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README_APPS.md

@@ -0,0 +1,58 @@
+# Breast Cancer Data Collection Tool
+
+This repository contains a Streamlit application for collecting breast cancer treatment data.
+
+## Files Overview
+
+### App Versions
+
+- **`app.py`** - Production version for Hugging Face Spaces deployment
+  - Uses `/tmp/data` directory for file storage (required for Hugging Face)
+  - Configured with Hugging Face metadata
+  - Includes patient ID sanitization for safe file paths
+
+- **`app_local.py`** - Local development version
+  - Uses local `data/` directory for file storage
+  - Optimized for local development and testing
+  - Full functionality without cloud deployment constraints
+
+### Supporting Files
+
+- **`requirements.txt`** - Python dependencies
+- **`districts.txt`** - Uganda districts list
+- **`Dockerfile`** - Container configuration for Hugging Face Spaces
+- **`.github/workflows/deploy.yml`** - CI/CD pipeline for automatic deployment
+
+## Quick Start
+
+### Local Development
+```bash
+# Install dependencies
+pip install -r requirements.txt
+
+# Run the local version
+streamlit run app_local.py
+```
+
+### Hugging Face Spaces Deployment
+The main `app.py` is automatically deployed via GitHub Actions to Hugging Face Spaces when changes are pushed to the main branch.
+
+## Features
+
+- **Baseline Data Collection**: Patient demographics, diagnosis, and treatment planning
+- **Treatment Cycle Management**: Progressive cycle data entry with dynamic medication tracking
+- **Data Validation**: Comprehensive form validation and error handling
+- **JSON Export**: Structured data storage for analysis
+- **Patient ID Support**: Handles special characters safely (e.g., "1275/17")
+
+## Data Storage
+
+- **Local**: Data saved to `./data/patient_[sanitized_id]/` directory
+- **Hugging Face**: Data saved to `/tmp/data/patient_[sanitized_id]/` directory
+- **Format**: JSON files with baseline data and treatment cycles
+
+## Development Notes
+
+Patient IDs with special characters (like "1275/17") are automatically sanitized for file paths while preserving the original ID in the data.
+
+Both versions include the same functionality - the only difference is the data storage location to accommodate different deployment environments.

app.py

@@ -1,6 +1,6 @@
 """
-Breast Cancer Data Collection Tool
-=====================================
+Breast Cancer Data Collection Tool - Hugging Face Spaces Version
+===============================================================
 Data capture tool for analysis of adherence patterns to chemotherapy and their 
 association with recurrence-free survival among breast cancer patients at UCI.
 
@@ -8,6 +8,9 @@ Study Period: 2016 - 2018
 Author: Data Collection Team
 Date: October 2025
 
+This version is configured for deployment on Hugging Face Spaces and uses /tmp/data
+for file storage to avoid permission issues. For local development, use app_local.py
+
 title: Breast Cancer Data Collection Tool
 emoji: 🎗️
 colorFrom: pink
@@ -562,7 +565,7 @@ def render_cycle_1_form(patient_id: str) -> Dict:
     return {
         "cycle_number": 1,
         "patient_id": patient_id,
-        "regimen_prescribed": regimen_prescribed if not regimen_prescribed.startswith("-- Select") else None,
+        "regimen_prescribed": regimen_prescribed if regimen_prescribed and not regimen_prescribed.startswith("-- Select") else None,
         "prescription_date": prescription_date.strftime("%Y-%m-%d"),
         "medications": medications,
         "chemo_received_date": chemo_received_date.strftime("%Y-%m-%d"),
@@ -847,8 +850,8 @@ def render_linear_baseline_form(districts: List[str]) -> Dict:
         "marital_status": marital_status,
         "income_source": income_source,
         "income_other": income_other if income_source == "Other" else None,
-        "district": district if not district.startswith("-- Select") else None,
-        "initial_diagnosis": initial_diagnosis if not initial_diagnosis.startswith("-- Select") else None,
+        "district": district if district and not district.startswith("-- Select") else None,
+        "initial_diagnosis": initial_diagnosis if initial_diagnosis and not initial_diagnosis.startswith("-- Select") else None,
         "immunohisto_present": immunohisto_present,
         "immunohisto_results": immunohisto_results if immunohisto_present == "Yes" else [],
         "immunohisto_other": immunohisto_other if "Other" in immunohisto_results else None,
@@ -862,7 +865,7 @@ def render_linear_baseline_form(districts: List[str]) -> Dict:
             "other_specify": commodities_other if other_comorbidities else None
         },
         "chemo_cycles_prescribed": chemo_cycles,
-        "regimen_prescribed": regimen_prescribed if not regimen_prescribed.startswith("-- Select") else None,
+        "regimen_prescribed": regimen_prescribed if regimen_prescribed and not regimen_prescribed.startswith("-- Select") else None,
         "treatment_started": treatment_started,
         "treatment_not_started_reason": treatment_not_started_reason if treatment_started == "No" else None
     }

app_local.py

@@ -0,0 +1,1062 @@
+"""
+Breast Cancer Data Collection Tool - Local Development Version
+=============================================================
+Data capture tool for analysis of adherence patterns to chemotherapy and their 
+association with recurrence-free survival among breast cancer patients at UCI.
