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+FROM ubuntu:latest
+
+RUN apt-get update
+RUN apt-get install python3 python3-pip -y
+# FROM ubuntu:22.04
+
+# RUN apt update
+# RUN apt-get update
+# RUN apt install python3.10 python3-pip -y 
+
+# https://stackoverflow.com/questions/75608323/how-do-i-solve-error-externally-managed-environment-every-time-i-use-pip-3
+# https://veronneau.org/python-311-pip-and-breaking-system-packages.html
+ENV PIP_BREAK_SYSTEM_PACKAGES 1
+
+
+##################################################
+# Ubuntu setup
+##################################################
+
+RUN  apt-get update \
+  && apt-get install -y wget \
+  && rm -rf /var/lib/apt/lists/*
+
+RUN apt-get update && apt-get -y upgrade \
+  && apt-get install -y --no-install-recommends \
+    unzip \
+    nano \
+    git \ 
+    g++ \
+    gcc \
+    htop \
+    zip \
+    ca-certificates \
+    && rm -rf /var/lib/apt/lists/*
+
+##################################################
+# ODTP setup
+##################################################
+
+# Set up a new user named "user" with user ID 1000
+#RUN useradd -m -u 1000 user
+
+# Switch to the "user" user
+USER 1000
+
+# Set home to the user's home directory
+ENV HOME=/home/user \
+	PATH=/home/user/.local/bin:$PATH
+
+# Set the working directory to the user's home directory
+WORKDIR $HOME/digiwild
+
+# Try and run pip command after setting the user with `USER user` to avoid permission issues with Python
+RUN pip install --no-cache-dir --upgrade pip
+
+# Copy the current directory contents into the container at $HOME/app setting the owner to the user
+COPY --chown=1000:1000 . $HOME/digiwild
+
+RUN pip3 install -r $HOME/digiwild/requirements.txt
+
+#RUN chown -R user:user /digiwild/data /digiwild/app/assets
+
+ENTRYPOINT ["python3", "/home/user/digiwild/app/main.py"]

LICENSE

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+                    GNU AFFERO GENERAL PUBLIC LICENSE
+                       Version 3, 19 November 2007
+
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+
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+License will continue to apply to the part which is the covered work,
+but the work with which it is combined will remain governed by version
+3 of the GNU General Public License.
+
+  14. Revised Versions of this License.
+
+  The Free Software Foundation may publish revised and/or new versions of
+the GNU Affero General Public License from time to time.  Such new versions
+will be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+  Each version is given a distinguishing version number.  If the
+Program specifies that a certain numbered version of the GNU Affero General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation.  If the Program does not specify a version number of the
+GNU Affero General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+  If the Program specifies that a proxy can decide which future
+versions of the GNU Affero General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+  Later license versions may give you additional or different
+permissions.  However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+  15. Disclaimer of Warranty.
+
+  THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+  16. Limitation of Liability.
+
+  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU Affero General Public License as published
+    by the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU Affero General Public License for more details.
+
+    You should have received a copy of the GNU Affero General Public License
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If your software can interact with users remotely through a computer
+network, you should also make sure that it provides a way for users to
+get its source.  For example, if your program is a web application, its
+interface could display a "Source" link that leads users to an archive
+of the code.  There are many ways you could offer source, and different
+solutions will be better for different programs; see section 13 for the
+specific requirements.
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU AGPL, see
+<https://www.gnu.org/licenses/>.

app/.env.dist

@@ -0,0 +1 @@
+PATH_ASSETS="YOUR_PATH_HERE"

app/assets/config/config_checkbox_behavior.json

@@ -0,0 +1,42 @@
+{
+    "Abnormal breathing":
+    {
+        "Description": "Problems breathing, breathing sounds"
+    },
+    "Crash, Falling from the sky":
+    {
+        "Description": "Suddenly falling from the sky"
+    },
+    "Diarrhea":
+    {
+        "Description": "Observed diarrhea"
+    },
+    "Lameness":
+    {
+        "Description": "Apparent limping or not able to walk properly"
+    },
+    "Neurological":
+    {
+        "Description": "Circling, incoordination, tremors, convulsions, fast eye movements"
+    },
+    "Other abnormal behavior":
+    {
+        "Description": "Other than weakness, other than neurologic"
+    },
+    "Unable to fly":
+    {
+        "Description": "Animal alert and tries to fly but can not take off"
+    },
+    "Vomiting":
+    {
+        "Description": "Throwing up undigested food, regurgitating"
+    },
+    "Weakness":
+    {
+        "Description": "Non responsive, does not fly away when approached, lethargy"
+    },
+    "No changes": 
+    {
+        "Description": "Animal is acting normally"
+    }
+}

