchema.ts +++ b/plugins/variants/src/VcfTabixAdapter/configSchema.ts @@ -39,9 +39,14 @@ const VcfTabixAdapter = ConfigurationSchema( /** * #slot */ - samples: { - type: 'frozen', - defaultValue: [], + samplesTsvLocation: { + type: 'fileLocation', + defaultValue: { + uri: '/path/to/samples.tsv', + description: + 'tsv with header like name\tpopulation\tetc. where the first column is required, and is the sample names', + locationType: 'UriLocation', + }, }, }, { explicitlyTyped: true }, diff --git a/plugins/variants/src/getMultiVariantFeaturesAutorun.ts b/plugins/variants/src/getMultiVariantFeaturesAutorun.ts index 134a1501e5..3119fc1f50 100644 --- a/plugins/variants/src/getMultiVariantFeaturesAutorun.ts +++ b/plugins/variants/src/getMultiVariantFeaturesAutorun.ts @@ -17,7 +17,7 @@ export interface Source { name: string color?: string group?: string - [key: string]: string | undefined + [key: string]: unknown } export function getMultiVariantFeaturesAutorun(self: { diff --git a/plugins/variants/src/shared/BulkEditPanel.tsx b/plugins/variants/src/shared/BulkEditPanel.tsx index 888d0c0e68..7a6816c249 100644 --- a/plugins/variants/src/shared/BulkEditPanel.tsx +++ b/plugins/variants/src/shared/BulkEditPanel.tsx @@ -1,9 +1,16 @@ import { useState } from 'react' import { ErrorMessage } from '@jbrowse/core/ui' -import { Button, TextField, Typography } from '@mui/material' +import { + Button, + DialogActions, + DialogContent, + TextField, + Typography, +} from '@mui/material' import { makeStyles } from 'tss-react/mui' -import { Source } from '../types' + +import type { Source } from '../types' const useStyles = makeStyles()({ textAreaFont: { @@ -12,127 +19,144 @@ const useStyles = makeStyles()({ }) export default function BulkEditPanel({ - setCurrLayout, + onClose, currLayout, }: { currLayout: Source[] - setCurrLayout: (arg: Source[]) => void + onClose: (arg?: Source[]) => void }) { const { classes } = useStyles() const [val, setVal] = useState('') const [error, setError] = useState() return ( -
- - Paste CSV or TSV. If a header column is present. First line is a header. - If a column called "name" is present, it uses that to connect to IDs in - the table, otherwise it uses the first column no. - - { - setVal(event.target.value) - }} - slotProps={{ - input: { - classes: { - input: classes.textAreaFont, - }, - }, - }} - /> - - - {error ? : null} -
+ onClose( + currLayout.map(record => ({ + ...record, + ...newData[record.name], + })), + ) + } else { + setError(new Error('No "name" column found on line 1')) + } + }} + > + Update rows + + + + + + ) } diff --git a/plugins/variants/src/shared/HelpfulTips.tsx b/plugins/variants/src/shared/HelpfulTips.tsx new file mode 100644 index 0000000000..bacb7e2e03 --- /dev/null +++ b/plugins/variants/src/shared/HelpfulTips.tsx @@ -0,0 +1,19 @@ +export default function HelpfulTips() { + return ( + <> + Helpful tips +
    +
  • You can select rows in the table with the checkboxes
    • +
  • Multi-select is enabled with shift-click and control-click
    • +
  • The "Move selected items up/down" can re-arrange subtracks
    • +
  • Sorting the data grid itself can also re-arrange subtracks
    • +
  • Changes are applied when you hit Submit
    • +
  • You can click and drag the dialog box to move it on the screen
    • +
