{"action":"created","comment":{"url":"https://api.github.com/repos/GMOD/Apollo/pulls/comments/61120728","id":61120728,"diff_hunk":"@@ -1078,6 +1081,12 @@ public void setTranslationEnd(Transcript transcript, int translationEnd) {\n             } else {\n                 gsolFeature.name = gsolFeature.uniqueName + \"-${type.get('name')}\"\n             }\n+            if (jsonFeature.has(FeatureStringEnum.SYMBOL.value)) {","path":"grails-app/services/org/bbop/apollo/FeatureService.groovy","position":57,"original_position":57,"commit_id":"d7e990f7e285098f5142384161271483e3fce91b","original_commit_id":"d7e990f7e285098f5142384161271483e3fce91b","user":{"login":"nathandunn","id":751274,"avatar_url":"https://avatars.githubusercontent.com/u/751274?v=3","gravatar_id":"","url":"https://api.github.com/users/nathandunn","html_url":"https://github.com/nathandunn","followers_url":"https://api.github.com/users/nathandunn/followers","following_url":"https://api.github.com/users/nathandunn/following{/other_user}","gists_url":"https://api.github.com/users/nathandunn/gists{/gist_id}","starred_url":"https://api.github.com/users/nathandunn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nathandunn/subscriptions","organizations_url":"https://api.github.com/users/nathandunn/orgs","repos_url":"https://api.github.com/users/nathandunn/repos","events_url":"https://api.github.com/users/nathandunn/events{/privacy}","received_events_url":"https://api.github.com/users/nathandunn/received_events","type":"User","site_admin":false},"body":"thanks for cathing this","created_at":"2016-04-26T16:44:03Z","updated_at":"2016-04-26T16:44:03Z","html_url":"https://github.com/GMOD/Apollo/pull/1002#discussion_r61120728","pull_request_url":"https://api.github.com/repos/GMOD/Apollo/pulls/1002","_links":{"self":{"href":"https://api.github.com/repos/GMOD/Apollo/pulls/comments/61120728"},"html":{"href":"https://github.com/GMOD/Apollo/pull/1002#discussion_r61120728"},"pull_request":{"href":"https://api.github.com/repos/GMOD/Apollo/pulls/1002"}}},"pull_request":{"url":"https://api.github.com/repos/GMOD/Apollo/pulls/1002","id":67270138,"html_url":"https://github.com/GMOD/Apollo/pull/1002","diff_url":"https://github.com/GMOD/Apollo/pull/1002.diff","patch_url":"https://github.com/GMOD/Apollo/pull/1002.patch","issue_url":"https://api.github.com/repos/GMOD/Apollo/issues/1002","number":1002,"state":"open","locked":false,"title":"Change annotation type (ready for review)","user":{"login":"deepakunni3","id":4530272,"avatar_url":"https://avatars.githubusercontent.com/u/4530272?v=3","gravatar_id":"","url":"https://api.github.com/users/deepakunni3","html_url":"https://github.com/deepakunni3","followers_url":"https://api.github.com/users/deepakunni3/followers","following_url":"https://api.github.com/users/deepakunni3/following{/other_user}","gists_url":"https://api.github.com/users/deepakunni3/gists{/gist_id}","starred_url":"https://api.github.com/users/deepakunni3/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/deepakunni3/subscriptions","organizations_url":"https://api.github.com/users/deepakunni3/orgs","repos_url":"https://api.github.com/users/deepakunni3/repos","events_url":"https://api.github.com/users/deepakunni3/events{/privacy}","received_events_url":"https://api.github.com/users/deepakunni3/received_events","type":"User","site_admin":false},"body":"This PR implements the ability to change a feature's type, once its added to the user created annotations track.\r\n\r\nFollowing are some of the issues observed while working on implementing this feature:\r\n* Bug where CDS was not being deleted in `addFeature()` if the transcript was a non-coding RNA. (fixed via 293b371).