rewrote test to check command line string

nipype/interfaces/tests/test_whitestripe.py

@@ -5,31 +5,43 @@
 
 import pytest
 import requests
+from pathlib import Path
+from string import Template
 from nipype.interfaces import whitestripe
 from nipype.interfaces.r import get_r_command
 
 
-@pytest.mark.skipif(get_r_command() is None, reason="R is not available")
 def test_whitestripe(tmpdir):
     cwd = tmpdir.chdir()
 
-    filename = "T1W.nii.gz"
-    req = requests.get(
-        "https://johnmuschelli.com/open_ms_data/cross_sectional/coregistered_resampled/patient01/T1W.nii.gz"
-    )
-    with open(filename, "wb") as fd:
-        for chunk in req.iter_content(chunk_size=128):
-            fd.write(chunk)
+    Path("T1W.nii.gz").touch()
 
     normalizer = whitestripe.WhiteStripe()
     normalizer.inputs.img_type = "T1"
     normalizer.inputs.in_file = "T1W.nii.gz"
-    normalizer.inputs.indices = normalizer.gen_indices()
     normalizer.inputs.out_file = "T1W_ws.nii.gz"
-    normalizer.run()
+    tmpfile, script = normalizer._cmdline(normalizer)
 
-    assert os.path.isfile(normalizer.inputs.out_file)
-    os.remove(normalizer.inputs.out_file)
+    expected_script = Template(
+        # the level of indentation needs to match what's in the whitestripe interface
+        """
+                library(neurobase)
+                library(WhiteStripe)
+                in_file = readnii('$in_file')
+                ind = whitestripe(in_file, "$img_type")$$whitestripe.ind
+                norm = whitestripe_norm(in_file, ind)
+                out_file = '$out_file'
+                writenii(norm, out_file)
+                """
+    ).substitute(
+        {
+            "in_file": normalizer.inputs.in_file,
+            "out_file": normalizer.inputs.out_file,
+            "img_type": normalizer.inputs.img_type,
+        }
+    )
+    assert tmpfile is False
+    assert script == expected_script
     os.remove(normalizer.inputs.in_file)
 
     cwd.chdir()

nipype/interfaces/whitestripe.py

@@ -29,6 +29,29 @@ class WhiteStripe(BaseInterface):
     output_spec = WhiteStripeOutputSpec
 
     def _run_interface(self, runtime):
+        tmpfile, script = self._cmdline(runtime)
+
+        # rfile = True  will create a .R file with your script and executed.
+        # Alternatively
+        # rfile can be set to False which will cause the R code to be
+        # passed
+        # as a commandline argument to the R executable
+        # (without creating any files).
+        # This, however, is less reliable and harder to debug
+        # (code will be reduced to
+        # a single line and stripped of any comments).
+        rcmd = RCommand(script=script, rfile=False)
+        result = rcmd.run()
+        if tmpfile:
+            os.remove(tmpfile)
+        return result.runtime
+
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+        outputs["out_file"] = os.path.abspath(self.inputs.out_file)
+        return outputs
+
+    def _cmdline(self, runtime):
         d = dict(
             in_file=self.inputs.in_file,
             out_file=self.inputs.out_file,
@@ -65,25 +88,7 @@ def _run_interface(self, runtime):
                 """
             ).substitute(d)
 
-        # rfile = True  will create a .R file with your script and executed.
-        # Alternatively
-        # rfile can be set to False which will cause the R code to be
-        # passed
-        # as a commandline argument to the R executable
-        # (without creating any files).
-        # This, however, is less reliable and harder to debug
-        # (code will be reduced to
-        # a single line and stripped of any comments).
-        rcmd = RCommand(script=script, rfile=False)
-        result = rcmd.run()
-        if tmpfile:
-            os.remove(tmpfile)
-        return result.runtime
-
-    def _list_outputs(self):
-        outputs = self._outputs().get()
-        outputs["out_file"] = os.path.abspath(self.inputs.out_file)
-        return outputs
+        return tmpfile, script
 
     def gen_indices(self):
         path = tempfile.mkstemp()[1]