medicafe 0.250529.1__py3-none-any.whl → 0.250529.2__py3-none-any.whl

MediBot/MediBot_Preprocessor_lib.py

@@ -1,743 +1,743 @@
-#MediBot_Preprocessor_lib.py
-from collections import OrderedDict, defaultdict
-from datetime import datetime, timedelta
-import os, csv, sys
-import chardet  # Ensure chardet is imported
-
-# Add the parent directory of the project to the Python path
-sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), "..")))
-
-# Attempt to import necessary modules, falling back if they are not found
-try:
-    import MediLink_ConfigLoader
-    import MediLink_DataMgmt
-except ImportError:
-    from MediLink import MediLink_ConfigLoader, MediLink_DataMgmt
-
-try:
-    from MediBot_UI import app_control
-    from MediBot_docx_decoder import parse_docx
-except ImportError:
-    from MediBot import MediBot_UI
-    app_control = MediBot_UI.app_control
-    from MediBot import MediBot_docx_decoder
-    parse_docx = MediBot_docx_decoder.parse_docx
-
-class InitializationError(Exception):
-    def __init__(self, message):
-        self.message = message
-        super().__init__(self.message)
-
-def initialize(config):
-    global AHK_EXECUTABLE, CSV_FILE_PATH, field_mapping, page_end_markers
-    
-    required_keys = {
-        'AHK_EXECUTABLE': "",
-        'CSV_FILE_PATH': "",
-        'field_mapping': {},
-        'page_end_markers': []
-    }
-    
-    for key, default in required_keys.items():
-        try:
-            globals()[key] = config.get(key, default) if key != 'field_mapping' else OrderedDict(config.get(key, default))
-        except AttributeError:
-            raise InitializationError("Error: '{}' not found in config.".format(key))
-
-def open_csv_for_editing(csv_file_path):
-    try:
-        # Open the CSV file with its associated application
-        os.system('start "" "{}"'.format(csv_file_path))
-        print("After saving the revised CSV, please re-run MediBot.")
-    except Exception as e:
-        print("Failed to open CSV file:", e)
-        
-# Function to clean the headers
-def clean_header(headers):
-    """
-    Cleans the header strings by removing unwanted characters and trimming whitespace.
-
-    Parameters:
-    headers (list of str): The original header strings.
-
-    Returns:
-    list of str: The cleaned header strings.
-    """
-    cleaned_headers = []
-    
-    for header in headers:
-        # Strip leading and trailing whitespace
-        cleaned_header = header.strip()
-        # Remove unwanted characters while keeping spaces, alphanumeric characters, hyphens, and underscores
-        cleaned_header = ''.join(char for char in cleaned_header if char.isalnum() or char.isspace() or char in ['-', '_'])
-        cleaned_headers.append(cleaned_header)
-
-    # Log the original and cleaned headers for debugging
-    MediLink_ConfigLoader.log("Original headers: {}".format(headers), level="INFO")
-    MediLink_ConfigLoader.log("Cleaned headers: {}".format(cleaned_headers), level="INFO")
-
-    # Check if 'Surgery Date' is in the cleaned headers
-    if 'Surgery Date' not in cleaned_headers:
-        MediLink_ConfigLoader.log("WARNING: 'Surgery Date' header not found after cleaning.", level="WARNING")
-        print("WARNING: 'Surgery Date' header not found after cleaning.")
-        raise ValueError("Error: 'Surgery Date' header not found after cleaning.")
-
-    return cleaned_headers
-
-# Function to load and process CSV data
-def load_csv_data(csv_file_path):
-    try:
-        # Check if the file exists
-        if not os.path.exists(csv_file_path):
-            raise FileNotFoundError("***Error: CSV file '{}' not found.".format(csv_file_path))
-        
-        # Detect the file encoding
-        with open(csv_file_path, 'rb') as f:
-            raw_data = f.read()
-            result = chardet.detect(raw_data)
-            encoding = result['encoding']
-            confidence = result['confidence']
-            print("Detected encoding: {} (Confidence: {:.2f})".format(encoding, confidence))
-
-        # Read the CSV file with the detected encoding
-        with open(csv_file_path, 'r', encoding=encoding) as csvfile:
-            reader = csv.DictReader(csvfile)
-            # Clean the headers
-            cleaned_headers = clean_header(reader.fieldnames)
-
-            # Create a mapping of cleaned headers to original headers
-            header_mapping = {cleaned_headers[i]: reader.fieldnames[i] for i in range(len(cleaned_headers))}
-
-            # Process the remaining rows
-            csv_data = []
-            for row in reader:
-                cleaned_row = {cleaned_headers[i]: row[header_mapping[cleaned_headers[i]]] for i in range(len(cleaned_headers))}
-                csv_data.append(cleaned_row)
-
-            return csv_data  # Return a list of dictionaries
-    except FileNotFoundError as e:
-        print(e)  # Print the informative error message
-        print("Hint: Check if CSV file is located in the expected directory or specify a different path in config file.")
-        print("Please correct the issue and re-run MediBot.")
-        sys.exit(1)  # Halt the script
-    except IOError as e:
-        print("Error reading CSV file: {}. Please check the file path and permissions.".format(e))
-        sys.exit(1)  # Halt the script in case of other IO errors
-
-# CSV Pre-processor Helper functions
-def add_columns(csv_data, column_headers):
-    """
-    Adds one or multiple columns to the CSV data.
-    
-    Parameters:
-    csv_data (list of dict): The CSV data where each row is represented as a dictionary.
-    column_headers (list of str or str): A list of column headers to be added to each row, or a single column header.
-    
-    Returns:
-    None: The function modifies the csv_data in place.
-    """
-    if isinstance(column_headers, str):
-        column_headers = [column_headers]
-    elif not isinstance(column_headers, list):
-        raise ValueError("column_headers should be a list or a string")
-
-    for row in csv_data:
-        for header in column_headers:
-            row[header] = ''  # Initialize the column with empty values
-
-# Extracting the list to a variable for future refactoring:
-def filter_rows(csv_data):
-    # TODO: This should be handled in the crosswalk.
-    excluded_insurance = {'AETNA', 'AETNA MEDICARE', 'HUMANA MED HMO'}
-    csv_data[:] = [row for row in csv_data if row.get('Patient ID') and row.get('Primary Insurance') not in excluded_insurance]
-
-def convert_surgery_date(csv_data):
-    for row in csv_data:
-        surgery_date_str = row.get('Surgery Date', '')
-        if not surgery_date_str:
-            MediLink_ConfigLoader.log("Warning: Surgery Date not found for row: {}".format(row), level="WARNING")
-            # BUG This needs a cleaning step for the Surgery Date string in case we're receiving damaged data.
-            row['Surgery Date'] = datetime.min  # Assign a minimum datetime value if empty
-            print("Surgery Date not found for row: {}".format(row))
-        else:
-            try:
-                row['Surgery Date'] = datetime.strptime(surgery_date_str, '%m/%d/%Y')
-            except ValueError as e:
-                MediLink_ConfigLoader.log("Error parsing Surgery Date '{}': {} for row: {}".format(surgery_date_str, e, row), level="ERROR")
-                row['Surgery Date'] = datetime.min  # Assign a minimum datetime value if parsing fails
-
-def sort_and_deduplicate(csv_data):
-    # Create a dictionary to hold unique patients based on Patient ID
-    unique_patients = {}
-    
-    # Iterate through the CSV data and populate the unique_patients dictionary
-    for row in csv_data:
-        patient_id = row.get('Patient ID')
-        if patient_id not in unique_patients:
-            unique_patients[patient_id] = row
-        else:
-            # If the patient ID already exists, compare surgery dates
-            existing_row = unique_patients[patient_id]
-            if row['Surgery Date'] < existing_row['Surgery Date']:
-                unique_patients[patient_id] = row
-
-    # Convert the unique_patients dictionary back to a list and sort it
-    csv_data[:] = sorted(unique_patients.values(), key=lambda x: (x['Surgery Date'], x.get('Patient Last', '').strip())) # TODO Does this need to be sorted twice? once before and once after?
-    
-    # TODO: Consider adding an option in the config to sort based on Surgery Schedules when available.
-    # If no schedule is available, the current sorting strategy will be used.
-
-def combine_fields(csv_data):
-    for row in csv_data:
-        # Safely handle the 'Surgery Date' conversion
-        surgery_date = row.get('Surgery Date')
-        row['Surgery Date'] = surgery_date.strftime('%m/%d/%Y') if surgery_date else ''
-        
-        first_name = '_'.join(part.strip() for part in row.get('Patient First', '').split()) # Join the first name parts with underscores after cleaning.
-        middle_name = row.get('Patient Middle', '').strip()
-        middle_name = middle_name[0] if len(middle_name) > 1 else ''  # Take only the first character or empty
-        last_name = '_'.join(part.strip() for part in row.get('Patient Last', '').split()) # Join the last name parts with underscores after cleaning.
