TEST: Test singular and decomposed interfaces

Author: effigies

niworkflows/interfaces/tests/test_bids.py

@@ -47,6 +47,7 @@
 BOLD_PATH = "ds054/sub-100185/func/sub-100185_task-machinegame_run-01_bold.nii.gz"
 
 
+@pytest.mark.parametrize("interface", [bintfs.DerivativesDataSink, bintfs.PrepareDerivative])
 @pytest.mark.parametrize("out_path_base", [None, "fmriprep"])
 @pytest.mark.parametrize(
     "source,input_files,entities,expectation,checksum",
@@ -258,6 +259,7 @@
 @pytest.mark.parametrize("dismiss_entities", [None, ("run", "session")])
 def test_DerivativesDataSink_build_path(
     tmp_path,
+    interface,
     out_path_base,
     source,
     input_files,
@@ -267,6 +269,8 @@ def test_DerivativesDataSink_build_path(
     dismiss_entities,
 ):
     """Check a few common derivatives generated by NiPreps."""
+    if interface is bintfs.PrepareDerivative and out_path_base is not None:
+        pytest.skip("PrepareDerivative does not support out_path_base")
     ds_inputs = []
     for input_file in input_files:
         fname = tmp_path / input_file
@@ -291,24 +295,41 @@ def test_DerivativesDataSink_build_path(
 
         ds_inputs.append(str(fname))
 
-    dds = bintfs.DerivativesDataSink(
+    base_directory = tmp_path / "output"
+    work_dir = tmp_path / "work"
+    base_directory.mkdir()
+    work_dir.mkdir()
+
+    prep = save = interface(
         in_file=ds_inputs,
-        base_directory=str(tmp_path),
         source_file=source,
-        out_path_base=out_path_base,
         dismiss_entities=dismiss_entities,
         **entities,
+        **({"out_path_base": out_path_base} if interface == bintfs.DerivativesDataSink else {}),
     )
+    if interface == bintfs.DerivativesDataSink:
+        prep.inputs.base_directory = str(base_directory)
+    else:
+        save = bintfs.SaveDerivative(base_directory=str(base_directory))
 
     if isinstance(expectation, type):
         with pytest.raises(expectation):
-            dds.run()
+            prep.run()
         return
 
-    output = dds.run().outputs.out_file
+    prep_outputs = save_outputs = prep.run().outputs
+
+    if save is not prep:
+        save.inputs.in_file = prep_outputs.out_file
+        save.inputs.relative_path = prep_outputs.out_path
+        save.inputs.metadata = prep_outputs.out_meta
+        save_outputs = save.run().outputs
+
+    output = save_outputs.out_file
     if isinstance(expectation, str):
         expectation = [expectation]
         output = [output]
+        checksum = [checksum]
 
     if dismiss_entities:
         if "run" in dismiss_entities:
@@ -320,26 +341,12 @@ def test_DerivativesDataSink_build_path(
                 for e in expectation
             ]
 
-    base = out_path_base or "niworkflows"
+    base = (out_path_base or "niworkflows") if interface == bintfs.DerivativesDataSink else ""
     for out, exp in zip(output, expectation):
-        assert Path(out).relative_to(tmp_path) == Path(base) / exp
-
-    os.chdir(str(tmp_path))  # Exercise without setting base_directory
-    dds = bintfs.DerivativesDataSink(
-        in_file=ds_inputs,
-        dismiss_entities=dismiss_entities,
-        source_file=source,
-        out_path_base=out_path_base,
-        **entities,
-    )
-
-    output = dds.run().outputs.out_file
-    if isinstance(output, str):
-        output = [output]
-        checksum = [checksum]
+        assert Path(out).relative_to(base_directory) == Path(base) / exp
 
     for out, exp in zip(output, expectation):
-        assert Path(out).relative_to(tmp_path) == Path(base) / exp
+        assert Path(out).relative_to(base_directory) == Path(base) / exp
         # Regression - some images were given nan scale factors
         if out.endswith(".nii") or out.endswith(".nii.gz"):
             img = nb.load(out)

niworkflows/utils/misc.py

@@ -282,8 +282,8 @@ def _copy_any(src, dst):
     from shutil import copyfileobj
     from nipype.utils.filemanip import copyfile
 
-    src_isgz = src.endswith(".gz")
-    dst_isgz = dst.endswith(".gz")
+    src_isgz = os.fspath(src).endswith(".gz")
+    dst_isgz = os.fspath(dst).endswith(".gz")
     if not src_isgz and not dst_isgz:
         copyfile(src, dst, copy=True, use_hardlink=True)
         return False  # Make sure we do not reuse the hardlink later