+
+Study Period: 2016 - 2018
+Author: Data Collection Team
+Date: October 2025
+
+This version is configured for local development and uses the local 'data' directory
+for file storage. For Hugging Face Spaces deployment, use app.py
+
+Usage: streamlit run app_local.py
+"""
+
+import streamlit as st
+from datetime import datetime, date
+import pandas as pd
+import json
+import os
+import time
+from typing import Dict, List, Optional
+
+
+# =========================================
+def render_linear_baseline_form(districts: List[str]) -> Dict:
+    """Render the linear baseline form following exact PDF numbering"""
+    st.header("Section 1: Baseline Data (Collected at First Visit Only)")
+    st.markdown("---")
+    
+    # 1. Patient ID=========================================
+# CONFIGURATION AND CONSTANTS
+# ========================================================================================
+
+class Config:
+    """Application configuration constants"""
+    STUDY_START_DATE = date(2016, 1, 1)
+    STUDY_END_DATE = date(2018, 12, 31)
+    DEFAULT_DATA_DIR = "data"
+    
+    # Form options
+    EDUCATION_OPTIONS = ["None", "Primary", "Secondary", "Tertiary", "Not captured"]
+    MARITAL_OPTIONS = ["Single", "Married", "Divorced", "Widowed", "Not captured"]
+    INCOME_OPTIONS = ["Farmer", "Business", "Professional", "Unemployed", "Other"]
+    DIAGNOSIS_OPTIONS = [
+        "Invasive ductal carcinoma",
+        "Moderately differentiated invasive ductal carcinoma",
+        "Moderately differentiated ductal carcinoma",
+        "Ductal carcinoma in situ",
+        "Infiltrating carcinoma",
+        "Poorly differentiated adenocarcinoma",
+        "Invasive adenocarcinoma",
+        "Invasive lobular carcinoma",
+        "Other"
+    ]
+    STAGE_OPTIONS = ["Stage 0", "Stage I", "Stage II", "Stage III", "Stage IV"]
+    
+    # Predefined medication options
+    MEDICATION_OPTIONS = [
+        "Adriamycin",
+        "Cyclophosphamide", 
+        "Doxorubicin",
+        "Dexamethasone",
+        "5-fluorouracil",
+        "Ondansetron",
+        "Ranitidine",
+        "Metoclopramide",
+        "Plasil",
+        "Ifosfamide",
+        "Mesna",
+        "Paclitaxel",
+        "Epirubicin",
+        "Carboplatin",
+        "Capecitabine (Xeloda)",
+        "Docetaxel",
+        "Epirubicin",
+        "Promethazine",
+        "Docetaxel",
+        "Tamoxifen",
+        "Anastrazole",
+        "Ifosfamide",
+        "Mesra",
+        "Promethazine"
+    ]
+    
+    IMMUNOHISTO_OPTIONS = [
+        "ER-positive (ER+)",
+        "PR-positive (PR+)", 
+        "HR-positive (HR+)",
+        "HR-negative (HR-)",
+        "HER2-positive (HER2+)",
+        "ER-negative (ER-)",
+        "HER2-negative (HER2-)"
+    ]
+    
+    REGIMEN_OPTIONS = [
+        "AC (Doxorubicin + Cyclophosphamide)",
+        "AC-T (Doxorubicin + Cyclophosphamide + Paclitaxel)",
+        "CMF (Cyclophosphamide + Methotrexate + 5-Fluorouracil)",
+        "FAC (5-Fluorouracil + Doxorubicin + Cyclophosphamide)",
+        "FEC (5-Fluorouracil + Epirubicin + Cyclophosphamide)",
+        "TC (Docetaxel + Cyclophosphamide)",
+        "TCH (Docetaxel + Carboplatin + Trastuzumab)",
+        "TAC (Docetaxel + Doxorubicin + Cyclophosphamide)",
+        "EC-T (Epirubicin + Cyclophosphamide + Paclitaxel)",
+        "Capecitabine (Xeloda) monotherapy",
+        "Tamoxifen monotherapy",
+        "Other"
+    ]
+    SIDE_EFFECTS_OPTIONS = ["Nausea", "Fatigue", "Vomiting", "Neuropathy", "None", "Other"]
+    CONDITION_OPTIONS = ["Better", "Weaker", "Other"]
+
+
+# ========================================================================================
+# UTILITY FUNCTIONS
+# ========================================================================================
+
+def sanitize_patient_id(patient_id: str) -> str:
+    """Sanitize patient ID for safe use in file paths"""
+    # Replace forward slashes and other problematic characters with underscores
+    return patient_id.replace("/", "_").replace("\\", "_").replace(":", "_").replace("*", "_").replace("?", "_").replace('"', "_").replace("<", "_").replace(">", "_").replace("|", "_")
+
+def load_uganda_districts() -> List[str]:
+    """Load Uganda districts from districts.txt file"""
+    try:
+        with open('districts.txt', 'r', encoding='utf-8') as f:
+            districts = [line.strip() for line in f.readlines() if line.strip()]
+        return sorted(districts)
+    except FileNotFoundError:
+        st.error("⚠️ districts.txt file not found. Please ensure the file exists in the same directory.")
