feat: simple physical and behavior definitions

app/assets/config/config_checkbox_behavior_simple.json

@@ -0,0 +1,18 @@
+{
+    "General weakness":
+    {
+        "Description": "Abnormal breathing (dyspnoea), sudden crash, apathy, lethargy, unable to fly but responsive."
+    },
+    "Vomiting":
+    {
+        "Description": "Throwing up undigested food, regurgitating"
+    },
+    "Atypical behavior":
+    {
+        "Description": "Circling, incoordination, tremors, convulsions"
+    },
+    "No changes": 
+    {
+        "Description": "Animal is acting normally"
+    }
+}

app/assets/config/config_checkbox_physical_simple.json

@@ -0,0 +1,30 @@
+{
+    "Common":
+    {
+        "Abnormal position": {
+            "Description": "Hanging wing, tilted head, lameness"},
+        "Injury": {
+            "Description": "Visible blood, fracture, missing limb, swelling without visible injury, foreign body"}
+    },
+    "Beak":
+    {
+        "Adhesion/Discharge": {
+            "Description": "Material (food, saliva) around/ in the beak, discharge from ears/ eyes/ beak/ nose"
+            }
+    },
+    "Body": 
+    {},
+    "Feathers/Wings/Tail":
+    {
+        "Feathers and skin change": {
+            "Description": "Blackened/ burnt skin or feathers, deformed feathers, ear changes (swollen, crusts, plugged, discharge), discolored/ missing/ broken/ stained feathers, fluffed up plumage, warts/ crusts/ tumor-like growth, parasites"}
+    },
+    "Head incl. eyes": 
+    {
+        "Eye changes": {
+            "Description": "Swollen, reddened, closed, discharge, crusts"}
+    },
+    "Legs":
+    {}
+
+}

app/behavior/behavior_checkbox.py

@@ -9,8 +9,12 @@ def on_select_behavior(behavior_checkbox, individual):
     individual = add_data_to_individual("behaviors_type", behavior_checkbox, individual)
     return individual
 
-def retrieve_behavior_options_description():
-    dropdown_config = get_custom_config_dropdowns("config_checkbox_behavior.json")
+def retrieve_behavior_options_description(mode:str):
+    print(mode)
+    if mode =="simple": 
+        dropdown_config = get_custom_config_dropdowns("config_checkbox_behavior_simple.json")
+    elif mode=="advanced": 
+        dropdown_config = get_custom_config_dropdowns("config_checkbox_behavior.json")
     options = list(dropdown_config.keys())
     options = [option.title() for option in options]
     descriptions =[]
@@ -18,14 +22,15 @@ def retrieve_behavior_options_description():
         descriptions.append(subdict["Description"])
     return options, descriptions
 
-def create_behavior_checkbox(section: str, visible):
-    options, descriptions = retrieve_behavior_options_description()
+def create_behavior_checkbox(section: str, mode: str, visible):
+    options, descriptions = retrieve_behavior_options_description(mode)
     label_checkbox = "Behavior changes observed"
     checkbox, text = create_checkbox("", section, label_checkbox, visible, options, descriptions)
     return checkbox, text
 
-def show_behavior(choice, section: str, individual): 
+def show_behavior(choice, section: str, mode: str, individual): 
+    print(mode)
     visible = set_visible(choice)
-    checkbox, text = create_behavior_checkbox(section, visible)
+    checkbox, text = create_behavior_checkbox(section, mode, visible)
     individual = add_data_to_individual("behaviors_radio", choice, individual)
     return checkbox, text, individual

app/behavior/class_behavior_simple.py

@@ -0,0 +1,36 @@
+from pydantic import BaseModel, Field
+from typing import Literal, List, Union, Optional
+
+class BehaviorSimple(BaseModel):
+    type: str
+    description: Optional[str] = None  # Making the description field optional
+
+# --- Specific BehaviorSimple classes ---
+class GeneralWeakness(BehaviorSimple):
+    type: Literal['general weakness']
+    description: Optional[Literal["Abnormal breathing (dyspnoea), sudden crash, apathy, lethargy, unable to fly but responsive"]] = None
+
+class Vomiting(BehaviorSimple):
+    type: Literal['vomiting']
+    description: Optional[Literal["Throwing up undigested food, regurgitating"]] = None
+
+class AtypicalBehavior(BehaviorSimple):
+    type: Literal['atypical behavior']
+    description: Optional[Literal["Circling, incoordination, tremors, convulsions"]] = None
+
+class NoChanges(BehaviorSimple):
+    type: Literal['no changes']
+    description: Optional[Literal["Animal is acting normally"]] = None
+
+# Union of all possible behaviors
+BehaviorSimpleType = Union[
+    GeneralWeakness,
+    Vomiting,
+    AtypicalBehavior,
+    NoChanges
+]
+
+# Main class that logs multiple behaviors
+class BehaviorsSimple(BaseModel):
+    behaviors_radio: str  # e.g., "Yes"
+    behaviors_type: Optional[List[BehaviorSimpleType]] = None

app/circumstances/circumstances.py

@@ -15,7 +15,7 @@ CAUSE_COL_WIDTH = "50px"
 
