Merge pull request #503 from theosanderson/fix-nexus

fix nexus comments implementation

taxonium_component/src/utils/nexusToNewick.js

@@ -26,37 +26,15 @@ function nexusToNewick(nexusString) {
  // get the Newick string from the tree block
  const newickString = treeBlock[0].match(/\((.*?)\).+;/gims)[0];
 
- let nodeProperties = {};
-
- // extract properties, which are indicated by [&key=value] or [&key={value1,value2,...}]
- newickString.replace(
- /\[&?(.*?)\]/gims,
- (match, contents, offset, inputString) => {
- let nodeId = inputString.slice(0, offset).match(/[^,\(\):]+$/g)[0];
- // use a regular expression to split on commas not inside curly brackets
- let properties = contents.split(/,(?![^{]*})/g);
- let propertyDict = {};
- for (let prop of properties) {
- let [key, value] = prop.split("=");
- propertyDict["meta_" + key] = value;
- }
- nodeProperties[nodeId] = propertyDict;
- }
- );
-
- // remove comments, which are indicated by [...]
-
- const newick = newickString.replace(/\[(.*?)\]/gims, "");
-
  // translate the taxon labels in the Newick string
- const translatedNewickString = newick.replace(
+ const translatedNewickString = newickString.replace(
  /([^:\,\(\)]+)/gims,
  (match) => {
  return translations[match] || match;
  }
  );
 
- return { newick: translatedNewickString, nodeProperties };
+ return { newick: translatedNewickString };
 }
 
 export default nexusToNewick;

taxonium_component/src/utils/processNewick.js

@@ -11,10 +11,6 @@ import reduceMaxOrMin from "./reduceMaxOrMin";
 import nexusToNewick from "../utils/nexusToNewick.js";
 const emptyList = [];
 
-function removeSquareBracketedComments(str) {
- return str.replace(/\[[^\]]*\]/g, "");
-}
-
 async function do_fetch(url, sendStatusMessage, whatIsBeingDownloaded) {
  if (!sendStatusMessage) {
  sendStatusMessage = () => {};
@@ -82,13 +78,29 @@ function fetch_or_extract(file_obj, sendStatusMessage, whatIsBeingDownloaded) {
  }
 }
 
+function parseNewickKeyValue(newickKVString, obj_to_set) {
+ // Regular expression that matches key=value pairs, accounting for commas within {}
+ const regex = /(&?\w+)=({[^}]*}|[^,]*)/g;
+
+ const result = [];
+ let match;
+
+ // Use the RegExp.exec() method to find all matches in the string
+ while ((match = regex.exec(newickKVString)) !== null) {
+ // Remove the '&' character if it's present at the start of the key
+ const key = match[1].startsWith("&") ? match[1].slice(1) : match[1];
+ // Push the key-value pair to the result array
+ obj_to_set["meta_" + key] = match[2];
+ }
+}
+
 async function cleanup(tree) {
  tree.node.forEach((node, i) => {
  node.node_id = i;
  });
 
  tree.node = tree.node.map((node, i) => {
- return {
+ const to_return = {
  name: node.name.replace(/'/g, ""),
  parent_id: node.parent ? node.parent.node_id : node.node_id,
  x_dist: node.x,
@@ -98,6 +110,12 @@ async function cleanup(tree) {
  is_tip: node.child.length === 0,
  node_id: node.node_id,
  };
+ // if node.meta is not empty, parse it.
+ // We need to parse things of the form "&name=blabla,mutations={T694A:1.0,C29870A:1.0},Ns={1-3,4-17,18-20,21-26,686-693,22029-22033,28248-28253,28271-28271}"
+ if (node.meta) {
+ parseNewickKeyValue(node.meta, to_return);
+ }
+ return to_return;
  });
 
  const scale_y = 2000;
@@ -117,30 +135,31 @@ async function cleanup(tree) {
 
 export async function processNewick(data, sendStatusMessage) {
  let the_data;
- let extra_metadata;
 
  the_data = await fetch_or_extract(data, sendStatusMessage, "tree");
 
  console.log("data.filetype", data.filetype);
  if (data.filetype == "nexus") {
  const result = nexusToNewick(the_data);
  the_data = result.newick;
- extra_metadata = result.nodeProperties;
  }
 
  sendStatusMessage({
  message: "Parsing Newick file",
  });
 
- // remove all square-bracketed comments from the string
- the_data = removeSquareBracketedComments(the_data);
+ // if starts with a "[", then trim to after the first "]"
+ if (the_data[0] === "[") {
+ the_data = the_data.slice(the_data.indexOf("]") + 1);
+ }
 
  // remove newlines from the string
 
  the_data = the_data.replaceAll("\n", "");
  the_data = the_data.replaceAll("\r", "");
 
  const tree = kn_parse(the_data);
+ console.log("tree", tree);
 
  function assignNumTips(node) {
  if (node.child.length === 0) {
@@ -189,6 +208,7 @@ export async function processNewick(data, sendStatusMessage) {
  });
 
  cleanup(tree);
+ console.log("tree", tree);
 
  const overallMaxX = reduceMaxOrMin(tree.node, (x) => x.x_dist, "max");
  const overallMinX = reduceMaxOrMin(tree.node, (x) => x.x_dist, "min");
@@ -208,7 +228,6 @@ export async function processNewick(data, sendStatusMessage) {
  rootMutations: [],
  rootId: 0,
  overwrite_config: { num_tips: total_tips, from_newick: true },
- extra_metadata,
  };
 
  return output;
@@ -299,37 +318,41 @@ export async function processNewickAndMetadata(data, sendStatusMessage) {
  headers.slice(1).map((x) => ["meta_" + x, ""])
  );
 
- if (tree.extra_metadata) {
- // loop over the extra metadata dict to find all the (sub)keys
- const all_extra_keys = new Set();
- Object.values(tree.extra_metadata).forEach((node_extra) => {
- Object.keys(node_extra).forEach((key) => {
- all_extra_keys.add(key);
- });
- });
- // add any misssing keys to blanks
- all_extra_keys.forEach((key) => {
- if (!blanks[key]) {
- blanks[key] = "";
- }
+ const all_keys = new Set();
+ tree.nodes.forEach((node) => {
+ // get all the keys that start with "meta_"
+ const meta_keys = Object.keys(node).filter((x) => x.startsWith("meta_"));
+ // add them to the set
+ meta_keys.forEach((key) => {
+ all_keys.add(key);
  });
- }
+ });
+ console.log("all_keys", all_keys);
+ // update the blanks object to include all the keys
+ all_keys.forEach((key) => {
+ if (!blanks[key]) {
+ blanks[key] = "";
+ }
+ });
+ console.log("blanks", blanks);
+
+ const blanksList = Object.entries(blanks);
 
  sendStatusMessage({
  message: "Assigning metadata to nodes",
  });
  tree.nodes.forEach((node) => {
  const this_metadata = metadata.get(node.name);
- Object.assign(node, blanks);
+ // add blanks for any properties not currently set
+ blanksList.forEach(([key, value]) => {
+ if (!node[key]) {
+ node[key] = value;
+ }
+ });
+
  if (this_metadata) {
  Object.assign(node, this_metadata);
  }
- if (tree.extra_metadata) {
- const node_extra = tree.extra_metadata[node.name];
- if (node_extra) {
- Object.assign(node, node_extra);
- }
- }
  });
 
  return tree;