+        return ["File not found - Please check districts.txt"]
+    except Exception as e:
+        st.error(f"⚠️ Error loading districts: {str(e)}")
+        return ["Error loading districts"]
+
+
+def initialize_session_state() -> None:
+    """Initialize Streamlit session state variables"""
+    if 'patient_data' not in st.session_state:
+        st.session_state.patient_data = {}
+    if 'data_directory' not in st.session_state:
+        st.session_state.data_directory = Config.DEFAULT_DATA_DIR
+    if 'current_patient_id' not in st.session_state:
+        st.session_state.current_patient_id = None
+    if 'baseline_completed' not in st.session_state:
+        st.session_state.baseline_completed = False
+    if 'current_cycle' not in st.session_state:
+        st.session_state.current_cycle = 0
+
+
+def clear_form_fields() -> None:
+    """Clear all form input fields"""
+    # Clear text inputs
+    for key in ['patient_id', 'income_other', 'immunohisto_other_specify', 'commodities_other', 'treatment_not_started_reason']:
+        if key in st.session_state:
+            del st.session_state[key]
+    
+    # Clear numeric inputs
+    for key in ['age_input', 'chemo_cycles']:
+        if key in st.session_state:
+            del st.session_state[key]
+    
+    # Clear radio button selections
+    for key in ['education_level', 'marital_status', 'income_source', 'immunohisto_present', 'disease_stage', 'treatment_started']:
+        if key in st.session_state:
+            del st.session_state[key]
+    
+    # Clear dropdown selections  
+    for key in ['district', 'initial_diagnosis', 'regimen_prescribed']:
+        if key in st.session_state:
+            del st.session_state[key]
+    
+    # Clear checkboxes
+    checkbox_keys = ['diabetes', 'hypertension', 'hiv', 'none_captured', 'other_comorbidities',
+                    'er_positive', 'er_negative', 'pr_positive', 'hr_positive', 'hr_negative', 
+                    'her2_positive', 'her2_negative', 'immunohisto_other_check']
+    for key in checkbox_keys:
+        if key in st.session_state:
+            del st.session_state[key]
+    
+    # Reset date to default
+    if 'date_admitted' in st.session_state:
+        del st.session_state['date_admitted']
+
+
+def validate_form_data(form_data: Dict) -> Optional[str]:
+    """Validate form data and return error message if any"""
+    patient_id = form_data.get("patient_id", "")
+    age = form_data.get("age", 0)
+    
+    if not patient_id or patient_id.strip() == "":
+        return "Patient ID is required!"
+    
+    if age <= 0:
+        return "Please enter a valid age!"
+    
+    if len(patient_id.strip()) < 3:
+        return "Patient ID must be at least 3 characters long!"
+    
+    # Check required radio button selections
+    if form_data.get("education_level") is None:
+        return "Please select an education level!"
+    
+    if form_data.get("marital_status") is None:
+        return "Please select a marital status!"
+    
+    if form_data.get("income_source") is None:
+        return "Please select an income source!"
+    
+    # Check dropdown selections (placeholder check)
+    if form_data.get("district", "").startswith("-- Select"):
+        return "Please select a district!"
+    
+    if form_data.get("initial_diagnosis", "").startswith("-- Select"):
+        return "Please select an initial diagnosis!"
+    
+    if form_data.get("immunohisto_present") is None:
+        return "Please select if immunohistochemistry results are present!"
+    
+    if form_data.get("disease_stage") is None:
+        return "Please select a disease stage!"
+    
+    # Check chemotherapy fields
+    if form_data.get("chemo_cycles_prescribed", 0) <= 0:
+        return "Please enter the number of chemotherapy cycles prescribed!"
+    
+    if form_data.get("regimen_prescribed", "").startswith("-- Select"):
+        return "Please select a prescribed regimen!"
+    
+    if form_data.get("treatment_started") is None:
+        return "Please select if the patient started treatment!"
+    
+    return None
+
+
+def save_patient_data(data: Dict, data_type: str = "baseline") -> tuple[bool, str]:
+    """Save patient data to JSON file"""
+    try:
+        # Create directory structure
+        base_dir = os.path.expanduser(st.session_state.data_directory)
+        sanitized_patient_id = sanitize_patient_id(data['patient_id'])
+        patient_folder = os.path.join(base_dir, f"patient_{sanitized_patient_id}")
+        
+        os.makedirs(base_dir, exist_ok=True)
+        os.makedirs(patient_folder, exist_ok=True)
+        
+        # Main patient file
+        main_filename = os.path.join(patient_folder, f"patient_{sanitized_patient_id}.json")
+        
+        # Load existing data or create new structure
+        if os.path.exists(main_filename):
+            with open(main_filename, "r") as f:
+                patient_data = json.load(f)
+        else:
+            patient_data = {
+                "patient_id": data['patient_id'],
+                "baseline_data": {},
+                "treatment_cycles": []
+            }
+        
+        if data_type == "baseline":
+            patient_data["baseline_data"] = data
+        elif data_type == "cycle":
+            # Add or update cycle data
+            cycle_num = data.get("cycle_number", 1)
+            # Check if cycle already exists
+            existing_cycle = next((c for c in patient_data["treatment_cycles"] if c.get("cycle_number") == cycle_num), None)
+            if existing_cycle:
+                # Update existing cycle
+                existing_cycle.update(data)
+            else:
+                # Add new cycle
+                patient_data["treatment_cycles"].append(data)
+        
+        # Save updated data
+        with open(main_filename, "w") as f:
+            json.dump(patient_data, f, indent=4, default=str)
+        
+        return True, main_filename
+    
+    except Exception as e:
+        return False, str(e)
+
+
