{"action":"created","issue":{"url":"https://api.github.com/repos/0u812/sbnw/issues/38","labels_url":"https://api.github.com/repos/0u812/sbnw/issues/38/labels{/name}","comments_url":"https://api.github.com/repos/0u812/sbnw/issues/38/comments","events_url":"https://api.github.com/repos/0u812/sbnw/issues/38/events","html_url":"https://github.com/0u812/sbnw/issues/38","id":112704090,"number":38,"title":"Bug in load SBML with layout?","user":{"login":"hsauro","id":1054990,"avatar_url":"https://avatars.githubusercontent.com/u/1054990?v=3","gravatar_id":"","url":"https://api.github.com/users/hsauro","html_url":"https://github.com/hsauro","followers_url":"https://api.github.com/users/hsauro/followers","following_url":"https://api.github.com/users/hsauro/following{/other_user}","gists_url":"https://api.github.com/users/hsauro/gists{/gist_id}","starred_url":"https://api.github.com/users/hsauro/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hsauro/subscriptions","organizations_url":"https://api.github.com/users/hsauro/orgs","repos_url":"https://api.github.com/users/hsauro/repos","events_url":"https://api.github.com/users/hsauro/events{/privacy}","received_events_url":"https://api.github.com/users/hsauro/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/0u812/sbnw/labels/bug","name":"bug","color":"fc2929"}],"state":"closed","locked":false,"assignee":{"login":"0u812","id":7402146,"avatar_url":"https://avatars.githubusercontent.com/u/7402146?v=3","gravatar_id":"","url":"https://api.github.com/users/0u812","html_url":"https://github.com/0u812","followers_url":"https://api.github.com/users/0u812/followers","following_url":"https://api.github.com/users/0u812/following{/other_user}","gists_url":"https://api.github.com/users/0u812/gists{/gist_id}","starred_url":"https://api.github.com/users/0u812/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/0u812/subscriptions","organizations_url":"https://api.github.com/users/0u812/orgs","repos_url":"https://api.github.com/users/0u812/repos","events_url":"https://api.github.com/users/0u812/events{/privacy}","received_events_url":"https://api.github.com/users/0u812/received_events","type":"User","site_admin":false},"milestone":null,"comments":1,"created_at":"2015-10-22T00:15:07Z","updated_at":"2015-10-22T17:43:48Z","closed_at":"2015-10-22T17:43:48Z","body":"I created this SBML model with layout information using version 0.4.6 of the library. However when I load it back in I get a the following errors:\r\n\r\nFailed to parse SBML\r\nError 0: Missing a required XML attribute. The species attribute 'compartment' is required.\r\nError 1: Missing a required XML attribute. The species attribute 'compartment' is required.\r\nError 2: Missing a required XML attribute. The species attribute 'compartment' is required.\r\nError 3: Missing a required XML attribute. The species attribute 'compartment' is required.\r\nError 4: Missing a required XML attribute. The species attribute 'compartment' is required.\r\nError 5: Missing a required XML attribute. The species attribute 'compartment' is required.\r\nError 6: Missing a required XML attribute. The species attribute 'compartment' is required.\r\n\r\nLooks like the species tag doesn't have a compartment. I checked the sbml validator and the file is an invalid sbml file. The original file fro which I generated it does have species with a compartment. The SBML generated by sbnw doesn't include a compartment which I think it should have.\r\n\r\nModel file attached to issue. Chance the extension of the file to xml.\r\n\r\n[_testLayoutWithLayout .txt](https://github.com/0u812/sbnw/files/18149/_testLayoutWithLayout.txt)\r\n"},"comment":{"url":"https://api.github.com/repos/0u812/sbnw/issues/comments/150302555","html_url":"https://github.com/0u812/sbnw/issues/38#issuecomment-150302555","issue_url":"https://api.github.com/repos/0u812/sbnw/issues/38","id":150302555,"user":{"login":"0u812","id":7402146,"avatar_url":"https://avatars.githubusercontent.com/u/7402146?v=3","gravatar_id":"","url":"https://api.github.com/users/0u812","html_url":"https://github.com/0u812","followers_url":"https://api.github.com/users/0u812/followers","following_url":"https://api.github.com/users/0u812/following{/other_user}","gists_url":"https://api.github.com/users/0u812/gists{/gist_id}","starred_url":"https://api.github.com/users/0u812/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/0u812/subscriptions","organizations_url":"https://api.github.com/users/0u812/orgs","repos_url":"https://api.github.com/users/0u812/repos","events_url":"https://api.github.com/users/0u812/events{/privacy}","received_events_url":"https://api.github.com/users/0u812/received_events","type":"User","site_admin":false},"created_at":"2015-10-22T17:43:47Z","updated_at":"2015-10-22T17:43:47Z","body":"This issue was moved to sys-bio/sbnw#17"}}