{"action":"created","issue":{"url":"https://api.github.com/repos/OpenTreeOfLife/opentree/issues/636","labels_url":"https://api.github.com/repos/OpenTreeOfLife/opentree/issues/636/labels{/name}","comments_url":"https://api.github.com/repos/OpenTreeOfLife/opentree/issues/636/comments","events_url":"https://api.github.com/repos/OpenTreeOfLife/opentree/issues/636/events","html_url":"https://github.com/OpenTreeOfLife/opentree/issues/636","id":73335514,"number":636,"title":"taxonomy subtree web service newick result not parseable by Mesquite","user":{"login":"balhoff","id":210210,"avatar_url":"https://avatars.githubusercontent.com/u/210210?v=3","gravatar_id":"","url":"https://api.github.com/users/balhoff","html_url":"https://github.com/balhoff","followers_url":"https://api.github.com/users/balhoff/followers","following_url":"https://api.github.com/users/balhoff/following{/other_user}","gists_url":"https://api.github.com/users/balhoff/gists{/gist_id}","starred_url":"https://api.github.com/users/balhoff/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/balhoff/subscriptions","organizations_url":"https://api.github.com/users/balhoff/orgs","repos_url":"https://api.github.com/users/balhoff/repos","events_url":"https://api.github.com/users/balhoff/events{/privacy}","received_events_url":"https://api.github.com/users/balhoff/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2015-05-05T14:47:40Z","updated_at":"2015-05-05T16:07:02Z","closed_at":null,"body":"I am trying retrieve the taxonomy for Chordata using the web services. I used this command line:\r\n\r\n```bash\r\ncurl -X POST http://api.opentreeoflife.org/v2/taxonomy/subtree -H 'Content-type:application/json' -d '{\"ott_id\":125642, \"label_format\": \"name\"}' >chordata.json\r\n```\r\n\r\nThe newick format result uses single quotes around names that contain some special characters such as parentheses or quotes. However some of these names contain single quotes as characters, which are not escaped in any way (and I am not sure how they should be escaped). After removing the surrounding JSON content, I tried to parse the newick text using Mesquite and a few online tree viewers. None could successfully parse the tree.\r\n\r\nSo, it would be good if all name characters were escaped however it is supposed to be done in newick. But for my own uses I would actually prefer if the tree itself were a JSON structure rather than a newick string. It would be a lot easier to parse for many consumers and there are libraries that take care of all the necessary escaping."},"comment":{"url":"https://api.github.com/repos/OpenTreeOfLife/opentree/issues/comments/99127065","html_url":"https://github.com/OpenTreeOfLife/opentree/issues/636#issuecomment-99127065","issue_url":"https://api.github.com/repos/OpenTreeOfLife/opentree/issues/636","id":99127065,"user":{"login":"balhoff","id":210210,"avatar_url":"https://avatars.githubusercontent.com/u/210210?v=3","gravatar_id":"","url":"https://api.github.com/users/balhoff","html_url":"https://github.com/balhoff","followers_url":"https://api.github.com/users/balhoff/followers","following_url":"https://api.github.com/users/balhoff/following{/other_user}","gists_url":"https://api.github.com/users/balhoff/gists{/gist_id}","starred_url":"https://api.github.com/users/balhoff/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/balhoff/subscriptions","organizations_url":"https://api.github.com/users/balhoff/orgs","repos_url":"https://api.github.com/users/balhoff/repos","events_url":"https://api.github.com/users/balhoff/events{/privacy}","received_events_url":"https://api.github.com/users/balhoff/received_events","type":"User","site_admin":false},"created_at":"2015-05-05T16:07:02Z","updated_at":"2015-05-05T16:07:02Z","body":"I did a little test with 3 taxa in Mesquite and it handled the quoted quotes. So I will need to put some more time into figuring out where it is going wrong. I will comment here if I figure it out. I changed the issue title since I'm not sure that there is actually any problem with your output."}}