  • + Columns in the table can be hidden using a vertical '...' menu on the + right side of each column +
    • +
+ + ) +} diff --git a/plugins/variants/src/shared/RowPalettizer.tsx b/plugins/variants/src/shared/RowPalettizer.tsx index 8f257f93a0..936bd1f6f5 100644 --- a/plugins/variants/src/shared/RowPalettizer.tsx +++ b/plugins/variants/src/shared/RowPalettizer.tsx @@ -2,7 +2,8 @@ import { set1 } from '@jbrowse/core/ui/colors' import { Button } from '@mui/material' import { randomColor } from '../util' -import { Source } from '../types' + +import type { Source } from '../types' export default function RowPalettizer({ setCurrLayout, @@ -12,41 +13,42 @@ export default function RowPalettizer({ setCurrLayout: (arg: Source[]) => void }) { return ( -
+
+ Assign palette based on... {Object.keys(currLayout[0] ?? []) .filter(f => f !== 'name' && f !== 'color') - .map(r => { - return ( - - ) - })} + setCurrLayout( + currLayout.map(row => ({ + ...row, + color: ret[row[r] as string], + })), + ) + }} + > + {r} + + ))}
) } diff --git a/plugins/variants/src/shared/SetColorDialog.tsx b/plugins/variants/src/shared/SetColorDialog.tsx index 7448f75420..dceadf4bf6 100644 --- a/plugins/variants/src/shared/SetColorDialog.tsx +++ b/plugins/variants/src/shared/SetColorDialog.tsx @@ -5,10 +5,12 @@ import { useLocalStorage } from '@jbrowse/core/util' import { Button, DialogActions, DialogContent } from '@mui/material' import { makeStyles } from 'tss-react/mui' -import SourcesGrid from './SourcesGrid' import BulkEditPanel from './BulkEditPanel' +import HelpfulTips from './HelpfulTips' import RowPalettizer from './RowPalettizer' -import { Source } from '../types' +import SourcesGrid from './SourcesGrid' + +import type { Source } from '../types' const useStyles = makeStyles()({ content: { @@ -50,97 +52,89 @@ export default function SetColorDialog({ maxWidth="xl" title="Multi-variant color/arrangement editor" > - -
- - -
-
- {showTips ? : null} - - {showBulkEditor ? ( - - ) : null} - + {showBulkEditor ? ( + { + if (arg) { + setCurrLayout(arg) + } - - - - - - - - - ) -} + /> + ) : ( + <> + +
+ + +
-function HelpfulTips() { - return ( - <> - Helpful tips -
    -
  • You can select rows in the table with the checkboxes
    • -
  • Multi-select is enabled with shift-click and control-click
    • -
  • The "Move selected items up/down" can re-arrange subtracks
    • -
  • Sorting the data grid itself can also re-arrange subtracks
    • -
  • Changes are applied when you hit Submit
    • -
  • You can click and drag the dialog box to move it on the screen
    • -
  • - Columns in the table can be hidden using a vertical '...' menu on the - right side of each column -
    • -
- + {showTips ? : null} +
+ + + + + + + + + + + )} + ) } diff --git a/plugins/wiggle/src/MultiLinearWiggleDisplay/util.ts b/plugins/wiggle/src/MultiLinearWiggleDisplay/util.ts new file mode 100644 index 0000000000..38d69f0c24 --- /dev/null +++ b/plugins/wiggle/src/MultiLinearWiggleDisplay/util.ts @@ -0,0 +1,8 @@ +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/products/jbrowse-web/src/__snapshots__/jbrowseModel.test.ts.snap b/products/jbrowse-web/src/__snapshots__/jbrowseModel.test.ts.snap index e484959036..b9f5ae2e69 100644 --- a/products/jbrowse-web/src/__snapshots__/jbrowseModel.test.ts.snap +++ b/products/jbrowse-web/src/__snapshots__/jbrowseModel.test.ts.snap @@ -486,6 +486,10 @@ exports[`JBrowse model creates with non-empty snapshot 1`] = ` "uri": "volvox.dup.vcf.gz.tbi", }, }, + "samplesTsvLocation": { + "locationType": "UriLocation", + "uri": "/path/to/samples.tsv", + }, "type": "VcfTabixAdapter", "vcfGzLocation": { "locationType": "UriLocation", @@ -533,6 +537,10 @@ exports[`JBrowse model creates with non-empty snapshot 1`] = ` "uri": "volvox.dup.renamed.vcf.gz.tbi", }, }, + "samplesTsvLocation": { + "locationType": "UriLocation", + "uri": "/path/to/samples.tsv", + }, "type": "VcfTabixAdapter", "vcfGzLocation": { "locationType": "UriLocation", @@ -1193,6 +1201,10 @@ exports[`JBrowse model creates with non-empty snapshot 1`] = ` "uri": "volvox.test.vcf.gz.tbi", }, }, + "samplesTsvLocation": { + "locationType": "UriLocation", + "uri": "1000genomes.tsv", + }, "type": "VcfTabixAdapter", "vcfGzLocation": { "locationType": "UriLocation", @@ -2132,6 +2144,10 @@ exports[`JBrowse model creates with non-empty snapshot 1`] = ` "uri": "volvox.filtered.vcf.gz.tbi", }, }, + "samplesTsvLocation": { + "locationType": "UriLocation", + "uri": "/path/to/samples.tsv", + }, "type": "VcfTabixAdapter", "vcfGzLocation": { "locationType": "UriLocation", @@ -2178,6 +2194,10 @@ exports[`JBrowse model creates with non-empty snapshot 1`] = ` "uri": "volvox.filtered.vcf.gz.tbi", }, }, + "samplesTsvLocation": { + "locationType": "UriLocation", + "uri": "/path/to/samples.tsv", + }, "type": "VcfTabixAdapter", "vcfGzLocation": { "locationType": "UriLocation", @@ -2808,6 +2828,10 @@ exports[`JBrowse model creates with non-empty snapshot 1`] = ` "uri": "volvox.filtered.vcf.gz.tbi", }, }, + "samplesTsvLocation": { + "locationType": "UriLocation", + "uri": "/path/to/samples.tsv", + }, "type": "VcfTabixAdapter", "vcfGzLocation": { "locationType": "UriLocation", @@ -3138,6 +3162,10 @@ exports[`JBrowse model creates with non-empty snapshot 1`] = ` "uri": "volvox.inv.vcf.gz.tbi", }, }, + "samplesTsvLocation": { + "locationType": "UriLocation", + "uri": "/path/to/samples.tsv", + }, "type": "VcfTabixAdapter", "vcfGzLocation": { "locationType": "UriLocation", @@ -3355,6 +3383,10 @@ exports[`JBrowse model creates with non-empty snapshot 1`] = ` }, { "adapter": { + "samplesTsvLocation": { + "locationType": "UriLocation", + "uri": "/path/to/samples.tsv", + }, "type": "VcfAdapter", "vcfLocation": { "locationType": "UriLocation", @@ -3461,6 +3493,10 @@ exports[`JBrowse model creates with non-empty snapshot 1`] = ` }, { "adapter": { + "samplesTsvLocation": { + "locationType": "UriLocation", + "uri": "/path/to/samples.tsv", + }, "type": "VcfAdapter", "vcfLocation": { "locationType": "UriLocation", @@ -3501,6 +3537,10 @@ exports[`JBrowse model creates with non-empty snapshot 1`] = ` }, { "adapter": { + "samplesTsvLocation": { + "locationType": "UriLocation", + "uri": "/path/to/samples.tsv", + }, "type": "VcfAdapter", "vcfLocation": { "locationType": "UriLocation", diff --git a/products/jbrowse-web/src/tests/VcfMatrix.test.tsx b/products/jbrowse-web/src/tests/VcfMatrix.test.tsx new file mode 100644 index 0000000000..ed439f131c --- /dev/null +++ b/products/jbrowse-web/src/tests/VcfMatrix.test.tsx @@ -0,0 +1,37 @@ +import { fireEvent } from '@testing-library/react' + +import { createView, doBeforeEach, expectCanvasMatch, hts, setup } from './util' + +setup() + +beforeEach(() => { + doBeforeEach() +}) + +const delay = { timeout: 30000 } +const opts = [{}, delay] + +test('matrix', async () => { + const { view, findByTestId, findByText } = await createView() + await view.navToLocString('ctgA') + fireEvent.click(await findByTestId(hts('volvox_test_vcf'), ...opts)) + + fireEvent.click(await findByTestId('track_menu_icon', ...opts)) + fireEvent.click(await findByText('Display types', ...opts)) + fireEvent.click(await findByText('Multi-variant display (matrix)', ...opts)) + fireEvent.click(await findByText('Force load', ...opts)) + expectCanvasMatch(await findByTestId(/prerendered_canvas/, ...opts)) +}, 40000) + +test('regular', async () => { + const { view, findByTestId, findByText, findAllByTestId } = await createView() + + await view.navToLocString('ctgA') + fireEvent.click(await findByTestId(hts('volvox_test_vcf'), ...opts)) + + fireEvent.click(await findByTestId('track_menu_icon', ...opts)) + fireEvent.click(await findByText('Display types', ...opts)) + fireEvent.click(await findByText('Multi-variant display (regular)', ...opts)) + fireEvent.click(await findByText('Force load', ...opts)) + expectCanvasMatch((await findAllByTestId(/prerendered_canvas/, ...opts))[0]!) +}, 40000) diff --git a/products/jbrowse-web/src/tests/__image_snapshots__/vcf-matrix-test-tsx-matrix-1-snap.png b/products/jbrowse-web/src/tests/__image_snapshots__/vcf-matrix-test-tsx-matrix-1-snap.png new file mode 100644 index 0000000000000000000000000000000000000000..bc163a4bd55d28e36210c6d52ced88be8b1efe04 GIT binary patch literal 46618 zcmYIvcRZEv8-JgYe9TnFF*`=G!m&d5AbTGxWS@*`lIuDobf#OeO>SCeZ8;u9jvAzON38_f8)jtB6+#z$Qw6s|GRPHpB_A1 za3y>k6$1XlHC2>-e&Y)I_qicA_Qs8eH{_p7XnK5FpR)Rr-R(VgG9$hxgq^C^v(s|b zI><20w(I8nSC=3@Ao@!f>GXHMu<%3)?x&Q`xQTHSOx{0inWcP0iTi##aOby^acCI_ zjGBv6zlyn%d8F9RwXl9H*J!OdsyTZ 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nonresistant e +NA20795 nonresistant e +NA20796 nonresistant e +NA20797 nonresistant e +NA20798 nonresistant e +NA20799 nonresistant e +NA20800 nonresistant e +NA20801 nonresistant e +NA20802 nonresistant e +NA20803 nonresistant e +NA20804 nonresistant e +NA20805 nonresistant e +NA20806 nonresistant e +NA20807 nonresistant e +NA20808 nonresistant e +NA20809 nonresistant e +NA20810 nonresistant e +NA20811 nonresistant e +NA20812 nonresistant e +NA20813 nonresistant e +NA20814 nonresistant e +NA20815 nonresistant e +NA20816 nonresistant e +NA20818 nonresistant e +NA20819 nonresistant e +NA20826 nonresistant e +NA20828 nonresistant e diff --git a/test_data/volvox/config.json b/test_data/volvox/config.json index db228fdb93..7a0679410a 100644 --- a/test_data/volvox/config.json +++ b/test_data/volvox/config.json @@ -365,7 +365,9 @@ "type": "LinearPileupDisplay", "displayId": "volvox_cram_pileup_pileup", "height": 400, - "colorBy": { "type": "mappingQuality" } + "colorBy": { + "type": "mappingQuality" + } } ] }, @@ -514,7 +516,9 @@ "pileupDisplay": { "type": "LinearPileupDisplay", "displayId": "volvox_bam_altname_alignments_pileup", - "colorBy": { "type": "mappingQuality" } + "colorBy": { + "type": "mappingQuality" + } } } ] @@ -662,6 +666,10 @@ "uri": "volvox.test.vcf.gz", "locationType": "UriLocation" }, + "samplesTsvLocation": { + "uri": "1000genomes.tsv", + "locationType": "UriLocation" + }, "index": { "location": { "uri": "volvox.test.vcf.gz.tbi", @@ -2219,7 +2227,6 @@ }, "assemblyNames": ["volvox"] }, - { "type": "AlignmentsTrack", "trackId": "volvox-sorted.noref.cram", diff --git a/test_data/volvox/trix/volvox-rev-del_meta.json b/test_data/volvox/trix/volvox-rev-del_meta.json index 43a7f4ee10..82c17e6b0a 100644 --- a/test_data/volvox/trix/volvox-rev-del_meta.json +++ b/test_data/volvox/trix/volvox-rev-del_meta.json @@ -1,5 +1,5 @@ { - "dateCreated": "2024-10-14T14:42:44.193Z", + "dateCreated": "2025-01-24T16:05:19.959Z", "tracks": [ { "trackId": "volvox-rev-del-annotations", diff --git a/test_data/volvox/trix/volvox_meta.json b/test_data/volvox/trix/volvox_meta.json index d3af26483e..817a316977 100644 --- a/test_data/volvox/trix/volvox_meta.json +++ b/test_data/volvox/trix/volvox_meta.json @@ -1,5 +1,5 @@ { - "dateCreated": "2024-10-14T14:42:44.177Z", + "dateCreated": "2025-01-24T16:05:19.939Z", "tracks": [ { "trackId": "volvox_sv_test", @@ -47,6 +47,10 @@ "uri": "volvox.test.vcf.gz", "locationType": "UriLocation" }, + "samplesTsvLocation": { + "uri": "1000genomes.tsv", + "locationType": "UriLocation" + }, "index": { "location": { "uri": "volvox.test.vcf.gz.tbi", diff --git a/yarn.lock b/yarn.lock index ec17b949ed..ce44eed4ec 100644 --- a/yarn.lock +++ b/yarn.lock @@ -635,7 +635,7 @@ "@smithy/types" "^4.1.0" tslib "^2.6.2" -"@babel/code-frame@^7.0.0", "@babel/code-frame@^7.10.4", "@babel/code-frame@^7.12.13", "@babel/code-frame@^7.16.0", "@babel/code-frame@^7.16.7", "@babel/code-frame@^7.25.9", "@babel/code-frame@^7.26.0", "@babel/code-frame@^7.26.2", "@babel/code-frame@^7.8.3": +"@babel/code-frame@^7.0.0", "@babel/code-frame@^7.10.4", "@babel/code-frame@^7.12.13", "@babel/code-frame@^7.16.0", "@babel/code-frame@^7.16.7", "@babel/code-frame@^7.25.9", "@babel/code-frame@^7.26.2", "@babel/code-frame@^7.8.3": version "7.26.2" resolved "https://registry.yarnpkg.com/@babel/code-frame/-/code-frame-7.26.2.tgz#4b5fab97d33338eff916235055f0ebc21e573a85" integrity sha512-RJlIHRueQgwWitWgF8OdFYGZX328Ax5BCemNGlqHfplnRT9ESi8JkFlvaVYbS+UubVY6dpv87Fs2u5M29iNFVQ== @@ -644,33 +644,33 @@ js-tokens "^4.0.0" picocolors "^1.0.0" -"@babel/compat-data@^7.22.6", "@babel/compat-data@^7.26.0", "@babel/compat-data@^7.26.5": +"@babel/compat-data@^7.22.6", "@babel/compat-data@^7.26.5": version "7.26.5" resolved "https://registry.yarnpkg.com/@babel/compat-data/-/compat-data-7.26.5.tgz#df93ac37f4417854130e21d72c66ff3d4b897fc7" integrity sha512-XvcZi1KWf88RVbF9wn8MN6tYFloU5qX8KjuF3E1PVBmJ9eypXfs4GRiJwLuTZL0iSnJUKn1BFPa5BPZZJyFzPg== 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"@babel/helpers" "^7.26.7" + "@babel/parser" "^7.26.7" "@babel/template" "^7.25.9" - "@babel/traverse" "^7.25.9" - "@babel/types" "^7.26.0" + "@babel/traverse" "^7.26.7" + "@babel/types" "^7.26.7" convert-source-map "^2.0.0" debug "^4.1.0" gensync "^1.0.0-beta.2" json5 "^2.2.3" semver "^6.3.1" -"@babel/generator@^7.26.0", "@babel/generator@^7.26.5", "@babel/generator@^7.7.2": +"@babel/generator@^7.26.5", "@babel/generator@^7.7.2": version "7.26.5" resolved "https://registry.yarnpkg.com/@babel/generator/-/generator-7.26.5.tgz#e44d4ab3176bbcaf78a5725da5f1dc28802a9458" integrity