refactor: folders for code subparts and pydantic classes

app/archive_main_old.py

@@ -1,199 +0,0 @@
-import gradio as gr
-from functools import partial
-from dead import show_section_dead
-from wounded import show_section_wounded
-from circumstances import show_causes
-from circumstances_dropdowns import *
-from physical_select_animal import show_physical, find_bounding_box
-from behavior_checkbox import show_behavior
-from maps import get_location
-from style import *
-from theme import theme, css
-
-with gr.Blocks(theme=theme, css=css) as demo:
-    # ---------------------------------------------------------
-    # Intro Text
-    with gr.Row():
-        with gr.Column(scale=1):
-            title = gr.Markdown("# Welcome to Digiwild", label="Title")
-            description = gr.Markdown("Please record your wildlife observations here !", label="description")
-
-    # ---------------------------------------------------------
-    # Camera
-    with gr.Row():
-        #with gr.Column(scale=1):
-        camera = gr.Image(elem_id="image")
-            
-    # ---------------------------------------------------------
-    # Location
-    #with gr.Row():
-        with gr.Column(scale=1):
-            location = gr.Textbox(visible=True, interactive=True, label="Location of Sighting")
-            #display location processing
-            identified_location= gr.Textbox(visible=False, interactive=False, 
-                                            label="Identified GPS Location")
-            with gr.Row():
-                #to clear it
-                clear_location = gr.ClearButton(components=[location], visible=True, interactive=True, scale=1
-                                                )
-                clear_location.click()
-                #to submit it
-                submit_location = gr.Button("Get GPS Coordinates", visible=True, interactive=True, scale=3)
-                submit_location.click(get_location, inputs=[location], outputs=[identified_location])
-    
-    # ---------------------------------------------------------
-    # ---------------------------------------------------------
-    # ---------------------------------------------------------
-    # ---------------------------------------------------------
-    with gr.Tab("Animal 1"):
-    # ---------------------------------------------------------
-        # Dead and Wounded Buttons
-        gr.Markdown("## The State of the Animal", label="Title")
-        gr.Markdown("Please tell us if the animal was wounded or dead.", label="description")
-        with gr.Row() as block_form:
-            with gr.Column(scale=1):
-                butt_wounded = gr.Button("Wounded", elem_id="wounded")
-            with gr.Column(scale=1):
-                butt_dead = gr.Button("Dead", elem_id="dead")
-
-        # ---------------------------------------------------------
-        # Initiate sections
-        section_dead, \
-            button_collision_dead, button_deliberate_destruction_dead, button_indirect_destruction_dead, button_natural_cause_dead, \
-                dropdown_dead, dropdown_level2_dead, openfield_level2_dead, dropdown_extra_level2_dead \
-                    = show_section_dead(False)
-        section_wounded, radio_cause_wounded, radio_behavior_wounded, radio_physical_wounded, \
-            button_collision_wounded, button_deliberate_destruction_wounded, button_indirect_destruction_wounded, button_natural_cause_wounded, \
-                dropdown_wounded, dropdown_level2_wounded, openfield_level2_wounded, dropdown_extra_level2_wounded, \
-                    behavior_checkbox, behavior_text, \
-                        physical_boxes_wounded, \
-                            checkbox_beak, text_beak, checkbox_body, text_body, checkbox_feathers, text_feathers, checkbox_head, text_head, checkbox_legs, text_legs \
-                            = show_section_wounded(False)
-    
-    # ---------------------------------------------------------
-    # ---------------------------------------------------------
-    # ---------------------------------------------------------
-    with gr.Tab("Animal 2"):
-    # ---------------------------------------------------------
-        # Dead and Wounded Buttons
-        gr.Markdown("## The State of the Animal", label="Title")
-        gr.Markdown("Please tell us if the animal was wounded or dead.", label="description")
-        with gr.Row() as block_form:
-            with gr.Column(scale=1):
-                butt_wounded = gr.Button("Wounded", elem_id="wounded")
-            with gr.Column(scale=1):
-                butt_dead = gr.Button("Dead", elem_id="dead")
-
-        # ---------------------------------------------------------
-        # Initiate sections
-        section_dead, \
-            button_collision_dead, button_deliberate_destruction_dead, button_indirect_destruction_dead, button_natural_cause_dead, \
-                dropdown_dead, dropdown_level2_dead, openfield_level2_dead, dropdown_extra_level2_dead \
-                    = show_section_dead(False)
-        section_wounded, radio_cause_wounded, radio_behavior_wounded, radio_physical_wounded, \
-            button_collision_wounded, button_deliberate_destruction_wounded, button_indirect_destruction_wounded, button_natural_cause_wounded, \
-                dropdown_wounded, dropdown_level2_wounded, openfield_level2_wounded, dropdown_extra_level2_wounded, \
-                    behavior_checkbox, behavior_text, \
-                        physical_boxes_wounded, \
-                            checkbox_beak, text_beak, checkbox_body, text_body, checkbox_feathers, text_feathers, checkbox_head, text_head, checkbox_legs, text_legs \
-                            = show_section_wounded(False)
-    # ---------------------------------------------------------
-    # ---------------------------------------------------------
-    # ---------------------------------------------------------
-        
-    # ---------------------------------------------------------
-    # Dead Button Logic
-    partial_show_section_dead = partial(show_section_dead, True)
-    partial_hide_section_wounded = partial(show_section_wounded, False)
-    butt_dead.click(partial_show_section_dead, 
-                    inputs=None, 
-                    outputs=[section_dead, 
-                            button_collision_dead, button_deliberate_destruction_dead, button_indirect_destruction_dead, button_natural_cause_dead, 
