feat: behavior circumstance processing with pydantic

app/assets/json_tmp/tmp_wounded_dead.json

@@ -1 +1 @@
-{}
+{"circumstance_radio": true, "circumstance": "collision with a means of transport", "cirumstance_type": {"type": "boat", "option_dropdown_label": "NA", "open_field_label": "NA", "extra_label": "NA"}, "behavior_radio": "Yes", "behaviors_observed": ["Crash, Falling From The Sky", "Diarrhea"], "physical_radio": "Yes", "physical_type_head": "head", "physical_anomaly_type_head": ["Injury", "Parasites"], "physical_type_legs": "legs", "physical_anomaly_type_legs": ["Missing Limb"], "fe_fe_collection": "no", "fe_fe_recipient": "local museum", "fe_fe_name_recipient": "reserve", "fe_fe_radio": "unknown", "fe_fe_answer": "police call", "fe_fe_collection_ref": "ref"}

app/behavior/behavior_checkbox.py

@@ -2,10 +2,10 @@ import gradio as gr
 from utils.utils_config import get_custom_config_dropdowns
 from utils.utils_checkbox import create_checkbox
 from utils.utils_visible import set_visible
-from validation_submission.add_json import add_data_to_individual 
+from validation_submission.add_json import add_data_tmp
 
 def on_select_behavior(behavior_checkbox): 
-    add_data_to_individual("behavior", behavior_checkbox)
+    add_data_tmp("wounded_dead", "behaviors_type", behavior_checkbox)
 
 def retrieve_behavior_options_description():
     dropdown_config = get_custom_config_dropdowns("config_checkbox_behavior.json")
@@ -25,4 +25,5 @@ def create_behavior_checkbox(section: str, visible):
 def show_behavior(choice, section: str): 
     visible = set_visible(choice)
     checkbox, text = create_behavior_checkbox(section, visible)
+    add_data_tmp("wounded_dead", "behaviors_radio", choice)
     return checkbox, text

app/behavior/class_behavior.py

@@ -63,4 +63,5 @@ BehaviorType = Union[
 
 # Main class that logs multiple behaviors
 class Behaviors(BaseModel):
-    observed_behaviors: List[BehaviorType] = Field(..., discriminator='type')
+    behaviors_radio: str  # e.g., "Yes"
+    behaviors_type: List[BehaviorType] = Field(..., discriminator='type')

app/circumstances/circumstances.py

@@ -17,7 +17,7 @@ def show_circumstances(choice):
     visible = set_visible(choice)
     add_data_tmp("wounded_dead", 
                     "circumstance_radio", 
-                    True)
+                    choice)
     button_collision, button_deliberate_destruction, button_indirect_destruction, button_natural_cause, dropdown, dropdown_level2, openfield_level2, dropdown_extra_level2 = create_circumstances(visible)
     return button_collision, button_deliberate_destruction, button_indirect_destruction, button_natural_cause, dropdown, dropdown_level2, openfield_level2, dropdown_extra_level2
 

app/follow_up/followup_events.py

@@ -1,6 +1,6 @@
 import gradio as gr
 from utils.utils_config import get_custom_config_dropdowns
-from validation_submission.add_json import add_data_to_individual
+from validation_submission.add_json import add_data_tmp
 
 def create_followup_dropdowns(visible, elem_id): 
     followup_config = get_custom_config_dropdowns("config_followup.json")
@@ -40,7 +40,7 @@ def create_fe_answer_dropdown(followup_config, visible, elem_id):
     return fe_answer_dropdown
 
 def save_fe(value, key): 
-    add_data_to_individual(key, value)
+    add_data_tmp("wounded_dead", key.lower(), value.lower())
 
 
     

app/geolocalisation/maps.py

@@ -1,6 +1,6 @@
 from geopy.geocoders import Nominatim
 import gradio as gr
-from app.validation_submission.utils_json import add_data_to_individual
+from validation_submission.add_json import add_data_to_individual
 from geolocalisation.class_geolocalisation import Geolocalisation
 
 

app/physical/class_physical.py

@@ -74,5 +74,6 @@ AnomalyType = Union[
 ]
 
 # Main PhysicalAnomaly class that logs anomalies across different body parts
-class PhysicalAnomaly(BaseModel):
-    body_part_anomalies: List[AnomalyType] = Field(..., discriminator='type')
+class PhysicalAnomalies(BaseModel):
+    physical_radio: str
+    physical_anomalies_type: List[AnomalyType] = Field(..., discriminator='type')

app/physical/physical_checkbox.py

@@ -1,7 +1,7 @@
 import gradio as gr
 from utils.utils_config import get_custom_config_dropdowns
 from utils.utils_checkbox import create_checkbox
-from validation_submission.add_json import add_data_to_individual 
+from validation_submission.add_json import add_data_tmp 
 #--------------------------------------------------------- 
 def get_body_parts():
     dropdown_config = get_custom_config_dropdowns("config_checkbox_physical.json")
@@ -72,7 +72,8 @@ def process_body_parts(section, matched_box):
 #--------------------------------------------------------- 
 
 def on_select_body_part(body_part_checkbox, body_part): 
-    add_data_to_individual("physical_changes_" + body_part, body_part_checkbox)
+    add_data_tmp("wounded_dead", "physical_type_"+body_part, body_part)
+    add_data_tmp("wounded_dead", "physical_anomaly_type_"+body_part, body_part_checkbox)
 
