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Use local data instead of remote data for LGV component test #3611

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merged 2 commits into from
Mar 24, 2023
+50 −323
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Use local data instead of remote data for LGV component test #3611

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8274fe4
Use volvox for component test lgv
cmdcolin Mar 24, 2023
504cb1d
Remove unneeded ui from cgv test too
cmdcolin Mar 24, 2023
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80 changes: 2 additions & 78 deletions component_tests/cgv/src/App.tsx
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@@ -1,5 +1,4 @@
import React, { useState, useEffect } from 'react'
import '@fontsource/roboto'
import {
createViewState,
JBrowseCircularGenomeView,
Expand All @@ -8,19 +7,14 @@ import {
import assembly from './assembly'
import tracks from './tracks'

function View() {
export default function View() {
const [viewState, setViewState] =
useState<ReturnType<typeof createViewState>>()
const [patches, setPatches] = useState('')
const [stateSnapshot, setStateSnapshot] = useState('')

useEffect(() => {
const state = createViewState({
assembly,
tracks,
onChange: (patch: any) => {
setPatches(previous => previous + JSON.stringify(patch) + '\n')
},
})
state.session.view.showTrack('volvox_sv_test_renamed')
setViewState(state)
Expand All @@ -30,75 +24,5 @@ function View() {
return null
}

return (
<>
<h1>
JBrowse 2 React Circular Genome View Demo (with create-react-app v4)
</h1>
<JBrowseCircularGenomeView viewState={viewState} />
<h3>Code</h3>
<p>
The code for this app is available at{' '}
<a
href="https://github.com/GMOD/jbrowse-components/tree/main/demos/jbrowse-react-circular-genome-view"
target="_blank"
rel="noreferrer"
>
https://github.com/GMOD/jbrowse-components/tree/main/demos/jbrowse-react-circular-genome-view
</a>
.
</p>
<h3>Control the view</h3>
<div>
<p>
This is an example of controlling the view from other elements on the
page. Clicking on a button will rotate the view.
</p>
<button
onClick={() => {
viewState.session.view.rotateClockwise()
}}
>
Rotate clockwise
</button>
<button
onClick={() => {
viewState.session.view.rotateCounterClockwise()
}}
>
Rotate counter clockwise
</button>
</div>
<h3>See the state</h3>
<div>
<p>
The button below will show you the current session, which includes
things like what region the view is showing and which tracks are open.
This session JSON object can be used in the{' '}
<code>defaultSession</code> of <code>createViewState</code>.
</p>
<button
onClick={() => {
setStateSnapshot(JSON.stringify(viewState.session, undefined, 2))
}}
>
Show session
</button>
</div>
<textarea value={stateSnapshot} readOnly rows={20} cols={80} />
<h3>React to the view</h3>
<p>
Using <code>onChange</code> in <code>createViewState</code>, you can
observe what is happening in the view and react to it. The changes in
the state of the view are emitted as{' '}
<a href="http://jsonpatch.com/" target="_blank" rel="noreferrer">
JSON patches
</a>
. The patches for the component on this page are shown below.
</p>
<textarea value={patches} readOnly rows={5} cols={80} wrap="off" />
</>
)
return <JBrowseCircularGenomeView viewState={viewState} />
}

export default View
12 changes: 1 addition & 11 deletions component_tests/lgv/cypress/integration/basic.spec.ts
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@@ -1,20 +1,10 @@
describe('JBrowse embedded view', () => {
it('page loads', () => {
Cypress.on(
// from https://github.com/cypress-io/cypress/issues/8418
'uncaught:exception',
// @ts-expect-error thinks we are es5 and don't have includes, may be able to update
err => !err.message.includes('ResizeObserver loop limit exceeded'),
)
cy.visit('/')
cy.contains('JBrowse 2 React Linear Genome View Demo')
})
it('track loads', () => {
cy.visit('/')

// eslint-disable-next-line testing-library/await-async-query,testing-library/prefer-screen-queries
cy.findByTestId('Blockset-pileup', { timeout: 30000 }).findByTestId(
'prerendered_canvas_{GRCh38}10:29838637..29838705-0_done',
'prerendered_canvas_{volvox}ctgA:1..82-0_done',
{ timeout: 30000 },
)
})
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134 changes: 7 additions & 127 deletions component_tests/lgv/src/App.tsx
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Original file line number Diff line number Diff line change
@@ -1,5 +1,4 @@
import React, { useState, useEffect } from 'react'
import '@fontsource/roboto'
import React, { useEffect, useState } from 'react'
import {
createViewState,
JBrowseLinearGenomeView,
Expand All @@ -8,143 +7,24 @@ import {
import assembly from './assembly'
import tracks from './tracks'