-                            dropdown_dead, dropdown_level2_dead, openfield_level2_dead, dropdown_extra_level2_dead
-                            ])
-    butt_dead.click(partial_hide_section_wounded, 
-                    inputs=None, 
-                    outputs=[section_wounded, 
-                            radio_cause_wounded, radio_behavior_wounded, radio_physical_wounded,
-                            button_collision_wounded, button_deliberate_destruction_wounded, button_indirect_destruction_wounded, button_natural_cause_wounded, 
-                            dropdown_wounded, dropdown_level2_wounded, openfield_level2_wounded, dropdown_extra_level2_wounded,
-                            behavior_checkbox, behavior_text, 
-                            physical_boxes_wounded, 
-                            checkbox_beak, text_beak, checkbox_body, text_body, checkbox_feathers, text_feathers, checkbox_head, text_head, checkbox_legs, text_legs
-                            ])
-    # ---------------------------------------------------------
-    # Wounded Button Logic
-    partial_show_section_wounded = partial(show_section_wounded, True)
-    partial_hide_section_dead = partial(show_section_dead, False)
-
-    butt_wounded.click(partial_show_section_wounded, 
-                       inputs=None, 
-                       outputs=[section_wounded, 
-                                radio_cause_wounded, radio_behavior_wounded, radio_physical_wounded,
-                                button_collision_wounded, button_deliberate_destruction_wounded, button_indirect_destruction_wounded, button_natural_cause_wounded, 
-                                dropdown_wounded, dropdown_level2_wounded, openfield_level2_wounded, dropdown_extra_level2_wounded,
-                                behavior_checkbox, behavior_text, 
-                                physical_boxes_wounded, 
-                                checkbox_beak, text_beak, checkbox_body, text_body, checkbox_feathers, text_feathers, checkbox_head, text_head, checkbox_legs, text_legs
-                                ])
-    butt_wounded.click(partial_hide_section_dead, inputs=None, outputs=[section_dead, 
-                                                                        button_collision_dead, button_deliberate_destruction_dead, button_indirect_destruction_dead, button_natural_cause_dead, 
-                                                                        dropdown_dead, dropdown_level2_dead, openfield_level2_dead, dropdown_extra_level2_dead
-                                                                        ])
-    # ---------------------------------------------------------
-    # Dropdowns Dead
-    button_collision_dead.click(dropdown_collision,  
-                                outputs=[dropdown_dead, dropdown_level2_dead, openfield_level2_dead, dropdown_extra_level2_dead])
-    button_deliberate_destruction_dead.click(dropdown_deliberate_destruction, outputs=[dropdown_dead, dropdown_level2_dead, openfield_level2_dead, dropdown_extra_level2_dead])
-    button_indirect_destruction_dead.click(dropdown_indirect_destruction, outputs=[dropdown_dead, dropdown_level2_dead, openfield_level2_dead, dropdown_extra_level2_dead])
-    button_natural_cause_dead.click(dropdown_natural_cause, outputs=[dropdown_dead, dropdown_level2_dead, openfield_level2_dead, dropdown_extra_level2_dead])
-
-    dropdown_dead.select(on_select, None, [dropdown_level2_dead, openfield_level2_dead, dropdown_extra_level2_dead])
-
-    # ---------------------------------------------------------
-    # Radio Cause Wounded
-    radio_cause_wounded.change(fn=show_causes,
-                              inputs=[radio_cause_wounded],
-                              outputs=[button_collision_wounded, button_deliberate_destruction_wounded, button_indirect_destruction_wounded, button_natural_cause_wounded, 
-                                        dropdown_wounded, dropdown_level2_wounded, openfield_level2_wounded, dropdown_extra_level2_wounded]
-                              )
-    
-    # Dropdowns Cause Wounded
-    button_collision_wounded.click(dropdown_collision,  
-                                outputs=[dropdown_wounded, dropdown_level2_wounded, openfield_level2_wounded, dropdown_extra_level2_wounded])
-    button_deliberate_destruction_wounded.click(dropdown_deliberate_destruction, outputs=[dropdown_wounded, dropdown_level2_wounded, openfield_level2_wounded, dropdown_extra_level2_wounded])
-    button_indirect_destruction_wounded.click(dropdown_indirect_destruction, outputs=[dropdown_wounded, dropdown_level2_wounded, openfield_level2_wounded, dropdown_extra_level2_wounded])
-    button_natural_cause_wounded.click(dropdown_natural_cause, outputs=[dropdown_wounded, dropdown_level2_wounded, openfield_level2_wounded, dropdown_extra_level2_wounded])
-    
-    dropdown_wounded.select(on_select, None, [dropdown_level2_wounded, openfield_level2_wounded, dropdown_extra_level2_wounded])
-
-    # ---------------------------------------------------------
-    # Radio Behavior Wounded
-    radio_behavior_wounded.change(fn=show_behavior,
-                                  inputs=[radio_behavior_wounded, gr.Text("wounded", visible=False)],
-                                  outputs=[behavior_checkbox, behavior_text])
-
-    # ---------------------------------------------------------
-    # Radio Physical Wounded
-    radio_physical_wounded.change(fn=show_physical,
-                                  inputs=[radio_physical_wounded, gr.Text("wounded", visible=False)],
-                                  outputs=[physical_boxes_wounded])
-
-    # Checkbox Physical Wounded
-    physical_boxes_wounded.select(find_bounding_box, 
-                     inputs=[physical_boxes_wounded, gr.Textbox(value="wounded", visible=False)], 
-                     outputs=[checkbox_beak, text_beak, checkbox_body, text_body, checkbox_feathers, text_feathers, checkbox_head, text_head, checkbox_legs, text_legs
-                                ])
-    
-    # ---------------------------------------------------------
-    #Submit Button
-    with gr.Column(scale=1):
-        subbutt = gr.Button("SUBMIT YOUR OBSERVATION TO ORNITHO", 
-                            elem_id="submit", 
-                            icon="https://cdn.iconscout.com/icon/free/png-256/free-send-2451554-2082560.png",
-                            scale=1)
-        output_message = gr.Markdown("Thank you, you are a champion of biodiversity conservation !")
-
-    
-
-demo.launch(server_name="0.0.0.0")