app/assets/config/config_checkbox_physical.json

@@ -0,0 +1,68 @@
+{
+    "Common":
+    {
+        "Blackened/burnt skin": {
+            "Description": "Burnt/ blackened/ charred skin or feathers"},
+        "Blood": {
+            "Description": "Visible blood"},
+        "Foreign body": {
+            "Description": "Objects in feathers"},
+        "Fracture": {
+            "Description": "Obvious bone fracture"},
+        "Injury": {
+            "Description": "Visible skin injury"},
+        "Parasite": {
+            "Description": "Maggots, fleas, lice, louseflies"},
+        "Swelling": {
+            "Description": "Marked swelling without injury"},
+        "Warty or tumor-like growth, crusts": {
+            "Description": "Unusual growth, crusty tumor-like growth"}
+    },
+    "Beak":
+    {
+        "Adhesion": {
+            "Description": "Material (food, saliva) around/ in the beak"
+            },
+        "Deformation": {
+            "Description": "Unusual beak growth"
+            }
+    },
+    "Body": 
+    {
+        "Emaciation": {
+            "Description": "Breast muscles are not well developed"},
+        "Fluffed up": {
+            "Description": "Plumage is fluffed up"},
+        "Stained feathers": {
+            "Description": "Feces, dirt, dried blood"}
+    },
+    "Feathers/Wings/Tail":
+    {
+        "Fluffed up": {
+            "Description": "Plumage is fluffed up"},
+        "Feather abnormalities": {
+            "Description": "Discoloration, broken/ missing feathers"},
+        "Stained feathers": {
+            "Description": "Feces, dirt, dried blood"},
+        "Abnormal wing posture": {
+            "Description": "Wing is not used/ hangs on the side"},
+        "Missing limb": {
+            "Description": "Missing limb"}
+    },
+    "Head incl. eyes": 
+    {
+        "Ear changes": {
+            "Description": "Swollen, crusts, plugged, discharge"},
+        "Eye changes": {
+            "Description": "Red, swollen, discharge, crusts, eyes shut"},
+        "Tilted head": {
+            "Description": "Wry neck, unusual neck posture, torticollis"}
+    },
+    "Legs":
+    {
+        "Missing limb": {
+            "Description": "Missing limb"},
+        "Deformation": {
+            "Description": "Abnormal form of limbs, toes, legs"}
+    }
+}

app/assets/config/config_dropdown_circumstances.json

@@ -0,0 +1,138 @@
+{
+    "Collision with a means of transport": 
+    {
+        "road vehicle": 
+        {
+            "Options": {
+                "road_type" : ["highway", "main road", "secondary road", "local road/path/trail", "parking lot", "other road", "unknown road"]
+            },
+            "Open": "Infrastructure_number"
+        },
+        "train": 
+        {
+            "Open": "Infrastructure_number"
+        },
+        "aircraft": {},
+        "boat": {},
+        "other transport collision": {},
+        "unknown": {}
+    },
+    "Destruction / Deliberatly removed" : 
+    {
+        "hunting": 
+        {
+            "Options": {
+                "method" : ["shooting", "bow", "falconry", 
+                "hounds hunting", "digging up", "other hunting", "unknow hunting"]
+            }
+        },
+        "trap": 
+        {
+            "Options": {
+                "method": ["killing trap", "pole trap", 
+                "trap cage", "corvids nasse", "net", "cage trap", 
+                "fall-trap", "glue trap", "insect trap", "other trap", "unknown trap"]
+            }
+        },
+        "poisoning": {},
+        "removal or direct capture": 
+        {
+            "Options": {"method": ["gassing", "raptor captured at nest", 
+            "brood destruction", "traffic/trade", "capture accident", 
+            "scientific sample", "other removal", "unknown removal"]
+        }
+        },
+        "fishing": 
+        {
+            "Options": {"method" : ["drowned/tangled", "beached with capture indications", 
+            "other fishing", "unknown fishing"]
+        }
+        },
+        "other destruction": {},
+        "unknown": {}
+    },
+   "Indirect destruction":
+   {
+         "pylone and electric grid":
+         {
+  
+            "Options": {
+                "infrastructure" : ["electric line", "pole/pylon", "other structure", "unknown structure"]
+            },
+            "Extra":
+            {
+                "Cause": ["collision", "electrocution"]
+            }
+         },
+         "windfarm": {},
+         "other collision": 
+         {
+            "Options": {
+                "object": ["window", "building", "lighthouse", "cable", "wire fence/barbed wire", "other crash", "unknown crash"]
+            }
+         },
+         "fall": 
+         {
+            "Options": {
+                "location": ["chimney", "empty pole", "hole/well", "other fall", "unknown fall"]
+            }
+         },
+         "development work": 
+         {
+            "Options": {
+                "work_type" : ["transport infrastructure", "building", "other work", "unknown work"]
+            }
+         },
+         "pollution / contamination": 
+         {
+            "Options": {
+                "pollution_type" : ["oil pollution", "chemical pollution", "heavy metals", 
+                "light", "noise", "plastic ingestion", "other pollution", "unknown pollution"]
+         },
+         "agricultural net protection": {},
+         "vegetal / forest work": 
+         {
+            "Options": {
+                "work_type" : ["clearing/mowing/plowing", "tree felling/pruning", 
+                "other forest work", "unknown forest work"]
+            }
+         }
+         },
+         "other indirect destruction": {},
+         "unknown": {}
+    },
+    "Natural cause": 
+    {
+        "predation": 
+        {
+            "Options": {
+                "predator" : ["cat", "dog", "rooster/hen", "other domestic animal", "wild birds",
+                "wild mammal", "other predator", "unknown predator"]
+            }
+        },
+        "weather": 
+        {
+            "Options": {
+                "condition" : ["cold wave", "drought", "hail", "lightening", "storm", "other weather", "unknown weather"]
+            }
+        },
+        "natural disaster": 
+        {
+            "Options": {
+                "disaster" : ["fire", "avalanche", "rock fall", "mudslide", "volcanic eruption/ashes", "other natural disaster", "unknown natural disaster"]
+            }
+        },
+        "nest fall": {},
+        "stranding due to exhaustion": {},
+        "disease/parasite": {},
+        "accidental drowing": 
+        {
+            "Options": {
+                "drowning_location" : ["drinking trough", "pool", "storm pool", "irrigation pool", "natural pool", "flood", "other location", "unknown location"]
+            }
+        },
+        "other natural cause": {},
+        "unknown": {}
+    },
+    "Unknown": {}
+}

