{"action":"created","issue":{"url":"https://api.github.com/repos/biocore/qiita/issues/1464","labels_url":"https://api.github.com/repos/biocore/qiita/issues/1464/labels{/name}","comments_url":"https://api.github.com/repos/biocore/qiita/issues/1464/comments","events_url":"https://api.github.com/repos/biocore/qiita/issues/1464/events","html_url":"https://github.com/biocore/qiita/pull/1464","id":104785461,"number":1464,"title":"Ebi step 3","user":{"login":"antgonza","id":2014559,"avatar_url":"https://avatars.githubusercontent.com/u/2014559?v=3","gravatar_id":"","url":"https://api.github.com/users/antgonza","html_url":"https://github.com/antgonza","followers_url":"https://api.github.com/users/antgonza/followers","following_url":"https://api.github.com/users/antgonza/following{/other_user}","gists_url":"https://api.github.com/users/antgonza/gists{/gist_id}","starred_url":"https://api.github.com/users/antgonza/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/antgonza/subscriptions","organizations_url":"https://api.github.com/users/antgonza/orgs","repos_url":"https://api.github.com/users/antgonza/repos","events_url":"https://api.github.com/users/antgonza/events{/privacy}","received_events_url":"https://api.github.com/users/antgonza/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-09-03T21:28:04Z","updated_at":"2015-09-06T00:56:29Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/biocore/qiita/pulls/1464","html_url":"https://github.com/biocore/qiita/pull/1464","diff_url":"https://github.com/biocore/qiita/pull/1464.diff","patch_url":"https://github.com/biocore/qiita/pull/1464.patch"},"body":"Sorry for the large amount of changes. Have no other idea of how to divide nicely, except making the DB changes in a different PR but that's small compared to the rest so decided to leave it here.\r\n\r\nGeneral comments:\r\n- Added scientific name (required for EBI submission) to the populate_test_db.sql so we can test \r\n- Remember that commands.submit_EBI is a work in progress and is just so we have an idea of how the calls will look\r\n- Removed iter_file_via_list_of_dicts, add_sample, add_sample_prep and add_samples_from_templates as these were required for from-file submission, which we will not support anymore as everything is being loaded from the DB\r\n- Removed _generate_library_descriptor as this was using/forcing to have some library design fields that are not required anymore\r\n- Removed all write_*_xml as now we simply call the write/generate functions\r\n- Removed write_all_xml_files cause this will defeat the idea of having networkx call/submit jobs. See point 2 of this list.\r\n- Replaced gzopen -> GzipFile cause this will allow us to set mtime (float to calculate gzip's timestamp) for testing. FYI: gzip incorporates the timestamp in the file so we need to know/define the timestamp for testing.\r\n- Removed all qiita_ware/test/test_data/* as now the files are generated and deleted on the fly.\r\n\r\nWho wants to review? "},"comment":{"url":"https://api.github.com/repos/biocore/qiita/issues/comments/138015822","html_url":"https://github.com/biocore/qiita/pull/1464#issuecomment-138015822","issue_url":"https://api.github.com/repos/biocore/qiita/issues/1464","id":138015822,"user":{"login":"mortonjt","id":4184797,"avatar_url":"https://avatars.githubusercontent.com/u/4184797?v=3","gravatar_id":"","url":"https://api.github.com/users/mortonjt","html_url":"https://github.com/mortonjt","followers_url":"https://api.github.com/users/mortonjt/followers","following_url":"https://api.github.com/users/mortonjt/following{/other_user}","gists_url":"https://api.github.com/users/mortonjt/gists{/gist_id}","starred_url":"https://api.github.com/users/mortonjt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mortonjt/subscriptions","organizations_url":"https://api.github.com/users/mortonjt/orgs","repos_url":"https://api.github.com/users/mortonjt/repos","events_url":"https://api.github.com/users/mortonjt/events{/privacy}","received_events_url":"https://api.github.com/users/mortonjt/received_events","type":"User","site_admin":false},"created_at":"2015-09-06T00:56:29Z","updated_at":"2015-09-06T00:56:29Z","body":"I did notice that in `ebi.py` is missing proper doc strings for `send_sequences()` and `send_xml()`.  Do you guys mind if I fix this in a future PR?"}}