Merge pull request #448 from gaurav/bug-with-double-single-quotes

Bug in escaping single quotes in Newick export

src/formats/newick.js

@@ -251,14 +251,15 @@ export function getNewick(annotator, root) {
  element_array.push(")");
  }
 
- if(n.data.name != 'root') {
- const node_label = n.data.name.replace("'", "''");
+ if(n.data.name !== 'root') {
+ const node_label = n.data.name.replaceAll("'", "''");
 
- // Escape the entire string if it contains any whitespace.
- if (/\w/.test(node_label)) {
+ // Surround the entire string with single quotes if it contains any
+ // non-alphanumeric characters.
+ if (/\W/.test(node_label)) {
  element_array.push("'" + node_label + "'");
  } else {
- element_array.push(n.data.name);
+ element_array.push(node_label);
  }
  }
  element_array.push(annotator(n));

test/formats-test.js

@@ -82,10 +82,10 @@ tape("Handle Newick strings with spaces", function(test) {
  * can read and write Newick strings correctly.
  */
 
- let nwk = "('Alpha beta', ('Alpha gamma', 'Delta''s epsilon'))";
+ let nwk = "('Alpha beta', ('Alpha gamma', ('Delta''s epsilon', 'Epsilon zeta ''alphonso''', 'test''s')))";
  let phylo = new phylotree.phylotree(nwk);
 
- let test_leaves = ['Alpha beta', 'Alpha gamma', "Delta's epsilon"];
+ let test_leaves = ['Alpha beta', 'Alpha gamma', "Delta's epsilon", "Epsilon zeta 'alphonso'", "test's"];
  test_leaves.forEach(function(leaf) {
  let node = phylo.getNodeByName(leaf);
  test.equal(node.data.name, leaf);
@@ -94,7 +94,7 @@ tape("Handle Newick strings with spaces", function(test) {
  // This would be identical to the original Newick string, but phylotree.js coerces
  // lengths to 1 (see https:/veg/phylotree.js/issues/440). So we expect
  // all lengths to be set to 1 on export.
- test.equal(phylo.getNewick(), "('Alpha beta':1,('Alpha gamma':1,'Delta''s epsilon':1):1):1;");
+ test.equal(phylo.getNewick(), "('Alpha beta':1,('Alpha gamma':1,('Delta''s epsilon':1,'Epsilon zeta ''alphonso''':1,'test''s':1):1):1):1;");
 
  test.end();
 });