REF: Repeated code for fetching SSH files into one function

Author: ashgillman

nipype/interfaces/io.py

@@ -2309,6 +2309,54 @@ def __init__(self, infields=None, outfields=None, **kwargs):
         ):
             self.inputs.template += '$'
 
+    def _get_files_over_ssh(self, template):
+        """Get the files matching template over an SSH connection."""
+        # Connect over SSH
+        client = self._get_ssh_client()
+        sftp = client.open_sftp()
+        sftp.chdir(self.inputs.base_directory)
+
+        # Get all files in the dir, and filter for desired files
+        template_dir = os.path.dirname(template)
+        template_base = os.path.basename(template)
+        filelist = sftp.listdir(template_dir)
+        if self.inputs.template_expression == 'fnmatch':
+            outfiles = fnmatch.filter(filelist, template_base)
+        elif self.inputs.template_expression == 'regexp':
+            regexp = re.compile(template_base)
+            outfiles = list(filter(regexp.match, filelist))
+        else:
+            raise ValueError('template_expression value invalid')
+
+        if len(outfiles) == 0:
+            # no files
+            msg = 'Output key: %s Template: %s returned no files' % (key, template)
+            if self.inputs.raise_on_empty:
+                raise IOError(msg)
+            else:
+                warn(msg)
+
+            # return value
+            outfiles = None
+
+        else:
+            # found files, sort and save to outputs
+            if self.inputs.sort_filelist:
+                outfiles = human_order_sorted(outfiles)
+
+            # actually download the files, if desired
+            if self.inputs.download_files:
+                for f in outfiles:
+                    try:
+                        sftp.get(os.path.join(template_dir, f), f)
+                    except IOError:
+                        iflogger.info('remote file %s not found' % f)
+
+            # return value
+            outfiles = list_to_filename(outfiles)
+
+        return outfiles
+
     def _list_outputs(self):
         try:
             paramiko
@@ -2340,39 +2388,7 @@ def _list_outputs(self):
                 template = self.inputs.field_template[key]
 
             if not args:
-                # Connect over SSH
-                client = self._get_ssh_client()
-                sftp = client.open_sftp()
-
-                # Get the files in the base dir, and filter for desired files
-                sftp.chdir(self.inputs.base_directory)
-                filelist = sftp.listdir()
-                if self.inputs.template_expression == 'fnmatch':
-                    filelist = fnmatch.filter(filelist, template)
-                elif self.inputs.template_expression == 'regexp':
-                    regexp = re.compile(template)
-                    filelist = list(filter(regexp.match, filelist))
-                else:
-                    raise ValueError('template_expression value invalid')
-
-                if len(filelist) == 0:
-                    # no files
-                    msg = 'Output key: %s Template: %s returned no files' % (
-                        key, template)
-                    if self.inputs.raise_on_empty:
-                        raise IOError(msg)
-                    else:
-                        warn(msg)
-                else:
-                    # found files, sort and save to outputs
-                    if self.inputs.sort_filelist:
-                        filelist = human_order_sorted(filelist)
-                    outputs[key] = list_to_filename(filelist)
-
-                    # actually download the files, if desired
-                    if self.inputs.download_files:
-                        for f in filelist:
-                            sftp.get(f, f)
+                outputs[key] = self._get_files_over_ssh(template)
 
             for argnum, arglist in enumerate(args):
                 maxlen = 1
@@ -2401,44 +2417,7 @@ def _list_outputs(self):
                         except TypeError as e:
                             raise TypeError(e.message + ": Template %s failed to convert with args %s" % (template, str(tuple(argtuple))))
 
-                    # Connect over SSH
-                    client = self._get_ssh_client()
-                    sftp = client.open_sftp()
-                    sftp.chdir(self.inputs.base_directory)
-
-                    # Get all files in the dir, and filter for desired files
-                    filledtemplate_dir = os.path.dirname(filledtemplate)
-                    filledtemplate_base = os.path.basename(filledtemplate)
-                    filelist = sftp.listdir(filledtemplate_dir)
-                    if self.inputs.template_expression == 'fnmatch':
-                        outfiles = fnmatch.filter(filelist, filledtemplate_base)
-                    elif self.inputs.template_expression == 'regexp':
-                        regexp = re.compile(filledtemplate_base)
-                        outfiles = list(filter(regexp.match, filelist))
-                    else:
-                        raise ValueError('template_expression value invalid')
-
-                    if len(outfiles) == 0:
-                        # no files
-                        msg = 'Output key: %s Template: %s returned no files' % (key, filledtemplate)
-                        if self.inputs.raise_on_empty:
-                            raise IOError(msg)
-                        else:
-                            warn(msg)
-                        outputs[key].append(None)
-                    else:
-                        # found files, sort and save to outputs
-                        if self.inputs.sort_filelist:
-                            outfiles = human_order_sorted(outfiles)
-                        outputs[key].append(list_to_filename(outfiles))
-
-                        # actually download the files, if desired
-                        if self.inputs.download_files:
-                            for f in outfiles:
-                                try:
-                                    sftp.get(os.path.join(filledtemplate_dir, f), f)
-                                except IOError:
-                                    iflogger.info('remote file %s not found' % f)
+                    outputs[key].append(self._get_files_over_ssh(filledtemplate))
 
             # disclude where there was any invalid matches
             if any([val is None for val in outputs[key]]):