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Fix attribute search with spaces, add more tests (GMOD#293)
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* More tests and quote query for search

* Fix sporadic error while testing

Usually the assembly selector box is empty, but sometimes it comes with
a preset assembly which caused the command to fail. Fix by accounting
for the possibility that the box is not empty.
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@dariober
dariober authored Oct 25, 2023
1 parent cfbaa39 commit 2f3e34e
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Showing 10 changed files with 316 additions and 45 deletions.
2 changes: 1 addition & 1 deletion packages/apollo-collaboration-server/src/features/features.service.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -443,7 +443,7 @@ export class FeaturesService {
.find({ assembly: assemblyIds })
.exec()
return this.featureModel
.find({ $text: { $search: term }, refSeq: refSeqs })
.find({ $text: { $search: `"${term}"` }, refSeq: refSeqs })
.populate('refSeq')
.exec()
}
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15 changes: 14 additions & 1 deletion packages/jbrowse-plugin-apollo/README.md
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Expand Up @@ -56,8 +56,21 @@ accordingly in `commands.ts`
`package.json`. Typically (again outside the dev container/vscode):

```
yarn --cwd packages/jbrowse-plugin-apollo run cypress open
yarn --cwd packages/jbrowse-plugin-apollo run cypress open --config baseUrl=http://localhost:3000
```

- For end-to-end testing, click "E2E Testing" `->` Chrome `->`
`Start E2E Testing`. Click on one of the available test scripts.

To run tests locally in headless mode:

```
yarn --cwd packages/jbrowse-plugin-apollo run cypress run \
--browser chrome \
--config '{"baseUrl": "http://localhost:3000",
"screenshotOnRunFailure": true,
"video": true,
"videoCompression": false,
"retries": {"runMode": 0}}' \
--spec cypress/e2e/editFeature.cy.ts
```
26 changes: 21 additions & 5 deletions packages/jbrowse-plugin-apollo/cypress/e2e/addAssembly.cy.ts
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Expand Up @@ -5,9 +5,9 @@ describe('Add Assembly', () => {
})

it('Can add assembly from fasta', () => {
cy.contains('Apollo').click()
cy.contains('button[data-testid="dropDownMenuButton"]', 'Apollo').click()
cy.contains('Add Assembly').click()
cy.get('input[type="TextField"]').type('volvox_deleteme')
cy.get('input[type="TextField"]').type('volvox.fa')
cy.get('input[value="text/x-fasta"]').check()
cy.get('input[type="file"]').selectFile('test_data/volvox.fa')

Expand All @@ -18,9 +18,9 @@ describe('Add Assembly', () => {
})

it('Can add assembly from gff3 with fasta', () => {
cy.contains('Apollo').click()
cy.contains('button[data-testid="dropDownMenuButton"]', 'Apollo').click()
cy.contains('Add Assembly').click()
cy.get('input[type="TextField"]').type('volvox_deleteme')
cy.get('input[type="TextField"]').type('volvox.fasta.gff3')
cy.get('input[value="text/x-gff3"]').check()
cy.get('input[type="file"]').selectFile('test_data/volvox.fasta.gff3')

Expand All @@ -30,8 +30,24 @@ describe('Add Assembly', () => {
cy.wait('@changes').its('response.statusCode').should('match', /2../)
})

it('Can import and add features', () => {
cy.addAssemblyFromGff('volvox.fasta', 'test_data/volvox.fasta.gff3')
cy.importFeatures('test_data/onegene.fasta.gff3', 'volvox.fasta', false)
cy.selectAssemblyToView('volvox.fasta')
cy.searchFeatures('gx1', 1)
cy.searchFeatures('EDEN', 1)
})

it('Can import and replace features', () => {
cy.addAssemblyFromGff('volvox.fasta', 'test_data/volvox.fasta.gff3')
cy.importFeatures('test_data/onegene.fasta.gff3', 'volvox.fasta', true)
cy.selectAssemblyToView('volvox.fasta')
cy.searchFeatures('gx1', 1)
cy.searchFeatures('EDEN', 0)
})

it('FIXME: Can add assembly from 2bit', () => {
cy.contains('Apollo').click()
cy.contains('button[data-testid="dropDownMenuButton"]', 'Apollo').click()
cy.contains('Add Assembly').click()
cy.get('input[type="TextField"]').type('volvox_deleteme')
cy.get('input[value="text/x-fasta"]').check()
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104 changes: 97 additions & 7 deletions packages/jbrowse-plugin-apollo/cypress/e2e/editFeature.cy.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -61,22 +61,112 @@ describe('Different ways of editing features', () => {
})
})