app/{behavior_checkbox.py → behavior/behavior_checkbox.py}

@@ -1,8 +1,8 @@
 import gradio as gr
-from utils_config import get_custom_config_dropdowns
-from utils_checkbox import create_checkbox
-from utils_visible import set_visible
-from utils_json import add_data_to_individual 
+from utils.utils_config import get_custom_config_dropdowns
+from utils.utils_checkbox import create_checkbox
+from utils.utils_visible import set_visible
+from utils.utils_json import add_data_to_individual 
 
 def on_select_behavior(behavior_checkbox): 
     add_data_to_individual("behavior", behavior_checkbox)

app/behavior/class_behavior.py

@@ -0,0 +1,66 @@
+from pydantic import BaseModel, Field
+from typing import Literal, List, Union
+
+
+class Behavior(BaseModel):
+    type: str
+    description: str
+
+# --- Specific Behavior classes ---
+class AbnormalBreathing(Behavior):
+    type: Literal['abnormal breathing']
+    description: Literal["Problems breathing, breathing sounds"]
+
+class CrashFalling(Behavior):
+    type: Literal['crash, falling from the sky']
+    description: Literal["Suddenly falling from the sky"]
+
+class Diarrhea(Behavior):
+    type: Literal['diarrhea']
+    description: Literal["Observed diarrhea"]
+
+class Lameness(Behavior):
+    type: Literal['lameness']
+    description: Literal["Apparent limping or not able to walk properly"]
+
+class Neurological(Behavior):
+    type: Literal['neurological']
+    description: Literal["Circling, incoordination, tremors, convulsions, fast eye movements"]
+
+class OtherAbnormalBehavior(Behavior):
+    type: Literal['other abnormal behavior']
+    description: Literal["Other than weakness, other than neurologic"]
+
+class UnableToFly(Behavior):
+    type: Literal['unable to fly']
+    description: Literal["Animal alert and tries to fly but can not take off"]
+
+class Vomiting(Behavior):
+    type: Literal['vomiting']
+    description: Literal["Throwing up undigested food, regurgitating"]
+
+class Weakness(Behavior):
+    type: Literal['weakness']
+    description: Literal["Non responsive, does not fly away when approached, lethargy"]
+
+class NoChanges(Behavior):
+    type: Literal['no changes']
+    description: Literal["Animal is acting normally"]
+
+# Union of all possible behaviors
+BehaviorType = Union[
+    AbnormalBreathing,
+    CrashFalling,
+    Diarrhea,
+    Lameness,
+    Neurological,
+    OtherAbnormalBehavior,
+    UnableToFly,
+    Vomiting,
+    Weakness,
+    NoChanges
+]
+
+# Main class that logs multiple behaviors
+class Behaviors(BaseModel):
+    observed_behaviors: List[BehaviorType]

app/{circumstances.py → circumstances/circumstances.py}

@@ -1,6 +1,6 @@
 import gradio as gr
 import os
-from utils_visible import set_visible
+from utils.utils_visible import set_visible
 from dotenv import load_dotenv
 import os
 load_dotenv()
@@ -11,17 +11,17 @@ LOGO_PATH = PATH + PATH_ASSETS + "logos"
 CAUSE_COL_WIDTH = "50px"
 