\r\n* User created annotations track displays `TypeError: Cannot read property 'className' of undefined` on UNDO operation on a pseudogene (#1001, fixed as part of this PR)\r\n* `convertJSONToFeature()` adds comments as a feature property of class `FeatureProperty` when it should be added as a feature property of class `Comment`. (fixed as part of this PR).\r\n* `OWNER` in `FeatureStringEnum.java` currently returns 'Owner' when it should return 'owner'. In many places to overcome this problem, `FeatureStringEnum.OWNER.value.toLowerCase()` is being used. It would be more optimal to change at the source, i.e. in `FeatureStringEnum.java`.\r\n* UNDO and REDO operation calls `addTranscript()` for non coding RNAs when it should actually be calling `addFeature()` (fixed as part of this PR).\r\n* `addFeature()` requires an input JSON object that must have a parent gene for non coding RNA features. That means when storing the JSON object for history tracking, the JSON object should include the parent gene, but this isn't the case right now. So far this went unnoticed because addFeature() was being called only for `repeat_region` and `transposable_element`. (Fixed as part of this PR).\r\n* Different assumptions made when converting a Feature to JSONObject (`FeatureService:convertFeatureToJSON`) and when converting a JSONObject back to a Feature (`FeatureService::convertJSONToFeature`). This leads to improper handling of feature properties, as noted in #1003 (fixed as part of this PR).","created_at":"2016-04-20T22:39:13Z","updated_at":"2016-04-26T16:44:03Z","closed_at":null,"merged_at":null,"merge_commit_sha":"d34e39c222f3088b223f8c1772141e56f170e91b","assignee":null,"milestone":{"url":"https://api.github.com/repos/GMOD/Apollo/milestones/23","html_url":"https://github.com/GMOD/Apollo/milestones/2.0.3","labels_url":"https://api.github.com/repos/GMOD/Apollo/milestones/23/labels","id":1299980,"number":23,"title":"2.0.3","description":"Bugfixes and Chado re-implementation.\r\n\r\n- Closed issued: https://github.com/GMOD/Apollo/issues?q=is%3Apr+milestone%3A2.0.3+is%3Aclosed\r\n- Closed pull requests: https://github.com/GMOD/Apollo/pulls?q=is%3Apr+milestone%3A2.0.3+is%3Aclosed","creator":{"login":"nathandunn","id":751274,"avatar_url":"https://avatars.githubusercontent.com/u/751274?v=3","gravatar_id":"","url":"https://api.github.com/users/nathandunn","html_url":"https://github.com/nathandunn","followers_url":"https://api.github.com/users/nathandunn/followers","following_url":"https://api.github.com/users/nathandunn/following{/other_user}","gists_url":"https://api.github.com/users/nathandunn/gists{/gist_id}","starred_url":"https://api.github.com/users/nathandunn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nathandunn/subscriptions","organizations_url":"https://api.github.com/users/nathandunn/orgs","repos_url":"https://api.github.com/users/nathandunn/repos","events_url":"https://api.github.com/users/nathandunn/events{/privacy}","received_events_url":"https://api.github.com/users/nathandunn/received_events","type":"User","site_admin":false},"open_issues":24,"closed_issues":78,"state":"open","created_at":"2015-09-10T19:58:08Z","updated_at":"2016-04-26T16:36:31Z","due_on":null,"closed_at":null},"commits_url":"https://api.github.com/repos/GMOD/Apollo/pulls/1002/commits","review_comments_url":"https://api.github.com/repos/GMOD/Apollo/pulls/1002/comments","review_comment_url":"https://api.github.com/repos/GMOD/Apollo/pulls/comments{/number}","comments_url":"https://api.github.com/repos/GMOD/Apollo/issues/1002/comments","statuses_url":"https://api.github.com/repos/GMOD/Apollo/statuses/d7e990f7e285098f5142384161271483e3fce91b","head":{"label":"deepakunni3:change_annotation_type","ref":"change_annotation_type","sha":"d7e990f7e285