allow newick files to be dragged & dropped

auspice.us/client-customisations/handleDroppedFiles.js

@@ -1,5 +1,5 @@
 import { createStateFromQueryOrJSONs } from "@auspice/actions/recomputeReduxState";
-
+import newickToAuspiceJson from "./newickToAuspiceJson";
 
 export const handleDroppedFiles = (dispatch, files) => {
   const file = files[0];
@@ -19,7 +19,11 @@ export const handleDroppedFiles = (dispatch, files) => {
     if (file.type === "application/json") {
       jsonData = JSON.parse(fileReader.result);
     } else if (file.name.endsWith(".new") || file.name.endsWith(".newick") || file.name.endsWith(".nwk")) {
-      console.log("attempting to parse a newick tree");
+      try {
+        jsonData = newickToAuspiceJson(file.name, fileReader.result);
+      } catch (err) {
+        return errorCB(err);
+      }
     } else {
       return errorCB("Unknown filetype");
     }

auspice.us/client-customisations/newickToAuspiceJson.js

@@ -0,0 +1,95 @@
+/**
+ * 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.
+ */
+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.strain = token;
+        } else if (x === ':') {
+          tree.div = parseFloat(token);
+        }
+    }
+  }
+  return tree;
+};
+
+const getTreeStruct = (nwk) => {
+  const tree = parseNewick(nwk);
+
+  /* ensure every node has a strain name */
+  let count = 10000;
+  const addNodeName = (node) => {
+    if (!node.strain) {
+      node.strain=`NODE${count}`;
+      count++;
+    }
+    if (node.children) {
+      node.children.forEach((child) => addNodeName(child));
+    }
+  };
+  addNodeName(tree);
+
+  /* div should be cumulative! */
+  const cumulativeDivs = (node, soFar=0) => {
+    node.div += soFar;
+    if (node.children) {
+      node.children.forEach((child) => cumulativeDivs(child, node.div));
+    }
+  };
+  cumulativeDivs(tree);
+
+
+  return tree;
+};
+
+/**
+ * Convert a newick string to an auspice (v2) JSON
+ * @param {string} nwk newick string
+ * @returns {object} auspice JSON
+ */
+const newickToAuspiceJson = (name, nwk) => {
+  const json = {
+    title: name,
+    tree: getTreeStruct(nwk),
+    panels: ["tree"],
+    version: "2.0"
+  };
+  return json;
+};
+
+
+export default newickToAuspiceJson;