LIMS-2015: Update d3-*, csv-file-validator and plotly.js libraries

[ndg63276]

JIRA ticket: LIMS-2015

Summary:

Upgrade some javascript libraries by a major version number

• d3-scale, d3-scale-chromatic, d3-selection
• csv-file-validator
• plotly.js

Changes:

• Update libraries in package.json and package-lock.json
• Update usage of d3-select to use arrow functions and remove let self = this syntax
• Remove pointless if clause in onCellClicked
• Bring in some csv-file-validator changes from LIMS-2037: Remove manual check for duplicate acronyms #1034
• csv-file-validator now passes errors as an object called inValidData rather than an array called inValidMessages
• Add a log message whenever plotly.js is used, to establish whether it can be safely removed in future

To test:

d3-

• Go to any mx proposal, go to any shipment, eg /shipments/sid/76923
• Click Add Container, set Container Type as Puck
• Check when you hover over a puck position, a circle appears to highlight it
• Create some samples, check they go green in the puck drawing
• Create the puck and view it, check when you hover over a puck position, a circle appears again
• Go back to the shipment and click Add Container again, but set the Container Type to be CrystalQuickX
• Fill in a unique barcode, container name and select an imager
• Check clicking on a well in the plate drawing updates the header for the lower section to eg "Sample Location 192"
• Check the well goes green when you select a protein and give a name
• Repeat for a few wells then click Add Container.
• Click to view the container, check the wells with samples are highlighted, and clicking on a well highlights it in blue

csv-file-validator

• Go to an I15-1 proposal, eg cm37261
• Go to Phases from the main menu, then click on a Phase
• Click "Add new simple sample"
• Choose "File upload for multiple samples"
• Select this file duplicate_acronym.csv, check an error appears about a duplicate acronym on row 3
• Select this file commas_in_comment.csv, check an error appears about having commas in the comment (the automatic message is a bit stilted so it is re-written)
• Select this file empty_file.csv, check an error appears to point out the file is empty
• Select this file valid_file.csv, check no errors occur, click "Add Sample" and check it uploads as expected

Plotly.js

• I'm not sure if/where plotly is used (seems to have been EM in the past), so I have copied a suitable plotly input file over another file
• Go to /dc/visit/cm44137-1/id/22240221, click the Auto Processing bar, select fast_dp (if not already) and click "Logs & Files"
• Click the View button next to "iotbx-merging-stats.json"
• Check a multiplicity plot appears, and all the plotly buttons are functional