098f5142384161271483e3fce91b","user":{"login":"deepakunni3","id":4530272,"avatar_url":"https://avatars.githubusercontent.com/u/4530272?v=3","gravatar_id":"","url":"https://api.github.com/users/deepakunni3","html_url":"https://github.com/deepakunni3","followers_url":"https://api.github.com/users/deepakunni3/followers","following_url":"https://api.github.com/users/deepakunni3/following{/other_user}","gists_url":"https://api.github.com/users/deepakunni3/gists{/gist_id}","starred_url":"https://api.github.com/users/deepakunni3/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/deepakunni3/subscriptions","organizations_url":"https://api.github.com/users/deepakunni3/orgs","repos_url":"https://api.github.com/users/deepakunni3/repos","events_url":"https://api.github.com/users/deepakunni3/events{/privacy}","received_events_url":"https://api.github.com/users/deepakunni3/received_events","type":"User","site_admin":false},"repo":{"id":48384268,"name":"Apollo","full_name":"deepakunni3/Apollo","owner":{"login":"deepakunni3","id":4530272,"avatar_url":"https://avatars.githubusercontent.com/u/4530272?v=3","gravatar_id":"","url":"https://api.github.com/users/deepakunni3","html_url":"https://github.com/deepakunni3","followers_url":"https://api.github.com/users/deepakunni3/followers","following_url":"https://api.github.com/users/deepakunni3/following{/other_user}","gists_url":"https://api.github.com/users/deepakunni3/gists{/gist_id}","starred_url":"https://api.github.com/users/deepakunni3/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/deepakunni3/subscriptions","organizations_url":"https://api.github.com/users/deepakunni3/orgs","repos_url":"https://api.github.com/users/deepakunni3/repos","events_url":"https://api.github.com/users/deepakunni3/events{/privacy}","received_events_url":"https://api.github.com/users/deepakunni3/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/deepakunni3/Apollo","description":"Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin","fork":true,"url":"https://api.github.com/repos/deepakunni3/Apollo","forks_url":"https://api.github.com/repos/deepakunni3/Apollo/forks","keys_url":"https://api.github.com/repos/deepakunni3/Apollo/keys{/key_id}","collaborators_url":"https://api.github.com/repos/deepakunni3/Apollo/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/deepakunni3/Apollo/teams","hooks_url":"https://api.github.com/repos/deepakunni3/Apollo/hooks","issue_events_url":"https://api.github.com/repos/deepakunni3/Apollo/issues/events{/number}","events_url":"https://api.github.com/repos/deepakunni3/Apollo/events","assignees_url":"https://api.github.com/repos/deepakunni3/Apollo/assignees{/user}","branches_url":"https://api.github.com/repos/deepakunni3/Apollo/branches{/branch}","tags_url":"https://api.github.com/repos/deepakunni3/Apollo/tags","blobs_url":"https://api.github.com/repos/deepakunni3/Apollo/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/deepakunni3/Apollo/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/deepakunni3/Apollo/git/refs{/sha}","trees_url":"https://api.github.com/repos/deepakunni3/Apollo/git/trees{/sha}","statuses_url":"https://api.github.com/repos/deepakunni3/Apollo/statuses/{sha}","languages_url":"https://api.github.com/repos/deepakunni3/Apollo/languages","stargazers_url":"https://api.github.com/repos/deepakunni3/Apollo/stargazers","contributors_url":"https://api.github.com/repos/deepakunni3/Apollo/contributors","subscribers_url":"https://api.github.com/repos/deepakunni3/Apollo/subscribers","subscription_url":"https://api.github.com/repos/deepakunni3/Apollo/subscription","commits_url":"https://api.github.com/repos/deepakunni3/Apollo/commits{/sha}","git_commits_url":"https://api.github.com/repos/deepakunni3/Apollo/git/commits{/sha}","comments_url":"https://api.github.com/repos/deepakunni3/Apollo/comments{/number}","issue_comment_url":"https://api.github.com/repos/deepakunni3/Apollo/issues/comments{/number}","contents_url":"https://api.github.com/repos/deepakunni3/Apollo/contents/{+path}","compare_url":"https://api.github.com/repos/deepakunni3/Apollo/compare/{base}...