 def show_circumstances(choice, individual): 
     visible = set_visible(choice)
-    individual = add_data_to_individual("wounded_dead", 
+    individual = add_data_to_individual(
                     "circumstance_radio", 
                     choice, individual)
     button_collision, button_deliberate_destruction, button_indirect_destruction, button_natural_cause, dropdown, dropdown_level2, openfield_level2, dropdown_extra_level2 = create_circumstances(visible)

app/circumstances/circumstances_dropdowns.py

@@ -23,22 +23,22 @@ def create_dropdown_level1(label, individual):
     
 def dropdown_collision(individual):
     label = "Collision with a means of transport"
-    individual = add_data_to_individual("wounded_dead", "circumstance", label.lower(), individual)
+    individual = add_data_to_individual("circumstance", label.lower(), individual)
     return create_dropdown_level1(label, individual)
 
 def dropdown_deliberate_destruction(individual):
     label = "Destruction / Deliberatly removed"
-    individual = add_data_to_individual("wounded_dead", "circumstance", label.lower(), individual)
+    individual = add_data_to_individual("circumstance", label.lower(), individual)
     return create_dropdown_level1(label, individual)     
 
 def dropdown_indirect_destruction(individual): 
     label = "Indirect destruction"
-    individual = add_data_to_individual("wounded_dead", "circumstance", label.lower(), individual)
+    individual = add_data_to_individual("circumstance", label.lower(), individual)
     return create_dropdown_level1(label, individual) 
 
 def dropdown_natural_cause(individual): 
     label = "Natural cause"
-    individual = add_data_to_individual("wounded_dead", "circumstance", label.lower(), individual)
+    individual = add_data_to_individual( "circumstance", label.lower(), individual)
     return create_dropdown_level1(label, individual)         
 
 
@@ -72,7 +72,7 @@ def get_options(value):
        
 def on_select(evt: gr.SelectData, individual):  # SelectData is a subclass of EventData
     options_label, options_dropdown, open_field, extras, extras_label = get_options(evt.value)
-    individual = add_data_to_individual("wounded_dead", 
+    individual = add_data_to_individual(
                     "circumstance_type", 
                     {"type": (evt.value).lower(),
                      "option_dropdown_label" : options_label.lower() if options_label is not None else 'NA',
@@ -96,20 +96,20 @@ def on_select(evt: gr.SelectData, individual):  # SelectData is a subclass of Ev
     return dropdown_level2, openfield_level2, dropdown_extra_level2, individual
 
 def on_select_dropdown_level2(evt: gr.SelectData, individual): 
-    individual = add_data_to_individual("wounded_dead", 
+    individual = add_data_to_individual( 
                 "circumstance_option_dropdown", 
                 evt.value.lower(), individual)
     return individual
 
 def on_select_dropdown_extra_level2(evt: gr.SelectData, individual):  
-    individual = add_data_to_individual("wounded_dead", 
+    individual = add_data_to_individual( 
                  "circumstance_extra", 
                  evt.value.lower(), individual)
     return individual
     
 def on_change_openfield_level2(openfield_level2_dead, individual): 
     print("Saving open field")
-    individual = add_data_to_individual("wounded_dead", 
+    individual = add_data_to_individual(
                 "circumstance_open_field", 
                 str(openfield_level2_dead).lower(), individual)
     return individual

app/dead.py

@@ -12,7 +12,7 @@ PATH = os.getcwd() + "/"
 PATH_ASSETS = os.getenv('PATH_ASSETS')
 PATH_ICONS = PATH + PATH_ASSETS + "icons/"
 
-def show_section_dead(visible, individual):
+def show_section_dead(visible, mode, individual):
     if visible==True: 
         individual = add_data_to_individual("wounded_state", "No", individual)
         individual = add_data_to_individual("dead_state", "Yes", individual)
@@ -33,7 +33,7 @@ def show_section_dead(visible, individual):
         with gr.Row():
             physical_boxes = create_bird_anatomy(False, "dead")
             with gr.Column():
-                checkbox_beak, text_beak, checkbox_body, text_body, checkbox_feathers, text_feathers, checkbox_head, text_head, checkbox_legs, text_legs = process_body_parts("dead", "None")
+                checkbox_beak, text_beak, checkbox_body, text_body, checkbox_feathers, text_feathers, checkbox_head, text_head, checkbox_legs, text_legs = process_body_parts("dead", mode, "None")
 
         gr.Button("Follow-Up Events",
                   icon=PATH_ICONS + "schedule.png",

app/mode_advanced.py

@@ -1,6 +1,8 @@
 import gradio as gr
 from gradio_modal import Modal
 
+from geolocalisation.js_geolocation import js_geocode, display_location
+from validation_submission.utils_individual import generate_random_md5
 from validation_submission.utils_individual import add_data_to_individual
 from validation_submission.submission import validate_save_individual
 from validation_submission.validation import reset_error_box
@@ -17,9 +19,6 @@ from follow_up.followup_events import save_fe
 from styling.style import *
 from credits import credits_text
 
-from geolocalisation.js_geolocation import js_geocode, display_location
-from validation_submission.utils_individual import generate_random_md5
-
 from dotenv import load_dotenv
 import os
 load_dotenv()
@@ -28,6 +27,7 @@ PATH_ASSETS = os.getenv('PATH_ASSETS')
 PATH_ICONS = PATH + PATH_ASSETS + "icons/"
 
 with gr.Blocks(theme='shivi/calm_seafoam') as advanced:
+    mode = "advanced"
     individual = gr.State({})
     individual.value = add_data_to_individual("image_md5", generate_random_md5(), individual.value)
 
