Dev

[ArtPoon]

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[GopiGugan]

• Checkout dev branch
• python3 setup.py install --user
• module load openmpi/gnu
• nohup python3 batch.py --dry-run > pr473.log &

[ArtPoon]

testing in progress

[GopiGugan]

Recombinants aren't being displayed:

Related to change made in 4f74df1286699b4934fc1f4ccfb24c26bdfdcbc7

[GopiGugan]

Checking the following:

• [x] Search
  • [x] Search by accession number
  • [x] Search by lineage
  • [x] Search by country
  • [x] Search by country (with date filter)
• [x] Tree filtering
• [x] Download Time-scaled tree (nwk)
• [x] Download Time-scaled tree (csv)
• [x] Download Beadplot (svg)
• [x] Download Beadplot (nwk)
• [x] Download mutation list (csv)
• [x] Beadplot cutoff slider
• [x] Expanding Beadplot
• [x] Translated pages
• [x] Changing the colour of the tree based on divergence, collection date, etc.
• [x] Left/Right arrow key to move between beads
• [x] Tooltips
• [x] Countries/Samples/Mutations tabs are populating the correct information
• [x] Toggle for displaying recombinants

[GopiGugan]

Unit tests are failing:

  11 passing (1m)
  3 failing

  1) Search Interface
       Searching 'China' results in selection and expected point count:
     AssertionError: Timed out retrying after 10000ms: Expected to find element: `.selectionH`, but never found it.
      at Context.eval (webpack:///./cypress/e2e/covizu.spec.cy.js:93:30)

  2) Search Interface
       Clicking the next button highlights the correct bead:
     TypeError: Cannot read properties of undefined (reading '0')
      at Context.eval (webpack:///./cypress/e2e/covizu.spec.cy.js:101:90)

  3) Search Interface
       Clear button resets search interface and cluster selection:
     CypressError: Timed out retrying after 10050ms: `cy.click()` failed because this element is `disabled`:

[GopiGugan]

Unit test did not timeout when re-running the tests

[GopiGugan]

Uncaught ReferenceError: Driver is not defined
    at HTMLDivElement.click (covizu.js:46:22)
    at HTMLButtonElement.<anonymous> (jquery-ui.min.js:11:4603)
    at HTMLButtonElement.dispatch (jquery.js:5429:27)
    at elemData.handle (jquery.js:5233:28)

To reproduce:

1. Click es to navigate to the Spanish translated page
2. Click on Tour rapido

[GopiGugan]

Uncaught DOMException: Failed to execute 'querySelector' on 'Document': '.lines#India-UT-VCSGGIMS&R-VCSG416285' is not a valid selector.
    at Object.select (http://localhost:8001/js/d3.js:1689:34)
    at SVGLineElement.<anonymous> (http://localhost:8001/js/beadplot.js:752:30)
    at SVGLineElement.<anonymous> (http://localhost:8001/js/d3.js:1526:16)

To reproduce:

1. Open the BA.2.75.5 beadplot
2. Hover over the vertical line connecting the India/UT-VCSGGIMS&R-VCSG416274 and India/UT-VCSGGIMS&R-VCSG416285 beads

[ArtPoon]

Can we deactivate the tests that are affected by the sporadic timeout issue, and run them manually with each PR?