 
-def show_causes(choice): 
+def show_circumstances(choice): 
     visible = set_visible(choice)
-    button_collision, button_deliberate_destruction, button_indirect_destruction, button_natural_cause, dropdown, dropdown_level2, openfield_level2, dropdown_extra_level2 = create_causes(visible)
+    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
 
-def create_causes(visible):
-    button_collision, button_deliberate_destruction, button_indirect_destruction, button_natural_cause = create_causes_buttons(visible)      
-    dropdown, dropdown_level2, openfield_level2, dropdown_extra_level2 = create_causes_dropdown(visible)
+def create_circumstances(visible):
+    button_collision, button_deliberate_destruction, button_indirect_destruction, button_natural_cause = create_circumstances_buttons(visible)      
+    dropdown, dropdown_level2, openfield_level2, dropdown_extra_level2 = create_circumstances_dropdown(visible)
     return button_collision, button_deliberate_destruction, button_indirect_destruction, button_natural_cause, dropdown, dropdown_level2, openfield_level2, dropdown_extra_level2
 
-def create_causes_buttons(visible): 
+def create_circumstances_buttons(visible): 
     with gr.Row() as image_row:
             with gr.Column(scale=1, min_width=CAUSE_COL_WIDTH):
                 button_collision = gr.Button("Collision with a means of transport", 
@@ -48,7 +48,7 @@ def create_causes_buttons(visible):
                                                  elem_id="buttons-conditions")
     return button_collision, button_deliberate_destruction, button_indirect_destruction, button_natural_cause
 
-def create_causes_dropdown(visible):
+def create_circumstances_dropdown(visible):
     with gr.Row() as dropdown_row:
         dropdown = gr.Dropdown(choices=[], 
                                label="Choices will appear here...",

app/{circumstances_dropdowns.py → circumstances/circumstances_dropdowns.py}

@@ -1,6 +1,6 @@
 import gradio as gr
-from utils_config import get_custom_config_dropdowns
-from utils_json import add_data_to_individual  
+from utils.utils_config import get_custom_config_dropdowns
+from utils.utils_json import add_data_to_individual  
 
 #--------------------------------------------------------- LEVEL 1 DROPDOWNS
 def retrieve_config_options(label, dropdown_config):
@@ -15,7 +15,7 @@ def reinitialise_level2():
     return dropdown_level2, openfield_level2, dropdown_extra_level2
 
 def create_dropdown_level1(label): 
-    dropdown_config = get_custom_config_dropdowns("config_dropdown_conditions.json")
+    dropdown_config = get_custom_config_dropdowns("config_dropdown_circumstances.json")
     options = retrieve_config_options(label, dropdown_config)
     dropdown = gr.Dropdown(choices=options, label=label, interactive=True, visible=True)
     dropdown_level2, openfield_level2, dropdown_extra_level2 = reinitialise_level2()
@@ -49,7 +49,7 @@ def get_options(value):
         open_field = None
         extras = None
         extras_label = None
-        dropdown_config = get_custom_config_dropdowns("config_dropdown_conditions.json")
+        dropdown_config = get_custom_config_dropdowns("config_dropdown_circumstances.json")
         for _, sub_dict in dropdown_config.items():
             nested_dict = sub_dict.get(value)
             if nested_dict is not None: 

