Merge branch 'cypress' of https://github.com/GMOD/Apollo3 into cypress

packages/jbrowse-plugin-apollo/cypress/e2e/add_assembly.cy.ts

@@ -0,0 +1,52 @@
+describe('Add Assembly', () => {
+  beforeEach(() => {
+    cy.fixture('tmp.json').then((config) => {
+      cy.exec(
+        `mongosh ${config.MONGODB_URI} --eval 'db.assemblies.deleteOne({name: "volvox_deleteme"})'`,
+      ).then((result) => {
+        cy.log(result.stdout)
+        cy.log(result.stderr)
+      })
+    })
+    cy.loginAsGuest('config.tmp.json')
+  })
+
+  it('Can add assembly from fasta', () => {
+    cy.contains('Apollo').click()
+    cy.contains('Add Assembly').click()
+    cy.get('input[type="TextField"]').type('volvox_deleteme')
+    cy.get('input[value="text/x-fasta"]').check()
+    cy.get('input[type="file"]').selectFile('test_data/volvox.fa')
+
+    cy.intercept('/changes').as('changes')
+    cy.contains('Submit').click()
+    cy.contains('is being added', { timeout: 10000 })
+    cy.wait('@changes').its('response.statusCode').should('match', /2../)
+  })
+
+  it('Can add assembly from 2bit', () => {
+    cy.contains('Apollo').click()
+    cy.contains('Add Assembly').click()
+    cy.get('input[type="TextField"]').type('volvox_deleteme')
+    cy.get('input[value="text/x-fasta"]').check()
+    cy.get('input[type="file"]').selectFile('test_data/volvox.2bit')
+
+    cy.intercept('/changes').as('changes')
+    cy.contains('Submit').click()
+    cy.contains('is being added', { timeout: 10000 })
+    cy.wait('@changes').its('response.statusCode').should('match', /2../)
+  })
+
+  it('Can add assembly from gff3 with fasta', () => {
+    cy.contains('Apollo').click()
+    cy.contains('Add Assembly').click()
+    cy.get('input[type="TextField"]').type('volvox_deleteme')
+    cy.get('input[value="text/x-gff3"]').check()
+    cy.get('input[type="file"]').selectFile('test_data/volvox.fasta.gff3')
+
+    cy.intercept('/changes').as('changes')
+    cy.contains('Submit').click()
+    cy.contains('is being added', { timeout: 10000 })
+    cy.wait('@changes').its('response.statusCode').should('match', /2../)
+  })
+})

packages/jbrowse-plugin-apollo/cypress/e2e/apollo.cy.ts

@@ -1,3 +1,4 @@
+/*
 describe('My First Test', () => {
   it('visits JBrowse with Apollo', () => {
     // You can put JBrowse 2 into any session you want this way at the beginning
@@ -13,4 +14,4 @@ describe('My First Test', () => {
       cy.contains('Log in to Demo Server')
     })
   })
-})
+}) */

packages/jbrowse-plugin-apollo/cypress/e2e/open_assembly.cy.ts

@@ -0,0 +1,11 @@
+describe('Open Assembly', () => {
+  it('Can open assembly', () => {
+    cy.loginAsGuest('config.tmp.json')
+    cy.contains('Select assembly to view', { timeout: 10000 })
+    cy.get('input[data-testid="assembly-selector"]').parent().click()
+    cy.contains('volvox_cy').click()
+    cy.contains('Open').click()
+    // It would be better to test that the screen contains "volvox_cy" somewhere (at the moment it doesn't)
+    cy.get('input[placeholder="Search for location"][value="ctgA:1..50,001"]')
+  })
+})

packages/jbrowse-plugin-apollo/cypress/e2e/search_features.cy.ts

@@ -0,0 +1,50 @@
+describe('Search features', () => {
+  beforeEach(() => {
+    cy.fixture('config.tmp.json').then((config) => {
+      cy.exec(
+        `mongosh ${config.MONGODB_URI} --eval 'db.assemblies.deleteMany({})'`,
+      ).then((result) => {
+        cy.log(result.stdout)
+        cy.log(result.stderr)
+      })
+    })
+    cy.loginAsGuest('config.tmp.json')
+  })
+
+  it('One hit, no children', () => {
+    cy.addAssemblyFromGff('volvox_cy', 'test_data/volvox.fasta.gff3')
+    cy.selectAssemblyToView('volvox_cy')
+    cy.searchFeatures('Match6')
+    cy.currentLocationEquals('ctgA', 8000, 9000, 10)
+  })
+
+  it('One matching Parent and multiple matching children', () => {
+    cy.addAssemblyFromGff('volvox_cy', 'test_data/volvox.fasta.gff3')
+    cy.selectAssemblyToView('volvox_cy')
+    cy.searchFeatures('EDEN')
+    cy.currentLocationEquals('ctgA', 1050, 9000, 10)
+  })
+
+  it.only('Can handle space in attribute values', () => {
+    cy.addAssemblyFromGff('volvox_cy', 'test_data/space.gff3')
+    cy.selectAssemblyToView('volvox_cy')
+    cy.searchFeatures('.1')
+    cy.contains('Error: Unknown reference sequence "SpamGene"')
+  })
+
+  it('Search only the selected assembly', () => {
+    cy.addAssemblyFromGff('volvox_cy', 'test_data/volvox.fasta.gff3')
+    cy.addAssemblyFromGff('volvox_spam', 'test_data/volvox2.fasta.gff3')
+
+    cy.selectAssemblyToView('volvox_spam')
+    cy.searchFeatures('SpamGene')
+    cy.currentLocationEquals('ctgA', 100, 200, 10)
+
+    cy.fixture('config.tmp.json').then((config) => {
+      cy.visit(config.apollo_url)
+    })
+    cy.selectAssemblyToView('volvox_cy')
+    cy.searchFeatures('SpamGene')
+    cy.contains('Error: Unknown reference sequence "SpamGene"')
+  })
+})

packages/jbrowse-plugin-apollo/cypress/fixtures/config.tmp.json

@@ -0,0 +1,4 @@
+{
+    "apollo_url": "http://localhost:3000/?config=http%3A%2F%2Flocalhost%3A9000%2Fjbrowse_config.json" ,
+    "MONGODB_URI": "mongodb://localhost:27017/apolloTestDb"
+}