TEST/RF: Check modified command + helper command

Author: effigies

nipype/interfaces/base/core.py

@@ -988,14 +988,26 @@ def _run_interface(self, runtime, correct_return_codes=(0, )):
 
         # which $cmd
         executable_name = self.cmd.split()[0]
-        cmd_path = which(executable_name, env=runtime.environ)
+
+        prefix_parts = self._cmd_prefix.split()
+        r_pre = prefix_parts.pop() if prefix_parts else ''
+
+        cmd_path = which(r_pre + executable_name, env=runtime.environ)
 
         if cmd_path is None:
             raise IOError(
                 'No command "%s" found on host %s. Please check that the '
                 'corresponding package is installed.' % (executable_name,
                                                          runtime.hostname))
 
+        if prefix_parts:
+            helper_command = which(prefix_parts[0], env=runtime.environ)
+            if helper_command is None:
+                raise IOError(
+                    'No command "%s" found on host %s. Please check that the '
+                    'corresponding package is installed.' % (helper_command,
+                                                             runtime.hostname))
+
         runtime.command_path = cmd_path
         runtime.dependencies = (get_dependencies(executable_name,
                                                  runtime.environ)

nipype/interfaces/base/tests/test_core.py

@@ -480,3 +480,38 @@ def test_global_CommandLine_output(tmpdir):
     # Check default affects derived interfaces
     ci = BET()
     assert ci.terminal_output == 'file'
+
+
+def test_CommandLine_prefix(tmpdir):
+    tmpdir.chdir()
+    oop = 'out/of/path'
+    os.makedirs(oop)
+
+    script_name = 'test_script.sh'
+    script_path = os.path.join(oop, script_name)
+    with open(script_path, 'w') as script_f:
+        script_f.write('#!/usr/bin/env bash\necho Success!')
+    os.chmod(script_path, mode=0o755)
+
+    ci = nib.CommandLine(command=script_name)
+    with pytest.raises(OSError):
+        ci.run()
+
+    class OOPCLI(nib.CommandLine):
+        _cmd_prefix = oop + '/'
+
+    ci = OOPCLI(command=script_name)
+    ci.run()
+
+    class OOPShell(nib.CommandLine):
+        _cmd_prefix = 'bash {}/'.format(oop)
+
+    ci = OOPShell(command=script_name)
+    ci.run()
+
+    class OOPBadShell(nib.CommandLine):
+        _cmd_prefix = 'shell_dne {}/'.format(oop)
+
+    ci = OOPBadShell(command=script_name)
+    with pytest.raises(OSError):
+        ci.run()