{"action":"created","issue":{"url":"https://api.github.com/repos/openmole/openmole/issues/9","labels_url":"https://api.github.com/repos/openmole/openmole/issues/9/labels{/name}","comments_url":"https://api.github.com/repos/openmole/openmole/issues/9/comments","events_url":"https://api.github.com/repos/openmole/openmole/issues/9/events","html_url":"https://github.com/openmole/openmole/issues/9","id":67408153,"number":9,"title":"File name extension not preserved when files are copied to remote","user":{"login":"schuhschuh","id":975451,"avatar_url":"https://avatars.githubusercontent.com/u/975451?v=3","gravatar_id":"","url":"https://api.github.com/users/schuhschuh","html_url":"https://github.com/schuhschuh","followers_url":"https://api.github.com/users/schuhschuh/followers","following_url":"https://api.github.com/users/schuhschuh/following{/other_user}","gists_url":"https://api.github.com/users/schuhschuh/gists{/gist_id}","starred_url":"https://api.github.com/users/schuhschuh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/schuhschuh/subscriptions","organizations_url":"https://api.github.com/users/schuhschuh/orgs","repos_url":"https://api.github.com/users/schuhschuh/repos","events_url":"https://api.github.com/users/schuhschuh/events{/privacy}","received_events_url":"https://api.github.com/users/schuhschuh/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":15,"created_at":"2015-04-09T17:14:18Z","updated_at":"2015-04-09T21:17:12Z","closed_at":null,"body":"I have an input File for a ScalaTask which runs an external program. This program uses the NIfTI-1 I/O library to read the NIfTI-1 image. It fails because apparently OpenMOLE copies the input image file to the remote with a cryptic random file name and “.bin” extension. Thus, the NIfTI-1 I/O library fails to find the image header file as it relies on specific file name extensions for the image header and raw image data (similar for other image processing libraries).\r\n\r\n> \"/homes/as12312/opt/bin/ireg\" \"/homes/as12312/.openmole/.tmp/ssh/5255b992-aae3-4fa6-8dce-a56079207f3d/tmp/1428599294970/f7aa5de4-88dd-420f-a74c-3711eb46bc1c/0d7f915e-6284-47ef-b3cd-32947d74f3\r\nc3/.tmp/6039562a-31d2-465b-9029-bf5be624e9e0/filef357ba84-536c-465d-949c-bbc00cf05855.bin\" \"/homes/as12312/.openmole/.tmp/ssh/5255b992-aae3-4fa6-8dce-a56079207f3d/tmp/1428599294970/f7aa5de4-88d\r\nd-420f-a74c-3711eb46bc1c/0d7f915e-6284-47ef-b3cd-32947d74f3c3/.tmp/6039562a-31d2-465b-9029-bf5be624e9e0/file66427b49-2517-4197-9347-6a807b55f887.bin\" \"-dofout\" \"/homes/as12312/.openmole/.tmp/ss\r\nh/5255b992-aae3-4fa6-8dce-a56079207f3d/tmp/1428599294970/f7aa5de4-88dd-420f-a74c-3711eb46bc1c/0d7f915e-6284-47ef-b3cd-32947d74f3c3/.tmp/6039562a-31d2-465b-9029-bf5be624e9e0/fileb565ef71-5505-41\r\n37-bce6-49de4dd2cdd0.bin\" \"-threads\" \"8\" \"-par\" \"Transformation model = Rigid\" \"-par\" \"Background value = 0\"\r\nireg 3.2 (rev 01ff3acc, built on Apr  9 2015)\r\n** ERROR (nifti_image_read): failed to find header file for '/homes/as12312/.openmole/.tmp/ssh/5255b992-aae3-4fa6-8dce-a56079207f3d/tmp/1428599294970/f7aa5de4-88dd-420f-a74c-3711eb46bc1c/0d7f91\r\n5e-6284-47ef-b3cd-32947d74f3c3/.tmp/6039562a-31d2-465b-9029-bf5be624e9e0/filef357ba84-536c-465d-949c-bbc00cf05855.bin’"},"comment":{"url":"https://api.github.com/repos/openmole/openmole/issues/comments/91358146","html_url":"https://github.com/openmole/openmole/issues/9#issuecomment-91358146","issue_url":"https://api.github.com/repos/openmole/openmole/issues/9","id":91358146,"user":{"login":"schuhschuh","id":975451,"avatar_url":"https://avatars.githubusercontent.com/u/975451?v=3","gravatar_id":"","url":"https://api.github.com/users/schuhschuh","html_url":"https://github.com/schuhschuh","followers_url":"https://api.github.com/users/schuhschuh/followers","following_url":"https://api.github.com/users/schuhschuh/following{/other_user}","gists_url":"https://api.github.com/users/schuhschuh/gists{/gist_id}","starred_url":"https://api.github.com/users/schuhschuh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/schuhschuh/subscriptions","organizations_url":"https://api.github.com/users/schuhschuh/orgs","repos_url":"https://api.github.com/users/schuhschuh/repos","events_url":"https://api.github.com/users/schuhschuh/events{/privacy}","received_events_url":"https://api.github.com/users/schuhschuh/received_events","type":"User","site_admin":false},"created_at":"2015-04-09T21:17:12Z","updated_at":"2015-04-09T21:17:12Z","body":"The previous code snippet gives me another error\r\n```\r\nErrors while compiling:\r\n\r\nnot found: value dof6\r\n              mapAsJavaMap(Map[String, Any](  \"dof6\" -> dof6, \"dof6Log\" -> dof6Log, \"srcId\" -> srcId, \"srcIm\" -> srcIm ))\r\n                                                        ^\r\non line 34\r\n\r\n\r\nnot found: value dof6Log\r\n              mapAsJavaMap(Map[String, Any](  \"dof6\" -> dof6, \"dof6Log\" -> dof6Log, \"srcId\" -> srcId, \"srcIm\" -> srcIm ))\r\n                                                                           ^\r\non line 34\r\n\r\n```"}}