 #--------------------------------------------------------- 
 

app/physical/physical_select_animal.py

@@ -40,6 +40,7 @@ def create_bird_anatomy(visible, section: str):
 def show_physical(choice, section: str): 
     visible = set_visible(choice)
     physical_boxes = create_bird_anatomy(visible, section)
+    add_data_tmp("wounded_dead", "physical_radio", choice)
     return physical_boxes
 
 

app/validation_submission/create_json.py

@@ -10,7 +10,7 @@ def create_json_all_individuals(all_individuals={}):
     with open("data/all_individuals.json", "w") as outfile:
         outfile.write(all_individuals)
 
-def create_tmp(tmp_name, tmp={}):
+def create_tmp(tmp_name="wounded_dead", tmp={}):
     tmp = json.dumps(tmp)
     with open(f"app/assets/json_tmp/tmp_{tmp_name}.json", "w") as outfile:
         outfile.write(tmp)

app/validation_submission/validation.py

@@ -1,6 +1,8 @@
 from validation_submission.get_json import get_json_tmp, get_json_one_individual
 from classes import Report
-from circumstances.class_circumstance import Circumstance
+from circumstances.class_circumstance import Circumstances
+from behavior.class_behavior import Behaviors
+from physical.class_physical import PhysicalAnomalies
 
 def get_fields(data_dict, keyword): 
     extract = {} 
@@ -11,8 +13,8 @@ def get_fields(data_dict, keyword):
 
 def validate_individual():
     data = get_json_tmp("wounded_dead")
-    validate_circumstance(data)
-    validate_behavior(data)
+    circumstance = validate_circumstance(data)
+    behaviors = validate_behavior(data)
     validate_physical(data)
     validate_follow_up(data)
     validate_individual()
@@ -22,16 +24,81 @@ def validate_individual():
 def validate_circumstance(data): 
     circumstance_raw = get_fields(data, "circumstance")
     circumstance_formatted = process_circumstance(circumstance_raw)
-    if not Circumstance(circumstance_formatted).validate(): 
+    if not Circumstances(**circumstance_formatted).validate(): 
         print("Validation failed for the circumstance.")
-    pass
+    else: 
+        return Circumstances(**circumstance_formatted)
+
 def process_circumstance(data):
-    pass
+    fields_to_check = ["option_dropdown", "open_field", "extra"]
+    for field in fields_to_check:
+        if data["circumstance_type"][field+"_label"] == "NA":
+            data["circumstance_type"].pop([field+"_label"])
+        else :
+            key = data[f"circumstance_{field}"]
+            val = data["circumstance_type"][field+"_label"]
+            data["circumstance_type"][key] = val
+            data["circumstance_type"].pop([field+"_label"])
+    # {"circumstance_radio": true, 
+    #  "circumstance": "destruction / deliberatly removed", 
+    #  "cirumstance_type": {"type": "removal or direct capture", 
+    #                       "option_dropdown_label": "method",
+    #                       "open_field_label": "NA", 
+    #                       "extra_label": "NA"}, 
+    # "circumstance_option_dropdown": "Traffic/Trade"}
+    return data
 
 def validate_behavior(data): 
-    pass
+    behaviors_raw = get_fields(data, "behaviours")
+    behaviors_formatted = process_behaviors(behaviors_raw)
+    if not Behaviors(**behaviors_formatted).validate(): 
+        print("Validation failed for the behaviours.")
+    else: 
+        return Behaviors(**behaviors_formatted)
+
+def process_behaviors(data):
+    # INPUT  : 
+    #"behaviors_radio": true, 
+    # "behaviors_type": ["Crash, Falling From The Sky", "Neurological"]
+    #OUTPUT: 
+#     "behaviors_radio": "Yes",
+#   "behaviors_type": [
+#     {
+#       "type": "abnormal breathing",
+#       "description": "Problems breathing, breathing sounds"
+#     }
+    behaviors =[]
+    for type in data["behaviors_type"]: 
+        new_behavior = {}
+        new_behavior["type"] = type
+        behaviors.append(new_behavior)
+    data["behaviors_type"] = behaviors
+    return data 
 
 def validate_physical(data): 
+    physical_raw = get_fields(data, "physical")
+    physical_formatted = process_physical(physical_raw)
+    if not PhysicalAnomalies(**physical_formatted).validate(): 
+        print("Validation failed for the physical anomalies.")
+    else: 
+        return PhysicalAnomalies(**physical_formatted)
+
+def process_physical(data):
+    # INPUT
+    # "physical_type_feathers": "feathers", 
+    # "physical_anomaly_type_feathers": ["Blood", "Swelling"]}
+    # OUTPUT
+#     "physical_radio": "Yes",
+#   "physical_anomalies_type": [
+#     {
+#       "type": "beak",
+#       "anomaly_type": "deformation"
+#     },
+#     {
+#       "type": "body",
+#       "anomaly_type": "fluffed up"
+#     },
+
     pass
 
 def validate_follow_up(data):