From da5adb3c027800e655ef899809dcaca5275c920e Mon Sep 17 00:00:00 2001 From: Demian Wassermann Date: Mon, 20 Apr 2015 11:14:32 +0200 Subject: [PATCH 1/3] SSHDataGrabber outputs now returns full path to the grabbed files --- nipype/interfaces/io.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/nipype/interfaces/io.py b/nipype/interfaces/io.py index 002582018c..cbef9ebcad 100644 --- a/nipype/interfaces/io.py +++ b/nipype/interfaces/io.py @@ -1775,13 +1775,20 @@ def _list_outputs(self): outputs[key].append(list_to_filename(outfiles)) if self.inputs.download_files: for f in outfiles: - sftp.get(os.path.join(filledtemplate_dir, f), f) + try: + sftp.get(os.path.join(filledtemplate_dir, f), f) + except IOError: + iflogger.info('remote file %s not found' % f) if any([val is None for val in outputs[key]]): outputs[key] = [] if len(outputs[key]) == 0: outputs[key] = None elif len(outputs[key]) == 1: outputs[key] = outputs[key][0] + + for k, v in outputs.items(): + outputs[k] = os.path.join(os.getcwd(), v) + return outputs def _get_ssh_client(self): From 26722836a6f3a4cb1c58b89b3feeb0dc0d649e71 Mon Sep 17 00:00:00 2001 From: Demian Wassermann Date: Mon, 20 Apr 2015 16:41:29 +0200 Subject: [PATCH 2/3] FIX: Added the updates to the CHANGES file --- CHANGES | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGES b/CHANGES index f72ca3a3bb..c6e2b9b54c 100644 --- a/CHANGES +++ b/CHANGES @@ -50,6 +50,7 @@ Next release * ENH: ANTs JointFusion() (https://github.com/nipy/nipype/pull/1042) * ENH: Added csvReader() utility (https://github.com/nipy/nipype/pull/1044) * FIX: typo in nipype.interfaces.freesurfer.utils.py Tkregister2 (https://github.com/nipy/nipype/pull/1083) +* FIX: SSHDataGrabber outputs now return full path to the grabbed/downloaded files. Release 0.10.0 (October 10, 2014) ============ From 9f5eb2cb47c54eb39a756aabe85dbc71a0ea77ca Mon Sep 17 00:00:00 2001 From: Demian Wassermann Date: Mon, 20 Apr 2015 16:45:19 +0200 Subject: [PATCH 3/3] FIX: Added the required URL to the CHANGES file --- CHANGES | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGES b/CHANGES index c6e2b9b54c..6ea2883c72 100644 --- a/CHANGES +++ b/CHANGES @@ -50,7 +50,7 @@ Next release * ENH: ANTs JointFusion() (https://github.com/nipy/nipype/pull/1042) * ENH: Added csvReader() utility (https://github.com/nipy/nipype/pull/1044) * FIX: typo in nipype.interfaces.freesurfer.utils.py Tkregister2 (https://github.com/nipy/nipype/pull/1083) -* FIX: SSHDataGrabber outputs now return full path to the grabbed/downloaded files. +* FIX: SSHDataGrabber outputs now return full path to the grabbed/downloaded files. (https://github.com/nipy/nipype/pull/1086) Release 0.10.0 (October 10, 2014) ============