-        row['Patient Name'] = ', '.join(filter(None, [last_name, first_name, middle_name]))  # Join non-empty parts
-        
-        address1 = row.get('Patient Address1', '').strip()
-        address2 = row.get('Patient Address2', '').strip()
-        row['Patient Street'] = ' '.join(filter(None, [address1, address2]))  # Join non-empty addresses
-
-def apply_replacements(csv_data, crosswalk):
-    replacements = crosswalk.get('csv_replacements', {})
-    for row in csv_data:
-        for old_value, new_value in replacements.items():
-            for key in ['Patient SSN', 'Primary Insurance', 'Ins1 Payer ID']:
-                if row.get(key) == old_value:
-                    row[key] = new_value
-                    break  # Exit the loop once a replacement is made
-
-import difflib
-from collections import defaultdict
-
-def find_best_medisoft_id(insurance_name, medisoft_ids, medisoft_to_mains_names):
-    """
-    Finds the best matching Medisoft ID for a given insurance name using fuzzy matching.
-
-    Parameters:
-    - insurance_name (str): The insurance name from the CSV row.
-    - medisoft_ids (list): List of Medisoft IDs associated with the Payer ID.
-    - medisoft_to_mains_names (dict): Mapping from Medisoft ID to list of MAINS names.
-
-    Returns:
-    - int or None: The best matching Medisoft ID or None if no match is found.
-    """
-    best_match_ratio = 0
-    best_medisoft_id = None
-
-    for medisoft_id in medisoft_ids:
-        mains_names = medisoft_to_mains_names.get(medisoft_id, [])
-        for mains_name in mains_names:
-            # Preprocess names by extracting non-numeric characters and converting to uppercase
-            processed_mains = ''.join(filter(lambda x: not x.isdigit(), mains_name)).upper()
-            processed_insurance = ''.join(filter(lambda x: not x.isdigit(), insurance_name)).upper()
-
-            # Log the processed names before computing the match ratio
-            MediLink_ConfigLoader.log("Processing Medisoft ID '{}': Comparing processed insurance '{}' with processed mains '{}'.".format(medisoft_id, processed_insurance, processed_mains), level="DEBUG")
-
-            # Compute the similarity ratio
-            match_ratio = difflib.SequenceMatcher(None, processed_insurance, processed_mains).ratio()
-
-            # Log the match ratio
-            MediLink_ConfigLoader.log("Match ratio for Medisoft ID '{}': {:.2f}".format(medisoft_id, match_ratio), level="DEBUG")
-
-            if match_ratio > best_match_ratio:
-                best_match_ratio = match_ratio
-                best_medisoft_id = medisoft_id
-                # Log the current best match
-                MediLink_ConfigLoader.log("New best match found: Medisoft ID '{}' with match ratio {:.2f}".format(best_medisoft_id, best_match_ratio), level="DEBUG")
-
-    # Log the final best match ratio and ID
-    MediLink_ConfigLoader.log("Final best match ratio: {:.2f} for Medisoft ID '{}'".format(best_match_ratio, best_medisoft_id), level="DEBUG")
-
-    # No threshold applied, return the best match found
-    return best_medisoft_id
-
-def NEW_update_insurance_ids(csv_data, config, crosswalk):
-    """
-    Updates the 'Ins1 Insurance ID' field in each row of csv_data based on the crosswalk and MAINS data.
-
-    Parameters:
-    - csv_data (list of dict): The CSV data where each row is represented as a dictionary.
-    - config (dict): Configuration object containing necessary paths and parameters.
-    - crosswalk (dict): Crosswalk data containing mappings between Payer IDs and Medisoft IDs.
-
-    Returns:
-    - None: The function modifies the csv_data in place.
-    """
-    processed_payer_ids = set()  # Track processed Payer IDs
-    MediLink_ConfigLoader.log("Starting update of insurance IDs.", level="INFO")
-
-    # Load MAINS data to get mapping from Medisoft ID to MAINS names
-    insurance_to_id = load_insurance_data_from_mains(config)  # Assuming it returns a dict mapping insurance names to IDs
-    MediLink_ConfigLoader.log("Loaded MAINS data for insurance to ID mapping.", level="DEBUG")
-    
-    # Invert the mapping to get Medisoft ID to MAINS names
-    medisoft_to_mains_names = defaultdict(list)
-    for insurance_name, medisoft_id in insurance_to_id.items():
-        medisoft_to_mains_names[medisoft_id].append(insurance_name)
-
-    for row in csv_data:
-        ins1_payer_id = row.get('Ins1 Payer ID', '').strip()
-        MediLink_ConfigLoader.log("Processing row with Ins1 Payer ID: '{}'.".format(ins1_payer_id), level="DEBUG")
-        
-        if ins1_payer_id:
-            # Mark this Payer ID as processed
-            if ins1_payer_id not in processed_payer_ids:
-                processed_payer_ids.add(ins1_payer_id)  # Add to set
-                MediLink_ConfigLoader.log("Marked Payer ID '{}' as processed.".format(ins1_payer_id), level="DEBUG")
-                
-                # Retrieve Medisoft IDs for the current Payer ID
-                medisoft_ids = crosswalk.get('payer_id', {}).get(ins1_payer_id, {}).get('medisoft_id', [])
-                MediLink_ConfigLoader.log("Retrieved Medisoft IDs for Payer ID '{}': {}".format(ins1_payer_id, medisoft_ids), level="DEBUG")
-
-        if not medisoft_ids:
-            MediLink_ConfigLoader.log("No Medisoft IDs available for Payer ID '{}', creating placeholder entry.".format(ins1_payer_id), level="WARNING")
-            # Create a placeholder entry in the crosswalk
-            if 'payer_id' not in crosswalk:
-                crosswalk['payer_id'] = {}
-            crosswalk['payer_id'][ins1_payer_id] = {
-                'medisoft_id': [],  # Placeholder for future Medisoft IDs
-                'medisoft_medicare_id': [],  # Placeholder for future Medicare IDs
-                'endpoint': None  # Placeholder for future endpoint
-            }
-            continue  # Skip further processing for this Payer ID
-
-        # If only one Medisoft ID is associated, assign it directly
-        if len(medisoft_ids) == 1:
-            try:
-                medisoft_id = int(medisoft_ids[0])
-                row['Ins1 Insurance ID'] = medisoft_id
-                MediLink_ConfigLoader.log("Assigned Medisoft ID '{}' to row number {} with Payer ID '{}'.".format(medisoft_id, csv_data.index(row) + 1, ins1_payer_id), level="DEBUG")
-            except ValueError as e:
-                MediLink_ConfigLoader.log("Error converting Medisoft ID '{}' to integer for Payer ID '{}': {}".format(medisoft_ids[0], ins1_payer_id, e), level="ERROR")
-                row['Ins1 Insurance ID'] = None
-            continue  # Move to the next row
-
-        # If multiple Medisoft IDs are associated, perform fuzzy matching
-        insurance_name = row.get('Primary Insurance', '').strip()
-        if not insurance_name:
-            MediLink_ConfigLoader.log("Row with Payer ID '{}' missing 'Primary Insurance', skipping assignment.".format(ins1_payer_id), level="WARNING")
-            continue  # Skip if insurance name is missing
-
-        best_medisoft_id = find_best_medisoft_id(insurance_name, medisoft_ids, medisoft_to_mains_names)
-
-        if best_medisoft_id:
-            row['Ins1 Insurance ID'] = best_medisoft_id
-            MediLink_ConfigLoader.log("Assigned Medisoft ID '{}' to row with Payer ID '{}' based on fuzzy match.".format(best_medisoft_id, ins1_payer_id), level="INFO")
-        else:
-            # Default to the first Medisoft ID if no good match is found
-            try:
-                default_medisoft_id = int(medisoft_ids[0])
-                row['Ins1 Insurance ID'] = default_medisoft_id
-                MediLink_ConfigLoader.log("No suitable match found. Defaulted to Medisoft ID '{}' for Payer ID '{}'.".format(default_medisoft_id, ins1_payer_id), level="INFO")
-            except ValueError as e:
-                MediLink_ConfigLoader.log("Error converting default Medisoft ID '{}' to integer for Payer ID '{}': {}".format(medisoft_ids[0], ins1_payer_id, e), level="ERROR")
-                row['Ins1 Insurance ID'] = None
-
-def update_insurance_ids(csv_data, config, crosswalk):
-    MediLink_ConfigLoader.log("Starting update_insurance_ids function.", level="DEBUG")
-    
-    # Create a dictionary to hold Medisoft IDs for each payer ID in the crosswalk
-    payer_id_to_medisoft = {}
-    MediLink_ConfigLoader.log("Initialized payer_id_to_medisoft dictionary.", level="DEBUG")
-    
-    # Populate the dictionary with data from the crosswalk
-    for payer_id, details in crosswalk.get('payer_id', {}).items():
-        medisoft_ids = details.get('medisoft_id', [])
-        # Filter out empty strings and take the first valid ID
-        medisoft_ids = [id for id in medisoft_ids if id]
-        payer_id_to_medisoft[payer_id] = int(medisoft_ids[0]) if medisoft_ids else None
-        MediLink_ConfigLoader.log("Processed Payer ID '{}': Medisoft IDs found: {}".format(payer_id, medisoft_ids), level="DEBUG")
-
-    # Process the csv_data
-    for row in csv_data:
-        ins1_payer_id = row.get('Ins1 Payer ID', '').strip()
-        MediLink_ConfigLoader.log("Processing row #{} with Ins1 Payer ID '{}'.".format(csv_data.index(row) + 1, ins1_payer_id), level="DEBUG")
-        
-        if ins1_payer_id not in payer_id_to_medisoft:
-            # Add placeholder entry for new payer ID
-            payer_id_to_medisoft[ins1_payer_id] = None  # No Medisoft ID available
-            crosswalk.setdefault('payer_id', {})[ins1_payer_id] = {
-                'medisoft_id': [],  # Placeholder for future Medisoft IDs
-                'medisoft_medicare_id': [],  # Placeholder for future Medicare IDs
-                'endpoint': None  # Placeholder for future endpoint
-            }
-            MediLink_ConfigLoader.log("Added placeholder entry for new Payer ID '{}'.".format(ins1_payer_id), level="INFO")
-        
-        # Assign the Medisoft ID to the row
-        row['Ins1 Insurance ID'] = payer_id_to_medisoft[ins1_payer_id]
-        MediLink_ConfigLoader.log("Assigned Medisoft ID '{}' to row with Ins1 Payer ID '{}'.".format(row['Ins1 Insurance ID'], ins1_payer_id), level="DEBUG")
-
-def update_procedure_codes(csv_data, crosswalk): 
-    
-    # Get Medisoft shorthand dictionary from crosswalk and reverse it
-    diagnosis_to_medisoft = crosswalk.get('diagnosis_to_medisoft', {}) # BUG We need to be careful here in case we decide we need to change the crosswalk data specifically with regard to the T8/H usage.