app/assets/config/config_followup.json

@@ -0,0 +1,23 @@
+{
+    "Event follow-up": 
+    {
+        "Animal collected": {
+            "Options": ["Yes", "No"]
+        },
+        "Recipient": {
+            "Options": ["Veterinary", "Care center", "Local Museum", "National Museum", "Other"]
+        },
+        "Radiography": {
+            "Options": ["Yes", "No", "Unknown"]
+        },
+        "Given answer": {
+            "Options": ["Nothing", "Complaint against X", "Complaint", "Police call", "Discussion with the speaker", "Press release", "Unknown"]
+        },
+        "Name of recipient / museum": {
+            "Open": {}
+        },
+        "Collection reference": {
+            "Open": {}
+        }
+    }
+}

app/assets/tmp_json/tmp_wounded_dead.json

@@ -0,0 +1 @@
+{}

app/behavior/behavior_checkbox.py

@@ -0,0 +1,30 @@
+import gradio as gr
+from utils.utils_config import get_custom_config_dropdowns
+from utils.utils_checkbox import create_checkbox
+from utils.utils_visible import set_visible
+from validation_submission.add_json import add_data_tmp
+
+def on_select_behavior(behavior_checkbox): 
+    behavior_checkbox = [behavior.lower() for behavior in behavior_checkbox]
+    add_data_tmp("wounded_dead", "behaviors_type", behavior_checkbox)
+
+def retrieve_behavior_options_description():
+    dropdown_config = get_custom_config_dropdowns("config_checkbox_behavior.json")
+    options = list(dropdown_config.keys())
+    options = [option.title() for option in options]
+    descriptions =[]
+    for _,subdict in dropdown_config.items():
+        descriptions.append(subdict["Description"])
+    return options, descriptions
+
+def create_behavior_checkbox(section: str, visible):
+    options, descriptions = retrieve_behavior_options_description()
+    label_checkbox = "Behavior changes observed"
+    checkbox, text = create_checkbox("", section, label_checkbox, visible, options, descriptions)
+    return checkbox, text
+
+def show_behavior(choice, section: str): 
+    visible = set_visible(choice)
+    checkbox, text = create_behavior_checkbox(section, visible)
+    add_data_tmp("wounded_dead", "behaviors_radio", choice)
+    return checkbox, text

