1st version of the creation of descriptors files.

redcap_bridge/test_redcap/test_utils.py

@@ -7,7 +7,7 @@
 import pytest
 
 from redcap_bridge.utils import compress_record
-from redcap_bridge.utils import conversion_csv_to_json
+from redcap_bridge.utils import conversion_csv_to_json, conversion_to_odml_table_descriptor
 test_directory = pathlib.Path(tempfile.gettempdir()) / 'diglabtools_testfiles'
 project_dir = test_directory / 'testfiles' / 'TestProject'
 
@@ -58,3 +58,7 @@ def test_conversion_csv_to_json(initialize_test_dir):
     elab_conversion = conversion_csv_to_json(test_dir / 'csvRecord.csv')
     assert elab_conversion == elab_final
 
+def test_conversion_to_odml_table_descriptor(initialize_test_dir):
+    test_dir = test_directory / 'testfiles' / 'conversionDescriptor'
+
+    conversion_to_odml_table_descriptor(test_dir / 'Vision4Action_DATA_2023-04-13_1110.csv', session_number=5)

redcap_bridge/test_redcap/testfiles/conversionDescriptor/Vision4Action_DATA_2023-04-13_1110.csv

@@ -0,0 +1,4 @@
+record_id,redcap_repeat_instrument,redcap_repeat_instance,redcap_survey_identifier,diglabform_v4a_timestamp,ethical_protocol_id,user,date,exp_name,guid,ses_number,ses_custom_field,modality___behaviour_eye,modality___behaviour_hand,modality___single_electrode,modality___multi_electrode,modality___emg,modality___int,modality___vsdi,modality___drug_injection,modality___neuronal_stimulation,modality___ecog,modality___seeg,weight,comments_exp,comments_setup,comments_animal,data_quality,incomplete,animal_behaviour___very_motivated,animal_behaviour___working,animal_behaviour___thirsty,animal_behaviour___sleepy,animal_behaviour___unmotivated,animal_behaviour___agitated,animal_behaviour_multi,time_last_trial,animal_behaviour_2___agitated,animal_behaviour_2___resting,animal_behaviour_2___sleeping,animal_behaviour_2___working,reward_fluid,reward_fluid_additional,reward_other___fruit_fresh,reward_other___fruit_dry,reward_other___seeds,reward_other___treats,reward_other___insects,special_event,special_event_time,kinarm_recorded_hand,kinarm_shoulder,kinarm_elbow,data_quality_hand,eyelink_recorded_eye,eyelink_offset_x,eyelink_offset_y,eyelink_gain_x,eyelink_gain_y,data_quality_eye,eye_screen_distance_x,eye_screen_distance_y,eye_screen_distance_z,diglabform_v4a_complete
+1,diglabform_v4a,1,,,APAFIS_13894_2018030217116218_v4,toto,2017-12-28,land,FRM10042901,1,,1,1,0,1,0,0,0,0,0,0,0,,,,,,,0,0,0,0,0,0,,,0,0,0,0,200,,0,0,0,0,0,,,right,6,115,,left,,,,,,9,20,18,2
+2,diglabform_v4a,1,,,APAFIS_13894_2018030217116218_v4,toto,2017-12-29,land,FRM10042901,5,,1,1,0,1,0,0,0,0,0,0,0,,,,,,,0,0,0,0,0,0,,,0,0,0,0,100,,0,0,0,0,0,,,right,6,115,,left,,,,,,9,20,18,2
+3,diglabform_v4a,1,,,APAFIS_13894_2018030217116218_v4,xxx,2018-01-04,land,FRM10042901,3,,1,1,0,1,0,0,0,0,0,0,0,,,,,,,0,0,0,0,0,0,,,0,0,0,0,,,0,0,0,0,0,,,right,6,115,,left,,,,,,9,20,18,2

redcap_bridge/utils.py

@@ -295,3 +295,30 @@ def parse_choices(choice_str, annotation_str):
     default_choice_label = re.sub(r'\{.*?\}', '', default_choice_label)
 
     return list(choice_labels), default_choice_label
+
+def conversion_to_odml_table_descriptor(full_elabbook_csv, session_number):
+    """
+    Create odml descriptor file base on the full elabbook csv file
+
+    Args:
+        full_elabbook_csv: path to the full csv file
+        session_number: number of the session you want to create descriptor csv file
+
+    Returns:
+        descriptor_elabbook_csv: csv descriptor file of the specific session given
+
+    """
+
+    df = pd.read_csv(full_elabbook_csv)
+
+    df_ses = df.loc[df['ses_number'] == session_number]
+
+    cols_to_melt = df_ses.columns[df_ses.columns.get_loc('ethical_protocol_id'):]
+
+    print(cols_to_melt)
+
+    df_melted = df_ses.melt(id_vars='record_id', value_vars=cols_to_melt)
+
+    df_melted = df_melted.rename(columns={'variable': 'Property name'})
+
+    print(df_melted.to_string())