-    medisoft_to_diagnosis = {v: k for k, v in diagnosis_to_medisoft.items()}
-
-    # Get procedure code to diagnosis dictionary from crosswalk and reverse it for easier lookup
-    diagnosis_to_procedure = {
-        diagnosis_code: procedure_code
-        for procedure_code, diagnosis_codes in crosswalk.get('procedure_to_diagnosis', {}).items()
-        for diagnosis_code in diagnosis_codes
-    }
-
-    # Initialize counter for updated rows
-    updated_count = 0
-
-    # Update the "Procedure Code" column in the CSV data
-    for row_num, row in enumerate(csv_data, start=1):
-        try:
-            medisoft_code = row.get('Default Diagnosis #1', '').strip()
-            diagnosis_code = medisoft_to_diagnosis.get(medisoft_code)
-            if diagnosis_code:
-                procedure_code = diagnosis_to_procedure.get(diagnosis_code)
-                if procedure_code:
-                    row['Procedure Code'] = procedure_code
-                    updated_count += 1
-                else:
-                    row['Procedure Code'] = "Unknown"  # Or handle as appropriate
-            else:
-                row['Procedure Code'] = "Unknown"  # Or handle as appropriate
-        except Exception as e:
-            MediLink_ConfigLoader.log("In update_procedure_codes, Error processing row {}: {}".format(row_num, e), level="ERROR")
-
-    # Log total count of updated rows
-    MediLink_ConfigLoader.log("Total {} 'Procedure Code' rows updated.".format(updated_count), level="INFO")
-
-    return True
-
-def update_diagnosis_codes(csv_data):
-    try:
-        # Load configuration and crosswalk
-        config, crosswalk = MediLink_ConfigLoader.load_configuration()
-        
-        # Extract the local storage path from the configuration
-        local_storage_path = config['MediLink_Config']['local_storage_path']
-        
-        # Initialize a dictionary to hold diagnosis codes from all DOCX files
-        all_patient_data = {}
-
-        # Convert surgery dates in CSV data
-        convert_surgery_date(csv_data)
-        
-        # Extract all valid surgery dates from csv_data
-        surgery_dates = [row['Surgery Date'] for row in csv_data if row['Surgery Date'] != datetime.min]
-        
-        if not surgery_dates:
-            raise ValueError("No valid surgery dates found in csv_data.")
-        
-        # Determine the minimum and maximum surgery dates
-        min_surgery_date = min(surgery_dates)
-        max_surgery_date = max(surgery_dates)
-        
-        # Apply a ±8-day margin to the surgery dates... Increased from 5 days.
-        margin = timedelta(days=8)
-        threshold_start = min_surgery_date - margin
-        threshold_end = max_surgery_date + margin
-        
-        # TODO (Low) This is a bad idea. We need a better way to handle this because it leaves 
-        # us with a situation where if we take 'too long' to download the DOCX files, it will presume that the DOCX files are out of range because 
-        # the modfied date is a bad proxy for the date of the surgery which would be contained inside the DOCX file. The processing overhead for extracting the
-        # date of the surgery from the DOCX file is non-trivial and computationally expensive so we need a smarter way to handle this.
-
-        MediLink_ConfigLoader.log("BAD IDEA: Processing DOCX files modified between {} and {}.".format(threshold_start, threshold_end), level="INFO")
-
-        # Gather all relevant DOCX files in the specified directory
-        docx_files = [
-            os.path.join(local_storage_path, filename)
-            for filename in os.listdir(local_storage_path)
-            if filename.endswith(".docx")
-        ]
-
-        # Filter files based on modification time
-        valid_files = [
-            filepath for filepath in docx_files
-            if threshold_start <= datetime.fromtimestamp(os.path.getmtime(filepath)) <= threshold_end
-        ]
-
-        # Process valid DOCX files
-        for filepath in valid_files:
-            MediLink_ConfigLoader.log("Processing DOCX file: {}".format(filepath), level="INFO")
-            try:
-                patient_data = parse_docx(filepath, surgery_dates)  # Pass surgery_dates to parse_docx
-                for patient_id, service_dates in patient_data.items():
-                    if patient_id not in all_patient_data:
-                        all_patient_data[patient_id] = {}
-                    for date_of_service, diagnosis_data in service_dates.items():
-                        all_patient_data[patient_id][date_of_service] = diagnosis_data
-            except Exception as e:
-                MediLink_ConfigLoader.log("Error parsing DOCX file {}: {}".format(filepath, e), level="ERROR")
-
-        # Log if no valid files were found
-        if not valid_files:
-            MediLink_ConfigLoader.log("No valid DOCX files found within the modification time threshold.", level="INFO")
-        
-        # Debug logging for all_patient_data
-        MediLink_ConfigLoader.log("All patient data collected from DOCX files: {}".format(all_patient_data), level="DEBUG")
-        
-        # Extract patient IDs from csv_data for efficient matching
-        patient_ids_in_csv = {row.get('Patient ID', '').strip() for row in csv_data}
-
-        # Check if any patient data was collected
-        if not all_patient_data or not patient_ids_in_csv.intersection(all_patient_data.keys()):
-            MediLink_ConfigLoader.log("No patient data collected or no matching Patient IDs found. Skipping further processing.", level="INFO")
-            return  # Exit the function early if no data is available
-
-        # Get Medisoft shorthand dictionary from crosswalk.
-        diagnosis_to_medisoft = crosswalk.get('diagnosis_to_medisoft', {})
-        
-        # Initialize counter for updated rows
-        updated_count = 0
-
-        # Update the "Default Diagnosis #1" column in the CSV data
-        for row_num, row in enumerate(csv_data, start=1):
-            patient_id = row.get('Patient ID', '').strip()
-            if patient_id not in patient_ids_in_csv:
-                continue  # Skip rows that do not match any patient ID
-
-            MediLink_ConfigLoader.log("Processing row number {}.".format(row_num), level="DEBUG")
-            surgery_date = row.get('Surgery Date', '')
-
-            # Convert surgery_date to string format for lookup
-            if surgery_date != datetime.min:
-                surgery_date_str = surgery_date.strftime("%m-%d-%Y")
-            else:
-                surgery_date_str = ''
-
-            MediLink_ConfigLoader.log("Patient ID: {}, Surgery Date: {}".format(patient_id, surgery_date_str), level="DEBUG")
-
-            if patient_id in all_patient_data:
-                if surgery_date_str in all_patient_data[patient_id]:
-                    diagnosis_code, left_or_right_eye, femto_yes_or_no = all_patient_data[patient_id][surgery_date_str]
-                    MediLink_ConfigLoader.log("Found diagnosis data for Patient ID: {}, Surgery Date: {}".format(patient_id, surgery_date_str), level="DEBUG")
-                    
-                    # Convert diagnosis code to Medisoft shorthand format.
-                    medisoft_shorthand = diagnosis_to_medisoft.get(diagnosis_code, None)
-                    if medisoft_shorthand is None and diagnosis_code:
-                        defaulted_code = diagnosis_code.lstrip('H').lstrip('T8').replace('.', '')[-5:]
-                        medisoft_shorthand = defaulted_code
-                    MediLink_ConfigLoader.log("Converted diagnosis code to Medisoft shorthand: {}".format(medisoft_shorthand), level="DEBUG")
-                    
-                    row['Default Diagnosis #1'] = medisoft_shorthand
-                    updated_count += 1
-                    MediLink_ConfigLoader.log("Updated row number {} with new diagnosis code.".format(row_num), level="INFO")
-                else:
-                    MediLink_ConfigLoader.log("No matching surgery date found for Patient ID: {} in row {}.".format(patient_id, row_num), level="INFO")
-            else:
-                MediLink_ConfigLoader.log("Patient ID: {} not found in DOCX data for row {}.".format(patient_id, row_num), level="INFO")
-
-        # Log total count of updated rows
-        MediLink_ConfigLoader.log("Total {} 'Default Diagnosis #1' rows updated.".format(updated_count), level="INFO")
-
-    except Exception as e:
-        message = "An error occurred while updating diagnosis codes. Please check the DOCX files and configuration: {}".format(e)
-        MediLink_ConfigLoader.log(message, level="ERROR")
-        print(message)
-
-def load_data_sources(config, crosswalk):
-    """Loads historical mappings from MAPAT and Carol's CSVs."""