app/behavior/class_behavior.py

@@ -0,0 +1,66 @@
+from pydantic import BaseModel, Field
+from typing import Literal, List, Union, Optional
+
+class Behavior(BaseModel):
+    type: str
+    description: Optional[str] = None  # Making the description field optional
+
+# --- Specific Behavior classes ---
+class AbnormalBreathing(Behavior):
+    type: Literal['abnormal breathing']
+    description: Optional[Literal["Problems breathing, breathing sounds"]] = None
+
+class CrashFalling(Behavior):
+    type: Literal['crash, falling from the sky']
+    description: Optional[Literal["Suddenly falling from the sky"]] = None
+
+class Diarrhea(Behavior):
+    type: Literal['diarrhea']
+    description: Optional[Literal["Observed diarrhea"]] = None
+
+class Lameness(Behavior):
+    type: Literal['lameness']
+    description: Optional[Literal["Apparent limping or not able to walk properly"]] = None
+
+class Neurological(Behavior):
+    type: Literal['neurological']
+    description: Optional[Literal["Circling, incoordination, tremors, convulsions, fast eye movements"]] = None
+
+class OtherAbnormalBehavior(Behavior):
+    type: Literal['other abnormal behavior']
+    description: Optional[Literal["Other than weakness, other than neurologic"]] = None
+
+class UnableToFly(Behavior):
+    type: Literal['unable to fly']
+    description: Optional[Literal["Animal alert and tries to fly but can not take off"]] = None
+
+class Vomiting(Behavior):
+    type: Literal['vomiting']
+    description: Optional[Literal["Throwing up undigested food, regurgitating"]] = None
+
+class Weakness(Behavior):
+    type: Literal['weakness']
+    description: Optional[Literal["Non responsive, does not fly away when approached, lethargy"]] = None
+
+class NoChanges(Behavior):
+    type: Literal['no changes']
+    description: Optional[Literal["Animal is acting normally"]] = None
+
+# 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):
+    behaviors_radio: str  # e.g., "Yes"
+    behaviors_type: Optional[List[BehaviorType]] = None

app/circumstances/circumstances.py

@@ -0,0 +1,67 @@
+import gradio as gr
+import os
+from dotenv import load_dotenv
+
+from utils.utils_visible import set_visible
+from validation_submission.add_json import add_data_tmp
+
+load_dotenv()
+PATH = os.getcwd() + "/"
+PATH_ASSETS = os.getenv('PATH_ASSETS')
+LOGO_PATH = PATH + PATH_ASSETS + "logos"
+
+CAUSE_COL_WIDTH = "50px"
+
+
+def show_circumstances(choice): 
+    visible = set_visible(choice)
+    add_data_tmp("wounded_dead", 
+                    "circumstance_radio", 
+                    choice)
+    button_collision, button_deliberate_destruction, button_indirect_destruction, button_natural_cause, dropdown, dropdown_level2, openfield_level2, dropdown_extra_level2 = create_circumstances(visible)
+    return button_collision, button_deliberate_destruction, button_indirect_destruction, button_natural_cause, dropdown, dropdown_level2, openfield_level2, dropdown_extra_level2
+
+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_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", 
+                                             visible=visible,
+                                             icon=LOGO_PATH +  '/van.png',
+                                             elem_id="buttons-conditions")
+                
+            with gr.Column(scale=1, min_width=CAUSE_COL_WIDTH):
+                button_deliberate_destruction = gr.Button("Destruction / Deliberatly removed", 
+                                                          icon=LOGO_PATH +  '/destruction.png',
+                                                          visible=visible,
+                                                          elem_id="buttons-conditions")
+ 
+            with gr.Column(scale=1, min_width=CAUSE_COL_WIDTH):
+                button_indirect_destruction = gr.Button("Indirect destruction", 
+                                                        icon=LOGO_PATH +  '/indirect.png',
+                                                        visible=visible,
+                                                        elem_id="buttons-conditions")
+
+            with gr.Column(scale=1, min_width=CAUSE_COL_WIDTH):
+                button_natural_cause = gr.Button("Natural cause", 
+                                                 icon=LOGO_PATH +  '/natural.png', 
+                                                 visible=visible,
+                                                 elem_id="buttons-conditions")
+    return button_collision, button_deliberate_destruction, button_indirect_destruction, button_natural_cause
+
+def create_circumstances_dropdown(visible):
+    with gr.Row() as dropdown_row:
+        dropdown = gr.Dropdown(choices=[], 
+                               label="Choices will appear here...",
+                               visible=visible, interactive=False, elem_id="dropdown-conditions")
+    openfield_level2 = gr.Textbox(visible=False, elem_id="dropdown-conditions")
+    dropdown_level2 = gr.Dropdown(choices=[], visible=False, elem_id="dropdown-conditions")
+    dropdown_extra_level2 = gr.Dropdown(choices=[], visible=False, elem_id="dropdown-conditions")
+    return dropdown, dropdown_level2, openfield_level2, dropdown_extra_level2
+
+
+     