sha512-2caSP6fN9I7HOe6nqhtft7V4g7/V/gfDsC3Ag4W7kEzzvRGKqiv0pu0HogPiZ3KaVSoNDhUws6IJjDjpfmYIXw== @@ -688,7 +688,7 @@ dependencies: "@babel/types" "^7.25.9" -"@babel/helper-compilation-targets@^7.22.6", "@babel/helper-compilation-targets@^7.25.9": +"@babel/helper-compilation-targets@^7.22.6", "@babel/helper-compilation-targets@^7.25.9", "@babel/helper-compilation-targets@^7.26.5": version "7.26.5" resolved 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"@babel/parser@^7.14.7", "@babel/parser@^7.20.7", "@babel/parser@^7.23.9", "@babel/parser@^7.24.4", "@babel/parser@^7.25.9", "@babel/parser@^7.26.0", "@babel/parser@^7.26.5": - version "7.26.5" - resolved "https://registry.yarnpkg.com/@babel/parser/-/parser-7.26.5.tgz#6fec9aebddef25ca57a935c86dbb915ae2da3e1f" - integrity sha512-SRJ4jYmXRqV1/Xc+TIVG84WjHBXKlxO9sHQnA2Pf12QQEAp1LOh6kDzNHXcUnbH1QI0FDoPPVOt+vyUDucxpaw== +"@babel/parser@^7.1.0", "@babel/parser@^7.14.7", "@babel/parser@^7.20.7", "@babel/parser@^7.23.9", "@babel/parser@^7.24.4", "@babel/parser@^7.25.9", "@babel/parser@^7.26.5", "@babel/parser@^7.26.7": + version "7.26.7" + resolved "https://registry.yarnpkg.com/@babel/parser/-/parser-7.26.7.tgz#e114cd099e5f7d17b05368678da0fb9f69b3385c" + integrity sha512-kEvgGGgEjRUutvdVvZhbn/BxVt+5VSpwXz1j3WYXQbXDo8KzFOPNG2GQbdAiNq8g6wn1yKk7C/qrke03a84V+w== dependencies: - "@babel/types" "^7.26.5" + "@babel/types" "^7.26.7" "@babel/plugin-bugfix-firefox-class-in-computed-class-key@^7.25.9": version "7.25.9" @@ -1045,7 +1045,7 @@ "@babel/helper-plugin-utils" "^7.25.9" "@babel/helper-remap-async-to-generator" "^7.25.9" -"@babel/plugin-transform-block-scoped-functions@^7.25.9": +"@babel/plugin-transform-block-scoped-functions@^7.26.5": version "7.26.5" resolved "https://registry.yarnpkg.com/@babel/plugin-transform-block-scoped-functions/-/plugin-transform-block-scoped-functions-7.26.5.tgz#3dc4405d31ad1cbe45293aa57205a6e3b009d53e" integrity sha512-chuTSY+hq09+/f5lMj8ZSYgCFpppV2CbYrhNFJ1BFoXpiWPnnAb7R0MqrafCpN8E1+YRrtM1MXZHJdIx8B6rMQ== @@ -1132,7 +1132,7 @@ dependencies: "@babel/helper-plugin-utils" "^7.25.9" -"@babel/plugin-transform-exponentiation-operator@^7.25.9": +"@babel/plugin-transform-exponentiation-operator@^7.26.3": version "7.26.3" resolved "https://registry.yarnpkg.com/@babel/plugin-transform-exponentiation-operator/-/plugin-transform-exponentiation-operator-7.26.3.tgz#e29f01b6de302c7c2c794277a48f04a9ca7f03bc" integrity sha512-7CAHcQ58z2chuXPWblnn1K6rLDnDWieghSOEmqQsrBenH0P9InCUtOJYD89pvngljmZlJcz3fcmgYsXFNGa1ZQ== @@ -1199,7 +1199,7 @@ "@babel/helper-module-transforms" "^7.25.9" "@babel/helper-plugin-utils" "^7.25.9" -"@babel/plugin-transform-modules-commonjs@^7.25.9": +"@babel/plugin-transform-modules-commonjs@^7.25.9", "@babel/plugin-transform-modules-commonjs@^7.26.3": version "7.26.3" resolved "https://registry.yarnpkg.com/@babel/plugin-transform-modules-commonjs/-/plugin-transform-modules-commonjs-7.26.3.tgz#8f011d44b20d02c3de44d8850d971d8497f981fb" integrity sha512-MgR55l4q9KddUDITEzEFYn5ZsGDXMSsU9E+kh7fjRXTIC3RHqfCo8RPRbyReYJh44HQ/yomFkqbOFohXvDCiIQ== @@ -1240,7 +1240,7 @@ dependencies: "@babel/helper-plugin-utils" "^7.25.9" -"@babel/plugin-transform-nullish-coalescing-operator@^7.25.9": +"@babel/plugin-transform-nullish-coalescing-operator@^7.26.6": version "7.26.6" resolved 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