app/circumstances/class_circumstance.py

@@ -0,0 +1,171 @@
+from pydantic import BaseModel, Field
+from typing import Literal, List, Union, Optional
+
+# Base class for CircumstanceType with a discriminator field 'type'
+class CircumstanceTypeBase(BaseModel):
+    type: str
+
+# Collision with means of transport
+class RoadVehicleCollision(CircumstanceTypeBase):
+    type: Literal['road_vehicle']
+    infrastructure_number: Optional[str] = None
+    road_type: Literal['highway', 'main road', 'secondary road', 'local road/path/trail', 'parking lot', 'other', 'unknown']
+
+class TrainCollision(CircumstanceTypeBase):
+    type: Literal['train']
+    infrastructure_number: str
+
+class AircraftCollision(CircumstanceTypeBase):
+    type: Literal['aircraft']
+
+class BoatCollision(CircumstanceTypeBase):
+    type: Literal['boat']
+
+class OtherTransportCollision(CircumstanceTypeBase):
+    type: Literal['other']
+
+class UnknownTransportCollision(CircumstanceTypeBase):
+    type: Literal['unknown']
+
+# Destruction / Deliberately removed
+class HuntingDestruction(CircumstanceTypeBase):
+    type: Literal['hunting']
+    method: Literal['shooting', 'bow', 'falconry', 'hounds hunting', 'digging up', 'other', 'unknown']
+
+class TrapDestruction(CircumstanceTypeBase):
+    type: Literal['trap']
+    method: Literal['killing trap', 'pole trap', 'trap cage', 'corvids nasse', 'net', 'cage trap', 'fall-trap', 'glue trap', 'insect trap', 'other', 'unknown']
+
+class PoisoningDestruction(CircumstanceTypeBase):
+    type: Literal['poisoning']
+
+class RemovalDestruction(CircumstanceTypeBase):
+    type: Literal['removal or direct capture']
+    method: Literal['gassing', 'raptor captured at nest', 'brood destruction', 'traffic/trade', 'capture accident', 'scientific sample', 'other', 'unknown']
+
+class FishingDestruction(CircumstanceTypeBase):
+    type: Literal['fishing']
+    method: Literal['drowned/tangled', 'beached with capture indications', 'other', 'unknown']
+
+class OtherDestruction(CircumstanceTypeBase):
+    type: Literal['other']
+
+class UnknownDestruction(CircumstanceTypeBase):
+    type: Literal['unknown']
+
+# Indirect destruction
+class PylonElectricGridDestruction(CircumstanceTypeBase):
+    type: Literal['pylone and electric grid']
+    infrastructure: Literal['electric line', 'pole/pylon', 'other', 'unknown']
+    cause: Literal['collision', 'electrocution', 'unknown']
+
+class WindfarmDestruction(CircumstanceTypeBase):
+    type: Literal['windfarm']
+
+class OtherCollisionDestruction(CircumstanceTypeBase):
+    type: Literal['other collision']
+    object: Literal['window', 'building', 'lighthouse', 'cable', 'wire fence/barbed wire', 'other crash', 'unknown']
+
+class FallDestruction(CircumstanceTypeBase):
+    type: Literal['fall']
+    location: Literal['chimney', 'empty pole', 'hole/well', 'other', 'unknown']
+
+class DevelopmentWorkDestruction(CircumstanceTypeBase):
+    type: Literal['development work']
+    work_type: Literal['transport infrastructure', 'building', 'other', 'unknown']
+
+class PollutionContaminationDestruction(CircumstanceTypeBase):
+    type: Literal['pollution / contamination']
+    pollution_type: Literal['oil pollution', 'chemical pollution', 'heavy metals', 'light', 'noise', 'plastic ingestion', 'other', 'unknown']
+
+class AgriculturalNetProtectionDestruction(CircumstanceTypeBase):
+    type: Literal['agricultural net protection']
+
+class VegetalForestWorkDestruction(CircumstanceTypeBase):
+    type: Literal['vegetal / forest work']
+    work_type: Literal['clearing/mowing/plowing', 'tree felling/pruning', 'other', 'unknown']
+
+class OtherIndirectDestruction(CircumstanceTypeBase):
+    type: Literal['other']
+
+class UnknownIndirectDestruction(CircumstanceTypeBase):
+    type: Literal['unknown']
+
+# Natural cause
+class Predation(CircumstanceTypeBase):
+    type: Literal['predation']
+    predator: Literal['cat', 'dog', 'rooster/hen', 'other domestic animal', 'wild birds', 'wild mammal', 'other', 'unknown']
+
+class Weather(CircumstanceTypeBase):
+    type: Literal['weather']
+    condition: Literal['cold wave', 'drought', 'hail', 'lightening', 'storm', 'other', 'unknown']
+
+class NaturalDisaster(CircumstanceTypeBase):
+    type: Literal['natural disaster']
+    disaster: Literal['fire', 'avalanche', 'rock fall', 'mudslide', 'volcanic eruption/ashes', 'other', 'unknown']
+
+class NestFall(CircumstanceTypeBase):
+    type: Literal['nest fall']
+
+class StrandingExhaustion(CircumstanceTypeBase):
+    type: Literal['stranding due to exhaustion']
+
+class DiseaseParasite(CircumstanceTypeBase):
+    type: Literal['disease/parasite']
+
+class AccidentalDrowning(CircumstanceTypeBase):
+    type: Literal['accidental drowning']
+    drowning_location: Literal['drinking trough', 'pool', 'storm pool', 'irrigation pool', 'natural pool', 'flood', 'other container', 'unknown']
+
+class OtherNaturalCause(CircumstanceTypeBase):
+    type: Literal['other']
+
+class UnknownNaturalCause(CircumstanceTypeBase):
+    type: Literal['unknown']
+
+# Unknown cause
+class UnknownCircumstance(CircumstanceTypeBase):
+    type: Literal['unknown']
+
+# Union of all possible CircumstanceTypes with 'type' as the discriminator
+CircumstanceType = Union[
+    RoadVehicleCollision,
+    TrainCollision,
+    AircraftCollision,
+    BoatCollision,
+    OtherTransportCollision,
+    UnknownTransportCollision,
+    HuntingDestruction,
+    TrapDestruction,
+    PoisoningDestruction,
+    RemovalDestruction,
+    FishingDestruction,
+    OtherDestruction,
+    UnknownDestruction,
+    PylonElectricGridDestruction,
+    WindfarmDestruction,
+    OtherCollisionDestruction,
+    FallDestruction,
+    DevelopmentWorkDestruction,
+    PollutionContaminationDestruction,
+    AgriculturalNetProtectionDestruction,
+    VegetalForestWorkDestruction,
+    OtherIndirectDestruction,
+    UnknownIndirectDestruction,
+    Predation,
+    Weather,
+    NaturalDisaster,
+    NestFall,
+    StrandingExhaustion,
+    DiseaseParasite,
+    AccidentalDrowning,
+    OtherNaturalCause,
+    UnknownNaturalCause,
+    UnknownCircumstance
+]
+
+# Main Circumstance class
+class Circumstances(BaseModel):
+    circumstance: str  # e.g., "COLLISION"
+    circumstance_radio: str  # e.g., "Yes"
+    circumstance_type: CircumstanceType = Field(..., discriminator='type')

