doc modified and errors replaced by warnings

Author: ISMAILI Adam

docs/Converters/GENFItoBIDS.md

@@ -99,7 +99,24 @@ where:
         - For `participants.tsv` : `blinded_code`, `blinded_family`, `blinded_site`, `gender`.
         - For `sessions.tsv` : `age_at_visit`, `date_of_assessment`, `diagnosis`, `education`, `ftld-cdr-nm-global`, `genetic_group`, `genetic_status_1`, `genetic_status_2`, `visit`. 
         <br> All the remaining clinical data is optional and added through the use of the `-full` flag.
-    - `--clinical-data-txt/-cdt` is a txt file containing the additional fields the user wants, written one field per line. The available data can be retrieved inside the installation of clinica at this location : `your_path_to_clinica/clinica/converters/genfi_to_bids/specifications/full_specs.csv`.
+    - `--clinical-data-txt/-cdt` is a txt file containing the additional fields the user wants. The available data can be retrieved inside the installation of clinica at this location : `your_path_to_clinica/clinica/converters/genfi_to_bids/specifications/full_specs.csv`. This file should be written one field per line such as in the example below :
+        ```diagnosis_1
+        diagnosis_1.1
+        diagnosis_2
+        diagnosis_3
+        diagnosis_4
+        diagnosis_5
+        diagnosis_6
+        diagnosis_7
+        diagnosis_8
+        diagnosis_child1
+        diagnosis_child2
+        digit_symbol
+        disinhibition
+        dob
+        drc_qc
+        drug_history
+        ...```
     - `-gif` allows the user to add all the clinical data related to the imaging volumes (GIF, Geodesic Information Flow) to `session.tsv`. The added clinical data also contain the mandatory ones.
     - `-full` allows the user to add all clinical data (mandatory, GIF, and the remaining optional ones) to `sessions.tsv`.
 

test/unittests/converters/test_genfi_to_bids_utils.py

@@ -579,7 +579,7 @@ def test_load_clinical_data_list_empty(tmp_path, clinical_data_list, expected):
     cdt_path = tmp_path / "additional_clinical_data.txt"
     cdt_path.write_text("".join(clinical_data_list), encoding="utf-8")
 
-    with pytest.raises(ValueError, match=re.escape(expected)):
+    with pytest.warns(UserWarning, match=re.escape(expected)):
         _load_clinical_data_list(cdt_path, FULL_SPECS_DF)
 
 
@@ -589,9 +589,9 @@ def test_load_clinical_data_list_unknown_field(tmp_path):
     cdt_path = tmp_path / "additional_clinical_data.txt"
     cdt_path.write_text("blinded_family\nfalse_field\naad\n", encoding="utf-8")
 
-    expected = "Error at line 2: 'false_field' not found in specifications."
+    expected = "Line 2: 'false_field' not found in specifications."
 
-    with pytest.raises(ValueError, match=re.escape(expected)):
+    with pytest.warns(UserWarning, match=re.escape(expected)):
         _load_clinical_data_list(cdt_path, FULL_SPECS_DF)