@@ -149,7 +149,7 @@ with gr.Blocks(theme='shivi/calm_seafoam') as advanced:
                 checkbox_beak_dead, text_beak_dead, checkbox_body_dead, text_body_dead, checkbox_feathers_dead, text_feathers_dead, checkbox_head_dead, text_head_dead, checkbox_legs_dead, text_legs_dead, \
                 fe_collection_dropdown_dead, fe_recepient_dropdown_dead, fe_radio_dropdown_dead, fe_answer_dropdown_dead, \
                 fe_name_recipient_dead, fe_collection_ref_dead \
-                = show_section_dead(False, individual)
+                = show_section_dead(False, mode, individual)
     
     section_wounded, individual, radio_circumstance_wounded, radio_behavior_wounded, radio_physical_wounded, \
         button_collision_wounded, button_deliberate_destruction_wounded, button_indirect_destruction_wounded, button_natural_cause_wounded, \
@@ -159,7 +159,7 @@ with gr.Blocks(theme='shivi/calm_seafoam') as advanced:
                         checkbox_beak_wounded, text_beak_wounded, checkbox_body_wounded, text_body_wounded, checkbox_feathers_wounded, text_feathers_wounded, checkbox_head_wounded, text_head_wounded, checkbox_legs_wounded, text_legs_wounded, \
                         fe_collection_dropdown_wounded, fe_recepient_dropdown_wounded, fe_radio_dropdown_wounded, fe_answer_dropdown_wounded, \
                             fe_name_recipient_wounded, fe_collection_ref_wounded \
-                            = show_section_wounded(False, individual)
+                            = show_section_wounded(False, mode, individual)
 
     # ---------------------------------------------------------
     # ---------------------------------------------------------
@@ -168,7 +168,8 @@ with gr.Blocks(theme='shivi/calm_seafoam') as advanced:
     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=[individual], 
+                    inputs=[gr.Text(mode, visible=False),
+                            individual], 
                     outputs=[section_dead, 
                             individual,
                             radio_circumstance_dead, radio_physical_dead,
@@ -181,7 +182,8 @@ with gr.Blocks(theme='shivi/calm_seafoam') as advanced:
                             ])
     
     butt_dead.click(partial_hide_section_wounded, 
-                    inputs=[individual], 
+                    inputs=[gr.Text(mode, visible=False),
+                            individual], 
                     outputs=[section_wounded, 
                             individual,
                             radio_circumstance_wounded, radio_behavior_wounded, radio_physical_wounded,
@@ -200,7 +202,8 @@ with gr.Blocks(theme='shivi/calm_seafoam') as advanced:
     partial_hide_section_dead = partial(show_section_dead, False)
 
     butt_wounded.click(partial_show_section_wounded, 
-                    inputs=[individual], 
+                    inputs=[gr.Text(mode, visible=False),
+                            individual], 
                     outputs=[section_wounded, 
                             individual,
                             radio_circumstance_wounded, radio_behavior_wounded, radio_physical_wounded,
@@ -214,7 +217,8 @@ with gr.Blocks(theme='shivi/calm_seafoam') as advanced:
                             ])
     
     butt_wounded.click(partial_hide_section_dead, 
-                        inputs=[individual], 
+                        inputs=[gr.Text(mode, visible=False),
+                                individual], 
                         outputs=[section_dead, 
                                 individual,
                                 radio_circumstance_dead, radio_physical_dead,
@@ -254,7 +258,9 @@ with gr.Blocks(theme='shivi/calm_seafoam') as advanced:
     # ---------------------------------------------------------
     # Radio Physical Dead
     radio_physical_dead.change(fn=show_physical,
-                                inputs=[radio_physical_dead, gr.Text("dead", visible=False), individual],
+                                inputs=[radio_physical_dead, 
+                                        gr.Text("dead", visible=False), 
+                                        individual],
                                 outputs=[physical_boxes_dead, individual])
 
     # Checkbox Physical Dead
@@ -299,7 +305,10 @@ with gr.Blocks(theme='shivi/calm_seafoam') as advanced:
     # ---------------------------------------------------------
     # Radio Behavior Wounded
     radio_behavior_wounded.change(fn=show_behavior,
-                                inputs=[radio_behavior_wounded, gr.Text("wounded / sick", visible=False), individual],
+                                inputs=[radio_behavior_wounded, 
+                                        gr.Text("wounded / sick", visible=False), 
+                                        gr.Text(mode, visible=False), 
+                                        individual],
                                 outputs=[behavior_checkbox, behavior_text, individual])
     behavior_checkbox.select(on_select_behavior, 
                                 inputs=[behavior_checkbox, individual],
@@ -307,7 +316,9 @@ with gr.Blocks(theme='shivi/calm_seafoam') as advanced:
     # ---------------------------------------------------------
     # Radio Physical Wounded
     radio_physical_wounded.change(fn=show_physical,
-                                inputs=[radio_physical_wounded, gr.Text("wounded / sick", visible=False), individual],
+                                inputs=[radio_physical_wounded, 
+                                        gr.Text("wounded / sick", visible=False), 
+                                        individual],
                                 outputs=[physical_boxes_wounded, individual])
 
