{"action":"created","issue":{"url":"https://api.github.com/repos/OpenMS/OpenMS/issues/2188","repository_url":"https://api.github.com/repos/OpenMS/OpenMS","labels_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/2188/labels{/name}","comments_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/2188/comments","events_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/2188/events","html_url":"https://github.com/OpenMS/OpenMS/issues/2188","id":179186827,"number":2188,"title":"Empty file test using file size is bad (can't read from named pipes)","user":{"login":"mcapuccini","id":1671397,"avatar_url":"https://avatars.githubusercontent.com/u/1671397?v=3","gravatar_id":"","url":"https://api.github.com/users/mcapuccini","html_url":"https://github.com/mcapuccini","followers_url":"https://api.github.com/users/mcapuccini/followers","following_url":"https://api.github.com/users/mcapuccini/following{/other_user}","gists_url":"https://api.github.com/users/mcapuccini/gists{/gist_id}","starred_url":"https://api.github.com/users/mcapuccini/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mcapuccini/subscriptions","organizations_url":"https://api.github.com/users/mcapuccini/orgs","repos_url":"https://api.github.com/users/mcapuccini/repos","events_url":"https://api.github.com/users/mcapuccini/events{/privacy}","received_events_url":"https://api.github.com/users/mcapuccini/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/OpenMS/OpenMS/labels/Good%20Ideas%20for%20upcoming%20releases","name":"Good Ideas for upcoming releases","color":"ffffff"}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-09-26T10:02:17Z","updated_at":"2016-09-26T23:01:29Z","closed_at":null,"body":"Hi! I am trying to reproduce a study in a distributed cloud environment using OpenMS. I have developed a tool to execute trivially parallelizable tasks in Spark (https://github.com/mcapuccini/EasyMapReduce). You have an empty file test in most of your tools, that checks the size of the file. This is making my life hard, as my parallelization tool uses named pipes to pass the data to OpenMS. Named pipes will always have file size equal to 0, but this doesn't mean that they are empty. It would be nice if you could fix this, in a way that your tools can read from named pipes. "},"comment":{"url":"https://api.github.com/repos/OpenMS/OpenMS/issues/comments/249722460","html_url":"https://github.com/OpenMS/OpenMS/issues/2188#issuecomment-249722460","issue_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/2188","id":249722460,"user":{"login":"hroest","id":464014,"avatar_url":"https://avatars.githubusercontent.com/u/464014?v=3","gravatar_id":"","url":"https://api.github.com/users/hroest","html_url":"https://github.com/hroest","followers_url":"https://api.github.com/users/hroest/followers","following_url":"https://api.github.com/users/hroest/following{/other_user}","gists_url":"https://api.github.com/users/hroest/gists{/gist_id}","starred_url":"https://api.github.com/users/hroest/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hroest/subscriptions","organizations_url":"https://api.github.com/users/hroest/orgs","repos_url":"https://api.github.com/users/hroest/repos","events_url":"https://api.github.com/users/hroest/events{/privacy}","received_events_url":"https://api.github.com/users/hroest/received_events","type":"User","site_admin":false},"created_at":"2016-09-26T23:01:29Z","updated_at":"2016-09-26T23:01:29Z","body":"this would actually be really cool but there are some limitations as some file formats require the computation of hashes across the whole datafile - not sure whether that would be a problem. I really like the idea to be able to do this - I guess this would be Linux only? \r\n\r\ndo you have an example of which tools use the empty file test that causes problems? Is it only the tests that cause problems or do the tools also fail to work? can you post the error messages you get? are these `Error: File empty` - can you run with `-debug 10` and report the results? I think we check \r\n\r\n`src/openms/source/APPLICATIONS/TOPPBase.cpp: TOPPBase::inputFileReadable_`\r\n\r\nhere we check `File::exists`, `File::readable` and `File::isDirectory` and `File::empty`\r\n\r\nwhere probably the last one causes issues, see https://github.com/OpenMS/OpenMS/blob/develop/src/openms/source/SYSTEM/File.cpp#L126"}}
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