feat: validation for follow up events

.gitignore

@@ -8,6 +8,7 @@ __pycache__/
 #Data 
 test/data/**
 data/**
+app/assets/tmp_json/** 
 
 # C extensions
 *.so

app/assets/json_tmp/tmp_wounded_dead.json

@@ -1 +0,0 @@
-{"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/classes.py

@@ -3,19 +3,19 @@ from typing import Literal, List, Union, Optional
 
 from behavior.class_behavior import Behaviors
 from circumstances.class_circumstance import Circumstances
-from physical.class_physical import PhysicalAnomaly
+from physical.class_physical import PhysicalAnomalies
 from follow_up.class_follow_up import FollowUpEvents
 from geolocalisation.class_geolocalisation import Geolocalisation
 
 class Wounded(BaseModel):
     circumstances: Circumstances
     behaviors: List[Behaviors]
-    physical_anomalies: List[PhysicalAnomaly]
+    physical_anomalies: List[PhysicalAnomalies]
     follow_up_events: List[FollowUpEvents]
 
 class Dead(BaseModel):
     circumstances: List[Circumstances] 
-    physical_anomalies: List[PhysicalAnomaly]
+    physical_anomalies: List[PhysicalAnomalies]
     follow_up_events: List[FollowUpEvents]
 
 class Image(BaseModel):

app/follow_up/class_follow_up.py

@@ -6,22 +6,22 @@ from typing import Literal, Union, Optional, List
 # Animal collected event
 class AnimalCollectedEvent(BaseModel):
     type: Literal['animal collected']
-    option: Literal['Yes', 'No']
+    collected: Literal['Yes', 'No']
 
 # Recipient event
 class RecipientEvent(BaseModel):
     type: Literal['recipient']
-    option: Literal['Veterinary', 'Care center', 'Local Museum', 'National Museum', 'Other']
-
+    recipient: Literal['Veterinary', 'Care center', 'Local Museum', 'National Museum', 'Other']
+    
 # Radiography event
 class RadiographyEvent(BaseModel):
     type: Literal['radiography']
-    option: Literal['Yes', 'No', 'Unknown']
+    radiography: Literal['Yes', 'No', 'Unknown']
 
 # Given answer event
 class GivenAnswerEvent(BaseModel):
     type: Literal['given answer']
-    option: Literal[
+    answer: Literal[
         'Nothing', 
         'Complaint against X', 
         'Complaint', 
@@ -33,7 +33,7 @@ class GivenAnswerEvent(BaseModel):
 
 # Name of recipient/museum (open text field)
 class NameOfRecipientEvent(BaseModel):
-    type: Literal['name of recipient / museum']
+    type: Literal['recipient name']
     name: str  # Open text field for entering the name
 
 # Collection reference (open text field)

app/follow_up/followup_events.py

@@ -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_tmp("wounded_dead", key.lower(), value.lower())
+    add_data_tmp("wounded_dead", "followup " + key.lower(), value.lower())
 
 
     

app/main_multianimal.py

@@ -210,21 +210,21 @@ with gr.Blocks(theme=theme, css=css) as demo:
         
         # ---------------------------------------------------------
         # Follow Up Events Wounded 
-        fe_collection_dropdown_wounded.select(save_fe, inputs=[fe_collection_dropdown_wounded, gr.Textbox("fe_collection", visible=False)])
-        fe_recepient_dropdown_wounded.select(save_fe, inputs=[fe_recepient_dropdown_wounded, gr.Textbox("fe_recipient", visible=False)])
-        fe_radio_dropdown_wounded.select(save_fe, inputs=[fe_radio_dropdown_wounded, gr.Textbox("fe_radio", visible=False)]) 
-        fe_answer_dropdown_wounded.select(save_fe, inputs=[fe_answer_dropdown_wounded, gr.Textbox("fe_answer", visible=False)])
-        fe_name_recipient_wounded.input(save_fe, inputs=[fe_name_recipient_wounded, gr.Textbox("fe_name_recipient", visible=False)])
-        fe_collection_ref_wounded.input(save_fe, inputs=[fe_collection_ref_wounded, gr.Textbox("fe_collection_ref", visible=False)])
+        fe_collection_dropdown_wounded.select(save_fe, inputs=[fe_collection_dropdown_wounded, gr.Textbox("animal collected", visible=False)])
+        fe_recepient_dropdown_wounded.select(save_fe, inputs=[fe_recepient_dropdown_wounded, gr.Textbox("recipient", visible=False)])
+        fe_radio_dropdown_wounded.select(save_fe, inputs=[fe_radio_dropdown_wounded, gr.Textbox("radiography", visible=False)]) 
+        fe_answer_dropdown_wounded.select(save_fe, inputs=[fe_answer_dropdown_wounded, gr.Textbox("given answer", visible=False)])
+        fe_name_recipient_wounded.input(save_fe, inputs=[fe_name_recipient_wounded, gr.Textbox("recipient name", visible=False)])
+        fe_collection_ref_wounded.input(save_fe, inputs=[fe_collection_ref_wounded, gr.Textbox("collection reference", visible=False)])
 