-    patient_id_to_insurance_id = load_insurance_data_from_mapat(config, crosswalk)
-    if not patient_id_to_insurance_id:
-        raise ValueError("Failed to load historical Patient ID to Insurance ID mappings from MAPAT.")
-
-    payer_id_to_patient_ids = load_historical_payer_to_patient_mappings(config)
-    if not payer_id_to_patient_ids:
-        raise ValueError("Failed to load historical Carol's CSVs.")
-
-    return patient_id_to_insurance_id, payer_id_to_patient_ids
-
-def map_payer_ids_to_insurance_ids(patient_id_to_insurance_id, payer_id_to_patient_ids):
-    """Maps Payer IDs to Insurance IDs based on the historical mappings."""
-    payer_id_to_details = {}
-    for payer_id, patient_ids in payer_id_to_patient_ids.items():
-        medisoft_ids = set()
-        for patient_id in patient_ids:
-            if patient_id in patient_id_to_insurance_id:
-                medisoft_id = patient_id_to_insurance_id[patient_id]
-                medisoft_ids.add(medisoft_id)
-                MediLink_ConfigLoader.log("Added Medisoft ID {} for Patient ID {} and Payer ID {}".format(medisoft_id, patient_id, payer_id))
-            else:
-                MediLink_ConfigLoader.log("No matching Insurance ID found for Patient ID {}".format(patient_id))
-        if medisoft_ids:
-            payer_id_to_details[payer_id] = {
-                "endpoint": "OPTUMEDI",  # TODO Default, to be refined via API poll. There are 2 of these defaults!
-                "medisoft_id": list(medisoft_ids),
-                "medisoft_medicare_id": []  # Placeholder for future implementation
-            }
-    return payer_id_to_details
-
-def load_insurance_data_from_mains(config):
-    """
-    Loads insurance data from MAINS and creates a mapping from insurance names to their respective IDs.
-    This mapping is critical for the crosswalk update process to correctly associate payer IDs with insurance IDs.
-
-    Args:
-        config (dict): Configuration object containing necessary paths and parameters.
-
-    Returns:
-        dict: A dictionary mapping insurance names to insurance IDs.
-    """
-    # Reset config pull to make sure its not using the MediLink config key subset
-    config, crosswalk = MediLink_ConfigLoader.load_configuration()
-    
-    # Retrieve MAINS path and slicing information from the configuration   
-    # TODO (Low) For secondary insurance, this needs to be pulling from the correct MAINS (there are 2)
-    # TODO (Low) Performance: There probably needs to be a dictionary proxy for MAINS that gets updated.
-    # Meh, this just has to be part of the new architecture plan where we make Medisoft a downstream 
-    # recipient from the db.
-    # TODO (High) The Medisoft Medicare flag needs to be brought in here.
-    mains_path = config['MAINS_MED_PATH']
-    mains_slices = crosswalk['mains_mapping']['slices']
-    
-    # Initialize the dictionary to hold the insurance to insurance ID mappings
-    insurance_to_id = {}
-    
-    # Read data from MAINS using a provided function to handle fixed-width data
-    for record, line_number in MediLink_DataMgmt.read_general_fixed_width_data(mains_path, mains_slices):
-        insurance_name = record['MAINSNAME']
-        # Assuming line_number gives the correct insurance ID without needing adjustment
-        insurance_to_id[insurance_name] = line_number
-    
-    return insurance_to_id
-
-def load_insurance_data_from_mapat(config, crosswalk):
-    """
-    Loads insurance data from MAPAT and creates a mapping from patient ID to insurance ID.
-    
-    Args:
-        config (dict): Configuration object containing necessary paths and parameters.
-        crosswalk ... ADD HERE.
-
-    Returns:
-        dict: A dictionary mapping patient IDs to insurance IDs.
-    """
-    # Retrieve MAPAT path and slicing information from the configuration
-    mapat_path = app_control.get_mapat_med_path()
-    mapat_slices = crosswalk['mapat_mapping']['slices']
-    
-    # Initialize the dictionary to hold the patient ID to insurance ID mappings
-    patient_id_to_insurance_id = {}
-    
-    # Read data from MAPAT using a provided function to handle fixed-width data
-    for record, _ in MediLink_DataMgmt.read_general_fixed_width_data(mapat_path, mapat_slices):
-        patient_id = record['MAPATPXID']
-        insurance_id = record['MAPATINID']
-        patient_id_to_insurance_id[patient_id] = insurance_id
-        
-    return patient_id_to_insurance_id
-
-def parse_z_dat(z_dat_path, config): # Why is this in MediBot and not MediLink?
-    """
-    Parses the Z.dat file to map Patient IDs to Insurance Names using the provided fixed-width file format.
-
-    Args:
-        z_dat_path (str): Path to the Z.dat file.
-        config (dict): Configuration object containing slicing information and other parameters.
-
-    Returns:
-        dict: A dictionary mapping Patient IDs to Insurance Names.
-    """
-    patient_id_to_insurance_name = {}
-
-    try:
-        # Reading blocks of fixed-width data (up to 5 lines per record)
-        for personal_info, insurance_info, service_info, service_info_2, service_info_3 in MediLink_DataMgmt.read_fixed_width_data(z_dat_path):
-            # Parsing the data using slice definitions from the config
-            parsed_data = MediLink_DataMgmt.parse_fixed_width_data(personal_info, insurance_info, service_info, service_info_2, service_info_3, config.get('MediLink_Config', config))
-
-            # Extract Patient ID and Insurance Name from parsed data
-            patient_id = parsed_data.get('PATID')
-            insurance_name = parsed_data.get('INAME')
-
-            if patient_id and insurance_name:
-                patient_id_to_insurance_name[patient_id] = insurance_name
-                MediLink_ConfigLoader.log("Mapped Patient ID {} to Insurance Name {}".format(patient_id, insurance_name), config, level="INFO")
-
-    except FileNotFoundError:
-        MediLink_ConfigLoader.log("File not found: {}".format(z_dat_path), config, level="INFO")
-    except Exception as e:
-        MediLink_ConfigLoader.log("Failed to parse Z.dat: {}".format(str(e)), config, level="INFO")
-
-    return patient_id_to_insurance_name
-
-def load_historical_payer_to_patient_mappings(config):
-    """
-    Loads historical mappings from multiple Carol's CSV files in a specified directory,
-    mapping Payer IDs to sets of Patient IDs.
-
-    Args:
-        config (dict): Configuration object containing the directory path for Carol's CSV files
-                       and other necessary parameters.
-
-    Returns:
-        dict: A dictionary where each key is a Payer ID and the value is a set of Patient IDs.
-    """
-    directory_path = os.path.dirname(config['CSV_FILE_PATH'])
-    payer_to_patient_ids = defaultdict(set)
-
-    try:
-        # Check if the directory exists
-        if not os.path.isdir(directory_path):
-            raise FileNotFoundError("Directory '{}' not found.".format(directory_path))
-
-        # Loop through each file in the directory containing Carol's historical CSVs
-        for filename in os.listdir(directory_path):
-            file_path = os.path.join(directory_path, filename)
-            if filename.endswith('.csv'):
-                try:
-                    with open(file_path, 'r', encoding='utf-8') as csvfile:
-                        reader = csv.DictReader(csvfile)
-                        patient_count = 0  # Counter for Patient IDs found in this CSV
-                        for row in reader:
-                            if 'Patient ID' not in row or 'Ins1 Payer ID' not in row:
-                                continue  # Skip this row if either key is missing
-                            if not row.get('Patient ID').strip() or not row.get('Ins1 Payer ID').strip():
-                                continue  # Skip this row if either value is missing or empty
-                            
-                            payer_id = row['Ins1 Payer ID'].strip()
-                            patient_id = row['Patient ID'].strip()
-                            payer_to_patient_ids[payer_id].add(patient_id)
-                            patient_count += 1  # Increment the counter for each valid mapping
-                        
-                        # Log the accumulated count for this CSV file
-                        if patient_count > 0:
-                            MediLink_ConfigLoader.log("CSV file '{}' has {} Patient IDs with Payer IDs.".format(filename, patient_count), level="DEBUG")
-                        else:
-                            MediLink_ConfigLoader.log("CSV file '{}' is empty or does not have valid Patient ID or Payer ID mappings.".format(filename), level="DEBUG")
-                except Exception as e:
-                    print("Error processing file {}: {}".format(filename, e))
-                    MediLink_ConfigLoader.log("Error processing file '{}': {}".format(filename, e), level="ERROR")
-    except FileNotFoundError as e:
-        print("Error: {}".format(e))
-
-    if not payer_to_patient_ids:
-        print("No historical mappings were generated.")
-    
-    return dict(payer_to_patient_ids)
-
-def capitalize_all_fields(csv_data):
-    """
-    Converts all text fields in the CSV data to uppercase.
-    
-    Parameters:
-    csv_data (list of dict): The CSV data where each row is represented as a dictionary.
-    
-    Returns:
-    None: The function modifies the csv_data in place.
