{"action":"created","issue":{"url":"https://api.github.com/repos/minoTour/linminUP/issues/7","repository_url":"https://api.github.com/repos/minoTour/linminUP","labels_url":"https://api.github.com/repos/minoTour/linminUP/issues/7/labels{/name}","comments_url":"https://api.github.com/repos/minoTour/linminUP/issues/7/comments","events_url":"https://api.github.com/repos/minoTour/linminUP/issues/7/events","html_url":"https://github.com/minoTour/linminUP/pull/7","id":174793402,"number":7,"title":"Cope with h5py error","user":{"login":"duncanparkes","id":56265,"avatar_url":"https://avatars.githubusercontent.com/u/56265?v=3","gravatar_id":"","url":"https://api.github.com/users/duncanparkes","html_url":"https://github.com/duncanparkes","followers_url":"https://api.github.com/users/duncanparkes/followers","following_url":"https://api.github.com/users/duncanparkes/following{/other_user}","gists_url":"https://api.github.com/users/duncanparkes/gists{/gist_id}","starred_url":"https://api.github.com/users/duncanparkes/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/duncanparkes/subscriptions","organizations_url":"https://api.github.com/users/duncanparkes/orgs","repos_url":"https://api.github.com/users/duncanparkes/repos","events_url":"https://api.github.com/users/duncanparkes/events{/privacy}","received_events_url":"https://api.github.com/users/duncanparkes/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-09-02T16:01:34Z","updated_at":"2016-09-27T13:28:08Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/minoTour/linminUP/pulls/7","html_url":"https://github.com/minoTour/linminUP/pull/7","diff_url":"https://github.com/minoTour/linminUP/pull/7.diff","patch_url":"https://github.com/minoTour/linminUP/pull/7.patch"},"body":"Hi Matt\r\n\r\nI'm getting a strange error from h5py\r\n\r\n```\r\nline 104, in make_fid\r\n  File \"h5f.pyx\", line 90, in h5py.h5f.create (h5py/h5f.c:1975)\r\nIOError: Unable to create file (Unable to open file: name =\r\n'<oddly lower cased fast5 file path>',\r\nerrno = 17, error message = 'file exists', flags = 15, o_flags = c2)\r\n```\r\nI suspect this is an example of https://github.com/h5py/h5py/issues/704.\r\n\r\nThis happens at https://github.com/minoTour/linminUP/blob/master/modules/folderDict.py#L41.\r\n\r\nThe problem appears to be that h5py can't parse the file and raises an exception. Because this happens as the file is opened in the `with` statement itself rather than in the block which follows it, the exception handling which should set `timestamp` to `-1` isn't triggered and instead the thread fails. I suggest swapping the try and the with so that in these circumstances the error does get handled.\r\n\r\nCheers,\r\n\r\nDuncan"},"comment":{"url":"https://api.github.com/repos/minoTour/linminUP/issues/comments/249864583","html_url":"https://github.com/minoTour/linminUP/pull/7#issuecomment-249864583","issue_url":"https://api.github.com/repos/minoTour/linminUP/issues/7","id":249864583,"user":{"login":"duncanparkes","id":56265,"avatar_url":"https://avatars.githubusercontent.com/u/56265?v=3","gravatar_id":"","url":"https://api.github.com/users/duncanparkes","html_url":"https://github.com/duncanparkes","followers_url":"https://api.github.com/users/duncanparkes/followers","following_url":"https://api.github.com/users/duncanparkes/following{/other_user}","gists_url":"https://api.github.com/users/duncanparkes/gists{/gist_id}","starred_url":"https://api.github.com/users/duncanparkes/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/duncanparkes/subscriptions","organizations_url":"https://api.github.com/users/duncanparkes/orgs","repos_url":"https://api.github.com/users/duncanparkes/repos","events_url":"https://api.github.com/users/duncanparkes/events{/privacy}","received_events_url":"https://api.github.com/users/duncanparkes/received_events","type":"User","site_admin":false},"created_at":"2016-09-27T13:28:08Z","updated_at":"2016-09-27T13:28:08Z","body":"Matt - the diff's a bit big for me to see, but did your latest commits include these changes?"}}
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