const defaultSession = {
name: 'this session',
view: {
id: 'linearGenomeView',
type: 'LinearGenomeView',
tracks: [
{
id: '7PWx6ki1_',
type: 'ReferenceSequenceTrack',
configuration: 'GRCh38-ReferenceSequenceTrack',
displays: [
{
id: 'pa_7lx6FDh',
type: 'LinearReferenceSequenceDisplay',
height: 210,
configuration:
'GRCh38-ReferenceSequenceTrack-LinearReferenceSequenceDisplay',
},
],
},
{
id: 'KHwe41KXk',
type: 'AlignmentsTrack',
configuration: 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome',
displays: [
{
id: '_-kwYVczT8',
type: 'LinearAlignmentsDisplay',
PileupDisplay: {
id: '1HTk32IDZJ',
type: 'LinearPileupDisplay',
height: 100,
configuration: {
type: 'LinearPileupDisplay',
displayId:
'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_pileup_xyz',
},
},
SNPCoverageDisplay: {
id: 'ZBXRXmuDrc',
type: 'LinearSNPCoverageDisplay',
height: 45,
configuration: {
type: 'LinearSNPCoverageDisplay',
displayId:
'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_snpcoverage_xyz',
},
},
configuration:
'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay',
height: 250,
},
],
},
],
},
}
type ViewModel = ReturnType<typeof createViewState>

function View() {
const [viewState, setViewState] =
useState<ReturnType<typeof createViewState>>()
const [patches, setPatches] = useState('')
const [stateSnapshot, setStateSnapshot] = useState('')
export default function View() {
const [viewState, setViewState] = useState<ViewModel>()

useEffect(() => {
const state = createViewState({
assembly,
tracks,
location: '10:29,838,655..29,838,737',
onChange: (patch: unknown) => {
setPatches(previous => previous + JSON.stringify(patch) + '\n')
},
defaultSession,
location: 'ctgA:1-100',
})
state.session.view.showTrack('volvox_cram')
setViewState(state)
}, [])

if (!viewState) {
return null
}

return (
<>
<h1>JBrowse 2 React Linear Genome View Demo</h1>
<JBrowseLinearGenomeView viewState={viewState} />
<h3>Control the view</h3>
<div>
<p>
This is an example of controlling the view from other elements on the
page. Clicking on a button will navigate the view to the location of
that gene.
</p>
<button
onClick={() => {
viewState.session.view.navToLocString('10:94762681..94855547')
}}
>
CYP2C19
</button>
<button
onClick={() => {
viewState.session.view.navToLocString('13:32315086..32400266')
}}
>
BRCA2
</button>
</div>
<h3>See the state</h3>
<div>
<p>
The button below will show you the current session, which includes
things like what region the view is showing and which tracks are open.
This session JSON object can be used in the{' '}
<code>defaultSession</code> of <code>createViewState</code>.
</p>
<button
onClick={() => {
setStateSnapshot(JSON.stringify(viewState.session, undefined, 2))
}}
>
Show session
</button>
</div>
<textarea value={stateSnapshot} readOnly rows={20} cols={80} />
<h3>React to the view</h3>
<p>
Using <code>onChange</code> in <code>createViewState</code>, you can
observe what is happening in the view and react to it. The changes in
the state of the view are emitted as{' '}
<a href="http://jsonpatch.com/" target="_blank" rel="noreferrer">
JSON patches
</a>
. The patches for the component on this page are shown below.
</p>
<textarea value={patches} readOnly rows={5} cols={80} wrap="off" />
</>
)
return <JBrowseLinearGenomeView viewState={viewState} />
}

export default View
54 changes: 28 additions & 26 deletions component_tests/lgv/src/assembly.ts
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@@ -1,38 +1,40 @@
const assembly = {
name: 'GRCh38',
aliases: ['hg38'],
name: 'volvox',
aliases: ['vvx'],
sequence: {
type: 'ReferenceSequenceTrack',
trackId: 'GRCh38-ReferenceSequenceTrack',
trackId: 'volvox_refseq',
metadata: {
date: '2020-08-20',
},
formatAbout: {
hideUris: true,
config: "jexl:{extraField:'important data'}",
},
adapter: {
type: 'BgzipFastaAdapter',
fastaLocation: {
uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz',
},
faiLocation: {
uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.fai',
},
gziLocation: {
uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi',
type: 'TwoBitAdapter',
twoBitLocation: {
uri: 'volvox.2bit',
locationType: 'UriLocation',
},
},
displays: [
{
type: 'LinearReferenceSequenceDisplay',
displayId:
'GRCh38-ReferenceSequenceTrack-LinearReferenceSequenceDisplay',
renderer: {
type: 'DivSequenceRenderer',
},
},
],
},
refNameAliases: {
adapter: {
type: 'RefNameAliasAdapter',
location: {
uri: '/GRCh38.aliases.txt',
},
type: 'FromConfigAdapter',
adapterId: 'W6DyPGJ0UU',
features: [
{
refName: 'ctgA',
uniqueId: 'alias1',
aliases: ['A', 'contigA'],
},
{
refName: 'ctgB',
uniqueId: 'alias2',
aliases: ['B', 'contigB'],
},
],
},
},
}
Expand Down
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