+def load_patient_data(patient_id: str) -> Dict:
+    """Load patient data from JSON file"""
+    try:
+        base_dir = os.path.expanduser(st.session_state.data_directory)
+        sanitized_patient_id = sanitize_patient_id(patient_id)
+        patient_folder = os.path.join(base_dir, f"patient_{sanitized_patient_id}")
+        filename = os.path.join(patient_folder, f"patient_{sanitized_patient_id}.json")
+        
+        if os.path.exists(filename):
+            with open(filename, "r") as f:
+                return json.load(f)
+        else:
+            return {
+                "patient_id": patient_id,
+                "baseline_data": {},
+                "treatment_cycles": []
+            }
+    except Exception as e:
+        return {
+            "patient_id": patient_id,
+            "baseline_data": {},
+            "treatment_cycles": []
+        }
+
+
+def render_dynamic_medications(cycle_num: int) -> List[Dict]:
+    """Render dynamic medication input fields with dropdown selection"""
+    st.markdown("**Medications & Dosages:**")
+    
+    # Initialize medications in session state
+    med_key = f"cycle_{cycle_num}_medications"
+    if med_key not in st.session_state:
+        st.session_state[med_key] = [{"name": "", "dose": "", "unit": "mg"}]
+    
+    medications = []
+    
+    for i, med in enumerate(st.session_state[med_key]):
+        col1, col2, col3, col4 = st.columns([3, 2, 1, 1])
+        
+        with col1:
+            # Medication dropdown with search
+            medication_options = ["-- Select Medication --"] + Config.MEDICATION_OPTIONS + ["Other (specify)"]
+            selected_med = st.selectbox(
+                f"Medication {i+1}:",
+                medication_options,
+                index=0 if not med.get("name") else (
+                    medication_options.index(med.get("name")) if med.get("name") in medication_options else 0
+                ),
+                key=f"med_name_{cycle_num}_{i}"
+            )
+            
+            # If "Other" is selected, show text input
+            if selected_med == "Other (specify)":
+                med_name = st.text_input(
+                    "Specify medication:",
+                    value=med.get("custom_name", ""),
+                    key=f"med_custom_{cycle_num}_{i}",
+                    placeholder="Enter medication name"
+                )
+            else:
+                med_name = selected_med if not selected_med.startswith("-- Select") else ""
+        
+        with col2:
+            med_dose = st.text_input(
+                f"Dose:",
+                value=med.get("dose", ""),
+                key=f"med_dose_{cycle_num}_{i}",
+                placeholder="e.g., 60, 1.5"
+            )
+        
+        with col3:
+            med_unit = st.selectbox(
+                f"Unit:",
+                ["mg", "mg/m2", "g", "mL", "tabs", "IU"],
+                index=0 if med.get("unit", "mg") == "mg" else ["mg", "mg/m2", "g", "mL", "tabs", "IU"].index(med.get("unit", "mg")),
+                key=f"med_unit_{cycle_num}_{i}"
+            )
+        
+        with col4:
+            if len(st.session_state[med_key]) > 1:
+                if st.button("🗑️", key=f"remove_med_{cycle_num}_{i}", help="Remove medication"):
+                    st.session_state[med_key].pop(i)
+                    st.rerun()
+        
+        # Only add to medications list if a medication is actually selected
+        if med_name and not med_name.startswith("-- Select"):
+            medications.append({
+                "name": med_name,
+                "dose": med_dose,
+                "unit": med_unit
+            })
+    
+    # Add medication button
+    if st.button("➕ Add Medication", key=f"add_med_{cycle_num}"):
+        st.session_state[med_key].append({"name": "", "dose": "", "unit": "mg"})
+        st.rerun()
+    
+    return medications
+
+
+def render_cycle_1_form(patient_id: str) -> Dict:
+    """Render Chemotherapy Treatment Cycle 1 form"""
+    st.header("Chemotherapy Treatment Cycle 1")
+    st.markdown("---")
+    
+    # Prescribed regimen for this cycle
+    regimen_options = ["-- Select Regimen --"] + Config.REGIMEN_OPTIONS
+    regimen_prescribed = st.selectbox(
+        "Prescribed regimen for this cycle:",
+        regimen_options,
+        key="cycle1_regimen_prescribed",
+        index=None,
+        help="Select the chemotherapy regimen prescribed for this treatment cycle"
+    )
+    
+    # Prescription date
+    prescription_date = st.date_input(
+        "Chemotherapy prescription date:",
+        value=date(2017, 7, 1),
+        min_value=Config.STUDY_START_DATE,
+        max_value=Config.STUDY_END_DATE,
+        key="cycle1_prescription_date"
+    )
+    
+    # Dynamic medications
+    medications = render_dynamic_medications(1)
+    
+    # Date chemotherapy received
+    chemo_received_date = st.date_input(
+        "Date chemotherapy received:",
+        value=date(2017, 7, 1),
+        min_value=Config.STUDY_START_DATE,
+        max_value=Config.STUDY_END_DATE,
+        key="cycle1_chemo_received_date"
+    )
+    
+    # Laboratory values
+    st.markdown("**Laboratory Results:**")
+    col1, col2, col3 = st.columns(3)
+    
+    with col1:
+        wbc = st.number_input(
+            "Total WBC:",
+            min_value=0.0,
+            max_value=50000.0,
+            step=100.0,
+            key="cycle1_wbc",
+            help="White Blood Cell count"
+        )
+    
+    with col2:
+        hemoglobin = st.number_input(
+            "Hemoglobin:",
+            min_value=0.0,
+            max_value=25.0,
+            step=0.1,
+            key="cycle1_hemoglobin",
+            help="Hemoglobin level (g/dL)"
+        )
+    
+    with col3:
+        platelets = st.number_input(
+            "Platelets:",
+            min_value=0,
+            max_value=1000000,
+            step=1000,
+            key="cycle1_platelets",
+            help="Platelet count"
+        )
+    
+    # Was chemotherapy received on prescription day?
