[REF TEST] Refactor data handling (#1045)

* Add error handling to caller of center_nifti_origin * start refactoring * continue refactoring and add tests * add test * refactor _create_merge_file_from_bids (BROKEN...) * better names and more tests * improve tests and code * refactor further * remove duplicate and broken tests * refactor pipeline handling * port changes from PR 1052 * port changes from PR 1055 * port changes from PR 1062 * fixes * fix broken test * some fixes and enhancements * fix broken exception
aramis-lab · Jul 25, 2024 · 7a6a7ca · 7a6a7ca
1 parent f2ec11b
commit 7a6a7ca
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diff --git a/clinica/iotools/converters/adni_to_bids/adni_utils.py b/clinica/iotools/converters/adni_to_bids/adni_utils.py
@@ -929,6 +929,7 @@ def _create_file(
                     ),
                     lvl="error",
                 )
+                raise ValueError(error_msg)
         else:
             shutil.copy(image_path, output_image)
 

diff --git a/clinica/iotools/utils/data_handling/__init__.py b/clinica/iotools/utils/data_handling/__init__.py
@@ -0,0 +1,21 @@
+from ._centering import (
+    center_all_nifti,
+    center_nifti_origin,
+    check_relative_volume_location_in_world_coordinate_system,
+    check_volume_location_in_world_coordinate_system,
+)
+from ._files import create_subs_sess_list, write_list_of_files
+from ._merging import create_merge_file
+from ._missing import compute_missing_mods, compute_missing_processing
+
+__all__ = [
+    "create_merge_file",
+    "center_nifti_origin",
+    "center_all_nifti",
+    "compute_missing_mods",
+    "compute_missing_processing",
+    "create_subs_sess_list",
+    "write_list_of_files",
+    "check_volume_location_in_world_coordinate_system",
+    "check_relative_volume_location_in_world_coordinate_system",
+]
-Original file line number
+Diff line change
@@ Expand Up / @@ -929,6 +929,7 @@ def _create_file( @@
                         ),
                         lvl="error",
                     )
+                    raise ValueError(error_msg)
             else:
                 shutil.copy(image_path, output_image)
@@ Expand Down @@