     # Checkbox Physical Wounded
@@ -405,7 +416,10 @@ with gr.Blocks(theme='shivi/calm_seafoam') as advanced:
    
     # ---------------------------------------------------------
     # VALIDATE ANIMAL 
-    button_df.click(validate_save_individual, inputs=[individual, error_box],
+    button_df.click(validate_save_individual, 
+                    inputs=[individual, 
+                            error_box,
+                            gr.Text(mode, visible=False)],
                     outputs=[error_box])
     # ---------------------------------------------------------
     #CREDITS

app/mode_simple.py

@@ -4,7 +4,6 @@ from gradio_modal import Modal
 from validation_submission.utils_individual import add_data_to_individual
 from validation_submission.submission import validate_save_individual
 from validation_submission.validation import reset_error_box
-from geolocalisation.maps import get_location
 from functools import partial
 from dead import show_section_dead
 from wounded import show_section_wounded
@@ -28,6 +27,7 @@ PATH_ASSETS = os.getenv('PATH_ASSETS')
 PATH_ICONS = PATH + PATH_ASSETS + "icons/"
 
 with gr.Blocks(theme='shivi/calm_seafoam') as simple:
+    mode = "simple"
     individual = gr.State({})
     individual.value = add_data_to_individual("image_md5", generate_random_md5(), individual.value)
 
@@ -99,6 +99,25 @@ with gr.Blocks(theme='shivi/calm_seafoam') as simple:
                     btn_gpslocation = gr.Button("Get Coordinates using GPS (Permission required)")
                     btn_gpslocation.click(None, [], [], js=js_geocode)
                     hidden_input.change(display_location, inputs=hidden_input, outputs=location_data)
+
+                    from geolocalisation.maps import get_location
+                    with gr.Column(scale=1):
+                        gr.Markdown("#### Location (Using address)")
+                        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 submit it
+                            submit_location = gr.Button("Get Coordinates using address", 
+                                                        visible=True, interactive=True, scale=3)
+                            submit_location.click(get_location, inputs=[location, individual], outputs=[identified_location, individual])
+                            #to clear it
+                            clear_location = gr.ClearButton(components=[location, identified_location], 
+                                                            visible=True, interactive=True, scale=1
+                                                            )
+                            clear_location.click()
             
     # ---------------------------------------------------------
     # Dead and Wounded Buttons
@@ -128,7 +147,7 @@ with gr.Blocks(theme='shivi/calm_seafoam') as simple:
                 checkbox_beak_dead, text_beak_dead, checkbox_body_dead, text_body_dead, checkbox_feathers_dead, text_feathers_dead, checkbox_head_dead, text_head_dead, checkbox_legs_dead, text_legs_dead, \
                 fe_collection_dropdown_dead, fe_recepient_dropdown_dead, fe_radio_dropdown_dead, fe_answer_dropdown_dead, \
                 fe_name_recipient_dead, fe_collection_ref_dead \
-                = show_section_dead(False, individual)
+                = show_section_dead(False, mode, individual)
     
     section_wounded, individual, radio_circumstance_wounded, radio_behavior_wounded, radio_physical_wounded, \
         button_collision_wounded, button_deliberate_destruction_wounded, button_indirect_destruction_wounded, button_natural_cause_wounded, \
@@ -138,7 +157,7 @@ with gr.Blocks(theme='shivi/calm_seafoam') as simple:
                         checkbox_beak_wounded, text_beak_wounded, checkbox_body_wounded, text_body_wounded, checkbox_feathers_wounded, text_feathers_wounded, checkbox_head_wounded, text_head_wounded, checkbox_legs_wounded, text_legs_wounded, \
                         fe_collection_dropdown_wounded, fe_recepient_dropdown_wounded, fe_radio_dropdown_wounded, fe_answer_dropdown_wounded, \
                             fe_name_recipient_wounded, fe_collection_ref_wounded \
-                            = show_section_wounded(False, individual)
+                            = show_section_wounded(False, mode, individual)
 
     # ---------------------------------------------------------
     # ---------------------------------------------------------
@@ -147,7 +166,8 @@ with gr.Blocks(theme='shivi/calm_seafoam') as simple:
     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=[individual], 
+                    inputs=[gr.Text(mode, visible=False),
+                            individual], 
                     outputs=[section_dead, 
                             individual,
                             radio_circumstance_dead, radio_physical_dead,
@@ -160,7 +180,8 @@ with gr.Blocks(theme='shivi/calm_seafoam') as simple:
                             ])
     
     butt_dead.click(partial_hide_section_wounded, 
-                    inputs=[individual], 
+                    inputs=[gr.Text(mode, visible=False), 
+                            individual], 
                     outputs=[section_wounded, 
                             individual,
                             radio_circumstance_wounded, radio_behavior_wounded, radio_physical_wounded,
@@ -179,7 +200,8 @@ with gr.Blocks(theme='shivi/calm_seafoam') as simple:
     partial_hide_section_dead = partial(show_section_dead, False)
 