-    """
-    for row in csv_data:
-        for key, value in row.items():
-            if isinstance(value, str):
-                row[key] = value.upper()
-            elif isinstance(value, datetime):
-                # Keep datetime objects as they are
-                pass
-            elif value is not None:
-                # Convert any other non-None values to string and then uppercase
+#MediBot_Preprocessor_lib.py
+from collections import OrderedDict, defaultdict
+from datetime import datetime, timedelta
+import os, csv, sys
+import chardet  # Ensure chardet is imported
+
+# Add the parent directory of the project to the Python path
+sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), "..")))
+
+# Attempt to import necessary modules, falling back if they are not found
+try:
+    import MediLink_ConfigLoader
+    import MediLink_DataMgmt
+except ImportError:
+    from MediLink import MediLink_ConfigLoader, MediLink_DataMgmt
+
+try:
+    from MediBot_UI import app_control
+    from MediBot_docx_decoder import parse_docx
+except ImportError:
+    from MediBot import MediBot_UI
+    app_control = MediBot_UI.app_control
+    from MediBot import MediBot_docx_decoder
+    parse_docx = MediBot_docx_decoder.parse_docx
+
+class InitializationError(Exception):
+    def __init__(self, message):
+        self.message = message
+        super().__init__(self.message)
+
+def initialize(config):
+    global AHK_EXECUTABLE, CSV_FILE_PATH, field_mapping, page_end_markers
+    
+    required_keys = {
+        'AHK_EXECUTABLE': "",
+        'CSV_FILE_PATH': "",
+        'field_mapping': {},
+        'page_end_markers': []
+    }
+    
+    for key, default in required_keys.items():
+        try:
+            globals()[key] = config.get(key, default) if key != 'field_mapping' else OrderedDict(config.get(key, default))
+        except AttributeError:
+            raise InitializationError("Error: '{}' not found in config.".format(key))
+
+def open_csv_for_editing(csv_file_path):
+    try:
+        # Open the CSV file with its associated application
+        os.system('start "" "{}"'.format(csv_file_path))
+        print("After saving the revised CSV, please re-run MediBot.")
+    except Exception as e:
+        print("Failed to open CSV file:", e)
+        
+# Function to clean the headers
+def clean_header(headers):
+    """
+    Cleans the header strings by removing unwanted characters and trimming whitespace.
+
+    Parameters:
+    headers (list of str): The original header strings.
+
+    Returns:
+    list of str: The cleaned header strings.
+    """
+    cleaned_headers = []
+    
+    for header in headers:
+        # Strip leading and trailing whitespace
+        cleaned_header = header.strip()
+        # Remove unwanted characters while keeping spaces, alphanumeric characters, hyphens, and underscores
+        cleaned_header = ''.join(char for char in cleaned_header if char.isalnum() or char.isspace() or char in ['-', '_'])
+        cleaned_headers.append(cleaned_header)
+
+    # Log the original and cleaned headers for debugging
+    MediLink_ConfigLoader.log("Original headers: {}".format(headers), level="INFO")
+    MediLink_ConfigLoader.log("Cleaned headers: {}".format(cleaned_headers), level="INFO")
+
+    # Check if 'Surgery Date' is in the cleaned headers
+    if 'Surgery Date' not in cleaned_headers:
+        MediLink_ConfigLoader.log("WARNING: 'Surgery Date' header not found after cleaning.", level="WARNING")
+        print("WARNING: 'Surgery Date' header not found after cleaning.")
+        raise ValueError("Error: 'Surgery Date' header not found after cleaning.")
+
+    return cleaned_headers
+
+# Function to load and process CSV data
+def load_csv_data(csv_file_path):
+    try:
+        # Check if the file exists
+        if not os.path.exists(csv_file_path):
+            raise FileNotFoundError("***Error: CSV file '{}' not found.".format(csv_file_path))
+        
+        # Detect the file encoding
+        with open(csv_file_path, 'rb') as f:
+            raw_data = f.read()
+            result = chardet.detect(raw_data)
+            encoding = result['encoding']
+            confidence = result['confidence']
+            print("Detected encoding: {} (Confidence: {:.2f})".format(encoding, confidence))
+
+        # Read the CSV file with the detected encoding
+        with open(csv_file_path, 'r', encoding=encoding) as csvfile:
+            reader = csv.DictReader(csvfile)
+            # Clean the headers
+            cleaned_headers = clean_header(reader.fieldnames)
+
+            # Create a mapping of cleaned headers to original headers
+            header_mapping = {cleaned_headers[i]: reader.fieldnames[i] for i in range(len(cleaned_headers))}
+
+            # Process the remaining rows
+            csv_data = []
+            for row in reader:
+                cleaned_row = {cleaned_headers[i]: row[header_mapping[cleaned_headers[i]]] for i in range(len(cleaned_headers))}
+                csv_data.append(cleaned_row)
+
+            return csv_data  # Return a list of dictionaries
+    except FileNotFoundError as e:
+        print(e)  # Print the informative error message
+        print("Hint: Check if CSV file is located in the expected directory or specify a different path in config file.")
+        print("Please correct the issue and re-run MediBot.")
+        sys.exit(1)  # Halt the script
+    except IOError as e:
+        print("Error reading CSV file: {}. Please check the file path and permissions.".format(e))
+        sys.exit(1)  # Halt the script in case of other IO errors
+
+# CSV Pre-processor Helper functions
+def add_columns(csv_data, column_headers):
+    """
+    Adds one or multiple columns to the CSV data.
+    
+    Parameters:
+    csv_data (list of dict): The CSV data where each row is represented as a dictionary.
+    column_headers (list of str or str): A list of column headers to be added to each row, or a single column header.
+    
+    Returns:
+    None: The function modifies the csv_data in place.
+    """
+    if isinstance(column_headers, str):
+        column_headers = [column_headers]
+    elif not isinstance(column_headers, list):
+        raise ValueError("column_headers should be a list or a string")
+
+    for row in csv_data:
+        for header in column_headers:
+            row[header] = ''  # Initialize the column with empty values
+
+# Extracting the list to a variable for future refactoring:
+def filter_rows(csv_data):
+    # TODO: This should be handled in the crosswalk.
+    excluded_insurance = {'AETNA', 'AETNA MEDICARE', 'HUMANA MED HMO'}
+    csv_data[:] = [row for row in csv_data if row.get('Patient ID') and row.get('Primary Insurance') not in excluded_insurance]
+
+def convert_surgery_date(csv_data):
+    for row in csv_data:
+        surgery_date_str = row.get('Surgery Date', '')
+        if not surgery_date_str:
+            MediLink_ConfigLoader.log("Warning: Surgery Date not found for row: {}".format(row), level="WARNING")
+            # BUG This needs a cleaning step for the Surgery Date string in case we're receiving damaged data.
+            row['Surgery Date'] = datetime.min  # Assign a minimum datetime value if empty
+            print("Surgery Date not found for row: {}".format(row))
+        else:
+            try:
+                row['Surgery Date'] = datetime.strptime(surgery_date_str, '%m/%d/%Y')
+            except ValueError as e:
+                MediLink_ConfigLoader.log("Error parsing Surgery Date '{}': {} for row: {}".format(surgery_date_str, e, row), level="ERROR")
+                row['Surgery Date'] = datetime.min  # Assign a minimum datetime value if parsing fails
+
+def sort_and_deduplicate(csv_data):
+    # Create a dictionary to hold unique patients based on Patient ID
+    unique_patients = {}
+    
+    # Iterate through the CSV data and populate the unique_patients dictionary
+    for row in csv_data:
+        patient_id = row.get('Patient ID')
+        if patient_id not in unique_patients:
+            unique_patients[patient_id] = row
+        else:
+            # If the patient ID already exists, compare surgery dates
+            existing_row = unique_patients[patient_id]
+            if row['Surgery Date'] < existing_row['Surgery Date']:
+                unique_patients[patient_id] = row
+
+    # Convert the unique_patients dictionary back to a list and sort it
+    csv_data[:] = sorted(unique_patients.values(), key=lambda x: (x['Surgery Date'], x.get('Patient Last', '').strip())) # TODO Does this need to be sorted twice? once before and once after?
+    
+    # TODO: Consider adding an option in the config to sort based on Surgery Schedules when available.
+    # If no schedule is available, the current sorting strategy will be used.
+
+def combine_fields(csv_data):
+    for row in csv_data:
+        # Safely handle the 'Surgery Date' conversion
+        surgery_date = row.get('Surgery Date')
+        row['Surgery Date'] = surgery_date.strftime('%m/%d/%Y') if surgery_date else ''
+        
+        first_name = '_'.join(part.strip() for part in row.get('Patient First', '').split()) # Join the first name parts with underscores after cleaning.
+        middle_name = row.get('Patient Middle', '').strip()
+        middle_name = middle_name[0] if len(middle_name) > 1 else ''  # Take only the first character or empty
+        last_name = '_'.join(part.strip() for part in row.get('Patient Last', '').split()) # Join the last name parts with underscores after cleaning.
+        row['Patient Name'] = ', '.join(filter(None, [last_name, first_name])) + (' ' + middle_name if middle_name else '')  # Comma between last and first, space before middle
+        
+        address1 = row.get('Patient Address1', '').strip()
+        address2 = row.get('Patient Address2', '').strip()
+        row['Patient Street'] = ' '.join(filter(None, [address1, address2]))  # Join non-empty addresses
+
+def apply_replacements(csv_data, crosswalk):
+    replacements = crosswalk.get('csv_replacements', {})
+    for row in csv_data:
+        for old_value, new_value in replacements.items():
+            for key in ['Patient SSN', 'Primary Insurance', 'Ins1 Payer ID']:
+                if row.get(key) == old_value:
+                    row[key] = new_value
+                    break  # Exit the loop once a replacement is made
+
+import difflib
+from collections import defaultdict
+
+def find_best_medisoft_id(insurance_name, medisoft_ids, medisoft_to_mains_names):
+    """
+    Finds the best matching Medisoft ID for a given insurance name using fuzzy matching.