app/circumstances/circumstances_dropdowns.py

@@ -0,0 +1,112 @@
+import gradio as gr
+from utils.utils_config import get_custom_config_dropdowns
+from validation_submission.add_json import add_data_tmp
+
+#--------------------------------------------------------- LEVEL 1 DROPDOWNS
+def retrieve_config_options(label, dropdown_config):
+    options = list(dropdown_config[label].keys())
+    options = [option.title() for option in options]
+    return options
+
+def reinitialise_level2(): 
+    dropdown_level2 = gr.Dropdown(choices=[], visible=False)
+    openfield_level2 = gr.Textbox(visible=False)
+    dropdown_extra_level2 = gr.Dropdown(choices=[], visible=False)
+    return dropdown_level2, openfield_level2, dropdown_extra_level2
+
+def create_dropdown_level1(label): 
+    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()
+    return dropdown, dropdown_level2, openfield_level2, dropdown_extra_level2
+    
+def dropdown_collision():
+    label = "Collision with a means of transport"
+    add_data_tmp("wounded_dead", "circumstance", label.lower())
+    return create_dropdown_level1(label)
+
+def dropdown_deliberate_destruction():
+    label = "Destruction / Deliberatly removed"
+    add_data_tmp("wounded_dead", "circumstance", label.lower())
+    return create_dropdown_level1(label)     
+
+def dropdown_indirect_destruction(): 
+    label = "Indirect destruction"
+    add_data_tmp("wounded_dead", "circumstance", label.lower())
+    return create_dropdown_level1(label) 
+
+def dropdown_natural_cause(): 
+    label = "Natural cause"
+    add_data_tmp("wounded_dead", "circumstance", label.lower())
+    return create_dropdown_level1(label)         
+
+
+#--------------------------------------------------------- LEVEL 2 DROPDOWNS
+def get_options(value):
+        value = value.lower()
+        options_label = None
+        options_dropdown= None
+        open_field = None
+        extras = None
+        extras_label = None
+        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: 
+                if "Options" in nested_dict.keys():
+                    options_dict = nested_dict["Options"]
+                    options_label = list(options_dict.keys())[0]
+                    options_dropdown = list(options_dict.values())[0]
+                    options_dropdown = [option.title() for option in options_dropdown]
+                if "Open" in nested_dict.keys():
+                    open_field = nested_dict["Open"]
+                    open_field = open_field.title()
+                if "Extra" in nested_dict.keys():
+                    for key, val in nested_dict["Extra"].items():
+                        extras_label = key
+                        extras = val
+                        extras = [extra.title() for extra in extras]
+        return options_label, options_dropdown, open_field, extras, extras_label
+
+       
+def on_select(evt: gr.SelectData):  # SelectData is a subclass of EventData
+    options_label, options_dropdown, open_field, extras, extras_label = get_options(evt.value)
+    add_data_tmp("wounded_dead", 
+                    "circumstance_type", 
+                    {"type": (evt.value).lower(),
+                     "option_dropdown_label" : options_label.lower() if options_label is not None else 'NA',
+                     "open_field_label" : open_field.lower() if open_field is not None else 'NA',
+                     "extra_label": extras_label.lower() if extras_label is not None else 'NA'
+                    })
+    if options_dropdown is not None:
+        dropdown_level2 = gr.Dropdown(choices=options_dropdown, label=evt.value, interactive=True, visible=True)
+    else: 
+        dropdown_level2 = gr.Dropdown(choices=[], visible=False)
+
+    if open_field is not None:
+        openfield_level2 = gr.Textbox(label=open_field, interactive=True, visible=True)
+    else: 
+        openfield_level2 = gr.Textbox(visible=False)
+
+    if extras is not None: 
+        dropdown_extra_level2 = gr.Dropdown(choices=extras, label=extras_label, interactive=True, visible=True)
+    else: 
+        dropdown_extra_level2 = gr.Dropdown(choices=[], visible=False)
+    return dropdown_level2, openfield_level2, dropdown_extra_level2
+
+def on_select_dropdown_level2(evt: gr.SelectData): 
+    add_data_tmp("wounded_dead", 
+                "circumstance_option_dropdown", 
+                evt.value.lower())
+
+def on_select_dropdown_extra_level2(evt: gr.SelectData):  
+    add_data_tmp("wounded_dead", 
+                 "circumstance_extra", 
+                 evt.value.lower())
+    
+def on_change_openfield_level2(openfield_level2_dead): 
+    print("Saving open field")
+    add_data_tmp("wounded_dead", 
+                "circumstance_open_field", 
+                str(openfield_level2_dead).lower())