it('Can add gene ontology attribute', () => {
cy.addAssemblyFromGff('onegene.fasta.gff3', 'test_data/onegene.fasta.gff3')
cy.selectAssemblyToView('onegene.fasta.gff3')
cy.searchFeatures('gx1', 1)
cy.contains('td', 'CDS1').rightclick()
cy.contains('Edit attributes').click()
cy.contains('Feature attributes')
.parent()
.within(() => {
cy.contains('button', 'Add new').click()
cy.get('input[value="Gene Ontology"]').click()
cy.contains('button', /^Add$/).click()
cy.contains('Gene Ontology')
.parent()
.parent()
.parent()
.within(() => {
cy.get('input').type('quiescence')
})
})
// This seems to take ~6 minutes in headless mode!
cy.contains('li', 'GO:0044838', { timeout: 600_000 }).click()
cy.contains('button', 'Submit changes').click()
cy.contains('td', 'Gene Ontology=GO:0044838')
})

it('Can delete feature', () => {
cy.addAssemblyFromGff('onegene.fasta.gff3', 'test_data/onegene.fasta.gff3')
cy.selectAssemblyToView('onegene.fasta.gff3')
cy.searchFeatures('gx1', 1)
cy.contains('td', '=CDS1')
cy.contains('td', '=tx1').rightclick()
cy.contains('Delete feature').click()
cy.contains('Are you sure you want to delete the selected feature?')
.parent()
.parent()
.within(() => {
cy.contains('button', /^yes$/, { matchCase: false }).click()
})
cy.contains('td', '=gx1')
cy.contains('td', '=tx1').should('not.exist')
cy.contains('td', '=CDS1').should('not.exist')
})

it('Suggest only valid SO terms from dropdown', () => {
cy.addAssemblyFromGff('onegene.fasta.gff3', 'test_data/onegene.fasta.gff3')
cy.selectAssemblyToView('onegene.fasta.gff3')
cy.searchFeatures('gx1')
cy.searchFeatures('gx1', 1)
// In headless mode it seems to take a long time for menus to be populated
cy.get('input[type="text"][value="exon"]', { timeout: 60_000 })
.eq(0)
.click({ timeout: 60_000, force: true })
cy.contains('li', /^CDS$/, { timeout: 60_000, matchCase: false }).should(
'exist',
)
cy.get('input[type="text"][value="CDS"]', { timeout: 60_000 }).click({
timeout: 60_000,
force: true,
})
cy.contains('li', /^start_codon$/, {
timeout: 60_000,
matchCase: false,
}).should('exist')
cy.contains('li', /^gene$/, { timeout: 60_000, matchCase: false }).should(
'not.exist',
)
})

it('Can add child feature via table editor', () => {
cy.addAssemblyFromGff('onegene.fasta.gff3', 'test_data/onegene.fasta.gff3')
cy.selectAssemblyToView('onegene.fasta.gff3')
cy.searchFeatures('gx1', 1)
// In headless mode it seems to take a long time for menus to be populated
cy.get('input[type="text"][value="CDS"]', { timeout: 60_000 }).rightclick({
timeout: 60_000,
force: true,
})
cy.contains('Add child feature').click()
cy.contains('Add new child feature')
.parent()
.within(() => {
cy.get('form').within(() => {
cy.contains('Start')
.parent()
.within(() => {
cy.get('input').type('{selectall}{backspace}1')
})
cy.contains('End')
.parent()
.within(() => {
cy.get('input').type('{selectall}{backspace}3')
})
cy.contains('Type')
.parent()
.within(() => {
cy.get('input').click({ timeout: 60_000 })
})
})
})
cy.contains('li', /^start_codon$/, {
timeout: 60_000,
matchCase: false,
}).click()
cy.get('button').contains('Submit').click()
cy.reload() // Ideally, you shouldn't need to reload to see the change?
cy.get('tbody', { timeout: 60_000 }).within(() => {
cy.get('input[value="start_codon"]').should('have.length', 1)
cy.get('input[value="1"]').should('have.length', 4)
cy.get('input[value="3"]').should('have.length', 1)
})
})

it.skip('Can select region on rubber-band and zoom into it', () => {
const assemblyName = 'space.gff3'
cy.addAssemblyFromGff(assemblyName, `test_data/${assemblyName}`)
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88 changes: 70 additions & 18 deletions packages/jbrowse-plugin-apollo/cypress/e2e/searchFeatures.cy.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -4,17 +4,55 @@ describe('Search features', () => {
cy.loginAsGuest()
})

it('One hit, no children', () => {
it('FIXME: Use of quotes', () => {
cy.addAssemblyFromGff('space.gff3', 'test_data/space.gff3')
cy.selectAssemblyToView('space.gff3')
cy.searchFeatures('"agt A"', 4) // Should return 2 matches
})

it('FIXME: Inconsistent substring matching', () => {
cy.addAssemblyFromGff('space.gff3', 'test_data/space.gff3')
cy.selectAssemblyToView('space.gff3')