+    st.markdown("**Was chemotherapy received on the day of prescription?**")
+    chemo_on_prescription_day = st.radio(
+        "Select option:",
+        ["Yes", "No"],
+        key="cycle1_chemo_on_prescription_day",
+        horizontal=True,
+        label_visibility="collapsed",
+        index=None
+    )
+    
+    # Conditional reason if No
+    chemo_delay_reason = ""
+    if chemo_on_prescription_day == "No":
+        chemo_delay_reason = st.text_input(
+            "If No, Why?:",
+            key="cycle1_chemo_delay_reason",
+            placeholder="Please specify reason..."
+        )
+    
+    # Side effects
+    st.markdown("**Documented side effects post treatment:**")
+    side_effects_present = st.radio(
+        "Are there documented side effects?",
+        ["Yes", "No"],
+        key="cycle1_side_effects_present",
+        horizontal=True,
+        index=None
+    )
+    
+    # Side effects checkboxes
+    side_effects = []
+    side_effects_other = ""
+    if side_effects_present == "Yes":
+        st.markdown("Select side effects:")
+        col1, col2, col3, col4, col5, col6 = st.columns(6)
+        
+        with col1:
+            if st.checkbox("Nausea", key="cycle1_nausea"):
+                side_effects.append("Nausea")
+        with col2:
+            if st.checkbox("Fatigue", key="cycle1_fatigue"):
+                side_effects.append("Fatigue")
+        with col3:
+            if st.checkbox("Vomiting", key="cycle1_vomiting"):
+                side_effects.append("Vomiting")
+        with col4:
+            if st.checkbox("Neuropathy", key="cycle1_neuropathy"):
+                side_effects.append("Neuropathy")
+        with col5:
+            if st.checkbox("None", key="cycle1_none_side_effects"):
+                side_effects.append("None")
+        with col6:
+            if st.checkbox("Other", key="cycle1_other_side_effects"):
+                side_effects.append("Other")
+                side_effects_other = st.text_input(
+                    "Specify other side effects:",
+                    key="cycle1_side_effects_other",
+                    placeholder="Please specify..."
+                )
+    
+    # Patient condition
+    st.markdown("**What is the general condition of the patient at the time of the clinic visit?**")
+    patient_condition = st.radio(
+        "Select condition:",
+        Config.CONDITION_OPTIONS,
+        key="cycle1_patient_condition",
+        horizontal=True,
+        label_visibility="collapsed",
+        index=None
+    )
+    
+    # Conditional input for "Other" condition
+    condition_other = ""
+    if patient_condition == "Other":
+        condition_other = st.text_input(
+            "Specify other condition:",
+            key="cycle1_condition_other",
+            placeholder="Please specify..."
+        )
+    
+    # Hospitalization
+    st.markdown("**Was there any hospitalization between this cycle and the previous cycle?**")
+    hospitalization = st.radio(
+        "Select option:",
+        ["Yes", "No"],
+        key="cycle1_hospitalization",
+        horizontal=True,
+        label_visibility="collapsed",
+        index=None
+    )
+    
+    # Conditional reason for hospitalization
+    hospitalization_reason = ""
+    if hospitalization == "Yes":
+        hospitalization_reason = st.text_input(
+            "If yes, specify the reason:",
+            key="cycle1_hospitalization_reason",
+            placeholder="Please specify reason..."
+        )
+    
+    # Return cycle data
+    return {
+        "cycle_number": 1,
+        "patient_id": patient_id,
+        "regimen_prescribed": regimen_prescribed if regimen_prescribed and not regimen_prescribed.startswith("-- Select") else None,
+        "prescription_date": prescription_date.strftime("%Y-%m-%d"),
+        "medications": medications,
+        "chemo_received_date": chemo_received_date.strftime("%Y-%m-%d"),
+        "laboratory": {
+            "wbc": wbc,
+            "hemoglobin": hemoglobin,
+            "platelets": platelets
+        },
+        "chemo_on_prescription_day": chemo_on_prescription_day,
+        "chemo_delay_reason": chemo_delay_reason if chemo_on_prescription_day == "No" else None,
+        "side_effects_present": side_effects_present,
+        "side_effects": side_effects if side_effects_present == "Yes" else [],
+        "side_effects_other": side_effects_other if "Other" in side_effects else None,
+        "patient_condition": patient_condition,
+        "condition_other": condition_other if patient_condition == "Other" else None,
+        "hospitalization": hospitalization,
+        "hospitalization_reason": hospitalization_reason if hospitalization == "Yes" else None
+    }
+
+
+# ========================================================================================
+# UI COMPONENTS
+# ========================================================================================
+
+def render_page_header() -> None:
+    """Render the main page header and description"""
+    st.set_page_config(page_title="Breast Cancer Data Collection", layout="centered")
+    st.title("Data Capture Tool for Analysis of Adherence Patterns to Chemotherapy")
+    st.markdown("---")
+
+def render_data_storage_config() -> None:
+    """Render data storage configuration in sidebar"""
+    with st.sidebar:
+        st.header("⚙️ Settings")
+        data_dir = st.text_input(
+            "Data Storage Directory",
+            value=st.session_state.data_directory,
+            help="Enter the path where you want to store the data files"
+        )
+        if data_dir != st.session_state.data_directory:
+            st.session_state.data_directory = data_dir
