Revert "Improve Newick parsing"

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.

auspice_client_customisation/parseNewick.js

@@ -1,46 +1,56 @@
-import { parse as _parseNewick } from "newick-js";
-
-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});
-  }
-
-  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 = [];
+/**
+ * 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.
+ */
 
-      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)
-        );
-      }
+/* 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)};
+        }
     }
-
-    return tree;
-  };
-
-  return constructTree(root, rootWeight);
+  }
+  return tree;
 };
 
+
 const getTreeStruct = (nwk) => {
   const tree = parseNewick(nwk);