app/classes.py

@@ -0,0 +1,42 @@
+from pydantic import BaseModel, Field
+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 follow_up.class_follow_up import FollowUpEvents
+from geolocalisation.class_geolocalisation import Geolocalisation
+
+class Wounded(BaseModel):
+    circumstances: List[Circumstances] 
+    behaviors: List[Behaviors]
+    physical_anomalies: List[PhysicalAnomaly]
+    follow_up_events: List[FollowUpEvents]
+
+class Dead(BaseModel):
+    circumstances: List[Circumstances] 
+    physical_anomalies: List[PhysicalAnomaly]
+    follow_up_events: List[FollowUpEvents]
+
+class Image(BaseModel):
+    image: List[float]
+
+class Report(BaseModel):
+    image: Image
+    geolocalisation: Geolocalisation
+    wounded_state: bool
+    wounded: Optional[Wounded] = None  
+    dead_state: bool
+    dead: Optional[Dead] = None 
+    
+# Example usage
+# json_data = {
+#     "circumstance": "COLLISION",
+#     "circumstance_radio": "Yes",
+#     "circumstance_type": {
+#         "type": "Train",
+#         "infrastructure_number": "56"
+#     }
+# }
+# circumstance_instance = Circumstance(**json_data)
+# circumstance_schema = Circumstance.schema_json(indent=2)

app/dead.py

@@ -1,7 +1,7 @@
 import gradio as gr
-from circumstances import create_causes
-from followup_events import create_followup_dropdowns, create_followup_open
-from utils_json import add_data_to_individual  
+from circumstances.circumstances import create_circumstances
+from follow_up.followup_events import create_followup_dropdowns, create_followup_open
+from utils.utils_json import add_data_to_individual  
 
 def show_section_dead(visible):
     if visible==True: 
@@ -12,7 +12,7 @@ def show_section_dead(visible):
         gr.Markdown("# Dead Animal")
         gr.Markdown("## Please describe the cause of death", label="description")
         
-        button_collision, button_deliberate_destruction, button_indirect_destruction, button_natural_cause, dropdown, dropdown_level2, openfield_level2, dropdown_extra_level2 = create_causes(visible)      
+        button_collision, button_deliberate_destruction, button_indirect_destruction, button_natural_cause, dropdown, dropdown_level2, openfield_level2, dropdown_extra_level2 = create_circumstances(visible)      
         
         gr.Markdown("## Follow-Up Events", label="Title")
         gr.Markdown("Please tell us what you did with the animal.", label="description")

app/follow_up/class_follow_up.py

@@ -0,0 +1,57 @@
+from pydantic import BaseModel, Field
+from typing import Literal, Union, Optional, List
+
+# --- Event follow-up classes ---
+
+# Animal collected event
+class AnimalCollectedEvent(BaseModel):
+    type: Literal['animal collected']
+    option: Literal['Yes', 'No']
+
+# Recipient event
+class RecipientEvent(BaseModel):
+    type: Literal['recipient']
+    option: Literal['Veterinary', 'Care center', 'Local Museum', 'National Museum', 'Other']
+
+# Radiography event
+class RadiographyEvent(BaseModel):
+    type: Literal['radiography']
+    option: Literal['Yes', 'No', 'Unknown']
+
+# Given answer event
+class GivenAnswerEvent(BaseModel):
+    type: Literal['given answer']
+    option: Literal[
+        'Nothing', 
+        'Complaint against X', 
+        'Complaint', 
+        'Police call', 
+        'Discussion with the speaker', 
+        'Press release', 
+        'Unknown'
+    ]
+
+# Name of recipient/museum (open text field)
+class NameOfRecipientEvent(BaseModel):
+    type: Literal['name of recipient / museum']
+    name: str  # Open text field for entering the name
+
+# Collection reference (open text field)
+class CollectionReferenceEvent(BaseModel):
+    type: Literal['collection reference']
+    reference: str  # Open text field for entering the reference
+
+# Union of all possible follow-up event types
+FollowUpEventType = Union[
+    AnimalCollectedEvent,
+    RecipientEvent,
+    RadiographyEvent,
+    GivenAnswerEvent,
+    NameOfRecipientEvent,
+    CollectionReferenceEvent
+]
+
+# Main class that logs multiple follow-up events
+class FollowUpEvents(BaseModel):
+    follow_up_events: List[FollowUpEventType]
+

app/{followup_events.py → follow_up/followup_events.py}

@@ -1,6 +1,6 @@
 import gradio as gr
-from utils_config import get_custom_config_dropdowns
-from utils_json import add_data_to_individual
+from utils.utils_config import get_custom_config_dropdowns
+from utils.utils_json import add_data_to_individual
 
