From 2413e3c9886c65e0f675379f793edc96e98c0379 Mon Sep 17 00:00:00 2001
From: James Hadfield <hadfield.james@gmail.com>
Date: Thu, 7 Dec 2023 12:10:25 +1300
Subject: [PATCH] Disallow newick trees with quotes

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.
---
 auspice_client_customisation/parseNewick.js | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/auspice_client_customisation/parseNewick.js b/auspice_client_customisation/parseNewick.js
index 768a72b..32e0d76 100644
--- a/auspice_client_customisation/parseNewick.js
+++ b/auspice_client_customisation/parseNewick.js
@@ -19,6 +19,17 @@
 export const parseNewick = (nwk) => {
   const ancestors = [];
   let tree = {};
+
+  /**
+   * This newick parser 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.
+   */
+  if (nwk.includes('"') || nwk.includes("'")) {
+    throw new Error("Auspice.us cannot currently parse Newick files with single or double quotes in them!")
+  }
+
+
   const tokens = nwk.split(/\s*(;|\(|\)|,|:)\s*/);
   for (let i=0; i<tokens.length; i++) {
     const token = tokens[i];