+        
+        st.markdown("---")
+        st.markdown("**Quick Stats**")
+        if os.path.exists(st.session_state.data_directory):
+            try:
+                patient_folders = [d for d in os.listdir(st.session_state.data_directory) 
+                                 if d.startswith('patient_') and os.path.isdir(os.path.join(st.session_state.data_directory, d))]
+                st.metric("Patients Recorded", len(patient_folders))
+            except:
+                st.metric("Patients Recorded", "0")
+        else:
+            st.metric("Patients Recorded", "0")
+
+
+def render_linear_baseline_form(districts: List[str]) -> Dict:
+    """Render the linear baseline form following exact PDF numbering"""
+    st.header("Section 1: Baseline Data (Collected at First Visit Only)")
+    st.markdown("---")
+    
+    # 1. Patient ID
+    patient_id = st.text_input(
+        "1. Patient ID:",
+        help="Enter unique patient identifier",
+        key="patient_id",
+        placeholder="e.g., WMJ11"
+    )
+    
+    # 2. Age and Date Admitted (on same line conceptually but separate inputs)
+    col1, col2 = st.columns(2)
+    with col1:
+        age = st.number_input(
+            "2. Age (years):",
+            min_value=0,
+            max_value=120,
+            step=1,
+            key="age_input"
+        )
+    
+    with col2:
+        date_admitted = st.date_input(
+            "Date Admitted:",
+            value=date(2017, 1, 1),
+            min_value=Config.STUDY_START_DATE,
+            max_value=Config.STUDY_END_DATE,
+            key="date_admitted",
+            help="Select date between 2016-2018"
+        )
+    
+    # 3. Education Level
+    st.markdown("**3. Highest level of education:**")
+    education_level = st.radio(
+        "Select education level:",
+        Config.EDUCATION_OPTIONS,
+        key="education_level",
+        horizontal=True,
+        label_visibility="collapsed",
+        index=None  # No default selection
+    )
+    
+    # 4. Marital Status  
+    st.markdown("**4. Current marital status:**")
+    marital_status = st.radio(
+        "Select marital status:",
+        Config.MARITAL_OPTIONS,
+        key="marital_status",
+        horizontal=True,
+        label_visibility="collapsed",
+        index=None  # No default selection
+    )
+    
+    # 5. Income Source
+    st.markdown("**5. Main source of income:**")
+    income_source = st.radio(
+        "Select income source:",
+        Config.INCOME_OPTIONS,
+        key="income_source",
+        horizontal=True,
+        label_visibility="collapsed",
+        index=None  # No default selection
+    )
+    
+    # Conditional input for "Other" income source
+    income_other = ""
+    if income_source == "Other":
+        income_other = st.text_input(
+            "Specify other source of income:",
+            key="income_other",
+            placeholder="Please specify..."
+        )
+    
+    # 6. District of residence
+    district_options = ["-- Select District --"] + districts
+    district = st.selectbox(
+        "6. District of residence:",
+        options=district_options,
+        key="district",
+        help=f"Select from {len(districts)} Uganda districts",
+        index=0  # Default to placeholder
+    )
+    
+    # 7. Initial diagnosis
+    diagnosis_options = ["-- Select Initial Diagnosis --"] + Config.DIAGNOSIS_OPTIONS
+    initial_diagnosis = st.selectbox(
+        "7. Initial diagnosis:",
+        diagnosis_options,
+        key="initial_diagnosis",
+        index=0  # Default to placeholder
+    )
+    
+    # 8. Immunohistochemistry results
+    st.markdown("**8. Immunohistochemistry results present:**")
+    immunohisto_present = st.radio(
+        "Select option:",
+        ["Yes", "No"],
+        key="immunohisto_present",
+        horizontal=True,
+        label_visibility="collapsed",
+        index=None  # No default selection
+    )
+    
+    # Conditional multiselect for immunohistochemistry results
+    immunohisto_results = []
+    immunohisto_other = ""
+    if immunohisto_present == "Yes":
+        st.markdown("**Select immunohistochemistry results (you can select multiple):**")
+        
+        # Create checkboxes in a grid layout
+        col1, col2, col3, col4 = st.columns(4)
+        
+        with col1:
+            if st.checkbox("ER-positive (ER+)", key="er_positive"):
+                immunohisto_results.append("ER-positive (ER+)")
+            if st.checkbox("ER-negative (ER-)", key="er_negative"):
+                immunohisto_results.append("ER-negative (ER-)")
+        
+        with col2:
+            if st.checkbox("PR-positive (PR+)", key="pr_positive"):
+                immunohisto_results.append("PR-positive (PR+)")
+            if st.checkbox("HR-positive (HR+)", key="hr_positive"):
+                immunohisto_results.append("HR-positive (HR+)")
+        
+        with col3:
+            if st.checkbox("HR-negative (HR-)", key="hr_negative"):
+                immunohisto_results.append("HR-negative (HR-)")
+            if st.checkbox("HER2-positive (HER2+)", key="her2_positive"):
+                immunohisto_results.append("HER2-positive (HER2+)")
+        
+        with col4:
+            if st.checkbox("HER2-negative (HER2-)", key="her2_negative"):
+                immunohisto_results.append("HER2-negative (HER2-)")
+            if st.checkbox("Other", key="immunohisto_other_check"):
+                immunohisto_results.append("Other")
+                immunohisto_other = st.text_input(
+                    "Specify other results:",
+                    key="immunohisto_other_specify",
+                    placeholder="Please specify..."
