{"action":"closed","number":227,"pull_request":{"url":"https://api.github.com/repos/nextstrain/augur/pulls/227","id":220481407,"node_id":"MDExOlB1bGxSZXF1ZXN0MjIwNDgxNDA3","html_url":"https://github.com/nextstrain/augur/pull/227","diff_url":"https://github.com/nextstrain/augur/pull/227.diff","patch_url":"https://github.com/nextstrain/augur/pull/227.patch","issue_url":"https://api.github.com/repos/nextstrain/augur/issues/227","number":227,"state":"closed","locked":false,"title":"Fix bugs in conversion of prepared JSONs to FASTA and metadata","user":{"login":"huddlej","id":85372,"node_id":"MDQ6VXNlcjg1Mzcy","avatar_url":"https://avatars3.githubusercontent.com/u/85372?v=4","gravatar_id":"","url":"https://api.github.com/users/huddlej","html_url":"https://github.com/huddlej","followers_url":"https://api.github.com/users/huddlej/followers","following_url":"https://api.github.com/users/huddlej/following{/other_user}","gists_url":"https://api.github.com/users/huddlej/gists{/gist_id}","starred_url":"https://api.github.com/users/huddlej/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/huddlej/subscriptions","organizations_url":"https://api.github.com/users/huddlej/orgs","repos_url":"https://api.github.com/users/huddlej/repos","events_url":"https://api.github.com/users/huddlej/events{/privacy}","received_events_url":"https://api.github.com/users/huddlej/received_events","type":"User","site_admin":false},"body":"Specifically, omit reference sequences when the prepared JSON explicitly states that they should not be included and rename any column named \"num_date\" to prevent conflicts with TreeTime in modular augur.\r\n\r\nAlthough this PR inspired issue #215 , it does not attempt to resolve that issue.\r\nIn this case, we can preemptively rename the conflicting column from flu's prepared JSON.\r\nWe will need additional code in `augur export` to throw an error when an unexpected conflict is discovered.","created_at":"2018-10-04T18:53:29Z","updated_at":"2018-10-04T19:11:43Z","closed_at":"2018-10-04T19:11:43Z","merged_at":"2018-10-04T19:11:43Z","merge_commit_sha":"fdc2ad96ee5805e6ad8b0f8387ef091e803e5697","assignee":null,"assignees":[],"requested_reviewers":[],"requested_teams":[],"labels":[],"milestone":null,"commits_url":"https://api.github.com/repos/nextstrain/augur/pulls/227/commits","review_comments_url":"https://api.github.com/repos/nextstrain/augur/pulls/227/comments","review_comment_url":"https://api.github.com/repos/nextstrain/augur/pulls/comments{/number}","comments_url":"https://api.github.com/repos/nextstrain/augur/issues/227/comments","statuses_url":"https://api.github.com/repos/nextstrain/augur/statuses/21f234aa20a1315f2106218a402ab230e2d1a1a9","head":{"label":"nextstrain:fix-prepared-json-to-fasta","ref":"fix-prepared-json-to-fasta","sha":"21f234aa20a1315f2106218a402ab230e2d1a1a9","user":{"login":"nextstrain","id":22159334,"node_id":"MDEyOk9yZ2FuaXphdGlvbjIyMTU5MzM0","avatar_url":"https://avatars3.githubusercontent.com/u/22159334?v=4","gravatar_id":"","url":"https://api.github.com/users/nextstrain","html_url":"https://github.com/nextstrain","followers_url":"https://api.github.com/users/nextstrain/followers","following_url":"https://api.github.com/users/nextstrain/following{/other_user}","gists_url":"https://api.github.com/users/nextstrain/gists{/gist_id}","starred_url":"https://api.github.com/users/nextstrain/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nextstrain/subscriptions","organizations_url":"https://api.github.com/users/nextstrain/orgs","repos_url":"https://api.github.com/users/nextstrain/repos","events_url":"https://api.github.com/users/nextstrain/events{/privacy}","received_events_url":"https://api.github.com/users/nextstrain/received_events","type":"Organization","site_admin":false},"repo":{"id":56883329,"node_id":"MDEwOlJlcG9zaXRvcnk1Njg4MzMyOQ==","name":"augur","full_name":"nextstrain/augur","private":false,"owner":{"login":"nextstrain","id":22159334,"node_id":"MDEyOk9yZ2FuaXphdGlvbjIyMTU5MzM0","avatar_url":"https://avatars3.githubusercontent.com/u/22