cy.searchFeatures('transmem', 0)
cy.searchFeatures('transmembrane', 1)
cy.currentLocationEquals('ctgA', 9520, 9900, 10)
cy.searchFeatures('7-transmembrane', 1)
cy.searchFeatures('someKeyWord', 1)
cy.searchFeatures('mRNA', 1)
cy.searchFeatures('UTRs', 1)
cy.searchFeatures('UTR', 1) // Why one match? Should be zero
cy.searchFeatures('with', 0) // Why zero matches?
cy.searchFeatures('both', 0) // Why zero matches?
cy.searchFeatures('and', 0) // Why zero matches?
})

it('One hit with no children', () => {
cy.addAssemblyFromGff('volvox.fasta.gff3', 'test_data/volvox.fasta.gff3')
cy.selectAssemblyToView('volvox.fasta.gff3')
cy.searchFeatures('Match6', 1)
cy.currentLocationEquals('ctgA', 8000, 9000, 10)
})

it('Match is not case sensitive', () => {
cy.addAssemblyFromGff('volvox.fasta.gff3', 'test_data/volvox.fasta.gff3')
cy.selectAssemblyToView('volvox.fasta.gff3')
cy.searchFeatures('Match6')
cy.searchFeatures('match6', 1)
cy.currentLocationEquals('ctgA', 8000, 9000, 10)
})

it('One matching Parent and multiple matching children', () => {
it('Decode URL escapes', () => {
cy.addAssemblyFromGff('volvox.fasta.gff3', 'test_data/volvox.fasta.gff3')
cy.selectAssemblyToView('volvox.fasta.gff3')
cy.searchFeatures('EDEN')
cy.searchFeatures('Some%2CNote', 0)
cy.searchFeatures('Some,Note', 1)
cy.currentLocationEquals('ctgA', 1000, 2000, 10)
})

it('One matching parent and multiple matching children', () => {
cy.addAssemblyFromGff('volvox.fasta.gff3', 'test_data/volvox.fasta.gff3')
cy.selectAssemblyToView('volvox.fasta.gff3')
cy.searchFeatures('EDEN', 1)
cy.currentLocationEquals('ctgA', 1050, 9000, 10)
})

Expand All @@ -23,29 +61,43 @@ describe('Search features', () => {
cy.addAssemblyFromGff('volvox2.fasta.gff3', 'test_data/volvox2.fasta.gff3')

cy.selectAssemblyToView('volvox2.fasta.gff3')
cy.searchFeatures('SpamGene')
cy.searchFeatures('SpamGene', 1)
cy.currentLocationEquals('ctgA', 100, 200, 10)

cy.visit('/?config=http://localhost:9000/jbrowse_config.json')
cy.selectAssemblyToView('volvox.fasta.gff3')
cy.searchFeatures('SpamGene')
cy.contains('Error: Unknown reference sequence "SpamGene"')
cy.searchFeatures('SpamGene', 0)
})

it('Can use quotes to handle spaces', () => {
cy.addAssemblyFromGff('space.gff3', 'test_data/space.gff3')
cy.selectAssemblyToView('space.gff3')
cy.searchFeatures('"agt A"')
cy.currentLocationEquals('ctgA', 7500, 8000, 10)
it('Select from multiple hits', () => {
cy.addAssemblyFromGff('volvox.fasta.gff3', 'test_data/volvox.fasta.gff3')
cy.selectAssemblyToView('volvox.fasta.gff3')
cy.searchFeatures('hga', 3)
cy.contains('td', 'ctgA:1000..2000')
.parent()
.within(() => {
cy.contains('button', /^Go$/, { matchCase: false }).click()
cy.wait('@search hga')
})
cy.currentLocationEquals('ctgA', 1000, 2000, 10)

cy.searchFeatures('hgb', 2)
})

it('FIXME: Can handle regex and space in attribute values', () => {
it('Can handle regex and space in attribute values', () => {
cy.addAssemblyFromGff('space.gff3', 'test_data/space.gff3')
cy.selectAssemblyToView('space.gff3')
cy.get('input[placeholder="Search for location"]').type('Ma*.1{enter}')
cy.contains('Search results')
// It should instead either:
// * Return only one hit for Match1, or
// * Return 'Error: Unknown reference sequence'
cy.searchFeatures('Ma.*1', 0)

cy.searchFeatures('agt 2', 1)
cy.currentLocationEquals('ctgA', 1150, 7200, 10)

cy.searchFeatures('spam"foo"eggs', 1)
cy.currentLocationEquals('ctgA', 1150, 7200, 10)

cy.searchFeatures('agt B', 1)
cy.currentLocationEquals('ctgA', 8000, 9000, 10)

cy.searchFeatures('agt 1', 2)
})
})
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