{"action":"created","issue":{"url":"https://api.github.com/repos/OpenTreeOfLife/opentree/issues/788","labels_url":"https://api.github.com/repos/OpenTreeOfLife/opentree/issues/788/labels{/name}","comments_url":"https://api.github.com/repos/OpenTreeOfLife/opentree/issues/788/comments","events_url":"https://api.github.com/repos/OpenTreeOfLife/opentree/issues/788/events","html_url":"https://github.com/OpenTreeOfLife/opentree/issues/788","id":110369303,"number":788,"title":"Failed upload prevents future uploads","user":{"login":"bomeara","id":1612612,"avatar_url":"https://avatars.githubusercontent.com/u/1612612?v=3","gravatar_id":"","url":"https://api.github.com/users/bomeara","html_url":"https://github.com/bomeara","followers_url":"https://api.github.com/users/bomeara/followers","following_url":"https://api.github.com/users/bomeara/following{/other_user}","gists_url":"https://api.github.com/users/bomeara/gists{/gist_id}","starred_url":"https://api.github.com/users/bomeara/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bomeara/subscriptions","organizations_url":"https://api.github.com/users/bomeara/orgs","repos_url":"https://api.github.com/users/bomeara/repos","events_url":"https://api.github.com/users/bomeara/events{/privacy}","received_events_url":"https://api.github.com/users/bomeara/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-10-08T04:02:04Z","updated_at":"2015-10-10T20:23:09Z","closed_at":null,"body":"I have finally gotten the Hedges et al 2015 time tree arranged for OpenTree: TRNSed the names, removed duplicate names or names failing TNRS, deleted any taxa with internal quotes or hyphens (OpenTree won't read them), removed any taxa with parentheses (represent uncertainty about placement), put all names in single quotes. Uploaded the tree: success! but 14% name match. It's fine; from past discussions, I know I have to change the taxonomy to All life (twice, due to a bug). However, clicking on the tree tab, the site froze: wasn't responsive to any other clicks. After a few minutes, tried reloading the page: no change. Tried again and got (in Safari) an option with warning to force reload the page. Did so -- my new tree isn't there. Tried to re-upload the tree, got ```An error occured, please reload the page``` (with reload a link). Clicked on reload, get ```The requested tree ('tree2') was not found. It has probably been deleted from this study.```. I don't mind re-uploading the tree, but it's problematic that its ghost somehow prevents this. I've tried the re-upload multiple times, and tried in both Safari (the original browser) and Chrome, with the same result. I imagine something has to be changed in the repo to delete the reference to the failed upload tree, but this is outside my current skill set (and, I hope, therefore outside my permissions).\r\n\r\nhttps://tree.opentreeoflife.org/curator/study/edit/ot_409 \r\n\r\nI've uploaded the nexus file at [NoAmbiguity.nex](https://tree.opentreeoflife.org/curator/supporting_files/download/supporting_files.doc.8e3e5f35527fa0b9.4e6f416d626967756974792e6e6578.nex)\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/OpenTreeOfLife/opentree/issues/comments/147122696","html_url":"https://github.com/OpenTreeOfLife/opentree/issues/788#issuecomment-147122696","issue_url":"https://api.github.com/repos/OpenTreeOfLife/opentree/issues/788","id":147122696,"user":{"login":"jimallman","id":446375,"avatar_url":"https://avatars.githubusercontent.com/u/446375?v=3","gravatar_id":"","url":"https://api.github.com/users/jimallman","html_url":"https://github.com/jimallman","followers_url":"https://api.github.com/users/jimallman/followers","following_url":"https://api.github.com/users/jimallman/following{/other_user}","gists_url":"https://api.github.com/users/jimallman/gists{/gist_id}","starred_url":"https://api.github.com/users/jimallman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jimallman/subscriptions","organizations_url":"https://api.github.com/users/jimallman/orgs","repos_url":"https://api.github.com/users/jimallman/repos","events_url":"https://api.github.com/users/jimallman/events{/privacy}","received_events_url":"https://api.github.com/users/jimallman/received_events","type":"User","site_admin":false},"created_at":"2015-10-10T20:23:09Z","updated_at":"2015-10-10T20:23:09Z","body":"I'm unable to reproduce these symptoms. That is, I can import this tree (albeit slowly) on **devtree**, but then I can't reload the study in the curation app.\r\n\r\nThere are two steps when adding a tree. The **file upload and conversion to nexson** took 2 minutes, which seems reasonable given the file size (2 MB with 48,000 nodes) and the constrained resources on our dev servers.\r\n\r\nThe second request, to **merge and consolidate OTUs** in the study, took even longer, 2.6 minutes. I've saved the results in [this unrelated study](https://devtree.opentreeoflife.org/curator/study/edit/tt_35?tab=trees). But it doesn't load back into the curation app, because the server times out after five minutes(!) trying to send the study data. In fact, I can't load other (known-good) studies either, or the curation home page. Hm, I think it's broken the devapi server... Will investigate further."}}