{"action":"created","issue":{"url":"https://api.github.com/repos/ga4gh/server/issues/1129","repository_url":"https://api.github.com/repos/ga4gh/server","labels_url":"https://api.github.com/repos/ga4gh/server/issues/1129/labels{/name}","comments_url":"https://api.github.com/repos/ga4gh/server/issues/1129/comments","events_url":"https://api.github.com/repos/ga4gh/server/issues/1129/events","html_url":"https://github.com/ga4gh/server/issues/1129","id":150133920,"number":1129,"title":"File handles being opened for ReadGroupSet search","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":[],"state":"open","locked":false,"assignee":{"login":"dcolligan","id":7422120,"avatar_url":"https://avatars.githubusercontent.com/u/7422120?v=3","gravatar_id":"","url":"https://api.github.com/users/dcolligan","html_url":"https://github.com/dcolligan","followers_url":"https://api.github.com/users/dcolligan/followers","following_url":"https://api.github.com/users/dcolligan/following{/other_user}","gists_url":"https://api.github.com/users/dcolligan/gists{/gist_id}","starred_url":"https://api.github.com/users/dcolligan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dcolligan/subscriptions","organizations_url":"https://api.github.com/users/dcolligan/orgs","repos_url":"https://api.github.com/users/dcolligan/repos","events_url":"https://api.github.com/users/dcolligan/events{/privacy}","received_events_url":"https://api.github.com/users/dcolligan/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/ga4gh/server/milestones/10","html_url":"https://github.com/ga4gh/server/milestones/sql%20data%20Repo","labels_url":"https://api.github.com/repos/ga4gh/server/milestones/10/labels","id":1707626,"number":10,"title":"sql data Repo","description":"This milestone covers the work required to complete the merge of the new sql data repository for the server. It includes changes to the server and the repo manager.","creator":{"login":"kozbo","id":17557555,"avatar_url":"https://avatars.githubusercontent.com/u/17557555?v=3","gravatar_id":"","url":"https://api.github.com/users/kozbo","html_url":"https://github.com/kozbo","followers_url":"https://api.github.com/users/kozbo/followers","following_url":"https://api.github.com/users/kozbo/following{/other_user}","gists_url":"https://api.github.com/users/kozbo/gists{/gist_id}","starred_url":"https://api.github.com/users/kozbo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kozbo/subscriptions","organizations_url":"https://api.github.com/users/kozbo/orgs","repos_url":"https://api.github.com/users/kozbo/repos","events_url":"https://api.github.com/users/kozbo/events{/privacy}","received_events_url":"https://api.github.com/users/kozbo/received_events","type":"User","site_admin":false},"open_issues":18,"closed_issues":1,"state":"open","created_at":"2016-04-14T20:13:50Z","updated_at":"2016-04-21T19:21:54Z","due_on":null,"closed_at":null},"comments":2,"created_at":"2016-04-21T17:03:21Z","updated_at":"2016-04-25T13:01:39Z","closed_at":null,"body":"When we run a readgroupsets/search operation in the SQL repo we should not have to look at the underlying file handles (indeed, it's essential that we don't, is this operation will be cripplingly slow when we're opening connections to thousands of remote URLs.)\r\n\r\nWe need to track down why this is happening and eliminate the open call. All the data we need to satisfy a search readgroupsets call should be derived from the BAM file at import time and stored in the DB.\r\n\r\nTo reproduce: Put a print statement into ``openFile``, and run a search-readgroupsets"},"comment":{"url":"https://api.github.com/repos/ga4gh/server/issues/comments/214305715","html_url":"https://github.com/ga4gh/server/issues/1129#issuecomment-214305715","issue_url":"https://api.github.com/repos/ga4gh/server/issues/1129","id":214305715,"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":"2016-04-25T13:01:39Z","updated_at":"2016-04-25T13:01:39Z","body":"Excellent --- these go into the ``Stats`` object, right? If so, we should populate this at load time and store the JSON in the DB."}}