{head}","merges_url":"https://api.github.com/repos/deepakunni3/Apollo/merges","archive_url":"https://api.github.com/repos/deepakunni3/Apollo/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/deepakunni3/Apollo/downloads","issues_url":"https://api.github.com/repos/deepakunni3/Apollo/issues{/number}","pulls_url":"https://api.github.com/repos/deepakunni3/Apollo/pulls{/number}","milestones_url":"https://api.github.com/repos/deepakunni3/Apollo/milestones{/number}","notifications_url":"https://api.github.com/repos/deepakunni3/Apollo/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/deepakunni3/Apollo/labels{/name}","releases_url":"https://api.github.com/repos/deepakunni3/Apollo/releases{/id}","deployments_url":"https://api.github.com/repos/deepakunni3/Apollo/deployments","created_at":"2015-12-21T17:12:23Z","updated_at":"2016-03-02T18:50:24Z","pushed_at":"2016-04-26T16:33:23Z","git_url":"git://github.com/deepakunni3/Apollo.git","ssh_url":"git@github.com:deepakunni3/Apollo.git","clone_url":"https://github.com/deepakunni3/Apollo.git","svn_url":"https://github.com/deepakunni3/Apollo","homepage":"http://genomearchitect.org","size":153293,"stargazers_count":0,"watchers_count":0,"language":"Groovy","has_issues":false,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":0,"mirror_url":null,"open_issues_count":0,"forks":0,"open_issues":0,"watchers":0,"default_branch":"master"}},"base":{"label":"GMOD:master","ref":"master","sha":"615929e423e70925e371a273c2d148555a1d3d2d","user":{"login":"GMOD","id":342482,"avatar_url":"https://avatars.githubusercontent.com/u/342482?v=3","gravatar_id":"","url":"https://api.github.com/users/GMOD","html_url":"https://github.com/GMOD","followers_url":"https://api.github.com/users/GMOD/followers","following_url":"https://api.github.com/users/GMOD/following{/other_user}","gists_url":"https://api.github.com/users/GMOD/gists{/gist_id}","starred_url":"https://api.github.com/users/GMOD/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/GMOD/subscriptions","organizations_url":"https://api.github.com/users/GMOD/orgs","repos_url":"https://api.github.com/users/GMOD/repos","events_url":"https://api.github.com/users/GMOD/events{/privacy}","received_events_url":"https://api.github.com/users/GMOD/received_events","type":"Organization","site_admin":false},"repo":{"id":13471446,"name":"Apollo","full_name":"GMOD/Apollo","owner":{"login":"GMOD","id":342482,"avatar_url":"https://avatars.githubusercontent.com/u/342482?v=3","gravatar_id":"","url":"https://api.github.com/users/GMOD","html_url":"https://github.com/GMOD","followers_url":"https://api.github.com/users/GMOD/followers","following_url":"https://api.github.com/users/GMOD/following{/other_user}","gists_url":"https://api.github.com/users/GMOD/gists{/gist_id}","starred_url":"https://api.github.com/users/GMOD/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/GMOD/subscriptions","organizations_url":"https://api.github.com/users/GMOD/orgs","repos_url":"https://api.github.com/users/GMOD/repos","events_url":"https://api.github.com/users/GMOD/events{/privacy}","received_events_url":"https://api.github.com/users/GMOD/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/GMOD/Apollo","description":"Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin","fork":false,"url":"https://api.github.com/repos/GMOD/Apollo","forks_url":"https://api.github.com/