app/circumstances/class_circumstance.py

@@ -0,0 +1,205 @@
+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']
+
+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 transport collision']
+
+class UnknownTransportCollision(CircumstanceTypeBase):
+    type: Literal['unknown transport collision']
+
+# Destruction / Deliberately removed
+class HuntingDestruction(CircumstanceTypeBase):
+    type: Literal['hunting']
+    method: Literal['shooting', 'bow', 'falconry', 
+                    'hounds hunting', 'digging up', 
+                    "other hunting", "unknow hunting"]
+
+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 trap", "unknown trap"]
+
+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 removal", "unknown removal"]
+
+class FishingDestruction(CircumstanceTypeBase):
+    type: Literal['fishing']
+    method: Literal['drowned/tangled', 'beached with capture indications', "other fishing", "unknown fishing"]
+
+class OtherDestruction(CircumstanceTypeBase):
+    type: Literal['other destruction']
+
+class UnknownDestruction(CircumstanceTypeBase):
+    type: Literal['unknown destruction']
+
+# Indirect destruction
+class PylonElectricGridDestruction(CircumstanceTypeBase):
+    type: Literal['pylone and electric grid']
+    infrastructure: Literal['electric line', 'pole/pylon', "other structure", "unknown structure"]
+    cause: Literal['collision', 'electrocution']
+
+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 crash']
+
+class FallDestruction(CircumstanceTypeBase):
+    type: Literal['fall']
+    location: Literal['chimney', 'empty pole', 'hole/well', 'other fall', 'unknown fall']
+
+class DevelopmentWorkDestruction(CircumstanceTypeBase):
+    type: Literal['development work']
+    work_type: Literal['transport infrastructure', 'building', 'other work', 'unknown work']
+
+class PollutionContaminationDestruction(CircumstanceTypeBase):
+    type: Literal['pollution / contamination']
+    pollution_type: Literal['oil pollution', 'chemical pollution', 'heavy metals', 
+                            'light', 'noise', 
+                            'plastic ingestion', 'other pollution', 'unknown pollution']
+
+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 forest work', 'unknown forest work']
+
+class OtherIndirectDestruction(CircumstanceTypeBase):
+    type: Literal['other indirect desctruction']
+
+class UnknownIndirectDestruction(CircumstanceTypeBase):
+    type: Literal['unknown indirect desctruction']
+
+# Natural cause
+class Predation(CircumstanceTypeBase):
+    type: Literal['predation']
+    predator: Literal['cat', 'dog', 'rooster/hen', 
+                      'other domestic animal', 'wild birds', 
+                      'wild mammal', 'other predator', 'unknown predator']
+
+class Weather(CircumstanceTypeBase):
+    type: Literal['weather']
+    condition: Literal['cold wave', 'drought', 'hail', 
+                       'lightening', 'storm', 
+                       'other weather', 'unknown weather']
+
+class NaturalDisaster(CircumstanceTypeBase):
+    type: Literal['natural disaster']
+    disaster: Literal['fire', 'avalanche', 'rock fall', 
+                      'mudslide', 'volcanic eruption/ashes', 
+                      'other natural disaster', 'unknown natural disaster']
+
+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 location', 'unknown location']
+
+class OtherNaturalCause(CircumstanceTypeBase):
+    type: Literal['other natural cause']
+
+class UnknownNaturalCause(CircumstanceTypeBase):
+    type: Literal['unknown natural cause']
+
+# 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_radio: str  # e.g., "Yes"
+    circumstance: Optional[str] = None  # e.g., "COLLISION"
+    circumstance_type: Optional[CircumstanceType] = Field(None, discriminator='type')
+
+
+# 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/classes.py

@@ -0,0 +1,46 @@
+from pydantic import BaseModel, Field
+from typing import Optional
+import numpy as np
+from PIL import Image
+import io
+import base64
+import uuid
+
+from behavior.class_behavior import Behaviors
+from circumstances.class_circumstance import Circumstances
+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: Behaviors
+    physical_anomalies: PhysicalAnomalies
+    follow_up_events: FollowUpEvents
+
+class Dead(BaseModel):
+    circumstances: Circumstances
+    physical_anomalies: PhysicalAnomalies
+    follow_up_events: FollowUpEvents
+
+class ImageBase64(BaseModel):
+    image: str  
+    @classmethod
+    def to_base64(cls, pixel_data: list):
+        img_array = np.array(pixel_data, dtype=np.uint8)
+        img = Image.fromarray(img_array)
+        # Save the image to a bytes buffer
+        buffer = io.BytesIO()
+        img.save(buffer, format="PNG")
+        buffer.seek(0)
+        base64_str = base64.b64encode(buffer.read()).decode('utf-8')
+        return cls(image=base64_str)
+    
+class Report(BaseModel):
+    identifier: str
+    image: ImageBase64
+    geolocalisation: Geolocalisation
+    wounded_state: str
+    wounded: Optional[Wounded] = None  
+    dead_state: str
+    dead: Optional[Dead] = None 