     butt_wounded.click(partial_show_section_wounded, 
-                    inputs=[individual], 
+                    inputs=[gr.Text(mode, visible=False), 
+                            individual], 
                     outputs=[section_wounded, 
                             individual,
                             radio_circumstance_wounded, radio_behavior_wounded, radio_physical_wounded,
@@ -193,7 +215,8 @@ with gr.Blocks(theme='shivi/calm_seafoam') as simple:
                             ])
     
     butt_wounded.click(partial_hide_section_dead, 
-                        inputs=[individual], 
+                        inputs=[gr.Text(mode, visible=False),
+                                individual], 
                         outputs=[section_dead, 
                                 individual,
                                 radio_circumstance_dead, radio_physical_dead,
@@ -233,12 +256,16 @@ with gr.Blocks(theme='shivi/calm_seafoam') as simple:
     # ---------------------------------------------------------
     # Radio Physical Dead
     radio_physical_dead.change(fn=show_physical,
-                                inputs=[radio_physical_dead, gr.Text("dead", visible=False), individual],
+                                inputs=[radio_physical_dead, 
+                                        gr.Text("dead", visible=False),
+                                        individual],
                                 outputs=[physical_boxes_dead, individual])
 
     # Checkbox Physical Dead
     physical_boxes_dead.select(find_bounding_box, 
-                    inputs=[physical_boxes_dead, gr.Textbox(value="dead", visible=False)], 
+                    inputs=[physical_boxes_dead, 
+                            gr.Textbox(value="dead", visible=False),
+                            gr.Text(mode, visible=False)], 
                     outputs=[checkbox_beak_dead, text_beak_dead, 
                                 checkbox_body_dead, text_body_dead, 
                                 checkbox_feathers_dead, text_feathers_dead, 
@@ -278,7 +305,10 @@ with gr.Blocks(theme='shivi/calm_seafoam') as simple:
     # ---------------------------------------------------------
     # Radio Behavior Wounded
     radio_behavior_wounded.change(fn=show_behavior,
-                                inputs=[radio_behavior_wounded, gr.Text("wounded / sick", visible=False), individual],
+                                inputs=[radio_behavior_wounded, 
+                                        gr.Text("wounded / sick", visible=False), 
+                                        gr.Text(mode, visible=False), 
+                                        individual],
                                 outputs=[behavior_checkbox, behavior_text, individual])
     behavior_checkbox.select(on_select_behavior, 
                                 inputs=[behavior_checkbox, individual],
@@ -286,12 +316,16 @@ with gr.Blocks(theme='shivi/calm_seafoam') as simple:
     # ---------------------------------------------------------
     # Radio Physical Wounded
     radio_physical_wounded.change(fn=show_physical,
-                                inputs=[radio_physical_wounded, gr.Text("wounded / sick", visible=False), individual],
+                                inputs=[radio_physical_wounded, 
+                                        gr.Text("wounded / sick", visible=False), 
+                                        individual],
                                 outputs=[physical_boxes_wounded, individual])
 
     # Checkbox Physical Wounded
     physical_boxes_wounded.select(find_bounding_box, 
-                    inputs=[physical_boxes_wounded, gr.Textbox(value="wounded / sick", visible=False)], 
+                    inputs=[physical_boxes_wounded, 
+                            gr.Textbox(value="wounded / sick", visible=False),
+                            gr.Text(mode, visible=False)], 
                     outputs=[checkbox_beak_wounded, text_beak_wounded, 
                                 checkbox_body_wounded, text_body_wounded, 
                                 checkbox_feathers_wounded, text_feathers_wounded, 
@@ -382,7 +416,10 @@ with gr.Blocks(theme='shivi/calm_seafoam') as simple:
    
     # ---------------------------------------------------------
     # VALIDATE ANIMAL 
-    button_df.click(validate_save_individual, inputs=[individual, error_box],
+    button_df.click(validate_save_individual, 
+                    inputs=[individual, 
+                            error_box,
+                            gr.Text(mode, visible=False)],
                     outputs=[error_box])
     # ---------------------------------------------------------
     #CREDITS

app/physical/class_physical_simple.py

@@ -0,0 +1,60 @@
+from pydantic import BaseModel, Field
+from typing import Literal, List, Union, Optional
+
+# Define common anomalies as a Literal type
+CommonAnomaliesSimple = Literal[
+    'injury',
+    'abnormal position'
+]
+
+# --- Beak-related Anomalies ---
+class BeakAnomaly(BaseModel):
+    type: Literal['beak']
+    anomaly_type: List[Literal[
+        'adhesion/discharge',
+        CommonAnomaliesSimple
+    ]]
+
+# --- Body-related Anomalies ---
+class BodyAnomaly(BaseModel):
+    type: Literal['body']
+    anomaly_type: List[Literal[
+        CommonAnomaliesSimple
+    ]]
+
+# --- Feathers/Wings/Tail-related Anomalies ---
+class FeathersWingsTailAnomaly(BaseModel):
+    type: Literal['feathers/wings/tail']
+    anomaly_type: List[Literal[
+        'feather and skin change',
+        CommonAnomaliesSimple
+    ]]
+
+# --- Head-related Anomalies (including eyes) ---
+class HeadAnomaly(BaseModel):
+    type: Literal['head incl. eyes']
+    anomaly_type: List[Literal[
+        'eye changes',
+        CommonAnomaliesSimple
+    ]]
+
+# --- Legs-related Anomalies ---
+class LegAnomaly(BaseModel):
+    type: Literal['legs']
+    anomaly_type: List[Literal[
+        CommonAnomaliesSimple
+    ]]
+
+# Union of all possible anomaly types for specific body parts
+AnomalyTypeSimple = Union[
+    BeakAnomaly,
+    BodyAnomaly,
+    LegAnomaly,
+    FeathersWingsTailAnomaly,
+    HeadAnomaly
+]
+
+# Main PhysicalAnomaly class that logs anomalies across different body parts
+class PhysicalAnomaliesSimple(BaseModel):
+    physical_radio: str
+    physical_anomalies_type: Optional[List[AnomalyTypeSimple]] = None