+
+    Parameters:
+    - insurance_name (str): The insurance name from the CSV row.
+    - medisoft_ids (list): List of Medisoft IDs associated with the Payer ID.
+    - medisoft_to_mains_names (dict): Mapping from Medisoft ID to list of MAINS names.
+
+    Returns:
+    - int or None: The best matching Medisoft ID or None if no match is found.
+    """
+    best_match_ratio = 0
+    best_medisoft_id = None
+
+    for medisoft_id in medisoft_ids:
+        mains_names = medisoft_to_mains_names.get(medisoft_id, [])
+        for mains_name in mains_names:
+            # Preprocess names by extracting non-numeric characters and converting to uppercase
+            processed_mains = ''.join(filter(lambda x: not x.isdigit(), mains_name)).upper()
+            processed_insurance = ''.join(filter(lambda x: not x.isdigit(), insurance_name)).upper()
+
+            # Log the processed names before computing the match ratio
+            MediLink_ConfigLoader.log("Processing Medisoft ID '{}': Comparing processed insurance '{}' with processed mains '{}'.".format(medisoft_id, processed_insurance, processed_mains), level="DEBUG")
+
+            # Compute the similarity ratio
+            match_ratio = difflib.SequenceMatcher(None, processed_insurance, processed_mains).ratio()
+
+            # Log the match ratio
+            MediLink_ConfigLoader.log("Match ratio for Medisoft ID '{}': {:.2f}".format(medisoft_id, match_ratio), level="DEBUG")
+
+            if match_ratio > best_match_ratio:
+                best_match_ratio = match_ratio
+                best_medisoft_id = medisoft_id
+                # Log the current best match
+                MediLink_ConfigLoader.log("New best match found: Medisoft ID '{}' with match ratio {:.2f}".format(best_medisoft_id, best_match_ratio), level="DEBUG")
+
+    # Log the final best match ratio and ID
+    MediLink_ConfigLoader.log("Final best match ratio: {:.2f} for Medisoft ID '{}'".format(best_match_ratio, best_medisoft_id), level="DEBUG")
+
+    # No threshold applied, return the best match found
+    return best_medisoft_id
+
+def NEW_update_insurance_ids(csv_data, config, crosswalk):
+    """
+    Updates the 'Ins1 Insurance ID' field in each row of csv_data based on the crosswalk and MAINS data.
+
+    Parameters:
+    - csv_data (list of dict): The CSV data where each row is represented as a dictionary.
+    - config (dict): Configuration object containing necessary paths and parameters.
+    - crosswalk (dict): Crosswalk data containing mappings between Payer IDs and Medisoft IDs.
+
+    Returns:
+    - None: The function modifies the csv_data in place.
+    """
+    processed_payer_ids = set()  # Track processed Payer IDs
+    MediLink_ConfigLoader.log("Starting update of insurance IDs.", level="INFO")
+
+    # Load MAINS data to get mapping from Medisoft ID to MAINS names
+    insurance_to_id = load_insurance_data_from_mains(config)  # Assuming it returns a dict mapping insurance names to IDs
+    MediLink_ConfigLoader.log("Loaded MAINS data for insurance to ID mapping.", level="DEBUG")
+    
+    # Invert the mapping to get Medisoft ID to MAINS names
+    medisoft_to_mains_names = defaultdict(list)
+    for insurance_name, medisoft_id in insurance_to_id.items():
+        medisoft_to_mains_names[medisoft_id].append(insurance_name)
+
+    for row in csv_data:
+        ins1_payer_id = row.get('Ins1 Payer ID', '').strip()
+        MediLink_ConfigLoader.log("Processing row with Ins1 Payer ID: '{}'.".format(ins1_payer_id), level="DEBUG")
+        
+        if ins1_payer_id:
+            # Mark this Payer ID as processed
+            if ins1_payer_id not in processed_payer_ids:
+                processed_payer_ids.add(ins1_payer_id)  # Add to set
+                MediLink_ConfigLoader.log("Marked Payer ID '{}' as processed.".format(ins1_payer_id), level="DEBUG")
+                
+                # Retrieve Medisoft IDs for the current Payer ID
+                medisoft_ids = crosswalk.get('payer_id', {}).get(ins1_payer_id, {}).get('medisoft_id', [])
+                MediLink_ConfigLoader.log("Retrieved Medisoft IDs for Payer ID '{}': {}".format(ins1_payer_id, medisoft_ids), level="DEBUG")
+
+        if not medisoft_ids:
+            MediLink_ConfigLoader.log("No Medisoft IDs available for Payer ID '{}', creating placeholder entry.".format(ins1_payer_id), level="WARNING")
+            # Create a placeholder entry in the crosswalk
+            if 'payer_id' not in crosswalk:
+                crosswalk['payer_id'] = {}
+            crosswalk['payer_id'][ins1_payer_id] = {
+                'medisoft_id': [],  # Placeholder for future Medisoft IDs
+                'medisoft_medicare_id': [],  # Placeholder for future Medicare IDs
+                'endpoint': None  # Placeholder for future endpoint
+            }
+            continue  # Skip further processing for this Payer ID
+
+        # If only one Medisoft ID is associated, assign it directly
+        if len(medisoft_ids) == 1:
+            try:
+                medisoft_id = int(medisoft_ids[0])
+                row['Ins1 Insurance ID'] = medisoft_id
+                MediLink_ConfigLoader.log("Assigned Medisoft ID '{}' to row number {} with Payer ID '{}'.".format(medisoft_id, csv_data.index(row) + 1, ins1_payer_id), level="DEBUG")
+            except ValueError as e:
+                MediLink_ConfigLoader.log("Error converting Medisoft ID '{}' to integer for Payer ID '{}': {}".format(medisoft_ids[0], ins1_payer_id, e), level="ERROR")
+                row['Ins1 Insurance ID'] = None
+            continue  # Move to the next row
+
+        # If multiple Medisoft IDs are associated, perform fuzzy matching
+        insurance_name = row.get('Primary Insurance', '').strip()
+        if not insurance_name:
+            MediLink_ConfigLoader.log("Row with Payer ID '{}' missing 'Primary Insurance', skipping assignment.".format(ins1_payer_id), level="WARNING")
+            continue  # Skip if insurance name is missing
+
+        best_medisoft_id = find_best_medisoft_id(insurance_name, medisoft_ids, medisoft_to_mains_names)
+
+        if best_medisoft_id:
+            row['Ins1 Insurance ID'] = best_medisoft_id
+            MediLink_ConfigLoader.log("Assigned Medisoft ID '{}' to row with Payer ID '{}' based on fuzzy match.".format(best_medisoft_id, ins1_payer_id), level="INFO")
+        else:
+            # Default to the first Medisoft ID if no good match is found
+            try:
+                default_medisoft_id = int(medisoft_ids[0])
+                row['Ins1 Insurance ID'] = default_medisoft_id
+                MediLink_ConfigLoader.log("No suitable match found. Defaulted to Medisoft ID '{}' for Payer ID '{}'.".format(default_medisoft_id, ins1_payer_id), level="INFO")
+            except ValueError as e:
+                MediLink_ConfigLoader.log("Error converting default Medisoft ID '{}' to integer for Payer ID '{}': {}".format(medisoft_ids[0], ins1_payer_id, e), level="ERROR")
+                row['Ins1 Insurance ID'] = None
+
+def update_insurance_ids(csv_data, config, crosswalk):
+    MediLink_ConfigLoader.log("Starting update_insurance_ids function.", level="DEBUG")
+    
+    # Create a dictionary to hold Medisoft IDs for each payer ID in the crosswalk
+    payer_id_to_medisoft = {}
+    MediLink_ConfigLoader.log("Initialized payer_id_to_medisoft dictionary.", level="DEBUG")
+    
+    # Populate the dictionary with data from the crosswalk
+    for payer_id, details in crosswalk.get('payer_id', {}).items():
+        medisoft_ids = details.get('medisoft_id', [])
+        # Filter out empty strings and take the first valid ID
+        medisoft_ids = [id for id in medisoft_ids if id]
+        payer_id_to_medisoft[payer_id] = int(medisoft_ids[0]) if medisoft_ids else None
+        MediLink_ConfigLoader.log("Processed Payer ID '{}': Medisoft IDs found: {}".format(payer_id, medisoft_ids), level="DEBUG")
+
+    # Process the csv_data
+    for row in csv_data:
+        ins1_payer_id = row.get('Ins1 Payer ID', '').strip()
+        MediLink_ConfigLoader.log("Processing row #{} with Ins1 Payer ID '{}'.".format(csv_data.index(row) + 1, ins1_payer_id), level="DEBUG")
+        
+        if ins1_payer_id not in payer_id_to_medisoft:
+            # Add placeholder entry for new payer ID
+            payer_id_to_medisoft[ins1_payer_id] = None  # No Medisoft ID available
+            crosswalk.setdefault('payer_id', {})[ins1_payer_id] = {
+                'medisoft_id': [],  # Placeholder for future Medisoft IDs
+                'medisoft_medicare_id': [],  # Placeholder for future Medicare IDs
+                'endpoint': None  # Placeholder for future endpoint
+            }
+            MediLink_ConfigLoader.log("Added placeholder entry for new Payer ID '{}'.".format(ins1_payer_id), level="INFO")
+        
+        # Assign the Medisoft ID to the row
+        row['Ins1 Insurance ID'] = payer_id_to_medisoft[ins1_payer_id]
+        MediLink_ConfigLoader.log("Assigned Medisoft ID '{}' to row with Ins1 Payer ID '{}'.".format(row['Ins1 Insurance ID'], ins1_payer_id), level="DEBUG")
+
+def update_procedure_codes(csv_data, crosswalk): 
+    
+    # Get Medisoft shorthand dictionary from crosswalk and reverse it
+    diagnosis_to_medisoft = crosswalk.get('diagnosis_to_medisoft', {}) # BUG We need to be careful here in case we decide we need to change the crosswalk data specifically with regard to the T8/H usage.