+                )
+    
+    # 9. Disease stage
+    st.markdown("**9. Disease stage at first diagnosis:**")
+    disease_stage = st.radio(
+        "Select stage:",
+        Config.STAGE_OPTIONS,
+        key="disease_stage",
+        horizontal=True,
+        label_visibility="collapsed",
+        index=None  # No default selection
+    )
+    
+    # 10. Comorbidities
+    st.markdown("**10. List of other comorbidities:**")
+    
+    # Create checkboxes in horizontal layout
+    col1, col2, col3, col4, col5 = st.columns(5)
+    
+    with col1:
+        diabetes = st.checkbox("Diabetes", key="diabetes")
+    with col2:
+        hypertension = st.checkbox("Hypertension", key="hypertension")
+    with col3:
+        hiv = st.checkbox("HIV", key="hiv")
+    with col4:
+        none_captured = st.checkbox("None captured", key="none_captured")
+    with col5:
+        other_comorbidities = st.checkbox("Other", key="other_comorbidities")
+    
+    # Conditional input for "Other" comorbidities
+    commodities_other = ""
+    if other_comorbidities:
+        commodities_other = st.text_input(
+            "Specify other comorbidities:",
+            key="commodities_other",
+            placeholder="Please specify..."
+        )
+    
+    # 11. Chemotherapy cycles prescribed
+    chemo_cycles = st.number_input(
+        "11. How many chemotherapy cycles have been prescribed:",
+        min_value=0,
+        max_value=50,
+        step=1,
+        key="chemo_cycles",
+        help="Enter the number of prescribed cycles"
+    )
+    
+    # 12. Regimen prescribed
+    regimen_options = ["-- Select Regimen --"] + Config.REGIMEN_OPTIONS
+    regimen_prescribed = st.selectbox(
+        "12. Which regimen was prescribed:",
+        regimen_options,
+        key="regimen_prescribed",
+        index=0  # Default to placeholder
+    )
+    
+    # 13. Treatment start status
+    st.markdown("**13. Did the patient start treatment:**")
+    treatment_started = st.radio(
+        "Select option:",
+        ["Yes", "No"],
+        key="treatment_started",
+        horizontal=True,
+        label_visibility="collapsed",
+        index=None  # No default selection
+    )
+    
+    # Conditional input for "No" treatment start
+    treatment_not_started_reason = ""
+    if treatment_started == "No":
+        treatment_not_started_reason = st.text_input(
+            "If No, why?:",
+            key="treatment_not_started_reason",
+            placeholder="Please specify reason..."
+        )
+    
+    # Return all collected data
+    return {
+        "patient_id": patient_id,
+        "age": age,
+        "date_admitted": date_admitted.strftime("%Y-%m-%d"),
+        "education_level": education_level,
+        "marital_status": marital_status,
+        "income_source": income_source,
+        "income_other": income_other if income_source == "Other" else None,
+        "district": district if district and not district.startswith("-- Select") else None,
+        "initial_diagnosis": initial_diagnosis if initial_diagnosis and not initial_diagnosis.startswith("-- Select") else None,
+        "immunohisto_present": immunohisto_present,
+        "immunohisto_results": immunohisto_results if immunohisto_present == "Yes" else [],
+        "immunohisto_other": immunohisto_other if "Other" in immunohisto_results else None,
+        "disease_stage": disease_stage,
+        "comorbidities": {
+            "diabetes": diabetes,
+            "hypertension": hypertension,
+            "hiv": hiv,
+            "none_captured": none_captured,
+            "other": other_comorbidities,
+            "other_specify": commodities_other if other_comorbidities else None
+        },
+        "chemo_cycles_prescribed": chemo_cycles,
+        "regimen_prescribed": regimen_prescribed if regimen_prescribed and not regimen_prescribed.startswith("-- Select") else None,
+        "treatment_started": treatment_started,
+        "treatment_not_started_reason": treatment_not_started_reason if treatment_started == "No" else None
+    }
+
+
+def render_cycle_actions(cycle_data, cycle_number):
+    """Render action buttons for cycle forms"""
+    st.markdown("---")
+    col1, col2, col3 = st.columns([2, 2, 1])
+    
+    with col1:
+        if st.button("💾 Save Cycle", type="primary", use_container_width=True):
+            if validate_cycle_data(cycle_data):
+                # Save cycle data
+                success, result = save_patient_data(cycle_data, data_type='cycle')
+                if success:
+                    st.success(f"✅ Treatment Cycle {cycle_number} data saved successfully!")
+                    # Reset current cycle to go back to cycle management
+                    st.session_state.current_cycle = 0
+                    time.sleep(1)
+                    st.rerun()
+                else:
+                    st.error(f"❌ Failed to save cycle data: {result}")
+            else:
+                st.error("❌ Please fill in all required fields before saving.")