app/physical/physical_checkbox.py

@@ -3,8 +3,11 @@ from utils.utils_config import get_custom_config_dropdowns
 from utils.utils_checkbox import create_checkbox
 from validation_submission.utils_individual import add_data_to_individual 
 #--------------------------------------------------------- 
-def get_body_parts():
-    dropdown_config = get_custom_config_dropdowns("config_checkbox_physical.json")
+def get_body_parts(mode):
+    if mode=="simple":
+        dropdown_config = get_custom_config_dropdowns("config_checkbox_physical_simple.json")
+    elif mode == "advanced":
+        dropdown_config = get_custom_config_dropdowns("config_checkbox_physical.json")
     return list(dropdown_config.keys())
 
 def retrieve_config_options(label, dropdown_config):
@@ -12,8 +15,12 @@ def retrieve_config_options(label, dropdown_config):
     options = [option.title() for option in options]
     return options
 
-def get_options_description(value):
-        dropdown_config = get_custom_config_dropdowns("config_checkbox_physical.json")
+def get_options_description(value, mode):
+        print(mode)
+        if mode=="simple":
+            dropdown_config = get_custom_config_dropdowns("config_checkbox_physical_simple.json")
+        elif mode == "advanced": 
+            dropdown_config = get_custom_config_dropdowns("config_checkbox_physical.json")
         # get options
         options_common = retrieve_config_options("Common", dropdown_config)
         options_for_value = retrieve_config_options(value, dropdown_config)
@@ -30,56 +37,56 @@ def get_options_description(value):
         return options, descriptions
 
 #--------------------------------------------------------- 
-def create_checkbox_beak(section, label_checkbox, visible):
+def create_checkbox_beak(section, mode, label_checkbox, visible):
     body_part="Beak"
-    options, descriptions = get_options_description(body_part)
+    options, descriptions = get_options_description(body_part, mode)
     return create_checkbox(body_part, section, label_checkbox, visible, options, descriptions)
 
-def create_checkbox_body(section, label_checkbox, visible):
+def create_checkbox_body(section, mode, label_checkbox, visible):
     body_part="Body"
-    options, descriptions = get_options_description(body_part)
+    options, descriptions = get_options_description(body_part, mode)
     return create_checkbox(body_part, section, label_checkbox, visible, options, descriptions)
 
-def create_checkbox_feathers(section, label_checkbox, visible):
+def create_checkbox_feathers(section, mode, label_checkbox, visible):
     body_part="Feathers/Wings/Tail"
-    options, descriptions = get_options_description(body_part)
+    options, descriptions = get_options_description(body_part, mode)
     return create_checkbox(body_part, section, label_checkbox, visible, options, descriptions)
 
-def create_checkbox_head(section, label_checkbox, visible):
+def create_checkbox_head(section, mode, label_checkbox, visible):
     body_part="Head incl. eyes"
-    options, descriptions = get_options_description(body_part)
+    options, descriptions = get_options_description(body_part, mode)
     return create_checkbox(body_part, section, label_checkbox, visible, options, descriptions)
 
-def create_checkbox_legs(section, label_checkbox, visible):
+def create_checkbox_legs(section, mode, label_checkbox, visible):
     body_part="Legs"
-    options, descriptions = get_options_description(body_part)
+    options, descriptions = get_options_description(body_part, mode)
     return create_checkbox(body_part, section, label_checkbox, visible, options, descriptions)
 
 #---------------------------------------------------------
-def process_body_parts(section, matched_box):
+def process_body_parts(section, mode, matched_box):
     #take all except "Common"
-    body_parts = get_body_parts()
+    body_parts = get_body_parts(mode)
     body_parts = body_parts[1:]
     label_checkbox = "Physical changes to "
     visibles = [True if matched_box==body_part else False for body_part in body_parts ]
-    checkbox_beak, text_beak = create_checkbox_beak(section, label_checkbox, visibles[0])
-    checkbox_body, text_body = create_checkbox_body(section, label_checkbox, visibles[1])
-    checkbox_feathers, text_feathers = create_checkbox_feathers(section, label_checkbox, visibles[2])
-    checkbox_head, text_head = create_checkbox_head(section, label_checkbox, visibles[3])
-    checkbox_legs, text_legs = create_checkbox_legs(section, label_checkbox, visibles[4])
+    checkbox_beak, text_beak = create_checkbox_beak(section, mode,  label_checkbox, visibles[0])
+    checkbox_body, text_body = create_checkbox_body(section, mode, label_checkbox, visibles[1])
+    checkbox_feathers, text_feathers = create_checkbox_feathers(section, mode, label_checkbox, visibles[2])
+    checkbox_head, text_head = create_checkbox_head(section, mode, label_checkbox, visibles[3])
+    checkbox_legs, text_legs = create_checkbox_legs(section, mode, label_checkbox, visibles[4])
     return checkbox_beak, text_beak, checkbox_body, text_body, checkbox_feathers, text_feathers, checkbox_head, text_head, checkbox_legs, text_legs
           