         # ---------------------------------------------------------
         # Follow Up Events Dead 
-        fe_collection_dropdown_dead.select(save_fe, inputs=[fe_collection_dropdown_dead, gr.Textbox("fe_collection", visible=False)])
-        fe_recepient_dropdown_dead.select(save_fe, inputs=[fe_recepient_dropdown_dead, gr.Textbox("fe_recipient", visible=False)])
-        fe_radio_dropdown_dead.select(save_fe, inputs=[fe_radio_dropdown_dead, gr.Textbox("fe_radio", visible=False)]) 
-        fe_answer_dropdown_dead.select(save_fe, inputs=[fe_answer_dropdown_dead, gr.Textbox("fe_answer", visible=False)])
-        fe_name_recipient_dead.input(save_fe, inputs=[fe_name_recipient_dead, gr.Textbox("fe_name_recipient", visible=False)])
-        fe_collection_ref_dead.input(save_fe, inputs=[fe_collection_ref_dead, gr.Textbox("fe_collection_ref", visible=False)])
+        fe_collection_dropdown_dead.select(save_fe, inputs=[fe_collection_dropdown_dead, gr.Textbox("animal collected", visible=False)])
+        fe_recepient_dropdown_dead.select(save_fe, inputs=[fe_recepient_dropdown_dead, gr.Textbox("recipient", visible=False)])
+        fe_radio_dropdown_dead.select(save_fe, inputs=[fe_radio_dropdown_dead, gr.Textbox("radiography", visible=False)]) 
+        fe_answer_dropdown_dead.select(save_fe, inputs=[fe_answer_dropdown_dead, gr.Textbox("given answer", visible=False)])
+        fe_name_recipient_dead.input(save_fe, inputs=[fe_name_recipient_dead, gr.Textbox("recipient name", visible=False)])
+        fe_collection_ref_dead.input(save_fe, inputs=[fe_collection_ref_dead, gr.Textbox("collection reference", visible=False)])
 
         # ---------------------------------------------------------
         # Add One Individual's Data to the Dataframe

app/validation_submission/validation.py

@@ -3,6 +3,7 @@ from classes import Report
 from circumstances.class_circumstance import Circumstances
 from behavior.class_behavior import Behaviors
 from physical.class_physical import PhysicalAnomalies
+from follow_up.class_follow_up import FollowUpEvents
 
 def get_fields(data_dict, keyword): 
     extract = {} 
@@ -20,14 +21,7 @@ def validate_individual():
     validate_individual()
     pass
 
-
-def validate_circumstance(data): 
-    circumstance_raw = get_fields(data, "circumstance")
-    circumstance_formatted = process_circumstance(circumstance_raw)
-    if not Circumstances(**circumstance_formatted).validate(): 
-        print("Validation failed for the circumstance.")
-    else: 
-        return Circumstances(**circumstance_formatted)
+#### PROCESS FUNCTIONS 
 
 def process_circumstance(data):
     fields_to_check = ["option_dropdown", "open_field", "extra"]
@@ -48,14 +42,6 @@ def process_circumstance(data):
     # "circumstance_option_dropdown": "Traffic/Trade"}
     return data
 
-def validate_behavior(data): 
-    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, 
@@ -75,18 +61,11 @@ def process_behaviors(data):
     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": [
@@ -98,11 +77,87 @@ def process_physical(data):
 #       "type": "body",
 #       "anomaly_type": "fluffed up"
 #     },
+    body_parts= ["beak", "body", "legs", "feathers", "head"]
+    anomalies=[]
+    reformatted = {}
+    reformatted["physical_radio"] = data["physical_radio"]
+    for body_part in body_parts:
+        anomaly = {}
+        for key, val in data.items(): 
+            if "type_"+ body_part in key:
+                anomaly["type"] = val
+            elif "anomaly_type_"+ body_part in key:
+                anomaly["anomaly_type"] = val
+        anomalies.append(anomaly)
+    reformatted["physical_anomalies_type"] = anomalies
+    return reformatted
 
-    pass
+def process_followup(data):
+    #     "follow_up_events": [
+#     {
+#       "type": "animal collected",
+#       "option": "Yes"
+#     },
+#     {
+#       "type": "recipient",
+#       "option": "Veterinary",
+#       "name_recipient": "Dr. Jane Smith"
+#     },
+#     {
+#       "type": "radiography",
+#       "option": "Unknown"
+#     },
+#     {
+#       "type": "given answer",
+#       "option": "Discussion with the speaker"
+#     },
+#     {
+#       "type": "collection reference",
+#       "reference": "Specimen ID: 12345, Collected on 2023-09-15"
+#     }
+#   ]
+    followup_events = []
+    for key, val in data.items(): 
+        followup_event={}
+        type = key.split("followup")[-1]
+        option = type.split(" ")[-1]
+        followup_event["type"] = type
+        followup_event[option] = val 
+        followup_events.append(followup_event)
+    return followup_events
+
+#### VALIDATION FUNCTIONS
+def validate_circumstance(data): 
+    circumstance_raw = get_fields(data, "circumstance")
+    circumstance_formatted = process_circumstance(circumstance_raw)
+    if not Circumstances(**circumstance_formatted).validate(): 
+        print("Validation failed for the circumstance.")
+    else: 
+        return Circumstances(**circumstance_formatted)
+
+def validate_behavior(data): 
+    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 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 validate_follow_up(data):
-    pass
+    followup_raw = get_fields(data, "followup")
+    followup_formatted = process_followup(followup_raw)
+    if not FollowUpEvents(**followup_formatted).validate(): 
+        print("Validation failed for the follow-up events.")
+    else:
+        return FollowUpEvents(**followup_formatted)
 
 def validate_individual():
     individual = get_json_one_individual()