+    medisoft_to_diagnosis = {v: k for k, v in diagnosis_to_medisoft.items()}
+
+    # Get procedure code to diagnosis dictionary from crosswalk and reverse it for easier lookup
+    diagnosis_to_procedure = {
+        diagnosis_code: procedure_code
+        for procedure_code, diagnosis_codes in crosswalk.get('procedure_to_diagnosis', {}).items()
+        for diagnosis_code in diagnosis_codes
+    }
+
+    # Initialize counter for updated rows
+    updated_count = 0
+
+    # Update the "Procedure Code" column in the CSV data
+    for row_num, row in enumerate(csv_data, start=1):
+        try:
+            medisoft_code = row.get('Default Diagnosis #1', '').strip()
+            diagnosis_code = medisoft_to_diagnosis.get(medisoft_code)
+            if diagnosis_code:
+                procedure_code = diagnosis_to_procedure.get(diagnosis_code)
+                if procedure_code:
+                    row['Procedure Code'] = procedure_code
+                    updated_count += 1
+                else:
+                    row['Procedure Code'] = "Unknown"  # Or handle as appropriate
+            else:
+                row['Procedure Code'] = "Unknown"  # Or handle as appropriate
+        except Exception as e:
+            MediLink_ConfigLoader.log("In update_procedure_codes, Error processing row {}: {}".format(row_num, e), level="ERROR")
+
+    # Log total count of updated rows
+    MediLink_ConfigLoader.log("Total {} 'Procedure Code' rows updated.".format(updated_count), level="INFO")
+
+    return True
+
+def update_diagnosis_codes(csv_data):
+    try:
+        # Load configuration and crosswalk
+        config, crosswalk = MediLink_ConfigLoader.load_configuration()
+        
+        # Extract the local storage path from the configuration
+        local_storage_path = config['MediLink_Config']['local_storage_path']
+        
+        # Initialize a dictionary to hold diagnosis codes from all DOCX files
+        all_patient_data = {}
+
+        # Convert surgery dates in CSV data
+        convert_surgery_date(csv_data)
+        
+        # Extract all valid surgery dates from csv_data
+        surgery_dates = [row['Surgery Date'] for row in csv_data if row['Surgery Date'] != datetime.min]
+        
+        if not surgery_dates:
+            raise ValueError("No valid surgery dates found in csv_data.")
+        
+        # Determine the minimum and maximum surgery dates
+        min_surgery_date = min(surgery_dates)
+        max_surgery_date = max(surgery_dates)
+        
+        # Apply a ±8-day margin to the surgery dates... Increased from 5 days.
+        margin = timedelta(days=8)
+        threshold_start = min_surgery_date - margin
+        threshold_end = max_surgery_date + margin
+        
+        # TODO (Low) This is a bad idea. We need a better way to handle this because it leaves 
+        # us with a situation where if we take 'too long' to download the DOCX files, it will presume that the DOCX files are out of range because 
+        # the modfied date is a bad proxy for the date of the surgery which would be contained inside the DOCX file. The processing overhead for extracting the
+        # date of the surgery from the DOCX file is non-trivial and computationally expensive so we need a smarter way to handle this.
+
+        MediLink_ConfigLoader.log("BAD IDEA: Processing DOCX files modified between {} and {}.".format(threshold_start, threshold_end), level="INFO")
+
+        # Gather all relevant DOCX files in the specified directory
+        docx_files = [
+            os.path.join(local_storage_path, filename)
+            for filename in os.listdir(local_storage_path)
+            if filename.endswith(".docx")
+        ]
+
+        # Filter files based on modification time
+        valid_files = [
+            filepath for filepath in docx_files
+            if threshold_start <= datetime.fromtimestamp(os.path.getmtime(filepath)) <= threshold_end
+        ]
+
+        # Process valid DOCX files
+        for filepath in valid_files:
+            MediLink_ConfigLoader.log("Processing DOCX file: {}".format(filepath), level="INFO")
+            try:
+                patient_data = parse_docx(filepath, surgery_dates)  # Pass surgery_dates to parse_docx
+                for patient_id, service_dates in patient_data.items():
+                    if patient_id not in all_patient_data:
+                        all_patient_data[patient_id] = {}
+                    for date_of_service, diagnosis_data in service_dates.items():
+                        all_patient_data[patient_id][date_of_service] = diagnosis_data
+            except Exception as e:
+                MediLink_ConfigLoader.log("Error parsing DOCX file {}: {}".format(filepath, e), level="ERROR")
+
+        # Log if no valid files were found
+        if not valid_files:
+            MediLink_ConfigLoader.log("No valid DOCX files found within the modification time threshold.", level="INFO")
+        
+        # Debug logging for all_patient_data
+        MediLink_ConfigLoader.log("All patient data collected from DOCX files: {}".format(all_patient_data), level="DEBUG")
+        
+        # Extract patient IDs from csv_data for efficient matching
+        patient_ids_in_csv = {row.get('Patient ID', '').strip() for row in csv_data}
+
+        # Check if any patient data was collected
+        if not all_patient_data or not patient_ids_in_csv.intersection(all_patient_data.keys()):
+            MediLink_ConfigLoader.log("No patient data collected or no matching Patient IDs found. Skipping further processing.", level="INFO")
+            return  # Exit the function early if no data is available
+
+        # Get Medisoft shorthand dictionary from crosswalk.
+        diagnosis_to_medisoft = crosswalk.get('diagnosis_to_medisoft', {})
+        
+        # Initialize counter for updated rows
+        updated_count = 0
+
+        # Update the "Default Diagnosis #1" column in the CSV data
+        for row_num, row in enumerate(csv_data, start=1):
+            patient_id = row.get('Patient ID', '').strip()
+            if patient_id not in patient_ids_in_csv:
+                continue  # Skip rows that do not match any patient ID
+
+            MediLink_ConfigLoader.log("Processing row number {}.".format(row_num), level="DEBUG")
+            surgery_date = row.get('Surgery Date', '')
+
+            # Convert surgery_date to string format for lookup
+            if surgery_date != datetime.min:
+                surgery_date_str = surgery_date.strftime("%m-%d-%Y")
+            else:
+                surgery_date_str = ''
+
+            MediLink_ConfigLoader.log("Patient ID: {}, Surgery Date: {}".format(patient_id, surgery_date_str), level="DEBUG")
+
+            if patient_id in all_patient_data:
+                if surgery_date_str in all_patient_data[patient_id]:
+                    diagnosis_code, left_or_right_eye, femto_yes_or_no = all_patient_data[patient_id][surgery_date_str]
+                    MediLink_ConfigLoader.log("Found diagnosis data for Patient ID: {}, Surgery Date: {}".format(patient_id, surgery_date_str), level="DEBUG")
+                    
+                    # Convert diagnosis code to Medisoft shorthand format.
+                    medisoft_shorthand = diagnosis_to_medisoft.get(diagnosis_code, None)
+                    if medisoft_shorthand is None and diagnosis_code:
+                        defaulted_code = diagnosis_code.lstrip('H').lstrip('T8').replace('.', '')[-5:]
+                        medisoft_shorthand = defaulted_code
+                    MediLink_ConfigLoader.log("Converted diagnosis code to Medisoft shorthand: {}".format(medisoft_shorthand), level="DEBUG")
+                    
+                    row['Default Diagnosis #1'] = medisoft_shorthand
+                    updated_count += 1
+                    MediLink_ConfigLoader.log("Updated row number {} with new diagnosis code.".format(row_num), level="INFO")
+                else:
+                    MediLink_ConfigLoader.log("No matching surgery date found for Patient ID: {} in row {}.".format(patient_id, row_num), level="INFO")
+            else:
+                MediLink_ConfigLoader.log("Patient ID: {} not found in DOCX data for row {}.".format(patient_id, row_num), level="INFO")
+
+        # Log total count of updated rows
+        MediLink_ConfigLoader.log("Total {} 'Default Diagnosis #1' rows updated.".format(updated_count), level="INFO")
+
+    except Exception as e:
+        message = "An error occurred while updating diagnosis codes. Please check the DOCX files and configuration: {}".format(e)
+        MediLink_ConfigLoader.log(message, level="ERROR")
+        print(message)
+
+def load_data_sources(config, crosswalk):
+    """Loads historical mappings from MAPAT and Carol's CSVs."""