app/dead.py

@@ -0,0 +1,40 @@
+import gradio as gr
+from circumstances.circumstances import create_circumstances
+from physical.physical_select_animal import create_bird_anatomy
+from physical.physical_checkbox import process_body_parts
+from follow_up.followup_events import create_followup_dropdowns, create_followup_open
+from validation_submission.add_json import add_data_to_individual
+
+def show_section_dead(visible):
+    if visible==True: 
+        add_data_to_individual("wounded_state", "No")
+        add_data_to_individual("dead_state", "Yes")
+        
+    with gr.Column(visible=visible, elem_id="dead") as section_dead:
+        gr.Markdown("# Dead Animal")
+        
+        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_circumstances(visible=False)      
+        
+        gr.Markdown("## Are there physical changes on the bird?" , label="description")
+        radio_physical = gr.Radio(["Yes", "No"], value=None, show_label=False, interactive=True)
+        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")
+
+        gr.Markdown("## Follow-Up Events", label="Title")
+        gr.Markdown("Please tell us what you did with the animal.", label="description")
+        with gr.Row(): 
+            fe_collection_dropdown, fe_recepient_dropdown, fe_radio_dropdown, fe_answer_dropdown = create_followup_dropdowns(visible, "dead")
+        with gr.Row(): 
+            fe_name_recipient, fe_collection_ref = create_followup_open(visible, "dead")
+
+
+    return section_dead, radio_cause, radio_physical,\
+         button_collision, button_deliberate_destruction, button_indirect_destruction, button_natural_cause, \
+          dropdown, dropdown_level2, openfield_level2, dropdown_extra_level2, \
+          physical_boxes, \
+          checkbox_beak, text_beak, checkbox_body, text_body, checkbox_feathers, text_feathers, checkbox_head, text_head, checkbox_legs, text_legs, \
+          fe_collection_dropdown, fe_recepient_dropdown, fe_radio_dropdown, fe_answer_dropdown, fe_name_recipient, fe_collection_ref

app/display.py

@@ -0,0 +1,120 @@
+import gradio as gr
+import pandas as pd
+from gradio_modal import Modal
+from PIL import Image
+from io import BytesIO
+import base64
+
+from validation_submission.submission import validate_save_individual
+from validation_submission.get_json import get_json_all_individuals
+
+HEADERS = ["Identifier", "Location", "Wounded", "Dead"]
+
+
+def save_display_individual(gallery, df, error_box):
+    individual, error_box = validate_save_individual(error_box)
+    if individual:
+        all_animals = get_json_all_individuals()
+        gallery_animals = process_animals_for_gallery(all_animals)
+        gallery = make_gallery(gallery_animals)
+        df_animals = process_animals_for_df(all_animals)
+        df = make_df(df_animals)
+    return gallery, df, error_box
+
+# ---------------------------------- 
+# GALLERY 
+
+def convert_image(image_base64_str): 
+    im = Image.open(BytesIO(base64.b64decode(image_base64_str)))
+    return im
+
+def set_gallery_size(len_animals): 
+    if len_animals < 10: 
+        num_cols=5
+        num_rows=2
+    else: 
+        num_cols = len_animals/2
+        num_rows = len_animals/(num_cols)
+    return num_cols, num_rows
+
+def process_animals_for_gallery(all_animals): 
+    gallery_animals = []
+    for _, animal in all_animals.items(): 
+        image = convert_image(animal["image"]["image"])
+        caption = animal["identifier"]
+        animal = (image, caption)
+        gallery_animals.append(animal)
+    return gallery_animals
+
+def make_gallery(gallery_animals):
+    num_cols, num_rows = set_gallery_size(len(gallery_animals))
+    gallery = gr.Gallery(
+        label="Gallery of Records", elem_id="gallery", 
+        columns=[num_cols], rows=[num_rows],
+        value=gallery_animals,
+        object_fit="contain", height="auto", interactive=False)
+    return gallery
+
+def keep_only_values(dict_to_filter): 
+    info_text = ""
+    values_to_ignore = ["Yes", "No", "NA"]
+    if dict_to_filter:
+        for key, val in dict_to_filter.items(): 
+            if type(val) is dict: 
+                subset_text = keep_only_values(val)
+                info_text += f"{subset_text}"
+            elif type(val) is list:
+                for item in val: 
+                    if type(item) is dict: 
+                        subset_text = keep_only_values(item)
+                        info_text += f"{subset_text}"
+            elif (val is not None) and (type(val) is not bool) and (val not in values_to_ignore): 
+                info_text += f" {key} : {val} |"
+            else:
+                print("Ignoring value: ", val)
+                print("Associated key: ", key)
+    else: 
+        info_text = "NaN"
+    return info_text
+
+# ---------------------------------- 
+# DATAFRAME 
+
+def process_animals_for_df(all_animals):
+    df_animals = {}
+    identifiers =[]
+    geo =[]
+    wounded =[]
+    dead =[]
+    for _, animal in all_animals.items(): 
+        identifier_value = animal["identifier"]
+        identifiers.append(identifier_value)
+        geo_dict = animal["geolocalisation"]
+        geo_values = keep_only_values(geo_dict)
+        geo.append(geo_values)
+        wounded_dict = animal["wounded"]
+        wounded_values = keep_only_values(wounded_dict)
+        wounded.append(wounded_values)
+        dead_dict = animal["dead"]
+        dead_values = keep_only_values(dead_dict)
+        dead.append(dead_values)
+    df_animals["Identifier"] = identifiers
+    df_animals["Location"] = geo
+    df_animals["Wounded"] = wounded
+    df_animals["Dead"] = dead
+    return df_animals
+
+
+def make_df(df_animals):
+    df = pd.DataFrame.from_dict(df_animals)
+    styled_df = df.style.set_properties(**{
+    'min-width': '25px',
+    'max-width': '50px',  # Adjust width as needed
+    'white-space': 'normal',  # Allows text to wrap to the next line
+    'word-wrap': 'break-word'  # Breaks long words to fit within the width
+    })
+    df_gradio = gr.DataFrame(visible=True,
+                         value=styled_df,
+                         headers=HEADERS, interactive=False)
+    return df_gradio
+

