{"action":"created","issue":{"url":"https://api.github.com/repos/kbase/data_api/issues/128","labels_url":"https://api.github.com/repos/kbase/data_api/issues/128/labels{/name}","comments_url":"https://api.github.com/repos/kbase/data_api/issues/128/comments","events_url":"https://api.github.com/repos/kbase/data_api/issues/128/events","html_url":"https://github.com/kbase/data_api/pull/128","id":120382947,"number":128,"title":"GenomeAnnotationAPI bug fixes","user":{"login":"mlhenderson","id":2807085,"avatar_url":"https://avatars.githubusercontent.com/u/2807085?v=3","gravatar_id":"","url":"https://api.github.com/users/mlhenderson","html_url":"https://github.com/mlhenderson","followers_url":"https://api.github.com/users/mlhenderson/followers","following_url":"https://api.github.com/users/mlhenderson/following{/other_user}","gists_url":"https://api.github.com/users/mlhenderson/gists{/gist_id}","starred_url":"https://api.github.com/users/mlhenderson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mlhenderson/subscriptions","organizations_url":"https://api.github.com/users/mlhenderson/orgs","repos_url":"https://api.github.com/users/mlhenderson/repos","events_url":"https://api.github.com/users/mlhenderson/events{/privacy}","received_events_url":"https://api.github.com/users/mlhenderson/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2015-12-04T11:27:53Z","updated_at":"2015-12-05T17:59:12Z","closed_at":"2015-12-05T17:59:12Z","pull_request":{"url":"https://api.github.com/repos/kbase/data_api/pulls/128","html_url":"https://github.com/kbase/data_api/pull/128","diff_url":"https://github.com/kbase/data_api/pull/128.diff","patch_url":"https://github.com/kbase/data_api/pull/128.patch"},"body":"Fixed a number of issues with GA methods found, including get_feature_ids() with different parameter permutations, inconsistent handling of genome region specifiers, etc.\r\n\r\nSome minor changes to wsfile.py and cache.py to set detailed logging info to debug.\r\n\r\nCurrently this command reveals at least one issue that is not addressed in this PR:\r\npython bin/genome_annotation_client_driver.py --ref \"OriginalReferenceGenomes/kb|g.166819\"\r\n\r\nTraceback (most recent call last):\r\n  File \"bin/genome_annotation_client_driver.py\", line 171, in <module>\r\n    test_client() # XXX: choose one with top-level args\r\n  File \"bin/genome_annotation_client_driver.py\", line 77, in test_client\r\n    print feature_ids[\"by_function\"].items()[0]\r\nIndexError: list index out of range\r\n\r\nSome debugging info:\r\n\r\nlen(features) == 1 ?\r\nfunction: PF00581 ; KOG1530 , filter: protein\r\n\r\nThis yields no results due to the filter not appearing in the single feature.  However there are more than 7,000 CDS, mRNA, gene features each, many of which contain \"protein\" in the function description.  This works fine for the new data type on disk, so I suspect something buggy in fetching the data from the old type on disk in either wsfile or cache."},"comment":{"url":"https://api.github.com/repos/kbase/data_api/issues/comments/162231094","html_url":"https://github.com/kbase/data_api/pull/128#issuecomment-162231094","issue_url":"https://api.github.com/repos/kbase/data_api/issues/128","id":162231094,"user":{"login":"dangunter","id":420923,"avatar_url":"https://avatars.githubusercontent.com/u/420923?v=3","gravatar_id":"","url":"https://api.github.com/users/dangunter","html_url":"https://github.com/dangunter","followers_url":"https://api.github.com/users/dangunter/followers","following_url":"https://api.github.com/users/dangunter/following{/other_user}","gists_url":"https://api.github.com/users/dangunter/gists{/gist_id}","starred_url":"https://api.github.com/users/dangunter/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dangunter/subscriptions","organizations_url":"https://api.github.com/users/dangunter/orgs","repos_url":"https://api.github.com/users/dangunter/repos","events_url":"https://api.github.com/users/dangunter/events{/privacy}","received_events_url":"https://api.github.com/users/dangunter/received_events","type":"User","site_admin":false},"created_at":"2015-12-05T17:59:12Z","updated_at":"2015-12-05T17:59:12Z","body":"I merged all the changes from this form into my fork and created a new PR, https://github.com/kbase/data_api/pull/131\r\n\r\nI am going to close this PR and approve in the new one"}}