+    patient_id_to_insurance_id = load_insurance_data_from_mapat(config, crosswalk)
+    if not patient_id_to_insurance_id:
+        raise ValueError("Failed to load historical Patient ID to Insurance ID mappings from MAPAT.")
+
+    payer_id_to_patient_ids = load_historical_payer_to_patient_mappings(config)
+    if not payer_id_to_patient_ids:
+        raise ValueError("Failed to load historical Carol's CSVs.")
+
+    return patient_id_to_insurance_id, payer_id_to_patient_ids
+
+def map_payer_ids_to_insurance_ids(patient_id_to_insurance_id, payer_id_to_patient_ids):
+    """Maps Payer IDs to Insurance IDs based on the historical mappings."""
+    payer_id_to_details = {}
+    for payer_id, patient_ids in payer_id_to_patient_ids.items():
+        medisoft_ids = set()
+        for patient_id in patient_ids:
+            if patient_id in patient_id_to_insurance_id:
+                medisoft_id = patient_id_to_insurance_id[patient_id]
+                medisoft_ids.add(medisoft_id)
+                MediLink_ConfigLoader.log("Added Medisoft ID {} for Patient ID {} and Payer ID {}".format(medisoft_id, patient_id, payer_id))
+            else:
+                MediLink_ConfigLoader.log("No matching Insurance ID found for Patient ID {}".format(patient_id))
+        if medisoft_ids:
+            payer_id_to_details[payer_id] = {
+                "endpoint": "OPTUMEDI",  # TODO Default, to be refined via API poll. There are 2 of these defaults!
+                "medisoft_id": list(medisoft_ids),
+                "medisoft_medicare_id": []  # Placeholder for future implementation
+            }
+    return payer_id_to_details
+
+def load_insurance_data_from_mains(config):
+    """
+    Loads insurance data from MAINS and creates a mapping from insurance names to their respective IDs.
+    This mapping is critical for the crosswalk update process to correctly associate payer IDs with insurance IDs.
+
+    Args:
+        config (dict): Configuration object containing necessary paths and parameters.
+
+    Returns:
+        dict: A dictionary mapping insurance names to insurance IDs.
+    """
+    # Reset config pull to make sure its not using the MediLink config key subset
+    config, crosswalk = MediLink_ConfigLoader.load_configuration()
+    
+    # Retrieve MAINS path and slicing information from the configuration   
+    # TODO (Low) For secondary insurance, this needs to be pulling from the correct MAINS (there are 2)
+    # TODO (Low) Performance: There probably needs to be a dictionary proxy for MAINS that gets updated.
+    # Meh, this just has to be part of the new architecture plan where we make Medisoft a downstream 
+    # recipient from the db.
+    # TODO (High) The Medisoft Medicare flag needs to be brought in here.
+    mains_path = config['MAINS_MED_PATH']
+    mains_slices = crosswalk['mains_mapping']['slices']
+    
+    # Initialize the dictionary to hold the insurance to insurance ID mappings
+    insurance_to_id = {}
+    
+    # Read data from MAINS using a provided function to handle fixed-width data
+    for record, line_number in MediLink_DataMgmt.read_general_fixed_width_data(mains_path, mains_slices):
+        insurance_name = record['MAINSNAME']
+        # Assuming line_number gives the correct insurance ID without needing adjustment
+        insurance_to_id[insurance_name] = line_number
+    
+    return insurance_to_id
+
+def load_insurance_data_from_mapat(config, crosswalk):
+    """
+    Loads insurance data from MAPAT and creates a mapping from patient ID to insurance ID.
+    
+    Args:
+        config (dict): Configuration object containing necessary paths and parameters.
+        crosswalk ... ADD HERE.
+
+    Returns:
+        dict: A dictionary mapping patient IDs to insurance IDs.
+    """
+    # Retrieve MAPAT path and slicing information from the configuration
+    mapat_path = app_control.get_mapat_med_path()
+    mapat_slices = crosswalk['mapat_mapping']['slices']
+    
+    # Initialize the dictionary to hold the patient ID to insurance ID mappings
+    patient_id_to_insurance_id = {}
+    
+    # Read data from MAPAT using a provided function to handle fixed-width data
+    for record, _ in MediLink_DataMgmt.read_general_fixed_width_data(mapat_path, mapat_slices):
+        patient_id = record['MAPATPXID']
+        insurance_id = record['MAPATINID']
+        patient_id_to_insurance_id[patient_id] = insurance_id
+        
+    return patient_id_to_insurance_id
+
+def parse_z_dat(z_dat_path, config): # Why is this in MediBot and not MediLink?
+    """
+    Parses the Z.dat file to map Patient IDs to Insurance Names using the provided fixed-width file format.
+
+    Args:
+        z_dat_path (str): Path to the Z.dat file.
+        config (dict): Configuration object containing slicing information and other parameters.
+
+    Returns:
+        dict: A dictionary mapping Patient IDs to Insurance Names.
+    """
+    patient_id_to_insurance_name = {}
+
+    try:
+        # Reading blocks of fixed-width data (up to 5 lines per record)
+        for personal_info, insurance_info, service_info, service_info_2, service_info_3 in MediLink_DataMgmt.read_fixed_width_data(z_dat_path):
+            # Parsing the data using slice definitions from the config
+            parsed_data = MediLink_DataMgmt.parse_fixed_width_data(personal_info, insurance_info, service_info, service_info_2, service_info_3, config.get('MediLink_Config', config))
+
+            # Extract Patient ID and Insurance Name from parsed data
+            patient_id = parsed_data.get('PATID')
+            insurance_name = parsed_data.get('INAME')
+
+            if patient_id and insurance_name:
+                patient_id_to_insurance_name[patient_id] = insurance_name
+                MediLink_ConfigLoader.log("Mapped Patient ID {} to Insurance Name {}".format(patient_id, insurance_name), config, level="INFO")
+
+    except FileNotFoundError:
+        MediLink_ConfigLoader.log("File not found: {}".format(z_dat_path), config, level="INFO")
+    except Exception as e:
+        MediLink_ConfigLoader.log("Failed to parse Z.dat: {}".format(str(e)), config, level="INFO")
+
+    return patient_id_to_insurance_name
+
+def load_historical_payer_to_patient_mappings(config):
+    """
+    Loads historical mappings from multiple Carol's CSV files in a specified directory,
+    mapping Payer IDs to sets of Patient IDs.
+
+    Args:
+        config (dict): Configuration object containing the directory path for Carol's CSV files
+                       and other necessary parameters.
+
+    Returns:
+        dict: A dictionary where each key is a Payer ID and the value is a set of Patient IDs.
+    """
+    directory_path = os.path.dirname(config['CSV_FILE_PATH'])
+    payer_to_patient_ids = defaultdict(set)
+
+    try:
+        # Check if the directory exists
+        if not os.path.isdir(directory_path):
+            raise FileNotFoundError("Directory '{}' not found.".format(directory_path))
+
+        # Loop through each file in the directory containing Carol's historical CSVs
+        for filename in os.listdir(directory_path):
+            file_path = os.path.join(directory_path, filename)
+            if filename.endswith('.csv'):
+                try:
+                    with open(file_path, 'r', encoding='utf-8') as csvfile:
+                        reader = csv.DictReader(csvfile)
+                        patient_count = 0  # Counter for Patient IDs found in this CSV
+                        for row in reader:
+                            if 'Patient ID' not in row or 'Ins1 Payer ID' not in row:
+                                continue  # Skip this row if either key is missing
+                            if not row.get('Patient ID').strip() or not row.get('Ins1 Payer ID').strip():
+                                continue  # Skip this row if either value is missing or empty
+                            
+                            payer_id = row['Ins1 Payer ID'].strip()
+                            patient_id = row['Patient ID'].strip()
+                            payer_to_patient_ids[payer_id].add(patient_id)
+                            patient_count += 1  # Increment the counter for each valid mapping
+                        
+                        # Log the accumulated count for this CSV file
+                        if patient_count > 0:
+                            MediLink_ConfigLoader.log("CSV file '{}' has {} Patient IDs with Payer IDs.".format(filename, patient_count), level="DEBUG")
+                        else:
+                            MediLink_ConfigLoader.log("CSV file '{}' is empty or does not have valid Patient ID or Payer ID mappings.".format(filename), level="DEBUG")
+                except Exception as e:
+                    print("Error processing file {}: {}".format(filename, e))
+                    MediLink_ConfigLoader.log("Error processing file '{}': {}".format(filename, e), level="ERROR")
+    except FileNotFoundError as e:
+        print("Error: {}".format(e))
+
+    if not payer_to_patient_ids:
+        print("No historical mappings were generated.")
+    
+    return dict(payer_to_patient_ids)
+
+def capitalize_all_fields(csv_data):
+    """
+    Converts all text fields in the CSV data to uppercase.
+    
+    Parameters:
+    csv_data (list of dict): The CSV data where each row is represented as a dictionary.
+    
+    Returns:
+    None: The function modifies the csv_data in place.
+    """
+    for row in csv_data:
+        for key, value in row.items():
+            if isinstance(value, str):
+                row[key] = value.upper()
+            elif isinstance(value, datetime):
+                # Keep datetime objects as they are
+                pass
+            elif value is not None:
+                # Convert any other non-None values to string and then uppercase
                 row[key] = str(value).upper()