more fixes in compliance with updated context

bids_prov/afni/afni_parser.py

@@ -130,17 +130,17 @@ def build_records(commands_bloc: list, agent_id: str, verbose: bool = False):
 
                 inputs, outputs, cmd_args_remain = get_entities(cmd_s[1:], df)
 
-                # if "used" in df:
-                #     arg = df["used"]
+                # if "Used" in df:
+                #     arg = df["Used"]
                 #     entities, args_consumed_list = get_entities(cmd_s, arg)
                 #     renamed_entities = [clean_label_suffix(
                 #         os.path.split(ent)[1]) for ent in entities]
                 #     inputs.extend(renamed_entities)
                 #     for arg in args_consumed_list:
                 #         cmd_args_remain.remove(arg)
 
-                # if "generatedBy" in df:
-                #     arg = df["generatedBy"]
+                # if "GeneratedBy" in df:
+                #     arg = df["GeneratedBy"]
                 #     entities, args_consumed_list = get_entities(cmd_s, arg)
                 #     renamed_entities = [clean_label_suffix(
                 #         os.path.split(ent)[1]) for ent in entities]
@@ -362,7 +362,7 @@ def fusion_activities(activities, label):
         return {
             "@id": f"urn:{get_id()}",
             "Label": label,
-            "AssociatedWith": activities[0]["associatedWith"],
+            "AssociatedWith": activities[0]["AssociatedWith"],
             "Command": command,
             "Used": used_entities,
         }
@@ -411,8 +411,8 @@ def get_extern_entities_from_activities(graph, activities, id_fusion_activity):
                         generated_entities.append(ent)
 
         # for ent in used_ents:
-        #     if "generatedBy" in ent:
-        #         ent["generatedBy"] = id_fusion_activity
+        #     if "GeneratedBy" in ent:
+        #         ent["GeneratedBy"] = id_fusion_activity
 
         for ent in generated_entities:
             if "GeneratedBy" in ent:

bids_prov/fsl/fsl_parser.py

@@ -143,7 +143,7 @@ def readlines(filename: str) -> Mapping[str, List[str]]:
 
 def _get_kwarg(serie,  with_value=True):
     """
-    Get the named arguments (kwarg) from a column ("used", "generatedBy", "parameters_value" or "parameters_no_value" ) of the dataframe coming frome in description_functions.json
+    Get the named arguments (kwarg) from a column ("Used", "GeneratedBy", "parameters_value" or "parameters_no_value" ) of the dataframe coming frome in description_functions.json
 
     Parameters
     ----------
@@ -201,7 +201,7 @@ def _get_kwarg(serie,  with_value=True):
 
 def _get_arg(serie, arg_rest):
     """
-    Get the ordinal arguments from a column ("used", "generatedBy") of the dataframe coming from in description_functions.json. _get_arg shoud be used when all named arguments are removed from the initial command.   
+    Get the ordinal arguments from a column ("Used", "GeneratedBy") of the dataframe coming from in description_functions.json. _get_arg shoud be used when all named arguments are removed from the initial command.   
 
     Parameters
     ----------
@@ -306,11 +306,11 @@ def get_entities(cmd_s, parameters):
     -------
 
     >>> df = {
-            "name": "command",
-            "used": [0, "-a"],
-            "generatedBy": [-1, "-b"]
+            "name": "Command",
+            "Used": [0, "-a"],
+            "GeneratedBy": [-1, "-b"]
         }
-    >>> cmd_s = ["command", "-a", "kwarg_0", "arg_0", "arg_1",  "-b", "kwarg_1"]
+    >>> cmd_s = ["Command", "-a", "kwarg_0", "arg_0", "arg_1",  "-b", "kwarg_1"]
     >>> inputs, outputs, parameters = get_entities(cmd_s[1:], df)
     >>> (["kwarg_0", "arg_0"], ["kwarg_1", "arg_1"], [])
 

bids_prov/spm/spm_parser.py

@@ -47,7 +47,7 @@ def get_input_entity(right: str) -> List[dict]:
     Returns
     -------
      dict[str, str]
-        else with key "@id", "label", "prov"
+        else with key "@id", "Label", "prov"
 
     """
 
@@ -62,8 +62,8 @@ def get_input_entity(right: str) -> List[dict]:
             entity_label_short = "_".join(file_location.split("/")[-2:])  # Sub01_con_0001.nii
             entity = {
                 "@id": "urn:" + get_id(),
-                "label": label_mapping(entity_label_short, "spm/spm_activity_labels.json"),
-                "prov:atLocation": file_location
+                "Label": label_mapping(entity_label_short, "spm/spm_activity_labels.json"),
+                "AtLocation": file_location
             }
 
             entities.append(entity)
@@ -159,7 +159,7 @@ def get_entities_from_ext_config(conf_dic: dict, activity_name: str, activity_id
     Returns
     -------
     list[dict]
-        each element is an entity dict with key    "@id", "label", "prov:atLocation", "wasGeneratedBy"
+        each element is an entity dict with key    "@id", "Label", "AtLocation", "wasGeneratedBy"
     """
 
     output_entities = list()
@@ -200,7 +200,7 @@ def find_closest_activity(activities: list, right: str) -> dict:
     dep_number = re.search(r"{(\d+)}", right)  # retrieve name of the output_entity
     closest_activity = None
     for act in activities:
-        if act["label"].endswith(dep_number.group(1)):
+        if act["Label"].endswith(dep_number.group(1)):
             closest_activity = act
             break
 
@@ -221,14 +221,14 @@ def find_output_id_from_closest(closest_activity: dict, records: dict) -> str:
     """
     for entity in records["Entities"]:
         if "GeneratedBy" in entity:
-            if entity["GeneratedBy"] == closest_activity["@id"]:  # entity["label"] == parts[-1]
+            if entity["GeneratedBy"] == closest_activity["@id"]:  # entity["Label"] == parts[-1]
                 output_id = entity["@id"]
                 break
     else:
         output_id = "urn:" + get_id()
     # output_id = next(
     #     (entity["@id"] for entity in records["prov:Entity"]
-    #                   if parts[-1] == entity["label"] and entity["generatedBy"] == closest_activity["@id"]
+    #                   if parts[-1] == entity["Label"] and entity["GeneratedBy"] == closest_activity["@id"]
     #     ), "urn:" + get_id()
     #     ) # find entity id generated by closest activity, if None new get_id
 
@@ -365,7 +365,7 @@ def get_records(task_groups: dict, agent_id: str, verbose=False) -> dict:
                     output_entity = {  # output for closest activity but input for current one
                         "@id": output_id,
                         "Label": out_label,  # label_mapping(parts[-1], "spm/spm_labels.json"),
-                        # "prov:atLocation": TODO
+                        # "AtLocation": TODO
                         "GeneratedBy": closest_activity["@id"],
                     }
                     output_entities.append(output_entity)