{"action":"created","comment":{"url":"https://api.github.com/repos/biocore/qiita/pulls/comments/33883432","id":33883432,"diff_hunk":"@@ -941,20 +1002,21 @@ def get_lat_longs():\n     list of [float, float]\n         The latitude and longitude for each sample in the database\n     \"\"\"\n-    conn = SQLConnectionHandler()\n-    sql = \"\"\"SELECT DISTINCT table_name\n-             FROM information_schema.columns\n-             WHERE SUBSTR(table_name, 1, 7) = 'sample_'\n-                AND table_schema = 'qiita'\n-                AND column_name IN ('latitude', 'longitude');\"\"\"\n-    tables_gen = (t[0] for t in conn.execute_fetchall(sql))\n+    with TRN:\n+        sql = \"\"\"SELECT DISTINCT table_name\n+                 FROM information_schema.columns\n+                 WHERE SUBSTR(table_name, 1, 7) = 'sample_'\n+                    AND table_schema = 'qiita'\n+                    AND column_name IN ('latitude', 'longitude');\"\"\"\n+        TRN.add(sql)\n+        tables_gen = (t[0] for t in TRN.execute_fetchindex())","path":"qiita_db/util.py","position":808,"original_position":808,"commit_id":"2e04a1d7e3f7a52c3a3397cd3dfaf3b29a91db9e","original_commit_id":"2e04a1d7e3f7a52c3a3397cd3dfaf3b29a91db9e","user":{"login":"josenavas","id":2501478,"avatar_url":"https://avatars.githubusercontent.com/u/2501478?v=3","gravatar_id":"","url":"https://api.github.com/users/josenavas","html_url":"https://github.com/josenavas","followers_url":"https://api.github.com/users/josenavas/followers","following_url":"https://api.github.com/users/josenavas/following{/other_user}","gists_url":"https://api.github.com/users/josenavas/gists{/gist_id}","starred_url":"https://api.github.com/users/josenavas/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/josenavas/subscriptions","organizations_url":"https://api.github.com/users/josenavas/orgs","repos_url":"https://api.github.com/users/josenavas/repos","events_url":"https://api.github.com/users/josenavas/events{/privacy}","received_events_url":"https://api.github.com/users/josenavas/received_events","type":"User","site_admin":false},"body":"Uhmmm... not sure, we were already doing this before. What others think? I have mixed feelings.","created_at":"2015-07-04T00:25:58Z","updated_at":"2015-07-04T00:25:58Z","html_url":"https://github.com/biocore/qiita/pull/1324#discussion_r33883432","pull_request_url":"https://api.github.com/repos/biocore/qiita/pulls/1324","_links":{"self":{"href":"https://api.github.com/repos/biocore/qiita/pulls/comments/33883432"},"html":{"href":"https://github.com/biocore/qiita/pull/1324#discussion_r33883432"},"pull_request":{"href":"https://api.github.com/repos/biocore/qiita/pulls/1324"}}},"pull_request":{"url":"https://api.github.com/repos/biocore/qiita/pulls/1324","id":39142845,"html_url":"https://github.com/biocore/qiita/pull/1324","diff_url":"https://github.com/biocore/qiita/pull/1324.diff","patch_url":"https://github.com/biocore/qiita/pull/1324.patch","issue_url":"https://api.github.com/repos/biocore/qiita/issues/1324","number":1324,"state":"open","locked":false,"title":"URGENT: Fix util","user":{"login":"josenavas","id":2501478,"avatar_url":"https://avatars.githubusercontent.com/u/2501478?v=3","gravatar_id":"","url":"https://api.github.com/users/josenavas","html_url":"https://github.com/josenavas","followers_url":"https://api.github.com/users/josenavas/followers","following_url":"https://api.github.com/users/josenavas/following{/other_user}","gists_url":"https://api.github.com/users/josenavas/gists{/gist_id}","starred_url":"https://api.github.com/users/josenavas/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/josenavas/subscriptions","organizations_url":"https://api.github.com/users/josenavas/orgs","repos_url":"https://api.github.com/users/josenavas/repos","events_url":"https://api.github.com/users/josenavas/events{/privacy}","received_events_url":"https://api.github.com/users/josenavas/received_events","type":"User","site_admin":false},"body":"This PR fixes the util.py file to use transactions.\r\nSince some function signatures changed, I had to fix other parts of the code to make the tests to pass.\r\nAny future PR will be based on this one, hence that is why it is urgent (the other ones will be in parallel, but they'll rely on the changes in util.py).\r\n\r\nSome comments:\r\n - `purge_filepaths` is tricky. 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However, I'd like to hear what others think.\r\n - `get_preprocessed_params_tables` was missing tests and it was incorrect.\r\n - `find_repeated` was not used anywhere, I removed it as we can use skbio's `find_duplicates`","created_at":"2015-07-03T03:05:32Z","updated_at":"2015-07-04T00:25:58Z","closed_at":null,"merged_at":null,"merge_commit_sha":"9e289005bf3551c2c24521074565893b1540cf03","assignee":null,"milestone":{"url":"https://api.github.com/repos/biocore/qiita/milestones/8","html_url":"https://github.com/biocore/qiita/milestones/Alpha%200.2","labels_url":"https://api.github.com/repos/biocore/qiita/milestones/8/labels","id":1049807,"number":8,"title":"Alpha 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