Add tests for newly added '-json-metadata' flag. Update other tests t…

…o be compatible with new 'json_metadata' param.

tests/test_create_json.py

@@ -21,7 +21,7 @@ def test_create_json(tmp_path):
     nifti_file.touch()
 
     # Call the function with modified=True
-    update_json(str(nifti_file), "Test Rater")
+    update_json(str(nifti_file), "Test Rater", json_metadata=None)
 
     # Check that the JSON file was created and contains the expected metadata
     expected_metadata = {'SpatialReference': 'orig',
@@ -35,6 +35,38 @@ def test_create_json(tmp_path):
     assert metadata == expected_metadata
 
 
+def test_create_json_custom_metadata(tmp_path):
+    """
+    Test that the function update_json() creates a JSON file with the expected metadata and includes custom metadata
+    provided by the user as a JSON file
+    """
+    # Create a temporary file for testing
+    fname_label = "sub-001_ses-01_T1w_seg-manual.nii.gz"
+    nifti_file = tmp_path / fname_label
+    nifti_file.touch()
+
+    custom_metada = {'Name': 'sct_deepseg_sc',
+                     'Author': "SCT v6.2",
+                     'Date': "2024-02-21"}
+
+    # Call the function with modified=True
+    update_json(str(nifti_file), "Test Rater", json_metadata=custom_metada)
+
+    # Check that the JSON file was created and contains the expected metadata
+    expected_metadata = {'SpatialReference': 'orig',
+                         'GeneratedBy': [{'Name': 'sct_deepseg_sc',
+                                          'Author': "SCT v6.2",
+                                          'Date': "2024-02-21"},
+                                         {'Name': 'Manual',
+                                          'Author': "Test Rater",
+                                          'Date': time.strftime('%Y-%m-%d %H:%M:%S')}]}
+    json_file = tmp_path / fname_label.replace(".nii.gz", ".json")
+    assert json_file.exists()
+    with open(str(json_file), "r") as f:
+        metadata = json.load(f)
+    assert metadata == expected_metadata
+
+
 def test_update_json(tmp_path):
     """
     Test that the function update_json() updates (appends to) the JSON file with the expected metadata.
@@ -52,7 +84,7 @@ def test_update_json(tmp_path):
                                          'Date': "2023-01-01 00:00:00"}]}, f)
 
     # Call the function with modified=True
-    update_json(str(nifti_file), "Test Rater 2")
+    update_json(str(nifti_file), "Test Rater 2", json_metadata=None)
 
     # Check that the JSON file was created and contains the expected metadata
     expected_metadata = {'SpatialReference': 'orig',