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Revert broken newick parsing #73

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merged 2 commits into from
Dec 6, 2023
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This reversion is not to say we shouldn't improve our newick parsing - we should! - but that improvements need to be well tested.

@nextstrain-bot nextstrain-bot temporarily deployed to auspice-us-revert-broke-rsv0nm December 6, 2023 23:15 Inactive
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Failure is due to Invalid: lock file's @types/react@18.2.42 does not satisfy @types/react@17.0.71. I didn't get this locally (nodejs 16.13), but can recreate now that I've upgraded to the 16.20 which Heroku is using.

package-lock.json Show resolved Hide resolved
Two recent issues (#71, #72) provide examples where the improved parsing
either didn't parse a valid newick tree or (much more worryingly)
returned an entirely incorrect tree structure, including nodes not
present in the newick. See those issues for details, including the tree
files. While this reversion will re-introduce bugs such as #66 and the
bug in
<https://discussion.nextstrain.org/t/displaying-trees-from-ncbi-pathogen-browser-in-auspice-us/1456/4>,
but they are lesser than the bugs introduced by #69.

This reverts commit cabba98, although
subsequent changes to package-lock.json mean it's not a clean revert.
The newick parser we use is known to have issues with quoted node names,
as it will parse the node name content as newick. As a quick fix,
disallow trees with quotes. The result is that the trees in #66 and
<https://discussion.nextstrain.org/t/displaying-trees-from-ncbi-pathogen-browser-in-auspice-us/1456/4>
will now result in an error. The downside is trees with quoted names but
no newick-like structure within the node name will also fail to load.
@jameshadfield jameshadfield force-pushed the revert-broken-newick-parsing branch from f7d4b5e to 2413e3c Compare December 6, 2023 23:27
@nextstrain-bot nextstrain-bot temporarily deployed to auspice-us-revert-broke-6hjsbg December 6, 2023 23:27 Inactive
@jameshadfield jameshadfield merged commit 23f8460 into master Dec 6, 2023
@jameshadfield jameshadfield deleted the revert-broken-newick-parsing branch December 6, 2023 23:30
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3 participants