app/follow_up/class_follow_up.py

@@ -0,0 +1,50 @@
+from pydantic import BaseModel, Field
+from typing import Literal, Union, Optional, List
+
+# --- Event follow-up classes ---
+
+class AnimalCollectedEvent(BaseModel):
+    type: Literal['animal collected']
+    collected: Literal['yes', 'no']
+
+class RecipientEvent(BaseModel):
+    type: Literal['recipient']
+    recipient: Literal['veterinary', 'care center', 
+                                'local museum', 'national museum', 
+                                'other']
+
+class RadiographyEvent(BaseModel):
+    type: Literal['radiography']
+    radiography: Literal['yes', 'no', 'unknown']
+
+class GivenAnswerEvent(BaseModel):
+    type: Literal['given answer']
+    answer: Literal[
+        'nothing', 
+        'complaint against x', 
+        'complaint', 
+        'police call', 
+        'discussion with the speaker', 
+        'press release', 
+        'unknown'
+    ]
+
+class NameOfRecipientEvent(BaseModel):
+    type: Literal['recipient name']
+    name: str
+
+class CollectionReferenceEvent(BaseModel):
+    type: Literal['collection reference']
+    reference: str
+
+FollowUpEventType = Union[
+    AnimalCollectedEvent,
+    RecipientEvent,
+    RadiographyEvent,
+    GivenAnswerEvent,
+    NameOfRecipientEvent,
+    CollectionReferenceEvent
+]
+
+class FollowUpEvents(BaseModel):
+    follow_up_events: Optional[List[FollowUpEventType]] = None

app/follow_up/followup_events.py

@@ -0,0 +1,46 @@
+import gradio as gr
+from utils.utils_config import get_custom_config_dropdowns
+from validation_submission.add_json import add_data_tmp
+
+def create_followup_dropdowns(visible, elem_id): 
+    followup_config = get_custom_config_dropdowns("config_followup.json")
+    followup_config = followup_config["Event follow-up"]
+    fe_collection_dropdown = create_fe_collection_dropdown(followup_config, visible, elem_id)
+    fe_recipient_dropdown = create_fe_recipient_dropdown(followup_config, visible, elem_id)
+    fe_radio_dropdown = create_fe_radio_dropdown(followup_config, visible, elem_id)
+    fe_answer_dropdown = create_fe_answer_dropdown(followup_config, visible, elem_id)
+    return fe_collection_dropdown, fe_recipient_dropdown, fe_radio_dropdown, fe_answer_dropdown
+
+def create_followup_open(visible, elem_id): 
+    fe_name_recipient = gr.Textbox(label="Name of recipient / museum", visible=visible, 
+                                   elem_id=elem_id, interactive=True)
+    fe_collection_ref = gr.Textbox(label="Collection reference", visible=visible, 
+                                   elem_id=elem_id, interactive=True)
+    return fe_name_recipient, fe_collection_ref
+
+
+def create_fe_collection_dropdown(followup_config, visible, elem_id):
+    fe_collection_dropdown = gr.Dropdown(choices=followup_config["Animal collected"]["Options"], label="Animal collected", 
+                                         visible=visible, elem_id=elem_id, interactive=True)
+    return fe_collection_dropdown
+
+def create_fe_recipient_dropdown(followup_config, visible, elem_id):
+    fe_recipient_dropdown = gr.Dropdown(choices=followup_config["Recipient"]["Options"], label="Recipient", 
+                                        visible=visible, elem_id=elem_id, interactive=True)
+    return fe_recipient_dropdown
+
+def create_fe_radio_dropdown(followup_config, visible, elem_id): 
+    fe_radio_dropdown = gr.Dropdown(choices=followup_config["Radiography"]["Options"], label="Radiography", 
+                                        visible=visible, elem_id=elem_id, interactive=True)
+    return fe_radio_dropdown
+
+def create_fe_answer_dropdown(followup_config, visible, elem_id): 
+    fe_answer_dropdown = gr.Dropdown(choices=followup_config["Given answer"]["Options"], label="Given answer", 
+                                        visible=visible, elem_id=elem_id, interactive=True)
+    return fe_answer_dropdown
+
+def save_fe(value, key): 
+    add_data_tmp("wounded_dead", "followup " + key.lower(), value.lower())
+
+
+