+    
+    with col2:
+        if st.button("🚫 Cancel Cycle", use_container_width=True):
+            st.session_state.current_cycle = 0
+            st.rerun()
+    
+    with col3:
+        if st.button("🗑️", help="Clear form", use_container_width=True):
+            clear_form_fields()
+            st.rerun()
+
+
+def validate_cycle_data(cycle_data):
+    """Validate cycle form data"""
+    if not cycle_data:
+        return False
+    
+    # Check required fields for cycle 1
+    required_fields = ['regimen_prescribed', 'prescription_date']
+    
+    for field in required_fields:
+        if field not in cycle_data or not cycle_data[field]:
+            return False
+    
+    # Validate medications
+    medications = cycle_data.get('medications', [])
+    if not medications:
+        return False
+    
+    for med in medications:
+        if not med.get('name') or not med.get('dose'):
+            return False
+    
+    return True
+
+
+def render_form_actions(form_data: Dict) -> None:
+    """Render form submission and action buttons"""
+    st.markdown("---")
+    
+    col1, col2 = st.columns([3, 1])
+    
+    with col1:
+        if st.button("💾 Save Baseline Data", type="primary", use_container_width=True):
+            # Validate form data
+            error_msg = validate_form_data(form_data)
+            
+            if error_msg:
+                st.error(f"❌ {error_msg}")
+            else:
+                # Save data
+                success, result = save_patient_data(form_data, "baseline")
+                
+                if success:
+                    st.success(f"✅ Baseline data for Patient {form_data['patient_id']} saved successfully!")
+                    st.success(f"📁 File saved to: {result}")
+                    
+                    # Update session state
+                    st.session_state.patient_data = form_data
+                    st.session_state.current_patient_id = form_data['patient_id']
+                    st.session_state.baseline_completed = True
+                    st.session_state.current_cycle = 0
+                    
+                    # Show success metrics
+                    with st.expander("📋 Saved Data Summary", expanded=True):
+                        col_a, col_b = st.columns(2)
+                        with col_a:
+                            st.metric("Patient ID", form_data['patient_id'])
+                            st.metric("Age", form_data['age'])
+                            st.metric("District", form_data['district'] or "Not selected")
+                        with col_b:
+                            st.metric("Education", form_data['education_level'] or "Not selected")
+                            st.metric("Diagnosis", form_data['initial_diagnosis'] or "Not selected")
+                            st.metric("Stage", form_data['disease_stage'] or "Not selected")
+                    
+                    st.rerun()  # Refresh to show cycle options
+                else:
+                    st.error(f"❌ Error saving data: {result}")
+    
+    with col2:
+        if st.button("🔄 Clear Form", use_container_width=True):
+            clear_form_fields()
+            st.rerun()
+
+
+def render_footer() -> None:
+    """Render application footer"""
+    st.markdown("---")
+    st.info(" **Note**: Please ensure all information is accurate before submission. Use 'Not captured' for missing information. Data will be exported to Excel/CSV for analysis.")
+
+
+# ========================================================================================
+# MAIN APPLICATION
+# ========================================================================================
+
+def main():
+    """Main application function"""
+    # Initialize session state
+    initialize_session_state()
+    
+    # Render page header
+    render_page_header()
+    
+    # Render sidebar configuration
+    render_data_storage_config()
+    
+    # Load districts data
+    uganda_districts = load_uganda_districts()
+    
+    # Check if baseline is completed
+    if not st.session_state.baseline_completed:
+        # Show baseline form
+        form_data = render_linear_baseline_form(uganda_districts)
+        render_form_actions(form_data)
+    else:
+        # Baseline completed - show cycle management
+        st.success(f"✅ Baseline data completed for Patient {st.session_state.current_patient_id}")
+        
+        # Load patient data to check existing cycles
+        patient_data = load_patient_data(st.session_state.current_patient_id)
+        existing_cycles = len(patient_data.get("treatment_cycles", []))
+        
+        st.markdown("---")
+        st.subheader("🔄 Treatment Cycles Management")
+        
+        col1, col2, col3 = st.columns([2, 2, 1])
+        
+        with col1:
+            st.metric("Patient ID", st.session_state.current_patient_id)
+        with col2:
+            st.metric("Completed Cycles", existing_cycles)
+        with col3:
+            if st.button("🔄 New Patient", help="Start with a new patient"):
+                # Reset session state
+                st.session_state.baseline_completed = False
+                st.session_state.current_patient_id = None
+                st.session_state.current_cycle = 0
+                clear_form_fields()
+                st.rerun()
+        
+        # Show cycle addition buttons
+        next_cycle = existing_cycles + 1
+        
+        if next_cycle == 1:
+            st.markdown("### Ready to add Treatment Cycle 1")
+            if st.button(f"📋 Add Treatment Cycle 1", type="primary", use_container_width=True):
+                st.session_state.current_cycle = 1
+                st.rerun()
+        else:
+            st.markdown(f"### Ready to add Treatment Cycle {next_cycle}")
+            col_a, col_b = st.columns(2)
+            with col_a:
+                if st.button(f"📋 Add Treatment Cycle {next_cycle}", type="primary", use_container_width=True):
+                    st.session_state.current_cycle = next_cycle
+                    st.rerun()
+            with col_b:
+                if st.button("✅ Complete Treatment", use_container_width=True):
+                    st.session_state.baseline_completed = False
+                    st.session_state.current_patient_id = None
+                    st.session_state.current_cycle = 0
+                    st.success("🎉 Treatment cycles completed! Ready for new patient.")
+                    st.rerun()
+        
+        # Show cycle form if current_cycle is set
+        if st.session_state.current_cycle > 0:
+            if st.session_state.current_cycle == 1:
+                cycle_data = render_cycle_1_form(st.session_state.current_patient_id)
+                render_cycle_actions(cycle_data, 1)
+            # TODO: Add cycle 2+ forms here
+    
+    # Footer
+    render_footer()
+
+
+if __name__ == "__main__":
+    main()