159334?v=4","gravatar_id":"","url":"https://api.github.com/users/nextstrain","html_url":"https://github.com/nextstrain","followers_url":"https://api.github.com/users/nextstrain/followers","following_url":"https://api.github.com/users/nextstrain/following{/other_user}","gists_url":"https://api.github.com/users/nextstrain/gists{/gist_id}","starred_url":"https://api.github.com/users/nextstrain/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nextstrain/subscriptions","organizations_url":"https://api.github.com/users/nextstrain/orgs","repos_url":"https://api.github.com/users/nextstrain/repos","events_url":"https://api.github.com/users/nextstrain/events{/privacy}","received_events_url":"https://api.github.com/users/nextstrain/received_events","type":"Organization","site_admin":false},"html_url":"https://github.com/nextstrain/augur","description":"Pipeline components for real-time virus analysis","fork":false,"url":"https://api.github.com/repos/nextstrain/augur","forks_url":"https://api.github.com/repos/nextstrain/augur/forks","keys_url":"https://api.github.com/repos/nextstrain/augur/keys{/key_id}","collaborators_url":"https://api.github.com/repos/nextstrain/augur/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/nextstrain/augur/teams","hooks_url":"https://api.github.com/repos/nextstrain/augur/hooks","issue_events_url":"https://api.github.com/repos/nextstrain/augur/issues/events{/number}","events_url":"https://api.github.com/repos/nextstrain/augur/events","assignees_url":"https://api.github.com/repos/nextstrain/augur/assignees{/user}","branches_url":"https://api.github.com/repos/nextstrain/augur/branches{/branch}","tags_url":"https://api.github.com/repos/nextstrain/augur/tags","blobs_url":"https://api.github.com/repos/nextstrain/augur/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/nextstrain/augur/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/nextstrain/augur/git/refs{/sha}","trees_url":"https://api.github.com/repos/nextstrain/augur/git/trees{/sha}","statuses_url":"https://api.github.com/repos/nextstrain/augur/statuses/{sha}","languages_url":"https://api.github.com/repos/nextstrain/augur/languages","stargazers_url":"https://api.github.com/repos/nextstrain/augur/stargazers","contributors_url":"https://api.github.com/repos/nextstrain/augur/contributors","subscribers_url":"https://api.github.com/repos/nextstrain/augur/subscribers","subscription_url":"https://api.github.com/repos/nextstrain/augur/subscription","commits_url":"https://api.github.com/repos/nextstrain/augur/commits{/sha}","git_commits_url":"https://api.github.com/repos/nextstrain/augur/git/commits{/sha}","comments_url":"https://api.github.com/repos/nextstrain/augur/comments{/number}","issue_comment_url":"https://api.github.com/repos/nextstrain/augur/issues/comments{/number}","contents_url":"https://api.github.com/repos/nextstrain/augur/contents/{+path}","compare_url":"https://api.github.com/repos/nextstrain/augur/compare/{base}...{head}","merges_url":"https://api.github.com/repos/nextstrain/augur/merges","archive_url":"https://api.github.com/repos/nextstrain/augur/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/nextstrain/augur/downloads","issues_url":"https://api.github.com/repos/nextstrain/augur/issues{/number}","pulls_url":"https://api.github.com/repos/nextstrain/augur/pulls{/number}","milestones_url":"https://api.github.com/repos/nextstrain/augur/milestones{/number}","notifications_url":"https://api.github.com/repos/nextstrain/augur/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/nextstrain/augur/labels{/name}","releases_url":"https://api.github.com/repos/nextstrain/augur/releases{/id}","deployments_url":"https://api.github.com/repos/nextstrain/augur/deployments","created_at":"2016-04-22T20:28:36Z","updated_at":"2018-10-04T19:11:02Z","pushed_at":"2018-10-04T19:11:43Z","git_url":"git://github.com/nextstrain/augur.git","ssh_url":"git@github.com:nextstrain/augur.git","clone_url":"https://github.com/nextstrain/augur.git","svn_url":"https://github.com/nextstrain/augur","homepage":"","size":12575,"stargazers_count":25,"watchers_count":25,"language":"Python","has_issues":true,"has_projects":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":10,"mirror_url":null,"archived":false,"open_issues_count":28,"license":{"key":"agpl-3.0","name":"GNU