Improve Newick parsing

[tsibley]

Replaces the basic Newick parser with an external one that handles single-quoted node names. Quoted names are allowed by the format¹ and occur in trees produced by NCBI Pathogens.²

The parser's API is a little awkward for our use case, but it's perfectly workable. Out of several parsers I tried on NPM, this was the only one which handled quoted names, so use it despite the slightly awkward API.

¹ See https://en.wikipedia.org/wiki/Newick_format#Notes for lack of
any formal spec.

² https://discussion.nextstrain.org/t/displaying-trees-from-ncbi-pathogen-browser-in-auspice-us/1456

Checklist

• Checks pass

[tsibley]

I tested this by dragging on a couple example Newick files to auspice.us vs. the review app for this PR (well, local server). The particular example that's fixed by this PR is this Newick tree:

((((((('clinical, 2021-06-01, USA, PNUSAS204121, PDT001057153.1':5,'clinical, 2020-07-22, USA, PNUSAS154799, PDT000794464.1':0.4,'clinical, 2020-11-05, USA, PNUSAS173850, PDT000878638.1':0.4):4,('clinical, 2021-11-12, USA, PNUSAS243890, PDT001173813.1':2,'clinical, 2021-07-12, USA, PNUSAS211661, PDT001088323.1':1):5):1,('clinical, 2021-07-23, USA, PNUSAS214401, PDT001095411.1':11,'clinical, 2020-12-07, USA, PNUSAS183708, PDT000905701.1':6):7):2,'clinical, 2019-12-30, USA, PNUSAS125933, PDT000651740.1':21,'clinical, 2022-11-28, USA, PNUSAS319288, PDT001503767.1':14):4,'clinical, 2021-12-06, USA, PNUSAS248727, PDT001197358.1':25):1,((('clinical, 2022-12-16, USA, PNUSAS322393, PDT001531480.1':4,'clinical, 2022-09-02, USA, PNUSAS296914, PDT001408059.1':0.4):12,'clinical, 2018-01-26, USA, stool, PNUSAS028961, PDT000281869.2':11):7,('clinical, 2023-10-25, PNUSAS395246, PDT001953269.1':6,'clinical, 2019-02-15, USA, PNUSAS056113, PDT000466197.1':7,'clinical, 2019-12-24, USA, PNUSAS124969, PDT000649918.1':8):2):12):9,('clinical, 2023-09-27, USA, PNUSAS386979, PDT001907074.1':2,'clinical, 2020-11-05, USA, PNUSAS173830, PDT000878827.1':1):6,'clinical, 2019-08-28, USA, PNUSAS093707, PDT000575200.1':20,'clinical, 2020-09-16, USA, PNUSAS167774, PDT000837790.1':5);

and it renders before/after like so:

[joverlee521]

Looks like switching the newick parser resolves #66 as well. Using the example tree.nwk that Cornelius provided in the test app, I see the auspice.us error notification

and the following error message in the console

tree.nwk failed to be read as a newick tree. Error: Error: End of buffer reached.

Should we catch errors raised by the parser and display a the more specific error message?

[victorlin]

Compared the following between review app and what's currently at auspice.us:

• The example file from discussion post does not show tip labels on auspice.us but does on the review app
• tree.nwk from local run of zika-tutorial - identical
• tree.nwk from local run of rsv - identical

[tsibley]

@victorlin Not just tip labels for the first test case you list, but the actual structure of the tree is vastly different (because the current parser misparses completely).

[tsibley]

@joverlee521

Should we catch errors raised by the parser and display a the more specific error message?

If we could turn the obtuse parser errors (e.g. End of buffer reached) into user-actionable errors (e.g. Check that your Newick tree file is well formed.) I'm not sure how feasible that is.

[tsibley]

Merging this since it improves the situation. We can improve user-reported errors in a subsequent PR as desired. With some light prodding of newick-js, I got these errors out of it:

Extra content beyond end of Newick tree: …
Not long enough to be a Newick string: …
End of buffer reached.

Grepping the source reveals two more that are applicable to its parsing routines:

At start of buffer.
Unexpected character "${token}" in Newick tree string at position ${buffer.pos - 1}.

These all basically boil down to "Check the syntax of your Newick tree."