 #--------------------------------------------------------- 
 
 def on_select_body_part(body_part_checkbox, body_part, individual): 
-    individual = add_data_to_individual("wounded_dead", "physical_type_"+body_part.lower(), body_part.lower(), individual)
+    individual = add_data_to_individual("physical_type_"+body_part.lower(), body_part.lower(), individual)
     body_part_checkbox = [body_part_check.lower() for body_part_check in body_part_checkbox]
-    individual = add_data_to_individual("wounded_dead", "physical_anomaly_"+body_part.lower(), body_part_checkbox, individual)
+    individual = add_data_to_individual("physical_anomaly_"+body_part.lower(), body_part_checkbox, individual)
     return individual
 
 #--------------------------------------------------------- 
 
-def hide_physical():
-    checkbox_beak, text_beak, checkbox_body, text_body, checkbox_feathers, text_feathers, checkbox_head, text_head, checkbox_legs, text_legs = process_body_parts("wounded", "None")
+def hide_physical(mode):
+    checkbox_beak, text_beak, checkbox_body, text_body, checkbox_feathers, text_feathers, checkbox_head, text_head, checkbox_legs, text_legs = process_body_parts("wounded", mode, "None")
     return checkbox_beak, text_beak, checkbox_body, text_body, checkbox_feathers, text_feathers, checkbox_head, text_head, checkbox_legs, text_legs
      

app/physical/physical_select_animal.py

@@ -8,20 +8,22 @@ from physical.physical_checkbox import *
 from physical.physical_boxes_define import gdf
 from utils.utils_visible import set_visible
 
+from validation_submission.utils_individual import add_data_to_individual
+
 load_dotenv()
 PATH_ASSETS = os.getenv('PATH_ASSETS')
 
 # Function to find the matching bounding box for a given point and return the image with boxes
-def find_bounding_box(evt: gr.SelectData, img, section: str):
+def find_bounding_box(evt: gr.SelectData, img, section: str, mode: str):
     x, y = evt.index[0], evt.index[1]
     point = Point(x, y)
     match = gdf[gdf.contains(point)]
     if not match.empty:
         matched_box = match.iloc[0]['name']
-        checkbox_beak, text_beak, checkbox_body, text_body, checkbox_feathers, text_feathers, checkbox_head, text_head, checkbox_legs, text_legs = process_body_parts(section, matched_box)
+        checkbox_beak, text_beak, checkbox_body, text_body, checkbox_feathers, text_feathers, checkbox_head, text_head, checkbox_legs, text_legs = process_body_parts(section, mode, matched_box)
     else:
         matched_box = None
-        checkbox_beak, text_beak, checkbox_body, text_body, checkbox_feathers, text_feathers, checkbox_head, text_head, checkbox_legs, text_legs = process_body_parts(section, matched_box)
+        checkbox_beak, text_beak, checkbox_body, text_body, checkbox_feathers, text_feathers, checkbox_head, text_head, checkbox_legs, text_legs = process_body_parts(section, mode, matched_box)
     return checkbox_beak, text_beak, checkbox_body, text_body, checkbox_feathers, text_feathers, checkbox_head, text_head, checkbox_legs, text_legs
 
     
@@ -39,7 +41,7 @@ def create_bird_anatomy(visible, section: str):
 def show_physical(choice, section: str, individual): 
     visible = set_visible(choice)
     physical_boxes = create_bird_anatomy(visible, section)
-    individual = add_data_tmp("wounded_dead", "physical_radio", choice, individual)
+    individual = add_data_to_individual("physical_radio", choice, individual)
     return physical_boxes, individual
 
 

app/validation_submission/submission.py

@@ -4,8 +4,8 @@ from validation_submission.validation import validate_individual
 from huggingface_hub import HfApi
 import os
 
-def validate_save_individual(data, error_box):
-    individual, error_box = validate_individual(data, error_box)
+def validate_save_individual(data, error_box, mode):
+    individual, error_box = validate_individual(data, error_box, mode)
     if individual:
         push_to_dataset_hf(individual.model_dump())
     return error_box
@@ -19,9 +19,10 @@ def push_to_dataset_hf(individual):
     f.flush()
     f.close()
     path_in_repo= f"data/{individual['image_md5']}.json"
-    api.upload_file(
-        path_or_fileobj=f.name,
-        path_in_repo=path_in_repo,
-        repo_id="SDSC/digiwild-dataset",
-        repo_type="dataset",
-    )
+    print(path_in_repo)
+    # api.upload_file(
+    #     path_or_fileobj=f.name,
+    #     path_in_repo=path_in_repo,
+    #     repo_id="SDSC/digiwild-dataset",
+    #     repo_type="dataset",
+    # )

