added cli test

pymedphys/_dicom/structure/merge.py

@@ -172,7 +172,12 @@ def create_new_contour_sequence(
 def merge_contours(  # pylint:disable = inconsistent-return-statements
     roi_contour_sequence, inplace=False
 ):
-    contour_sequence = roi_contour_sequence.ContourSequence
+    try:
+        contour_sequence = roi_contour_sequence.ContourSequence
+    except AttributeError:
+        print(roi_contour_sequence)
+        raise
+
     contours_by_z, image_sequence_by_z = extract_contours_and_image_sequences(
         contour_sequence
     )
@@ -197,5 +202,8 @@ def merge_contours(  # pylint:disable = inconsistent-return-statements
 
 def merge_contours_cli(args):
     dicom_dataset = pydicom.read_file(args.input_file, force=True)
-    merge_contours(dicom_dataset.ROIContourSequence, inplace=True)
+
+    for roi_contour_sequence in dicom_dataset.ROIContourSequence:
+        merge_contours(roi_contour_sequence, inplace=True)
+
     pydicom.write_file(args.output_file, dicom_dataset)

tests/dicom/test_structure_dedupe.py

@@ -12,6 +12,10 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+import pathlib
+import subprocess
+import tempfile
+
 import pydicom
 
 import pymedphys
@@ -36,3 +40,16 @@ def test_structure_dedupe():
             pymedphys.dicom.merge_contours(item, inplace=True)
 
         assert str(input_dcm) == str(baseline_dcm)
+
+        with tempfile.TemporaryDirectory() as temp_dir:
+            output_filename = str(pathlib.Path(temp_dir).joinpath("temp.dcm"))
+
+            command = "pymedphys dicom merge-contours".split() + [
+                str(input_path),
+                output_filename,
+            ]
+            subprocess.check_call(command)
+
+            cli_dcm = pydicom.read_file(output_filename, force=True)
+
+        assert str(cli_dcm) == str(baseline_dcm)