{"action":"created","issue":{"url":"https://api.github.com/repos/ga4gh/server/issues/1079","repository_url":"https://api.github.com/repos/ga4gh/server","labels_url":"https://api.github.com/repos/ga4gh/server/issues/1079/labels{/name}","comments_url":"https://api.github.com/repos/ga4gh/server/issues/1079/comments","events_url":"https://api.github.com/repos/ga4gh/server/issues/1079/events","html_url":"https://github.com/ga4gh/server/pull/1079","id":147455349,"number":1079,"title":"Sql repo initial work","user":{"login":"jeromekelleher","id":2664569,"avatar_url":"https://avatars.githubusercontent.com/u/2664569?v=3","gravatar_id":"","url":"https://api.github.com/users/jeromekelleher","html_url":"https://github.com/jeromekelleher","followers_url":"https://api.github.com/users/jeromekelleher/followers","following_url":"https://api.github.com/users/jeromekelleher/following{/other_user}","gists_url":"https://api.github.com/users/jeromekelleher/gists{/gist_id}","starred_url":"https://api.github.com/users/jeromekelleher/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jeromekelleher/subscriptions","organizations_url":"https://api.github.com/users/jeromekelleher/orgs","repos_url":"https://api.github.com/users/jeromekelleher/repos","events_url":"https://api.github.com/users/jeromekelleher/events{/privacy}","received_events_url":"https://api.github.com/users/jeromekelleher/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/ga4gh/server/labels/in%20progress","name":"in progress","color":"ededed"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-04-11T14:55:36Z","updated_at":"2016-04-11T19:41:03Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/ga4gh/server/pulls/1079","html_url":"https://github.com/ga4gh/server/pull/1079","diff_url":"https://github.com/ga4gh/server/pull/1079.diff","patch_url":"https://github.com/ga4gh/server/pull/1079.patch"},"body":"This is a proposal for changing the DataRepository from a file system derived structure to an explicit SQLite database, containing tables for all container objects. See #1069 for an overview of the design and initial comments and feedback. This PR is against the ``sql_repo`` topic branch so that work can proceed on it until it's ready to merge into master.\r\n\r\nI plan on adding a few further updates on the repo manager side, and will summarise the changes in a comment once this is done. In the mean time, any review would be much appreciated."},"comment":{"url":"https://api.github.com/repos/ga4gh/server/issues/comments/208521539","html_url":"https://github.com/ga4gh/server/pull/1079#issuecomment-208521539","issue_url":"https://api.github.com/repos/ga4gh/server/issues/1079","id":208521539,"user":{"login":"jeromekelleher","id":2664569,"avatar_url":"https://avatars.githubusercontent.com/u/2664569?v=3","gravatar_id":"","url":"https://api.github.com/users/jeromekelleher","html_url":"https://github.com/jeromekelleher","followers_url":"https://api.github.com/users/jeromekelleher/followers","following_url":"https://api.github.com/users/jeromekelleher/following{/other_user}","gists_url":"https://api.github.com/users/jeromekelleher/gists{/gist_id}","starred_url":"https://api.github.com/users/jeromekelleher/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jeromekelleher/subscriptions","organizations_url":"https://api.github.com/users/jeromekelleher/orgs","repos_url":"https://api.github.com/users/jeromekelleher/repos","events_url":"https://api.github.com/users/jeromekelleher/events{/privacy}","received_events_url":"https://api.github.com/users/jeromekelleher/received_events","type":"User","site_admin":false},"created_at":"2016-04-11T19:41:03Z","updated_at":"2016-04-11T19:41:03Z","body":"Status:\r\n\r\n1. Variant annotations work needs to be completed and the tests re-enabled.\r\n2. Repo manager CLI needs to be built out and tested following pattern for add-dataset.\r\n3. Test data needs to be converted into a SQL repo so that we can fully remove the FileSystemRepository and FileSystemDataset.\r\n\r\nI propose making these changes after merging this initial PR to the topic branch, and tackling these issues as follow up PRs. Then, once we're happy that the code in the topic branch we can merge it into master. Does this sound like a sensible plan?\r\n\r\nIn any case, this is ready for review (with the caveats above). Please weigh in @macieksmuga, @david4096 , @dcolligan, @diekhans, @kozbo or anyone else that's interested!"}}