 def create_followup_dropdowns(visible, elem_id): 
     followup_config = get_custom_config_dropdowns("config_followup.json")

app/{utils_gallery.py → gallery.py}

@@ -2,9 +2,11 @@ import gradio as gr
 import pandas as pd
 import numpy as np
 from dotenv import load_dotenv
-from utils_config import load_config
-from utils_json import get_json_one_individual, save_to_all_individuals
+
+from utils.utils_config import load_config
+from utils.utils_json import get_json_one_individual, save_to_all_individuals
 import os
+
 load_dotenv()
 PATH = os.getcwd() + "/"
 PATH_ASSETS = os.getenv('PATH_ASSETS')

app/geolocalisation/class_geolocalisation.py

@@ -0,0 +1,16 @@
+from pydantic import BaseModel, Field
+from typing import Literal, List, Union
+
+class Longitude(BaseModel):
+    type: Literal['longitude']
+    value: float
+
+class Latitude(BaseModel):
+    type: Literal['latitude']
+    value: float
+
+class Geolocalisation(BaseModel):
+    longitude: Longitude
+    latitude: Latitude
+    name: str
+

app/{maps.py → geolocalisation/maps.py}

@@ -1,6 +1,6 @@
 from geopy.geocoders import Nominatim
 import gradio as gr
-from utils_json import add_data_to_individual
+from utils.utils_json import add_data_to_individual
  
 def get_location(address):
     # try: 

app/main_multianimal.py

@@ -1,20 +1,20 @@
 import gradio as gr
 from gradio_modal import Modal
 
-from utils_json import *
-from utils_gallery import save_individual_to_gallery
-from maps import get_location
+from utils.utils_json import *
+from gallery import save_individual_to_gallery
+from geolocalisation.maps import get_location
 from functools import partial
 from dead import show_section_dead
 from wounded import show_section_wounded
-from circumstances import show_causes
-from circumstances_dropdowns import *
-from physical_select_animal import show_physical, find_bounding_box
-from physical_checkbox import on_select_body_part, hide_physical
-from behavior_checkbox import show_behavior, on_select_behavior
-from followup_events import save_fe
-from style import *
-from theme import theme, css
+from circumstances.circumstances import show_circumstances
+from circumstances.circumstances_dropdowns import *
+from physical.physical_select_animal import show_physical, find_bounding_box
+from physical.physical_checkbox import on_select_body_part, hide_physical
+from behavior.behavior_checkbox import show_behavior, on_select_behavior
+from follow_up.followup_events import save_fe
+from styling.style import *
+from styling.theme import theme, css
 
 with gr.Blocks(theme=theme, css=css) as demo:
     create_json_all_individuals()
@@ -155,7 +155,7 @@ with gr.Blocks(theme=theme, css=css) as demo:
         dropdown_extra_level2_dead.select(on_select_dropdown_extra_level2)
         # ---------------------------------------------------------
         # Radio Cause Wounded
-        radio_cause_wounded.change(fn=show_causes,
+        radio_cause_wounded.change(fn=show_circumstances,
                                 inputs=[radio_cause_wounded],
                                 outputs=[button_collision_wounded, button_deliberate_destruction_wounded, button_indirect_destruction_wounded, button_natural_cause_wounded, 
                                             dropdown_wounded, dropdown_level2_wounded, openfield_level2_wounded, dropdown_extra_level2_wounded]
@@ -257,7 +257,7 @@ with gr.Blocks(theme=theme, css=css) as demo:
     show_modal.click(lambda: Modal(visible=True), None, modal)
     show_modal.click(create_json_one_individual)
     #submit_button.click(save_and_rest_df, inputs=[df], outputs=[df])
-    #submit_button.click(save_individual_to_gallery)
+    submit_button.click(save_individual_to_gallery)
 
 
      

app/physical/class_physical.py

@@ -0,0 +1,78 @@
+from pydantic import BaseModel, Field
+from typing import Literal, List, Union, Optional
+
+# Define common anomalies as a Literal type
+CommonAnomalies = Literal[
+    'blackened/burnt skin',
+    'blood',
+    'foreign body',
+    'fracture',
+    'injury',
+    'parasite',
+    'swelling',
+    'warty or tumor-like growth, crusts'
+]
+
+# --- Beak-related Anomalies ---
+class BeakAnomaly(BaseModel):
+    type: Literal['beak']
+    anomaly_type: Literal[
+        'adhesion',
+        'deformation',
+        CommonAnomalies
+    ]
+
+# --- Body-related Anomalies ---
+class BodyAnomaly(BaseModel):
+    type: Literal['body']
+    anomaly_type: Literal[
+        'emaciation',
+        'fluffed up',
+        'stained feathers',
+        CommonAnomalies
+    ]
+
+# --- Legs-related Anomalies ---
+class LegAnomaly(BaseModel):
+    type: Literal['legs']
+    anomaly_type: Literal[
+        'missing limb',
+        'deformation',
+        CommonAnomalies
+    ]
+
+# --- Feathers/Wings/Tail-related Anomalies ---
+class FeathersWingsTailAnomaly(BaseModel):
+    type: Literal['feathers/wings/tail']
+    anomaly_type: Literal[
+        'fluffed up',
+        'feather abnormalities',
+        'stained feathers',
+        'abnormal wing posture',
+        'missing limb',
+        CommonAnomalies
+    ]
+
+# --- Head-related Anomalies (including eyes) ---
+class HeadAnomaly(BaseModel):
+    type: Literal['head']
+    anomaly_type: Literal[
+        'ear changes',
+        'eye changes',
+        'tilted head',
+        CommonAnomalies
+    ]
+
+
+# Union of all possible anomaly types for specific body parts
+AnomalyType = Union[
+    BeakAnomaly,
+    BodyAnomaly,
+    LegAnomaly,
+    FeathersWingsTailAnomaly,
+    HeadAnomaly
+]
+
+# Main PhysicalAnomaly class that logs anomalies across different body parts
+class PhysicalAnomaly(BaseModel):
+    body_part_anomalies: List[AnomalyType]  # List of anomalies across different body parts