Affero General Public License v3.0","spdx_id":"AGPL-3.0","url":"https://api.github.com/licenses/agpl-3.0","node_id":"MDc6TGljZW5zZTE="},"forks":10,"open_issues":28,"watchers":25,"default_branch":"master"}},"base":{"label":"nextstrain:master","ref":"master","sha":"85614f6cc280f27e6492a15bf06b4011833f6da4","user":{"login":"nextstrain","id":22159334,"node_id":"MDEyOk9yZ2FuaXphdGlvbjIyMTU5MzM0","avatar_url":"https://avatars3.githubusercontent.com/u/22159334?v=4","gravatar_id":"","url":"https://api.github.com/users/nextstrain","html_url":"https://github.com/nextstrain","followers_url":"https://api.github.com/users/nextstrain/followers","following_url":"https://api.github.com/users/nextstrain/following{/other_user}","gists_url":"https://api.github.com/users/nextstrain/gists{/gist_id}","starred_url":"https://api.github.com/users/nextstrain/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nextstrain/subscriptions","organizations_url":"https://api.github.com/users/nextstrain/orgs","repos_url":"https://api.github.com/users/nextstrain/repos","events_url":"https://api.github.com/users/nextstrain/events{/privacy}","received_events_url":"https://api.github.com/users/nextstrain/received_events","type":"Organization","site_admin":false},"repo":{"id":56883329,"node_id":"MDEwOlJlcG9zaXRvcnk1Njg4MzMyOQ==","name":"augur","full_name":"nextstrain/augur","private":false,"owner":{"login":"nextstrain","id":22159334,"node_id":"MDEyOk9yZ2FuaXphdGlvbjIyMTU5MzM0","avatar_url":"https://avatars3.githubusercontent.com/u/22159334?v=4","gravatar_id":"","url":"https://api.github.com/users/nextstrain","html_url":"https://github.com/nextstrain","followers_url":"https://api.github.com/users/nextstrain/followers","following_url":"https://api.github.com/users/nextstrain/following{/other_user}","gists_url":"https://api.github.com/users/nextstrain/gists{/gist_id}","starred_url":"https://api.github.com/users/nextstrain/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nextstrain/subscriptions","organizations_url":"https://api.github.com/users/nextstrain/orgs","repos_url":"https://api.github.com/users/nextstrain/repos","events_url":"https://api.github.com/users/nextstrain/events{/privacy}","received_events_url":"https://api.github.com/users/nextstrain/received_events","type":"Organization","site_admin":false},"html_url":"https://github.com/nextstrain/augur","description":"Pipeline components for real-time virus analysis","fork":false,"url":"https://api.github.com/repos/nextstrain/augur","forks_url":"https://api.github.com/repos/nextstrain/augur/forks","keys_url":"https://api.github.com/repos/nextstrain/augur/keys{/key_id}","collaborators_url":"https://api.github.com/repos/nextstrain/augur/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/nextstrain/augur/teams","hooks_url":"https://api.github.com/repos/nextstrain/augur/hooks","issue_events_url":"https://api.github.com/repos/nextstrain/augur/issues/events{/number}","events_url":"https://api.github.com/repos/nextstrain/augur/events","assignees_url":"https://api.github.com/repos/nextstrain/augur/assignees{/user}","branches_url":"https://api.github.com/repos/nextstrain/augur/branches{/branch}","tags_url":"https://api.github.com/repos/nextstrain/augur/tags","blobs_url":"https://api.github.com/repos/nextstrain/augur/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/nextstrain/augur/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/nextstrain/augur/git/refs{/sha}","trees_url":"https://api.github.com/repos/nextstrain/augur/git/trees{/sha}","statuses_url":"https://api.github.com/repos/nextstrain/augur/statuses/{sha}","languages_url":"https://api.github.com/repos/nextstrain/augur/languages","stargazers_url":"https://api.github.com/repos/nextstrain/augur/stargazers","contributors_url":"https://api.github.com/