Tweaks to tests. Add downloads to gitignore

packages/jbrowse-plugin-apollo/.gitignore

@@ -3,3 +3,4 @@
 # Cypress specific files
 cypress/videos
 cypress/screenshots
+cypress/downloads

packages/jbrowse-plugin-apollo/README.md

@@ -1,8 +1,6 @@
 # Testing with cypress
 
-These are some notes to setup cypress and run tests. These notes are likely to
-change and temporary.
-
+These notes setup cypress and run tests. These notes are likely to change.
 
 * One time step: **Outside** the Apollo dev container [install
   cypress](https://docs.cypress.io/guides/getting-started/installing-cypress).
@@ -23,6 +21,16 @@ Add these lines to the `packageExtensions` section of `.yarnrc.yml`:
 
 Then run `yarn` again.
 
+-----
+
+* Start [jbrowse](https://github.com/GMOD/jbrowse-components): You may want to pull the latest code to be consistent with the GitHub workflow
+
+```
+cd /path/to/jbrowse-components
+git pull
+yarn --cwd products/jbrowse-web start
+```
+
 * Start Apollo server. Within the docker container (*i.e* within vscode) and in distinct terminals run:
 
 ```

packages/jbrowse-plugin-apollo/cypress.config.js

@@ -4,6 +4,8 @@ const { defineConfig } = require('cypress')
 const { configurePlugin } = require('cypress-mongodb')
 
 module.exports = defineConfig({
+  // Make viewport long and thin to avoid the scrollbar on the right intefere
+  // with the coordinates
   viewportHeight: 2000,
   viewportWidth: 1000,
   env: {

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

@@ -9,7 +9,7 @@ describe('Download GFF', () => {
     cy.loginAsGuest()
   })
 
-  it('FIXME: Can download gff', () => {
+  it('Can download gff', () => {
     cy.addAssemblyFromGff('volvox.fasta.gff3', 'test_data/volvox.fasta.gff3')
     cy.get('button[data-testid="dropDownMenuButton"]')
       .contains('Apollo')
@@ -28,13 +28,12 @@ describe('Download GFF', () => {
     // TODO 1: Wait for download to complete
     // TODO 2: Be sure you scan the right gff file! There may be other gffs
     // in downloadsFolder, possibly even from the same assembly used here
-    /*
-    cy.exec(`wc -l ${Cypress.config('downloadsFolder')}/*_apollo.gff3`).then(
-      (result) => {
-        expect(result.stdout).eq(242)
-        cy.log(result.stderr)
-      },
-    )
-    */
+    // eslint-disable-next-line prettier/prettier
+    const cmd = `grep -v -P '^#' ${Cypress.config('downloadsFolder')}/*_apollo.gff3 | wc -l`
+    cy.log(cmd)
+    cy.exec(cmd).then((result) => {
+      expect(result.stdout).eq('242')
+      cy.log(result.stderr)
+    })
   })
 })

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

@@ -4,25 +4,6 @@ describe('Different ways of editing features', () => {
     cy.loginAsGuest()
   })
 
-  it.skip('Can select region on rubber-band and zoom into it', () => {
-    const assemblyName = 'space.gff3'
-    cy.addAssemblyFromGff(assemblyName, `test_data/${assemblyName}`)
-    cy.selectAssemblyToView(assemblyName)
-    cy.get('input[placeholder="Search for location"]').type(
-      'ctgA:1..10000{enter}',
-    )
-    cy.get('[data-testid="rubberband_controls"]').trigger('mouseover')
-    cy.get('[data-testid="rubberband_controls"]').trigger('mousedown', 100, 5)
-    cy.get('[data-testid="rubberband_controls"]').trigger('mousemove', 200, 5)
-    cy.get('[data-testid="rubberband_controls"]').trigger('mouseup', 200, 5, {
-      force: true,
-    })
-    cy.intercept('POST', '/users/userLocation').as('done')
-    cy.contains('Zoom to region').click()
-    cy.wait('@done')
-    cy.currentLocationEquals('ctgA', 1021, 2041, 10)
-  })
-
   it('FIXME: edit feature via table editor', () => {
     const assemblyName = 'space.gff3'
     cy.addAssemblyFromGff(assemblyName, `test_data/${assemblyName}`)
@@ -56,7 +37,7 @@ describe('Different ways of editing features', () => {
       'ctgA:9400..9600{enter}',
     )
 
-    cy.get('tbody')
+    cy.get('tbody', { timeout: 10_000 })
       .contains('tr', 'Match5')
       .within(() => {
         cy.get('input[type="text"][value="EST_match"]').type('CDS{enter}', {
@@ -70,16 +51,36 @@ describe('Different ways of editing features', () => {
         })
       })
     cy.get('body').click(0, 0)
+
     // Check edit is done
     cy.reload()
-    cy.get('tbody').within(() => {
+    cy.get('tbody', { timeout: 10_000 }).within(() => {
       cy.get('input[type="text"][value="CDS"]')
       cy.contains('9432')
       // FIXME: It *should* contain 9567
       cy.contains('9567').should('not.exist')
     })
   })
 
+  it.skip('Can select region on rubber-band and zoom into it', () => {
+    const assemblyName = 'space.gff3'
+    cy.addAssemblyFromGff(assemblyName, `test_data/${assemblyName}`)
+    cy.selectAssemblyToView(assemblyName)
+    cy.get('input[placeholder="Search for location"]').type(
+      'ctgA:1..10000{enter}',
+    )
+    cy.get('[data-testid="rubberband_controls"]').trigger('mouseover')
+    cy.get('[data-testid="rubberband_controls"]').trigger('mousedown', 100, 5)
+    cy.get('[data-testid="rubberband_controls"]').trigger('mousemove', 200, 5)
+    cy.get('[data-testid="rubberband_controls"]').trigger('mouseup', 200, 5, {
+      force: true,
+    })
+    cy.intercept('POST', '/users/userLocation').as('done')
+    cy.contains('Zoom to region').click()
+    cy.wait('@done')
+    cy.currentLocationEquals('ctgA', 1021, 2041, 10)
+  })
+
   it.skip('Can drag and move position', () => {
     const assemblyName = 'space.gff3'
     cy.addAssemblyFromGff(assemblyName, `test_data/${assemblyName}`)

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

@@ -34,10 +34,20 @@ describe('Search features', () => {
     cy.contains('Error: Unknown reference sequence "SpamGene"')
   })
 
-  it('FIXME: Can handle space in attribute values', () => {
+  it('Can use quotes to handle spaces', () => {
     cy.addAssemblyFromGff('space.gff3', 'test_data/space.gff3')
     cy.selectAssemblyToView('space.gff3')
-    cy.searchFeatures('.1')
-    cy.contains('Error: Unknown reference sequence')
+    cy.searchFeatures('"agt A"')
+    cy.currentLocationEquals('ctgA', 7500, 8000, 10)
+  })
+
+  it('FIXME: 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'
   })
 })