{"action":"created","issue":{"url":"https://api.github.com/repos/hammerlab/cycledash/issues/527","labels_url":"https://api.github.com/repos/hammerlab/cycledash/issues/527/labels{/name}","comments_url":"https://api.github.com/repos/hammerlab/cycledash/issues/527/comments","events_url":"https://api.github.com/repos/hammerlab/cycledash/issues/527/events","html_url":"https://github.com/hammerlab/cycledash/issues/527","id":60440318,"number":527,"title":"gene_annotator fails with \"has no attribute 'db'\"","user":{"login":"arahuja","id":455755,"avatar_url":"https://avatars.githubusercontent.com/u/455755?v=3","gravatar_id":"","url":"https://api.github.com/users/arahuja","html_url":"https://github.com/arahuja","followers_url":"https://api.github.com/users/arahuja/followers","following_url":"https://api.github.com/users/arahuja/following{/other_user}","gists_url":"https://api.github.com/users/arahuja/gists{/gist_id}","starred_url":"https://api.github.com/users/arahuja/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/arahuja/subscriptions","organizations_url":"https://api.github.com/users/arahuja/orgs","repos_url":"https://api.github.com/users/arahuja/repos","events_url":"https://api.github.com/users/arahuja/events{/privacy}","received_events_url":"https://api.github.com/users/arahuja/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-03-10T02:09:51Z","updated_at":"2015-10-12T15:15:40Z","closed_at":"2015-10-12T15:15:40Z","body":"Maybe this already known, but I didn't see any issue on it:\r\n\r\n```\r\nTraceback (most recent call last):\r\n  File \"/home/cycledash/cycledash/venv/lib/python2.7/site-packages/celery/app/trace.py\", line 240, in trace_task\r\n    R = retval = fun(*args, **kwargs)\r\n  File \"/home/cycledash/cycledash/venv/lib/python2.7/site-packages/celery/app/trace.py\", line 437, in __protected_call__\r\n    return self.run(*args, **kwargs)\r\n  File \"/home/cycledash/cycledash/workers/gene_annotator.py\", line 44, in annotate\r\n    connection, metadata, vcf_id, ensembl_release_num=75)\r\n  File \"/home/cycledash/cycledash/workers/gene_annotator.py\", line 101, in get_gene_names\r\n    str(contig), int(position))\r\n  File \"/home/cycledash/cycledash/venv/lib/python2.7/site-packages/pyensembl/ensembl_release.py\", line 165, in gene_names_at_locus\r\n    strand=strand)\r\n  File \"/home/cycledash/cycledash/venv/lib/python2.7/site-packages/pyensembl/database.py\", line 226, in distinct_column_values_at_locus\r\n    sorted=True)\r\n  File \"/home/cycledash/cycledash/venv/lib/python2.7/site-packages/pyensembl/database.py\", line 150, in column_values_at_locus\r\n    if not self.column_exists(column_name):\r\n  File \"/home/cycledash/cycledash/venv/lib/python2.7/site-packages/pyensembl/database.py\", line 120, in column_exists\r\n    return column_name in self.columns()\r\n  File \"/home/cycledash/cycledash/venv/lib/python2.7/site-packages/pyensembl/database.py\", line 116, in columns\r\n    table_info = self.connection.execute(sql).fetchall()\r\n  File \"/home/cycledash/cycledash/venv/lib/python2.7/site-packages/pyensembl/database.py\", line 111, in connection\r\n    self._connection = self._connect_or_create_database()\r\n  File \"/home/cycledash/cycledash/venv/lib/python2.7/site-packages/pyensembl/database.py\", line 99, in _connect_or_create_database\r\n    if datacache.db.db_table_exists(db, 'ensembl'):\r\nAttributeError: 'module' object has no attribute 'db'\r\n```"},"comment":{"url":"https://api.github.com/repos/hammerlab/cycledash/issues/comments/147429959","html_url":"https://github.com/hammerlab/cycledash/issues/527#issuecomment-147429959","issue_url":"https://api.github.com/repos/hammerlab/cycledash/issues/527","id":147429959,"user":{"login":"ihodes","id":167803,"avatar_url":"https://avatars.githubusercontent.com/u/167803?v=3","gravatar_id":"","url":"https://api.github.com/users/ihodes","html_url":"https://github.com/ihodes","followers_url":"https://api.github.com/users/ihodes/followers","following_url":"https://api.github.com/users/ihodes/following{/other_user}","gists_url":"https://api.github.com/users/ihodes/gists{/gist_id}","starred_url":"https://api.github.com/users/ihodes/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ihodes/subscriptions","organizations_url":"https://api.github.com/users/ihodes/orgs","repos_url":"https://api.github.com/users/ihodes/repos","events_url":"https://api.github.com/users/ihodes/events{/privacy}","received_events_url":"https://api.github.com/users/ihodes/received_events","type":"User","site_admin":false},"created_at":"2015-10-12T15:15:40Z","updated_at":"2015-10-12T15:15:40Z","body":"Fixed a while back"}}