app/validation_submission/validation.py

@@ -5,7 +5,9 @@ import gradio as gr
 # from validation_submission.get_json import get_json_tmp, get_json_one_individual
 from circumstances.class_circumstance import Circumstances
 from behavior.class_behavior import Behaviors
+from behavior.class_behavior_simple import BehaviorsSimple
 from physical.class_physical import PhysicalAnomalies
+from physical.class_physical_simple import PhysicalAnomaliesSimple
 from follow_up.class_follow_up import FollowUpEvents
 from classes import Report, Wounded, Dead, ImageBase64
 from validation_submission.processing import process_circumstance, process_behaviors, process_physical, process_followup
@@ -17,7 +19,7 @@ def get_fields(data_dict, keyword):
             extract[key] = val
     return extract
 
-def validate_individual(data, error_box):
+def validate_individual(data, error_box, mode:str):
     error_box = reset_error_box(error_box)
     #data = get_json_one_individual() # TODO: This should change
     data["identifier"] = str(uuid.uuid4())
@@ -40,13 +42,14 @@ def validate_individual(data, error_box):
         data["dead_state"] = "No"
     if (data["wounded_state"] == "Yes") or (data["dead_state"] == "Yes"):
         data_wounded_dead = data #get_json_tmp("wounded_dead")
+        print(data_wounded_dead)
         circumstance, error_circumstance = validate_circumstance(data_wounded_dead)
-        physical, error_physical = validate_physical(data_wounded_dead)
+        physical, error_physical = validate_physical(data_wounded_dead, mode)
         followup, error_followup = validate_follow_up(data_wounded_dead)
 
         if data["wounded_state"]=="Yes":
             print(physical)
-            behavior, error_behavior = validate_behavior(data_wounded_dead)
+            behavior, error_behavior = validate_behavior(data_wounded_dead, mode)
             try : 
                 individual = Report(identifier = data["identifier"],
                                     image = img,
@@ -130,12 +133,16 @@ def validate_circumstance(data):
     return circumstances, error
         
 
-def validate_behavior(data): 
+def validate_behavior(data, mode): 
     behaviors_raw = get_fields(data, "behaviors")
     behaviors_formatted = process_behaviors(behaviors_raw)
     try:
-        Behaviors.model_validate(behaviors_formatted)
-        behavior = Behaviors(**behaviors_formatted)
+        if mode=="simple":
+            BehaviorsSimple.model_validate(behaviors_formatted)
+            behavior = BehaviorsSimple(**behaviors_formatted)
+        elif mode=="advanced": 
+            Behaviors.model_validate(behaviors_formatted)
+            behavior = Behaviors(**behaviors_formatted)
         error = None
     except ValidationError as e:
         print(e)
@@ -145,12 +152,17 @@ def validate_behavior(data):
     return behavior, error
         
 
-def validate_physical(data): 
+def validate_physical(data, mode): 
     physical_raw = get_fields(data, "physical")
     physical_formatted = process_physical(physical_raw)
+    print(physical_formatted)
     try: 
-        PhysicalAnomalies.model_validate(physical_formatted)
-        physical = PhysicalAnomalies(**physical_formatted)
+        if mode=="simple":
+            PhysicalAnomaliesSimple.model_validate(physical_formatted)
+            physical = PhysicalAnomaliesSimple(**physical_formatted)
+        elif mode=="advanced":
+            PhysicalAnomalies.model_validate(physical_formatted)
+            physical = PhysicalAnomalies(**physical_formatted)
         error = None
     except ValidationError as e:
         print(e)

app/wounded.py

@@ -13,7 +13,7 @@ PATH = os.getcwd() + "/"
 PATH_ASSETS = os.getenv('PATH_ASSETS')
 PATH_ICONS = PATH + PATH_ASSETS + "icons/"
 
-def show_section_wounded(visible, individual):
+def show_section_wounded(visible, mode, individual):
     if visible==True: 
         individual = add_data_to_individual("wounded_state", "Yes", individual)
         individual = add_data_to_individual("dead_state", "No", individual)
@@ -32,7 +32,7 @@ def show_section_wounded(visible, individual):
                   variant= "primary")
         radio_behaviour = gr.Radio(["Yes", "No"], value=None, show_label=False, interactive=True)
         with gr.Row():
-            behavior_checkbox, behavior_text = create_behavior_checkbox("wounded", False)
+            behavior_checkbox, behavior_text = create_behavior_checkbox("wounded", mode, False)
 
         gr.Button("Are there physical changes on the animal?",
                   icon=PATH_ICONS + "cardiogram.png",
@@ -41,7 +41,7 @@ def show_section_wounded(visible, individual):
         with gr.Row():
             physical_boxes = create_bird_anatomy(False, "wounded")
             with gr.Column():
-                checkbox_beak, text_beak, checkbox_body, text_body, checkbox_feathers, text_feathers, checkbox_head, text_head, checkbox_legs, text_legs = process_body_parts("wounded", "None")
+                checkbox_beak, text_beak, checkbox_body, text_body, checkbox_feathers, text_feathers, checkbox_head, text_head, checkbox_legs, text_legs = process_body_parts("wounded", mode, "None")
 
             
         gr.Button("Follow-Up Events",