repos/GMOD/Apollo/forks","keys_url":"https://api.github.com/repos/GMOD/Apollo/keys{/key_id}","collaborators_url":"https://api.github.com/repos/GMOD/Apollo/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/GMOD/Apollo/teams","hooks_url":"https://api.github.com/repos/GMOD/Apollo/hooks","issue_events_url":"https://api.github.com/repos/GMOD/Apollo/issues/events{/number}","events_url":"https://api.github.com/repos/GMOD/Apollo/events","assignees_url":"https://api.github.com/repos/GMOD/Apollo/assignees{/user}","branches_url":"https://api.github.com/repos/GMOD/Apollo/branches{/branch}","tags_url":"https://api.github.com/repos/GMOD/Apollo/tags","blobs_url":"https://api.github.com/repos/GMOD/Apollo/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/GMOD/Apollo/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/GMOD/Apollo/git/refs{/sha}","trees_url":"https://api.github.com/repos/GMOD/Apollo/git/trees{/sha}","statuses_url":"https://api.github.com/repos/GMOD/Apollo/statuses/{sha}","languages_url":"https://api.github.com/repos/GMOD/Apollo/languages","stargazers_url":"https://api.github.com/repos/GMOD/Apollo/stargazers","contributors_url":"https://api.github.com/repos/GMOD/Apollo/contributors","subscribers_url":"https://api.github.com/repos/GMOD/Apollo/subscribers","subscription_url":"https://api.github.com/repos/GMOD/Apollo/subscription","commits_url":"https://api.github.com/repos/GMOD/Apollo/commits{/sha}","git_commits_url":"https://api.github.com/repos/GMOD/Apollo/git/commits{/sha}","comments_url":"https://api.github.com/repos/GMOD/Apollo/comments{/number}","issue_comment_url":"https://api.github.com/repos/GMOD/Apollo/issues/comments{/number}","contents_url":"https://api.github.com/repos/GMOD/Apollo/contents/{+path}","compare_url":"https://api.github.com/repos/GMOD/Apollo/compare/{base}...{head}","merges_url":"https://api.github.com/repos/GMOD/Apollo/merges","archive_url":"https://api.github.com/repos/GMOD/Apollo/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/GMOD/Apollo/downloads","issues_url":"https://api.github.com/repos/GMOD/Apollo/issues{/number}","pulls_url":"https://api.github.com/repos/GMOD/Apollo/pulls{/number}","milestones_url":"https://api.github.com/repos/GMOD/Apollo/milestones{/number}","notifications_url":"https://api.github.com/repos/GMOD/Apollo/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/GMOD/Apollo/labels{/name}","releases_url":"https://api.github.com/repos/GMOD/Apollo/releases{/id}","deployments_url":"https://api.github.com/repos/GMOD/Apollo/deployments","created_at":"2013-10-10T13:05:28Z","updated_at":"2016-03-30T15:18:13Z","pushed_at":"2016-04-26T16:33:24Z","git_url":"git://github.com/GMOD/Apollo.git","ssh_url":"git@github.com:GMOD/Apollo.git","clone_url":"https://github.com/GMOD/Apollo.git","svn_url":"https://github.com/GMOD/Apollo","homepage":"http://genomearchitect.org","size":155403,"stargazers_count":19,"watchers_count":19,"language":"Groovy","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":25,"mirror_url":null,"open_issues_count":246,"forks":25,"open_issues":246,"watchers":19,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/GMOD/Apollo/pulls/1002"},"html":{"href":"https://github.com/GMOD/Apollo/pull/1002"},"issue":{"href":"https://api.github.com/repos/GMOD/Apollo/issues/1002"},"comments":{"href":"https://api.github.com/repos/GMOD/Apollo/issues/1002/comments"},"review_comments":{"href":"https://api.github.com/repos/GMOD/Apollo/pulls/1002/comments"},"review_comment":{"href":"https://api.github.com/repos/GMOD/Apollo/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/GMOD/Apollo/pulls/1002/commits"},"statuses":{"href":"https://api.github.com/repos/GMOD/Apollo/statuses/d7e990f7e285098f5142384161271483e3fce91b"}}}}