repos/nextstrain/augur/contributors","subscribers_url":"https://api.github.com/repos/nextstrain/augur/subscribers","subscription_url":"https://api.github.com/repos/nextstrain/augur/subscription","commits_url":"https://api.github.com/repos/nextstrain/augur/commits{/sha}","git_commits_url":"https://api.github.com/repos/nextstrain/augur/git/commits{/sha}","comments_url":"https://api.github.com/repos/nextstrain/augur/comments{/number}","issue_comment_url":"https://api.github.com/repos/nextstrain/augur/issues/comments{/number}","contents_url":"https://api.github.com/repos/nextstrain/augur/contents/{+path}","compare_url":"https://api.github.com/repos/nextstrain/augur/compare/{base}...{head}","merges_url":"https://api.github.com/repos/nextstrain/augur/merges","archive_url":"https://api.github.com/repos/nextstrain/augur/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/nextstrain/augur/downloads","issues_url":"https://api.github.com/repos/nextstrain/augur/issues{/number}","pulls_url":"https://api.github.com/repos/nextstrain/augur/pulls{/number}","milestones_url":"https://api.github.com/repos/nextstrain/augur/milestones{/number}","notifications_url":"https://api.github.com/repos/nextstrain/augur/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/nextstrain/augur/labels{/name}","releases_url":"https://api.github.com/repos/nextstrain/augur/releases{/id}","deployments_url":"https://api.github.com/repos/nextstrain/augur/deployments","created_at":"2016-04-22T20:28:36Z","updated_at":"2018-10-04T19:11:02Z","pushed_at":"2018-10-04T19:11:43Z","git_url":"git://github.com/nextstrain/augur.git","ssh_url":"git@github.com:nextstrain/augur.git","clone_url":"https://github.com/nextstrain/augur.git","svn_url":"https://github.com/nextstrain/augur","homepage":"","size":12575,"stargazers_count":25,"watchers_count":25,"language":"Python","has_issues":true,"has_projects":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":10,"mirror_url":null,"archived":false,"open_issues_count":28,"license":{"key":"agpl-3.0","name":"GNU Affero General Public License v3.0","spdx_id":"AGPL-3.0","url":"https://api.github.com/licenses/agpl-3.0","node_id":"MDc6TGljZW5zZTE="},"forks":10,"open_issues":28,"watchers":25,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/nextstrain/augur/pulls/227"},"html":{"href":"https://github.com/nextstrain/augur/pull/227"},"issue":{"href":"https://api.github.com/repos/nextstrain/augur/issues/227"},"comments":{"href":"https://api.github.com/repos/nextstrain/augur/issues/227/comments"},"review_comments":{"href":"https://api.github.com/repos/nextstrain/augur/pulls/227/comments"},"review_comment":{"href":"https://api.github.com/repos/nextstrain/augur/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/nextstrain/augur/pulls/227/commits"},"statuses":{"href":"https://api.github.com/repos/nextstrain/augur/statuses/21f234aa20a1315f2106218a402ab230e2d1a1a9"}},"author_association":"CONTRIBUTOR","merged":true,"mergeable":null,"rebaseable":null,"mergeable_state":"unknown","merged_by":{"login":"huddlej","id":85372,"node_id":"MDQ6VXNlcjg1Mzcy","avatar_url":"https://avatars3.githubusercontent.com/u/85372?v=4","gravatar_id":"","url":"https://api.github.com/users/huddlej","html_url":"https://github.com/huddlej","followers_url":"https://api.github.com/users/huddlej/followers","following_url":"https://api.github.com/users/huddlej/following{/other_user}","gists_url":"https://api.github.com/users/huddlej/gists{/gist_id}","starred_url":"https://api.github.com/users/huddlej/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/huddlej/subscriptions","organizations_url":"https://api.github.com/users/huddlej/orgs","repos_url":"https://api.github.com/users/huddlej/repos","events_url":"https://api.github.com/users/huddlej/events{/privacy}","received_events_url":"https://api.github.com/users/huddlej/received_events","type":"User","site_admin":false},"comments":0,"review_comments":0,"maintainer_can_modify":false,"commits":1,"additions":2,"deletions":5,"changed_files":1}}
{"actor":{"display_login":"huddlej"}}