From cabba988539a320c6624e2dd04b533f0fc5fd6fb Mon Sep 17 00:00:00 2001
From: Thomas Sibley <tsibley@fredhutch.org>
Date: Thu, 2 Nov 2023 12:12:52 -0700
Subject: [PATCH] Improve Newick parsing
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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>
---
 auspice_client_customisation/parseNewick.js | 88 +++++++++------------
 package-lock.json                           | 13 ++-
 package.json                                |  3 +-
 3 files changed, 53 insertions(+), 51 deletions(-)

diff --git a/auspice_client_customisation/parseNewick.js b/auspice_client_customisation/parseNewick.js
index 768a72b..ae61864 100644
--- a/auspice_client_customisation/parseNewick.js
+++ b/auspice_client_customisation/parseNewick.js
@@ -1,55 +1,45 @@
-/**
- * Newick format parser in JavaScript.
- *
- * Copyright (c) Jason Davies 2010.
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in
- * all copies or substantial portions of the Software.
- */
+import { parse as _parseNewick } from "newick-js";
 
-/* NOTE: parseNewick function slightly modified to produce an object better suited for Nextstrain. */
-
-export const parseNewick = (nwk) => {
-  const ancestors = [];
-  let tree = {};
-  const tokens = nwk.split(/\s*(;|\(|\)|,|:)\s*/);
-  for (let i=0; i<tokens.length; i++) {
-    const token = tokens[i];
-    const subtree = {};
-    switch (token) {
-      case '(': // new child nodes up next
-        tree.children = [subtree];
-        ancestors.push(tree);
-        tree = subtree;
-        break;
-      case ',': // next node: another child of the last ancestor
-        ancestors[ancestors.length-1].children.push(subtree);
-        tree = subtree;
-        break;
-      case ')': // optional name next
-        tree = ancestors.pop();
-        break;
-      case ':': // optional length next
-        break;
-      default:
-        const x = tokens[i-1];
-        if (x === ')' || x === '(' || x === ',') {
-          tree.name = token;
-        } else if (x === ':') {
-          tree.node_attrs = {div: parseFloat(token)};
-        }
-    }
+const parseNewick = (nwk) => {
+  const {root, rootWeight, graph: [,edges]} = _parseNewick(nwk);
+  const edgesByParent = new Map();
+
+  for (const [parent, child, weight] of edges) {
+    if (!edgesByParent.has(parent))
+      edgesByParent.set(parent, new Set());
+    edgesByParent.get(parent).add({child, weight});
   }
-  return tree;
-};
 
+  const constructTree = (parent, weight) => {
+    const tree = {
+      // Particulars of this object are tied to getTreeStruct() below.
+      name: parent.label ?? "",
+      node_attrs: {
+        div: Number.isFinite(weight) ? weight : 0,
+      }
+    };
+
+    const childEdges = edgesByParent.get(parent);
+
+    if (childEdges?.size) {
+      tree.children = [];
+
+      for (const {child, weight} of childEdges) {
+        /* childEdges is reversed relative to the order given by the Newick input
+         * due to a side-effect of the parser's internals, so we unshift()
+         * instead of push() to restore the input order.
+         */
+        tree.children.unshift(
+          constructTree(child, weight)
+        );
+      }
+    }
+
+    return tree;
+  };
+
+  return constructTree(root, rootWeight);
+};
 
 const getTreeStruct = (nwk) => {
   const tree = parseNewick(nwk);
diff --git a/package-lock.json b/package-lock.json
index 2b87c6a..91e690e 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -11,7 +11,8 @@
       "license": "AGPL-3.0-only",
       "dependencies": {
         "auspice": "2.50.0",
-        "heroku-ssl-redirect": "0.0.4"
+        "heroku-ssl-redirect": "0.0.4",
+        "newick-js": "^1.2.1"
       },
       "engines": {
         "node": "16.x"
@@ -4781,6 +4782,11 @@
       "resolved": "https://registry.npmjs.org/neo-async/-/neo-async-2.6.2.tgz",
       "integrity": "sha512-Yd3UES5mWCSqR+qNT93S3UoYUkqAZ9lLg8a7g9rimsWmYGK8cVToA4/sF3RrshdyV3sAGMXVUmpMYOw+dLpOuw=="
     },
+    "node_modules/newick-js": {
+      "version": "1.2.1",
+      "resolved": "https://registry.npmjs.org/newick-js/-/newick-js-1.2.1.tgz",
+      "integrity": "sha512-qyZVNtlXmORBf2w9vg2S/5N5mQlU46xDFdPX7SEDZTeSElafNQUelNzR7HWSKcVOpjXiDnBqkvjd5RlEG7/SEA=="
+    },
     "node_modules/no-case": {
       "version": "3.0.4",
       "resolved": "https://registry.npmjs.org/no-case/-/no-case-3.0.4.tgz",
@@ -10609,6 +10615,11 @@
       "resolved": "https://registry.npmjs.org/neo-async/-/neo-async-2.6.2.tgz",
       "integrity": "sha512-Yd3UES5mWCSqR+qNT93S3UoYUkqAZ9lLg8a7g9rimsWmYGK8cVToA4/sF3RrshdyV3sAGMXVUmpMYOw+dLpOuw=="
     },
+    "newick-js": {
+      "version": "1.2.1",
+      "resolved": "https://registry.npmjs.org/newick-js/-/newick-js-1.2.1.tgz",
+      "integrity": "sha512-qyZVNtlXmORBf2w9vg2S/5N5mQlU46xDFdPX7SEDZTeSElafNQUelNzR7HWSKcVOpjXiDnBqkvjd5RlEG7/SEA=="
+    },
     "no-case": {
       "version": "3.0.4",
       "resolved": "https://registry.npmjs.org/no-case/-/no-case-3.0.4.tgz",
diff --git a/package.json b/package.json
index 60835a5..8295f8b 100644
--- a/package.json
+++ b/package.json
@@ -15,6 +15,7 @@
   },
   "dependencies": {
     "auspice": "2.50.0",
-    "heroku-ssl-redirect": "0.0.4"
+    "heroku-ssl-redirect": "0.0.4",
+    "newick-js": "^1.2.1"
   }
 }