app/{physical_checkbox.py → physical/physical_checkbox.py}

@@ -1,7 +1,7 @@
 import gradio as gr
-from utils_config import get_custom_config_dropdowns
-from utils_checkbox import create_checkbox
-from utils_json import add_data_to_individual 
+from utils.utils_config import get_custom_config_dropdowns
+from utils.utils_checkbox import create_checkbox
+from utils.utils_json import add_data_to_individual 
 #--------------------------------------------------------- 
 def get_body_parts():
     dropdown_config = get_custom_config_dropdowns("config_checkbox_physical.json")

app/{physical_select_animal.py → physical/physical_select_animal.py}

@@ -1,12 +1,13 @@
 import gradio as gr
-# from gradio_image_prompter import ImagePrompter
-from typing import List
-from shapely.geometry import Point
-from physical_checkbox import *
-from physical_boxes_define import gdf
-from utils_visible import set_visible
 from dotenv import load_dotenv
 import os
+from typing import List
+from shapely.geometry import Point
+
+from physical.physical_checkbox import *
+from physical.physical_boxes_define import gdf
+from utils.utils_visible import set_visible
+
 load_dotenv()
 PATH_ASSETS = os.getenv('PATH_ASSETS')
 

app/tests.py

@@ -0,0 +1,25 @@
+import gradio as gr
+
+# Example initial image list
+images = [
+    "https://via.placeholder.com/150/0000FF",
+    "https://via.placeholder.com/150/FF0000",
+    "https://via.placeholder.com/150/00FF00"
+]
+
+# Function to remove a selected image from the gallery
+def delete_image(selected_image, image_list):
+    if selected_image in image_list:
+        image_list.remove(selected_image)  # Remove the selected image
+    return image_list  # Return the updated image list
+
+# Gradio app
+with gr.Blocks() as demo:
+    gallery = gr.Gallery(value=images, label="Gallery")  # Gallery of images
+    selected_image = gr.Dropdown(choices=images, label="Select Image to Delete")  # Dropdown for selection
+    delete_button = gr.Button("Delete Selected Image")  # Button to delete
+    
+    # When button is clicked, delete the selected image and update gallery
+    delete_button.click(fn=delete_image, inputs=[selected_image, gallery], outputs=gallery)
+    
+demo.launch(server_name="0.0.0.0", server_port=3232)

app/wounded.py

@@ -1,10 +1,10 @@
 import gradio as gr
-from circumstances import create_causes
-from physical_select_animal import create_bird_anatomy
-from physical_checkbox import process_body_parts
-from behavior_checkbox import create_behavior_checkbox
-from followup_events import create_followup_dropdowns, create_followup_open
-from utils_json import add_data_to_individual  
+from circumstances.circumstances import create_circumstances
+from physical.physical_select_animal import create_bird_anatomy
+from physical.physical_checkbox import process_body_parts
+from behavior.behavior_checkbox import create_behavior_checkbox
+from follow_up.followup_events import create_followup_dropdowns, create_followup_open
+from utils.utils_json import add_data_to_individual  
 
 def show_section_wounded(visible):
     if visible==True: 
@@ -16,7 +16,7 @@ def show_section_wounded(visible):
         
         gr.Markdown("## Do you know what conditions caused this?", label="description")
         radio_cause = gr.Radio(["Yes", "No"], value=None, show_label=False, interactive=True)
-        button_collision, button_deliberate_destruction, button_indirect_destruction, button_natural_cause, dropdown, dropdown_level2, openfield_level2, dropdown_extra_level2 = create_causes(visible=False)
+        button_collision, button_deliberate_destruction, button_indirect_destruction, button_natural_cause, dropdown, dropdown_level2, openfield_level2, dropdown_extra_level2 = create_circumstances(visible=False)
 
         gr.Markdown("## Is the bird displaying behavioural changes?" , label="description")
         radio_behaviour = gr.Radio(["Yes", "No"], value=None, show_label=False, interactive=True)